diff --git a/tools/moltemplate/LICENSE.TXT b/tools/moltemplate/LICENSE.TXT new file mode 100644 index 0000000000..73eec32380 --- /dev/null +++ b/tools/moltemplate/LICENSE.TXT @@ -0,0 +1,28 @@ + +Author: Andrew Jewett, Shea Group, http://www.chem.ucsb.edu/~sheagroup/ +Copyright (c) 2014, Regents of the University of California +All rights reserved. +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + * Neither the name of the University of California, Santa Barbara nor the + names of its contributors may be used to endorse or promote products + derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF +THE POSSIBILITY OF SUCH DAMAGE. + diff --git a/tools/moltemplate/README.TXT b/tools/moltemplate/README.TXT new file mode 100644 index 0000000000..773464d01b --- /dev/null +++ b/tools/moltemplate/README.TXT @@ -0,0 +1,61 @@ + -- Description: -- + +Moltemplate is a cross-platform text-based molecule builder for LAMMPS. + + -- Typical usage: -- + +moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] [-vmd] system.lt + + -- Web page: -- + +Documentation, examples, and supporting code can be downloaded at: + + http://www.moltemplate.org +The most up-to-date version of moltemplate can be downloaded here. +(After download, you can unpack the archive using: + tar xzf moltemplate_2012-3-31.tar.gz +The date will vary from version to version.) + +---------------------------------------------------- +---------- INSTALLATION INSTRUCTIONS: ------------ +---------------------------------------------------- + +This directory should contain two folders: + src/ <-- location of all python and bash scripts + common/ <-- location of shared force fields and molecules + +The ``moltemplate.sh'' script and the python scripts that it invokes are +located in the ``src/'' subdirectory. You should update your PATH environment +variable to include this directory. + +If you do not know what a PATH environment variable is, read: + http://www.linfo.org/path_env_var.html +(I receive this question often.) + +It is also a good idea to set your MOLTEMPLATE_PATH environment variable to +point to the ``common/'' subdirectory. +(Force fields and commonly used molecules will eventually be located here.) + + -- Installation example --- + +Suppose the directory with this README.TXT file is located at ~/moltemplate. + +If you use the bash shell, typically you would edit your +~/.profile, ~/.bash_profile or ~/.bashrc files to contain the following lines: + export PATH="$PATH:$HOME/moltemplate/src" + export MOLTEMPLATE_PATH="$HOME/moltemplate/common" +If you use the tcsh shell, typically you would edit your +~/.login, ~/.cshrc, or ~/.tcshrc files to contain the following lines: + setenv PATH "$PATH:$HOME/moltemplate/src" + setenv MOLTEMPLATE_PATH "$HOME/moltemplate/common" + + -- Requirements: -- + +Moltemplate requires the Bourne-shell, and a recent version of python +(2.7, 3.0 or higher), and can run on OS X, linux, or windows (if a +suitable shell environment has been installed). + + -- License: -- + +Moltemplate is available under the terms of the open-source 3-clause BSD +license. (See LICENSE.TXT.) diff --git a/tools/moltemplate/common/amber/README.TXT b/tools/moltemplate/common/amber/README.TXT new file mode 100644 index 0000000000..20b4d7ed2d --- /dev/null +++ b/tools/moltemplate/common/amber/README.TXT @@ -0,0 +1,74 @@ +This directory contains scripts used for converting AMBER parameter files +into moltemplate (.LT) format. When a newer version of the AMBER parameters +is eventually published, you can use these scripts to convert the new files +again. (Some tinkering may be necessary.) + +The main bash script is a wrapper which simply splits up the parameter (".dat") +file into fragments which (it thinks) correspond to the mass, pair, bond, +angle, dihedral, and improper section of the original .dat file. +(However sometimes it gets this wrong and you have to split it up manually!) + +Then this bash script invokes the relevant python script to convert +each section into .LT format: +amberparm_to_mass.py +amberparm_to_pair.py +amberparm_to_bond.py +amberparm_to_angle.py +amberparm_to_dihedral.py +amberparm_to_improper.py +In case this goes wrong, you may have to run these scripts manaully. + + +Find out how to run this bash script by invoking it without any arguments: + +./amberparm2lt.sh + +------------ IMPORTANT ------------ + +BEFORE YOU RUN THIS SCRIPT, BE SURE TO CHANGE THE ORDER OF THE IMPROPER DIHEDRAL +PARAMETERS SO THAT THE "SPECIFIC" IMPROPER DIHEDRALS APPEAR LAST, AND THE +"GENERIC" IMPROPER DIHEDRALS APPEAR FIRST. + +For example replace these two lines: + +X -o -c -o 1.1 180. 2. JCC,7,(1986),230 +X -X -c -o 10.5 180. 2. JCC,7,(1986),230 + +with these two lines: + +X -X -c -o 10.5 180. 2. JCC,7,(1986),230 +X -o -c -o 1.1 180. 2. JCC,7,(1986),230 + +Why: +This is the order that moltemplate expects: generic first. specific last. +So far only the improper dihedral parameters in the gaff.dat file seem +to violate this order. The bonds, angles and dihedrals seem to obey this, +but check to make sure. + + +There is a discussion of these parameters here: +http://structbio.vanderbilt.edu/archives/amber-archive/2005/3444.php + +excerpt: + +> > In the parm99 file (for example), sometimes the wild-card is used, as it +> > is done in the following example: +> > +> > X -X -C -O 10.5 180. 2. JCC,7,(1986),230 +> > +> > The first example is the specific case while the second one is the generic +> > case. In page # 257 of the AMBER Manual, it is talking about Dihedral +> > Angle, and how these dihedral parameters are used to calculate the +> > energies. I am wondering what the difference between generic and specific +> > case is for improper torsions. +> +> "specific" torsions are search for first, and used if a match is found. If +> no match is found, then a search is made to see if a "generic" (aka wild-card) +> torsion with match. +> ...good luck...dac + +Good luck + +-Andrew +2014-4-19 + diff --git a/tools/moltemplate/common/amber/amberparm2lt.sh b/tools/moltemplate/common/amber/amberparm2lt.sh new file mode 100755 index 0000000000..7ef489d5f0 --- /dev/null +++ b/tools/moltemplate/common/amber/amberparm2lt.sh @@ -0,0 +1,203 @@ +#!/bin/sh + +SYNTAX_MSG=$(cat < gaff.lt + + You can also try: +amberparm2lt.sh parm94.dat "AMBERFF94 inherits GAFF" > amberff94.lt + (However, this later usage may not work. + You may need to manually split the .dat file and run these scripts instead: + amberparm_pair_to_lt.py, amberparm_bond_to_lt.py, amberparm_angle_to_lt.py...) + Be sure that all of these .py files are in your PATH as well.) + +EOF +) + +if [ "$#" != "2" ]; then + echo "${SYNTAX_MSG}" >&2 + echo "" >&2 + echo "Error: This script requires two arguments," >&2 + echo " 1) the name of the amber parm file to be converted (eg \"gaff.dat\")" >&2 + echo " 2) the name of the moltemplate object to be created (eg \"GAFF\")" >&2 + echo " (This may include the \"inherits\" keyword and parent classes.)" >&2 + exit 1 +fi + +MOLTEMPLATE_USAGE_MSG=$(cat < /dev/null; then + echo "\nError: \"amberparm_mass_to_lt.py\" not found.\n" >&2 + echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 + exit 2 +fi +if ! which ./amberparm_pair_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_pair_to_lt.py\" not found.\n" >&2 + echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 + exit 2 +fi +if ! which ./amberparm_bond_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_bond_to_lt.py\" not found.\n" >&2 + echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 + exit 2 +fi +if ! which ./amberparm_angle_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_angle_to_lt.py\" not found.\n" >&2 + echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 + exit 2 +fi +if ! which ./amberparm_dihedral_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_dihedral_to_lt.py\" not found.\n" >&2 + echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 + exit 2 +fi +if ! which ./amberparm_improper_to_lt.py > /dev/null; then + echo "\nError: \"amberparm_improper_to_lt.py\" not found. (Update your PATH?)\n" >&2 + echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 + exit 2 +fi + + +#PARM_FILE='gaff.dat' +PARM_FILE=$1 + +# sections are separated by blank lines +# some sections have comment lines at the beginning + +# The 1st section is the mass (note: skip the first line) +tail -n +2 < "$PARM_FILE" | \ + awk -v n=1 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + > "${PARM_FILE}.mass" + +# The 2nd section has the list of 2-body bond force-field params +awk -v n=2 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + | tail -n +2 \ + > "${PARM_FILE}.bond" + +# The 3rd section has the list of 3-body angle force-field params +awk -v n=3 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + > "${PARM_FILE}.angle" + +# The 4th section has the list of 4-body dihedral force-field params +awk -v n=4 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + > "${PARM_FILE}.dihedral" + +# The 5th section has the list of 4-body improper force-field params +awk -v n=5 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + > "${PARM_FILE}.improper" + +# The 6th section has the hbond-parameters (no-longer used. ignore) +awk -v n=6 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + > "${PARM_FILE}.hbond" + +# The 7th "section" is just a blank line. (skip that) + +# The 8th section has the list of non-bonded ("pair") force-field parameters +awk -v n=8 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ + < "$PARM_FILE" \ + | tail -n +2 \ + > "${PARM_FILE}.pair" + + +./amberparm_mass_to_lt.py < "${PARM_FILE}.mass" > "${PARM_FILE}.mass.lt" +./amberparm_pair_to_lt.py < "${PARM_FILE}.pair" > "${PARM_FILE}.pair.lt" +./amberparm_bond_to_lt.py < "${PARM_FILE}.bond" > "${PARM_FILE}.bond.lt" +./amberparm_angle_to_lt.py < "${PARM_FILE}.angle" > "${PARM_FILE}.angle.lt" +./amberparm_dihedral_to_lt.py \ + < "${PARM_FILE}.dihedral" > "${PARM_FILE}.dihedral.lt" +./amberparm_improper_to_lt.py \ + < "${PARM_FILE}.improper" > "${PARM_FILE}.improper.lt" + +echo "$2 {" +echo "" +echo " # ----------------------------------------------------------------------" +#echo " # This file was automatically generated by \"common/amber/amberparm2lt.sh\"" +echo " # The basic atom nomenclature and conventions are explained here:" +echo " # http://ambermd.org/antechamber/gaff.pdf" +echo " # For reference, the original gaff.dat file and format documenation are here:" +echo " # http://ambermd.org/AmberTools-get.html" +echo " # http://ambermd.org/formats.html#parm.dat" +echo " # ----------------------------------------------------------------------" +echo "" + +cat "$PARM_FILE.mass.lt" \ + "$PARM_FILE.pair.lt" \ + "$PARM_FILE.bond.lt" \ + "$PARM_FILE.angle.lt" \ + "$PARM_FILE.dihedral.lt" \ + "$PARM_FILE.improper.lt" + +AMBER_STYLES_INIT=$(cat <0): + # sys.stderr.write('prev_n='+str(in_dihedral_coeffs[i-1][-3])+'\n') + #sys.stderr.write('n='+str(n)+'\n') + + if ((i>0) and (in_dihedral_coeffs[i-1][-3] < 0)): + + #sys.stdout.write('interation_before_append: '+str(in_dihedral_coeffs[i-1])+'\n') + assert(in_dihedral_coeffs[i-1][0] == in_dihedral_coeffs[i][0]) + in_dihedral_coeffs[i-1][-3] = -in_dihedral_coeffs[i-1][-3] + comments = in_dihedral_coeffs[i-1][-1] + in_dihedral_coeffs[i-1][-1] = Kn + in_dihedral_coeffs[i-1].append(n) + in_dihedral_coeffs[i-1].append(dn) + in_dihedral_coeffs[i-1].append(comments) + #sys.stdout.write('interation_after_append: '+str(in_dihedral_coeffs[i-1])+'\n') + del in_dihedral_coeffs[i] + + #elif len(in_dihedral_coeffs) < 3: + # del in_dihedral_coeffs[i] + else: + i += 1 + + + +for i in range(0, len(in_dihedral_coeffs)): + type_str = in_dihedral_coeffs[i][0] + params = in_dihedral_coeffs[i][1:] + params = map(str, params) + num_fourier_terms = (len(params)-1)/3 + dihedral_coeff_str = 'dihedral_coeff '+type_str+' '+\ + dihedral_style_name+' '+\ + str(num_fourier_terms)+' '+ \ + ' '.join(params) + in_dihedral_coeffs[i] = dihedral_coeff_str + +# ---- finished processing dihedral fourier series ---- + + +sys.stdout.write(' write_once(\"In Settings\") {\n ') +sys.stdout.write('\n '.join(in_dihedral_coeffs)+'\n') +sys.stdout.write(' } # (end of dihedral_coeffs)\n') + + + + + +sys.stdout.write('\n') + +sys.stdout.write(' write_once("Data Dihedrals By Type") {\n') + +for i in range(0, len(lines_gaff)): + line = lines_gaff[i] + atypes = line[:11].split('-') + atype1 = atypes[0].strip() + atype2 = atypes[1].strip() + atype3 = atypes[2].strip() + atype4 = atypes[3].strip() + at1 = atype1.replace('X','*') + at2 = atype2.replace('X','*') + at3 = atype3.replace('X','*') + at4 = atype4.replace('X','*') + dihedraltype = '@dihedral:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4 + + sys.stdout.write(' '+dihedraltype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n') + +sys.stdout.write(' } # (end of Dihedrals By Type)\n') +sys.stdout.write('\n') + + +""" + - 6 - ***** INPUT FOR DIHEDRAL PARAMETERS ***** + + IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN + + FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2) + + IPT, ... The atom symbols for the atoms forming a dihedral + angle. If IPT .eq. 'X ' .and. LPT .eq. 'X ' then + any dihedrals in the system involving the atoms "JPT" and + and "KPT" are assigned the same parameters. This is + called the general dihedral type and is of the form + "X "-"JPT"-"KPT"-"X ". + + IDIVF The factor by which the torsional barrier is divided. + Consult Weiner, et al., JACS 106:765 (1984) p. 769 for + details. Basically, the actual torsional potential is + + (PK/IDIVF) * (1 + cos(PN*phi - PHASE)) + + PK The barrier height divided by a factor of 2. + + PHASE The phase shift angle in the torsional function. + + The unit is degrees. + + PN The periodicity of the torsional barrier. + NOTE: If PN .lt. 0.0 then the torsional potential + is assumed to have more than one term, and the + values of the rest of the terms are read from the + next cards until a positive PN is encountered. The + negative value of pn is used only for identifying + the existence of the next term and only the + absolute value of PN is kept. + + The input is terminated by a blank card. +""" diff --git a/tools/moltemplate/common/amber/amberparm_improper_to_lt.py b/tools/moltemplate/common/amber/amberparm_improper_to_lt.py new file mode 100755 index 0000000000..7123d03beb --- /dev/null +++ b/tools/moltemplate/common/amber/amberparm_improper_to_lt.py @@ -0,0 +1,90 @@ +#!/usr/bin/env python + +import sys + +lines_gaff = sys.stdin.readlines() +improper_style_name = 'cvff' + +sys.stdout.write(' write_once("In Settings") {\n') + +for i in range(0, len(lines_gaff)): + line = lines_gaff[i] + atypes = line[:11].split('-') + atype1 = atypes[0].strip() + atype2 = atypes[1].strip() + atype3 = atypes[2].strip() + atype4 = atypes[3].strip() + at1 = atype1.replace('X','*') + at2 = atype2.replace('X','*') + at3 = atype3.replace('X','*') + at4 = atype4.replace('X','*') + #impropertype = '@improper:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4 + #sys.stdout.write(' '+impropertype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n') + # Oops. This is incorrect. + # In moltemplate, the central atom is the first atom, + # In "gaff.dat", the central atom is the third atom + # http://archive.ambermd.org/201307/0519.html + impropertype = '@improper:'+atype3+'-'+atype1+'-'+atype2+'-'+atype4 + + tokens= line[11:].split() + Kn = float(tokens[0]) + dn = float(tokens[1]) + n = int(float(tokens[2])) + comments=' '.join(tokens[3:]) + + if (dn < 0.001): + sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' 1 '+str(n)+' # '+comments+'\n') + elif (179.999 < abs(dn) < 180.001): + sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' -1 '+str(n)+' # '+comments+'\n') + else: + sys.stderr.write('Error: Illegal bondImproper parameters:\n' + ' As of 2013-8-03, LAMMPS doens hot have an improper style\n' + ' which can handle impropers with gamma != 0 or 180\n') + exit(-1) + + + +sys.stdout.write(' } # (end of improper_coeffs)\n') +sys.stdout.write('\n') +sys.stdout.write(' write_once("Data Impropers By Type") {\n') + +for i in range(0, len(lines_gaff)): + line = lines_gaff[i] + atypes = line[:11].split('-') + atype1 = atypes[0].strip() + atype2 = atypes[1].strip() + atype3 = atypes[2].strip() + atype4 = atypes[3].strip() + at1 = atype1.replace('X','*') + at2 = atype2.replace('X','*') + at3 = atype3.replace('X','*') + at4 = atype4.replace('X','*') + + #impropertype = '@improper:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4 + #sys.stdout.write(' '+impropertype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n') + # Oops. This is incorrect. + # In moltemplate, the central atom is the first atom, + # In "gaff.dat", the central atom is the third atom + # http://archive.ambermd.org/201307/0519.html + impropertype = '@improper:'+atype3+'-'+atype1+'-'+atype2+'-'+atype4 + sys.stdout.write(' '+impropertype+' @atom:'+at3+' @atom:'+at1+' @atom:'+at2+' @atom:'+at4+'\n') + + +sys.stdout.write(' } # (end of Impropers By Type)\n') +sys.stdout.write('\n') + +# NOTE: AMBER documentation is not clear how the improper angle is defined. +# It's not clear if we should be using the dihedral angle between +# planes I-J-K and J-K-L. As of 2014-4, improper_style cvff does this. +# Even if we create improper interactions with the angle defined between +# the wrong planes, at least the minima should be the same +# (0 degrees or 180 degrees). +# So I'm not too worried we are getting this detail wrong long as +# we generate new impropers realizing that the 3rd atom (K) is the +# central atom (according to AMBER conventions). +# +# http://structbio.vanderbilt.edu/archives/amber-archive/2007/0408.php +# +# Currently, we only apply improper torsional angles for atoms +# in a planar conformations. Is it clear? +# Junmei diff --git a/tools/moltemplate/common/amber/amberparm_mass_to_lt.py b/tools/moltemplate/common/amber/amberparm_mass_to_lt.py new file mode 100755 index 0000000000..818b1fa303 --- /dev/null +++ b/tools/moltemplate/common/amber/amberparm_mass_to_lt.py @@ -0,0 +1,19 @@ +#!/usr/bin/env python + +import sys + +lines_gaff = sys.stdin.readlines() + +sys.stdout.write(' write_once(\"Data Masses\") {\n') + +for i in range(0, len(lines_gaff)): + line = lines_gaff[i] + tokens= line.split() + atype = tokens[0] + mass=tokens[1] + # what is the next number? (the one in tokens[2]?) + comments=' '.join(tokens[3:]) + sys.stdout.write(' @atom:'+atype+' '+mass+' # '+comments+'\n') + +sys.stdout.write(' } # (end of masses)\n') +sys.stdout.write('\n') diff --git a/tools/moltemplate/common/amber/amberparm_pair_to_lt.py b/tools/moltemplate/common/amber/amberparm_pair_to_lt.py new file mode 100755 index 0000000000..587e9b047c --- /dev/null +++ b/tools/moltemplate/common/amber/amberparm_pair_to_lt.py @@ -0,0 +1,32 @@ +#!/usr/bin/env python + +import sys + +lines_gaff = sys.stdin.readlines() + +#pair_style = 'lj/charmm/coul/long' + + # NOTE: Long-range coulombic forces were disabled intentionally. (See below) + # If you want to use long-range electrostatics, uncomment these lines: + # Instead I use hybrid lj/charmm/coul/charmm by default, because + # LAMMPS complains if you attempt to use lj/charmm/coul/long on a + # system if it does not contain any charged particles. + # Currently, moltemplate does not assign atomic charge, + # so this problem occurs frequently. + +#pair_style = 'lj/charmm/coul/charmm' +pair_style = 'lj/charmm/coul/long' + +sys.stdout.write(' write_once(\"In Settings\") {\n') + +for i in range(0, len(lines_gaff)): + line = lines_gaff[i] + tokens= line.split() + atype = tokens[0] + sig=tokens[1] + eps=tokens[2] + comments=' '.join(tokens[3:]) + sys.stdout.write(' pair_coeff @atom:'+atype+' @atom:'+atype+' '+pair_style+' '+eps+' '+sig+' # '+comments+'\n') + +sys.stdout.write(' } # (end of pair_coeffs)\n') +sys.stdout.write('\n') diff --git a/tools/moltemplate/common/gaff.lt b/tools/moltemplate/common/gaff.lt new file mode 100644 index 0000000000..a83824e271 --- /dev/null +++ b/tools/moltemplate/common/gaff.lt @@ -0,0 +1,11780 @@ +# This is the April 2014 version of GAFF (from AmberTools14). +#################################################################### +# To use this, LAMMPS currently must be compiled with the USER-MISC package. +# (Type "make yes-user-misc" into the shell before compiling LAMMPS.) +#################################################################### +# This moltemplate (LT) file was generated automatically using +# amberparm2lt.sh gaff.dat GAFF +#################################################################### +# Background information and usage explanation: +# This file contanis a list of atom types and rules for generating bonded +# interactions between these atoms (hopefully) according to AMBER conventions. +# By using the atom types shown below in your own molecules, bonds and angular +# interactions will be automatically generated. +# AMBER (GAFF) force-field parameters will also be assigned to each angle +# interaction (according to these atom types). +# One way to apply the GAFF force field to a particular type of molecule, is +# to use the "inherits" keyword when you define that molecule. For example: +# import("gaff.lt") +# MoleculeType inherits GAFF { +# write_once("Data Atoms") { +# $atom:C1 $mol:... @atom:cx 0.0 4.183 3.194 13.285 +# $atom:C2 $mol:... @atom:cx 0.0 4.291 4.618 13.382 +# : : : +# } +# } +#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.) +#################################################################### +# Moltemplate can not assign atom charge. You must assign atomic +# charges yourself. (Moltemplate is only a simple text manipulation tool.) +#################################################################### + + +GAFF { + + # ---------------------------------------------------------------------- + # The basic atom nomenclature and conventions are explained here: + # http://ambermd.org/antechamber/gaff.pdf + # For reference, the original gaff.dat file and format documenation are here: + # http://ambermd.org/AmberTools-get.html + # http://ambermd.org/formats.html#parm.dat + # ---------------------------------------------------------------------- + + write_once("Data Masses") { + @atom:c 12.01 # Sp2 C carbonyl group + @atom:c1 12.01 # Sp C + @atom:c2 12.01 # Sp2 C + @atom:c3 12.01 # Sp3 C + @atom:ca 12.01 # Sp2 C in pure aromatic systems + @atom:cp 12.01 # Head Sp2 C that connect two rings in biphenyl sys. + @atom:cq 12.01 # Head Sp2 C that connect two rings in biphenyl sys. identical to cp + @atom:cc 12.01 # Sp2 carbons in non-pure aromatic systems + @atom:cd 12.01 # Sp2 carbons in non-pure aromatic systems, identical to cc + @atom:ce 12.01 # Inner Sp2 carbons in conjugated systems + @atom:cf 12.01 # Inner Sp2 carbons in conjugated systems, identical to ce + @atom:cg 12.01 # Inner Sp carbons in conjugated systems + @atom:ch 12.01 # Inner Sp carbons in conjugated systems, identical to cg + @atom:cx 12.01 # Sp3 carbons in triangle systems + @atom:cy 12.01 # Sp3 carbons in square systems + @atom:cu 12.01 # Sp2 carbons in triangle systems + @atom:cv 12.01 # Sp2 carbons in square systems + @atom:cz 12.01 # Sp2 carbon in guanidine group + @atom:h1 1.008 # H bonded to aliphatic carbon with 1 electrwd. group + @atom:h2 1.008 # H bonded to aliphatic carbon with 2 electrwd. group + @atom:h3 1.008 # H bonded to aliphatic carbon with 3 electrwd. group + @atom:h4 1.008 # H bonded to non-sp3 carbon with 1 electrwd. group + @atom:h5 1.008 # H bonded to non-sp3 carbon with 2 electrwd. group + @atom:ha 1.008 # H bonded to aromatic carbon + @atom:hc 1.008 # H bonded to aliphatic carbon without electrwd. group + @atom:hn 1.008 # H bonded to nitrogen atoms + @atom:ho 1.008 # Hydroxyl group + @atom:hp 1.008 # H bonded to phosphate + @atom:hs 1.008 # Hydrogen bonded to sulphur + @atom:hw 1.008 # Hydrogen in water + @atom:hx 1.008 # H bonded to C next to positively charged group + @atom:f 19.00 # Fluorine + @atom:cl 35.45 # Chlorine + @atom:br 79.90 # Bromine + @atom:i 126.9 # Iodine + @atom:n 14.01 # Sp2 nitrogen in amide groups + @atom:n1 14.01 # Sp N + @atom:n2 14.01 # aliphatic Sp2 N with two connected atoms + @atom:n3 14.01 # Sp3 N with three connected atoms + @atom:n4 14.01 # Sp3 N with four connected atoms + @atom:na 14.01 # Sp2 N with three connected atoms + @atom:nb 14.01 # Sp2 N in pure aromatic systems + @atom:nc 14.01 # Sp2 N in non-pure aromatic systems + @atom:nd 14.01 # Sp2 N in non-pure aromatic systems, identical to nc + @atom:ne 14.01 # Inner Sp2 N in conjugated systems + @atom:nf 14.01 # Inner Sp2 N in conjugated systems, identical to ne + @atom:nh 14.01 # Amine N connected one or more aromatic rings + @atom:no 14.01 # Nitro N + @atom:o 16.00 # Oxygen with one connected atom + @atom:oh 16.00 # Oxygen in hydroxyl group + @atom:os 16.00 # Ether and ester oxygen + @atom:ow 16.00 # Oxygen in water + @atom:p2 30.97 # Phosphate with two connected atoms + @atom:p3 30.97 # Phosphate with three connected atoms, such as PH3 + @atom:p4 30.97 # Phosphate with three connected atoms, such as O=P(CH3)2 + @atom:p5 30.97 # Phosphate with four connected atoms, such as O=P(OH)3 + @atom:pb 30.97 # Sp2 P in pure aromatic systems + @atom:pc 30.97 # Sp2 P in non-pure aromatic systems + @atom:pd 30.97 # Sp2 P in non-pure aromatic systems, identical to pc + @atom:pe 30.97 # Inner Sp2 P in conjugated systems + @atom:pf 30.97 # Inner Sp2 P in conjugated systems, identical to pe + @atom:px 30.97 # Special p4 in conjugated systems + @atom:py 30.97 # Special p5 in conjugated systems + @atom:s 32.06 # S with one connected atom + @atom:s2 32.06 # S with two connected atom, involved at least one double bond + @atom:s4 32.06 # S with three connected atoms + @atom:s6 32.06 # S with four connected atoms + @atom:sh 32.06 # Sp3 S connected with hydrogen + @atom:ss 32.06 # Sp3 S in thio-ester and thio-ether + @atom:sx 32.06 # Special s4 in conjugated systems + @atom:sy 32.06 # Special s6 in conjugated systems + } # (end of masses) + + write_once("In Settings") { + pair_coeff @atom:h1 @atom:h1 lj/charmm/coul/long 0.0157 1.3870 # Veenstra et al JCC,8,(1992),963 + pair_coeff @atom:h2 @atom:h2 lj/charmm/coul/long 0.0157 1.2870 # Veenstra et al JCC,8,(1992),963 + pair_coeff @atom:h3 @atom:h3 lj/charmm/coul/long 0.0157 1.1870 # Veenstra et al JCC,8,(1992),963 + pair_coeff @atom:h4 @atom:h4 lj/charmm/coul/long 0.0150 1.4090 # Spellmeyer, one electrowithdr. neighbor + pair_coeff @atom:h5 @atom:h5 lj/charmm/coul/long 0.0150 1.3590 # Spellmeyer, two electrowithdr. neighbor + pair_coeff @atom:ha @atom:ha lj/charmm/coul/long 0.0150 1.4590 # Spellmeyer + pair_coeff @atom:hc @atom:hc lj/charmm/coul/long 0.0157 1.4870 # OPLS + pair_coeff @atom:hn @atom:hn lj/charmm/coul/long 0.0157 0.6000 # !Ferguson base pair geom. + pair_coeff @atom:ho @atom:ho lj/charmm/coul/long 0.0000 0.0000 # OPLS Jorgensen, JACS,110,(1988),1657 + pair_coeff @atom:hp @atom:hp lj/charmm/coul/long 0.0157 0.6000 # same to hs (be careful !) + pair_coeff @atom:hs @atom:hs lj/charmm/coul/long 0.0157 0.6000 # W. Cornell CH3SH --> CH3OH FEP + pair_coeff @atom:hw @atom:hw lj/charmm/coul/long 0.0000 0.0000 # OPLS Jorgensen, JACS,110,(1988),1657 + pair_coeff @atom:hx @atom:hx lj/charmm/coul/long 0.0157 1.1000 # Veenstra et al JCC,8,(1992),963 + pair_coeff @atom:o @atom:o lj/charmm/coul/long 0.2100 1.6612 # OPLS + pair_coeff @atom:oh @atom:oh lj/charmm/coul/long 0.2104 1.7210 # OPLS + pair_coeff @atom:os @atom:os lj/charmm/coul/long 0.1700 1.6837 # OPLS ether + pair_coeff @atom:ow @atom:ow lj/charmm/coul/long 0.1520 1.7683 # TIP3P water model + pair_coeff @atom:c @atom:c lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:c1 @atom:c1 lj/charmm/coul/long 0.2100 1.9080 # cp C DLM 11/2007 well depth from OPLS replacing 0.0860 + pair_coeff @atom:c2 @atom:c2 lj/charmm/coul/long 0.0860 1.9080 # sp2 atom in the middle of C=CD-CD=C + pair_coeff @atom:c3 @atom:c3 lj/charmm/coul/long 0.1094 1.9080 # OPLS + pair_coeff @atom:ca @atom:ca lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:cc @atom:cc lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:cd @atom:cd lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:ce @atom:ce lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:cf @atom:cf lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:cg @atom:cg lj/charmm/coul/long 0.2100 1.9080 # DLM 12/2007 as c1 + pair_coeff @atom:ch @atom:ch lj/charmm/coul/long 0.2100 1.9080 # DLM 12/2007 as c1 + pair_coeff @atom:cp @atom:cp lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:cq @atom:cq lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:cu @atom:cu lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:cv @atom:cv lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:cx @atom:cx lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:cy @atom:cy lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:cz @atom:cz lj/charmm/coul/long 0.0860 1.9080 # OPLS + pair_coeff @atom:n @atom:n lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:n1 @atom:n1 lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:n2 @atom:n2 lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:n3 @atom:n3 lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:n4 @atom:n4 lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:na @atom:na lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:nb @atom:nb lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:nc @atom:nc lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:nd @atom:nd lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:ne @atom:ne lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:nf @atom:nf lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:nh @atom:nh lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:no @atom:no lj/charmm/coul/long 0.1700 1.8240 # OPLS + pair_coeff @atom:s @atom:s lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:s2 @atom:s2 lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:s4 @atom:s4 lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:s6 @atom:s6 lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:sx @atom:sx lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:sy @atom:sy lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:sh @atom:sh lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:ss @atom:ss lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's + pair_coeff @atom:p2 @atom:p2 lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:p3 @atom:p3 lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:p4 @atom:p4 lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:p5 @atom:p5 lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:pb @atom:pb lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:pc @atom:pc lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:pd @atom:pd lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:pe @atom:pe lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:pf @atom:pf lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:px @atom:px lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:py @atom:py lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230; + pair_coeff @atom:f @atom:f lj/charmm/coul/long 0.061 1.75 # Gough et al. JCC 13,(1992),963. + pair_coeff @atom:cl @atom:cl lj/charmm/coul/long 0.265 1.948 # Fox, JPCB,102,8070,(98),flex.mdl CHCl3 + pair_coeff @atom:br @atom:br lj/charmm/coul/long 0.420 2.02 # Junmei, 2010 + pair_coeff @atom:i @atom:i lj/charmm/coul/long 0.50 2.15 # Junmei, 2010 + } # (end of pair_coeffs) + + write_once("In Settings") { + bond_coeff @bond:ow-hw harmonic 553.0 0.9572 # TIP3P_Water 1 + bond_coeff @bond:hw-hw harmonic 553.0 1.5136 # TIP3P_Water 1 + bond_coeff @bond:br-br harmonic 123.2 2.5420 # SOURCE1 4 0.0000 + bond_coeff @bond:br-c1 harmonic 352.7 1.7870 # SOURCE2 4 0.0024 + bond_coeff @bond:br-c2 harmonic 278.7 1.8830 # SOURCE1 31 0.0000 + bond_coeff @bond:br-c harmonic 240.3 1.9460 # SOURCE2 2 0.0285 + bond_coeff @bond:br-c3 harmonic 229.5 1.9660 # SOURCE1 100 0.0000 + bond_coeff @bond:br-ca harmonic 269.6 1.8970 # SOURCE1 127 0.0058 + bond_coeff @bond:br-cc harmonic 277.6 1.8847 # SOURCE4 39 0.0068 + bond_coeff @bond:br-cx harmonic 261.4 1.9100 # SOURCE1 8 0.0000 + bond_coeff @bond:br-i harmonic 142.4 2.6710 # SOURCE1 2 0.0245 + bond_coeff @bond:br-n1 harmonic 330.4 1.8600 # SOUECE3 1 + bond_coeff @bond:br-n2 harmonic 219.0 2.0380 # SOURCE3 5 0.1082 + bond_coeff @bond:br-n harmonic 320.2 1.8730 # SOURCE3 4 0.0046 + bond_coeff @bond:br-n3 harmonic 265.9 1.9520 # SOURCE3 2 0.0000 + bond_coeff @bond:br-n4 harmonic 282.4 1.9260 # SOURCE3 3 0.0013 + bond_coeff @bond:br-na harmonic 237.3 2.0020 # SOURCE3 7 0.2156 + bond_coeff @bond:br-nh harmonic 270.9 1.9440 # SOURCE3 1 0.0000 + bond_coeff @bond:br-no harmonic 191.0 2.1010 # SOURCE3 1 0.0000 + bond_coeff @bond:br-o harmonic 278.9 1.8000 # SOUECE3 1 + bond_coeff @bond:br-oh harmonic 237.2 1.8660 # SOURCE3 1 0.0000 + bond_coeff @bond:br-os harmonic 225.6 1.8870 # SOURCE3 2 0.0000 + bond_coeff @bond:br-p2 harmonic 174.3 2.2100 # SOURCE3 9 0.0510 + bond_coeff @bond:br-p3 harmonic 167.0 2.2310 # SOURCE3 3 0.0101 + bond_coeff @bond:br-p4 harmonic 188.8 2.1710 # SOUECE3 1 + bond_coeff @bond:br-p5 harmonic 179.3 2.1960 # SOURCE3 3 0.0099 + bond_coeff @bond:br-s harmonic 170.6 2.2200 # SOUECE3 1 + bond_coeff @bond:br-s4 harmonic 134.3 2.3410 # SOURCE3 1 0.0000 + bond_coeff @bond:br-s6 harmonic 172.7 2.2140 # SOURCE3 3 0.0443 + bond_coeff @bond:br-sh harmonic 174.4 2.2090 # SOURCE3 1 0.0000 + bond_coeff @bond:br-ss harmonic 176.6 2.2030 # SOURCE3 3 0.0035 + bond_coeff @bond:c1-c1 harmonic 986.2 1.1810 # SOURCE1 265 0.0031 + bond_coeff @bond:c1-c2 harmonic 625.0 1.3070 # SOURCE1 18 0.0000 + bond_coeff @bond:c1-c3 harmonic 368.3 1.4700 # SOURCE1 215 0.0017 + bond_coeff @bond:c1-ca harmonic 404.1 1.4400 # SOUECE3 1 + bond_coeff @bond:c1-ce harmonic 607.4 1.3153 # SOURCE4 6 0.0086 + bond_coeff @bond:c1-cg harmonic 845.8 1.2220 # SOURCE3 22 0.0101 + bond_coeff @bond:c1-ch harmonic 845.8 1.2220 # SOURCE3 22 same_as_c1-cg + bond_coeff @bond:c1-cl harmonic 419.7 1.6310 # SOURCE2 6 0.0050 + bond_coeff @bond:c1-cx harmonic 399.1 1.4440 # SOURCE1 38 0.0000 + bond_coeff @bond:c1-f harmonic 469.4 1.2700 # SOURCE2 2 0.0085 + bond_coeff @bond:c1-ha harmonic 375.9 1.0660 # SOURCE3 63 0.0035 + bond_coeff @bond:c1-hc harmonic 385.6 1.0600 # SOUECE3 1 + bond_coeff @bond:c1-i harmonic 318.8 1.9890 # SOURCE2 4 0.0032 + bond_coeff @bond:c1-n1 harmonic 1014.5 1.1380 # SOURCE1 170 0.0055 + bond_coeff @bond:c1-n2 harmonic 769.8 1.2100 # SOURCE3 5 0.0115 + bond_coeff @bond:c1-n3 harmonic 409.8 1.3920 # SOURCE2 1 0.0000 + bond_coeff @bond:c1-n4 harmonic 378.2 1.4170 # SOURCE3 3 0.0032 + bond_coeff @bond:c1-n harmonic 503.0 1.3300 # SOUECE3 1 + bond_coeff @bond:c1-na harmonic 452.0 1.3620 # SOURCE3 8 0.0034 + bond_coeff @bond:c1-ne harmonic 803.3 1.1986 # SOURCE4 10 0.0088 + bond_coeff @bond:c1-nf harmonic 803.3 1.1986 # SOURCE4 10 same_as_c1-ne + bond_coeff @bond:c1-nh harmonic 485.0 1.3408 # SOURCE4 11 0.0037 + bond_coeff @bond:c1-no harmonic 393.0 1.4050 # SOURCE3 3 0.0005 + bond_coeff @bond:c1-o harmonic 777.0 1.1660 # SOURCE2 9 0.0052 + bond_coeff @bond:c1-oh harmonic 435.6 1.3260 # SOURCE3 1 0.0000 + bond_coeff @bond:c1-os harmonic 437.1 1.3250 # SOURCE3 3 0.0148 + bond_coeff @bond:c1-p2 harmonic 289.3 1.7700 # SOUECE3 1 + bond_coeff @bond:c1-p3 harmonic 275.1 1.7900 # SOUECE3 1 + bond_coeff @bond:c1-p4 harmonic 275.1 1.7900 # SOUECE3 1 + bond_coeff @bond:c1-p5 harmonic 302.2 1.7530 # SOURCE3 2 0.0000 + bond_coeff @bond:c1-s2 harmonic 410.0 1.5950 # SOURCE3 1 0.0000 + bond_coeff @bond:c1-s harmonic 371.8 1.6300 # SOURCE1 14 0.0000 + bond_coeff @bond:c1-s4 harmonic 272.9 1.7460 # SOURCE3 2 0.0000 + bond_coeff @bond:c1-s6 harmonic 290.4 1.7220 # SOURCE3 2 0.0000 + bond_coeff @bond:c1-sh harmonic 324.5 1.6800 # SOUECE3 1 + bond_coeff @bond:c1-ss harmonic 325.4 1.6790 # SOURCE1 10 0.0000 + bond_coeff @bond:c2-c2 harmonic 589.7 1.3240 # SOURCE1 974 0.0096 + bond_coeff @bond:c2-c3 harmonic 328.3 1.5080 # SOURCE1 2536 0.0021 + bond_coeff @bond:c2-ca harmonic 357.2 1.4800 # SOUECE3 1 + bond_coeff @bond:c2-cc harmonic 522.6 1.3600 # SOURCE1 771 0.0185 + bond_coeff @bond:c2-cd harmonic 522.6 1.3600 # SOURCE1 771 0.0185 + bond_coeff @bond:c2-ce harmonic 560.5 1.3390 # SOURCE3 62 0.0128 + bond_coeff @bond:c2-cf harmonic 560.5 1.3390 # SOURCE3 62 same_as_c2-ce + bond_coeff @bond:c2-cl harmonic 328.8 1.7220 # SOURCE1 163 0.0098 + bond_coeff @bond:c2-cu harmonic 573.9 1.3320 # SOURCE2 1 0.0000 + bond_coeff @bond:c2-cx harmonic 353.3 1.4836 # SOURCE4 26 0.0064 + bond_coeff @bond:c2-cy harmonic 331.7 1.5046 # SOURCE4 9 0.0053 + bond_coeff @bond:c2-f harmonic 368.7 1.3400 # SOURCE1 34 0.0000 + bond_coeff @bond:c2-h4 harmonic 348.6 1.0840 # SOURCE3 40 0.0058 + bond_coeff @bond:c2-h5 harmonic 338.0 1.0915 # SOURCE4 42 0.0017 + bond_coeff @bond:c2-ha harmonic 344.3 1.0870 # SOURCE3 797 0.0046 + bond_coeff @bond:c2-hc harmonic 344.3 1.0870 # SOURCE3 789 0.0046 + bond_coeff @bond:c2-hx harmonic 350.1 1.0830 # SOURCE3 3 0.0008 + bond_coeff @bond:c2-i harmonic 223.2 2.1530 # SOURCE3 2 0.0000 + bond_coeff @bond:c2-n1 harmonic 546.0 1.3060 # SOURCE3 4 0.0161 + bond_coeff @bond:c2-n2 harmonic 581.1 1.2880 # SOURCE1 103 0.0100 + bond_coeff @bond:c2-n3 harmonic 486.3 1.3400 # SOUECE3 1 + bond_coeff @bond:c2-n harmonic 390.5 1.4070 # SOURCE3 9 0.0124 + bond_coeff @bond:c2-n4 harmonic 309.1 1.4820 # SOURCE3 5 0.0064 + bond_coeff @bond:c2-na harmonic 411.1 1.3910 # SOURCE3 31 0.0289 + bond_coeff @bond:c2-nc harmonic 533.0 1.3130 # SOURCE1 99 0.0095 + bond_coeff @bond:c2-nd harmonic 533.0 1.3130 # SOURCE1 99 same_as_c2-nc + bond_coeff @bond:c2-ne harmonic 597.7 1.2800 # SOURCE3 37 0.0110 + bond_coeff @bond:c2-nf harmonic 597.7 1.2800 # SOURCE3 37 same_as_c2-ne + bond_coeff @bond:c2-nh harmonic 462.6 1.3550 # SOURCE3 38 0.0413 + bond_coeff @bond:c2-no harmonic 345.6 1.4457 # SOURCE4 7 0.0087 + bond_coeff @bond:c2-o harmonic 623.6 1.2244 # SOURCE4 15 0.0036 + bond_coeff @bond:c2-oh harmonic 425.4 1.3330 # SOURCE1 53 0.0000 + bond_coeff @bond:c2-os harmonic 392.6 1.3570 # SOURCE1 315 0.0097 + bond_coeff @bond:c2-p2 harmonic 375.9 1.6700 # SOURCE3 62 0.0147 + bond_coeff @bond:c2-p3 harmonic 246.6 1.8340 # SOURCE3 5 0.0042 + bond_coeff @bond:c2-p4 harmonic 254.0 1.8220 # SOUECE3 1 + bond_coeff @bond:c2-p5 harmonic 228.2 1.8658 # SOURCE4 5 0.0025 + bond_coeff @bond:c2-pe harmonic 355.3 1.6910 # SOURCE3 52 0.0542 + bond_coeff @bond:c2-pf harmonic 355.3 1.6910 # SOURCE3 52 same_as_c2-pe + bond_coeff @bond:c2-s2 harmonic 393.1 1.6100 # SOURCE2 1 0.0000 + bond_coeff @bond:c2-s harmonic 281.5 1.7340 # SOURCE3 4 0.0034 + bond_coeff @bond:c2-s4 harmonic 263.2 1.7600 # SOUECE3 1 + bond_coeff @bond:c2-s6 harmonic 263.2 1.7600 # SOUECE3 1 + bond_coeff @bond:c2-sh harmonic 252.0 1.7771 # SOURCE4 5 0.0037 + bond_coeff @bond:c2-ss harmonic 280.0 1.7360 # SOURCE1 209 0.0155 + bond_coeff @bond:c3-c3 harmonic 303.1 1.5350 # SOURCE1 14664 0.0048 + bond_coeff @bond:c3-ca harmonic 323.5 1.5130 # SOURCE1 1813 0.0000 + bond_coeff @bond:c3-cc harmonic 337.3 1.4990 # SOURCE3 50 0.0096 + bond_coeff @bond:c3-cd harmonic 337.3 1.4990 # SOURCE3 50 0.0096 + bond_coeff @bond:c3-ce harmonic 331.3 1.5050 # SOURCE3 9 0.0024 + bond_coeff @bond:c3-cf harmonic 331.3 1.5050 # SOURCE3 9 same_as_c3-ce + bond_coeff @bond:c3-cl harmonic 279.0 1.7860 # SOURCE1 267 0.0194 + bond_coeff @bond:c3-cu harmonic 359.4 1.4780 # SOURCE1 7 0.0000 + bond_coeff @bond:c3-cv harmonic 347.6 1.4890 # SOURCE1 11 0.0000 + bond_coeff @bond:c3-cx harmonic 322.5 1.5140 # SOURCE1 712 0.0045 + bond_coeff @bond:c3-cy harmonic 308.5 1.5290 # SOURCE1 376 0.0000 + bond_coeff @bond:c3-f harmonic 363.8 1.3440 # SOURCE1 617 0.0281 + bond_coeff @bond:c3-h1 harmonic 335.9 1.0930 # SOURCE3 2175 0.0082 + bond_coeff @bond:c3-h2 harmonic 326.4 1.1000 # SOURCE3 66 0.0280 + bond_coeff @bond:c3-h3 harmonic 333.4 1.0948 # SOURCE4 25 0.0026 + bond_coeff @bond:c3-hc harmonic 337.3 1.0920 # SOURCE3 2815 0.0059 + bond_coeff @bond:c3-hx harmonic 338.7 1.0910 # SOURCE3 146 0.0066 + bond_coeff @bond:c3-i harmonic 219.1 2.1620 # SOURCE1 15 0.0000 + bond_coeff @bond:c3-n1 harmonic 325.1 1.4700 # SOURCE3 0 + bond_coeff @bond:c3-n2 harmonic 313.8 1.4770 # SOURCE1 129 0.0138 + bond_coeff @bond:c3-n harmonic 330.6 1.4600 # SOURCE1 187 0.0079 + bond_coeff @bond:c3-n3 harmonic 320.6 1.4700 # SOURCE1 1678 0.0017 + bond_coeff @bond:c3-n4 harmonic 293.6 1.4990 # SOURCE1 1370 0.0000 + bond_coeff @bond:c3-na harmonic 334.7 1.4560 # SOURCE3 23 0.0119 + bond_coeff @bond:c3-nc harmonic 334.7 1.4560 # SOURCE3 9 0.0109 + bond_coeff @bond:c3-nd harmonic 334.7 1.4560 # SOURCE3 9 same_as_c3-nc + bond_coeff @bond:c3-nh harmonic 332.7 1.4580 # SOURCE3 27 0.0085 + bond_coeff @bond:c3-no harmonic 265.4 1.5330 # SOURCE1 83 0.0212 + bond_coeff @bond:c3-o harmonic 449.9 1.3165 # SOURCE4 8 0.0193 + bond_coeff @bond:c3-oh harmonic 314.1 1.4260 # SOURCE1 914 0.0129 + bond_coeff @bond:c3-os harmonic 301.5 1.4390 # SOURCE1 3123 0.0126 + bond_coeff @bond:c3-p2 harmonic 234.3 1.8550 # SOURCE3 9 0.0125 + bond_coeff @bond:c3-p3 harmonic 240.6 1.8440 # SOURCE3 109 0.0107 + bond_coeff @bond:c3-p4 harmonic 247.2 1.8330 # SOURCE3 29 0.0138 + bond_coeff @bond:c3-p5 harmonic 259.7 1.8130 # SOURCE1 84 0.0000 + bond_coeff @bond:c3-px harmonic 252.7 1.8240 # SOURCE3 28 0.0098 + bond_coeff @bond:c3-py harmonic 259.7 1.8130 # SOURCE3 13 0.0163 + bond_coeff @bond:c3-s harmonic 212.9 1.8450 # SOURCE3 4 0.0185 + bond_coeff @bond:c3-s4 harmonic 233.8 1.8070 # SOURCE1 139 0.0023 + bond_coeff @bond:c3-s6 harmonic 254.0 1.7740 # SOURCE1 118 0.0103 + bond_coeff @bond:c3-sh harmonic 225.3 1.8220 # SOURCE3 12 0.0051 + bond_coeff @bond:c3-ss harmonic 225.8 1.8210 # SOURCE1 358 0.0075 + bond_coeff @bond:c3-sx harmonic 232.6 1.8090 # SOURCE3 30 0.0067 + bond_coeff @bond:c3-sy harmonic 248.9 1.7820 # SOURCE3 31 0.0039 + bond_coeff @bond:ca-ca harmonic 478.4 1.3870 # SOURCE1 6228 0.0147 + bond_coeff @bond:ca-cc harmonic 411.7 1.4340 # SOURCE1 80 0.0000 + bond_coeff @bond:ca-cd harmonic 411.7 1.4340 # SOURCE1 80 0.0000 + bond_coeff @bond:ca-ce harmonic 366.0 1.4720 # SOURCE1 71 0.0030 + bond_coeff @bond:ca-cf harmonic 366.0 1.4720 # SOURCE1 71 0.0030 + bond_coeff @bond:ca-cg harmonic 406.6 1.4380 # SOURCE1 71 0.0045 + bond_coeff @bond:ca-ch harmonic 406.6 1.4380 # SOURCE1 71 0.0045 + bond_coeff @bond:ca-cl harmonic 322.8 1.7290 # SOURCE1 704 0.0095 + bond_coeff @bond:ca-cp harmonic 461.8 1.3980 # CORR 28 + bond_coeff @bond:ca-cq harmonic 461.8 1.3980 # CORR 28 + bond_coeff @bond:ca-cx harmonic 350.8 1.4860 # SOURCE1 98 0.0118 + bond_coeff @bond:ca-cy harmonic 323.0 1.5135 # SOURCE4 8 0.0043 + bond_coeff @bond:ca-f harmonic 363.8 1.3440 # SOURCE1 205 0.0089 + bond_coeff @bond:ca-h4 harmonic 342.9 1.0880 # SOURCE3 57 0.0026 + bond_coeff @bond:ca-h5 harmonic 347.2 1.0850 # SOURCE3 15 0.0048 + bond_coeff @bond:ca-ha harmonic 344.3 1.0870 # SOURCE3 1496 0.0045 + bond_coeff @bond:ca-i harmonic 252.4 2.0950 # SOURCE1 51 0.0000 + bond_coeff @bond:ca-n1 harmonic 398.1 1.4000 # SOURCE3 0 + bond_coeff @bond:ca-n2 harmonic 551.6 1.3030 # SOURCE4 7 0.0058 + bond_coeff @bond:ca-n harmonic 372.3 1.4220 # SOURCE3 9 0.0098 + bond_coeff @bond:ca-n4 harmonic 325.6 1.4650 # SOURCE1 23 0.0000 + bond_coeff @bond:ca-na harmonic 470.3 1.3500 # SOURCE1 150 0.0103 + bond_coeff @bond:ca-nb harmonic 483.1 1.3420 # SOURCE3 104 0.0076 + bond_coeff @bond:ca-nc harmonic 492.9 1.3360 # SOURCE1 1826 0.0020 + bond_coeff @bond:ca-nd harmonic 492.9 1.3360 # SOURCE1 1826 0.0020 + bond_coeff @bond:ca-ne harmonic 361.8 1.4310 # SOURCE1 52 0.0000 + bond_coeff @bond:ca-nf harmonic 361.8 1.4310 # SOURCE1 52 0.0000 + bond_coeff @bond:ca-nh harmonic 449.0 1.3640 # SOURCE1 137 0.0085 + bond_coeff @bond:ca-no harmonic 322.6 1.4680 # SOURCE1 556 0.0000 + bond_coeff @bond:ca-o harmonic 610.0 1.2304 # SOURCE4 5 0.0026 + bond_coeff @bond:ca-oh harmonic 386.1 1.3620 # SOURCE1 551 0.0000 + bond_coeff @bond:ca-os harmonic 372.4 1.3730 # SOURCE1 1092 0.0071 + bond_coeff @bond:ca-p2 harmonic 243.0 1.8400 # SOUECE3 1 + bond_coeff @bond:ca-p3 harmonic 252.7 1.8240 # SOURCE1 145 0.0187 + bond_coeff @bond:ca-p4 harmonic 264.3 1.8060 # SOUECE3 1 + bond_coeff @bond:ca-p5 harmonic 271.6 1.7950 # SOURCE1 571 0.0028 + bond_coeff @bond:ca-pe harmonic 249.6 1.8290 # SOURCE3 10 0.0042 + bond_coeff @bond:ca-pf harmonic 249.6 1.8290 # SOURCE3 10 0.0042 + bond_coeff @bond:ca-px harmonic 252.1 1.8250 # SOURCE3 5 0.0168 + bond_coeff @bond:ca-py harmonic 268.3 1.7999 # SOURCE4 5 0.0072 + bond_coeff @bond:ca-s harmonic 277.9 1.7390 # SOURCE3 2 0.0000 + bond_coeff @bond:ca-s4 harmonic 245.2 1.7880 # SOURCE1 51 0.0048 + bond_coeff @bond:ca-s6 harmonic 263.9 1.7590 # SOURCE1 229 0.0036 + bond_coeff @bond:ca-sh harmonic 251.3 1.7783 # SOURCE4 12 0.0041 + bond_coeff @bond:ca-ss harmonic 256.6 1.7700 # SOURCE1 297 0.0041 + bond_coeff @bond:ca-sx harmonic 223.5 1.8252 # SOURCE4 24 0.0032 + bond_coeff @bond:ca-sy harmonic 247.7 1.7840 # SOURCE3 13 0.0094 + bond_coeff @bond:c-c1 harmonic 379.8 1.4600 # SOUECE3 1 + bond_coeff @bond:c-c2 harmonic 449.9 1.4060 # SOURCE3 2 0.0370 + bond_coeff @bond:c-c harmonic 290.1 1.5500 # SOURCE1 31 0.0100 + bond_coeff @bond:c-c3 harmonic 328.3 1.5080 # SOURCE1 2949 0.0060 + bond_coeff @bond:c-ca harmonic 349.7 1.4870 # SOURCE1 480 0.0055 + bond_coeff @bond:c-cc harmonic 377.4 1.4620 # SOURCE3 132 0.0210 + bond_coeff @bond:cc-cc harmonic 418.3 1.4290 # SOURCE1 740 0.0069 + bond_coeff @bond:cc-cd harmonic 504.0 1.3710 # SOURCE3 523 0.0217 + bond_coeff @bond:cc-ce harmonic 387.9 1.4532 # CORR 249 + bond_coeff @bond:cc-cf harmonic 511.3 1.3666 # CORR 70 + bond_coeff @bond:cc-cg harmonic 420.9 1.4270 # SOURCE1 560 0.0000 + bond_coeff @bond:cc-ch harmonic 420.9 1.4270 # SOURCE1 560 0.0000 + bond_coeff @bond:cc-cl harmonic 317.1 1.7359 # CORR 66 + bond_coeff @bond:cc-cx harmonic 366.6 1.4715 # CORR 24 + bond_coeff @bond:c-cd harmonic 377.4 1.4620 # SOURCE3 132 0.0210 + bond_coeff @bond:c-ce harmonic 363.8 1.4740 # SOURCE1 601 0.0105 + bond_coeff @bond:c-cf harmonic 363.8 1.4740 # SOURCE1 601 0.0105 + bond_coeff @bond:cc-f harmonic 368.6 1.3401 # SOURCE4 24 0.0034 + bond_coeff @bond:c-cg harmonic 389.3 1.4520 # SOURCE3 2 0.0000 + bond_coeff @bond:c-ch harmonic 389.3 1.4520 # SOURCE3 2 same_as_c-cg + bond_coeff @bond:cc-h4 harmonic 350.1 1.0830 # SOURCE3 599 0.0037 + bond_coeff @bond:cc-h5 harmonic 356.0 1.0790 # SOURCE3 40 0.0051 + bond_coeff @bond:cc-ha harmonic 347.2 1.0850 # SOURCE3 740 0.0039 + bond_coeff @bond:c-cl harmonic 293.5 1.7660 # SOURCE3 6 0.0250 + bond_coeff @bond:cc-n2 harmonic 573.8 1.2917 # CORR 81 + bond_coeff @bond:cc-n harmonic 426.0 1.3800 # SOURCE3 56 0.0109 + bond_coeff @bond:cc-n4 harmonic 299.0 1.4930 # SOURCE4 7 0.0148 + bond_coeff @bond:cc-na harmonic 438.8 1.3710 # SOURCE3 440 0.0144 + bond_coeff @bond:cc-nc harmonic 431.6 1.3760 # SOURCE1 88 0.0000 + bond_coeff @bond:cc-nd harmonic 494.6 1.3350 # SOURCE3 203 0.0239 + bond_coeff @bond:cc-ne harmonic 427.4 1.3790 # SOURCE4 30 0.0126 + bond_coeff @bond:cc-nf harmonic 565.4 1.2960 # CORR 23 + bond_coeff @bond:cc-nh harmonic 449.0 1.3640 # SOURCE3 6 0.0040 + bond_coeff @bond:cc-no harmonic 367.4 1.4262 # SOURCE4 133 0.0061 + bond_coeff @bond:cc-oh harmonic 408.5 1.3451 # CORR 121 + bond_coeff @bond:cc-os harmonic 376.1 1.3700 # SOURCE3 86 0.0192 + bond_coeff @bond:cc-pd harmonic 318.2 1.7330 # SOURCE3 84 0.0161 + bond_coeff @bond:cc-sh harmonic 257.9 1.7681 # SOURCE4 8 0.0027 + bond_coeff @bond:cc-ss harmonic 279.3 1.7370 # SOURCE3 52 0.0194 + bond_coeff @bond:cc-sx harmonic 231.3 1.8113 # SOURCE4 16 0.0050 + bond_coeff @bond:cc-sy harmonic 248.1 1.7834 # CORR 55 + bond_coeff @bond:c-cu harmonic 441.4 1.4120 # SOURCE2 1 0.0000 + bond_coeff @bond:c-cx harmonic 350.8 1.4860 # SOURCE1 105 0.0000 + bond_coeff @bond:c-cy harmonic 308.5 1.5290 # SOURCE1 18 0.0000 + bond_coeff @bond:cd-cd harmonic 418.3 1.4290 # SOURCE1 740 0.0069 + bond_coeff @bond:cd-ce harmonic 511.3 1.3666 # CORR 70 + bond_coeff @bond:cd-cf harmonic 387.9 1.4532 # CORR 249 + bond_coeff @bond:cd-cg harmonic 420.9 1.4270 # SOURCE1 560 0.0000 + bond_coeff @bond:cd-ch harmonic 420.9 1.4270 # SOURCE1 560 0.0000 + bond_coeff @bond:cd-cl harmonic 317.1 1.7359 # CORR 66 + bond_coeff @bond:cd-cx harmonic 366.6 1.4715 # CORR 24 + bond_coeff @bond:cd-cy harmonic 330.9 1.5054 # SOURCE4 10 0.0008 + bond_coeff @bond:cd-h4 harmonic 350.1 1.0830 # SOURCE3 599 0.0037 + bond_coeff @bond:cd-h5 harmonic 356.0 1.0790 # SOURCE3 40 0.0051 + bond_coeff @bond:cd-ha harmonic 347.2 1.0850 # SOURCE3 740 0.0039 + bond_coeff @bond:cd-n2 harmonic 573.8 1.2917 # CORR 81 + bond_coeff @bond:cd-n harmonic 426.0 1.3800 # SOURCE3 56 0.0109 + bond_coeff @bond:cd-na harmonic 438.8 1.3710 # SOURCE3 440 0.0144 + bond_coeff @bond:cd-nc harmonic 494.6 1.3350 # SOURCE3 203 0.0239 + bond_coeff @bond:cd-nd harmonic 431.6 1.3760 # SOURCE1 88 0.0000 + bond_coeff @bond:cd-ne harmonic 565.4 1.2960 # CORR 23 + bond_coeff @bond:cd-nh harmonic 449.0 1.3640 # SOURCE3 6 0.0040 + bond_coeff @bond:cd-oh harmonic 408.5 1.3451 # CORR 121 + bond_coeff @bond:cd-os harmonic 376.1 1.3700 # SOURCE3 86 0.0192 + bond_coeff @bond:cd-pc harmonic 318.2 1.7330 # SOURCE3 84 same_as_cc-pd + bond_coeff @bond:cd-ss harmonic 279.3 1.7370 # SOURCE3 52 0.0194 + bond_coeff @bond:cd-sy harmonic 248.1 1.7834 # CORR 55 + bond_coeff @bond:ce-ce harmonic 390.5 1.4510 # SOURCE1 66 0.0060 + bond_coeff @bond:ce-cf harmonic 562.4 1.3380 # SOURCE1 543 0.0045 + bond_coeff @bond:ce-cg harmonic 415.6 1.4310 # SOURCE1 22 0.0000 + bond_coeff @bond:ce-ch harmonic 415.6 1.4310 # SOURCE1 22 0.0000 + bond_coeff @bond:ce-cl harmonic 292.6 1.7671 # SOURCE4 24 0.0062 + bond_coeff @bond:ce-cx harmonic 337.0 1.4993 # SOURCE4 5 0.0066 + bond_coeff @bond:ce-cy harmonic 323.0 1.5135 # SOURCE4 17 0.0024 + bond_coeff @bond:ce-h4 harmonic 337.4 1.0919 # CORR 144 + bond_coeff @bond:ce-ha harmonic 341.5 1.0890 # SOURCE3 55 0.0056 + bond_coeff @bond:ce-n1 harmonic 536.1 1.3113 # CORR 13 + bond_coeff @bond:ce-n2 harmonic 599.8 1.2790 # SOURCE1 75 0.0000 + bond_coeff @bond:ce-n harmonic 368.9 1.4249 # CORR 136 + bond_coeff @bond:ce-na harmonic 373.8 1.4207 # SOURCE4 5 0.0051 + bond_coeff @bond:ce-ne harmonic 381.8 1.4140 # SOURCE3 7 0.0103 + bond_coeff @bond:ce-nf harmonic 574.0 1.2916 # CORR 42 + bond_coeff @bond:ce-nh harmonic 412.3 1.3901 # CORR 168 + bond_coeff @bond:ce-oh harmonic 402.9 1.3493 # CORR 37 + bond_coeff @bond:ce-os harmonic 372.8 1.3727 # CORR 45 + bond_coeff @bond:ce-p2 harmonic 259.1 1.8140 # SOUECE3 1 + bond_coeff @bond:ce-pe harmonic 256.5 1.8180 # SOURCE3 8 0.0108 + bond_coeff @bond:ce-px harmonic 254.6 1.8210 # SOURCE3 6 0.0046 + bond_coeff @bond:ce-py harmonic 272.3 1.7940 # SOURCE3 5 0.0045 + bond_coeff @bond:ce-s harmonic 324.5 1.6800 # SOUECE3 1 + bond_coeff @bond:ce-ss harmonic 243.6 1.7906 # SOURCE4 10 0.0064 + bond_coeff @bond:ce-sx harmonic 239.7 1.7970 # SOURCE3 5 0.0082 + bond_coeff @bond:ce-sy harmonic 248.9 1.7820 # SOURCE3 5 0.0114 + bond_coeff @bond:c-f harmonic 387.9 1.3250 # SOURCE2 6 0.0147 + bond_coeff @bond:cf-cf harmonic 390.5 1.4510 # SOURCE1 66 0.0060 + bond_coeff @bond:cf-cg harmonic 415.6 1.4310 # SOURCE1 22 0.0000 + bond_coeff @bond:cf-ch harmonic 415.6 1.4310 # SOURCE1 22 0.0000 + bond_coeff @bond:cf-h4 harmonic 337.4 1.0919 # CORR 144 + bond_coeff @bond:cf-ha harmonic 341.5 1.0890 # SOURCE3 55 0.0056 + bond_coeff @bond:cf-n1 harmonic 536.1 1.3113 # CORR 13 + bond_coeff @bond:cf-n2 harmonic 599.8 1.2790 # SOURCE1 75 same_as_ce-n2 + bond_coeff @bond:cf-n harmonic 368.9 1.4249 # CORR 136 + bond_coeff @bond:cf-ne harmonic 574.0 1.2916 # CORR 42 + bond_coeff @bond:cf-nf harmonic 381.8 1.4140 # SOURCE3 7 same_as_ce-ne + bond_coeff @bond:cf-nh harmonic 412.3 1.3901 # CORR 168 + bond_coeff @bond:cf-oh harmonic 402.9 1.3493 # CORR 37 + bond_coeff @bond:cf-os harmonic 372.8 1.3727 # CORR 45 + bond_coeff @bond:cf-p2 harmonic 259.1 1.8140 # SOUECE3 1 same_as_ce-p2 + bond_coeff @bond:cf-pf harmonic 256.5 1.8180 # SOURCE3 8 same_as_ce-pe + bond_coeff @bond:cf-px harmonic 254.6 1.8210 # SOURCE3 6 same_as_ce-px + bond_coeff @bond:cf-py harmonic 272.3 1.7940 # SOURCE3 5 same_as_ce-py + bond_coeff @bond:cf-s harmonic 324.5 1.6800 # SOUECE3 1 same_as_ce-s + bond_coeff @bond:cf-sx harmonic 239.7 1.7970 # SOURCE3 5 same_as_ce-sx + bond_coeff @bond:cf-sy harmonic 248.9 1.7820 # SOURCE3 5 same_as_ce-sy + bond_coeff @bond:cg-cg harmonic 494.2 1.3770 # SOURCE1 42 0.0000 + bond_coeff @bond:cg-ch harmonic 949.5 1.1910 # SOURCE1 80 0.0015 + bond_coeff @bond:cg-n1 harmonic 994.7 1.1430 # SOURCE1 316 0.0018 + bond_coeff @bond:cg-ne harmonic 509.5 1.3262 # SOURCE4 17 0.0009 + bond_coeff @bond:cg-pe harmonic 429.8 1.6210 # SOURCE3 11 0.2008 + bond_coeff @bond:c-h4 harmonic 310.5 1.1123 # SOURCE4 125 0.0023 + bond_coeff @bond:c-h5 harmonic 319.4 1.1053 # SOURCE4 42 0.0028 + bond_coeff @bond:c-ha harmonic 325.1 1.1010 # SOURCE3 53 0.0102 + bond_coeff @bond:ch-ch harmonic 494.2 1.3770 # SOURCE1 42 0.0000 + bond_coeff @bond:ch-n1 harmonic 994.7 1.1430 # SOURCE1 316 0.0018 + bond_coeff @bond:ch-nf harmonic 509.5 1.3262 # SOURCE4 17 same_as_cg-ne + bond_coeff @bond:ch-pf harmonic 429.8 1.6210 # SOURCE3 11 same_as_cg-pe + bond_coeff @bond:c-i harmonic 198.9 2.2090 # SOURCE3 4 0.0365 + bond_coeff @bond:cl-cl harmonic 143.3 2.2670 # SOURCE1 2 0.0395 + bond_coeff @bond:cl-cx harmonic 301.8 1.7550 # SOURCE1 64 0.0000 + bond_coeff @bond:cl-cy harmonic 292.0 1.7680 # SOURCE2 2 0.0070 + bond_coeff @bond:cl-f harmonic 298.6 1.6480 # SOURCE2 2 0.0500 + bond_coeff @bond:cl-i harmonic 163.5 2.5500 # SOURCE1 6 0.0893 + bond_coeff @bond:cl-n1 harmonic 431.6 1.6300 # SOUECE3 1 + bond_coeff @bond:cl-n2 harmonic 263.4 1.8190 # SOURCE3 6 0.1020 + bond_coeff @bond:cl-n3 harmonic 290.4 1.7800 # SOURCE4 5 0.0021 + bond_coeff @bond:cl-n harmonic 344.2 1.7140 # SOURCE4 5 0.0005 + bond_coeff @bond:cl-n4 harmonic 311.1 1.7530 # SOURCE3 4 0.0098 + bond_coeff @bond:cl-na harmonic 253.2 1.8350 # SOURCE3 7 0.2083 + bond_coeff @bond:cl-nh harmonic 303.2 1.7630 # SOURCE3 1 0.0000 + bond_coeff @bond:cl-no harmonic 250.1 1.8400 # SOURCE2 1 0.0000 + bond_coeff @bond:cl-o harmonic 557.6 1.4830 # SOURCE3 4 0.0000 + bond_coeff @bond:cl-oh harmonic 309.7 1.6900 # SOURCE2 1 0.0000 + bond_coeff @bond:cl-os harmonic 278.8 1.7300 # SOURCE3 4 0.0000 + bond_coeff @bond:cl-p2 harmonic 217.5 2.0700 # SOURCE3 6 0.0108 + bond_coeff @bond:cl-p3 harmonic 249.4 2.0080 # SOURCE1 111 0.0000 + bond_coeff @bond:cl-p4 harmonic 249.4 2.0080 # SOURCE1 111 0.0000 + bond_coeff @bond:cl-p5 harmonic 249.4 2.0080 # SOURCE1 111 0.0000 + bond_coeff @bond:cl-pb harmonic 255.6 1.9970 # SOURCE1 46 0.0000 + bond_coeff @bond:cl-s harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-s2 harmonic 172.7 2.1610 # SOURCE2 1 0.0000 + bond_coeff @bond:cl-s4 harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-s6 harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-sh harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-ss harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-sx harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:cl-sy harmonic 208.7 2.0720 # SOURCE1 6 0.0000 + bond_coeff @bond:c-n2 harmonic 374.6 1.4200 # SOUECE3 1 + bond_coeff @bond:c-n4 harmonic 255.5 1.5460 # SOURCE3 4 0.0388 + bond_coeff @bond:c-n harmonic 478.2 1.3450 # SOURCE1 1235 0.0215 + bond_coeff @bond:c-nc harmonic 412.1 1.3906 # CORR 124 + bond_coeff @bond:c-nd harmonic 412.1 1.3906 # CORR 124 + bond_coeff @bond:c-ne harmonic 408.2 1.3932 # CORR 52 + bond_coeff @bond:c-nf harmonic 408.2 1.3932 # CORR 52 + bond_coeff @bond:c-no harmonic 260.1 1.5400 # SOUECE3 1 + bond_coeff @bond:c-o harmonic 648.0 1.2140 # SOURCE1 3682 0.0165 + bond_coeff @bond:c-oh harmonic 466.4 1.3060 # SOURCE1 271 0.0041 + bond_coeff @bond:c-os harmonic 411.3 1.3430 # SOURCE1 1044 0.0171 + bond_coeff @bond:c-p2 harmonic 210.3 1.9000 # SOUECE3 1 + bond_coeff @bond:c-p3 harmonic 219.0 1.8830 # SOURCE3 6 0.0129 + bond_coeff @bond:c-p4 harmonic 220.6 1.8800 # SOUECE3 1 + bond_coeff @bond:c-p5 harmonic 219.8 1.8815 # SOURCE4 11 0.0078 + bond_coeff @bond:cp-cp harmonic 346.5 1.4900 # SOURCE1 242 0.0010 + bond_coeff @bond:cp-cq harmonic 419.3 1.4282 # SOURCE4 7 0.0034 + bond_coeff @bond:c-pe harmonic 204.9 1.9110 # SOURCE3 3 0.0025 + bond_coeff @bond:c-pf harmonic 204.9 1.9110 # SOURCE3 3 same_as_c-pe + bond_coeff @bond:cp-na harmonic 420.5 1.3840 # SOURCE4 7 0.0181 + bond_coeff @bond:cp-nb harmonic 486.7 1.3398 # SOURCE4 70 0.0062 + bond_coeff @bond:c-px harmonic 208.3 1.9040 # SOURCE3 1 0.0000 + bond_coeff @bond:c-py harmonic 227.6 1.8670 # SOURCE3 6 0.0199 + bond_coeff @bond:cq-cq harmonic 346.5 1.4900 # SOURCE1 242 0.0010 + bond_coeff @bond:c-s harmonic 328.9 1.6750 # SOURCE1 401 0.0128 + bond_coeff @bond:c-s4 harmonic 200.4 1.8700 # SOUECE3 1 + bond_coeff @bond:c-s6 harmonic 200.4 1.8700 # SOUECE3 1 + bond_coeff @bond:c-sh harmonic 249.6 1.7810 # SOURCE3 6 0.0171 + bond_coeff @bond:c-ss harmonic 261.9 1.7620 # SOURCE1 20 0.0000 + bond_coeff @bond:c-sx harmonic 193.3 1.8850 # SOURCE3 5 0.0088 + bond_coeff @bond:c-sy harmonic 202.8 1.8650 # SOURCE3 5 0.0085 + bond_coeff @bond:cu-cu harmonic 653.7 1.2940 # SOURCE1 10 0.0000 + bond_coeff @bond:cu-cx harmonic 327.3 1.5090 # SOURCE1 20 0.0000 + bond_coeff @bond:cu-ha harmonic 353.0 1.0810 # SOURCE2 3 0.0111 + bond_coeff @bond:cv-cv harmonic 568.1 1.3350 # SOURCE1 25 0.0000 + bond_coeff @bond:cv-cy harmonic 323.5 1.5130 # SOURCE1 50 0.0000 + bond_coeff @bond:cv-ha harmonic 344.3 1.0870 # SOURCE3 2 0.0000 + bond_coeff @bond:cx-cv harmonic 328.3 1.5080 # SOURCE1 2536 as + bond_coeff @bond:cx-cx harmonic 337.3 1.4990 # SOURCE1 1204 0.0183 + bond_coeff @bond:cx-cy harmonic 321.5 1.5150 # SOURCE3 2 0.0000 + bond_coeff @bond:cx-f harmonic 347.2 1.3580 # SOURCE2 3 0.0050 + bond_coeff @bond:cx-h1 harmonic 344.3 1.0870 # SOURCE3 10 0.0017 + bond_coeff @bond:cx-h2 harmonic 350.1 1.0830 # SOURCE3 2 0.0000 + bond_coeff @bond:cx-hc harmonic 345.8 1.0860 # SOURCE3 44 0.0011 + bond_coeff @bond:cx-hx harmonic 347.2 1.0850 # SOURCE4 5 0.0002 + bond_coeff @bond:cx-n2 harmonic 309.1 1.4820 # SOURCE3 2 0.0000 + bond_coeff @bond:cx-n3 harmonic 318.7 1.4720 # SOURCE1 134 0.0000 + bond_coeff @bond:cx-n harmonic 350.6 1.4411 # SOURCE4 11 0.0092 + bond_coeff @bond:cx-na harmonic 329.0 1.4616 # SOURCE4 11 0.0016 + bond_coeff @bond:cx-nh harmonic 336.7 1.4541 # SOURCE4 83 0.0076 + bond_coeff @bond:cx-oh harmonic 387.4 1.3610 # SOURCE3 3 0.0018 + bond_coeff @bond:cx-os harmonic 320.1 1.4200 # SOURCE3 7 0.0222 + bond_coeff @bond:cx-p3 harmonic 227.6 1.8670 # SOURCE2 1 0.0000 + bond_coeff @bond:cx-s4 harmonic 225.3 1.8220 # SOURCE2 1 0.0000 + bond_coeff @bond:cx-s6 harmonic 283.7 1.7310 # SOURCE2 1 0.0000 + bond_coeff @bond:cx-ss harmonic 229.2 1.8150 # SOURCE2 1 0.0000 + bond_coeff @bond:cy-cy harmonic 286.8 1.5540 # SOURCE1 742 0.0041 + bond_coeff @bond:cy-f harmonic 355.5 1.3509 # SOURCE4 8 0.0047 + bond_coeff @bond:cy-h1 harmonic 330.4 1.0970 # SOURCE3 17 0.0058 + bond_coeff @bond:cy-h2 harmonic 335.8 1.0931 # SOURCE4 80 0.0019 + bond_coeff @bond:cy-hc harmonic 334.5 1.0940 # SOURCE3 63 0.0014 + bond_coeff @bond:cy-n harmonic 321.3 1.4693 # SOURCE4 250 0.0102 + bond_coeff @bond:cy-n3 harmonic 307.2 1.4840 # SOURCE1 21 0.0000 + bond_coeff @bond:cy-oh harmonic 325.2 1.4150 # SOURCE3 2 0.0000 + bond_coeff @bond:cy-os harmonic 308.6 1.4316 # SOURCE4 23 0.0136 + bond_coeff @bond:cy-s6 harmonic 209.6 1.8514 # SOURCE4 9 0.0166 + bond_coeff @bond:cy-ss harmonic 211.3 1.8481 # SOURCE4 78 0.0080 + bond_coeff @bond:cz-nh harmonic 487.8 1.3391 # SOURCE4 32 0.0045 + bond_coeff @bond:f-n1 harmonic 375.7 1.4100 # SOUECE3 1 + bond_coeff @bond:f-n2 harmonic 337.5 1.4440 # SOURCE3 5 0.0377 + bond_coeff @bond:f-n3 harmonic 380.6 1.4060 # SOURCE1 9 0.0000 + bond_coeff @bond:f-n harmonic 391.7 1.3970 # SOURCE3 3 0.0112 + bond_coeff @bond:f-n4 harmonic 526.8 1.3080 # SOURCE3 2 0.0000 + bond_coeff @bond:f-na harmonic 374.5 1.4110 # SOURCE3 7 0.0611 + bond_coeff @bond:f-nh harmonic 357.1 1.4260 # SOURCE3 3 0.0085 + bond_coeff @bond:f-no harmonic 314.4 1.4670 # SOURCE2 1 0.0000 + bond_coeff @bond:f-o harmonic 442.2 1.3300 # SOUECE3 1 + bond_coeff @bond:f-oh harmonic 305.4 1.4440 # SOURCE3 1 0.0000 + bond_coeff @bond:f-os harmonic 326.2 1.4230 # SOURCE3 2 0.0000 + bond_coeff @bond:f-p2 harmonic 287.3 1.5360 # SOURCE3 7 0.2054 + bond_coeff @bond:f-p3 harmonic 254.5 1.5780 # SOURCE2 8 0.0103 + bond_coeff @bond:f-p4 harmonic 246.0 1.5900 # SOUECE3 1 + bond_coeff @bond:f-p5 harmonic 253.8 1.5790 # SOURCE1 72 0.0000 + bond_coeff @bond:f-s2 harmonic 244.4 1.6430 # SOURCE2 1 0.0000 + bond_coeff @bond:f-s harmonic 233.3 1.6600 # SOUECE3 1 + bond_coeff @bond:f-s4 harmonic 282.4 1.5910 # SOURCE2 4 0.0065 + bond_coeff @bond:f-s6 harmonic 312.1 1.5560 # SOURCE2 5 0.0220 + bond_coeff @bond:f-sh harmonic 240.4 1.6490 # SOURCE3 1 0.0000 + bond_coeff @bond:f-ss harmonic 250.5 1.6340 # SOURCE3 3 0.0156 + bond_coeff @bond:hn-n1 harmonic 455.1 0.9860 # SOURCE2 1 0.0000 + bond_coeff @bond:hn-n2 harmonic 375.5 1.0290 # SOURCE3 108 0.0096 + bond_coeff @bond:hn-n3 harmonic 394.1 1.0180 # SOURCE3 157 0.0086 + bond_coeff @bond:hn-n harmonic 410.2 1.0090 # SOURCE3 149 0.0098 + bond_coeff @bond:hn-n4 harmonic 369.0 1.0330 # SOURCE3 264 0.0082 + bond_coeff @bond:hn-na harmonic 406.6 1.0110 # SOURCE3 46 0.0107 + bond_coeff @bond:hn-nh harmonic 401.2 1.0140 # SOURCE3 209 0.0091 + bond_coeff @bond:hn-no harmonic 385.6 1.0230 # SOURCE3 1 0.0000 + bond_coeff @bond:ho-o harmonic 357.9 0.9810 # SOURCE3 1 0.0000 + bond_coeff @bond:ho-oh harmonic 369.6 0.9740 # SOURCE3 367 0.0105 + bond_coeff @bond:hp-p2 harmonic 385.1 1.3360 # SOURCE3 87 0.1706 + bond_coeff @bond:hp-p3 harmonic 303.1 1.4090 # SOURCE3 101 0.0617 + bond_coeff @bond:hp-p4 harmonic 368.7 1.3490 # SOURCE3 17 0.1577 + bond_coeff @bond:hp-p5 harmonic 305.0 1.4070 # SOURCE3 7 0.0062 + bond_coeff @bond:hs-s harmonic 286.4 1.3530 # SOURCE3 1 0.0000 + bond_coeff @bond:hs-s4 harmonic 266.4 1.3750 # SOURCE3 5 0.0004 + bond_coeff @bond:hs-s6 harmonic 280.8 1.3590 # SOURCE3 5 0.0015 + bond_coeff @bond:hs-sh harmonic 302.2 1.3370 # SOURCE3 98 0.0486 + bond_coeff @bond:i-i harmonic 109.2 2.9170 # SOURCE1 1 0.0000 + bond_coeff @bond:i-n1 harmonic 302.1 2.0600 # SOUECE3 1 + bond_coeff @bond:i-n2 harmonic 182.6 2.3040 # SOURCE3 6 0.1186 + bond_coeff @bond:i-n harmonic 278.3 2.0980 # SOURCE3 5 0.0156 + bond_coeff @bond:i-n3 harmonic 231.8 2.1850 # SOURCE3 3 0.0437 + bond_coeff @bond:i-n4 harmonic 246.6 2.1550 # SOURCE3 3 0.0168 + bond_coeff @bond:i-na harmonic 260.5 2.1290 # SOURCE3 8 0.1276 + bond_coeff @bond:i-nh harmonic 249.2 2.1500 # SOURCE3 1 0.0000 + bond_coeff @bond:i-no harmonic 211.0 2.2310 # SOURCE3 1 0.0000 + bond_coeff @bond:i-o harmonic 323.8 1.9800 # SOUECE3 1 + bond_coeff @bond:i-oh harmonic 247.9 2.1010 # SOURCE3 2 0.0000 + bond_coeff @bond:i-os harmonic 233.6 2.1290 # SOURCE3 3 0.0146 + bond_coeff @bond:i-p2 harmonic 108.2 2.6430 # SOURCE3 6 0.0297 + bond_coeff @bond:i-p3 harmonic 123.6 2.5660 # SOURCE3 3 0.0016 + bond_coeff @bond:i-p4 harmonic 183.0 2.3520 # SOURCE3 4 0.2600 + bond_coeff @bond:i-p5 harmonic 117.3 2.5960 # SOURCE3 3 0.0143 + bond_coeff @bond:i-s harmonic 175.1 2.4300 # SOUECE3 1 + bond_coeff @bond:i-s4 harmonic 82.8 2.8700 # SOUECE3 1 + bond_coeff @bond:i-s6 harmonic 82.8 2.8700 # SOURCE3 1 0.0000 + bond_coeff @bond:i-sh harmonic 138.5 2.5600 # SOUECE3 1 + bond_coeff @bond:i-ss harmonic 135.9 2.5710 # SOURCE3 3 0.0065 + bond_coeff @bond:n1-n1 harmonic 1221.7 1.1240 # SOURCE1 19 0.0000 + bond_coeff @bond:n1-n2 harmonic 857.4 1.2160 # SOURCE1 19 0.0000 + bond_coeff @bond:n1-n3 harmonic 535.7 1.3500 # SOUECE3 1 + bond_coeff @bond:n1-n4 harmonic 518.2 1.3600 # SOUECE3 1 + bond_coeff @bond:n1-na harmonic 535.7 1.3500 # SOUECE3 1 + bond_coeff @bond:n1-nc harmonic 857.4 1.2160 # SOURCE1 38 0.0000 + bond_coeff @bond:n1-nd harmonic 857.4 1.2160 # SOURCE1 38 0.0000 + bond_coeff @bond:n1-ne harmonic 751.9 1.2520 # SOURCE2 1 0.0000 + bond_coeff @bond:n1-nf harmonic 751.9 1.2520 # SOURCE2 1 same_as_n1-ne + bond_coeff @bond:n1-nh harmonic 553.9 1.3400 # SOUECE3 1 + bond_coeff @bond:n1-no harmonic 454.8 1.4000 # SOUECE3 1 + bond_coeff @bond:n1-o harmonic 617.5 1.2770 # SOURCE3 5 0.0438 + bond_coeff @bond:n1-oh harmonic 569.8 1.3000 # SOUECE3 1 + bond_coeff @bond:n1-os harmonic 550.5 1.3100 # SOUECE3 1 + bond_coeff @bond:n1-p2 harmonic 358.8 1.6780 # SOURCE3 2 0.0282 + bond_coeff @bond:n1-p3 harmonic 376.7 1.6600 # SOUECE3 1 + bond_coeff @bond:n1-p4 harmonic 353.0 1.6800 # SOURCE3 0 + bond_coeff @bond:n1-p5 harmonic 482.7 1.5710 # SOURCE1 132 0.0000 + bond_coeff @bond:n1-s2 harmonic 604.3 1.4490 # SOURCE2 2 0.0010 + bond_coeff @bond:n1-s harmonic 328.7 1.6590 # SOURCE3 6 0.0789 + bond_coeff @bond:n1-s4 harmonic 336.8 1.6500 # SOUECE3 1 + bond_coeff @bond:n1-s6 harmonic 670.3 1.4160 # SOURCE2 2 0.0000 + bond_coeff @bond:n1-sh harmonic 376.1 1.6100 # SOUECE3 1 + bond_coeff @bond:n1-ss harmonic 376.1 1.6100 # SOUECE3 1 + bond_coeff @bond:n2-n2 harmonic 702.7 1.2710 # SOURCE3 27 0.0347 + bond_coeff @bond:n2-n3 harmonic 574.8 1.3290 # SOURCE2 1 0.0000 + bond_coeff @bond:n2-n4 harmonic 200.8 1.6790 # SOURCE3 7 0.3138 + bond_coeff @bond:n2-na harmonic 503.9 1.3685 # SOURCE4 18 0.0066 + bond_coeff @bond:n2-nc harmonic 743.9 1.2550 # SOURCE1 13 0.0000 + bond_coeff @bond:n2-nd harmonic 743.9 1.2550 # SOURCE1 13 same_as_n2_nc + bond_coeff @bond:n2-ne harmonic 685.5 1.2780 # SOURCE3 30 0.0302 + bond_coeff @bond:n2-nf harmonic 685.5 1.2780 # SOURCE3 30 same_as_n2-ne + bond_coeff @bond:n2-nh harmonic 525.1 1.3560 # SOURCE3 22 0.0300 + bond_coeff @bond:n2-no harmonic 231.9 1.6260 # SOURCE3 4 0.1933 + bond_coeff @bond:n2-o harmonic 789.9 1.2090 # SOURCE3 20 0.0344 + bond_coeff @bond:n2-oh harmonic 416.2 1.3940 # SOURCE1 67 0.0000 + bond_coeff @bond:n2-os harmonic 400.5 1.4060 # SOURCE3 10 0.0147 + bond_coeff @bond:n2-p2 harmonic 438.3 1.6050 # SOURCE3 35 0.0737 + bond_coeff @bond:n2-p3 harmonic 286.5 1.7640 # SOURCE3 7 0.0374 + bond_coeff @bond:n2-p4 harmonic 317.7 1.7240 # SOUECE3 1 + bond_coeff @bond:n2-p5 harmonic 445.8 1.5990 # SOURCE1 7 0.0000 + bond_coeff @bond:n2-pe harmonic 527.9 1.5400 # SOURCE3 20 0.1392 + bond_coeff @bond:n2-pf harmonic 527.9 1.5400 # SOURCE3 20 same_as_n2-pe + bond_coeff @bond:n2-s2 harmonic 499.0 1.5120 # SOURCE2 1 0.0000 + bond_coeff @bond:n2-s4 harmonic 376.1 1.6100 # SOUECE3 1 + bond_coeff @bond:n2-s harmonic 458.1 1.5410 # SOURCE1 37 0.0000 + bond_coeff @bond:n2-s6 harmonic 444.6 1.5513 # SOURCE4 5 0.0011 + bond_coeff @bond:n2-sh harmonic 266.6 1.7380 # SOURCE3 5 0.0511 + bond_coeff @bond:n2-ss harmonic 331.4 1.6560 # SOURCE1 36 0.0000 + bond_coeff @bond:n3-n3 harmonic 383.6 1.4540 # SOURCE1 44 0.0000 + bond_coeff @bond:n3-n4 harmonic 434.9 1.4140 # SOURCE1 13 0.0000 + bond_coeff @bond:n3-na harmonic 426.7 1.4200 # SOURCE1 68 0.0000 + bond_coeff @bond:n3-nh harmonic 426.7 1.4200 # SOURCE1 68 0.0000 + bond_coeff @bond:n3-no harmonic 394.5 1.4450 # SOURCE3 3 0.0208 + bond_coeff @bond:n3-o harmonic 564.0 1.3030 # SOURCE3 4 0.1217 + bond_coeff @bond:n3-oh harmonic 413.5 1.3960 # SOURCE1 28 0.0000 + bond_coeff @bond:n3-os harmonic 359.6 1.4400 # SOURCE1 34 0.0315 + bond_coeff @bond:n3-p2 harmonic 366.6 1.6700 # SOUECE3 1 + bond_coeff @bond:n3-p3 harmonic 312.8 1.7300 # SOURCE1 40 0.0000 + bond_coeff @bond:n3-p4 harmonic 341.1 1.6970 # SOURCE1 88 0.0000 + bond_coeff @bond:n3-p5 harmonic 373.6 1.6630 # SOURCE1 501 0.0086 + bond_coeff @bond:n3-py harmonic 338.1 1.7003 # SOURCE4 6 0.0044 + bond_coeff @bond:n3-s harmonic 232.3 1.7920 # SOURCE3 3 0.0178 + bond_coeff @bond:n3-s4 harmonic 251.3 1.7610 # SOURCE3 6 0.0766 + bond_coeff @bond:n3-s6 harmonic 353.8 1.6320 # SOURCE1 99 0.0136 + bond_coeff @bond:n3-sh harmonic 265.9 1.7390 # SOURCE3 3 0.0154 + bond_coeff @bond:n3-ss harmonic 277.9 1.7220 # SOURCE3 5 0.0207 + bond_coeff @bond:n3-sy harmonic 297.3 1.6964 # SOURCE4 226 0.0081 + bond_coeff @bond:n4-n4 harmonic 349.9 1.4840 # SOURCE3 4 0.0089 + bond_coeff @bond:n4-na harmonic 407.0 1.4350 # SOURCE3 9 0.0390 + bond_coeff @bond:n4-nh harmonic 369.7 1.4660 # SOURCE3 5 0.0108 + bond_coeff @bond:n4-no harmonic 354.2 1.4800 # SOUECE3 1 + bond_coeff @bond:n4-o harmonic 463.6 1.3610 # SOURCE3 3 0.0041 + bond_coeff @bond:n4-oh harmonic 408.2 1.4000 # SOURCE3 3 0.0115 + bond_coeff @bond:n4-os harmonic 381.8 1.4210 # SOURCE3 5 0.0249 + bond_coeff @bond:n4-p2 harmonic 185.9 1.9420 # SOURCE3 10 0.0643 + bond_coeff @bond:n4-p3 harmonic 215.1 1.8800 # SOURCE3 5 0.0146 + bond_coeff @bond:n4-p4 harmonic 187.6 1.9380 # SOURCE3 1 0.0000 + bond_coeff @bond:n4-p5 harmonic 242.9 1.8300 # SOURCE3 5 0.0087 + bond_coeff @bond:n4-py harmonic 204.2 1.9020 # SOURCE3 4 0.0000 + bond_coeff @bond:n4-s harmonic 210.3 1.8320 # SOURCE3 3 0.0004 + bond_coeff @bond:n4-s4 harmonic 151.0 1.9720 # SOURCE3 3 0.0198 + bond_coeff @bond:n4-s6 harmonic 172.7 1.9140 # SOURCE3 5 0.0432 + bond_coeff @bond:n4-sh harmonic 221.5 1.8110 # SOURCE3 3 0.0027 + bond_coeff @bond:n4-ss harmonic 221.0 1.8120 # SOURCE3 5 0.0064 + bond_coeff @bond:na-na harmonic 453.3 1.4010 # SOURCE1 40 0.0000 + bond_coeff @bond:na-nb harmonic 546.5 1.3440 # SOURCE4 5 0.0070 + bond_coeff @bond:na-nc harmonic 535.7 1.3500 # SOURCE3 152 0.0180 + bond_coeff @bond:na-nd harmonic 535.7 1.3500 # SOURCE3 152 0.0180 + bond_coeff @bond:na-nh harmonic 453.3 1.4010 # SOURCE1 40 0.0000 + bond_coeff @bond:na-no harmonic 401.9 1.4390 # SOURCE3 9 0.0289 + bond_coeff @bond:na-o harmonic 644.3 1.2650 # SOURCE1 25 0.0347 + bond_coeff @bond:na-oh harmonic 412.2 1.3970 # SOURCE3 9 0.0217 + bond_coeff @bond:na-os harmonic 355.2 1.4440 # SOURCE3 45 0.0423 + bond_coeff @bond:na-p2 harmonic 297.8 1.7490 # SOURCE3 11 0.0192 + bond_coeff @bond:na-p3 harmonic 288.0 1.7620 # SOURCE3 8 0.0113 + bond_coeff @bond:na-p4 harmonic 492.4 1.5640 # SOURCE3 5 0.2161 + bond_coeff @bond:na-p5 harmonic 325.3 1.7150 # SOURCE3 11 0.0238 + bond_coeff @bond:na-pc harmonic 311.1 1.7320 # SOURCE3 81 0.0207 + bond_coeff @bond:na-pd harmonic 311.1 1.7320 # SOURCE3 81 same_as_na-pc + bond_coeff @bond:na-py harmonic 327.8 1.7120 # SOURCE3 2 0.0000 + bond_coeff @bond:na-s harmonic 248.7 1.7650 # SOURCE3 8 0.0095 + bond_coeff @bond:na-s4 harmonic 231.7 1.7930 # SOURCE3 10 0.0421 + bond_coeff @bond:na-s6 harmonic 274.3 1.7270 # SOURCE3 10 0.0201 + bond_coeff @bond:na-sh harmonic 278.6 1.7210 # SOURCE3 9 0.0113 + bond_coeff @bond:na-ss harmonic 270.1 1.7330 # SOURCE3 38 0.0412 + bond_coeff @bond:na-sy harmonic 274.3 1.7270 # SOURCE3 1 + bond_coeff @bond:nb-nb harmonic 550.2 1.3420 # SOURCE1 15 0.0314 + bond_coeff @bond:nb-pb harmonic 461.1 1.5870 # SOURCE1 162 0.0091 + bond_coeff @bond:nc-nc harmonic 486.8 1.3790 # SOURCE3 9 0.0164 + bond_coeff @bond:nc-nd harmonic 602.9 1.3150 # SOURCE3 9 0.0221 + bond_coeff @bond:nc-os harmonic 414.9 1.3950 # SOURCE1 46 0.0188 + bond_coeff @bond:nc-ss harmonic 433.5 1.5600 # SOURCE1 74 0.0000 + bond_coeff @bond:nc-sy harmonic 439.8 1.5550 # SOURCE3 2 + bond_coeff @bond:nd-nd harmonic 486.8 1.3790 # SOURCE3 9 0.0164 + bond_coeff @bond:nd-os harmonic 414.9 1.3950 # SOURCE1 46 0.0188 + bond_coeff @bond:nd-ss harmonic 433.5 1.5600 # SOURCE1 74 0.0000 + bond_coeff @bond:nd-sy harmonic 439.8 1.5550 # SOURCE3 2 + bond_coeff @bond:ne-ne harmonic 355.3 1.4790 # SOURCE3 19 0.1705 + bond_coeff @bond:ne-nf harmonic 721.6 1.2635 # SOURCE4 25 0.0034 + bond_coeff @bond:ne-o harmonic 736.4 1.2280 # SOURCE3 40 0.0255 + bond_coeff @bond:ne-p2 harmonic 493.9 1.5630 # SOURCE3 14 0.1325 + bond_coeff @bond:ne-pe harmonic 327.8 1.7120 # SOURCE3 28 0.1076 + bond_coeff @bond:ne-px harmonic 336.6 1.7020 # SOURCE3 11 0.0883 + bond_coeff @bond:ne-py harmonic 425.4 1.6157 # SOURCE4 10 0.0094 + bond_coeff @bond:ne-s harmonic 463.5 1.5370 # SOURCE3 22 0.1708 + bond_coeff @bond:ne-sx harmonic 207.3 1.8380 # SOURCE3 7 0.1060 + bond_coeff @bond:ne-sy harmonic 257.1 1.7520 # SOURCE3 7 0.0814 + bond_coeff @bond:nf-nf harmonic 355.3 1.4790 # SOURCE3 19 same_as_ne-ne + bond_coeff @bond:nf-o harmonic 736.4 1.2280 # SOURCE3 40 same_as_ne-o + bond_coeff @bond:nf-p2 harmonic 493.9 1.5630 # SOURCE3 14 same_as_ne-p2 + bond_coeff @bond:nf-pf harmonic 327.8 1.7120 # SOURCE3 28 same_as_ne-pe + bond_coeff @bond:nf-px harmonic 336.6 1.7020 # SOURCE3 11 same_as_ne-px + bond_coeff @bond:nf-py harmonic 425.4 1.6157 # SOURCE4 10 same_as_ne-py + bond_coeff @bond:nf-s harmonic 463.5 1.5370 # SOURCE3 22 same_as_ne-s + bond_coeff @bond:nf-sx harmonic 207.3 1.8380 # SOURCE3 7 same_as_ne-sx + bond_coeff @bond:nf-sy harmonic 257.1 1.7520 # SOURCE3 7 same_as_ne-sy + bond_coeff @bond:nh-nh harmonic 453.3 1.4010 # SOURCE1 40 0.0000 + bond_coeff @bond:nh-no harmonic 477.4 1.3850 # SOURCE4 7 0.0036 + bond_coeff @bond:nh-o harmonic 596.2 1.2870 # SOURCE3 3 0.0450 + bond_coeff @bond:nh-oh harmonic 389.9 1.4144 # SOURCE4 19 0.0064 + bond_coeff @bond:nh-os harmonic 387.8 1.4161 # SOURCE4 6 0.0039 + bond_coeff @bond:nh-p2 harmonic 357.8 1.6790 # SOURCE3 17 0.0872 + bond_coeff @bond:nh-p3 harmonic 312.8 1.7300 # SOURCE3 3 0.0016 + bond_coeff @bond:nh-p4 harmonic 333.1 1.7060 # SOURCE3 3 0.0008 + bond_coeff @bond:nh-p5 harmonic 365.6 1.6710 # SOURCE3 3 0.0007 + bond_coeff @bond:nh-s harmonic 237.0 1.7840 # SOURCE3 3 0.0076 + bond_coeff @bond:nh-s4 harmonic 259.1 1.7490 # SOURCE3 3 0.0203 + bond_coeff @bond:nh-s6 harmonic 297.2 1.6965 # SOURCE4 33 0.0062 + bond_coeff @bond:nh-sh harmonic 288.3 1.7080 # SOURCE3 1 0.0000 + bond_coeff @bond:nh-ss harmonic 288.3 1.7080 # SOURCE1 52 0.0015 + bond_coeff @bond:nh-sy harmonic 283.5 1.7144 # SOURCE4 80 0.0066 + bond_coeff @bond:n-n1 harmonic 553.9 1.3400 # SOUECE3 1 + bond_coeff @bond:n-n2 harmonic 499.7 1.3710 # SOURCE3 9 0.0200 + bond_coeff @bond:n-n3 harmonic 443.3 1.4080 # SOURCE3 5 0.0087 + bond_coeff @bond:n-n4 harmonic 410.8 1.4320 # SOURCE3 5 0.0098 + bond_coeff @bond:n-n harmonic 469.7 1.3900 # SOURCE3 5 0.0038 + bond_coeff @bond:n-na harmonic 486.8 1.3790 # SOURCE3 11 0.0071 + bond_coeff @bond:n-nc harmonic 523.7 1.3568 # CORR 76 + bond_coeff @bond:n-nd harmonic 523.7 1.3568 # CORR 76 + bond_coeff @bond:n-nh harmonic 451.2 1.4025 # SOURCE4 20 0.0074 + bond_coeff @bond:n-no harmonic 381.2 1.4560 # SOURCE3 4 0.0327 + bond_coeff @bond:n-o harmonic 646.6 1.2640 # SOURCE3 9 0.0381 + bond_coeff @bond:n-oh harmonic 395.4 1.4100 # SOURCE3 6 0.0106 + bond_coeff @bond:no-no harmonic 138.3 1.8240 # SOURCE3 1 0.0000 + bond_coeff @bond:no-o harmonic 761.2 1.2190 # SOURCE1 1838 0.0049 + bond_coeff @bond:no-oh harmonic 400.5 1.4060 # SOURCE2 1 0.0000 + bond_coeff @bond:no-os harmonic 379.5 1.4229 # SOURCE4 53 0.0076 + bond_coeff @bond:no-p2 harmonic 306.3 1.7380 # SOURCE3 10 0.2231 + bond_coeff @bond:no-p3 harmonic 234.7 1.8440 # SOURCE3 3 0.0005 + bond_coeff @bond:no-p4 harmonic 220.4 1.8700 # SOURCE3 3 0.0006 + bond_coeff @bond:no-p5 harmonic 240.5 1.8340 # SOURCE3 4 0.0020 + bond_coeff @bond:no-s harmonic 263.8 1.7420 # SOURCE3 2 0.0000 + bond_coeff @bond:n-os harmonic 395.0 1.4103 # SOURCE4 30 0.0112 + bond_coeff @bond:no-s4 harmonic 143.0 1.9960 # SOURCE3 3 0.0313 + bond_coeff @bond:no-s6 harmonic 149.6 1.9760 # SOURCE3 3 0.0520 + bond_coeff @bond:no-sh harmonic 225.4 1.8040 # SOURCE3 1 0.0000 + bond_coeff @bond:no-ss harmonic 212.4 1.8280 # SOURCE3 3 0.0244 + bond_coeff @bond:n-p2 harmonic 310.3 1.7330 # SOURCE3 8 0.0217 + bond_coeff @bond:n-p3 harmonic 282.2 1.7700 # SOURCE3 9 0.0118 + bond_coeff @bond:n-p4 harmonic 309.5 1.7340 # SOURCE3 1 0.0000 + bond_coeff @bond:n-p5 harmonic 331.3 1.7080 # SOURCE4 6 0.0022 + bond_coeff @bond:n-pc harmonic 304.8 1.7400 # SOURCE3 3 0.0010 + bond_coeff @bond:n-pd harmonic 304.8 1.7400 # SOURCE3 3 same_as_n-pc + bond_coeff @bond:n-s harmonic 247.5 1.7670 # SOURCE3 3 0.0011 + bond_coeff @bond:n-s4 harmonic 238.2 1.7820 # SOURCE3 4 0.0214 + bond_coeff @bond:n-s6 harmonic 283.0 1.7151 # SOURCE4 13 0.0138 + bond_coeff @bond:n-sh harmonic 273.6 1.7280 # SOURCE3 4 0.0128 + bond_coeff @bond:n-ss harmonic 281.6 1.7170 # SOURCE3 7 0.0133 + bond_coeff @bond:n-sy harmonic 282.9 1.7152 # SOURCE4 51 0.0079 + bond_coeff @bond:oh-oh harmonic 340.5 1.4690 # SOURCE3 1 0.0000 + bond_coeff @bond:oh-os harmonic 355.8 1.4547 # SOURCE4 19 0.0050 + bond_coeff @bond:oh-p2 harmonic 316.8 1.6300 # SOURCE3 8 0.0916 + bond_coeff @bond:oh-p3 harmonic 278.8 1.6770 # SOURCE3 3 0.0148 + bond_coeff @bond:oh-p4 harmonic 307.4 1.6410 # SOURCE3 4 0.0092 + bond_coeff @bond:oh-p5 harmonic 321.2 1.6250 # SOURCE3 92 0.0451 + bond_coeff @bond:oh-py harmonic 332.1 1.6130 # SOURCE3 79 0.0138 + bond_coeff @bond:oh-s harmonic 190.0 1.8120 # SOURCE3 2 0.0000 + bond_coeff @bond:oh-s4 harmonic 256.3 1.6954 # SOURCE4 10 0.0091 + bond_coeff @bond:oh-s6 harmonic 344.1 1.5880 # SOURCE3 13 0.0091 + bond_coeff @bond:oh-sh harmonic 258.6 1.6920 # SOURCE3 2 0.0003 + bond_coeff @bond:oh-ss harmonic 265.6 1.6820 # SOURCE3 4 0.0131 + bond_coeff @bond:oh-sy harmonic 290.4 1.6490 # SOURCE4 33 0.0044 + bond_coeff @bond:o-o harmonic 384.3 1.4300 # SOURCE3 2 0.0500 + bond_coeff @bond:o-oh harmonic 294.6 1.5170 # SOURCE3 2 0.0000 + bond_coeff @bond:o-os harmonic 306.3 1.5040 # SOURCE3 3 0.0117 + bond_coeff @bond:o-p2 harmonic 449.7 1.5080 # SOURCE3 17 0.0306 + bond_coeff @bond:o-p3 harmonic 440.4 1.5150 # SOURCE3 35 0.0297 + bond_coeff @bond:o-p4 harmonic 456.4 1.5030 # SOURCE3 42 0.0749 + bond_coeff @bond:o-p5 harmonic 487.7 1.4810 # SOURCE1 263 0.0205 + bond_coeff @bond:o-pe harmonic 432.6 1.5210 # SOURCE3 20 0.0171 + bond_coeff @bond:o-pf harmonic 432.6 1.5210 # SOURCE3 20 same_as_o-pe + bond_coeff @bond:o-px harmonic 459.2 1.5010 # SOURCE3 37 0.0160 + bond_coeff @bond:o-py harmonic 477.5 1.4880 # SOURCE3 63 0.0091 + bond_coeff @bond:o-s harmonic 194.8 1.8020 # SOURCE3 2 0.0000 + bond_coeff @bond:o-s2 harmonic 333.6 1.5990 # SOURCE3 3 0.0707 + bond_coeff @bond:o-s4 harmonic 448.7 1.4970 # SOURCE1 90 0.0000 + bond_coeff @bond:o-s6 harmonic 541.1 1.4360 # SOURCE1 1038 0.0128 + bond_coeff @bond:o-sh harmonic 328.0 1.6050 # SOURCE3 2 0.0000 + bond_coeff @bond:os-os harmonic 343.6 1.4660 # SOURCE1 20 0.0067 + bond_coeff @bond:os-p2 harmonic 371.9 1.5730 # SOURCE1 16 0.0000 + bond_coeff @bond:os-p3 harmonic 272.2 1.6860 # SOURCE3 6 0.0201 + bond_coeff @bond:os-p4 harmonic 311.6 1.6360 # SOURCE3 4 0.0057 + bond_coeff @bond:os-p5 harmonic 342.5 1.6020 # SOURCE1 248 0.0400 + bond_coeff @bond:os-py harmonic 328.5 1.6170 # SOURCE3 17 0.0139 + bond_coeff @bond:os-s harmonic 195.8 1.8000 # SOURCE3 3 0.0052 + bond_coeff @bond:o-ss harmonic 398.5 1.5370 # SOURCE3 3 0.0501 + bond_coeff @bond:os-s4 harmonic 253.9 1.6990 # SOURCE3 8 0.0223 + bond_coeff @bond:os-s6 harmonic 355.0 1.5770 # SOURCE1 75 0.0030 + bond_coeff @bond:os-sh harmonic 273.6 1.6710 # SOURCE3 3 0.0106 + bond_coeff @bond:os-ss harmonic 250.5 1.7040 # SOURCE3 9 0.0277 + bond_coeff @bond:os-sy harmonic 253.9 1.6990 # SOURCE3 1 0.0000 + bond_coeff @bond:o-sx harmonic 434.2 1.5080 # SOURCE3 40 0.0130 + bond_coeff @bond:o-sy harmonic 493.0 1.4660 # SOURCE3 92 0.0114 + bond_coeff @bond:p2-p2 harmonic 490.3 1.7860 # SOURCE3 25 0.3488 + bond_coeff @bond:p2-p3 harmonic 211.9 2.1520 # SOURCE3 9 0.1777 + bond_coeff @bond:p2-p4 harmonic 200.4 2.1790 # SOUECE3 1 + bond_coeff @bond:p2-p5 harmonic 199.9 2.1800 # SOUECE3 1 + bond_coeff @bond:p2-pe harmonic 401.6 1.8670 # SOURCE3 16 0.3571 + bond_coeff @bond:p2-pf harmonic 401.6 1.8670 # SOURCE3 16 same_as_p2-pe + bond_coeff @bond:p2-s harmonic 361.6 1.7720 # SOURCE3 26 0.3014 + bond_coeff @bond:p2-s4 harmonic 139.4 2.1900 # SOUECE3 1 + bond_coeff @bond:p2-s6 harmonic 142.3 2.1800 # SOUECE3 1 + bond_coeff @bond:p2-sh harmonic 224.0 1.9710 # SOURCE3 10 0.2829 + bond_coeff @bond:p2-ss harmonic 226.6 1.9660 # SOURCE3 10 0.2739 + bond_coeff @bond:p3-p3 harmonic 186.5 2.2140 # SOURCE1 41 0.0000 + bond_coeff @bond:p3-p4 harmonic 185.7 2.2160 # SOURCE3 3 0.0011 + bond_coeff @bond:p3-p5 harmonic 186.9 2.2130 # SOURCE3 9 0.0265 + bond_coeff @bond:p3-s harmonic 179.7 2.0700 # SOUECE3 1 + bond_coeff @bond:p3-s4 harmonic 173.2 2.0870 # SOURCE3 8 0.2235 + bond_coeff @bond:p3-s6 harmonic 176.9 2.0770 # SOURCE3 11 0.1420 + bond_coeff @bond:p3-sh harmonic 157.3 2.1320 # SOURCE3 3 0.0078 + bond_coeff @bond:p3-ss harmonic 161.0 2.1210 # SOURCE3 3 0.0059 + bond_coeff @bond:p4-p4 harmonic 273.1 2.0340 # SOURCE1 1 0.0000 + bond_coeff @bond:p4-p5 harmonic 178.0 2.2370 # SOUECE3 1 + bond_coeff @bond:p4-s harmonic 152.7 2.1460 # SOURCE3 5 0.0601 + bond_coeff @bond:p4-s4 harmonic 123.2 2.2510 # SOUECE3 1 + bond_coeff @bond:p4-s6 harmonic 118.9 2.2690 # SOUECE3 1 + bond_coeff @bond:p4-sh harmonic 163.1 2.1150 # SOURCE3 4 0.0008 + bond_coeff @bond:p4-ss harmonic 167.0 2.1040 # SOURCE3 4 0.0044 + bond_coeff @bond:p5-p5 harmonic 261.4 2.0540 # SOURCE1 1 0.0000 + bond_coeff @bond:p5-s harmonic 250.8 1.9220 # SOURCE1 89 0.0140 + bond_coeff @bond:p5-s4 harmonic 191.9 2.0400 # SOUECE3 1 + bond_coeff @bond:p5-s6 harmonic 191.9 2.0400 # SOUECE3 1 + bond_coeff @bond:p5-sh harmonic 175.0 2.0820 # SOURCE3 3 0.0035 + bond_coeff @bond:p5-ss harmonic 163.1 2.1149 # SOURCE4 24 0.0106 + bond_coeff @bond:pe-pe harmonic 240.7 2.0920 # SOURCE3 7 0.1369 + bond_coeff @bond:pe-pf harmonic 260.8 2.0550 # SOURCE3 1 0.0000 + bond_coeff @bond:pe-px harmonic 291.4 2.0050 # SOURCE3 12 0.2609 + bond_coeff @bond:pe-py harmonic 278.6 2.0250 # SOURCE3 12 0.2617 + bond_coeff @bond:pe-s harmonic 374.7 1.7580 # SOURCE3 31 0.3197 + bond_coeff @bond:pe-sx harmonic 145.9 2.1680 # SOURCE3 9 0.1743 + bond_coeff @bond:pe-sy harmonic 133.0 2.2130 # SOURCE3 6 0.0127 + bond_coeff @bond:pf-pf harmonic 240.7 2.0920 # SOURCE3 7 same_as_pe-pe + bond_coeff @bond:pf-px harmonic 291.4 2.0050 # SOURCE3 12 same_as_pe-px + bond_coeff @bond:pf-py harmonic 278.6 2.0250 # SOURCE3 12 same_as_pe-py + bond_coeff @bond:pf-s harmonic 374.7 1.7580 # SOURCE3 31 same_as_pe-s + bond_coeff @bond:pf-sx harmonic 145.9 2.1680 # SOURCE3 9 same_as_pe-sx + bond_coeff @bond:pf-sy harmonic 133.0 2.2130 # SOURCE3 6 same_as_pe-sy + bond_coeff @bond:px-py harmonic 192.3 2.1990 # SOURCE3 5 0.0238 + bond_coeff @bond:px-sx harmonic 125.4 2.2420 # SOURCE3 3 0.0119 + bond_coeff @bond:px-sy harmonic 123.7 2.2490 # SOURCE3 3 0.0272 + bond_coeff @bond:py-py harmonic 197.5 2.1860 # SOURCE3 8 0.0132 + bond_coeff @bond:py-sx harmonic 121.2 2.2590 # SOURCE3 7 0.0603 + bond_coeff @bond:py-sy harmonic 141.7 2.1820 # SOURCE3 5 0.0047 + bond_coeff @bond:s4-s4 harmonic 151.5 2.0800 # SOUECE3 1 + bond_coeff @bond:s4-s6 harmonic 151.5 2.0800 # SOUECE3 1 + bond_coeff @bond:s4-sh harmonic 125.7 2.1680 # SOURCE3 3 0.0227 + bond_coeff @bond:s4-ss harmonic 126.2 2.1660 # SOURCE3 5 0.0247 + bond_coeff @bond:s6-s6 harmonic 151.5 2.0800 # SOUECE3 1 + bond_coeff @bond:s6-sh harmonic 142.6 2.1080 # SOURCE3 3 0.0144 + bond_coeff @bond:s6-ss harmonic 139.6 2.1180 # SOURCE3 5 0.0209 + bond_coeff @bond:sh-sh harmonic 158.9 2.0580 # SOURCE2 1 0.0000 + bond_coeff @bond:sh-ss harmonic 155.8 2.0670 # SOURCE3 3 0.0029 + bond_coeff @bond:s-s harmonic 169.0 2.0300 # SOURCE3 1 0.0000 + bond_coeff @bond:s-s2 harmonic 229.2 1.8970 # SOURCE1 5 0.0000 + bond_coeff @bond:s-s4 harmonic 152.8 2.0760 # SOURCE3 4 0.0345 + bond_coeff @bond:s-s6 harmonic 166.0 2.0380 # SOURCE3 3 0.0311 + bond_coeff @bond:s-sh harmonic 142.0 2.1100 # SOURCE3 2 0.0000 + bond_coeff @bond:s-ss harmonic 148.5 2.0890 # SOURCE3 1 0.0000 + bond_coeff @bond:ss-ss harmonic 161.7 2.0500 # SOURCE1 225 0.0015 + bond_coeff @bond:sx-sx harmonic 80.9 2.3910 # SOURCE3 3 0.0185 + bond_coeff @bond:sx-sy harmonic 105.3 2.2550 # SOURCE3 5 0.0737 + bond_coeff @bond:sy-sy harmonic 106.4 2.2500 # SOURCE3 3 0.0289 + bond_coeff @bond:br-cd harmonic 277.6 1.8847 # NEW 39 + bond_coeff @bond:c1-cf harmonic 607.4 1.3153 # NEW 6 + bond_coeff @bond:cd-f harmonic 368.6 1.3401 # NEW 24 + bond_coeff @bond:cd-n4 harmonic 299.0 1.4930 # NEW 7 + bond_coeff @bond:cd-nf harmonic 427.4 1.3790 # NEW 30 + bond_coeff @bond:cd-no harmonic 367.4 1.4262 # NEW 133 + bond_coeff @bond:cd-sh harmonic 257.9 1.7681 # NEW 8 + bond_coeff @bond:cd-sx harmonic 231.3 1.8113 # NEW 16 + bond_coeff @bond:cc-cy harmonic 330.9 1.5054 # NEW 10 + bond_coeff @bond:cf-cl harmonic 292.6 1.7671 # NEW 24 + bond_coeff @bond:cf-cx harmonic 337.0 1.4993 # NEW 5 + bond_coeff @bond:cf-cy harmonic 323.0 1.5135 # NEW 17 + bond_coeff @bond:cf-na harmonic 373.8 1.4207 # NEW 5 + bond_coeff @bond:cf-ss harmonic 243.6 1.7906 # NEW 10 + bond_coeff @bond:cq-na harmonic 420.5 1.3840 # NEW 7 + bond_coeff @bond:cq-nb harmonic 486.7 1.3398 # NEW 70 + } # (end of bond_coeffs) + + write_once("Data Bonds By Type") { + @bond:ow-hw @atom:ow @atom:hw + @bond:hw-hw @atom:hw @atom:hw + @bond:br-br @atom:br @atom:br + @bond:br-c1 @atom:br @atom:c1 + @bond:br-c2 @atom:br @atom:c2 + @bond:br-c @atom:br @atom:c + @bond:br-c3 @atom:br @atom:c3 + @bond:br-ca @atom:br @atom:ca + @bond:br-cc @atom:br @atom:cc + @bond:br-cx @atom:br @atom:cx + @bond:br-i @atom:br @atom:i + @bond:br-n1 @atom:br @atom:n1 + @bond:br-n2 @atom:br @atom:n2 + @bond:br-n @atom:br @atom:n + @bond:br-n3 @atom:br @atom:n3 + @bond:br-n4 @atom:br @atom:n4 + @bond:br-na @atom:br @atom:na + @bond:br-nh @atom:br @atom:nh + @bond:br-no @atom:br @atom:no + @bond:br-o @atom:br @atom:o + @bond:br-oh @atom:br @atom:oh + @bond:br-os @atom:br @atom:os + @bond:br-p2 @atom:br @atom:p2 + @bond:br-p3 @atom:br @atom:p3 + @bond:br-p4 @atom:br @atom:p4 + @bond:br-p5 @atom:br @atom:p5 + @bond:br-s @atom:br @atom:s + @bond:br-s4 @atom:br @atom:s4 + @bond:br-s6 @atom:br @atom:s6 + @bond:br-sh @atom:br @atom:sh + @bond:br-ss @atom:br @atom:ss + @bond:c1-c1 @atom:c1 @atom:c1 + @bond:c1-c2 @atom:c1 @atom:c2 + @bond:c1-c3 @atom:c1 @atom:c3 + @bond:c1-ca @atom:c1 @atom:ca + @bond:c1-ce @atom:c1 @atom:ce + @bond:c1-cg @atom:c1 @atom:cg + @bond:c1-ch @atom:c1 @atom:ch + @bond:c1-cl @atom:c1 @atom:cl + @bond:c1-cx @atom:c1 @atom:cx + @bond:c1-f @atom:c1 @atom:f + @bond:c1-ha @atom:c1 @atom:ha + @bond:c1-hc @atom:c1 @atom:hc + @bond:c1-i @atom:c1 @atom:i + @bond:c1-n1 @atom:c1 @atom:n1 + @bond:c1-n2 @atom:c1 @atom:n2 + @bond:c1-n3 @atom:c1 @atom:n3 + @bond:c1-n4 @atom:c1 @atom:n4 + @bond:c1-n @atom:c1 @atom:n + @bond:c1-na @atom:c1 @atom:na + @bond:c1-ne @atom:c1 @atom:ne + @bond:c1-nf @atom:c1 @atom:nf + @bond:c1-nh @atom:c1 @atom:nh + @bond:c1-no @atom:c1 @atom:no + @bond:c1-o @atom:c1 @atom:o + @bond:c1-oh @atom:c1 @atom:oh + @bond:c1-os @atom:c1 @atom:os + @bond:c1-p2 @atom:c1 @atom:p2 + @bond:c1-p3 @atom:c1 @atom:p3 + @bond:c1-p4 @atom:c1 @atom:p4 + @bond:c1-p5 @atom:c1 @atom:p5 + @bond:c1-s2 @atom:c1 @atom:s2 + @bond:c1-s @atom:c1 @atom:s + @bond:c1-s4 @atom:c1 @atom:s4 + @bond:c1-s6 @atom:c1 @atom:s6 + @bond:c1-sh @atom:c1 @atom:sh + @bond:c1-ss @atom:c1 @atom:ss + @bond:c2-c2 @atom:c2 @atom:c2 + @bond:c2-c3 @atom:c2 @atom:c3 + @bond:c2-ca @atom:c2 @atom:ca + @bond:c2-cc @atom:c2 @atom:cc + @bond:c2-cd @atom:c2 @atom:cd + @bond:c2-ce @atom:c2 @atom:ce + @bond:c2-cf @atom:c2 @atom:cf + @bond:c2-cl @atom:c2 @atom:cl + @bond:c2-cu @atom:c2 @atom:cu + @bond:c2-cx @atom:c2 @atom:cx + @bond:c2-cy @atom:c2 @atom:cy + @bond:c2-f @atom:c2 @atom:f + @bond:c2-h4 @atom:c2 @atom:h4 + @bond:c2-h5 @atom:c2 @atom:h5 + @bond:c2-ha @atom:c2 @atom:ha + @bond:c2-hc @atom:c2 @atom:hc + @bond:c2-hx @atom:c2 @atom:hx + @bond:c2-i @atom:c2 @atom:i + @bond:c2-n1 @atom:c2 @atom:n1 + @bond:c2-n2 @atom:c2 @atom:n2 + @bond:c2-n3 @atom:c2 @atom:n3 + @bond:c2-n @atom:c2 @atom:n + @bond:c2-n4 @atom:c2 @atom:n4 + @bond:c2-na @atom:c2 @atom:na + @bond:c2-nc @atom:c2 @atom:nc + @bond:c2-nd @atom:c2 @atom:nd + @bond:c2-ne @atom:c2 @atom:ne + @bond:c2-nf @atom:c2 @atom:nf + @bond:c2-nh @atom:c2 @atom:nh + @bond:c2-no @atom:c2 @atom:no + @bond:c2-o @atom:c2 @atom:o + @bond:c2-oh @atom:c2 @atom:oh + @bond:c2-os @atom:c2 @atom:os + @bond:c2-p2 @atom:c2 @atom:p2 + @bond:c2-p3 @atom:c2 @atom:p3 + @bond:c2-p4 @atom:c2 @atom:p4 + @bond:c2-p5 @atom:c2 @atom:p5 + @bond:c2-pe @atom:c2 @atom:pe + @bond:c2-pf @atom:c2 @atom:pf + @bond:c2-s2 @atom:c2 @atom:s2 + @bond:c2-s @atom:c2 @atom:s + @bond:c2-s4 @atom:c2 @atom:s4 + @bond:c2-s6 @atom:c2 @atom:s6 + @bond:c2-sh @atom:c2 @atom:sh + @bond:c2-ss @atom:c2 @atom:ss + @bond:c3-c3 @atom:c3 @atom:c3 + @bond:c3-ca @atom:c3 @atom:ca + @bond:c3-cc @atom:c3 @atom:cc + @bond:c3-cd @atom:c3 @atom:cd + @bond:c3-ce @atom:c3 @atom:ce + @bond:c3-cf @atom:c3 @atom:cf + @bond:c3-cl @atom:c3 @atom:cl + @bond:c3-cu @atom:c3 @atom:cu + @bond:c3-cv @atom:c3 @atom:cv + @bond:c3-cx @atom:c3 @atom:cx + @bond:c3-cy @atom:c3 @atom:cy + @bond:c3-f @atom:c3 @atom:f + @bond:c3-h1 @atom:c3 @atom:h1 + @bond:c3-h2 @atom:c3 @atom:h2 + @bond:c3-h3 @atom:c3 @atom:h3 + @bond:c3-hc @atom:c3 @atom:hc + @bond:c3-hx @atom:c3 @atom:hx + @bond:c3-i @atom:c3 @atom:i + @bond:c3-n1 @atom:c3 @atom:n1 + @bond:c3-n2 @atom:c3 @atom:n2 + @bond:c3-n @atom:c3 @atom:n + @bond:c3-n3 @atom:c3 @atom:n3 + @bond:c3-n4 @atom:c3 @atom:n4 + @bond:c3-na @atom:c3 @atom:na + @bond:c3-nc @atom:c3 @atom:nc + @bond:c3-nd @atom:c3 @atom:nd + @bond:c3-nh @atom:c3 @atom:nh + @bond:c3-no @atom:c3 @atom:no + @bond:c3-o @atom:c3 @atom:o + @bond:c3-oh @atom:c3 @atom:oh + @bond:c3-os @atom:c3 @atom:os + @bond:c3-p2 @atom:c3 @atom:p2 + @bond:c3-p3 @atom:c3 @atom:p3 + @bond:c3-p4 @atom:c3 @atom:p4 + @bond:c3-p5 @atom:c3 @atom:p5 + @bond:c3-px @atom:c3 @atom:px + @bond:c3-py @atom:c3 @atom:py + @bond:c3-s @atom:c3 @atom:s + @bond:c3-s4 @atom:c3 @atom:s4 + @bond:c3-s6 @atom:c3 @atom:s6 + @bond:c3-sh @atom:c3 @atom:sh + @bond:c3-ss @atom:c3 @atom:ss + @bond:c3-sx @atom:c3 @atom:sx + @bond:c3-sy @atom:c3 @atom:sy + @bond:ca-ca @atom:ca @atom:ca + @bond:ca-cc @atom:ca @atom:cc + @bond:ca-cd @atom:ca @atom:cd + @bond:ca-ce @atom:ca @atom:ce + @bond:ca-cf @atom:ca @atom:cf + @bond:ca-cg @atom:ca @atom:cg + @bond:ca-ch @atom:ca @atom:ch + @bond:ca-cl @atom:ca @atom:cl + @bond:ca-cp @atom:ca @atom:cp + @bond:ca-cq @atom:ca @atom:cq + @bond:ca-cx @atom:ca @atom:cx + @bond:ca-cy @atom:ca @atom:cy + @bond:ca-f @atom:ca @atom:f + @bond:ca-h4 @atom:ca @atom:h4 + @bond:ca-h5 @atom:ca @atom:h5 + @bond:ca-ha @atom:ca @atom:ha + @bond:ca-i @atom:ca @atom:i + @bond:ca-n1 @atom:ca @atom:n1 + @bond:ca-n2 @atom:ca @atom:n2 + @bond:ca-n @atom:ca @atom:n + @bond:ca-n4 @atom:ca @atom:n4 + @bond:ca-na @atom:ca @atom:na + @bond:ca-nb @atom:ca @atom:nb + @bond:ca-nc @atom:ca @atom:nc + @bond:ca-nd @atom:ca @atom:nd + @bond:ca-ne @atom:ca @atom:ne + @bond:ca-nf @atom:ca @atom:nf + @bond:ca-nh @atom:ca @atom:nh + @bond:ca-no @atom:ca @atom:no + @bond:ca-o @atom:ca @atom:o + @bond:ca-oh @atom:ca @atom:oh + @bond:ca-os @atom:ca @atom:os + @bond:ca-p2 @atom:ca @atom:p2 + @bond:ca-p3 @atom:ca @atom:p3 + @bond:ca-p4 @atom:ca @atom:p4 + @bond:ca-p5 @atom:ca @atom:p5 + @bond:ca-pe @atom:ca @atom:pe + @bond:ca-pf @atom:ca @atom:pf + @bond:ca-px @atom:ca @atom:px + @bond:ca-py @atom:ca @atom:py + @bond:ca-s @atom:ca @atom:s + @bond:ca-s4 @atom:ca @atom:s4 + @bond:ca-s6 @atom:ca @atom:s6 + @bond:ca-sh @atom:ca @atom:sh + @bond:ca-ss @atom:ca @atom:ss + @bond:ca-sx @atom:ca @atom:sx + @bond:ca-sy @atom:ca @atom:sy + @bond:c-c1 @atom:c @atom:c1 + @bond:c-c2 @atom:c @atom:c2 + @bond:c-c @atom:c @atom:c + @bond:c-c3 @atom:c @atom:c3 + @bond:c-ca @atom:c @atom:ca + @bond:c-cc @atom:c @atom:cc + @bond:cc-cc @atom:cc @atom:cc + @bond:cc-cd @atom:cc @atom:cd + @bond:cc-ce @atom:cc @atom:ce + @bond:cc-cf @atom:cc @atom:cf + @bond:cc-cg @atom:cc @atom:cg + @bond:cc-ch @atom:cc @atom:ch + @bond:cc-cl @atom:cc @atom:cl + @bond:cc-cx @atom:cc @atom:cx + @bond:c-cd @atom:c @atom:cd + @bond:c-ce @atom:c @atom:ce + @bond:c-cf @atom:c @atom:cf + @bond:cc-f @atom:cc @atom:f + @bond:c-cg @atom:c @atom:cg + @bond:c-ch @atom:c @atom:ch + @bond:cc-h4 @atom:cc @atom:h4 + @bond:cc-h5 @atom:cc @atom:h5 + @bond:cc-ha @atom:cc @atom:ha + @bond:c-cl @atom:c @atom:cl + @bond:cc-n2 @atom:cc @atom:n2 + @bond:cc-n @atom:cc @atom:n + @bond:cc-n4 @atom:cc @atom:n4 + @bond:cc-na @atom:cc @atom:na + @bond:cc-nc @atom:cc @atom:nc + @bond:cc-nd @atom:cc @atom:nd + @bond:cc-ne @atom:cc @atom:ne + @bond:cc-nf @atom:cc @atom:nf + @bond:cc-nh @atom:cc @atom:nh + @bond:cc-no @atom:cc @atom:no + @bond:cc-oh @atom:cc @atom:oh + @bond:cc-os @atom:cc @atom:os + @bond:cc-pd @atom:cc @atom:pd + @bond:cc-sh @atom:cc @atom:sh + @bond:cc-ss @atom:cc @atom:ss + @bond:cc-sx @atom:cc @atom:sx + @bond:cc-sy @atom:cc @atom:sy + @bond:c-cu @atom:c @atom:cu + @bond:c-cx @atom:c @atom:cx + @bond:c-cy @atom:c @atom:cy + @bond:cd-cd @atom:cd @atom:cd + @bond:cd-ce @atom:cd @atom:ce + @bond:cd-cf @atom:cd @atom:cf + @bond:cd-cg @atom:cd @atom:cg + @bond:cd-ch @atom:cd @atom:ch + @bond:cd-cl @atom:cd @atom:cl + @bond:cd-cx @atom:cd @atom:cx + @bond:cd-cy @atom:cd @atom:cy + @bond:cd-h4 @atom:cd @atom:h4 + @bond:cd-h5 @atom:cd @atom:h5 + @bond:cd-ha @atom:cd @atom:ha + @bond:cd-n2 @atom:cd @atom:n2 + @bond:cd-n @atom:cd @atom:n + @bond:cd-na @atom:cd @atom:na + @bond:cd-nc @atom:cd @atom:nc + @bond:cd-nd @atom:cd @atom:nd + @bond:cd-ne @atom:cd @atom:ne + @bond:cd-nh @atom:cd @atom:nh + @bond:cd-oh @atom:cd @atom:oh + @bond:cd-os @atom:cd @atom:os + @bond:cd-pc @atom:cd @atom:pc + @bond:cd-ss @atom:cd @atom:ss + @bond:cd-sy @atom:cd @atom:sy + @bond:ce-ce @atom:ce @atom:ce + @bond:ce-cf @atom:ce @atom:cf + @bond:ce-cg @atom:ce @atom:cg + @bond:ce-ch @atom:ce @atom:ch + @bond:ce-cl @atom:ce @atom:cl + @bond:ce-cx @atom:ce @atom:cx + @bond:ce-cy @atom:ce @atom:cy + @bond:ce-h4 @atom:ce @atom:h4 + @bond:ce-ha @atom:ce @atom:ha + @bond:ce-n1 @atom:ce @atom:n1 + @bond:ce-n2 @atom:ce @atom:n2 + @bond:ce-n @atom:ce @atom:n + @bond:ce-na @atom:ce @atom:na + @bond:ce-ne @atom:ce @atom:ne + @bond:ce-nf @atom:ce @atom:nf + @bond:ce-nh @atom:ce @atom:nh + @bond:ce-oh @atom:ce @atom:oh + @bond:ce-os @atom:ce @atom:os + @bond:ce-p2 @atom:ce @atom:p2 + @bond:ce-pe @atom:ce @atom:pe + @bond:ce-px @atom:ce @atom:px + @bond:ce-py @atom:ce @atom:py + @bond:ce-s @atom:ce @atom:s + @bond:ce-ss @atom:ce @atom:ss + @bond:ce-sx @atom:ce @atom:sx + @bond:ce-sy @atom:ce @atom:sy + @bond:c-f @atom:c @atom:f + @bond:cf-cf @atom:cf @atom:cf + @bond:cf-cg @atom:cf @atom:cg + @bond:cf-ch @atom:cf @atom:ch + @bond:cf-h4 @atom:cf @atom:h4 + @bond:cf-ha @atom:cf @atom:ha + @bond:cf-n1 @atom:cf @atom:n1 + @bond:cf-n2 @atom:cf @atom:n2 + @bond:cf-n @atom:cf @atom:n + @bond:cf-ne @atom:cf @atom:ne + @bond:cf-nf @atom:cf @atom:nf + @bond:cf-nh @atom:cf @atom:nh + @bond:cf-oh @atom:cf @atom:oh + @bond:cf-os @atom:cf @atom:os + @bond:cf-p2 @atom:cf @atom:p2 + @bond:cf-pf @atom:cf @atom:pf + @bond:cf-px @atom:cf @atom:px + @bond:cf-py @atom:cf @atom:py + @bond:cf-s @atom:cf @atom:s + @bond:cf-sx @atom:cf @atom:sx + @bond:cf-sy @atom:cf @atom:sy + @bond:cg-cg @atom:cg @atom:cg + @bond:cg-ch @atom:cg @atom:ch + @bond:cg-n1 @atom:cg @atom:n1 + @bond:cg-ne @atom:cg @atom:ne + @bond:cg-pe @atom:cg @atom:pe + @bond:c-h4 @atom:c @atom:h4 + @bond:c-h5 @atom:c @atom:h5 + @bond:c-ha @atom:c @atom:ha + @bond:ch-ch @atom:ch @atom:ch + @bond:ch-n1 @atom:ch @atom:n1 + @bond:ch-nf @atom:ch @atom:nf + @bond:ch-pf @atom:ch @atom:pf + @bond:c-i @atom:c @atom:i + @bond:cl-cl @atom:cl @atom:cl + @bond:cl-cx @atom:cl @atom:cx + @bond:cl-cy @atom:cl @atom:cy + @bond:cl-f @atom:cl @atom:f + @bond:cl-i @atom:cl @atom:i + @bond:cl-n1 @atom:cl @atom:n1 + @bond:cl-n2 @atom:cl @atom:n2 + @bond:cl-n3 @atom:cl @atom:n3 + @bond:cl-n @atom:cl @atom:n + @bond:cl-n4 @atom:cl @atom:n4 + @bond:cl-na @atom:cl @atom:na + @bond:cl-nh @atom:cl @atom:nh + @bond:cl-no @atom:cl @atom:no + @bond:cl-o @atom:cl @atom:o + @bond:cl-oh @atom:cl @atom:oh + @bond:cl-os @atom:cl @atom:os + @bond:cl-p2 @atom:cl @atom:p2 + @bond:cl-p3 @atom:cl @atom:p3 + @bond:cl-p4 @atom:cl @atom:p4 + @bond:cl-p5 @atom:cl @atom:p5 + @bond:cl-pb @atom:cl @atom:pb + @bond:cl-s @atom:cl @atom:s + @bond:cl-s2 @atom:cl @atom:s2 + @bond:cl-s4 @atom:cl @atom:s4 + @bond:cl-s6 @atom:cl @atom:s6 + @bond:cl-sh @atom:cl @atom:sh + @bond:cl-ss @atom:cl @atom:ss + @bond:cl-sx @atom:cl @atom:sx + @bond:cl-sy @atom:cl @atom:sy + @bond:c-n2 @atom:c @atom:n2 + @bond:c-n4 @atom:c @atom:n4 + @bond:c-n @atom:c @atom:n + @bond:c-nc @atom:c @atom:nc + @bond:c-nd @atom:c @atom:nd + @bond:c-ne @atom:c @atom:ne + @bond:c-nf @atom:c @atom:nf + @bond:c-no @atom:c @atom:no + @bond:c-o @atom:c @atom:o + @bond:c-oh @atom:c @atom:oh + @bond:c-os @atom:c @atom:os + @bond:c-p2 @atom:c @atom:p2 + @bond:c-p3 @atom:c @atom:p3 + @bond:c-p4 @atom:c @atom:p4 + @bond:c-p5 @atom:c @atom:p5 + @bond:cp-cp @atom:cp @atom:cp + @bond:cp-cq @atom:cp @atom:cq + @bond:c-pe @atom:c @atom:pe + @bond:c-pf @atom:c @atom:pf + @bond:cp-na @atom:cp @atom:na + @bond:cp-nb @atom:cp @atom:nb + @bond:c-px @atom:c @atom:px + @bond:c-py @atom:c @atom:py + @bond:cq-cq @atom:cq @atom:cq + @bond:c-s @atom:c @atom:s + @bond:c-s4 @atom:c @atom:s4 + @bond:c-s6 @atom:c @atom:s6 + @bond:c-sh @atom:c @atom:sh + @bond:c-ss @atom:c @atom:ss + @bond:c-sx @atom:c @atom:sx + @bond:c-sy @atom:c @atom:sy + @bond:cu-cu @atom:cu @atom:cu + @bond:cu-cx @atom:cu @atom:cx + @bond:cu-ha @atom:cu @atom:ha + @bond:cv-cv @atom:cv @atom:cv + @bond:cv-cy @atom:cv @atom:cy + @bond:cv-ha @atom:cv @atom:ha + @bond:cx-cv @atom:cx @atom:cv + @bond:cx-cx @atom:cx @atom:cx + @bond:cx-cy @atom:cx @atom:cy + @bond:cx-f @atom:cx @atom:f + @bond:cx-h1 @atom:cx @atom:h1 + @bond:cx-h2 @atom:cx @atom:h2 + @bond:cx-hc @atom:cx @atom:hc + @bond:cx-hx @atom:cx @atom:hx + @bond:cx-n2 @atom:cx @atom:n2 + @bond:cx-n3 @atom:cx @atom:n3 + @bond:cx-n @atom:cx @atom:n + @bond:cx-na @atom:cx @atom:na + @bond:cx-nh @atom:cx @atom:nh + @bond:cx-oh @atom:cx @atom:oh + @bond:cx-os @atom:cx @atom:os + @bond:cx-p3 @atom:cx @atom:p3 + @bond:cx-s4 @atom:cx @atom:s4 + @bond:cx-s6 @atom:cx @atom:s6 + @bond:cx-ss @atom:cx @atom:ss + @bond:cy-cy @atom:cy @atom:cy + @bond:cy-f @atom:cy @atom:f + @bond:cy-h1 @atom:cy @atom:h1 + @bond:cy-h2 @atom:cy @atom:h2 + @bond:cy-hc @atom:cy @atom:hc + @bond:cy-n @atom:cy @atom:n + @bond:cy-n3 @atom:cy @atom:n3 + @bond:cy-oh @atom:cy @atom:oh + @bond:cy-os @atom:cy @atom:os + @bond:cy-s6 @atom:cy @atom:s6 + @bond:cy-ss @atom:cy @atom:ss + @bond:cz-nh @atom:cz @atom:nh + @bond:f-n1 @atom:f @atom:n1 + @bond:f-n2 @atom:f @atom:n2 + @bond:f-n3 @atom:f @atom:n3 + @bond:f-n @atom:f @atom:n + @bond:f-n4 @atom:f @atom:n4 + @bond:f-na @atom:f @atom:na + @bond:f-nh @atom:f @atom:nh + @bond:f-no @atom:f @atom:no + @bond:f-o @atom:f @atom:o + @bond:f-oh @atom:f @atom:oh + @bond:f-os @atom:f @atom:os + @bond:f-p2 @atom:f @atom:p2 + @bond:f-p3 @atom:f @atom:p3 + @bond:f-p4 @atom:f @atom:p4 + @bond:f-p5 @atom:f @atom:p5 + @bond:f-s2 @atom:f @atom:s2 + @bond:f-s @atom:f @atom:s + @bond:f-s4 @atom:f @atom:s4 + @bond:f-s6 @atom:f @atom:s6 + @bond:f-sh @atom:f @atom:sh + @bond:f-ss @atom:f @atom:ss + @bond:hn-n1 @atom:hn @atom:n1 + @bond:hn-n2 @atom:hn @atom:n2 + @bond:hn-n3 @atom:hn @atom:n3 + @bond:hn-n @atom:hn @atom:n + @bond:hn-n4 @atom:hn @atom:n4 + @bond:hn-na @atom:hn @atom:na + @bond:hn-nh @atom:hn @atom:nh + @bond:hn-no @atom:hn @atom:no + @bond:ho-o @atom:ho @atom:o + @bond:ho-oh @atom:ho @atom:oh + @bond:hp-p2 @atom:hp @atom:p2 + @bond:hp-p3 @atom:hp @atom:p3 + @bond:hp-p4 @atom:hp @atom:p4 + @bond:hp-p5 @atom:hp @atom:p5 + @bond:hs-s @atom:hs @atom:s + @bond:hs-s4 @atom:hs @atom:s4 + @bond:hs-s6 @atom:hs @atom:s6 + @bond:hs-sh @atom:hs @atom:sh + @bond:i-i @atom:i @atom:i + @bond:i-n1 @atom:i @atom:n1 + @bond:i-n2 @atom:i @atom:n2 + @bond:i-n @atom:i @atom:n + @bond:i-n3 @atom:i @atom:n3 + @bond:i-n4 @atom:i @atom:n4 + @bond:i-na @atom:i @atom:na + @bond:i-nh @atom:i @atom:nh + @bond:i-no @atom:i @atom:no + @bond:i-o @atom:i @atom:o + @bond:i-oh @atom:i @atom:oh + @bond:i-os @atom:i @atom:os + @bond:i-p2 @atom:i @atom:p2 + @bond:i-p3 @atom:i @atom:p3 + @bond:i-p4 @atom:i @atom:p4 + @bond:i-p5 @atom:i @atom:p5 + @bond:i-s @atom:i @atom:s + @bond:i-s4 @atom:i @atom:s4 + @bond:i-s6 @atom:i @atom:s6 + @bond:i-sh @atom:i @atom:sh + @bond:i-ss @atom:i @atom:ss + @bond:n1-n1 @atom:n1 @atom:n1 + @bond:n1-n2 @atom:n1 @atom:n2 + @bond:n1-n3 @atom:n1 @atom:n3 + @bond:n1-n4 @atom:n1 @atom:n4 + @bond:n1-na @atom:n1 @atom:na + @bond:n1-nc @atom:n1 @atom:nc + @bond:n1-nd @atom:n1 @atom:nd + @bond:n1-ne @atom:n1 @atom:ne + @bond:n1-nf @atom:n1 @atom:nf + @bond:n1-nh @atom:n1 @atom:nh + @bond:n1-no @atom:n1 @atom:no + @bond:n1-o @atom:n1 @atom:o + @bond:n1-oh @atom:n1 @atom:oh + @bond:n1-os @atom:n1 @atom:os + @bond:n1-p2 @atom:n1 @atom:p2 + @bond:n1-p3 @atom:n1 @atom:p3 + @bond:n1-p4 @atom:n1 @atom:p4 + @bond:n1-p5 @atom:n1 @atom:p5 + @bond:n1-s2 @atom:n1 @atom:s2 + @bond:n1-s @atom:n1 @atom:s + @bond:n1-s4 @atom:n1 @atom:s4 + @bond:n1-s6 @atom:n1 @atom:s6 + @bond:n1-sh @atom:n1 @atom:sh + @bond:n1-ss @atom:n1 @atom:ss + @bond:n2-n2 @atom:n2 @atom:n2 + @bond:n2-n3 @atom:n2 @atom:n3 + @bond:n2-n4 @atom:n2 @atom:n4 + @bond:n2-na @atom:n2 @atom:na + @bond:n2-nc @atom:n2 @atom:nc + @bond:n2-nd @atom:n2 @atom:nd + @bond:n2-ne @atom:n2 @atom:ne + @bond:n2-nf @atom:n2 @atom:nf + @bond:n2-nh @atom:n2 @atom:nh + @bond:n2-no @atom:n2 @atom:no + @bond:n2-o @atom:n2 @atom:o + @bond:n2-oh @atom:n2 @atom:oh + @bond:n2-os @atom:n2 @atom:os + @bond:n2-p2 @atom:n2 @atom:p2 + @bond:n2-p3 @atom:n2 @atom:p3 + @bond:n2-p4 @atom:n2 @atom:p4 + @bond:n2-p5 @atom:n2 @atom:p5 + @bond:n2-pe @atom:n2 @atom:pe + @bond:n2-pf @atom:n2 @atom:pf + @bond:n2-s2 @atom:n2 @atom:s2 + @bond:n2-s4 @atom:n2 @atom:s4 + @bond:n2-s @atom:n2 @atom:s + @bond:n2-s6 @atom:n2 @atom:s6 + @bond:n2-sh @atom:n2 @atom:sh + @bond:n2-ss @atom:n2 @atom:ss + @bond:n3-n3 @atom:n3 @atom:n3 + @bond:n3-n4 @atom:n3 @atom:n4 + @bond:n3-na @atom:n3 @atom:na + @bond:n3-nh @atom:n3 @atom:nh + @bond:n3-no @atom:n3 @atom:no + @bond:n3-o @atom:n3 @atom:o + @bond:n3-oh @atom:n3 @atom:oh + @bond:n3-os @atom:n3 @atom:os + @bond:n3-p2 @atom:n3 @atom:p2 + @bond:n3-p3 @atom:n3 @atom:p3 + @bond:n3-p4 @atom:n3 @atom:p4 + @bond:n3-p5 @atom:n3 @atom:p5 + @bond:n3-py @atom:n3 @atom:py + @bond:n3-s @atom:n3 @atom:s + @bond:n3-s4 @atom:n3 @atom:s4 + @bond:n3-s6 @atom:n3 @atom:s6 + @bond:n3-sh @atom:n3 @atom:sh + @bond:n3-ss @atom:n3 @atom:ss + @bond:n3-sy @atom:n3 @atom:sy + @bond:n4-n4 @atom:n4 @atom:n4 + @bond:n4-na @atom:n4 @atom:na + @bond:n4-nh @atom:n4 @atom:nh + @bond:n4-no @atom:n4 @atom:no + @bond:n4-o @atom:n4 @atom:o + @bond:n4-oh @atom:n4 @atom:oh + @bond:n4-os @atom:n4 @atom:os + @bond:n4-p2 @atom:n4 @atom:p2 + @bond:n4-p3 @atom:n4 @atom:p3 + @bond:n4-p4 @atom:n4 @atom:p4 + @bond:n4-p5 @atom:n4 @atom:p5 + @bond:n4-py @atom:n4 @atom:py + @bond:n4-s @atom:n4 @atom:s + @bond:n4-s4 @atom:n4 @atom:s4 + @bond:n4-s6 @atom:n4 @atom:s6 + @bond:n4-sh @atom:n4 @atom:sh + @bond:n4-ss @atom:n4 @atom:ss + @bond:na-na @atom:na @atom:na + @bond:na-nb @atom:na @atom:nb + @bond:na-nc @atom:na @atom:nc + @bond:na-nd @atom:na @atom:nd + @bond:na-nh @atom:na @atom:nh + @bond:na-no @atom:na @atom:no + @bond:na-o @atom:na @atom:o + @bond:na-oh @atom:na @atom:oh + @bond:na-os @atom:na @atom:os + @bond:na-p2 @atom:na @atom:p2 + @bond:na-p3 @atom:na @atom:p3 + @bond:na-p4 @atom:na @atom:p4 + @bond:na-p5 @atom:na @atom:p5 + @bond:na-pc @atom:na @atom:pc + @bond:na-pd @atom:na @atom:pd + @bond:na-py @atom:na @atom:py + @bond:na-s @atom:na @atom:s + @bond:na-s4 @atom:na @atom:s4 + @bond:na-s6 @atom:na @atom:s6 + @bond:na-sh @atom:na @atom:sh + @bond:na-ss @atom:na @atom:ss + @bond:na-sy @atom:na @atom:sy + @bond:nb-nb @atom:nb @atom:nb + @bond:nb-pb @atom:nb @atom:pb + @bond:nc-nc @atom:nc @atom:nc + @bond:nc-nd @atom:nc @atom:nd + @bond:nc-os @atom:nc @atom:os + @bond:nc-ss @atom:nc @atom:ss + @bond:nc-sy @atom:nc @atom:sy + @bond:nd-nd @atom:nd @atom:nd + @bond:nd-os @atom:nd @atom:os + @bond:nd-ss @atom:nd @atom:ss + @bond:nd-sy @atom:nd @atom:sy + @bond:ne-ne @atom:ne @atom:ne + @bond:ne-nf @atom:ne @atom:nf + @bond:ne-o @atom:ne @atom:o + @bond:ne-p2 @atom:ne @atom:p2 + @bond:ne-pe @atom:ne @atom:pe + @bond:ne-px @atom:ne @atom:px + @bond:ne-py @atom:ne @atom:py + @bond:ne-s @atom:ne @atom:s + @bond:ne-sx @atom:ne @atom:sx + @bond:ne-sy @atom:ne @atom:sy + @bond:nf-nf @atom:nf @atom:nf + @bond:nf-o @atom:nf @atom:o + @bond:nf-p2 @atom:nf @atom:p2 + @bond:nf-pf @atom:nf @atom:pf + @bond:nf-px @atom:nf @atom:px + @bond:nf-py @atom:nf @atom:py + @bond:nf-s @atom:nf @atom:s + @bond:nf-sx @atom:nf @atom:sx + @bond:nf-sy @atom:nf @atom:sy + @bond:nh-nh @atom:nh @atom:nh + @bond:nh-no @atom:nh @atom:no + @bond:nh-o @atom:nh @atom:o + @bond:nh-oh @atom:nh @atom:oh + @bond:nh-os @atom:nh @atom:os + @bond:nh-p2 @atom:nh @atom:p2 + @bond:nh-p3 @atom:nh @atom:p3 + @bond:nh-p4 @atom:nh @atom:p4 + @bond:nh-p5 @atom:nh @atom:p5 + @bond:nh-s @atom:nh @atom:s + @bond:nh-s4 @atom:nh @atom:s4 + @bond:nh-s6 @atom:nh @atom:s6 + @bond:nh-sh @atom:nh @atom:sh + @bond:nh-ss @atom:nh @atom:ss + @bond:nh-sy @atom:nh @atom:sy + @bond:n-n1 @atom:n @atom:n1 + @bond:n-n2 @atom:n @atom:n2 + @bond:n-n3 @atom:n @atom:n3 + @bond:n-n4 @atom:n @atom:n4 + @bond:n-n @atom:n @atom:n + @bond:n-na @atom:n @atom:na + @bond:n-nc @atom:n @atom:nc + @bond:n-nd @atom:n @atom:nd + @bond:n-nh @atom:n @atom:nh + @bond:n-no @atom:n @atom:no + @bond:n-o @atom:n @atom:o + @bond:n-oh @atom:n @atom:oh + @bond:no-no @atom:no @atom:no + @bond:no-o @atom:no @atom:o + @bond:no-oh @atom:no @atom:oh + @bond:no-os @atom:no @atom:os + @bond:no-p2 @atom:no @atom:p2 + @bond:no-p3 @atom:no @atom:p3 + @bond:no-p4 @atom:no @atom:p4 + @bond:no-p5 @atom:no @atom:p5 + @bond:no-s @atom:no @atom:s + @bond:n-os @atom:n @atom:os + @bond:no-s4 @atom:no @atom:s4 + @bond:no-s6 @atom:no @atom:s6 + @bond:no-sh @atom:no @atom:sh + @bond:no-ss @atom:no @atom:ss + @bond:n-p2 @atom:n @atom:p2 + @bond:n-p3 @atom:n @atom:p3 + @bond:n-p4 @atom:n @atom:p4 + @bond:n-p5 @atom:n @atom:p5 + @bond:n-pc @atom:n @atom:pc + @bond:n-pd @atom:n @atom:pd + @bond:n-s @atom:n @atom:s + @bond:n-s4 @atom:n @atom:s4 + @bond:n-s6 @atom:n @atom:s6 + @bond:n-sh @atom:n @atom:sh + @bond:n-ss @atom:n @atom:ss + @bond:n-sy @atom:n @atom:sy + @bond:oh-oh @atom:oh @atom:oh + @bond:oh-os @atom:oh @atom:os + @bond:oh-p2 @atom:oh @atom:p2 + @bond:oh-p3 @atom:oh @atom:p3 + @bond:oh-p4 @atom:oh @atom:p4 + @bond:oh-p5 @atom:oh @atom:p5 + @bond:oh-py @atom:oh @atom:py + @bond:oh-s @atom:oh @atom:s + @bond:oh-s4 @atom:oh @atom:s4 + @bond:oh-s6 @atom:oh @atom:s6 + @bond:oh-sh @atom:oh @atom:sh + @bond:oh-ss @atom:oh @atom:ss + @bond:oh-sy @atom:oh @atom:sy + @bond:o-o @atom:o @atom:o + @bond:o-oh @atom:o @atom:oh + @bond:o-os @atom:o @atom:os + @bond:o-p2 @atom:o @atom:p2 + @bond:o-p3 @atom:o @atom:p3 + @bond:o-p4 @atom:o @atom:p4 + @bond:o-p5 @atom:o @atom:p5 + @bond:o-pe @atom:o @atom:pe + @bond:o-pf @atom:o @atom:pf + @bond:o-px @atom:o @atom:px + @bond:o-py @atom:o @atom:py + @bond:o-s @atom:o @atom:s + @bond:o-s2 @atom:o @atom:s2 + @bond:o-s4 @atom:o @atom:s4 + @bond:o-s6 @atom:o @atom:s6 + @bond:o-sh @atom:o @atom:sh + @bond:os-os @atom:os @atom:os + @bond:os-p2 @atom:os @atom:p2 + @bond:os-p3 @atom:os @atom:p3 + @bond:os-p4 @atom:os @atom:p4 + @bond:os-p5 @atom:os @atom:p5 + @bond:os-py @atom:os @atom:py + @bond:os-s @atom:os @atom:s + @bond:o-ss @atom:o @atom:ss + @bond:os-s4 @atom:os @atom:s4 + @bond:os-s6 @atom:os @atom:s6 + @bond:os-sh @atom:os @atom:sh + @bond:os-ss @atom:os @atom:ss + @bond:os-sy @atom:os @atom:sy + @bond:o-sx @atom:o @atom:sx + @bond:o-sy @atom:o @atom:sy + @bond:p2-p2 @atom:p2 @atom:p2 + @bond:p2-p3 @atom:p2 @atom:p3 + @bond:p2-p4 @atom:p2 @atom:p4 + @bond:p2-p5 @atom:p2 @atom:p5 + @bond:p2-pe @atom:p2 @atom:pe + @bond:p2-pf @atom:p2 @atom:pf + @bond:p2-s @atom:p2 @atom:s + @bond:p2-s4 @atom:p2 @atom:s4 + @bond:p2-s6 @atom:p2 @atom:s6 + @bond:p2-sh @atom:p2 @atom:sh + @bond:p2-ss @atom:p2 @atom:ss + @bond:p3-p3 @atom:p3 @atom:p3 + @bond:p3-p4 @atom:p3 @atom:p4 + @bond:p3-p5 @atom:p3 @atom:p5 + @bond:p3-s @atom:p3 @atom:s + @bond:p3-s4 @atom:p3 @atom:s4 + @bond:p3-s6 @atom:p3 @atom:s6 + @bond:p3-sh @atom:p3 @atom:sh + @bond:p3-ss @atom:p3 @atom:ss + @bond:p4-p4 @atom:p4 @atom:p4 + @bond:p4-p5 @atom:p4 @atom:p5 + @bond:p4-s @atom:p4 @atom:s + @bond:p4-s4 @atom:p4 @atom:s4 + @bond:p4-s6 @atom:p4 @atom:s6 + @bond:p4-sh @atom:p4 @atom:sh + @bond:p4-ss @atom:p4 @atom:ss + @bond:p5-p5 @atom:p5 @atom:p5 + @bond:p5-s @atom:p5 @atom:s + @bond:p5-s4 @atom:p5 @atom:s4 + @bond:p5-s6 @atom:p5 @atom:s6 + @bond:p5-sh @atom:p5 @atom:sh + @bond:p5-ss @atom:p5 @atom:ss + @bond:pe-pe @atom:pe @atom:pe + @bond:pe-pf @atom:pe @atom:pf + @bond:pe-px @atom:pe @atom:px + @bond:pe-py @atom:pe @atom:py + @bond:pe-s @atom:pe @atom:s + @bond:pe-sx @atom:pe @atom:sx + @bond:pe-sy @atom:pe @atom:sy + @bond:pf-pf @atom:pf @atom:pf + @bond:pf-px @atom:pf @atom:px + @bond:pf-py @atom:pf @atom:py + @bond:pf-s @atom:pf @atom:s + @bond:pf-sx @atom:pf @atom:sx + @bond:pf-sy @atom:pf @atom:sy + @bond:px-py @atom:px @atom:py + @bond:px-sx @atom:px @atom:sx + @bond:px-sy @atom:px @atom:sy + @bond:py-py @atom:py @atom:py + @bond:py-sx @atom:py @atom:sx + @bond:py-sy @atom:py @atom:sy + @bond:s4-s4 @atom:s4 @atom:s4 + @bond:s4-s6 @atom:s4 @atom:s6 + @bond:s4-sh @atom:s4 @atom:sh + @bond:s4-ss @atom:s4 @atom:ss + @bond:s6-s6 @atom:s6 @atom:s6 + @bond:s6-sh @atom:s6 @atom:sh + @bond:s6-ss @atom:s6 @atom:ss + @bond:sh-sh @atom:sh @atom:sh + @bond:sh-ss @atom:sh @atom:ss + @bond:s-s @atom:s @atom:s + @bond:s-s2 @atom:s @atom:s2 + @bond:s-s4 @atom:s @atom:s4 + @bond:s-s6 @atom:s @atom:s6 + @bond:s-sh @atom:s @atom:sh + @bond:s-ss @atom:s @atom:ss + @bond:ss-ss @atom:ss @atom:ss + @bond:sx-sx @atom:sx @atom:sx + @bond:sx-sy @atom:sx @atom:sy + @bond:sy-sy @atom:sy @atom:sy + @bond:br-cd @atom:br @atom:cd + @bond:c1-cf @atom:c1 @atom:cf + @bond:cd-f @atom:cd @atom:f + @bond:cd-n4 @atom:cd @atom:n4 + @bond:cd-nf @atom:cd @atom:nf + @bond:cd-no @atom:cd @atom:no + @bond:cd-sh @atom:cd @atom:sh + @bond:cd-sx @atom:cd @atom:sx + @bond:cc-cy @atom:cc @atom:cy + @bond:cf-cl @atom:cf @atom:cl + @bond:cf-cx @atom:cf @atom:cx + @bond:cf-cy @atom:cf @atom:cy + @bond:cf-na @atom:cf @atom:na + @bond:cf-ss @atom:cf @atom:ss + @bond:cq-na @atom:cq @atom:na + @bond:cq-nb @atom:cq @atom:nb + } # (end of Bonds By Type) + + write_once("In Settings") { + angle_coeff @angle:hw-ow-hw harmonic 100.00 104.52 # AMBER 1 TIP3P_water + angle_coeff @angle:hw-hw-ow harmonic 0.00 127.74 # AMBER 1 (found_in_crystallographic_water_with_3_bonds) + angle_coeff @angle:br-c1-br harmonic 57.76 180.00 # Guess 0 + angle_coeff @angle:br-c1-c1 harmonic 54.93 180.00 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-c1 harmonic 64.41 180.00 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-c2 harmonic 60.84 180.00 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-c3 harmonic 56.28 178.46 # SOURCE4 188 0.6631 + angle_coeff @angle:c1-c1-ca harmonic 56.92 180.00 # SOURCE3 1 + angle_coeff @angle:c1-c1-cl harmonic 51.40 180.00 # SOURCE3 1 + angle_coeff @angle:c1-c1-f harmonic 61.02 180.00 # SOURCE3 1 + angle_coeff @angle:c1-c1-ha harmonic 44.84 178.38 # SOURCE3 41 2.0683 + angle_coeff @angle:c1-c1-hc harmonic 44.73 180.00 # SOURCE3 1 + angle_coeff @angle:c1-c1-i harmonic 49.80 180.00 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-n1 harmonic 67.17 180.00 # SOURCE3 1 + angle_coeff @angle:c1-c1-n2 harmonic 65.17 180.00 # SOURCE3 1 + angle_coeff @angle:c1-c1-n3 harmonic 59.77 180.00 # SOURCE3 1 + angle_coeff @angle:c1-c1-n4 harmonic 59.09 179.56 # SOURCE3 3 0.3096 + angle_coeff @angle:c1-c1-n harmonic 62.13 177.18 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-na harmonic 61.23 176.75 # SOURCE3 8 2.9328 + angle_coeff @angle:c1-c1-nh harmonic 61.44 179.27 # SOURCE3 3 0.2357 + angle_coeff @angle:c1-c1-no harmonic 59.38 180.00 # SOURCE3 3 0.0000 + angle_coeff @angle:c1-c1-o harmonic 66.79 180.00 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-oh harmonic 62.70 176.65 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-os harmonic 62.77 176.42 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-p2 harmonic 65.19 180.00 # SOURCE3 1 + angle_coeff @angle:c1-c1-p3 harmonic 66.41 169.63 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-p4 harmonic 64.47 180.00 # SOURCE3 1 + angle_coeff @angle:c1-c1-p5 harmonic 66.52 176.17 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-s4 harmonic 54.12 167.47 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-s6 harmonic 53.74 174.38 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-c1-s harmonic 55.65 179.97 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c1-sh harmonic 54.14 180.00 # SOURCE3 1 + angle_coeff @angle:c1-c1-ss harmonic 55.22 173.22 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-c1-c2 harmonic 58.20 180.00 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-c1-ce harmonic 58.18 179.01 # SOURCE4 6 0.4656 + angle_coeff @angle:c2-c1-n1 harmonic 63.14 180.00 # HF/6-31G* 1 + angle_coeff @angle:c2-c1-o harmonic 63.07 179.50 # SOURCE2 1 0.0000 + angle_coeff @angle:c2-c1-s2 harmonic 56.73 172.98 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-c1-c3 harmonic 51.75 180.00 # Guess 0 + angle_coeff @angle:c3-c1-cg harmonic 55.79 178.52 # SOURCE4 39 0.5063 + angle_coeff @angle:c3-c1-n1 harmonic 58.10 178.50 # SOURCE4 77 0.5443 + angle_coeff @angle:ca-c1-ca harmonic 52.83 180.00 # Guess 0 + angle_coeff @angle:c-c1-c1 harmonic 56.33 180.00 # SOURCE3 1 + angle_coeff @angle:cg-c1-ha harmonic 43.98 177.41 # SOURCE3 22 2.4947 + angle_coeff @angle:ch-c1-ha harmonic 43.98 177.41 # SOURCE3 22 same_as_cg-c1-ha + angle_coeff @angle:cl-c1-cl harmonic 46.64 180.00 # Guess 0 + angle_coeff @angle:f-c1-f harmonic 58.19 180.00 # Guess 0 + angle_coeff @angle:i-c1-i harmonic 53.41 180.00 # Guess 0 + angle_coeff @angle:n1-c1-n1 harmonic 93.20 102.01 # SOURCE3 1 + angle_coeff @angle:n1-c1-n3 harmonic 63.71 169.70 # SOURCE2 1 0.0000 + angle_coeff @angle:n1-c1-nh harmonic 64.02 177.43 # SOURCE4 7 0.7877 + angle_coeff @angle:n1-c1-os harmonic 64.72 178.59 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-c1-p3 harmonic 67.69 171.20 # SOURCE2 1 0.0000 + angle_coeff @angle:n1-c1-ss harmonic 55.82 178.68 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-c1-n2 harmonic 65.99 180.00 # Guess 0 + angle_coeff @angle:n2-c1-o harmonic 69.15 171.79 # SOURCE3 2 0.3594 + angle_coeff @angle:n2-c1-s harmonic 57.48 176.01 # SOURCE4 9 0.1123 + angle_coeff @angle:n3-c1-n3 harmonic 57.36 180.00 # Guess 0 + angle_coeff @angle:n4-c1-n4 harmonic 56.35 180.00 # Guess 0 + angle_coeff @angle:na-c1-na harmonic 58.62 180.00 # Guess 0 + angle_coeff @angle:ne-c1-o harmonic 69.39 172.33 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-c1-s harmonic 57.59 175.81 # SOURCE4 8 0.2356 + angle_coeff @angle:nf-c1-o harmonic 69.39 172.33 # SOURCE3 1 same_as_ne-c1-o + angle_coeff @angle:nh-c1-nh harmonic 59.55 180.00 # Guess 0 + angle_coeff @angle:n-c1-n harmonic 60.03 180.00 # Guess 0 + angle_coeff @angle:no-c1-no harmonic 56.83 180.00 # Guess 0 + angle_coeff @angle:oh-c1-oh harmonic 60.91 180.00 # Guess 0 + angle_coeff @angle:o-c1-o harmonic 69.27 180.00 # Guess 0 + angle_coeff @angle:os-c1-os harmonic 60.96 180.00 # Guess 0 + angle_coeff @angle:p2-c1-p2 harmonic 80.59 180.00 # Guess 0 + angle_coeff @angle:p3-c1-p3 harmonic 79.69 180.00 # Guess 0 + angle_coeff @angle:p4-c1-p4 harmonic 79.69 180.00 # Guess 0 + angle_coeff @angle:p5-c1-p5 harmonic 81.37 180.00 # Guess 0 + angle_coeff @angle:s2-c1-s2 harmonic 55.83 180.00 # Guess 0 + angle_coeff @angle:s4-c1-s4 harmonic 51.00 180.00 # Guess 0 + angle_coeff @angle:s6-c1-s6 harmonic 51.72 180.00 # Guess 0 + angle_coeff @angle:sh-c1-sh harmonic 53.01 180.00 # Guess 0 + angle_coeff @angle:s-c1-s harmonic 54.63 180.00 # Guess 0 + angle_coeff @angle:ss-c1-ss harmonic 53.04 180.00 # Guess 0 + angle_coeff @angle:br-c2-br harmonic 68.56 115.06 # SOURCE3 1 0.0000 + angle_coeff @angle:br-c2-c2 harmonic 63.97 118.96 # SOURCE4 6 0.4902 + angle_coeff @angle:br-c2-c3 harmonic 63.71 115.33 # SOURCE4 6 0.5872 + angle_coeff @angle:br-c2-ce harmonic 63.21 121.59 # SOURCE4 7 0.7078 + angle_coeff @angle:br-c2-h4 harmonic 43.04 113.94 # SOURCE4 6 0.4017 + angle_coeff @angle:br-c2-ha harmonic 43.18 113.28 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-c2-c1 harmonic 72.26 116.77 # SOURCE3 1 + angle_coeff @angle:c1-c2-c2 harmonic 70.34 121.62 # SOURCE3 1 + angle_coeff @angle:c1-c2-c3 harmonic 64.22 124.92 # SOURCE4 17 0.7576 + angle_coeff @angle:c1-c2-f harmonic 67.99 124.90 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-c2-ha harmonic 50.43 121.37 # SOURCE3 8 0.0055 + angle_coeff @angle:c2-c2-c2 harmonic 69.84 121.81 # SOURCE3 10 0.3843 + angle_coeff @angle:c2-c2-c3 harmonic 64.33 123.42 # SOURCE3 41 2.6057 + angle_coeff @angle:c2-c2-ca harmonic 66.88 117.00 # SOURCE3 1 + angle_coeff @angle:c2-c2-cc harmonic 70.22 117.21 # SOURCE3 2 0.3418 + angle_coeff @angle:c2-c2-cd harmonic 70.22 117.21 # SOURCE3 2 same_as_c2-c2-cc + angle_coeff @angle:c2-c2-cl harmonic 58.43 122.85 # SOURCE4 23 0.6711 + angle_coeff @angle:c2-c2-cx harmonic 64.50 125.40 # SOURCE4 12 1.8494 + angle_coeff @angle:c2-c2-cy harmonic 70.42 103.30 # SOURCE2 1 0.0000 + angle_coeff @angle:c2-c2-f harmonic 68.11 122.92 # SOURCE4 12 0.5301 + angle_coeff @angle:c2-c2-h4 harmonic 49.75 122.54 # SOURCE4 69 1.1900 + angle_coeff @angle:c2-c2-ha harmonic 50.04 120.94 # SOURCE3 254 1.3150 + angle_coeff @angle:c2-c2-hc harmonic 50.30 119.70 # SOURCE3 1 + angle_coeff @angle:c2-c2-hx harmonic 48.98 126.45 # SOURCE3 3 0.0219 + angle_coeff @angle:c2-c2-i harmonic 56.28 121.03 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-c2-n1 harmonic 71.69 122.98 # HF/6-31G* 1 + angle_coeff @angle:c2-c2-n2 harmonic 71.29 126.01 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-c2-n3 harmonic 70.33 124.55 # SOURCE3 1 + angle_coeff @angle:c2-c2-n4 harmonic 67.18 121.52 # SOURCE3 5 1.2656 + angle_coeff @angle:c2-c2-n harmonic 68.86 123.20 # SOURCE4 15 1.8657 + angle_coeff @angle:c2-c2-na harmonic 69.83 121.38 # SOURCE3 26 6.9463 + angle_coeff @angle:c2-c2-nh harmonic 69.80 124.99 # SOURCE3 7 0.9929 + angle_coeff @angle:c2-c2-no harmonic 67.52 124.09 # SOURCE4 6 1.2772 + angle_coeff @angle:c2-c2-o harmonic 71.92 130.89 # SOURCE3 2 0.0201 + angle_coeff @angle:c2-c2-oh harmonic 71.64 122.07 # SOURCE4 6 1.0883 + angle_coeff @angle:c2-c2-os harmonic 71.04 121.89 # SOURCE4 33 1.3457 + angle_coeff @angle:c2-c2-p2 harmonic 84.73 115.10 # SOURCE3 1 + angle_coeff @angle:c2-c2-p3 harmonic 75.19 124.83 # SOURCE3 5 2.1222 + angle_coeff @angle:c2-c2-p4 harmonic 77.22 119.76 # SOURCE3 1 + angle_coeff @angle:c2-c2-p5 harmonic 73.70 125.97 # SOURCE3 1 + angle_coeff @angle:c2-c2-s4 harmonic 62.85 119.84 # SOURCE3 1 + angle_coeff @angle:c2-c2-s6 harmonic 62.81 120.01 # SOURCE3 1 + angle_coeff @angle:c2-c2-s harmonic 61.25 129.37 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-c2-sh harmonic 60.87 125.70 # SOURCE3 3 1.3390 + angle_coeff @angle:c2-c2-ss harmonic 62.79 122.86 # SOURCE4 13 1.7467 + angle_coeff @angle:c3-c2-c3 harmonic 62.70 116.52 # SOURCE3 15 3.1001 + angle_coeff @angle:c3-c2-cc harmonic 63.22 125.39 # CORR 27 + angle_coeff @angle:c3-c2-cd harmonic 63.22 125.39 # CORR 27 + angle_coeff @angle:c3-c2-ce harmonic 64.17 123.08 # CORR 1288 + angle_coeff @angle:c3-c2-cf harmonic 64.17 123.08 # CORR 1288 + angle_coeff @angle:c3-c2-h4 harmonic 45.30 119.25 # SOURCE4 22 2.1707 + angle_coeff @angle:c3-c2-ha harmonic 45.66 117.30 # SOURCE3 33 1.7453 + angle_coeff @angle:c3-c2-hc harmonic 45.15 120.00 # SOURCE3 1 + angle_coeff @angle:c3-c2-n2 harmonic 66.47 123.52 # SOURCE4 141 2.2935 + angle_coeff @angle:c3-c2-n harmonic 66.79 114.80 # SOURCE4 12 1.8112 + angle_coeff @angle:c3-c2-na harmonic 64.95 122.54 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-c2-ne harmonic 66.96 122.15 # SOURCE3 4 0.2197 + angle_coeff @angle:c3-c2-nf harmonic 66.96 122.15 # SOURCE3 4 same_as_c3-c2-ne + angle_coeff @angle:c3-c2-nh harmonic 66.69 118.59 # SOURCE3 6 2.2622 + angle_coeff @angle:c3-c2-o harmonic 67.88 123.18 # SOURCE4 5 0.9226 + angle_coeff @angle:c3-c2-oh harmonic 68.50 115.04 # SOURCE4 36 2.0110 + angle_coeff @angle:c3-c2-os harmonic 68.77 112.69 # SOURCE4 50 2.4254 + angle_coeff @angle:c3-c2-p2 harmonic 78.98 122.74 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-c2-s harmonic 62.79 115.44 # SOURCE3 2 0.0115 + angle_coeff @angle:c3-c2-ss harmonic 61.62 119.66 # SOURCE4 45 1.9732 + angle_coeff @angle:ca-c2-ca harmonic 63.51 117.88 # SOURCE3 1 + angle_coeff @angle:ca-c2-hc harmonic 45.28 123.30 # SOURCE3 1 + angle_coeff @angle:c-c2-c2 harmonic 67.93 120.70 # SOURCE3 1 + angle_coeff @angle:c-c2-c3 harmonic 63.87 119.70 # SOURCE3 1 + angle_coeff @angle:c-c2-c harmonic 66.57 118.88 # SOURCE3 1 + angle_coeff @angle:cc-c2-h4 harmonic 49.19 120.33 # SOURCE4 7 0.0865 + angle_coeff @angle:cc-c2-ha harmonic 49.07 120.76 # SOURCE3 11 1.4155 + angle_coeff @angle:cc-c2-nh harmonic 69.46 122.96 # SOURCE4 10 0.7347 + angle_coeff @angle:cc-c2-o harmonic 72.80 123.59 # SOURCE4 6 0.0560 + angle_coeff @angle:cd-c2-ha harmonic 49.07 120.76 # SOURCE3 11 1.4155 + angle_coeff @angle:ce-c2-cl harmonic 58.06 123.90 # SOURCE4 11 0.3570 + angle_coeff @angle:ce-c2-h4 harmonic 49.38 122.29 # SOURCE4 75 1.4008 + angle_coeff @angle:ce-c2-ha harmonic 49.57 121.19 # SOURCE3 122 0.5318 + angle_coeff @angle:ce-c2-na harmonic 68.82 123.71 # SOURCE4 6 2.0109 + angle_coeff @angle:ce-c2-nh harmonic 70.64 120.72 # SOURCE4 93 2.2537 + angle_coeff @angle:ce-c2-no harmonic 68.45 119.65 # SOURCE4 5 0.9817 + angle_coeff @angle:ce-c2-o harmonic 73.66 123.08 # SOURCE4 5 0.2391 + angle_coeff @angle:ce-c2-oh harmonic 70.90 123.27 # SOURCE4 42 1.8111 + angle_coeff @angle:ce-c2-os harmonic 70.47 122.52 # SOURCE4 51 2.4680 + angle_coeff @angle:cf-c2-ha harmonic 49.57 121.19 # SOURCE3 122 same_as_ce-c2-ha + angle_coeff @angle:c-c2-ha harmonic 47.67 121.33 # SOURCE3 4 0.2462 + angle_coeff @angle:c-c2-hc harmonic 48.00 119.70 # SOURCE3 1 + angle_coeff @angle:cl-c2-cl harmonic 55.44 114.27 # SOURCE4 10 0.5850 + angle_coeff @angle:cl-c2-h4 harmonic 40.76 113.77 # SOURCE4 9 0.6228 + angle_coeff @angle:cl-c2-ha harmonic 40.86 113.20 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-c2-ha harmonic 46.61 115.89 # SOURCE4 15 0.3682 + angle_coeff @angle:f-c2-f harmonic 70.67 109.60 # SOURCE2 2 0.6000 + angle_coeff @angle:f-c2-ha harmonic 51.25 110.00 # SOURCE2 1 0.0000 + angle_coeff @angle:h4-c2-n2 harmonic 52.40 120.69 # SOURCE4 13 1.3105 + angle_coeff @angle:h4-c2-n harmonic 50.48 113.57 # SOURCE4 26 1.0283 + angle_coeff @angle:h4-c2-na harmonic 51.03 113.22 # SOURCE4 9 0.6345 + angle_coeff @angle:h4-c2-ne harmonic 52.87 119.63 # SOURCE4 10 1.6786 + angle_coeff @angle:h4-c2-nh harmonic 51.55 115.64 # SOURCE4 31 1.0081 + angle_coeff @angle:h4-c2-no harmonic 49.39 113.38 # SOURCE4 6 0.1240 + angle_coeff @angle:h4-c2-os harmonic 52.23 113.70 # SOURCE3 13 2.0464 + angle_coeff @angle:h4-c2-ss harmonic 42.85 118.47 # SOURCE3 9 2.5335 + angle_coeff @angle:h5-c2-n2 harmonic 52.41 120.16 # SOURCE4 27 1.8999 + angle_coeff @angle:h5-c2-na harmonic 48.23 126.39 # SOURCE3 4 0.3299 + angle_coeff @angle:h5-c2-ne harmonic 52.76 119.62 # SOURCE4 17 1.3235 + angle_coeff @angle:h5-c2-nh harmonic 51.85 113.93 # SOURCE4 50 0.8394 + angle_coeff @angle:ha-c2-ha harmonic 38.02 117.65 # SOURCE3 349 1.3426 + angle_coeff @angle:ha-c2-n1 harmonic 51.83 120.76 # SOURCE3 8 0.6632 + angle_coeff @angle:ha-c2-n2 harmonic 52.39 120.54 # SOURCE3 92 1.4571 + angle_coeff @angle:ha-c2-n3 harmonic 52.44 113.54 # SOURCE3 1 + angle_coeff @angle:ha-c2-n harmonic 50.49 113.40 # SOURCE3 4 1.2182 + angle_coeff @angle:ha-c2-na harmonic 51.18 112.42 # SOURCE3 8 0.6507 + angle_coeff @angle:ha-c2-ne harmonic 52.48 121.18 # SOURCE3 68 0.6824 + angle_coeff @angle:ha-c2-nf harmonic 52.48 121.18 # SOURCE3 68 same_as_ha-c2-ne + angle_coeff @angle:ha-c2-nh harmonic 51.29 116.68 # SOURCE3 13 2.5734 + angle_coeff @angle:ha-c2-no harmonic 49.64 112.14 # SOURCE3 2 0.0264 + angle_coeff @angle:ha-c2-o harmonic 55.30 117.23 # SOURCE3 2 0.0201 + angle_coeff @angle:ha-c2-oh harmonic 52.34 116.18 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-os harmonic 52.43 112.69 # SOURCE3 13 2.5851 + angle_coeff @angle:ha-c2-p2 harmonic 55.74 121.48 # SOURCE3 122 0.4329 + angle_coeff @angle:ha-c2-p3 harmonic 52.04 114.31 # SOURCE3 3 0.0000 + angle_coeff @angle:ha-c2-p4 harmonic 51.62 117.86 # SOURCE3 1 + angle_coeff @angle:ha-c2-p5 harmonic 49.81 120.10 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-pe harmonic 55.05 121.46 # SOURCE3 104 0.7821 + angle_coeff @angle:ha-c2-pf harmonic 55.05 121.46 # SOURCE3 104 same_as_ha-c2-pe + angle_coeff @angle:ha-c2-s2 harmonic 46.19 118.74 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-s4 harmonic 42.81 115.30 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-s harmonic 43.42 115.70 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-s6 harmonic 42.58 116.60 # SOURCE3 2 0.0000 + angle_coeff @angle:ha-c2-sh harmonic 43.04 111.74 # SOURCE3 1 0.0000 + angle_coeff @angle:ha-c2-ss harmonic 43.18 116.72 # SOURCE3 7 2.7543 + angle_coeff @angle:hc-c2-hc harmonic 37.81 118.92 # SOURCE3 1 + angle_coeff @angle:hc-c2-n2 harmonic 52.42 120.40 # SOURCE3 1 + angle_coeff @angle:hc-c2-n harmonic 50.35 114.04 # SOURCE3 1 + angle_coeff @angle:hc-c2-na harmonic 49.73 119.10 # SOURCE3 1 + angle_coeff @angle:hc-c2-nh harmonic 52.03 113.36 # SOURCE3 1 + angle_coeff @angle:hc-c2-no harmonic 49.64 112.12 # SOURCE3 1 + angle_coeff @angle:hc-c2-oh harmonic 52.33 116.22 # SOURCE3 1 + angle_coeff @angle:hc-c2-os harmonic 51.65 116.11 # SOURCE3 1 + angle_coeff @angle:hc-c2-p3 harmonic 51.40 117.19 # SOURCE3 1 + angle_coeff @angle:hc-c2-p5 harmonic 49.92 119.58 # SOURCE3 1 + angle_coeff @angle:hc-c2-s4 harmonic 42.66 116.12 # SOURCE3 1 + angle_coeff @angle:hc-c2-s6 harmonic 42.79 115.45 # SOURCE3 1 + angle_coeff @angle:hc-c2-sh harmonic 42.31 115.63 # SOURCE3 1 + angle_coeff @angle:hc-c2-ss harmonic 43.38 115.62 # SOURCE3 1 + angle_coeff @angle:hx-c2-n4 harmonic 48.42 113.03 # SOURCE3 3 0.3873 + angle_coeff @angle:i-c2-i harmonic 60.96 117.94 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-c2-n1 harmonic 73.61 124.15 # HF/6-31G* 1 + angle_coeff @angle:n2-c2-n2 harmonic 77.96 113.82 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-c2-n4 harmonic 72.03 113.05 # SOURCE4 6 0.3318 + angle_coeff @angle:n2-c2-na harmonic 71.71 123.62 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-c2-nh harmonic 72.62 124.27 # SOURCE3 12 2.4114 + angle_coeff @angle:n2-c2-oh harmonic 74.36 122.08 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-c2-os harmonic 74.32 119.82 # SOURCE4 20 1.2664 + angle_coeff @angle:n2-c2-ss harmonic 62.86 129.77 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-c2-n3 harmonic 73.45 118.47 # SOURCE3 1 + angle_coeff @angle:n4-c2-n4 harmonic 67.72 113.93 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-c2-ss harmonic 64.40 116.26 # SOURCE4 7 2.4226 + angle_coeff @angle:na-c2-na harmonic 73.65 109.33 # SOURCE3 3 3.0187 + angle_coeff @angle:ne-c2-nh harmonic 73.03 123.56 # CORR 128 + angle_coeff @angle:ne-c2-os harmonic 74.86 118.76 # SOURCE4 5 0.3382 + angle_coeff @angle:ne-c2-ss harmonic 65.41 120.06 # SOURCE4 9 1.3423 + angle_coeff @angle:nf-c2-nh harmonic 73.03 123.56 # CORR 128 + angle_coeff @angle:nh-c2-nh harmonic 74.46 112.72 # SOURCE4 257 1.8176 + angle_coeff @angle:nh-c2-oh harmonic 74.05 117.16 # SOURCE4 7 0.8698 + angle_coeff @angle:nh-c2-os harmonic 74.32 114.29 # SOURCE4 18 1.0900 + angle_coeff @angle:nh-c2-ss harmonic 67.23 111.55 # SOURCE4 37 1.1778 + angle_coeff @angle:n-c2-n2 harmonic 70.56 125.95 # SOURCE3 2 5.0202 + angle_coeff @angle:n-c2-n harmonic 71.55 113.23 # SOURCE3 1 0.0000 + angle_coeff @angle:n-c2-na harmonic 74.57 105.42 # SOURCE3 1 0.0000 + angle_coeff @angle:n-c2-ne harmonic 70.89 125.38 # SOURCE4 10 1.6819 + angle_coeff @angle:n-c2-nh harmonic 74.20 109.14 # SOURCE4 22 1.5634 + angle_coeff @angle:no-c2-no harmonic 69.43 113.90 # SOURCE3 1 0.0000 + angle_coeff @angle:n-c2-ss harmonic 66.83 111.06 # SOURCE4 9 0.5522 + angle_coeff @angle:oh-c2-oh harmonic 76.03 114.33 # SOURCE3 1 0.0000 + angle_coeff @angle:o-c2-o harmonic 80.23 121.69 # SOURCE3 1 + angle_coeff @angle:o-c2-oh harmonic 76.69 121.23 # SOURCE4 6 0.0958 + angle_coeff @angle:o-c2-s harmonic 64.15 127.68 # SOURCE3 2 0.0547 + angle_coeff @angle:os-c2-os harmonic 74.21 115.80 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-c2-p2 harmonic 100.59 129.80 # SOURCE3 1 + angle_coeff @angle:p3-c2-p3 harmonic 97.08 115.54 # SOURCE3 1 0.0000 + angle_coeff @angle:p5-c2-p5 harmonic 92.92 121.85 # SOURCE3 1 + angle_coeff @angle:s4-c2-s4 harmonic 61.89 120.32 # SOURCE3 1 + angle_coeff @angle:s4-c2-s6 harmonic 61.98 119.95 # SOURCE3 1 + angle_coeff @angle:s6-c2-s6 harmonic 61.98 119.97 # SOURCE3 1 + angle_coeff @angle:sh-c2-sh harmonic 63.96 110.48 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-c2-ss harmonic 62.65 117.82 # SOURCE3 1 + angle_coeff @angle:s-c2-s harmonic 62.47 121.67 # SOURCE3 1 + angle_coeff @angle:ss-c2-ss harmonic 62.77 120.24 # SOURCE3 1 0.0000 + angle_coeff @angle:br-c3-br harmonic 67.46 109.03 # SOURCE4 6 0.5435 + angle_coeff @angle:br-c3-c1 harmonic 62.77 111.80 # SOURCE2 3 0.2160 + angle_coeff @angle:br-c3-c3 harmonic 63.03 109.25 # SOURCE3 10 0.5685 + angle_coeff @angle:br-c3-c harmonic 62.92 110.37 # SOURCE4 13 2.4747 + angle_coeff @angle:br-c3-h1 harmonic 43.12 103.04 # SOURCE3 5 0.3092 + angle_coeff @angle:br-c3-h2 harmonic 42.34 107.10 # SOURCE4 7 0.2378 + angle_coeff @angle:br-c3-hc harmonic 42.40 106.50 # SOURCE3 1 + angle_coeff @angle:c1-c3-c1 harmonic 66.50 109.00 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-c3-c2 harmonic 65.00 111.11 # SOURCE4 12 0.7366 + angle_coeff @angle:c1-c3-c3 harmonic 64.29 111.42 # SOURCE4 197 1.2106 + angle_coeff @angle:c1-c3-ca harmonic 64.93 110.95 # SOURCE4 28 1.1203 + angle_coeff @angle:c1-c3-cc harmonic 64.32 114.20 # CORR 13 + angle_coeff @angle:c1-c3-cd harmonic 64.32 114.20 # CORR 13 + angle_coeff @angle:c1-c3-cl harmonic 58.49 110.63 # SOURCE2 3 1.2257 + angle_coeff @angle:c1-c3-h1 harmonic 48.35 109.29 # SOURCE4 133 0.5701 + angle_coeff @angle:c1-c3-hc harmonic 48.25 109.75 # SOURCE3 12 0.8436 + angle_coeff @angle:c1-c3-hx harmonic 47.76 112.05 # SOURCE4 17 0.2587 + angle_coeff @angle:c1-c3-n3 harmonic 67.03 112.59 # SOURCE4 28 0.9555 + angle_coeff @angle:c1-c3-n4 harmonic 66.53 112.04 # SOURCE4 11 0.5701 + angle_coeff @angle:c1-c3-n harmonic 67.41 112.08 # SOURCE4 18 0.9568 + angle_coeff @angle:c1-c3-nh harmonic 67.25 112.79 # SOURCE4 8 0.9453 + angle_coeff @angle:c1-c3-oh harmonic 69.49 109.14 # SOURCE4 39 0.6500 + angle_coeff @angle:c1-c3-os harmonic 69.27 108.88 # SOURCE4 31 0.9597 + angle_coeff @angle:c2-c3-c2 harmonic 63.93 112.08 # SOURCE4 153 0.7742 + angle_coeff @angle:c2-c3-c3 harmonic 63.53 111.44 # SOURCE4 2891 1.7167 + angle_coeff @angle:c2-c3-ca harmonic 63.71 112.45 # SOURCE4 141 1.6755 + angle_coeff @angle:c2-c3-cc harmonic 64.24 111.64 # CORR 32 + angle_coeff @angle:c2-c3-cd harmonic 64.24 111.64 # CORR 32 + angle_coeff @angle:c2-c3-ce harmonic 64.05 111.87 # CORR 38 + angle_coeff @angle:c2-c3-cf harmonic 64.05 111.87 # CORR 38 + angle_coeff @angle:c2-c3-cl harmonic 57.71 112.07 # SOURCE4 6 0.9936 + angle_coeff @angle:c2-c3-cx harmonic 63.65 112.62 # SOURCE4 17 1.3287 + angle_coeff @angle:c2-c3-cy harmonic 66.76 101.33 # SOURCE4 58 0.9262 + angle_coeff @angle:c2-c3-f harmonic 66.52 110.96 # SOURCE4 25 0.2829 + angle_coeff @angle:c2-c3-h1 harmonic 47.03 110.46 # SOURCE3 17 1.1525 + angle_coeff @angle:c2-c3-h2 harmonic 46.84 111.19 # SOURCE4 17 0.8311 + angle_coeff @angle:c2-c3-hc harmonic 47.03 110.49 # SOURCE3 159 0.7479 + angle_coeff @angle:c2-c3-hx harmonic 46.83 111.45 # SOURCE4 20 0.9004 + angle_coeff @angle:c2-c3-n2 harmonic 67.09 108.99 # SOURCE4 10 1.2025 + angle_coeff @angle:c2-c3-n3 harmonic 66.47 111.52 # SOURCE4 158 1.4012 + angle_coeff @angle:c2-c3-n harmonic 66.73 111.38 # SOURCE4 67 1.7559 + angle_coeff @angle:c2-c3-na harmonic 66.24 113.30 # SOURCE4 27 1.2945 + angle_coeff @angle:c2-c3-nh harmonic 67.10 110.27 # SOURCE4 56 1.8018 + angle_coeff @angle:c2-c3-oh harmonic 68.18 110.21 # SOURCE4 220 1.4197 + angle_coeff @angle:c2-c3-os harmonic 68.45 108.48 # SOURCE4 204 1.6082 + angle_coeff @angle:c2-c3-s4 harmonic 62.57 109.73 # SOURCE4 6 0.1722 + angle_coeff @angle:c2-c3-ss harmonic 63.62 104.97 # SOURCE3 2 2.2248 + angle_coeff @angle:c3-c3-c3 harmonic 63.21 110.63 # SOURCE3 507 2.7845 + angle_coeff @angle:c3-c3-ca harmonic 63.25 112.09 # SOURCE4 3859 1.5523 + angle_coeff @angle:c3-c3-cc harmonic 63.58 111.89 # CORR 700 + angle_coeff @angle:c3-c3-cd harmonic 63.58 111.89 # CORR 700 + angle_coeff @angle:c3-c3-ce harmonic 63.70 111.06 # CORR 490 + angle_coeff @angle:c3-c3-cf harmonic 63.70 111.06 # CORR 490 + angle_coeff @angle:c3-c3-cl harmonic 57.85 110.33 # SOURCE3 20 1.1495 + angle_coeff @angle:c3-c3-cx harmonic 63.30 111.82 # SOURCE4 179 2.4814 + angle_coeff @angle:c3-c3-cy harmonic 63.63 109.62 # SOURCE3 5 2.0747 + angle_coeff @angle:c3-c3-f harmonic 66.22 109.41 # SOURCE3 18 1.1878 + angle_coeff @angle:c3-c3-h1 harmonic 46.36 110.07 # SOURCE3 457 1.1542 + angle_coeff @angle:c3-c3-h2 harmonic 46.02 111.59 # SOURCE3 8 1.1217 + angle_coeff @angle:c3-c3-hc harmonic 46.37 110.05 # SOURCE3 2092 0.6991 + angle_coeff @angle:c3-c3-hx harmonic 46.02 111.74 # SOURCE3 15 1.2365 + angle_coeff @angle:c3-c3-i harmonic 58.48 110.96 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-c3-n1 harmonic 66.64 108.86 # SOURCE4 9 0.8093 + angle_coeff @angle:c3-c3-n2 harmonic 66.40 109.16 # SOURCE3 8 1.4079 + angle_coeff @angle:c3-c3-n3 harmonic 66.18 110.38 # SOURCE3 69 2.9054 + angle_coeff @angle:c3-c3-n4 harmonic 64.45 114.32 # SOURCE4 567 2.4412 + angle_coeff @angle:c3-c3-n harmonic 65.85 112.13 # SOURCE3 31 2.0700 + angle_coeff @angle:c3-c3-na harmonic 65.73 112.81 # SOURCE4 595 1.5050 + angle_coeff @angle:c3-c3-nh harmonic 66.39 110.45 # SOURCE4 1514 1.3881 + angle_coeff @angle:c3-c3-no harmonic 65.21 109.27 # SOURCE4 25 1.1817 + angle_coeff @angle:c3-c3-o harmonic 68.59 112.97 # SOURCE4 14 1.0277 + angle_coeff @angle:c3-c3-oh harmonic 67.72 109.43 # SOURCE3 48 1.5023 + angle_coeff @angle:c3-c3-os harmonic 67.78 108.42 # SOURCE3 122 1.6759 + angle_coeff @angle:c3-c3-p3 harmonic 76.46 113.19 # SOURCE4 15 0.2974 + angle_coeff @angle:c3-c3-p5 harmonic 77.70 112.32 # SOURCE4 106 1.1753 + angle_coeff @angle:c3-c3-s4 harmonic 62.16 110.07 # SOURCE4 38 0.8510 + angle_coeff @angle:c3-c3-s6 harmonic 62.98 110.00 # SOURCE4 152 1.4278 + angle_coeff @angle:c3-c3-sh harmonic 60.98 113.02 # SOURCE4 80 1.3442 + angle_coeff @angle:c3-c3-ss harmonic 61.10 112.69 # SOURCE3 24 2.1842 + angle_coeff @angle:c3-c3-sy harmonic 62.81 109.91 # SOURCE4 22 0.9248 + angle_coeff @angle:ca-c3-ca harmonic 63.66 112.26 # SOURCE4 385 1.7047 + angle_coeff @angle:ca-c3-cc harmonic 63.92 112.38 # CORR 69 + angle_coeff @angle:ca-c3-cd harmonic 63.92 112.38 # CORR 69 + angle_coeff @angle:ca-c3-ce harmonic 63.81 112.33 # SOURCE4 51 1.1929 + angle_coeff @angle:ca-c3-cl harmonic 57.85 111.31 # SOURCE4 16 0.8077 + angle_coeff @angle:ca-c3-cx harmonic 63.69 112.10 # SOURCE4 5 2.1117 + angle_coeff @angle:ca-c3-f harmonic 66.14 111.76 # SOURCE4 449 0.3492 + angle_coeff @angle:ca-c3-h1 harmonic 46.78 110.95 # SOURCE3 12 1.1170 + angle_coeff @angle:ca-c3-h2 harmonic 47.03 109.66 # SOURCE4 29 1.2184 + angle_coeff @angle:ca-c3-hc harmonic 46.96 110.15 # SOURCE3 47 1.2602 + angle_coeff @angle:ca-c3-hx harmonic 46.69 111.44 # SOURCE4 33 0.4691 + angle_coeff @angle:ca-c3-n2 harmonic 65.92 112.49 # SOURCE4 22 1.1043 + angle_coeff @angle:ca-c3-n3 harmonic 66.18 112.13 # SOURCE4 387 1.2309 + angle_coeff @angle:ca-c3-n4 harmonic 64.87 114.54 # SOURCE4 22 2.3986 + angle_coeff @angle:ca-c3-n harmonic 66.29 112.43 # SOURCE4 201 1.5133 + angle_coeff @angle:ca-c3-na harmonic 66.27 112.81 # SOURCE4 104 1.5807 + angle_coeff @angle:ca-c3-nc harmonic 68.20 106.51 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-c3-nd harmonic 68.20 106.51 # SOURCE3 1 same_as_ca-c3-nc + angle_coeff @angle:ca-c3-nh harmonic 66.64 111.41 # SOURCE4 147 1.0074 + angle_coeff @angle:ca-c3-oh harmonic 67.94 110.55 # SOURCE4 348 1.2310 + angle_coeff @angle:ca-c3-os harmonic 68.19 108.89 # SOURCE4 411 1.0102 + angle_coeff @angle:ca-c3-p5 harmonic 77.64 113.41 # SOURCE4 19 1.4444 + angle_coeff @angle:ca-c3-s6 harmonic 62.87 111.36 # SOURCE4 15 1.4775 + angle_coeff @angle:ca-c3-ss harmonic 61.90 110.66 # SOURCE4 78 1.4797 + angle_coeff @angle:ca-c3-sx harmonic 62.16 110.80 # SOURCE4 16 0.5396 + angle_coeff @angle:c-c3-c1 harmonic 64.56 112.64 # SOURCE4 11 1.0678 + angle_coeff @angle:c-c3-c2 harmonic 64.14 111.32 # SOURCE4 92 1.8522 + angle_coeff @angle:c-c3-c3 harmonic 63.79 110.53 # SOURCE3 62 1.9636 + angle_coeff @angle:c-c3-c harmonic 64.06 111.61 # SOURCE4 151 2.1872 + angle_coeff @angle:c-c3-ca harmonic 64.13 110.99 # SOURCE4 481 1.7257 + angle_coeff @angle:c-c3-cc harmonic 63.89 112.89 # CORR 104 + angle_coeff @angle:cc-c3-cc harmonic 64.61 111.05 # CORR 19 + angle_coeff @angle:cc-c3-cd harmonic 67.30 102.35 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-c3-cx harmonic 63.85 112.55 # SOURCE4 5 1.4317 + angle_coeff @angle:c-c3-cd harmonic 63.89 112.89 # CORR 104 + angle_coeff @angle:c-c3-ce harmonic 64.02 111.98 # SOURCE4 16 2.1388 + angle_coeff @angle:cc-c3-f harmonic 66.70 111.22 # CORR 69 + angle_coeff @angle:cc-c3-h1 harmonic 47.03 111.62 # SOURCE3 20 1.0215 + angle_coeff @angle:cc-c3-hc harmonic 47.20 110.86 # SOURCE3 85 1.0276 + angle_coeff @angle:cc-c3-hx harmonic 47.17 111.02 # SOURCE4 9 0.7503 + angle_coeff @angle:c-c3-cl harmonic 57.94 111.16 # SOURCE4 41 1.2257 + angle_coeff @angle:cc-c3-n2 harmonic 66.85 110.47 # SOURCE4 11 0.5153 + angle_coeff @angle:cc-c3-n3 harmonic 66.79 111.17 # CORR 111 + angle_coeff @angle:cc-c3-n4 harmonic 64.88 115.58 # SOURCE4 6 1.1723 + angle_coeff @angle:cc-c3-n harmonic 66.84 111.71 # CORR 32 + angle_coeff @angle:cc-c3-na harmonic 66.43 113.39 # SOURCE4 8 0.8010 + angle_coeff @angle:cc-c3-nc harmonic 68.37 107.04 # SOURCE3 2 0.0000 + angle_coeff @angle:cc-c3-nh harmonic 66.68 112.38 # CORR 21 + angle_coeff @angle:cc-c3-oh harmonic 68.13 111.10 # CORR 116 + angle_coeff @angle:cc-c3-os harmonic 68.51 109.01 # CORR 91 + angle_coeff @angle:cc-c3-p5 harmonic 76.89 116.23 # SOURCE4 6 0.7766 + angle_coeff @angle:cc-c3-sh harmonic 61.11 114.02 # SOURCE3 1 same_as_cd-c3-sh + angle_coeff @angle:cc-c3-ss harmonic 61.95 111.06 # CORR 43 + angle_coeff @angle:c-c3-cx harmonic 64.08 111.09 # SOURCE4 9 1.2357 + angle_coeff @angle:cd-c3-cd harmonic 64.61 111.05 # CORR 19 + angle_coeff @angle:cd-c3-f harmonic 66.70 111.22 # CORR 69 + angle_coeff @angle:cd-c3-h1 harmonic 47.03 111.62 # SOURCE3 20 1.0215 + angle_coeff @angle:cd-c3-hc harmonic 47.20 110.86 # SOURCE3 85 1.0276 + angle_coeff @angle:cd-c3-n3 harmonic 66.79 111.17 # CORR 111 + angle_coeff @angle:cd-c3-n harmonic 66.84 111.71 # CORR 32 + angle_coeff @angle:cd-c3-nd harmonic 68.37 107.04 # SOURCE3 2 same_as_cc-c3-nc + angle_coeff @angle:cd-c3-nh harmonic 66.68 112.38 # CORR 21 + angle_coeff @angle:cd-c3-oh harmonic 68.13 111.10 # CORR 116 + angle_coeff @angle:cd-c3-os harmonic 68.51 109.01 # CORR 91 + angle_coeff @angle:cd-c3-sh harmonic 61.11 114.02 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-c3-ss harmonic 61.95 111.06 # CORR 43 + angle_coeff @angle:ce-c3-ce harmonic 64.24 111.44 # SOURCE4 18 0.3695 + angle_coeff @angle:ce-c3-cy harmonic 66.33 102.85 # CORR 55 + angle_coeff @angle:ce-c3-h1 harmonic 47.30 109.59 # CORR 119 + angle_coeff @angle:ce-c3-hc harmonic 47.00 110.98 # SOURCE3 27 0.1559 + angle_coeff @angle:ce-c3-n3 harmonic 66.45 111.83 # CORR 28 + angle_coeff @angle:ce-c3-n harmonic 67.09 110.41 # SOURCE4 6 1.1405 + angle_coeff @angle:ce-c3-oh harmonic 68.00 111.05 # SOURCE4 17 1.5159 + angle_coeff @angle:ce-c3-os harmonic 68.64 108.10 # SOURCE4 16 1.9583 + angle_coeff @angle:ce-c3-ss harmonic 61.87 111.10 # SOURCE4 7 2.0156 + angle_coeff @angle:c-c3-f harmonic 66.82 109.98 # SOURCE4 38 0.9895 + angle_coeff @angle:cf-c3-cy harmonic 66.33 102.85 # CORR 55 + angle_coeff @angle:cf-c3-h1 harmonic 47.30 109.59 # CORR 119 + angle_coeff @angle:cf-c3-hc harmonic 47.00 110.98 # SOURCE3 27 same_as_ce-c3-hc + angle_coeff @angle:cf-c3-n3 harmonic 66.45 111.83 # CORR 28 + angle_coeff @angle:c-c3-h1 harmonic 47.63 107.66 # SOURCE3 66 1.4015 + angle_coeff @angle:c-c3-h2 harmonic 47.16 109.69 # SOURCE4 38 1.0614 + angle_coeff @angle:c-c3-hc harmonic 47.20 109.68 # SOURCE3 614 0.6426 + angle_coeff @angle:c-c3-hx harmonic 47.23 109.54 # SOURCE4 47 0.6627 + angle_coeff @angle:cl-c3-cl harmonic 54.23 111.03 # SOURCE2 6 1.1324 + angle_coeff @angle:cl-c3-f harmonic 59.15 109.02 # SOURCE4 15 0.3609 + angle_coeff @angle:cl-c3-h1 harmonic 40.66 105.93 # SOURCE3 19 1.1883 + angle_coeff @angle:cl-c3-h2 harmonic 40.44 107.14 # SOURCE4 50 0.5973 + angle_coeff @angle:cl-c3-hc harmonic 40.33 107.65 # SOURCE2 2 2.2500 + angle_coeff @angle:cl-c3-os harmonic 60.38 111.40 # SOURCE4 8 0.8275 + angle_coeff @angle:cl-c3-ss harmonic 57.60 112.94 # SOURCE4 10 1.4625 + angle_coeff @angle:c-c3-n2 harmonic 66.92 109.55 # SOURCE4 55 1.4579 + angle_coeff @angle:c-c3-n3 harmonic 66.59 111.14 # SOURCE4 629 1.6673 + angle_coeff @angle:c-c3-n4 harmonic 65.07 114.21 # SOURCE4 27 1.5388 + angle_coeff @angle:c-c3-n harmonic 66.67 111.56 # SOURCE3 28 1.7981 + angle_coeff @angle:c-c3-na harmonic 66.81 111.37 # SOURCE4 31 1.6229 + angle_coeff @angle:c-c3-nh harmonic 67.36 109.43 # SOURCE4 42 1.7022 + angle_coeff @angle:c-c3-oh harmonic 68.65 108.70 # SOURCE4 299 1.3415 + angle_coeff @angle:c-c3-os harmonic 68.03 109.82 # SOURCE3 10 2.0612 + angle_coeff @angle:c-c3-p5 harmonic 78.76 110.41 # SOURCE4 15 2.2683 + angle_coeff @angle:c-c3-s6 harmonic 63.26 110.22 # SOURCE4 5 2.0076 + angle_coeff @angle:c-c3-sh harmonic 62.46 108.82 # SOURCE4 12 0.8354 + angle_coeff @angle:c-c3-ss harmonic 61.70 111.58 # SOURCE3 5 1.9506 + angle_coeff @angle:cx-c3-cx harmonic 63.53 112.58 # SOURCE4 7 1.2211 + angle_coeff @angle:cx-c3-h1 harmonic 47.04 109.64 # SOURCE4 175 0.8822 + angle_coeff @angle:cx-c3-hc harmonic 46.92 110.20 # SOURCE4 356 0.8798 + angle_coeff @angle:cx-c3-hx harmonic 46.38 112.81 # SOURCE4 12 0.0977 + angle_coeff @angle:cx-c3-n3 harmonic 65.83 113.22 # SOURCE4 33 1.3978 + angle_coeff @angle:cx-c3-n4 harmonic 68.88 101.51 # SOURCE4 12 0.0760 + angle_coeff @angle:cx-c3-n harmonic 66.22 112.59 # SOURCE4 22 0.8034 + angle_coeff @angle:cx-c3-oh harmonic 68.10 109.97 # SOURCE4 25 1.3176 + angle_coeff @angle:cx-c3-os harmonic 68.40 108.16 # SOURCE4 26 1.0162 + angle_coeff @angle:cy-c3-h1 harmonic 47.00 107.88 # SOURCE4 162 0.9624 + angle_coeff @angle:cy-c3-hc harmonic 46.51 110.17 # SOURCE3 16 0.5693 + angle_coeff @angle:cy-c3-n3 harmonic 65.63 112.72 # SOURCE4 7 1.0639 + angle_coeff @angle:cy-c3-oh harmonic 67.22 111.56 # SOURCE4 138 0.5051 + angle_coeff @angle:cy-c3-os harmonic 68.45 106.79 # SOURCE4 5 1.0955 + angle_coeff @angle:f-c3-f harmonic 71.26 107.16 # SOURCE2 10 1.1324 + angle_coeff @angle:f-c3-h1 harmonic 51.57 107.85 # SOURCE3 14 0.9537 + angle_coeff @angle:f-c3-h2 harmonic 51.36 108.41 # SOURCE3 6 0.5081 + angle_coeff @angle:f-c3-h3 harmonic 51.05 110.01 # SOURCE4 19 0.6811 + angle_coeff @angle:f-c3-hc harmonic 51.33 108.92 # SOURCE2 5 3.0534 + angle_coeff @angle:f-c3-n2 harmonic 69.23 110.40 # SOURCE2 3 2.6470 + angle_coeff @angle:f-c3-os harmonic 70.66 110.61 # SOURCE4 45 1.1755 + angle_coeff @angle:f-c3-p5 harmonic 80.63 107.25 # SOURCE4 11 1.1735 + angle_coeff @angle:f-c3-s6 harmonic 64.18 109.67 # SOURCE4 24 0.4116 + angle_coeff @angle:f-c3-ss harmonic 62.13 111.89 # SOURCE4 11 0.9479 + angle_coeff @angle:h1-c3-h1 harmonic 39.18 109.55 # SOURCE3 1888 1.1205 + angle_coeff @angle:h1-c3-n1 harmonic 49.99 107.31 # HF/6-31G* 1 + angle_coeff @angle:h1-c3-n2 harmonic 49.26 109.61 # SOURCE3 63 1.0452 + angle_coeff @angle:h1-c3-n3 harmonic 49.39 109.92 # SOURCE3 313 1.1810 + angle_coeff @angle:h1-c3-n harmonic 49.82 109.32 # SOURCE3 91 1.0325 + angle_coeff @angle:h1-c3-na harmonic 49.90 109.45 # SOURCE3 53 0.9555 + angle_coeff @angle:h1-c3-nc harmonic 50.11 108.57 # SOURCE3 6 0.0764 + angle_coeff @angle:h1-c3-nd harmonic 50.11 108.57 # SOURCE3 6 same_as_h1-c3-nc + angle_coeff @angle:h1-c3-nh harmonic 49.73 109.96 # SOURCE3 70 0.7000 + angle_coeff @angle:h1-c3-no harmonic 48.66 105.15 # SOURCE4 16 0.4950 + angle_coeff @angle:h1-c3-o harmonic 52.53 117.19 # SOURCE3 6 0.0003 + angle_coeff @angle:h1-c3-oh harmonic 50.97 109.88 # SOURCE3 63 1.3172 + angle_coeff @angle:h1-c3-os harmonic 50.84 108.82 # SOURCE3 541 0.8042 + angle_coeff @angle:h1-c3-p5 harmonic 54.25 107.99 # SOURCE4 72 1.1862 + angle_coeff @angle:h1-c3-s4 harmonic 42.89 108.66 # SOURCE3 201 0.3834 + angle_coeff @angle:h1-c3-s harmonic 41.18 112.60 # SOURCE3 6 0.0026 + angle_coeff @angle:h1-c3-s6 harmonic 43.86 108.11 # SOURCE3 160 0.5518 + angle_coeff @angle:h1-c3-sh harmonic 42.40 109.21 # SOURCE3 22 1.2028 + angle_coeff @angle:h1-c3-ss harmonic 42.40 109.34 # SOURCE3 356 0.6573 + angle_coeff @angle:h1-c3-sx harmonic 42.83 108.69 # SOURCE3 90 0.2749 + angle_coeff @angle:h1-c3-sy harmonic 43.65 108.09 # SOURCE3 93 0.2556 + angle_coeff @angle:h2-c3-h2 harmonic 39.00 109.19 # SOURCE3 29 3.1352 + angle_coeff @angle:h2-c3-i harmonic 38.69 104.99 # SOURCE3 2 0.0000 + angle_coeff @angle:h2-c3-n2 harmonic 49.08 110.22 # SOURCE3 6 0.2133 + angle_coeff @angle:h2-c3-n3 harmonic 49.37 109.80 # SOURCE4 189 1.2893 + angle_coeff @angle:h2-c3-n harmonic 50.22 107.38 # SOURCE4 258 1.3140 + angle_coeff @angle:h2-c3-na harmonic 50.27 107.66 # SOURCE3 6 1.4096 + angle_coeff @angle:h2-c3-nc harmonic 49.85 109.47 # SOURCE3 10 0.3133 + angle_coeff @angle:h2-c3-nd harmonic 49.85 109.47 # SOURCE3 10 same_as_h2-c3-nc + angle_coeff @angle:h2-c3-nh harmonic 49.60 110.33 # SOURCE4 102 1.0596 + angle_coeff @angle:h2-c3-no harmonic 47.83 108.69 # SOURCE3 4 0.0000 + angle_coeff @angle:h2-c3-o harmonic 54.38 108.97 # SOURCE3 4 0.0000 + angle_coeff @angle:h2-c3-oh harmonic 51.29 108.30 # SOURCE3 6 0.5715 + angle_coeff @angle:h2-c3-os harmonic 50.84 108.58 # SOURCE3 44 1.2773 + angle_coeff @angle:h2-c3-s4 harmonic 42.93 108.58 # SOURCE3 8 0.2408 + angle_coeff @angle:h2-c3-s harmonic 42.32 106.75 # SOURCE3 4 0.0000 + angle_coeff @angle:h2-c3-s6 harmonic 44.20 106.54 # SOURCE4 27 0.9934 + angle_coeff @angle:h2-c3-sh harmonic 42.68 107.87 # SOURCE3 6 0.4376 + angle_coeff @angle:h2-c3-ss harmonic 42.34 109.75 # SOURCE3 10 0.3442 + angle_coeff @angle:h3-c3-n3 harmonic 49.73 108.39 # SOURCE4 12 1.7932 + angle_coeff @angle:h3-c3-nc harmonic 49.91 109.37 # SOURCE3 1 0.0000 + angle_coeff @angle:h3-c3-nd harmonic 49.91 109.37 # SOURCE3 1 same_as_h3-c3-nc + angle_coeff @angle:h3-c3-nh harmonic 49.53 110.78 # SOURCE4 5 1.5993 + angle_coeff @angle:h3-c3-os harmonic 50.09 112.03 # SOURCE4 17 1.0957 + angle_coeff @angle:h3-c3-ss harmonic 42.42 109.27 # SOURCE4 8 0.8367 + angle_coeff @angle:hc-c3-hc harmonic 39.43 108.35 # SOURCE3 2380 0.9006 + angle_coeff @angle:hc-c3-i harmonic 38.62 104.99 # SOURCE3 1 + angle_coeff @angle:hc-c3-n2 harmonic 49.29 109.50 # SOURCE3 1 + angle_coeff @angle:hc-c3-n3 harmonic 49.42 109.80 # SOURCE2 5 2.0070 + angle_coeff @angle:hc-c3-n4 harmonic 49.01 107.90 # SOURCE3 1 + angle_coeff @angle:hc-c3-n harmonic 49.78 109.50 # SOURCE3 1 + angle_coeff @angle:hc-c3-na harmonic 49.90 109.50 # SOURCE3 1 + angle_coeff @angle:hc-c3-nh harmonic 49.38 111.54 # SOURCE3 1 + angle_coeff @angle:hc-c3-no harmonic 48.19 107.20 # SOURCE2 1 0.0000 + angle_coeff @angle:hc-c3-oh harmonic 51.07 109.50 # SOURCE3 1 + angle_coeff @angle:hc-c3-os harmonic 50.87 108.70 # SOURCE2 13 2.3739 + angle_coeff @angle:hc-c3-p2 harmonic 52.37 110.18 # SOURCE3 25 0.4057 + angle_coeff @angle:hc-c3-p3 harmonic 52.73 110.14 # SOURCE3 325 0.5126 + angle_coeff @angle:hc-c3-p4 harmonic 53.21 109.59 # SOURCE3 87 0.3196 + angle_coeff @angle:hc-c3-p5 harmonic 53.84 109.64 # SOURCE3 69 0.8112 + angle_coeff @angle:hc-c3-px harmonic 53.46 109.74 # SOURCE3 84 0.3474 + angle_coeff @angle:hc-c3-py harmonic 53.86 109.54 # SOURCE3 39 0.1999 + angle_coeff @angle:hc-c3-s4 harmonic 43.12 107.50 # SOURCE2 1 0.0000 + angle_coeff @angle:hc-c3-s6 harmonic 43.84 108.20 # SOURCE3 1 + angle_coeff @angle:hc-c3-sh harmonic 42.66 107.87 # SOURCE2 3 2.0981 + angle_coeff @angle:hc-c3-ss harmonic 42.51 108.76 # SOURCE2 3 1.6891 + angle_coeff @angle:hx-c3-hx harmonic 39.04 110.74 # SOURCE3 137 0.5531 + angle_coeff @angle:hx-c3-n4 harmonic 49.02 107.91 # SOURCE3 148 0.5899 + angle_coeff @angle:i-c3-i harmonic 61.98 113.12 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-c3-n1 harmonic 71.09 105.07 # HF/6-31G* 1 + angle_coeff @angle:n2-c3-n2 harmonic 69.89 107.70 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-c3-nh harmonic 69.26 111.06 # SOURCE4 5 0.7868 + angle_coeff @angle:n2-c3-oh harmonic 70.15 111.82 # SOURCE4 10 0.3451 + angle_coeff @angle:n2-c3-os harmonic 70.04 111.23 # SOURCE4 6 1.0463 + angle_coeff @angle:n3-c3-n3 harmonic 69.61 109.59 # SOURCE4 27 1.8125 + angle_coeff @angle:n3-c3-nc harmonic 68.79 113.29 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-c3-nd harmonic 68.79 113.29 # SOURCE3 1 same_as_n3-c3-nc + angle_coeff @angle:n3-c3-nh harmonic 69.74 110.08 # SOURCE4 21 1.0686 + angle_coeff @angle:n3-c3-oh harmonic 70.71 110.63 # SOURCE4 20 1.0177 + angle_coeff @angle:n3-c3-os harmonic 71.15 108.33 # SOURCE4 17 1.9545 + angle_coeff @angle:n3-c3-p5 harmonic 81.55 109.51 # SOURCE4 10 1.5002 + angle_coeff @angle:n3-c3-ss harmonic 64.75 107.73 # SOURCE4 18 1.7621 + angle_coeff @angle:n4-c3-n4 harmonic 67.13 113.32 # SOURCE3 1 0.0000 + angle_coeff @angle:na-c3-na harmonic 69.06 113.49 # SOURCE3 1 0.0000 + angle_coeff @angle:na-c3-os harmonic 71.27 109.06 # SOURCE4 170 0.5450 + angle_coeff @angle:nc-c3-nc harmonic 69.96 110.61 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-c3-nh harmonic 69.34 112.43 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-c3-os harmonic 69.28 115.41 # SOURCE3 3 1.0288 + angle_coeff @angle:nd-c3-nd harmonic 69.96 110.61 # SOURCE3 1 same_as_nc-c3-nc + angle_coeff @angle:nd-c3-nh harmonic 69.34 112.43 # SOURCE3 1 same_as_nc-c3-nh + angle_coeff @angle:nd-c3-os harmonic 69.28 115.41 # SOURCE3 3 same_as_nc-c3-os + angle_coeff @angle:nh-c3-nh harmonic 71.41 105.87 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-c3-oh harmonic 70.47 112.36 # SOURCE4 12 0.7775 + angle_coeff @angle:nh-c3-os harmonic 71.26 108.93 # SOURCE4 17 1.3775 + angle_coeff @angle:nh-c3-p5 harmonic 80.62 112.50 # SOURCE4 5 1.7371 + angle_coeff @angle:nh-c3-ss harmonic 64.53 108.88 # SOURCE4 8 2.1521 + angle_coeff @angle:n-c3-n2 harmonic 68.82 112.34 # SOURCE4 5 1.1443 + angle_coeff @angle:n-c3-n3 harmonic 69.39 111.03 # SOURCE4 15 1.8216 + angle_coeff @angle:n-c3-n harmonic 68.78 113.81 # SOURCE3 1 0.0000 + angle_coeff @angle:n-c3-nh harmonic 70.54 108.34 # SOURCE4 11 2.1727 + angle_coeff @angle:n-c3-oh harmonic 70.36 112.54 # SOURCE4 31 1.1295 + angle_coeff @angle:no-c3-no harmonic 68.37 104.47 # SOURCE4 5 0.9726 + angle_coeff @angle:n-c3-os harmonic 71.14 109.16 # SOURCE4 153 0.8778 + angle_coeff @angle:n-c3-p5 harmonic 81.48 110.05 # SOURCE4 5 1.2965 + angle_coeff @angle:oh-c3-oh harmonic 72.71 109.23 # SOURCE4 8 1.4978 + angle_coeff @angle:oh-c3-os harmonic 72.38 109.21 # SOURCE4 85 1.1964 + angle_coeff @angle:oh-c3-p5 harmonic 82.83 108.86 # SOURCE4 33 1.2025 + angle_coeff @angle:oh-c3-sh harmonic 63.30 115.46 # SOURCE3 1 0.0000 + angle_coeff @angle:o-c3-o harmonic 74.43 122.30 # SOURCE3 1 0.0000 + angle_coeff @angle:os-c3-os harmonic 71.72 110.24 # SOURCE3 17 2.1340 + angle_coeff @angle:os-c3-p5 harmonic 82.86 108.36 # SOURCE4 22 2.1937 + angle_coeff @angle:os-c3-ss harmonic 65.36 107.98 # SOURCE4 20 1.7464 + angle_coeff @angle:p2-c3-p2 harmonic 98.16 110.48 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-c3-p3 harmonic 98.88 110.16 # SOURCE3 1 0.0000 + angle_coeff @angle:p5-c3-p5 harmonic 100.59 110.13 # SOURCE4 33 2.4116 + angle_coeff @angle:p5-c3-ss harmonic 78.88 111.30 # SOURCE4 5 2.0560 + angle_coeff @angle:s4-c3-s4 harmonic 62.40 112.29 # SOURCE3 2 1.2724 + angle_coeff @angle:s4-c3-s6 harmonic 62.62 113.52 # SOURCE3 1 + angle_coeff @angle:s6-c3-s6 harmonic 63.71 111.75 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-c3-sh harmonic 60.82 116.26 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-c3-ss harmonic 62.33 110.73 # SOURCE3 1 + angle_coeff @angle:s-c3-s harmonic 58.31 123.35 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-c3-ss harmonic 62.40 110.57 # SOURCE4 15 1.4311 + angle_coeff @angle:br-ca-br harmonic 67.31 117.60 # SOURCE3 1 + angle_coeff @angle:br-ca-ca harmonic 63.48 118.13 # SOURCE3 8 0.6041 + angle_coeff @angle:c1-ca-c1 harmonic 64.70 120.00 # SOURCE3 1 + angle_coeff @angle:c1-ca-ca harmonic 65.86 120.00 # SOURCE3 1 + angle_coeff @angle:c2-ca-c2 harmonic 62.95 120.00 # SOURCE3 1 + angle_coeff @angle:c2-ca-ca harmonic 64.69 120.60 # SOURCE3 1 + angle_coeff @angle:c3-ca-c2 harmonic 62.24 120.00 # SOURCE3 1 + angle_coeff @angle:c3-ca-c3 harmonic 62.41 116.80 # SOURCE3 1 + angle_coeff @angle:c3-ca-ca harmonic 63.84 120.63 # SOURCE3 60 0.7175 + angle_coeff @angle:c3-ca-cp harmonic 63.64 120.63 # CORR 120 + angle_coeff @angle:c3-ca-cq harmonic 63.64 120.63 # CORR 120 + angle_coeff @angle:c3-ca-na harmonic 66.59 118.78 # SOURCE4 59 1.1184 + angle_coeff @angle:c3-ca-nb harmonic 67.33 116.66 # SOURCE4 408 0.9380 + angle_coeff @angle:ca-ca-ca harmonic 67.18 119.97 # SOURCE3 1969 0.3480 + angle_coeff @angle:ca-ca-cc harmonic 65.99 120.10 # SOURCE3 103 0.3451 + angle_coeff @angle:ca-ca-cd harmonic 65.99 120.10 # SOURCE3 103 0.3451 + angle_coeff @angle:ca-ca-ce harmonic 64.88 120.66 # SOURCE3 14 0.1564 + angle_coeff @angle:ca-ca-cf harmonic 64.88 120.66 # SOURCE3 14 same_as_ca-ca-ce + angle_coeff @angle:ca-ca-cg harmonic 65.90 120.05 # SOURCE3 6 0.2397 + angle_coeff @angle:ca-ca-ch harmonic 65.90 120.05 # SOURCE3 6 same_as_ca-ca-cg + angle_coeff @angle:ca-ca-cl harmonic 58.52 119.40 # SOURCE4 2459 0.5283 + angle_coeff @angle:ca-ca-cp harmonic 67.16 119.07 # CORR 28 + angle_coeff @angle:ca-ca-cq harmonic 67.16 119.07 # CORR 28 + angle_coeff @angle:ca-ca-cx harmonic 64.48 120.83 # SOURCE4 71 1.3062 + angle_coeff @angle:ca-ca-cy harmonic 63.77 120.86 # SOURCE4 17 2.0287 + angle_coeff @angle:ca-ca-f harmonic 67.51 118.95 # SOURCE4 967 0.3369 + angle_coeff @angle:ca-ca-h4 harmonic 48.24 121.09 # SOURCE3 57 1.4696 + angle_coeff @angle:ca-ca-ha harmonic 48.46 120.01 # SOURCE3 2980 0.2511 + angle_coeff @angle:ca-ca-i harmonic 58.59 118.47 # SOURCE3 10 0.6181 + angle_coeff @angle:ca-ca-n1 harmonic 68.92 118.50 # HF/6-31G* 1 + angle_coeff @angle:ca-ca-n2 harmonic 70.95 119.57 # SOURCE3 1 + angle_coeff @angle:ca-ca-n4 harmonic 67.28 118.41 # SOURCE3 6 0.1691 + angle_coeff @angle:ca-ca-n harmonic 67.97 119.89 # SOURCE3 18 0.2095 + angle_coeff @angle:ca-ca-na harmonic 70.21 118.34 # SOURCE3 54 3.6168 + angle_coeff @angle:ca-ca-nb harmonic 69.16 122.63 # SOURCE3 83 1.1249 + angle_coeff @angle:ca-ca-nc harmonic 70.14 119.72 # SOURCE3 22 3.3994 + angle_coeff @angle:ca-ca-nd harmonic 70.14 119.72 # SOURCE3 22 3.3994 + angle_coeff @angle:ca-ca-ne harmonic 67.74 119.88 # SOURCE3 24 0.3637 + angle_coeff @angle:ca-ca-nf harmonic 67.74 119.88 # SOURCE3 24 0.3637 + angle_coeff @angle:ca-ca-nh harmonic 69.34 120.13 # SOURCE3 193 0.6341 + angle_coeff @angle:ca-ca-no harmonic 66.88 119.54 # SOURCE3 10 1.3187 + angle_coeff @angle:ca-ca-o harmonic 71.85 123.29 # SOURCE4 11 1.2526 + angle_coeff @angle:ca-ca-oh harmonic 69.85 119.94 # SOURCE3 14 0.1627 + angle_coeff @angle:ca-ca-os harmonic 69.79 119.20 # SOURCE3 52 0.5240 + angle_coeff @angle:ca-ca-p2 harmonic 77.87 114.36 # SOURCE3 1 + angle_coeff @angle:ca-ca-p3 harmonic 76.34 120.73 # SOURCE3 6 0.1273 + angle_coeff @angle:ca-ca-p4 harmonic 77.11 120.30 # SOURCE3 1 + angle_coeff @angle:ca-ca-p5 harmonic 77.50 120.28 # SOURCE4 5 0.0177 + angle_coeff @angle:ca-ca-pe harmonic 76.26 120.45 # SOURCE3 20 0.2719 + angle_coeff @angle:ca-ca-pf harmonic 76.26 120.45 # SOURCE3 20 0.2719 + angle_coeff @angle:ca-ca-px harmonic 76.37 120.53 # SOURCE3 10 0.4509 + angle_coeff @angle:ca-ca-py harmonic 77.43 119.98 # SOURCE3 6 0.0670 + angle_coeff @angle:ca-ca-s4 harmonic 61.72 119.15 # SOURCE3 1 + angle_coeff @angle:ca-ca-s6 harmonic 62.18 120.54 # SOURCE4 36 1.2154 + angle_coeff @angle:ca-ca-s harmonic 62.22 122.55 # SOURCE3 4 0.0000 + angle_coeff @angle:ca-ca-sh harmonic 61.32 121.78 # SOURCE4 17 1.2849 + angle_coeff @angle:ca-ca-ss harmonic 62.03 119.93 # SOURCE3 16 0.3901 + angle_coeff @angle:ca-ca-sx harmonic 60.68 119.18 # SOURCE3 6 0.0434 + angle_coeff @angle:ca-ca-sy harmonic 61.64 119.89 # SOURCE3 24 1.8813 + angle_coeff @angle:c-ca-c3 harmonic 62.61 118.06 # SOURCE3 1 + angle_coeff @angle:c-ca-c harmonic 62.65 120.00 # SOURCE3 1 + angle_coeff @angle:c-ca-ca harmonic 64.64 120.14 # SOURCE3 40 0.4788 + angle_coeff @angle:cc-ca-cp harmonic 64.63 124.30 # SOURCE4 10 0.6423 + angle_coeff @angle:cc-ca-nb harmonic 69.19 118.02 # CORR 64 + angle_coeff @angle:cd-ca-nb harmonic 69.19 118.02 # CORR 64 + angle_coeff @angle:ce-ca-na harmonic 67.44 119.85 # SOURCE4 9 0.7001 + angle_coeff @angle:ce-ca-nb harmonic 68.24 117.59 # CORR 44 + angle_coeff @angle:cf-ca-nb harmonic 68.24 117.59 # CORR 44 + angle_coeff @angle:cg-ca-cp harmonic 65.26 121.53 # SOURCE4 12 0.1831 + angle_coeff @angle:c-ca-ha harmonic 46.51 115.90 # SOURCE3 1 + angle_coeff @angle:cl-ca-cl harmonic 54.17 118.72 # SOURCE3 1 + angle_coeff @angle:cl-ca-cp harmonic 58.19 120.31 # SOURCE4 18 0.5607 + angle_coeff @angle:cl-ca-nb harmonic 61.21 116.15 # SOURCE4 50 0.6047 + angle_coeff @angle:c-ca-nb harmonic 67.71 117.94 # SOURCE4 91 1.0536 + angle_coeff @angle:c-ca-nc harmonic 64.40 130.80 # SOURCE3 1 + angle_coeff @angle:c-ca-nd harmonic 64.40 130.80 # SOURCE3 1 same_as_c-ca-nc + angle_coeff @angle:cp-ca-f harmonic 67.10 119.39 # SOURCE4 16 0.1724 + angle_coeff @angle:cp-ca-h4 harmonic 48.15 120.03 # SOURCE4 27 0.4431 + angle_coeff @angle:cp-ca-ha harmonic 47.94 121.08 # CORR 24 + angle_coeff @angle:cp-ca-na harmonic 72.91 108.79 # SOURCE4 165 0.5166 + angle_coeff @angle:cp-ca-nb harmonic 68.56 123.72 # SOURCE4 50 0.8176 + angle_coeff @angle:cp-ca-nh harmonic 68.66 121.52 # SOURCE4 11 0.5438 + angle_coeff @angle:cp-ca-oh harmonic 69.26 120.96 # SOURCE4 12 1.1400 + angle_coeff @angle:cp-ca-ss harmonic 63.87 112.75 # SOURCE4 8 0.6216 + angle_coeff @angle:cp-ca-sy harmonic 63.91 111.18 # CORR 4 + angle_coeff @angle:cq-ca-ha harmonic 47.94 121.08 # CORR 24 + angle_coeff @angle:cq-ca-sy harmonic 63.91 111.18 # CORR 4 + angle_coeff @angle:f-ca-f harmonic 68.05 117.50 # SOURCE3 1 + angle_coeff @angle:f-ca-nb harmonic 71.69 114.58 # SOURCE4 19 0.2987 + angle_coeff @angle:h4-ca-n harmonic 49.48 116.02 # SOURCE3 1 + angle_coeff @angle:h4-ca-na harmonic 51.88 114.65 # SOURCE3 5 1.5484 + angle_coeff @angle:h4-ca-nb harmonic 51.82 115.94 # SOURCE3 52 0.7370 + angle_coeff @angle:h4-ca-nc harmonic 51.46 118.36 # SOURCE3 1 + angle_coeff @angle:h4-ca-nd harmonic 51.46 118.36 # SOURCE3 1 same_as_h4-ca-nc + angle_coeff @angle:h4-ca-os harmonic 52.30 111.15 # SOURCE3 1 + angle_coeff @angle:h4-ca-ss harmonic 42.40 116.19 # SOURCE3 1 + angle_coeff @angle:h5-ca-nb harmonic 51.76 116.35 # SOURCE3 30 0.5545 + angle_coeff @angle:h5-ca-nc harmonic 50.70 122.11 # SOURCE3 1 + angle_coeff @angle:h5-ca-nd harmonic 50.70 122.11 # SOURCE3 1 same_as_h5-ca-nc + angle_coeff @angle:ha-ca-n2 harmonic 52.97 116.00 # SOURCE2 1 0.0000 + angle_coeff @angle:ha-ca-p2 harmonic 50.08 122.56 # SOURCE3 1 + angle_coeff @angle:i-ca-i harmonic 62.29 119.28 # SOURCE3 1 + angle_coeff @angle:n1-ca-n1 harmonic 70.73 117.03 # HF/6-31G* 1 + angle_coeff @angle:n2-ca-n2 harmonic 75.05 120.00 # SOURCE3 1 + angle_coeff @angle:n2-ca-na harmonic 73.80 119.60 # SOURCE3 1 + angle_coeff @angle:n4-ca-n4 harmonic 67.65 116.82 # SOURCE3 1 + angle_coeff @angle:na-ca-na harmonic 76.48 107.65 # SOURCE4 5 0.8751 + angle_coeff @angle:na-ca-nb harmonic 70.60 127.07 # SOURCE4 237 1.9392 + angle_coeff @angle:na-ca-nh harmonic 72.48 118.62 # SOURCE4 29 0.9759 + angle_coeff @angle:nb-ca-nb harmonic 70.78 127.19 # SOURCE4 585 1.1793 + angle_coeff @angle:nb-ca-nc harmonic 71.12 126.53 # CORR 22 + angle_coeff @angle:nb-ca-nd harmonic 71.12 126.53 # CORR 22 + angle_coeff @angle:nb-ca-nh harmonic 73.20 116.95 # SOURCE4 765 0.8040 + angle_coeff @angle:nb-ca-oh harmonic 73.57 117.30 # SOURCE4 64 0.9290 + angle_coeff @angle:nb-ca-os harmonic 72.54 119.66 # SOURCE4 76 0.6493 + angle_coeff @angle:nb-ca-sh harmonic 64.31 117.59 # SOURCE4 15 1.4616 + angle_coeff @angle:nb-ca-ss harmonic 64.10 119.30 # SOURCE4 41 1.3420 + angle_coeff @angle:nc-ca-nc harmonic 70.67 128.74 # SOURCE3 1 + angle_coeff @angle:nc-ca-nh harmonic 72.77 118.86 # SOURCE3 1 + angle_coeff @angle:nd-ca-nd harmonic 70.67 128.74 # SOURCE3 1 same_as_nc-ca-nc + angle_coeff @angle:nd-ca-nh harmonic 72.77 118.86 # SOURCE3 1 same_as_nc-ca-nh + angle_coeff @angle:nh-ca-nh harmonic 71.40 120.98 # SOURCE3 1 + angle_coeff @angle:n-ca-nc harmonic 69.66 123.86 # SOURCE3 1 + angle_coeff @angle:n-ca-nd harmonic 69.66 123.86 # SOURCE3 1 same_as_n-ca-nc + angle_coeff @angle:n-ca-nh harmonic 71.29 116.16 # SOURCE3 1 + angle_coeff @angle:no-ca-no harmonic 67.42 117.14 # SOURCE3 1 + angle_coeff @angle:oh-ca-oh harmonic 72.63 120.00 # SOURCE3 1 + angle_coeff @angle:o-ca-o harmonic 78.21 126.82 # SOURCE3 1 + angle_coeff @angle:os-ca-os harmonic 74.01 113.73 # SOURCE3 1 + angle_coeff @angle:p2-ca-p2 harmonic 94.48 121.20 # SOURCE3 1 + angle_coeff @angle:p3-ca-p3 harmonic 95.21 121.46 # SOURCE3 1 + angle_coeff @angle:p5-ca-p5 harmonic 97.33 120.00 # SOURCE3 1 + angle_coeff @angle:s4-ca-s4 harmonic 64.96 105.81 # SOURCE3 1 + angle_coeff @angle:s6-ca-s6 harmonic 66.03 105.81 # SOURCE3 1 + angle_coeff @angle:sh-ca-sh harmonic 61.27 120.24 # SOURCE3 1 + angle_coeff @angle:s-ca-s harmonic 61.42 125.14 # SOURCE3 1 + angle_coeff @angle:ss-ca-ss harmonic 62.91 115.15 # SOURCE3 1 + angle_coeff @angle:br-c-br harmonic 66.91 113.10 # SOURCE3 1 + angle_coeff @angle:br-c-c3 harmonic 63.34 110.74 # SOURCE3 1 0.0000 + angle_coeff @angle:br-c-o harmonic 63.19 121.46 # SOURCE3 5 1.6264 + angle_coeff @angle:c1-c-c1 harmonic 65.09 115.32 # SOURCE3 1 + angle_coeff @angle:c1-c-o harmonic 69.92 122.34 # SOURCE3 1 + angle_coeff @angle:c2-c-c2 harmonic 67.17 116.78 # SOURCE3 1 + angle_coeff @angle:c2-c-ha harmonic 48.65 115.95 # SOURCE3 1 + angle_coeff @angle:c2-c-o harmonic 72.77 119.12 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-c-s harmonic 64.67 119.16 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-c-c3 harmonic 62.82 116.05 # SOURCE3 11 1.0986 + angle_coeff @angle:c3-c-ca harmonic 62.59 118.54 # SOURCE4 240 1.3614 + angle_coeff @angle:c3-c-cc harmonic 63.38 117.47 # CORR 46 + angle_coeff @angle:c3-c-cd harmonic 63.38 117.47 # CORR 46 + angle_coeff @angle:c3-c-ce harmonic 63.44 116.37 # CORR 233 + angle_coeff @angle:c3-c-cf harmonic 63.44 116.37 # CORR 233 + angle_coeff @angle:c3-c-cg harmonic 64.26 115.00 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-c-ch harmonic 64.26 115.00 # SOURCE2 1 same_as_c3-c-cg + angle_coeff @angle:c3-c-cl harmonic 58.18 111.99 # SOURCE3 2 0.0125 + angle_coeff @angle:c3-c-f harmonic 66.93 110.70 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-c-h4 harmonic 46.11 114.40 # SOURCE4 57 0.4032 + angle_coeff @angle:c3-c-ha harmonic 46.01 115.22 # SOURCE3 15 0.3181 + angle_coeff @angle:c3-c-i harmonic 56.87 112.94 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-c-n2 harmonic 66.62 114.53 # SOURCE3 1 + angle_coeff @angle:c3-c-n4 harmonic 64.61 112.26 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-c-n harmonic 67.86 115.15 # SOURCE3 153 2.7443 + angle_coeff @angle:c3-c-ne harmonic 68.03 111.56 # CORR 12 + angle_coeff @angle:c3-c-nf harmonic 68.03 111.56 # CORR 12 + angle_coeff @angle:c3-c-o harmonic 68.03 123.11 # SOURCE3 267 3.0977 + angle_coeff @angle:c3-c-oh harmonic 69.84 112.20 # SOURCE3 14 1.8324 + angle_coeff @angle:c3-c-os harmonic 69.26 111.96 # SOURCE3 15 2.3072 + angle_coeff @angle:c3-c-p3 harmonic 74.55 116.42 # SOURCE3 3 0.1291 + angle_coeff @angle:c3-c-p5 harmonic 73.81 118.90 # SOURCE3 1 + angle_coeff @angle:c3-c-pe harmonic 74.19 114.85 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-c-pf harmonic 74.19 114.85 # SOURCE3 1 same_as_c3-c-pe + angle_coeff @angle:c3-c-px harmonic 74.17 115.60 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-c-py harmonic 74.48 118.16 # SOURCE3 3 1.0735 + angle_coeff @angle:c3-c-s4 harmonic 59.64 114.79 # SOURCE3 1 + angle_coeff @angle:c3-c-s6 harmonic 59.65 114.72 # SOURCE3 1 + angle_coeff @angle:c3-c-s harmonic 62.03 123.73 # SOURCE3 9 1.4528 + angle_coeff @angle:c3-c-sh harmonic 61.97 114.21 # SOURCE3 3 2.3916 + angle_coeff @angle:c3-c-ss harmonic 62.41 114.32 # SOURCE3 5 2.7478 + angle_coeff @angle:c3-c-sx harmonic 59.48 113.97 # SOURCE3 3 0.0610 + angle_coeff @angle:c3-c-sy harmonic 59.89 114.28 # SOURCE3 3 0.7341 + angle_coeff @angle:ca-c-ca harmonic 63.03 118.58 # SOURCE4 144 2.1146 + angle_coeff @angle:ca-c-cc harmonic 64.24 116.07 # CORR 257 + angle_coeff @angle:ca-c-cd harmonic 64.24 116.07 # CORR 257 + angle_coeff @angle:ca-c-ce harmonic 63.21 118.92 # CORR 36 + angle_coeff @angle:ca-c-cf harmonic 63.21 118.92 # CORR 36 + angle_coeff @angle:ca-c-h4 harmonic 46.52 115.14 # SOURCE4 30 0.7320 + angle_coeff @angle:ca-c-ha harmonic 46.80 114.12 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-c-n harmonic 68.47 115.14 # SOURCE4 571 1.4648 + angle_coeff @angle:ca-c-ne harmonic 67.74 114.39 # SOURCE4 5 0.2958 + angle_coeff @angle:ca-c-o harmonic 68.67 123.44 # SOURCE3 18 2.5574 + angle_coeff @angle:ca-c-oh harmonic 70.11 113.44 # SOURCE4 222 0.8421 + angle_coeff @angle:ca-c-os harmonic 68.78 115.54 # SOURCE3 5 2.6708 + angle_coeff @angle:ca-c-s harmonic 62.52 123.04 # SOURCE4 12 0.7935 + angle_coeff @angle:ca-c-sh harmonic 61.05 118.63 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-c-ss harmonic 62.45 115.13 # SOURCE4 12 1.0069 + angle_coeff @angle:br-cc-c harmonic 63.98 115.68 # SOURCE4 8 0.4970 + angle_coeff @angle:br-cc-cc harmonic 61.82 124.89 # SOURCE4 8 1.9479 + angle_coeff @angle:br-cc-cd harmonic 62.26 124.56 # SOURCE4 32 2.4696 + angle_coeff @angle:br-cc-na harmonic 64.60 121.42 # SOURCE4 6 0.5507 + angle_coeff @angle:c2-cc-c3 harmonic 63.27 126.11 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-cc-ca harmonic 65.34 124.66 # CORR 16 + angle_coeff @angle:c2-cc-cc harmonic 66.24 121.77 # CORR 32 + angle_coeff @angle:c2-cc-cd harmonic 69.09 117.02 # SOURCE3 2 0.0703 + angle_coeff @angle:c2-cc-ha harmonic 48.69 122.72 # SOURCE3 2 0.0092 + angle_coeff @angle:c2-cc-n harmonic 67.74 126.90 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-cc-os harmonic 70.10 120.79 # CORR 13 + angle_coeff @angle:c-c-c3 harmonic 61.72 116.86 # SOURCE3 5 0.1653 + angle_coeff @angle:c3-cc-ca harmonic 61.96 125.89 # CORR 127 + angle_coeff @angle:c3-cc-cc harmonic 64.66 115.97 # SOURCE3 4 3.0507 + angle_coeff @angle:c3-cc-cd harmonic 64.81 119.45 # SOURCE3 35 8.2040 + angle_coeff @angle:c3-cc-cf harmonic 65.34 117.84 # CORR 2 + angle_coeff @angle:c3-cc-ha harmonic 45.11 121.52 # SOURCE3 32 3.2091 + angle_coeff @angle:c3-cc-n2 harmonic 65.80 126.87 # CORR 9 + angle_coeff @angle:c3-cc-n harmonic 66.33 119.11 # CORR 68 + angle_coeff @angle:c3-cc-na harmonic 65.50 122.78 # CORR 632 + angle_coeff @angle:c3-cc-nc harmonic 65.90 120.94 # CORR 309 + angle_coeff @angle:c3-cc-nd harmonic 66.32 122.13 # CORR 475 + angle_coeff @angle:c3-cc-os harmonic 67.54 116.88 # CORR 203 + angle_coeff @angle:c3-cc-ss harmonic 61.21 121.66 # CORR 171 + angle_coeff @angle:c-c-c harmonic 62.30 111.68 # SOURCE3 2 6.1226 + angle_coeff @angle:c-c-ca harmonic 61.73 118.34 # SOURCE4 26 1.0692 + angle_coeff @angle:ca-cc-cc harmonic 67.66 111.04 # SOURCE3 9 7.9455 + angle_coeff @angle:ca-cc-cd harmonic 68.23 113.51 # SOURCE3 26 7.4229 + angle_coeff @angle:ca-cc-ce harmonic 62.51 127.87 # SOURCE4 11 1.7579 + angle_coeff @angle:ca-cc-h4 harmonic 45.57 128.66 # SOURCE3 10 3.1167 + angle_coeff @angle:ca-cc-ha harmonic 46.40 124.04 # SOURCE3 34 3.6691 + angle_coeff @angle:ca-cc-n harmonic 68.46 117.67 # CORR 18 + angle_coeff @angle:ca-cc-nc harmonic 67.69 120.67 # CORR 162 + angle_coeff @angle:ca-cc-nd harmonic 67.92 123.02 # CORR 188 + angle_coeff @angle:ca-cc-nh harmonic 67.46 122.45 # SOURCE4 9 1.4092 + angle_coeff @angle:ca-cc-oh harmonic 69.61 117.71 # CORR 21 + angle_coeff @angle:ca-cc-os harmonic 69.82 115.16 # CORR 134 + angle_coeff @angle:ca-cc-ss harmonic 62.30 120.51 # CORR 43 + angle_coeff @angle:c-cc-c2 harmonic 65.60 120.92 # CORR 22 + angle_coeff @angle:c-cc-c3 harmonic 63.60 117.42 # CORR 126 + angle_coeff @angle:c-cc-c harmonic 63.42 121.17 # CORR 64 + angle_coeff @angle:c-c-cc harmonic 64.02 111.67 # SOURCE3 4 5.5146 + angle_coeff @angle:c-cc-ca harmonic 63.55 122.95 # SOURCE3 1 0.0000 + angle_coeff @angle:c-cc-cc harmonic 63.72 122.69 # SOURCE3 2 0.0000 + angle_coeff @angle:cc-c-cc harmonic 64.80 116.04 # CORR 56 + angle_coeff @angle:cc-cc-cc harmonic 67.88 110.70 # SOURCE3 54 3.4091 + angle_coeff @angle:cc-cc-cd harmonic 68.16 114.19 # SOURCE3 517 6.5960 + angle_coeff @angle:cc-cc-ce harmonic 62.78 127.20 # CORR 42 + angle_coeff @angle:cc-cc-cf harmonic 65.88 122.59 # CORR 39 + angle_coeff @angle:cc-cc-cg harmonic 63.63 126.15 # CORR 27 + angle_coeff @angle:c-cc-cd harmonic 65.25 121.42 # CORR 1708 + angle_coeff @angle:cc-c-cd harmonic 65.73 112.79 # SOURCE3 1 0.0000 + angle_coeff @angle:c-cc-ce harmonic 63.20 122.73 # CORR 10 + angle_coeff @angle:cc-c-ce harmonic 64.64 115.68 # SOURCE4 6 1.2033 + angle_coeff @angle:cc-cc-f harmonic 66.35 119.41 # SOURCE4 7 0.4917 + angle_coeff @angle:c-cc-cg harmonic 64.98 118.14 # SOURCE4 7 0.7745 + angle_coeff @angle:cc-cc-h4 harmonic 45.56 129.47 # SOURCE3 171 2.2734 + angle_coeff @angle:cc-cc-ha harmonic 47.14 120.86 # CORR 1751 + angle_coeff @angle:c-cc-cl harmonic 58.39 116.05 # CORR 24 + angle_coeff @angle:cc-cc-n2 harmonic 69.48 121.15 # CORR 12 + angle_coeff @angle:cc-cc-n harmonic 67.95 119.89 # SOURCE3 36 0.2095 + angle_coeff @angle:cc-cc-na harmonic 72.21 106.80 # SOURCE3 33 0.6297 + angle_coeff @angle:cc-cc-nc harmonic 67.53 121.69 # CORR 105 + angle_coeff @angle:cc-cc-nd harmonic 71.15 112.56 # SOURCE3 141 4.2871 + angle_coeff @angle:cc-cc-nh harmonic 68.41 119.51 # CORR 228 + angle_coeff @angle:cc-cc-oh harmonic 68.53 121.96 # CORR 27 + angle_coeff @angle:cc-cc-os harmonic 69.34 117.23 # CORR 211 + angle_coeff @angle:cc-cc-pd harmonic 80.79 115.36 # SOURCE3 84 same_as_cd-cd-pc + angle_coeff @angle:cc-cc-ss harmonic 62.45 120.12 # CORR 31 + angle_coeff @angle:cc-cc-sy harmonic 59.22 128.36 # SOURCE4 8 0.9813 + angle_coeff @angle:c-c-cd harmonic 64.02 111.67 # SOURCE3 4 5.5146 + angle_coeff @angle:cd-cc-cd harmonic 67.89 120.23 # CORR 133 + angle_coeff @angle:cd-cc-ce harmonic 63.67 128.41 # CORR 210 + angle_coeff @angle:cd-cc-cl harmonic 57.46 123.70 # CORR 62 + angle_coeff @angle:cd-cc-f harmonic 67.42 121.08 # SOURCE4 28 0.8788 + angle_coeff @angle:cd-cc-h4 harmonic 47.19 129.11 # SOURCE3 418 3.1355 + angle_coeff @angle:cd-cc-ha harmonic 48.35 122.89 # SOURCE3 584 2.9334 + angle_coeff @angle:cd-cc-n harmonic 70.72 115.52 # SOURCE3 52 1.3322 + angle_coeff @angle:cd-cc-na harmonic 72.91 109.42 # SOURCE3 265 2.6051 + angle_coeff @angle:cd-cc-nc harmonic 72.01 111.75 # CORR 1101 + angle_coeff @angle:cd-cc-nh harmonic 68.69 123.89 # CORR 106 + angle_coeff @angle:cd-cc-no harmonic 65.78 128.95 # SOURCE4 117 1.4740 + angle_coeff @angle:cd-cc-oh harmonic 69.56 123.89 # CORR 106 + angle_coeff @angle:cd-cc-os harmonic 69.96 120.30 # SOURCE3 64 5.4354 + angle_coeff @angle:cd-cc-ss harmonic 65.44 111.55 # CORR 884 + angle_coeff @angle:cd-cc-sy harmonic 60.54 124.91 # CORR 41 + angle_coeff @angle:ce-cc-na harmonic 66.32 124.22 # CORR 48 + angle_coeff @angle:ce-cc-nc harmonic 67.01 121.29 # CORR 37 + angle_coeff @angle:ce-cc-nd harmonic 67.80 121.51 # CORR 37 + angle_coeff @angle:ce-cc-os harmonic 68.17 119.03 # CORR 66 + angle_coeff @angle:ce-cc-ss harmonic 61.83 121.44 # CORR 38 + angle_coeff @angle:c-cc-f harmonic 66.16 116.87 # SOURCE4 16 0.5322 + angle_coeff @angle:cg-cc-na harmonic 67.51 122.35 # SOURCE4 5 0.8112 + angle_coeff @angle:cg-cc-ss harmonic 62.33 120.70 # SOURCE4 12 0.9090 + angle_coeff @angle:cc-c-h4 harmonic 47.13 115.45 # SOURCE4 5 0.8021 + angle_coeff @angle:c-cc-ha harmonic 46.99 117.02 # SOURCE3 56 1.9713 + angle_coeff @angle:cl-cc-na harmonic 59.37 121.61 # SOURCE4 12 0.3436 + angle_coeff @angle:cl-cc-nd harmonic 59.35 122.97 # CORR 6 + angle_coeff @angle:cl-cc-ss harmonic 58.09 119.85 # SOURCE4 11 1.0626 + angle_coeff @angle:c-cc-n2 harmonic 68.54 120.89 # CORR 2 + angle_coeff @angle:c-cc-n harmonic 68.11 116.32 # CORR 21 + angle_coeff @angle:cc-c-n harmonic 70.19 111.86 # SOURCE3 36 2.3407 + angle_coeff @angle:c-cc-nc harmonic 66.19 123.47 # CORR 24 + angle_coeff @angle:cc-c-nd harmonic 67.92 116.21 # CORR 33 + angle_coeff @angle:c-cc-nd harmonic 67.50 121.67 # CORR 47 + angle_coeff @angle:c-cc-ne harmonic 67.11 119.88 # SOURCE4 6 0.3139 + angle_coeff @angle:cc-c-o harmonic 68.91 125.71 # SOURCE3 66 2.4784 + angle_coeff @angle:c-cc-oh harmonic 70.04 113.64 # CORR 53 + angle_coeff @angle:cc-c-oh harmonic 71.00 113.10 # CORR 85 + angle_coeff @angle:c-cc-os harmonic 67.83 119.39 # CORR 78 + angle_coeff @angle:cc-c-os harmonic 70.50 112.30 # SOURCE3 6 2.7842 + angle_coeff @angle:cc-c-s harmonic 61.67 127.94 # SOURCE4 12 0.9342 + angle_coeff @angle:cc-c-ss harmonic 63.47 112.52 # SOURCE4 10 0.6933 + angle_coeff @angle:cx-cc-nd harmonic 65.61 127.75 # SOURCE4 12 1.7156 + angle_coeff @angle:cx-cc-os harmonic 67.94 118.08 # SOURCE4 10 0.0955 + angle_coeff @angle:cd-c-cd harmonic 64.80 116.04 # CORR 56 + angle_coeff @angle:cd-c-cx harmonic 63.88 117.46 # SOURCE4 13 0.1625 + angle_coeff @angle:cd-c-n harmonic 70.19 111.86 # SOURCE3 36 2.3407 + angle_coeff @angle:cd-c-nc harmonic 67.92 116.21 # CORR 33 + angle_coeff @angle:cd-c-nd harmonic 68.65 113.75 # SOURCE4 14 0.0860 + angle_coeff @angle:cd-c-o harmonic 68.91 125.71 # SOURCE3 66 2.4784 + angle_coeff @angle:cd-c-oh harmonic 71.00 113.10 # CORR 85 + angle_coeff @angle:cd-c-os harmonic 70.50 112.30 # SOURCE3 6 2.7842 + angle_coeff @angle:ce-c-ce harmonic 64.34 115.80 # CORR 74 + angle_coeff @angle:ce-c-cf harmonic 64.04 116.89 # SOURCE4 11 1.6021 + angle_coeff @angle:ce-c-cx harmonic 63.95 116.25 # SOURCE4 6 0.6351 + angle_coeff @angle:ce-c-h4 harmonic 46.93 114.88 # SOURCE4 19 0.3355 + angle_coeff @angle:ce-c-ha harmonic 46.93 115.22 # SOURCE3 7 2.4188 + angle_coeff @angle:ce-c-n harmonic 68.80 115.27 # CORR 32 + angle_coeff @angle:ce-c-o harmonic 69.27 122.92 # SOURCE3 17 3.5085 + angle_coeff @angle:ce-c-oh harmonic 70.32 114.09 # CORR 128 + angle_coeff @angle:ce-c-os harmonic 70.16 112.28 # CORR 149 + angle_coeff @angle:ce-c-s harmonic 64.09 117.80 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-c-ss harmonic 63.94 110.39 # SOURCE4 5 0.6050 + angle_coeff @angle:cf-c-cf harmonic 64.34 115.80 # CORR 74 + angle_coeff @angle:cf-c-ha harmonic 46.93 115.22 # SOURCE3 7 same_as_ce-c-ha + angle_coeff @angle:cf-c-n harmonic 68.80 115.27 # CORR 32 + angle_coeff @angle:cf-c-o harmonic 69.27 122.92 # SOURCE3 17 3.5085 + angle_coeff @angle:cf-c-oh harmonic 70.32 114.09 # CORR 128 + angle_coeff @angle:cf-c-os harmonic 70.16 112.28 # CORR 149 + angle_coeff @angle:cf-c-s harmonic 64.09 117.80 # SOURCE3 1 same_as_ce-c-s + angle_coeff @angle:cg-c-cg harmonic 65.44 115.38 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-c-ha harmonic 47.80 113.90 # SOURCE2 1 0.0000 + angle_coeff @angle:cg-c-o harmonic 70.21 122.31 # SOURCE3 2 0.0000 + angle_coeff @angle:c-c-h4 harmonic 44.62 116.36 # SOURCE4 5 0.5586 + angle_coeff @angle:h4-cc-n harmonic 50.39 117.62 # SOURCE3 53 0.9721 + angle_coeff @angle:h4-cc-na harmonic 50.22 119.66 # SOURCE3 294 2.4702 + angle_coeff @angle:h4-cc-nc harmonic 50.00 120.03 # SOURCE3 16 2.3863 + angle_coeff @angle:h4-cc-nd harmonic 51.39 119.11 # SOURCE3 135 1.6946 + angle_coeff @angle:h4-cc-os harmonic 52.27 111.89 # SOURCE3 61 2.3500 + angle_coeff @angle:h4-cc-ss harmonic 42.95 117.75 # SOURCE3 40 3.1156 + angle_coeff @angle:h5-cc-n harmonic 50.84 115.72 # CORR 20 + angle_coeff @angle:h5-cc-na harmonic 49.76 122.10 # SOURCE3 16 1.4626 + angle_coeff @angle:h5-cc-nc harmonic 49.29 123.70 # SOURCE3 6 0.3547 + angle_coeff @angle:h5-cc-nd harmonic 50.13 125.38 # SOURCE3 40 2.2157 + angle_coeff @angle:h5-cc-os harmonic 51.30 116.33 # SOURCE3 12 3.2919 + angle_coeff @angle:h5-cc-ss harmonic 42.19 122.00 # SOURCE3 6 0.7237 + angle_coeff @angle:c-c-ha harmonic 44.85 115.43 # SOURCE2 3 0.6549 + angle_coeff @angle:ha-cc-na harmonic 49.82 121.50 # SOURCE2 1 0.0000 + angle_coeff @angle:ha-cc-nc harmonic 50.73 116.54 # SOURCE3 5 1.4482 + angle_coeff @angle:ha-cc-nd harmonic 51.41 118.88 # SOURCE3 20 2.8923 + angle_coeff @angle:ha-cc-os harmonic 52.49 110.86 # SOURCE3 7 1.3846 + angle_coeff @angle:ha-cc-pd harmonic 53.59 121.76 # SOURCE3 84 same_as_ha-cd-pc + angle_coeff @angle:ha-cc-ss harmonic 42.26 121.64 # SOURCE2 5 1.3276 + angle_coeff @angle:ch-c-ch harmonic 65.44 115.38 # SOURCE3 1 same_as_cg-c-cg + angle_coeff @angle:ch-c-ha harmonic 47.80 113.90 # SOURCE2 1 same_as_cg-c-ha + angle_coeff @angle:ch-c-o harmonic 70.21 122.31 # SOURCE3 2 same_as_cg-c-o + angle_coeff @angle:cl-c-cl harmonic 54.78 111.30 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-c-f harmonic 59.05 112.00 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-c-ha harmonic 40.42 109.90 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-c-o harmonic 59.78 121.51 # SOURCE3 6 1.6987 + angle_coeff @angle:cl-c-s harmonic 56.74 127.60 # SOURCE2 1 0.0000 + angle_coeff @angle:c-c-n harmonic 67.53 112.14 # SOURCE4 53 2.1247 + angle_coeff @angle:na-cc-nc harmonic 70.72 121.62 # CORR 231 + angle_coeff @angle:na-cc-nd harmonic 74.78 112.02 # SOURCE3 17 2.2434 + angle_coeff @angle:na-cc-no harmonic 68.48 124.90 # SOURCE4 48 0.7933 + angle_coeff @angle:na-cc-oh harmonic 73.25 117.26 # SOURCE4 16 0.9090 + angle_coeff @angle:na-cc-sx harmonic 63.25 117.04 # SOURCE4 13 0.4187 + angle_coeff @angle:na-cc-sy harmonic 63.13 120.55 # SOURCE4 7 1.7547 + angle_coeff @angle:nc-cc-nd harmonic 73.35 115.96 # CORR 222 + angle_coeff @angle:nc-cc-nh harmonic 72.33 116.85 # CORR 35 + angle_coeff @angle:nc-cc-no harmonic 69.31 121.54 # SOURCE4 7 0.9221 + angle_coeff @angle:nc-cc-ss harmonic 64.63 119.86 # SOURCE3 2 0.0000 + angle_coeff @angle:nd-cc-nd harmonic 70.88 128.17 # SOURCE4 7 0.0269 + angle_coeff @angle:nd-cc-ne harmonic 69.29 129.66 # SOURCE4 7 0.4306 + angle_coeff @angle:nd-cc-nh harmonic 72.41 120.11 # SOURCE3 5 0.9313 + angle_coeff @angle:nd-cc-no harmonic 69.90 122.68 # SOURCE4 16 0.3393 + angle_coeff @angle:nd-cc-oh harmonic 72.93 121.54 # CORR 22 + angle_coeff @angle:nd-cc-os harmonic 73.85 116.29 # CORR 209 + angle_coeff @angle:nd-cc-sh harmonic 62.75 124.92 # SOURCE4 5 0.9563 + angle_coeff @angle:nd-cc-ss harmonic 66.51 114.51 # SOURCE3 8 0.3449 + angle_coeff @angle:nd-cc-sx harmonic 60.81 127.60 # SOURCE4 14 1.1650 + angle_coeff @angle:nd-cc-sy harmonic 62.75 123.08 # SOURCE4 13 1.0531 + angle_coeff @angle:ne-cc-ss harmonic 65.39 116.99 # SOURCE4 7 0.1657 + angle_coeff @angle:nh-cc-nh harmonic 72.93 115.96 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-cc-os harmonic 72.96 116.69 # CORR 25 + angle_coeff @angle:nh-cc-ss harmonic 64.19 121.94 # CORR 91 + angle_coeff @angle:n-cc-n2 harmonic 74.78 114.48 # SOURCE4 15 2.3208 + angle_coeff @angle:n-cc-na harmonic 70.47 122.14 # CORR 59 + angle_coeff @angle:n-cc-nc harmonic 69.35 125.66 # CORR 64 + angle_coeff @angle:n-cc-nd harmonic 71.12 122.98 # CORR 229 + angle_coeff @angle:n-cc-nh harmonic 72.22 116.87 # CORR 79 + angle_coeff @angle:no-cc-os harmonic 71.01 117.59 # SOURCE4 62 0.2199 + angle_coeff @angle:no-cc-ss harmonic 63.76 121.10 # SOURCE4 10 0.0957 + angle_coeff @angle:n-cc-ss harmonic 63.75 123.03 # CORR 45 + angle_coeff @angle:c-c-o harmonic 67.16 120.99 # SOURCE4 233 2.0333 + angle_coeff @angle:c-c-oh harmonic 68.20 113.23 # SOURCE3 5 0.5615 + angle_coeff @angle:c-c-os harmonic 68.18 111.39 # SOURCE4 14 0.4038 + angle_coeff @angle:os-cc-ss harmonic 61.99 132.01 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-cc-ss harmonic 62.44 121.37 # CORR 22 + angle_coeff @angle:ss-cc-sy harmonic 61.51 121.70 # CORR 39 + angle_coeff @angle:cx-c-cx harmonic 85.45 64.60 # SOURCE2 1 0.0000 + angle_coeff @angle:cx-c-n harmonic 68.69 114.49 # SOURCE4 23 1.4914 + angle_coeff @angle:cx-c-o harmonic 68.88 122.82 # SOURCE4 97 2.2075 + angle_coeff @angle:cx-c-oh harmonic 70.49 112.32 # SOURCE4 10 0.6413 + angle_coeff @angle:cx-c-os harmonic 70.06 111.48 # SOURCE4 16 1.3998 + angle_coeff @angle:cy-c-cy harmonic 70.14 90.55 # SOURCE2 2 2.4500 + angle_coeff @angle:cy-c-n harmonic 75.43 91.54 # SOURCE4 249 0.5104 + angle_coeff @angle:cy-c-o harmonic 64.27 135.04 # SOURCE4 253 1.3450 + angle_coeff @angle:cy-c-oh harmonic 69.09 112.48 # SOURCE4 5 1.0793 + angle_coeff @angle:cy-c-os harmonic 74.55 94.89 # SOURCE4 8 0.6016 + angle_coeff @angle:c2-cd-c3 harmonic 63.27 126.11 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-cd-ca harmonic 65.34 124.66 # CORR 16 + angle_coeff @angle:c2-cd-cc harmonic 69.09 117.02 # SOURCE3 2 same_as_c2-cc-cd + angle_coeff @angle:c2-cd-cd harmonic 66.24 121.77 # CORR 32 + angle_coeff @angle:c2-cd-ha harmonic 48.69 122.72 # SOURCE3 2 same_as_c2-cc-ha + angle_coeff @angle:c2-cd-n harmonic 67.74 126.90 # SOURCE3 1 same_as_c2-cc-n + angle_coeff @angle:c2-cd-os harmonic 70.10 120.79 # CORR 13 + angle_coeff @angle:c3-cd-ca harmonic 61.96 125.89 # CORR 127 + angle_coeff @angle:c3-cd-cc harmonic 64.81 119.45 # SOURCE3 35 8.2040 + angle_coeff @angle:c3-cd-cd harmonic 64.66 115.97 # SOURCE3 4 3.0507 + angle_coeff @angle:c3-cd-ce harmonic 65.34 117.84 # CORR 2 + angle_coeff @angle:c3-cd-ha harmonic 45.11 121.52 # SOURCE3 32 3.2091 + angle_coeff @angle:c3-cd-n2 harmonic 65.80 126.87 # CORR 9 + angle_coeff @angle:c3-cd-n harmonic 66.33 119.11 # CORR 68 + angle_coeff @angle:c3-cd-na harmonic 65.50 122.78 # CORR 632 + angle_coeff @angle:c3-cd-nc harmonic 66.32 122.13 # CORR 475 + angle_coeff @angle:c3-cd-nd harmonic 65.90 120.94 # CORR 309 + angle_coeff @angle:c3-cd-os harmonic 67.54 116.88 # CORR 203 + angle_coeff @angle:c3-cd-ss harmonic 61.21 121.66 # CORR 171 + angle_coeff @angle:ca-cd-cc harmonic 68.23 113.51 # SOURCE3 26 7.4229 + angle_coeff @angle:ca-cd-cd harmonic 67.66 111.04 # SOURCE3 9 7.9455 + angle_coeff @angle:ca-cd-ce harmonic 65.09 125.10 # SOURCE4 9 1.9265 + angle_coeff @angle:ca-cd-h4 harmonic 45.57 128.66 # SOURCE3 10 3.1167 + angle_coeff @angle:ca-cd-ha harmonic 46.40 124.04 # SOURCE3 34 3.6691 + angle_coeff @angle:ca-cd-n harmonic 68.46 117.67 # CORR 18 + angle_coeff @angle:ca-cd-na harmonic 67.03 123.45 # SOURCE4 39 1.9138 + angle_coeff @angle:ca-cd-nc harmonic 67.92 123.02 # CORR 188 + angle_coeff @angle:ca-cd-nd harmonic 67.69 120.67 # CORR 162 + angle_coeff @angle:ca-cd-oh harmonic 69.61 117.71 # CORR 21 + angle_coeff @angle:ca-cd-os harmonic 69.82 115.16 # CORR 134 + angle_coeff @angle:ca-cd-ss harmonic 62.30 120.51 # CORR 43 + angle_coeff @angle:c-cd-c2 harmonic 65.60 120.92 # CORR 22 + angle_coeff @angle:c-cd-c3 harmonic 63.60 117.42 # CORR 126 + angle_coeff @angle:c-cd-c harmonic 63.42 121.17 # CORR 64 + angle_coeff @angle:c-cd-ca harmonic 63.55 122.95 # SOURCE3 1 same_as_c-cc-ca + angle_coeff @angle:c-cd-cc harmonic 65.25 121.42 # CORR 1708 + angle_coeff @angle:cc-cd-cc harmonic 67.89 120.23 # CORR 133 + angle_coeff @angle:cc-cd-cd harmonic 68.16 114.19 # SOURCE3 517 6.5960 + angle_coeff @angle:cc-cd-cf harmonic 63.67 128.41 # CORR 210 + angle_coeff @angle:cc-cd-ch harmonic 64.92 126.05 # SOURCE4 30 1.4695 + angle_coeff @angle:cc-cd-cl harmonic 57.46 123.70 # CORR 62 + angle_coeff @angle:cc-cd-cy harmonic 63.93 122.13 # SOURCE4 10 0.8509 + angle_coeff @angle:c-cd-cd harmonic 63.72 122.69 # SOURCE3 2 0.0000 + angle_coeff @angle:c-cd-cf harmonic 63.20 122.73 # CORR 10 + angle_coeff @angle:cc-cd-h4 harmonic 47.19 129.11 # SOURCE3 418 3.1355 + angle_coeff @angle:cc-cd-ha harmonic 48.35 122.89 # SOURCE3 584 2.9334 + angle_coeff @angle:c-cd-cl harmonic 58.39 116.05 # CORR 24 + angle_coeff @angle:cc-cd-n harmonic 70.72 115.52 # SOURCE3 52 1.3322 + angle_coeff @angle:cc-cd-na harmonic 72.91 109.42 # SOURCE3 265 2.6051 + angle_coeff @angle:cc-cd-nc harmonic 69.42 123.82 # SOURCE4 14 0.3678 + angle_coeff @angle:cc-cd-nd harmonic 72.01 111.75 # CORR 1101 + angle_coeff @angle:cc-cd-nh harmonic 68.69 123.89 # CORR 106 + angle_coeff @angle:cc-cd-oh harmonic 69.56 123.89 # CORR 106 + angle_coeff @angle:cc-cd-os harmonic 69.96 120.30 # SOURCE3 64 5.4354 + angle_coeff @angle:cc-cd-ss harmonic 65.44 111.55 # CORR 884 + angle_coeff @angle:cc-cd-sy harmonic 60.54 124.91 # CORR 41 + angle_coeff @angle:cd-cd-cd harmonic 67.88 110.70 # SOURCE3 54 3.4091 + angle_coeff @angle:cd-cd-ce harmonic 65.88 122.59 # CORR 39 + angle_coeff @angle:cd-cd-cf harmonic 62.78 127.20 # CORR 42 + angle_coeff @angle:cd-cd-ch harmonic 63.63 126.15 # CORR 27 + angle_coeff @angle:cd-cd-cy harmonic 63.17 120.93 # SOURCE4 6 1.2205 + angle_coeff @angle:cd-cd-h4 harmonic 45.56 129.47 # SOURCE3 171 2.2734 + angle_coeff @angle:cd-cd-ha harmonic 47.14 120.86 # CORR 1751 + angle_coeff @angle:cd-cd-n2 harmonic 69.48 121.15 # CORR 12 + angle_coeff @angle:cd-cd-n harmonic 67.95 119.89 # SOURCE3 36 0.2095 + angle_coeff @angle:cd-cd-na harmonic 72.21 106.80 # SOURCE3 33 same_as_cc-cc-na + angle_coeff @angle:cd-cd-nc harmonic 71.15 112.56 # SOURCE3 141 4.2871 + angle_coeff @angle:cd-cd-nd harmonic 67.53 121.69 # CORR 105 + angle_coeff @angle:cd-cd-nh harmonic 68.41 119.51 # CORR 228 + angle_coeff @angle:cd-cd-oh harmonic 68.53 121.96 # CORR 27 + angle_coeff @angle:cd-cd-os harmonic 69.34 117.23 # CORR 211 + angle_coeff @angle:cd-cd-pc harmonic 80.79 115.36 # SOURCE3 84 3.2889 + angle_coeff @angle:cd-cd-ss harmonic 62.45 120.12 # CORR 31 + angle_coeff @angle:ce-cd-nd harmonic 68.22 124.90 # SOURCE4 5 2.3975 + angle_coeff @angle:cf-cd-na harmonic 66.32 124.22 # CORR 48 + angle_coeff @angle:cf-cd-nc harmonic 67.80 121.51 # CORR 37 + angle_coeff @angle:cf-cd-nd harmonic 67.01 121.29 # CORR 37 + angle_coeff @angle:cf-cd-os harmonic 68.17 119.03 # CORR 66 + angle_coeff @angle:cf-cd-ss harmonic 61.83 121.44 # CORR 38 + angle_coeff @angle:c-cd-h4 harmonic 46.77 118.19 # SOURCE4 8 0.2226 + angle_coeff @angle:c-cd-ha harmonic 46.99 117.02 # SOURCE3 56 1.9713 + angle_coeff @angle:cl-cd-nc harmonic 59.35 122.97 # CORR 6 + angle_coeff @angle:c-cd-n2 harmonic 68.54 120.89 # CORR 2 + angle_coeff @angle:c-cd-n harmonic 68.11 116.32 # CORR 21 + angle_coeff @angle:c-cd-nc harmonic 67.50 121.67 # CORR 47 + angle_coeff @angle:c-cd-nd harmonic 66.19 123.47 # CORR 24 + angle_coeff @angle:c-cd-oh harmonic 70.04 113.64 # CORR 53 + angle_coeff @angle:c-cd-os harmonic 67.83 119.39 # CORR 78 + angle_coeff @angle:h4-cd-n harmonic 50.39 117.62 # SOURCE3 53 0.9721 + angle_coeff @angle:h4-cd-na harmonic 50.22 119.66 # SOURCE3 294 2.4702 + angle_coeff @angle:h4-cd-nc harmonic 51.39 119.11 # SOURCE3 135 1.6946 + angle_coeff @angle:h4-cd-nd harmonic 50.00 120.03 # SOURCE3 16 2.3863 + angle_coeff @angle:h4-cd-os harmonic 52.27 111.89 # SOURCE3 61 2.3500 + angle_coeff @angle:h4-cd-ss harmonic 42.95 117.75 # SOURCE3 40 3.1156 + angle_coeff @angle:h5-cd-n harmonic 50.84 115.72 # CORR 20 + angle_coeff @angle:h5-cd-na harmonic 49.76 122.10 # SOURCE3 16 1.4626 + angle_coeff @angle:h5-cd-nc harmonic 50.13 125.38 # SOURCE3 40 2.2157 + angle_coeff @angle:h5-cd-nd harmonic 49.29 123.70 # SOURCE3 6 0.3547 + angle_coeff @angle:h5-cd-os harmonic 51.30 116.33 # SOURCE3 12 3.2919 + angle_coeff @angle:h5-cd-ss harmonic 42.19 122.00 # SOURCE3 6 0.7237 + angle_coeff @angle:ha-cd-na harmonic 49.82 121.50 # SOURCE2 1 same_as_ha-cc-na + angle_coeff @angle:ha-cd-nc harmonic 51.41 118.88 # SOURCE3 20 2.8923 + angle_coeff @angle:ha-cd-nd harmonic 50.73 116.54 # SOURCE3 5 1.4482 + angle_coeff @angle:ha-cd-os harmonic 52.49 110.86 # SOURCE3 7 1.3846 + angle_coeff @angle:ha-cd-pc harmonic 53.59 121.76 # SOURCE3 84 2.2216 + angle_coeff @angle:ha-cd-ss harmonic 42.26 121.64 # SOURCE2 5 same_as_ha-cc-ss + angle_coeff @angle:na-cd-nc harmonic 74.78 112.02 # SOURCE3 17 2.2434 + angle_coeff @angle:na-cd-nd harmonic 70.72 121.62 # CORR 231 + angle_coeff @angle:na-cd-nh harmonic 72.43 116.98 # SOURCE4 46 1.4937 + angle_coeff @angle:na-cd-ss harmonic 67.07 111.46 # SOURCE4 20 0.8600 + angle_coeff @angle:nc-cd-nd harmonic 73.35 115.96 # CORR 222 + angle_coeff @angle:nc-cd-nh harmonic 72.41 120.11 # SOURCE3 5 0.9313 + angle_coeff @angle:nc-cd-oh harmonic 72.93 121.54 # CORR 22 + angle_coeff @angle:nc-cd-os harmonic 73.85 116.29 # CORR 209 + angle_coeff @angle:nc-cd-ss harmonic 66.51 114.51 # SOURCE3 8 0.3449 + angle_coeff @angle:nd-cd-nd harmonic 69.47 125.58 # SOURCE4 13 0.4672 + angle_coeff @angle:nd-cd-nh harmonic 72.33 116.85 # CORR 35 + angle_coeff @angle:nd-cd-ss harmonic 64.63 119.86 # SOURCE3 2 same_as_nc-cc-ss + angle_coeff @angle:nh-cd-nh harmonic 72.93 115.96 # SOURCE3 1 same_as_nh-cc-nh + angle_coeff @angle:nh-cd-os harmonic 72.96 116.69 # CORR 25 + angle_coeff @angle:nh-cd-ss harmonic 64.19 121.94 # CORR 91 + angle_coeff @angle:n-cd-na harmonic 70.47 122.14 # CORR 59 + angle_coeff @angle:n-cd-nc harmonic 71.12 122.98 # CORR 229 + angle_coeff @angle:n-cd-nd harmonic 69.35 125.66 # CORR 64 + angle_coeff @angle:n-cd-nh harmonic 72.22 116.87 # CORR 79 + angle_coeff @angle:n-cd-ss harmonic 63.75 123.03 # CORR 45 + angle_coeff @angle:oh-cd-os harmonic 75.54 111.61 # SOURCE4 6 1.1909 + angle_coeff @angle:os-cd-ss harmonic 61.99 132.01 # SOURCE3 1 same_as_os-cc-ss + angle_coeff @angle:ss-cd-ss harmonic 62.44 121.37 # CORR 22 + angle_coeff @angle:ss-cd-sy harmonic 61.51 121.70 # CORR 39 + angle_coeff @angle:c2-ce-c3 harmonic 64.30 122.89 # SOURCE3 7 1.0449 + angle_coeff @angle:c2-ce-ca harmonic 65.16 123.08 # SOURCE3 6 2.1589 + angle_coeff @angle:c2-ce-cc harmonic 65.62 123.27 # CORR 72 + angle_coeff @angle:c2-ce-ce harmonic 65.73 123.08 # SOURCE3 12 0.6518 + angle_coeff @angle:c2-ce-cg harmonic 66.66 121.67 # CORR 21 + angle_coeff @angle:c2-ce-cl harmonic 57.87 119.51 # SOURCE4 24 1.4963 + angle_coeff @angle:c2-ce-h4 harmonic 48.64 125.58 # SOURCE4 11 0.9381 + angle_coeff @angle:c2-ce-ha harmonic 49.56 121.10 # SOURCE3 46 2.4054 + angle_coeff @angle:c2-ce-n1 harmonic 72.67 117.85 # SOURCE4 7 0.3180 + angle_coeff @angle:c2-ce-n2 harmonic 70.34 128.70 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-ce-na harmonic 69.29 119.19 # SOURCE4 5 0.8452 + angle_coeff @angle:c2-ce-ne harmonic 69.73 118.32 # SOURCE3 7 1.0468 + angle_coeff @angle:c2-ce-oh harmonic 70.32 123.78 # SOURCE4 10 1.8182 + angle_coeff @angle:c2-ce-p2 harmonic 77.91 118.24 # SOURCE3 1 + angle_coeff @angle:c2-ce-pe harmonic 77.59 118.76 # SOURCE3 8 2.3984 + angle_coeff @angle:c2-ce-px harmonic 77.17 119.72 # SOURCE3 6 0.5213 + angle_coeff @angle:c2-ce-py harmonic 77.39 122.13 # SOURCE3 5 3.1367 + angle_coeff @angle:c2-ce-sx harmonic 61.64 119.87 # SOURCE3 5 0.8557 + angle_coeff @angle:c2-ce-sy harmonic 61.96 120.35 # SOURCE3 5 0.5401 + angle_coeff @angle:c3-ce-ca harmonic 62.76 119.28 # CORR 178 + angle_coeff @angle:c3-ce-cc harmonic 63.42 118.22 # CORR 39 + angle_coeff @angle:c3-ce-ce harmonic 63.80 116.99 # CORR 244 + angle_coeff @angle:c3-ce-cf harmonic 64.52 122.11 # CORR 221 + angle_coeff @angle:c3-ce-cg harmonic 63.79 118.48 # SOURCE4 8 1.4756 + angle_coeff @angle:c3-ce-n2 harmonic 66.92 122.70 # CORR 81 + angle_coeff @angle:c3-ce-nf harmonic 67.26 120.75 # SOURCE4 6 2.1938 + angle_coeff @angle:c3-ce-nh harmonic 65.76 119.90 # SOURCE4 5 0.9634 + angle_coeff @angle:ca-ce-ca harmonic 63.94 117.58 # CORR 112 + angle_coeff @angle:ca-ce-cc harmonic 64.21 118.06 # CORR 17 + angle_coeff @angle:ca-ce-ce harmonic 63.84 119.62 # SOURCE4 14 1.9171 + angle_coeff @angle:ca-ce-cf harmonic 64.07 127.39 # CORR 318 + angle_coeff @angle:ca-ce-cl harmonic 57.99 114.22 # SOURCE4 6 1.3164 + angle_coeff @angle:ca-ce-h4 harmonic 46.71 116.86 # SOURCE4 74 0.9179 + angle_coeff @angle:ca-ce-ha harmonic 47.07 115.16 # CORR 345 + angle_coeff @angle:ca-ce-n2 harmonic 68.51 120.72 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-ce-nf harmonic 67.74 122.66 # CORR 22 + angle_coeff @angle:ca-ce-nh harmonic 67.87 115.51 # SOURCE4 93 0.9284 + angle_coeff @angle:ca-ce-oh harmonic 68.85 116.37 # CORR 11 + angle_coeff @angle:ca-ce-os harmonic 68.60 115.58 # SOURCE4 8 1.0735 + angle_coeff @angle:ca-ce-ss harmonic 61.21 117.73 # SOURCE4 5 1.1596 + angle_coeff @angle:c-ce-c2 harmonic 65.82 120.42 # SOURCE3 13 1.8877 + angle_coeff @angle:c-ce-c3 harmonic 63.35 116.92 # CORR 188 + angle_coeff @angle:c-ce-c harmonic 62.59 122.38 # CORR 23 + angle_coeff @angle:c-ce-ca harmonic 63.79 117.98 # SOURCE4 8 1.5129 + angle_coeff @angle:cc-ce-cd harmonic 63.28 130.36 # SOURCE4 5 2.3402 + angle_coeff @angle:cc-ce-cf harmonic 64.87 126.20 # CORR 88 + angle_coeff @angle:c-ce-cd harmonic 63.81 126.07 # CORR 2 + angle_coeff @angle:c-ce-ce harmonic 63.46 120.89 # SOURCE4 16 1.8719 + angle_coeff @angle:c-ce-cf harmonic 64.26 126.41 # SOURCE3 2 5.7847 + angle_coeff @angle:c-ce-cg harmonic 64.57 118.32 # SOURCE4 15 1.0595 + angle_coeff @angle:cc-ce-h4 harmonic 47.52 115.40 # SOURCE4 29 0.8744 + angle_coeff @angle:cc-ce-ha harmonic 47.53 115.45 # CORR 113 + angle_coeff @angle:c-ce-cl harmonic 57.67 115.40 # SOURCE4 6 1.0958 + angle_coeff @angle:cc-ce-n2 harmonic 68.94 121.28 # CORR 69 + angle_coeff @angle:cc-ce-nh harmonic 67.31 119.17 # SOURCE4 8 2.1378 + angle_coeff @angle:c-ce-cy harmonic 72.72 88.22 # SOURCE4 19 0.3234 + angle_coeff @angle:cd-ce-ce harmonic 64.81 124.49 # CORR 12 + angle_coeff @angle:cd-ce-ha harmonic 49.97 115.48 # CORR 39 + angle_coeff @angle:ce-ce-ce harmonic 64.55 118.74 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-ce-cf harmonic 65.46 124.19 # CORR 341 + angle_coeff @angle:ce-ce-cl harmonic 57.29 117.93 # SOURCE4 12 0.2639 + angle_coeff @angle:ce-ce-h4 harmonic 47.06 117.97 # CORR 19 + angle_coeff @angle:ce-ce-ha harmonic 47.50 115.90 # SOURCE3 12 0.4670 + angle_coeff @angle:ce-ce-n1 harmonic 66.79 127.15 # CORR 4 + angle_coeff @angle:ce-ce-n2 harmonic 69.57 119.33 # CORR 13 + angle_coeff @angle:ce-ce-oh harmonic 69.29 116.89 # SOURCE4 11 2.0380 + angle_coeff @angle:cf-ce-cg harmonic 66.10 123.79 # CORR 41 + angle_coeff @angle:cf-ce-cy harmonic 60.53 137.74 # SOURCE4 13 0.3952 + angle_coeff @angle:cf-ce-h4 harmonic 49.02 123.76 # SOURCE4 5 1.0909 + angle_coeff @angle:cf-ce-ha harmonic 50.21 118.12 # CORR 655 + angle_coeff @angle:cf-ce-n1 harmonic 72.03 120.03 # SOURCE4 6 1.9451 + angle_coeff @angle:cf-ce-n harmonic 72.60 108.25 # CORR 64 + angle_coeff @angle:cf-ce-nh harmonic 69.48 121.52 # SOURCE4 12 2.0106 + angle_coeff @angle:cf-ce-oh harmonic 70.92 121.78 # CORR 24 + angle_coeff @angle:cg-ce-cg harmonic 65.58 118.26 # CORR 7 + angle_coeff @angle:cg-ce-ha harmonic 47.93 116.54 # CORR 18 + angle_coeff @angle:cg-ce-n1 harmonic 69.49 119.50 # CORR 2 + angle_coeff @angle:cg-ce-n2 harmonic 69.59 121.43 # SOURCE4 6 0.8382 + angle_coeff @angle:c-ce-ha harmonic 46.59 117.26 # SOURCE3 11 2.7158 + angle_coeff @angle:c-ce-n harmonic 66.20 118.62 # CORR 137 + angle_coeff @angle:c-ce-nh harmonic 67.79 115.62 # CORR 19 + angle_coeff @angle:c-ce-oh harmonic 68.34 117.92 # SOURCE4 5 1.4580 + angle_coeff @angle:c-ce-os harmonic 69.09 113.78 # SOURCE4 21 1.8258 + angle_coeff @angle:h4-ce-n1 harmonic 52.58 116.36 # SOURCE4 7 0.2182 + angle_coeff @angle:h4-ce-n2 harmonic 52.36 121.58 # CORR 116 + angle_coeff @angle:h4-ce-ne harmonic 49.72 115.81 # SOURCE4 7 1.9836 + angle_coeff @angle:ha-ce-n1 harmonic 52.70 115.96 # CORR 4 + angle_coeff @angle:ha-ce-n2 harmonic 52.85 119.51 # SOURCE3 2 0.4623 + angle_coeff @angle:ha-ce-ne harmonic 49.16 118.59 # SOURCE3 5 1.1113 + angle_coeff @angle:ha-ce-nh harmonic 50.62 114.99 # CORR 2 + angle_coeff @angle:ha-ce-p2 harmonic 51.40 120.11 # SOURCE3 1 + angle_coeff @angle:ha-ce-pe harmonic 51.44 119.33 # SOURCE3 6 0.8966 + angle_coeff @angle:ha-ce-px harmonic 51.66 117.90 # SOURCE3 6 0.1809 + angle_coeff @angle:ha-ce-py harmonic 52.32 118.72 # SOURCE3 3 0.3064 + angle_coeff @angle:ha-ce-sx harmonic 41.85 115.45 # SOURCE3 3 0.6640 + angle_coeff @angle:ha-ce-sy harmonic 42.34 114.86 # SOURCE3 3 0.4717 + angle_coeff @angle:n2-ce-nh harmonic 71.56 124.96 # CORR 92 + angle_coeff @angle:n2-ce-os harmonic 74.58 118.13 # SOURCE4 6 0.1367 + angle_coeff @angle:n2-ce-ss harmonic 64.40 117.23 # SOURCE4 6 2.0518 + angle_coeff @angle:ne-ce-ne harmonic 68.07 123.87 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-ce-nh harmonic 71.89 112.91 # SOURCE4 12 1.1263 + angle_coeff @angle:nf-ce-nh harmonic 73.31 118.13 # SOURCE4 6 0.5842 + angle_coeff @angle:pe-ce-pe harmonic 92.40 129.79 # SOURCE3 1 0.0000 + angle_coeff @angle:py-ce-py harmonic 102.62 108.06 # SOURCE3 1 0.0000 + angle_coeff @angle:sx-ce-sx harmonic 60.61 120.32 # SOURCE3 1 0.0000 + angle_coeff @angle:sy-ce-sy harmonic 61.21 119.97 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-cf-c3 harmonic 64.30 122.89 # SOURCE3 7 same_as_c2-ce-c3 + angle_coeff @angle:c2-cf-ca harmonic 65.16 123.08 # SOURCE3 6 same_as_c2-ce-ca + angle_coeff @angle:c2-cf-cd harmonic 65.62 123.27 # CORR 72 + angle_coeff @angle:c2-cf-cf harmonic 65.73 123.08 # SOURCE3 12 same_as_c2-ce-ce + angle_coeff @angle:c2-cf-ch harmonic 66.66 121.67 # CORR 21 + angle_coeff @angle:c2-cf-ha harmonic 49.56 121.10 # SOURCE3 46 same_as_c2-ce-ha + angle_coeff @angle:c2-cf-n2 harmonic 70.34 128.70 # SOURCE3 1 same_as_c2-ce-n2 + angle_coeff @angle:c2-cf-nf harmonic 69.73 118.32 # SOURCE3 7 same_as_c2-ce-ne + angle_coeff @angle:c2-cf-p2 harmonic 77.91 118.24 # SOURCE3 1 same_as_c2-ce-p2 + angle_coeff @angle:c2-cf-pf harmonic 77.59 118.76 # SOURCE3 8 same_as_c2-ce-pe + angle_coeff @angle:c2-cf-px harmonic 77.17 119.72 # SOURCE3 6 same_as_c2-ce-px + angle_coeff @angle:c2-cf-py harmonic 77.39 122.13 # SOURCE3 5 same_as_c2-ce-py + angle_coeff @angle:c2-cf-sx harmonic 61.64 119.87 # SOURCE3 5 same_as_c2-ce-sx + angle_coeff @angle:c2-cf-sy harmonic 61.96 120.35 # SOURCE3 5 same_as_c2-ce-sy + angle_coeff @angle:c3-cf-ca harmonic 62.76 119.28 # CORR 178 + angle_coeff @angle:c3-cf-cd harmonic 63.42 118.22 # CORR 39 + angle_coeff @angle:c3-cf-ce harmonic 64.52 122.11 # CORR 221 + angle_coeff @angle:c3-cf-cf harmonic 63.80 116.99 # CORR 244 + angle_coeff @angle:c3-cf-n2 harmonic 66.92 122.70 # CORR 81 + angle_coeff @angle:ca-cf-ca harmonic 63.94 117.58 # CORR 112 + angle_coeff @angle:ca-cf-cc harmonic 62.70 130.80 # SOURCE4 12 1.2696 + angle_coeff @angle:ca-cf-cd harmonic 64.21 118.06 # CORR 17 + angle_coeff @angle:ca-cf-ce harmonic 64.07 127.39 # CORR 318 + angle_coeff @angle:ca-cf-ha harmonic 47.07 115.16 # CORR 345 + angle_coeff @angle:ca-cf-n2 harmonic 68.51 120.72 # SOURCE3 1 same_as_ca-ce-n2 + angle_coeff @angle:ca-cf-ne harmonic 67.74 122.66 # CORR 22 + angle_coeff @angle:ca-cf-oh harmonic 68.85 116.37 # CORR 11 + angle_coeff @angle:c-cf-c2 harmonic 65.82 120.42 # SOURCE3 13 same_as_c-ce-c2 + angle_coeff @angle:c-cf-c3 harmonic 63.35 116.92 # CORR 188 + angle_coeff @angle:c-cf-c harmonic 62.59 122.38 # CORR 23 + angle_coeff @angle:c-cf-cc harmonic 63.81 126.07 # CORR 2 + angle_coeff @angle:cc-cf-cf harmonic 64.81 124.49 # CORR 12 + angle_coeff @angle:c-cf-cd harmonic 64.25 117.76 # SOURCE4 10 1.2451 + angle_coeff @angle:c-cf-ce harmonic 64.26 126.41 # SOURCE3 2 same_as_c-ce-cf + angle_coeff @angle:cc-cf-ha harmonic 49.97 115.48 # CORR 39 + angle_coeff @angle:cd-cf-ce harmonic 64.87 126.20 # CORR 88 + angle_coeff @angle:cd-cf-ha harmonic 47.53 115.45 # CORR 113 + angle_coeff @angle:cd-cf-n2 harmonic 68.94 121.28 # CORR 69 + angle_coeff @angle:ce-cf-cf harmonic 65.46 124.19 # CORR 341 + angle_coeff @angle:ce-cf-ch harmonic 66.10 123.79 # CORR 41 + angle_coeff @angle:ce-cf-ha harmonic 50.21 118.12 # CORR 655 + angle_coeff @angle:ce-cf-n harmonic 72.60 108.25 # CORR 64 + angle_coeff @angle:ce-cf-oh harmonic 70.92 121.78 # CORR 24 + angle_coeff @angle:cf-cf-cf harmonic 64.55 118.74 # SOURCE3 1 same_as_ce-ce-ce + angle_coeff @angle:cf-cf-h4 harmonic 47.06 117.97 # CORR 19 + angle_coeff @angle:cf-cf-ha harmonic 47.50 115.90 # SOURCE3 12 0.4670 + angle_coeff @angle:cf-cf-n1 harmonic 66.79 127.15 # CORR 4 + angle_coeff @angle:cf-cf-n2 harmonic 69.57 119.33 # CORR 13 + angle_coeff @angle:c-cf-ha harmonic 46.59 117.26 # SOURCE3 11 2.7158 + angle_coeff @angle:ch-cf-ch harmonic 65.58 118.26 # CORR 7 + angle_coeff @angle:ch-cf-ha harmonic 47.93 116.54 # CORR 18 + angle_coeff @angle:ch-cf-n1 harmonic 69.49 119.50 # CORR 2 + angle_coeff @angle:c-cf-n2 harmonic 70.16 114.88 # SOURCE4 5 1.3647 + angle_coeff @angle:c-cf-n harmonic 66.20 118.62 # CORR 137 + angle_coeff @angle:c-cf-nh harmonic 67.79 115.62 # CORR 19 + angle_coeff @angle:f-c-f harmonic 72.22 107.35 # SOURCE2 2 0.2500 + angle_coeff @angle:h4-cf-n2 harmonic 52.36 121.58 # CORR 116 + angle_coeff @angle:h4-cf-ne harmonic 52.29 120.21 # SOURCE4 6 0.8104 + angle_coeff @angle:ha-cf-n1 harmonic 52.70 115.96 # CORR 4 + angle_coeff @angle:ha-cf-n2 harmonic 52.85 119.51 # SOURCE3 2 same_as_ha-ce-n2 + angle_coeff @angle:ha-cf-nf harmonic 49.16 118.59 # SOURCE3 5 same_as_ha-ce-ne + angle_coeff @angle:ha-cf-nh harmonic 50.62 114.99 # CORR 2 + angle_coeff @angle:ha-cf-p2 harmonic 51.40 120.11 # SOURCE3 1 same_as_ha-ce-p2 + angle_coeff @angle:ha-cf-pf harmonic 51.44 119.33 # SOURCE3 6 same_as_ha-ce-pe + angle_coeff @angle:ha-cf-px harmonic 51.66 117.90 # SOURCE3 6 same_as_ha-ce-px + angle_coeff @angle:ha-cf-py harmonic 52.32 118.72 # SOURCE3 3 same_as_ha-ce-py + angle_coeff @angle:ha-cf-sx harmonic 41.85 115.45 # SOURCE3 3 same_as_ha-ce-sx + angle_coeff @angle:ha-cf-sy harmonic 42.34 114.86 # SOURCE3 3 same_as_ha-ce-sy + angle_coeff @angle:n2-cf-nh harmonic 71.56 124.96 # CORR 92 + angle_coeff @angle:nf-cf-nf harmonic 68.07 123.87 # SOURCE3 1 same_as_ne-ce-ne + angle_coeff @angle:f-c-o harmonic 73.21 123.44 # SOURCE3 1 + angle_coeff @angle:pf-cf-pf harmonic 92.40 129.79 # SOURCE3 1 same_as_pe-ce-pe + angle_coeff @angle:py-cf-py harmonic 102.62 108.06 # SOURCE3 1 same_as_py-ce-py + angle_coeff @angle:f-c-s harmonic 63.41 124.00 # SOURCE2 1 0.0000 + angle_coeff @angle:sx-cf-sx harmonic 60.61 120.32 # SOURCE3 1 same_as_sx-ce-sx + angle_coeff @angle:sy-cf-sy harmonic 61.21 119.97 # SOURCE3 1 same_as_sy-ce-sy + angle_coeff @angle:c1-cg-ca harmonic 56.52 179.52 # CORR 19 + angle_coeff @angle:c1-cg-cc harmonic 56.97 178.60 # SOURCE4 6 0.3822 + angle_coeff @angle:c1-cg-ce harmonic 56.95 178.05 # CORR 7 + angle_coeff @angle:c1-cg-cg harmonic 58.17 179.70 # CORR 18 + angle_coeff @angle:c1-cg-ne harmonic 62.73 170.02 # SOURCE3 4 1.1724 + angle_coeff @angle:c1-cg-pe harmonic 71.80 173.29 # SOURCE3 11 4.9305 + angle_coeff @angle:ca-cg-ch harmonic 56.91 179.64 # CORR 13 + angle_coeff @angle:ca-cg-n1 harmonic 58.93 179.43 # CORR 103 + angle_coeff @angle:c-cg-c1 harmonic 56.19 179.14 # SOURCE3 2 0.0000 + angle_coeff @angle:cc-cg-n1 harmonic 59.43 178.54 # CORR 50 + angle_coeff @angle:ce-cg-ch harmonic 57.39 177.94 # CORR 17 + angle_coeff @angle:ce-cg-n1 harmonic 59.39 177.97 # CORR 67 + angle_coeff @angle:n1-cg-ne harmonic 64.98 174.44 # CORR 17 + angle_coeff @angle:h4-c-o harmonic 54.28 120.93 # SOURCE4 129 0.5769 + angle_coeff @angle:h5-c-n harmonic 52.39 112.19 # SOURCE4 33 0.4220 + angle_coeff @angle:h5-c-o harmonic 53.89 123.26 # SOURCE4 38 0.4806 + angle_coeff @angle:ha-c-ha harmonic 37.86 115.61 # SOURCE3 4 0.0458 + angle_coeff @angle:ha-c-i harmonic 36.71 110.58 # SOURCE3 1 0.0000 + angle_coeff @angle:ha-c-n harmonic 52.40 112.37 # SOURCE3 4 0.6424 + angle_coeff @angle:ha-c-o harmonic 54.27 121.94 # SOURCE3 51 2.3235 + angle_coeff @angle:ha-c-oh harmonic 53.97 111.82 # SOURCE3 4 1.9375 + angle_coeff @angle:ha-c-os harmonic 53.24 110.34 # SOURCE3 8 1.9344 + angle_coeff @angle:ha-c-s harmonic 44.27 119.56 # SOURCE3 3 0.7586 + angle_coeff @angle:c1-ch-ca harmonic 56.52 179.52 # CORR 19 + angle_coeff @angle:c1-ch-cf harmonic 56.95 178.05 # CORR 7 + angle_coeff @angle:c1-ch-ch harmonic 58.17 179.70 # CORR 18 + angle_coeff @angle:c1-ch-nf harmonic 62.73 170.02 # SOURCE3 4 same_as_c1-cg-ne + angle_coeff @angle:c1-ch-pf harmonic 71.80 173.29 # SOURCE3 11 same_as_c1-cg-pe + angle_coeff @angle:ca-ch-cg harmonic 56.91 179.64 # CORR 13 + angle_coeff @angle:ca-ch-n1 harmonic 58.93 179.43 # CORR 103 + angle_coeff @angle:c-ch-c1 harmonic 56.19 179.14 # SOURCE3 2 same_as_c-cg-c1 + angle_coeff @angle:cd-ch-n1 harmonic 59.43 178.54 # CORR 50 + angle_coeff @angle:cf-ch-cg harmonic 57.39 177.94 # CORR 17 + angle_coeff @angle:cf-ch-n1 harmonic 59.39 177.97 # CORR 67 + angle_coeff @angle:cg-ch-ch harmonic 58.68 179.67 # SOURCE4 7 0.1439 + angle_coeff @angle:n1-ch-nf harmonic 64.98 174.44 # CORR 17 + angle_coeff @angle:i-c-i harmonic 59.79 116.45 # SOURCE3 1 0.0000 + angle_coeff @angle:i-c-o harmonic 55.51 122.02 # SOURCE3 4 1.2961 + angle_coeff @angle:f-cl-f harmonic 0.00 87.50 # SOURCE2 1 estimated_force_constant + angle_coeff @angle:n2-c-n2 harmonic 71.83 110.31 # SOURCE3 1 + angle_coeff @angle:n2-c-o harmonic 73.02 122.50 # SOURCE3 1 + angle_coeff @angle:n4-c-n4 harmonic 64.71 114.64 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-c-o harmonic 69.58 118.83 # SOURCE3 4 3.8516 + angle_coeff @angle:nc-c-o harmonic 73.92 122.97 # CORR 121 + angle_coeff @angle:nd-c-o harmonic 73.92 122.97 # CORR 121 + angle_coeff @angle:ne-c-ne harmonic 73.21 110.31 # CORR 2 + angle_coeff @angle:ne-c-o harmonic 72.96 125.91 # CORR 42 + angle_coeff @angle:nf-c-nf harmonic 73.21 110.31 # CORR 2 + angle_coeff @angle:nf-c-o harmonic 72.96 125.91 # CORR 42 + angle_coeff @angle:n-c-n harmonic 74.80 113.38 # SOURCE4 635 1.4358 + angle_coeff @angle:n-c-nc harmonic 72.35 117.05 # CORR 77 + angle_coeff @angle:n-c-nd harmonic 72.35 117.05 # CORR 77 + angle_coeff @angle:n-c-ne harmonic 74.43 110.37 # SOURCE4 10 1.7492 + angle_coeff @angle:n-c-o harmonic 75.83 122.03 # SOURCE3 221 2.3565 + angle_coeff @angle:n-c-oh harmonic 76.22 113.63 # SOURCE4 5 1.1209 + angle_coeff @angle:no-c-no harmonic 66.54 109.28 # SOURCE3 1 + angle_coeff @angle:no-c-o harmonic 67.95 125.36 # SOURCE3 1 + angle_coeff @angle:n-c-os harmonic 76.68 109.28 # SOURCE4 318 0.8749 + angle_coeff @angle:n-c-s harmonic 65.73 123.88 # SOURCE3 5 1.2935 + angle_coeff @angle:n-c-sh harmonic 65.61 112.61 # SOURCE4 8 1.2601 + angle_coeff @angle:n-c-ss harmonic 66.85 110.42 # SOURCE4 59 1.5507 + angle_coeff @angle:oh-c-oh harmonic 78.91 110.56 # SOURCE3 2 0.5498 + angle_coeff @angle:oh-c-s harmonic 66.64 123.44 # SOURCE3 1 0.0000 + angle_coeff @angle:o-c-o harmonic 78.17 130.38 # SOURCE4 429 1.0315 + angle_coeff @angle:o-c-oh harmonic 77.38 122.88 # SOURCE3 33 2.1896 + angle_coeff @angle:o-c-os harmonic 75.93 123.33 # SOURCE4 1708 1.0632 + angle_coeff @angle:o-c-p2 harmonic 75.65 123.10 # SOURCE3 1 + angle_coeff @angle:o-c-p3 harmonic 77.08 120.79 # SOURCE3 1 + angle_coeff @angle:o-c-p5 harmonic 77.01 121.20 # SOURCE4 8 1.2117 + angle_coeff @angle:o-c-pe harmonic 75.23 123.02 # SOURCE3 3 0.1404 + angle_coeff @angle:o-c-pf harmonic 75.23 123.02 # SOURCE3 3 same_as_o-c-pe + angle_coeff @angle:o-c-px harmonic 76.75 119.10 # SOURCE3 1 0.0000 + angle_coeff @angle:o-c-py harmonic 77.45 121.71 # SOURCE4 5 0.3133 + angle_coeff @angle:o-c-s4 harmonic 61.24 121.15 # SOURCE3 1 + angle_coeff @angle:o-c-s6 harmonic 61.67 119.45 # SOURCE3 1 + angle_coeff @angle:o-c-s harmonic 68.21 120.44 # SOURCE3 2 0.0000 + angle_coeff @angle:o-c-sh harmonic 64.19 121.41 # SOURCE3 4 1.4052 + angle_coeff @angle:os-c-os harmonic 76.45 111.38 # SOURCE4 12 0.8309 + angle_coeff @angle:o-c-ss harmonic 64.62 122.29 # SOURCE3 7 1.9240 + angle_coeff @angle:os-c-s harmonic 65.82 125.03 # SOURCE4 18 0.9978 + angle_coeff @angle:os-c-ss harmonic 66.30 113.63 # SOURCE4 5 0.7367 + angle_coeff @angle:o-c-sx harmonic 60.75 121.15 # SOURCE3 5 3.6452 + angle_coeff @angle:o-c-sy harmonic 61.88 119.32 # SOURCE3 5 2.4495 + angle_coeff @angle:p2-c-p2 harmonic 94.44 113.75 # SOURCE3 1 + angle_coeff @angle:p3-c-p3 harmonic 93.55 118.04 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-c-py harmonic 107.54 90.08 # SOURCE3 1 0.0000 + angle_coeff @angle:p5-c-p5 harmonic 91.43 123.76 # SOURCE3 1 + angle_coeff @angle:ca-cp-ca harmonic 67.11 118.33 # CORR 526 + angle_coeff @angle:ca-cp-cp harmonic 64.09 121.13 # CORR 991 + angle_coeff @angle:ca-cp-na harmonic 68.78 119.43 # SOURCE4 21 0.6591 + angle_coeff @angle:ca-cp-nb harmonic 69.19 121.65 # SOURCE4 63 0.6564 + angle_coeff @angle:cp-cp-cp harmonic 72.20 90.00 # SOURCE3 4 0.0000 + angle_coeff @angle:cp-cp-cq harmonic 62.64 124.47 # CORR 10 + angle_coeff @angle:cp-cp-nb harmonic 68.05 116.60 # SOURCE4 88 1.1887 + angle_coeff @angle:pe-c-pe harmonic 93.89 113.77 # SOURCE3 1 0.0000 + angle_coeff @angle:pf-c-pf harmonic 93.89 113.77 # SOURCE3 1 same_as_pe-c-pe + angle_coeff @angle:nb-cp-nb harmonic 71.31 125.72 # SOURCE4 5 0.6674 + angle_coeff @angle:py-c-py harmonic 92.13 123.80 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-cq-ca harmonic 67.11 118.33 # CORR 526 + angle_coeff @angle:ca-cq-cq harmonic 64.09 121.13 # CORR 991 + angle_coeff @angle:ca-cq-nb harmonic 69.19 121.65 # SOURCE4 63 same as ca-cp-nb + angle_coeff @angle:cp-cq-cq harmonic 62.64 124.47 # CORR 10 + angle_coeff @angle:cq-cq-cq harmonic 72.20 90.00 # SOURCE3 4 0.0000 + angle_coeff @angle:cq-cq-nb harmonic 68.05 116.60 # SOURCE4 88 same as cp-cp-nb + angle_coeff @angle:s4-c-s4 harmonic 61.25 108.81 # SOURCE3 1 + angle_coeff @angle:s6-c-s6 harmonic 59.39 115.75 # SOURCE3 1 + angle_coeff @angle:sh-c-sh harmonic 62.47 115.33 # SOURCE3 1 0.0000 + angle_coeff @angle:s-c-s harmonic 65.01 120.40 # SOURCE3 2 1.2766 + angle_coeff @angle:s-c-sh harmonic 62.29 122.76 # SOURCE4 11 1.5734 + angle_coeff @angle:s-c-ss harmonic 61.88 125.90 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-c-ss harmonic 63.79 113.00 # SOURCE3 1 0.0000 + angle_coeff @angle:sx-c-sx harmonic 60.77 108.80 # SOURCE3 1 0.0000 + angle_coeff @angle:sy-c-sy harmonic 59.54 115.78 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-cu-cx harmonic 58.56 148.21 # SOURCE4 6 1.8305 + angle_coeff @angle:c-cu-cu harmonic 94.97 62.60 # SOURCE2 1 0.0000 + angle_coeff @angle:cu-cu-cx harmonic 100.97 50.80 # SOURCE2 1 0.0000 + angle_coeff @angle:cu-cu-ha harmonic 46.11 147.73 # SOURCE2 3 2.0950 + angle_coeff @angle:cv-cv-cy harmonic 73.28 94.17 # SOURCE3 2 0.0000 + angle_coeff @angle:cv-cv-ha harmonic 47.30 133.70 # SOURCE3 2 0.0000 + angle_coeff @angle:cx-cv-cx harmonic 84.66 63.90 # SOURCE2 1 0.0000 + angle_coeff @angle:cy-cv-ha harmonic 42.89 132.14 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-cx-cx harmonic 63.10 120.66 # SOURCE4 9 0.9067 + angle_coeff @angle:c2-cx-cx harmonic 62.33 120.54 # SOURCE4 51 2.2377 + angle_coeff @angle:c2-cx-h1 harmonic 46.63 115.78 # SOURCE4 8 0.2332 + angle_coeff @angle:c2-cx-hc harmonic 46.77 115.10 # SOURCE4 12 0.7463 + angle_coeff @angle:c2-cx-os harmonic 67.14 116.17 # SOURCE4 14 1.2782 + angle_coeff @angle:c3-cx-c3 harmonic 63.00 114.48 # SOURCE4 46 1.9627 + angle_coeff @angle:c3-cx-cx harmonic 61.82 120.06 # SOURCE4 448 2.1467 + angle_coeff @angle:c3-cx-h1 harmonic 45.87 115.42 # SOURCE4 89 1.1096 + angle_coeff @angle:c3-cx-hc harmonic 46.12 114.16 # SOURCE4 85 1.1118 + angle_coeff @angle:c3-cx-n3 harmonic 64.31 118.50 # SOURCE4 17 2.4897 + angle_coeff @angle:c3-cx-os harmonic 66.57 115.50 # SOURCE4 161 1.3016 + angle_coeff @angle:ca-cx-cx harmonic 61.86 122.18 # SOURCE4 65 1.6898 + angle_coeff @angle:ca-cx-h1 harmonic 46.81 114.57 # SOURCE4 7 0.6498 + angle_coeff @angle:ca-cx-hc harmonic 47.05 113.41 # SOURCE4 18 0.7843 + angle_coeff @angle:ca-cx-oh harmonic 69.25 112.93 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-cx-os harmonic 66.42 118.50 # SOURCE4 6 0.7514 + angle_coeff @angle:c-cx-c3 harmonic 62.91 116.93 # SOURCE4 18 1.8253 + angle_coeff @angle:cc-cx-cx harmonic 62.90 119.31 # CORR 39 + angle_coeff @angle:cc-cx-hc harmonic 47.37 113.84 # SOURCE4 15 0.6682 + angle_coeff @angle:c-cx-cx harmonic 62.96 117.96 # SOURCE4 147 1.8483 + angle_coeff @angle:cd-cx-cx harmonic 62.90 119.31 # CORR 39 + angle_coeff @angle:c-cx-h1 harmonic 46.27 117.25 # SOURCE4 24 0.7935 + angle_coeff @angle:c-cx-hc harmonic 46.42 116.53 # SOURCE4 36 1.2830 + angle_coeff @angle:cl-cx-cl harmonic 54.42 114.20 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-cx-cx harmonic 56.53 120.10 # SOURCE4 15 0.5917 + angle_coeff @angle:cl-cx-h1 harmonic 40.37 111.43 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-cx-hc harmonic 39.60 115.80 # SOURCE2 1 0.0000 + angle_coeff @angle:c-cx-os harmonic 67.25 115.59 # SOURCE4 36 0.8227 + angle_coeff @angle:cu-cx-cu harmonic 91.53 54.60 # SOURCE2 1 0.0000 + angle_coeff @angle:cu-cx-cx harmonic 88.72 58.50 # SOURCE4 7 0.1333 + angle_coeff @angle:cu-cx-hc harmonic 45.49 118.09 # SOURCE4 7 1.0126 + angle_coeff @angle:cx-cx-cx harmonic 87.90 60.00 # SOURCE4 681 0.6259 + angle_coeff @angle:cx-cx-cy harmonic 67.54 100.53 # SOURCE3 4 0.0000 + angle_coeff @angle:cx-cx-f harmonic 64.53 117.93 # SOURCE4 7 1.1613 + angle_coeff @angle:cx-cx-h1 harmonic 45.45 119.66 # SOURCE3 12 0.4529 + angle_coeff @angle:cx-cx-hc harmonic 45.79 117.92 # SOURCE3 92 1.1927 + angle_coeff @angle:cx-cx-hx harmonic 45.47 119.62 # SOURCE4 9 0.1118 + angle_coeff @angle:cx-cx-n3 harmonic 91.17 59.59 # SOURCE4 154 0.3104 + angle_coeff @angle:cx-cx-na harmonic 62.94 125.85 # SOURCE4 16 2.0385 + angle_coeff @angle:cx-cx-nh harmonic 92.03 59.15 # SOURCE4 116 0.6758 + angle_coeff @angle:cx-cx-os harmonic 93.61 59.07 # SOURCE4 306 0.5253 + angle_coeff @angle:cy-cx-hc harmonic 43.98 125.43 # SOURCE3 2 0.0000 + angle_coeff @angle:f-cx-f harmonic 70.61 106.90 # SOURCE2 2 1.4000 + angle_coeff @angle:f-cx-h1 harmonic 50.35 111.68 # SOURCE3 1 0.0000 + angle_coeff @angle:f-cx-hc harmonic 50.22 112.30 # SOURCE2 1 0.0000 + angle_coeff @angle:h1-cx-h1 harmonic 38.38 115.45 # SOURCE4 230 0.3302 + angle_coeff @angle:h1-cx-n3 harmonic 47.97 116.43 # SOURCE4 173 1.4531 + angle_coeff @angle:h1-cx-n harmonic 49.06 115.42 # SOURCE4 12 1.0443 + angle_coeff @angle:h1-cx-na harmonic 49.96 108.67 # SOURCE4 8 1.6134 + angle_coeff @angle:h1-cx-nh harmonic 48.50 116.32 # SOURCE4 151 1.0310 + angle_coeff @angle:h1-cx-os harmonic 50.01 115.17 # SOURCE3 8 0.0226 + angle_coeff @angle:h2-cx-h2 harmonic 37.87 119.43 # SOURCE3 1 0.0000 + angle_coeff @angle:h2-cx-n2 harmonic 47.55 117.18 # SOURCE3 4 0.0000 + angle_coeff @angle:hc-cx-hc harmonic 38.58 114.47 # SOURCE3 19 0.3295 + angle_coeff @angle:hc-cx-os harmonic 50.25 114.10 # SOURCE2 1 0.0000 + angle_coeff @angle:hx-cx-n4 harmonic 49.89 114.47 # SOURCE4 8 0.1059 + angle_coeff @angle:n2-cx-n2 harmonic 102.06 50.16 # SOURCE3 1 0.0000 + angle_coeff @angle:n-cx-oh harmonic 70.16 119.75 # SOURCE3 2 0.0000 + angle_coeff @angle:n-cx-os harmonic 92.71 65.98 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-cx-oh harmonic 76.67 107.85 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-cx-os harmonic 71.64 118.12 # SOURCE3 4 1.3581 + angle_coeff @angle:os-cx-os harmonic 70.90 115.84 # SOURCE4 7 2.0760 + angle_coeff @angle:c2-cy-cy harmonic 66.57 100.40 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-cy-c3 harmonic 63.19 111.58 # SOURCE4 15 1.0060 + angle_coeff @angle:c3-cy-cy harmonic 60.76 118.70 # SOURCE4 293 1.8510 + angle_coeff @angle:c3-cy-h1 harmonic 46.16 111.77 # SOURCE4 119 0.4412 + angle_coeff @angle:c3-cy-hc harmonic 46.21 111.55 # SOURCE3 5 0.6276 + angle_coeff @angle:c3-cy-n3 harmonic 65.28 112.92 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-cy-n harmonic 68.32 104.05 # SOURCE4 122 0.5745 + angle_coeff @angle:c3-cy-os harmonic 66.99 111.96 # SOURCE4 11 1.0668 + angle_coeff @angle:c-cy-c3 harmonic 61.78 116.72 # SOURCE4 129 0.5236 + angle_coeff @angle:cc-cy-cy harmonic 60.58 121.17 # CORR 19 + angle_coeff @angle:c-cy-cy harmonic 71.81 84.99 # SOURCE4 263 0.6952 + angle_coeff @angle:cd-cy-cy harmonic 60.58 121.17 # CORR 19 + angle_coeff @angle:ce-cy-h2 harmonic 45.50 117.25 # SOURCE4 17 0.5351 + angle_coeff @angle:ce-cy-n harmonic 74.69 88.02 # SOURCE4 14 0.1416 + angle_coeff @angle:ce-cy-ss harmonic 58.47 121.33 # SOURCE4 13 0.1599 + angle_coeff @angle:c-cy-h1 harmonic 45.89 113.10 # SOURCE4 71 0.7655 + angle_coeff @angle:c-cy-hc harmonic 45.75 113.85 # SOURCE3 8 0.2067 + angle_coeff @angle:cl-cy-cy harmonic 57.58 112.00 # SOURCE3 2 0.0000 + angle_coeff @angle:cl-cy-h1 harmonic 40.98 106.59 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-cy-hc harmonic 39.62 114.00 # SOURCE2 1 0.0000 + angle_coeff @angle:c-cy-n harmonic 64.32 117.39 # SOURCE4 70 1.0742 + angle_coeff @angle:c-cy-os harmonic 66.27 114.42 # SOURCE4 6 1.2052 + angle_coeff @angle:cv-cy-cy harmonic 71.46 86.67 # SOURCE4 6 1.1600 + angle_coeff @angle:cv-cy-hc harmonic 46.06 114.47 # SOURCE4 7 0.4307 + angle_coeff @angle:cx-cy-cy harmonic 66.08 101.23 # SOURCE3 4 0.0000 + angle_coeff @angle:cx-cy-hc harmonic 45.25 118.30 # SOURCE2 3 5.7799 + angle_coeff @angle:cy-cy-cy harmonic 70.16 87.61 # SOURCE3 32 1.5407 + angle_coeff @angle:cy-cy-f harmonic 64.55 112.87 # SOURCE4 13 1.6772 + angle_coeff @angle:cy-cy-h1 harmonic 44.87 114.84 # SOURCE3 20 2.5651 + angle_coeff @angle:cy-cy-h2 harmonic 44.51 116.77 # SOURCE4 83 0.8683 + angle_coeff @angle:cy-cy-hc harmonic 44.82 115.14 # SOURCE3 114 0.8364 + angle_coeff @angle:cy-cy-n3 harmonic 73.47 87.58 # SOURCE3 4 0.6135 + angle_coeff @angle:cy-cy-n harmonic 65.22 112.13 # SOURCE3 31 2.0700 + angle_coeff @angle:cy-cy-na harmonic 63.12 119.70 # SOURCE4 9 0.3333 + angle_coeff @angle:cy-cy-oh harmonic 66.00 114.19 # SOURCE3 4 0.0000 + angle_coeff @angle:cy-cy-os harmonic 66.41 111.77 # SOURCE4 18 2.1334 + angle_coeff @angle:cy-cy-s6 harmonic 58.93 117.46 # SOURCE4 7 1.2423 + angle_coeff @angle:cy-cy-ss harmonic 58.83 118.18 # SOURCE4 55 0.9860 + angle_coeff @angle:h1-cy-h1 harmonic 39.01 109.72 # SOURCE3 6 0.8087 + angle_coeff @angle:h1-cy-n3 harmonic 48.21 113.36 # SOURCE3 6 1.4509 + angle_coeff @angle:h1-cy-n harmonic 49.10 111.18 # SOURCE4 141 0.5848 + angle_coeff @angle:h1-cy-oh harmonic 50.89 111.49 # SOURCE3 2 0.0000 + angle_coeff @angle:h1-cy-os harmonic 50.53 110.94 # SOURCE3 8 0.6522 + angle_coeff @angle:h1-cy-s6 harmonic 41.05 112.57 # SOURCE4 5 1.2943 + angle_coeff @angle:h2-cy-n harmonic 48.42 114.44 # SOURCE4 88 0.7114 + angle_coeff @angle:h2-cy-os harmonic 50.97 109.19 # SOURCE4 6 0.4162 + angle_coeff @angle:h2-cy-s6 harmonic 42.11 106.85 # SOURCE4 6 0.3975 + angle_coeff @angle:h2-cy-ss harmonic 41.64 109.73 # SOURCE4 92 0.7424 + angle_coeff @angle:hc-cy-hc harmonic 39.24 109.04 # SOURCE3 28 0.5962 + angle_coeff @angle:n-cy-os harmonic 71.62 107.50 # SOURCE4 9 2.3773 + angle_coeff @angle:n-cy-s6 harmonic 65.24 103.45 # SOURCE4 6 0.7197 + angle_coeff @angle:n-cy-ss harmonic 64.81 105.12 # SOURCE4 69 0.3987 + angle_coeff @angle:nh-cz-nh harmonic 72.97 120.17 # SOURCE4 26 0.3964 + angle_coeff @angle:br-n1-c1 harmonic 51.10 180.00 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c1 harmonic 64.91 179.92 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c2 harmonic 60.25 177.73 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c3 harmonic 54.83 180.00 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-ca harmonic 56.97 179.99 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-cl harmonic 50.10 179.95 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-f harmonic 55.86 179.96 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-hn harmonic 45.62 179.98 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-i harmonic 46.23 179.95 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n1 harmonic 66.89 180.00 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n2 harmonic 65.70 171.56 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n3 harmonic 60.69 175.59 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n4 harmonic 59.68 179.69 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-na harmonic 59.95 180.00 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-nh harmonic 60.88 176.35 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-o harmonic 62.62 179.95 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-oh harmonic 62.88 174.31 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-os harmonic 62.15 176.61 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p2 harmonic 68.11 172.83 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p3 harmonic 68.68 173.51 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p4 harmonic 67.87 173.64 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p5 harmonic 71.49 177.28 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s2 harmonic 60.33 178.11 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s4 harmonic 55.20 169.60 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s harmonic 53.31 179.99 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s6 harmonic 61.81 175.92 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-sh harmonic 55.72 174.25 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-ss harmonic 55.44 176.06 # HF/6-31G* 1 + angle_coeff @angle:c2-n1-n1 harmonic 61.58 180.00 # HF/6-31G* 1 + angle_coeff @angle:c2-n1-o harmonic 73.09 116.94 # SOURCE3 2 0.0060 + angle_coeff @angle:c2-n1-s harmonic 64.71 118.00 # SOURCE3 2 0.0121 + angle_coeff @angle:c3-n1-n1 harmonic 56.30 180.00 # HF/6-31G* 1 + angle_coeff @angle:ca-n1-n1 harmonic 58.54 180.00 # HF/6-31G* 1 + angle_coeff @angle:ce-n1-o harmonic 71.28 122.40 # CORR 2 + angle_coeff @angle:ce-n1-s harmonic 64.84 117.34 # CORR 2 + angle_coeff @angle:cf-n1-o harmonic 71.28 122.40 # CORR 2 + angle_coeff @angle:cf-n1-s harmonic 64.84 117.34 # CORR 2 + angle_coeff @angle:cl-n1-n1 harmonic 51.37 179.94 # HF/6-31G* 1 + angle_coeff @angle:f-n1-n1 harmonic 57.39 179.93 # HF/6-31G* 1 + angle_coeff @angle:hn-n1-n1 harmonic 47.14 179.91 # HF/6-31G* 1 + angle_coeff @angle:i-n1-n1 harmonic 47.26 179.94 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n1 harmonic 68.97 179.97 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n2 harmonic 67.65 171.57 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n3 harmonic 62.49 175.09 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n4 harmonic 61.31 179.91 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-na harmonic 61.63 179.97 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-nh harmonic 62.66 176.00 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-o harmonic 64.43 179.94 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-oh harmonic 64.78 173.77 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-os harmonic 64.01 176.12 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-p2 harmonic 69.42 174.71 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-p3 harmonic 70.24 174.27 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-s harmonic 54.64 180.00 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-n1-sh harmonic 57.01 175.07 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-ss harmonic 56.92 175.61 # HF/6-31G* 1 + angle_coeff @angle:o-n1-p2 harmonic 84.67 116.05 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n1-s harmonic 80.34 119.93 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n2-br harmonic 63.89 106.60 # SOURCE3 1 + angle_coeff @angle:br-n2-c2 harmonic 59.13 112.40 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n2-n2 harmonic 61.08 110.42 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n2-o harmonic 60.10 114.47 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n2-p2 harmonic 80.05 111.03 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n2-s harmonic 62.40 115.78 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-n2-c1 harmonic 74.41 121.10 # SOURCE3 1 + angle_coeff @angle:c1-n2-c3 harmonic 58.67 151.88 # SOURCE3 4 15.8282 + angle_coeff @angle:c1-n2-cl harmonic 55.36 118.80 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-n2-hn harmonic 51.47 126.50 # SOURCE2 3 7.6267 + angle_coeff @angle:c1-n2-n2 harmonic 76.75 113.40 # SOURCE3 1 + angle_coeff @angle:c1-n2-o harmonic 79.20 113.59 # SOURCE3 1 + angle_coeff @angle:c1-n2-p2 harmonic 84.76 119.57 # SOURCE3 1 + angle_coeff @angle:c1-n2-s harmonic 69.80 117.67 # SOURCE3 1 + angle_coeff @angle:c2-n2-c2 harmonic 70.76 118.18 # SOURCE3 1 + angle_coeff @angle:c2-n2-c3 harmonic 66.13 115.30 # SOURCE3 8 4.2940 + angle_coeff @angle:c2-n2-ca harmonic 69.83 119.94 # SOURCE3 1 + angle_coeff @angle:c2-n2-cl harmonic 56.69 112.64 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n2-f harmonic 68.30 108.14 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n2-hn harmonic 52.63 110.33 # SOURCE3 9 0.6498 + angle_coeff @angle:c2-n2-i harmonic 51.86 114.74 # SOURCE3 2 0.0139 + angle_coeff @angle:c2-n2-n1 harmonic 75.45 115.09 # HF/6-31G* 1 + angle_coeff @angle:c2-n2-n2 harmonic 77.94 103.59 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-n2-n3 harmonic 71.34 118.14 # SOURCE3 1 + angle_coeff @angle:c2-n2-n4 harmonic 62.39 112.22 # SOURCE3 3 0.0406 + angle_coeff @angle:c2-n2-n harmonic 70.16 117.98 # SOURCE4 11 0.9019 + angle_coeff @angle:c2-n2-na harmonic 70.35 117.58 # SOURCE3 8 1.6671 + angle_coeff @angle:c2-n2-nh harmonic 70.71 117.61 # SOURCE3 6 3.2642 + angle_coeff @angle:c2-n2-no harmonic 64.22 111.54 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n2-o harmonic 75.47 116.94 # SOURCE3 1 + angle_coeff @angle:c2-n2-oh harmonic 72.08 110.89 # SOURCE4 22 1.2709 + angle_coeff @angle:c2-n2-os harmonic 71.83 110.51 # SOURCE4 13 0.7888 + angle_coeff @angle:c2-n2-p2 harmonic 85.03 116.00 # SOURCE3 1 + angle_coeff @angle:c2-n2-p3 harmonic 77.54 119.30 # SOURCE3 3 2.8489 + angle_coeff @angle:c2-n2-p4 harmonic 79.28 118.77 # SOURCE3 1 + angle_coeff @angle:c2-n2-s4 harmonic 68.12 112.29 # SOURCE3 1 + angle_coeff @angle:c2-n2-s6 harmonic 68.85 116.24 # SOURCE3 1 + angle_coeff @angle:c2-n2-s harmonic 68.67 118.00 # SOURCE3 1 + angle_coeff @angle:c2-n2-sh harmonic 63.09 115.48 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n2-ss harmonic 64.97 118.04 # SOURCE3 4 2.2804 + angle_coeff @angle:c3-n2-c3 harmonic 63.76 110.70 # SOURCE3 1 + angle_coeff @angle:c3-n2-ca harmonic 65.97 114.95 # SOURCE4 5 0.9744 + angle_coeff @angle:c3-n2-ce harmonic 65.37 118.53 # CORR 123 + angle_coeff @angle:c3-n2-cf harmonic 65.37 118.53 # CORR 123 + angle_coeff @angle:c3-n2-hn harmonic 45.18 118.40 # SOURCE3 1 + angle_coeff @angle:c3-n2-n1 harmonic 68.64 116.20 # SOURCE4 12 0.5407 + angle_coeff @angle:c3-n2-n2 harmonic 69.29 111.18 # SOURCE3 7 0.4349 + angle_coeff @angle:c3-n2-nh harmonic 68.08 109.99 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n2-o harmonic 70.29 112.40 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-n2-p2 harmonic 82.11 114.21 # SOURCE3 2 2.2772 + angle_coeff @angle:c3-n2-s6 harmonic 66.28 113.84 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n2-s harmonic 65.70 116.72 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-n2-ca harmonic 71.79 112.20 # SOURCE3 1 + angle_coeff @angle:ca-n2-hn harmonic 50.01 120.00 # SOURCE3 1 + angle_coeff @angle:ca-n2-n2 harmonic 74.00 113.53 # SOURCE3 1 + angle_coeff @angle:ca-n2-o harmonic 75.26 116.00 # SOURCE2 1 0.0000 + angle_coeff @angle:ca-n2-p2 harmonic 84.03 118.11 # SOURCE3 1 + angle_coeff @angle:ca-n2-s harmonic 67.84 120.11 # SOURCE3 1 + angle_coeff @angle:c-n2-c2 harmonic 66.22 120.97 # SOURCE3 1 + angle_coeff @angle:c-n2-c harmonic 62.71 123.80 # SOURCE3 1 + angle_coeff @angle:c-n2-ca harmonic 66.05 120.50 # SOURCE3 1 + angle_coeff @angle:cc-n2-cl harmonic 55.90 115.79 # CORR 2 + angle_coeff @angle:cc-n2-hn harmonic 52.42 110.72 # CORR 20 + angle_coeff @angle:cc-n2-na harmonic 73.01 108.92 # SOURCE4 9 1.6245 + angle_coeff @angle:cc-n2-nh harmonic 70.37 118.47 # SOURCE4 6 1.7995 + angle_coeff @angle:cd-n2-cl harmonic 55.90 115.79 # CORR 2 + angle_coeff @angle:cd-n2-hn harmonic 52.42 110.72 # CORR 20 + angle_coeff @angle:ce-n2-hn harmonic 52.74 111.05 # CORR 69 + angle_coeff @angle:ce-n2-n harmonic 70.35 118.04 # CORR 101 + angle_coeff @angle:ce-n2-nh harmonic 70.64 118.57 # CORR 54 + angle_coeff @angle:ce-n2-o harmonic 77.37 112.16 # SOURCE3 1 + angle_coeff @angle:ce-n2-oh harmonic 71.48 113.38 # CORR 37 + angle_coeff @angle:ce-n2-os harmonic 71.23 112.97 # CORR 40 + angle_coeff @angle:ce-n2-s harmonic 69.30 116.28 # SOURCE3 1 + angle_coeff @angle:cf-n2-hn harmonic 52.74 111.05 # CORR 69 + angle_coeff @angle:cf-n2-n harmonic 70.35 118.04 # CORR 101 + angle_coeff @angle:cf-n2-nh harmonic 70.64 118.57 # CORR 54 + angle_coeff @angle:cf-n2-o harmonic 77.37 112.16 # SOURCE3 1 same_as_ce-n2-o + angle_coeff @angle:cf-n2-oh harmonic 71.48 113.38 # CORR 37 + angle_coeff @angle:cf-n2-os harmonic 71.23 112.97 # CORR 40 + angle_coeff @angle:cf-n2-s harmonic 69.30 116.28 # SOURCE3 1 same_as_ce-n2-s + angle_coeff @angle:cl-n2-n1 harmonic 59.29 108.70 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-n2-n2 harmonic 58.70 110.47 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-n2-o harmonic 58.23 114.03 # SOURCE3 1 + angle_coeff @angle:cl-n2-p2 harmonic 73.98 112.98 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-n2-s harmonic 58.50 115.77 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-n2-n2 harmonic 90.46 64.92 # SOURCE3 2 0.0000 + angle_coeff @angle:f-n2-n2 harmonic 68.29 114.60 # SOURCE2 1 0.0000 + angle_coeff @angle:f-n2-o harmonic 71.17 110.10 # SOURCE2 1 0.0000 + angle_coeff @angle:f-n2-p2 harmonic 84.30 107.10 # SOURCE3 1 0.0000 + angle_coeff @angle:f-n2-s harmonic 67.14 110.73 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-hn harmonic 38.61 120.00 # SOURCE3 1 + angle_coeff @angle:hn-n2-n1 harmonic 55.33 114.10 # SOURCE2 1 0.0000 + angle_coeff @angle:hn-n2-n2 harmonic 55.84 105.01 # SOURCE3 19 1.5183 + angle_coeff @angle:hn-n2-ne harmonic 54.69 108.56 # SOURCE3 29 5.5708 + angle_coeff @angle:hn-n2-nf harmonic 54.69 108.56 # SOURCE3 29 same_as_hn-n2-ne + angle_coeff @angle:hn-n2-o harmonic 57.61 107.37 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-p2 harmonic 58.61 112.09 # SOURCE3 18 4.0663 + angle_coeff @angle:hn-n2-p4 harmonic 54.50 111.33 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-p5 harmonic 56.32 122.34 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-pe harmonic 61.28 111.41 # SOURCE3 20 4.9895 + angle_coeff @angle:hn-n2-pf harmonic 61.28 111.41 # SOURCE3 20 same_as_hn-n2-pe + angle_coeff @angle:hn-n2-s2 harmonic 48.34 115.80 # SOURCE2 1 0.0000 + angle_coeff @angle:hn-n2-s4 harmonic 46.34 111.21 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-s harmonic 49.11 108.17 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n2-s6 harmonic 47.82 112.59 # SOURCE3 2 0.0000 + angle_coeff @angle:i-n2-n2 harmonic 53.71 111.79 # SOURCE3 1 0.0000 + angle_coeff @angle:i-n2-o harmonic 52.33 116.82 # SOURCE3 1 0.0000 + angle_coeff @angle:i-n2-p2 harmonic 72.31 113.26 # SOURCE3 1 0.0000 + angle_coeff @angle:i-n2-s harmonic 56.35 116.85 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-n2-n1 harmonic 80.82 112.00 # HF/6-31G* 1 + angle_coeff @angle:n2-n2-n1 harmonic 62.28 180.00 # dac_for_azides 0 + angle_coeff @angle:n2-n2-n2 harmonic 78.20 109.49 # SOURCE3 2 0.0000 + angle_coeff @angle:n2-n2-n3 harmonic 76.59 108.88 # SOURCE3 1 + angle_coeff @angle:n2-n2-n4 harmonic 65.78 106.45 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-na harmonic 74.18 112.23 # SOURCE3 1 + angle_coeff @angle:n2-n2-nh harmonic 74.76 111.70 # SOURCE3 5 0.3475 + angle_coeff @angle:n2-n2-no harmonic 67.68 105.97 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-o harmonic 80.17 110.43 # SOURCE3 1 + angle_coeff @angle:n2-n2-oh harmonic 74.02 111.51 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-os harmonic 74.69 108.38 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-p2 harmonic 90.07 109.15 # SOURCE3 1 + angle_coeff @angle:n2-n2-p3 harmonic 81.73 113.05 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-p4 harmonic 81.37 118.77 # SOURCE3 1 + angle_coeff @angle:n2-n2-p5 harmonic 89.80 110.46 # SOURCE3 1 + angle_coeff @angle:n2-n2-s4 harmonic 71.60 107.30 # SOURCE3 1 + angle_coeff @angle:n2-n2-s6 harmonic 72.35 111.25 # SOURCE3 1 + angle_coeff @angle:n2-n2-s harmonic 71.24 115.91 # SOURCE3 1 + angle_coeff @angle:n2-n2-sh harmonic 66.00 111.10 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n2-ss harmonic 68.46 112.14 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-n2-n3 harmonic 72.95 115.07 # SOURCE3 1 + angle_coeff @angle:n3-n2-o harmonic 76.86 114.00 # SOURCE2 1 0.0000 + angle_coeff @angle:n3-n2-p2 harmonic 86.69 115.34 # SOURCE3 1 + angle_coeff @angle:n3-n2-s harmonic 69.96 117.13 # SOURCE3 1 + angle_coeff @angle:n4-n2-n4 harmonic 59.97 106.70 # SOURCE3 1 + angle_coeff @angle:n4-n2-o harmonic 64.86 112.20 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-n2-p2 harmonic 79.54 113.07 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-n2-s harmonic 62.44 118.50 # SOURCE3 1 0.0000 + angle_coeff @angle:na-n2-na harmonic 73.47 107.00 # SOURCE3 1 + angle_coeff @angle:na-n2-o harmonic 75.74 113.09 # SOURCE3 1 0.0000 + angle_coeff @angle:na-n2-p2 harmonic 84.58 119.16 # SOURCE3 1 0.0000 + angle_coeff @angle:na-n2-s harmonic 68.94 118.26 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-n2-nh harmonic 74.13 113.09 # CORR 12 + angle_coeff @angle:ne-n2-o harmonic 79.97 110.31 # SOURCE3 1 + angle_coeff @angle:ne-n2-s harmonic 71.04 116.22 # SOURCE3 1 + angle_coeff @angle:nf-n2-nh harmonic 74.13 113.09 # CORR 12 + angle_coeff @angle:nf-n2-o harmonic 79.97 110.31 # SOURCE3 1 same_as_ne-n2-o + angle_coeff @angle:nf-n2-s harmonic 71.04 116.22 # SOURCE3 1 same_as_ne-n2-s + angle_coeff @angle:nh-n2-nh harmonic 69.67 121.20 # SOURCE3 1 + angle_coeff @angle:nh-n2-o harmonic 76.02 113.60 # SOURCE4 13 1.0945 + angle_coeff @angle:nh-n2-p2 harmonic 84.93 118.83 # SOURCE3 2 0.1024 + angle_coeff @angle:nh-n2-s harmonic 69.56 116.90 # SOURCE3 2 0.2276 + angle_coeff @angle:n-n2-n2 harmonic 75.48 108.18 # SOURCE4 8 0.3496 + angle_coeff @angle:n-n2-o harmonic 74.99 115.10 # SOURCE4 31 0.2796 + angle_coeff @angle:no-n2-no harmonic 62.81 103.70 # SOURCE3 1 + angle_coeff @angle:no-n2-o harmonic 70.40 100.76 # SOURCE3 1 0.0000 + angle_coeff @angle:no-n2-p2 harmonic 81.32 111.95 # SOURCE3 1 0.0000 + angle_coeff @angle:n-n2-p2 harmonic 85.20 117.30 # SOURCE3 1 0.0000 + angle_coeff @angle:n-n2-s harmonic 69.64 115.74 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-n2-oh harmonic 74.84 101.70 # SOURCE3 1 + angle_coeff @angle:oh-n2-p2 harmonic 86.05 115.11 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-n2-s harmonic 69.52 116.08 # SOURCE3 1 0.0000 + angle_coeff @angle:o-n2-o harmonic 81.02 115.37 # SOURCE3 1 + angle_coeff @angle:o-n2-oh harmonic 75.56 112.15 # SOURCE2 2 1.4500 + angle_coeff @angle:o-n2-os harmonic 75.73 110.35 # SOURCE3 2 0.0042 + angle_coeff @angle:o-n2-p2 harmonic 88.65 116.08 # SOURCE3 1 + angle_coeff @angle:o-n2-p3 harmonic 82.37 113.43 # SOURCE3 1 0.0000 + angle_coeff @angle:o-n2-p4 harmonic 85.23 110.61 # SOURCE3 1 + angle_coeff @angle:o-n2-p5 harmonic 91.73 109.11 # SOURCE3 1 + angle_coeff @angle:o-n2-pe harmonic 85.18 134.56 # SOURCE3 1 + angle_coeff @angle:o-n2-pf harmonic 85.18 134.56 # SOURCE3 1 same_as_o-n2-pe + angle_coeff @angle:o-n2-s4 harmonic 72.12 108.91 # SOURCE3 1 + angle_coeff @angle:o-n2-s6 harmonic 73.56 111.34 # SOURCE3 1 + angle_coeff @angle:o-n2-s harmonic 72.09 117.18 # SOURCE3 1 + angle_coeff @angle:o-n2-sh harmonic 65.55 114.98 # SOURCE3 1 0.0000 + angle_coeff @angle:os-n2-os harmonic 71.25 110.29 # SOURCE3 1 + angle_coeff @angle:os-n2-p2 harmonic 87.70 110.20 # SOURCE3 1 0.0000 + angle_coeff @angle:o-n2-ss harmonic 68.39 115.34 # SOURCE3 1 0.0000 + angle_coeff @angle:os-n2-s harmonic 70.47 112.23 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n2-p2 harmonic 107.12 116.80 # SOURCE3 1 + angle_coeff @angle:p2-n2-p3 harmonic 98.43 124.48 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n2-p4 harmonic 98.27 128.37 # SOURCE3 1 + angle_coeff @angle:p2-n2-p5 harmonic 104.38 123.47 # SOURCE3 1 + angle_coeff @angle:p2-n2-s4 harmonic 86.26 112.10 # SOURCE3 1 + angle_coeff @angle:p2-n2-s6 harmonic 86.44 115.70 # SOURCE3 1 + angle_coeff @angle:p2-n2-s harmonic 85.91 117.84 # SOURCE3 1 + angle_coeff @angle:p2-n2-sh harmonic 80.45 118.45 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n2-ss harmonic 82.01 120.43 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-n2-p3 harmonic 96.00 120.40 # SOURCE3 1 + angle_coeff @angle:p3-n2-s harmonic 80.08 120.86 # SOURCE3 1 0.0000 + angle_coeff @angle:p4-n2-s harmonic 77.83 131.84 # SOURCE3 1 + angle_coeff @angle:p5-n2-p5 harmonic 105.81 120.60 # SOURCE3 1 + angle_coeff @angle:p5-n2-s harmonic 85.34 119.89 # SOURCE3 1 + angle_coeff @angle:pe-n2-s harmonic 88.59 115.73 # SOURCE3 1 + angle_coeff @angle:pf-n2-s harmonic 88.59 115.73 # SOURCE3 1 same_as_pe-n2-s + angle_coeff @angle:s4-n2-s4 harmonic 66.00 119.18 # SOURCE3 1 + angle_coeff @angle:s4-n2-s6 harmonic 67.18 119.18 # SOURCE3 1 + angle_coeff @angle:s6-n2-s6 harmonic 68.49 119.18 # SOURCE3 1 + angle_coeff @angle:sh-n2-sh harmonic 59.95 123.93 # SOURCE3 1 + angle_coeff @angle:sh-n2-ss harmonic 61.33 123.93 # SOURCE3 1 + angle_coeff @angle:s-n2-s harmonic 68.47 120.88 # SOURCE3 1 + angle_coeff @angle:s-n2-s4 harmonic 69.20 113.00 # SOURCE3 1 + angle_coeff @angle:s-n2-s6 harmonic 68.60 119.61 # SOURCE3 1 + angle_coeff @angle:s-n2-sh harmonic 63.58 122.05 # SOURCE3 1 0.0000 + angle_coeff @angle:s-n2-ss harmonic 66.58 118.19 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-n2-ss harmonic 62.92 123.93 # SOURCE3 1 + angle_coeff @angle:br-n3-br harmonic 66.54 107.15 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n3-c3 harmonic 62.70 106.93 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-n3-c1 harmonic 64.09 123.34 # SOURCE3 1 + angle_coeff @angle:c1-n3-f harmonic 68.22 104.70 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-n3-hn harmonic 47.74 118.31 # SOURCE3 1 + angle_coeff @angle:c1-n3-o harmonic 70.01 116.63 # SOURCE3 1 + angle_coeff @angle:c2-n3-c2 harmonic 66.22 124.68 # SOURCE3 1 + angle_coeff @angle:c2-n3-hn harmonic 49.11 119.38 # SOURCE3 1 + angle_coeff @angle:c3-n3-c3 harmonic 64.01 110.90 # SOURCE3 40 2.3048 + angle_coeff @angle:c3-n3-cl harmonic 57.82 107.23 # SOURCE3 3 0.3673 + angle_coeff @angle:c3-n3-cx harmonic 62.45 116.32 # SOURCE4 24 0.5119 + angle_coeff @angle:c3-n3-cy harmonic 61.69 118.26 # SOURCE4 14 0.8788 + angle_coeff @angle:c3-n3-f harmonic 66.81 103.13 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-n3-hn harmonic 47.13 109.92 # SOURCE3 120 2.2590 + angle_coeff @angle:c3-n3-i harmonic 56.98 108.48 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-n3-n2 harmonic 66.23 118.75 # SOURCE2 2 2.6500 + angle_coeff @angle:c3-n3-n3 harmonic 66.76 108.15 # SOURCE3 15 1.3999 + angle_coeff @angle:c3-n3-n4 harmonic 67.18 109.65 # SOURCE3 3 0.1146 + angle_coeff @angle:c3-n3-n harmonic 66.67 111.75 # SOURCE4 50 1.6777 + angle_coeff @angle:c3-n3-nh harmonic 66.37 111.89 # SOURCE4 21 1.3006 + angle_coeff @angle:c3-n3-no harmonic 66.02 111.27 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n3-o harmonic 68.68 113.31 # SOURCE3 5 8.9081 + angle_coeff @angle:c3-n3-oh harmonic 69.07 106.14 # SOURCE4 14 1.1040 + angle_coeff @angle:c3-n3-os harmonic 68.48 104.95 # SOURCE4 9 0.9687 + angle_coeff @angle:c3-n3-p3 harmonic 75.79 121.93 # SOURCE3 3 5.6009 + angle_coeff @angle:c3-n3-p5 harmonic 78.53 119.81 # SOURCE4 58 1.8367 + angle_coeff @angle:c3-n3-s4 harmonic 61.45 112.91 # SOURCE3 3 0.8983 + angle_coeff @angle:c3-n3-s6 harmonic 63.67 116.57 # SOURCE4 73 1.8772 + angle_coeff @angle:c3-n3-s harmonic 61.46 110.02 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n3-sh harmonic 62.06 112.70 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n3-ss harmonic 61.59 116.01 # SOURCE3 3 1.1944 + angle_coeff @angle:c3-n3-sy harmonic 62.43 115.27 # SOURCE4 108 1.7647 + angle_coeff @angle:cl-n3-cl harmonic 53.49 108.28 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-n3-hn harmonic 39.61 104.39 # SOURCE3 2 0.0000 + angle_coeff @angle:cl-n3-n3 harmonic 59.29 107.65 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-n3-cx harmonic 86.39 60.71 # SOURCE4 57 0.2359 + angle_coeff @angle:cx-n3-hn harmonic 47.15 109.57 # SOURCE4 26 0.7439 + angle_coeff @angle:cx-n3-p5 harmonic 78.66 119.32 # SOURCE4 71 1.1948 + angle_coeff @angle:cx-n3-py harmonic 76.73 121.75 # SOURCE4 10 1.0295 + angle_coeff @angle:cy-n3-cy harmonic 70.04 90.87 # SOURCE4 10 0.5777 + angle_coeff @angle:cy-n3-hn harmonic 46.25 112.12 # SOURCE4 9 1.9058 + angle_coeff @angle:f-n3-f harmonic 67.71 102.22 # SOURCE2 4 0.7562 + angle_coeff @angle:f-n3-hn harmonic 50.78 99.80 # SOURCE2 1 0.0000 + angle_coeff @angle:hn-n3-hn harmonic 41.30 107.13 # SOURCE3 44 1.9687 + angle_coeff @angle:hn-n3-i harmonic 35.43 109.98 # SOURCE3 2 0.0000 + angle_coeff @angle:hn-n3-n1 harmonic 52.05 110.17 # HF/6-31G* 1 + angle_coeff @angle:hn-n3-n2 harmonic 51.40 115.94 # SOURCE3 1 + angle_coeff @angle:hn-n3-n3 harmonic 50.16 103.98 # SOURCE3 18 1.8593 + angle_coeff @angle:hn-n3-n4 harmonic 50.87 106.40 # SOURCE3 5 0.5863 + angle_coeff @angle:hn-n3-n harmonic 51.02 106.57 # SOURCE3 6 1.0767 + angle_coeff @angle:hn-n3-na harmonic 50.32 107.89 # SOURCE3 1 + angle_coeff @angle:hn-n3-nh harmonic 50.44 107.39 # SOURCE3 11 1.6294 + angle_coeff @angle:hn-n3-no harmonic 50.25 104.78 # SOURCE3 3 1.1126 + angle_coeff @angle:hn-n3-o harmonic 53.14 113.32 # SOURCE3 3 4.3945 + angle_coeff @angle:hn-n3-oh harmonic 53.08 101.11 # SOURCE3 4 0.9921 + angle_coeff @angle:hn-n3-os harmonic 51.67 100.92 # SOURCE3 6 0.7295 + angle_coeff @angle:hn-n3-p2 harmonic 54.24 120.26 # SOURCE3 1 + angle_coeff @angle:hn-n3-p3 harmonic 52.93 116.89 # SOURCE3 9 3.8816 + angle_coeff @angle:hn-n3-p4 harmonic 54.97 113.05 # SOURCE3 2 0.0000 + angle_coeff @angle:hn-n3-p5 harmonic 56.04 113.68 # SOURCE3 6 2.1781 + angle_coeff @angle:hn-n3-s4 harmonic 42.47 108.93 # SOURCE3 7 1.7819 + angle_coeff @angle:hn-n3-s harmonic 41.53 109.47 # SOURCE3 1 + angle_coeff @angle:hn-n3-s6 harmonic 46.06 109.33 # SOURCE4 86 0.9610 + angle_coeff @angle:hn-n3-sh harmonic 43.12 108.67 # SOURCE3 3 2.5025 + angle_coeff @angle:hn-n3-ss harmonic 43.36 109.85 # SOURCE3 5 2.3215 + angle_coeff @angle:hn-n3-sy harmonic 44.15 109.49 # SOURCE4 278 0.7897 + angle_coeff @angle:i-n3-i harmonic 60.04 111.27 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-n3-n1 harmonic 72.40 113.21 # HF/6-31G* 1 + angle_coeff @angle:n2-n3-n2 harmonic 71.82 118.73 # SOURCE3 1 + angle_coeff @angle:n2-n3-o harmonic 74.13 114.91 # SOURCE3 1 + angle_coeff @angle:n3-n3-n3 harmonic 69.57 105.71 # SOURCE3 3 0.3561 + angle_coeff @angle:n4-n3-n4 harmonic 69.04 113.48 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-n3-nh harmonic 70.91 107.14 # SOURCE3 1 + angle_coeff @angle:na-n3-na harmonic 69.21 112.00 # SOURCE3 1 + angle_coeff @angle:nh-n3-nh harmonic 70.75 107.15 # SOURCE3 1 0.0000 + angle_coeff @angle:n-n3-n harmonic 70.25 110.55 # SOURCE3 1 0.0000 + angle_coeff @angle:no-n3-no harmonic 67.04 115.26 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-n3-oh harmonic 72.79 107.18 # SOURCE3 1 0.0000 + angle_coeff @angle:o-n3-o harmonic 71.89 126.14 # SOURCE3 1 + angle_coeff @angle:o-n3-p2 harmonic 84.34 117.02 # SOURCE3 1 + angle_coeff @angle:o-n3-p4 harmonic 83.38 116.65 # SOURCE3 1 + angle_coeff @angle:o-n3-s4 harmonic 64.56 114.09 # SOURCE3 1 + angle_coeff @angle:o-n3-s6 harmonic 68.82 113.80 # SOURCE3 1 + angle_coeff @angle:o-n3-s harmonic 62.04 119.81 # SOURCE3 1 + angle_coeff @angle:os-n3-os harmonic 70.79 106.52 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n3-p2 harmonic 97.53 130.13 # SOURCE3 1 + angle_coeff @angle:p3-n3-p3 harmonic 98.56 118.74 # SOURCE3 3 3.3755 + angle_coeff @angle:p4-n3-p4 harmonic 101.51 116.35 # SOURCE3 1 + angle_coeff @angle:p5-n3-p5 harmonic 102.24 119.42 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-n3-s4 harmonic 60.13 120.02 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-n3-s6 harmonic 61.99 120.95 # SOURCE3 1 + angle_coeff @angle:s6-n3-s6 harmonic 63.29 126.13 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-n3-sh harmonic 61.24 118.63 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-n3-ss harmonic 61.27 119.67 # SOURCE3 1 + angle_coeff @angle:s-n3-s harmonic 56.48 131.36 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-n3-ss harmonic 61.60 119.57 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n4-br harmonic 65.14 114.82 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n4-hn harmonic 41.38 108.44 # SOURCE3 7 0.5630 + angle_coeff @angle:c1-n4-c1 harmonic 65.53 113.87 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-n4-hn harmonic 48.62 110.19 # SOURCE3 7 1.0847 + angle_coeff @angle:c2-n4-c2 harmonic 63.01 112.58 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n4-c3 harmonic 63.10 110.96 # SOURCE4 13 2.4632 + angle_coeff @angle:c2-n4-hn harmonic 46.43 111.36 # SOURCE3 13 1.2672 + angle_coeff @angle:c3-n4-c3 harmonic 62.84 110.64 # SOURCE3 13 1.3060 + angle_coeff @angle:c3-n4-ca harmonic 63.61 110.40 # SOURCE4 46 1.4643 + angle_coeff @angle:c3-n4-cc harmonic 62.84 111.09 # SOURCE4 7 0.7065 + angle_coeff @angle:c3-n4-cl harmonic 57.92 108.04 # SOURCE3 3 0.0000 + angle_coeff @angle:c3-n4-hn harmonic 46.19 110.11 # SOURCE3 100 1.3136 + angle_coeff @angle:c3-n4-n3 harmonic 66.73 108.72 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-n4-n4 harmonic 63.72 114.07 # SOURCE3 4 0.0000 + angle_coeff @angle:c3-n4-n harmonic 66.20 109.26 # SOURCE4 7 1.9859 + angle_coeff @angle:c3-n4-nh harmonic 64.76 111.73 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-no harmonic 65.25 109.08 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-o harmonic 67.25 111.66 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-oh harmonic 65.90 113.73 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-os harmonic 67.38 107.42 # SOURCE3 3 3.5920 + angle_coeff @angle:c3-n4-p2 harmonic 71.92 112.52 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-p3 harmonic 74.40 110.73 # SOURCE3 3 2.1084 + angle_coeff @angle:c3-n4-p5 harmonic 75.11 113.22 # SOURCE3 3 0.4021 + angle_coeff @angle:c3-n4-s4 harmonic 57.21 108.23 # SOURCE3 3 0.4195 + angle_coeff @angle:c3-n4-s6 harmonic 57.75 111.56 # SOURCE3 3 1.8851 + angle_coeff @angle:c3-n4-s harmonic 59.21 113.55 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-sh harmonic 59.13 115.81 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-n4-ss harmonic 59.66 113.68 # SOURCE3 3 1.1405 + angle_coeff @angle:ca-n4-ca harmonic 63.21 114.48 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-n4-hn harmonic 47.54 108.52 # SOURCE3 5 1.1693 + angle_coeff @angle:c-n4-c harmonic 61.50 108.61 # SOURCE3 1 0.0000 + angle_coeff @angle:c-n4-hn harmonic 44.68 110.86 # SOURCE3 10 1.0073 + angle_coeff @angle:cl-n4-cl harmonic 52.73 114.91 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-n4-hn harmonic 39.53 108.87 # SOURCE3 7 0.7719 + angle_coeff @angle:f-n4-f harmonic 70.47 109.05 # SOURCE3 1 0.0000 + angle_coeff @angle:f-n4-hn harmonic 51.67 108.39 # SOURCE3 4 0.0000 + angle_coeff @angle:hn-n4-hn harmonic 40.52 108.11 # SOURCE3 208 1.4126 + angle_coeff @angle:hn-n4-i harmonic 36.44 108.72 # SOURCE3 7 1.2717 + angle_coeff @angle:hn-n4-n1 harmonic 51.79 109.39 # HF/6-31G* 1 + angle_coeff @angle:hn-n4-n2 harmonic 42.29 109.68 # SOURCE3 19 0.6266 + angle_coeff @angle:hn-n4-n3 harmonic 49.85 110.40 # SOURCE3 11 0.7307 + angle_coeff @angle:hn-n4-n4 harmonic 48.09 108.66 # SOURCE3 18 1.2967 + angle_coeff @angle:hn-n4-n harmonic 49.59 109.08 # SOURCE3 13 1.6047 + angle_coeff @angle:hn-n4-na harmonic 49.43 109.38 # SOURCE3 25 1.0758 + angle_coeff @angle:hn-n4-nh harmonic 48.36 109.92 # SOURCE3 12 0.7304 + angle_coeff @angle:hn-n4-no harmonic 49.19 104.38 # SOURCE3 2 0.0000 + angle_coeff @angle:hn-n4-o harmonic 52.09 109.26 # SOURCE3 6 2.1203 + angle_coeff @angle:hn-n4-oh harmonic 51.12 108.09 # SOURCE3 6 1.6728 + angle_coeff @angle:hn-n4-os harmonic 50.15 109.39 # SOURCE3 10 1.4403 + angle_coeff @angle:hn-n4-p2 harmonic 47.71 110.50 # SOURCE3 25 1.0664 + angle_coeff @angle:hn-n4-p3 harmonic 49.73 109.89 # SOURCE3 10 2.3870 + angle_coeff @angle:hn-n4-p4 harmonic 47.65 111.33 # SOURCE3 3 0.0000 + angle_coeff @angle:hn-n4-p5 harmonic 51.29 110.00 # SOURCE3 10 1.0282 + angle_coeff @angle:hn-n4-py harmonic 47.36 117.89 # SOURCE3 8 0.0000 + angle_coeff @angle:hn-n4-s4 harmonic 37.07 110.10 # SOURCE3 6 0.8471 + angle_coeff @angle:hn-n4-s harmonic 41.06 106.89 # SOURCE3 6 1.0775 + angle_coeff @angle:hn-n4-s6 harmonic 38.64 108.94 # SOURCE3 10 0.5715 + angle_coeff @angle:hn-n4-sh harmonic 41.29 108.56 # SOURCE3 6 0.8535 + angle_coeff @angle:hn-n4-ss harmonic 41.15 109.17 # SOURCE3 10 0.8455 + angle_coeff @angle:i-n4-i harmonic 58.99 118.49 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-n4-n1 harmonic 72.69 110.67 # HF/6-31G* 1 + angle_coeff @angle:n2-n4-n2 harmonic 59.43 108.64 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-n4-n3 harmonic 69.79 111.07 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-n4-n4 harmonic 65.21 115.49 # SOURCE3 1 0.0000 + angle_coeff @angle:na-n4-na harmonic 66.27 119.60 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-n4-nh harmonic 67.83 109.38 # SOURCE3 1 0.0000 + angle_coeff @angle:n-n4-n harmonic 66.68 118.62 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-n4-oh harmonic 72.25 108.19 # SOURCE3 1 0.0000 + angle_coeff @angle:o-n4-o harmonic 70.28 120.97 # SOURCE3 1 0.0000 + angle_coeff @angle:os-n4-os harmonic 72.46 104.40 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n4-p2 harmonic 89.65 113.91 # SOURCE3 2 0.0000 + angle_coeff @angle:p3-n4-p3 harmonic 89.71 121.38 # SOURCE3 1 0.0000 + angle_coeff @angle:p5-n4-p5 harmonic 98.15 107.02 # SOURCE3 1 0.0000 + angle_coeff @angle:py-n4-py harmonic 116.94 69.79 # SOURCE3 2 0.0000 + angle_coeff @angle:s4-n4-s4 harmonic 54.75 115.43 # SOURCE3 1 + angle_coeff @angle:s6-n4-s6 harmonic 57.91 109.51 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-n4-sh harmonic 60.37 112.59 # SOURCE3 1 0.0000 + angle_coeff @angle:s-n4-s harmonic 56.74 124.55 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-n4-ss harmonic 61.26 109.20 # SOURCE3 1 0.0000 + angle_coeff @angle:br-na-br harmonic 60.55 123.00 # SOURCE3 1 + angle_coeff @angle:br-na-c2 harmonic 63.61 100.48 # SOURCE3 2 1.0536 + angle_coeff @angle:br-na-ca harmonic 57.15 124.81 # SOURCE3 1 + angle_coeff @angle:br-na-cc harmonic 57.16 124.62 # SOURCE3 3 0.5348 + angle_coeff @angle:br-na-cd harmonic 57.16 124.62 # SOURCE3 3 same_as_br-na-cc + angle_coeff @angle:br-na-nc harmonic 59.86 119.42 # SOURCE3 4 1.6703 + angle_coeff @angle:br-na-nd harmonic 59.86 119.42 # SOURCE3 4 same_as_br-na-nc + angle_coeff @angle:br-na-os harmonic 63.92 104.99 # SOURCE3 1 0.0000 + angle_coeff @angle:br-na-p2 harmonic 75.91 121.01 # SOURCE3 1 + angle_coeff @angle:br-na-pc harmonic 76.39 120.26 # SOURCE3 3 2.1456 + angle_coeff @angle:br-na-pd harmonic 76.39 120.26 # SOURCE3 3 same_as_br-na-pc + angle_coeff @angle:br-na-ss harmonic 62.46 112.28 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-na-c1 harmonic 67.20 117.20 # SOURCE3 1 + angle_coeff @angle:c1-na-c2 harmonic 64.32 125.20 # SOURCE3 1 + angle_coeff @angle:c1-na-ca harmonic 66.54 120.57 # SOURCE3 1 + angle_coeff @angle:c1-na-cc harmonic 65.82 121.35 # SOURCE3 6 0.6517 + angle_coeff @angle:c1-na-cd harmonic 65.82 121.35 # SOURCE3 6 0.6517 + angle_coeff @angle:c1-na-nc harmonic 68.27 120.24 # SOURCE3 4 1.6849 + angle_coeff @angle:c1-na-nd harmonic 68.27 120.24 # SOURCE3 4 same_as_c1-na-nc + angle_coeff @angle:c1-na-os harmonic 70.24 106.96 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-na-p2 harmonic 76.49 122.25 # SOURCE3 1 + angle_coeff @angle:c1-na-pc harmonic 77.33 121.48 # SOURCE3 3 2.1681 + angle_coeff @angle:c1-na-pd harmonic 77.33 121.48 # SOURCE3 3 same_as_c1-na-pc + angle_coeff @angle:c1-na-ss harmonic 61.89 118.30 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-na-c2 harmonic 67.80 110.37 # SOURCE3 6 0.5121 + angle_coeff @angle:c2-na-c3 harmonic 64.23 117.20 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-na-ca harmonic 64.55 125.33 # SOURCE4 7 0.5648 + angle_coeff @angle:c2-na-cc harmonic 63.98 125.75 # SOURCE3 10 1.5856 + angle_coeff @angle:c2-na-cd harmonic 63.98 125.75 # SOURCE3 10 1.5856 + angle_coeff @angle:c2-na-cl harmonic 58.85 101.01 # SOURCE3 2 1.5799 + angle_coeff @angle:c2-na-f harmonic 68.64 103.11 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-na-hn harmonic 47.62 119.28 # SOURCE3 14 6.6027 + angle_coeff @angle:c2-na-i harmonic 58.98 106.74 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-na-n1 harmonic 66.27 124.81 # HF/6-31G* 1 + angle_coeff @angle:c2-na-n2 harmonic 65.80 125.00 # SOURCE3 1 + angle_coeff @angle:c2-na-n3 harmonic 64.64 124.80 # SOURCE3 1 + angle_coeff @angle:c2-na-n4 harmonic 65.19 121.32 # SOURCE3 1 + angle_coeff @angle:c2-na-n harmonic 65.63 124.70 # SOURCE3 1 + angle_coeff @angle:c2-na-na harmonic 65.14 124.60 # SOURCE3 1 + angle_coeff @angle:c2-na-nc harmonic 67.42 120.61 # CORR 9 + angle_coeff @angle:c2-na-nd harmonic 67.42 120.61 # CORR 9 + angle_coeff @angle:c2-na-nh harmonic 65.04 124.98 # SOURCE3 1 + angle_coeff @angle:c2-na-no harmonic 64.34 124.20 # SOURCE3 1 + angle_coeff @angle:c2-na-o harmonic 68.21 125.90 # SOURCE3 1 + angle_coeff @angle:c2-na-oh harmonic 65.80 123.90 # SOURCE3 1 + angle_coeff @angle:c2-na-os harmonic 68.53 110.33 # SOURCE3 4 3.2172 + angle_coeff @angle:c2-na-p2 harmonic 76.19 122.14 # SOURCE3 1 + angle_coeff @angle:c2-na-p3 harmonic 74.55 126.10 # SOURCE3 1 + angle_coeff @angle:c2-na-p4 harmonic 81.58 125.00 # SOURCE3 1 + angle_coeff @angle:c2-na-p5 harmonic 76.43 125.10 # SOURCE3 1 + angle_coeff @angle:c2-na-pc harmonic 76.96 121.56 # SOURCE3 3 1.6252 + angle_coeff @angle:c2-na-pd harmonic 76.96 121.56 # SOURCE3 3 same_as_c2-na-pc + angle_coeff @angle:c2-na-s4 harmonic 58.37 124.90 # SOURCE3 1 + angle_coeff @angle:c2-na-s6 harmonic 60.24 124.40 # SOURCE3 1 + angle_coeff @angle:c2-na-s harmonic 58.90 125.80 # SOURCE3 1 + angle_coeff @angle:c2-na-sh harmonic 60.23 125.10 # SOURCE3 1 + angle_coeff @angle:c2-na-ss harmonic 62.34 115.53 # SOURCE3 5 1.4036 + angle_coeff @angle:c3-na-c3 harmonic 60.72 125.59 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-na-ca harmonic 63.15 124.36 # SOURCE3 5 4.2557 + angle_coeff @angle:c3-na-cc harmonic 62.56 125.09 # SOURCE3 18 1.2138 + angle_coeff @angle:c3-na-cd harmonic 62.56 125.09 # SOURCE3 18 1.2138 + angle_coeff @angle:c3-na-cp harmonic 63.76 119.46 # SOURCE4 7 0.4108 + angle_coeff @angle:c3-na-n2 harmonic 65.48 120.05 # SOURCE4 5 0.8795 + angle_coeff @angle:c3-na-n harmonic 67.37 112.68 # SOURCE4 12 0.5122 + angle_coeff @angle:c3-na-nc harmonic 65.74 120.46 # SOURCE3 8 2.1625 + angle_coeff @angle:c3-na-nd harmonic 65.74 120.46 # SOURCE3 8 2.1625 + angle_coeff @angle:c3-na-os harmonic 68.91 104.39 # SOURCE3 3 1.2017 + angle_coeff @angle:c3-na-p2 harmonic 75.04 123.12 # SOURCE3 1 + angle_coeff @angle:c3-na-pc harmonic 75.89 122.11 # SOURCE3 3 2.8504 + angle_coeff @angle:c3-na-pd harmonic 75.89 122.11 # SOURCE3 3 same_as_c3-na-pc + angle_coeff @angle:c3-na-sh harmonic 63.38 110.28 # SOURCE3 1 + angle_coeff @angle:c3-na-ss harmonic 62.90 110.87 # SOURCE3 3 0.8260 + angle_coeff @angle:ca-na-ca harmonic 66.98 120.09 # SOURCE4 321 1.7366 + angle_coeff @angle:ca-na-cc harmonic 68.46 113.15 # SOURCE3 18 9.8644 + angle_coeff @angle:ca-na-cd harmonic 68.46 113.15 # SOURCE3 18 9.8644 + angle_coeff @angle:ca-na-cl harmonic 53.17 124.79 # SOURCE3 1 + angle_coeff @angle:ca-na-cp harmonic 65.88 120.96 # SOURCE4 20 1.2820 + angle_coeff @angle:ca-na-cx harmonic 63.07 124.09 # SOURCE4 12 1.8167 + angle_coeff @angle:ca-na-f harmonic 65.51 116.40 # SOURCE3 1 + angle_coeff @angle:ca-na-hn harmonic 47.63 125.59 # SOURCE4 437 1.1893 + angle_coeff @angle:ca-na-i harmonic 55.21 121.62 # SOURCE3 1 + angle_coeff @angle:ca-na-n2 harmonic 68.21 119.85 # SOURCE4 6 1.2043 + angle_coeff @angle:ca-na-n4 harmonic 66.37 120.19 # SOURCE3 1 + angle_coeff @angle:ca-na-n harmonic 67.34 122.00 # SOURCE3 1 + angle_coeff @angle:ca-na-na harmonic 66.29 123.76 # SOURCE3 1 + angle_coeff @angle:ca-na-nb harmonic 68.18 122.16 # SOURCE4 7 0.8543 + angle_coeff @angle:ca-na-nc harmonic 69.27 117.85 # SOURCE3 6 3.6536 + angle_coeff @angle:ca-na-nd harmonic 69.27 117.85 # SOURCE3 6 same_as_ca-na-nc + angle_coeff @angle:ca-na-nh harmonic 66.14 124.33 # SOURCE4 7 1.3855 + angle_coeff @angle:ca-na-o harmonic 71.14 119.99 # SOURCE4 51 1.2671 + angle_coeff @angle:ca-na-oh harmonic 66.69 124.08 # SOURCE3 1 + angle_coeff @angle:ca-na-os harmonic 69.70 109.46 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-na-p2 harmonic 75.51 125.85 # SOURCE3 1 + angle_coeff @angle:ca-na-p3 harmonic 75.50 124.38 # SOURCE3 1 + angle_coeff @angle:ca-na-p4 harmonic 82.41 124.97 # SOURCE3 1 + angle_coeff @angle:ca-na-p5 harmonic 77.51 123.30 # SOURCE3 1 + angle_coeff @angle:ca-na-pc harmonic 77.26 122.13 # SOURCE3 3 2.2393 + angle_coeff @angle:ca-na-pd harmonic 77.26 122.13 # SOURCE3 3 same_as_ca-na-pc + angle_coeff @angle:ca-na-py harmonic 72.61 140.88 # SOURCE3 2 0.0000 + angle_coeff @angle:ca-na-s4 harmonic 60.55 117.23 # SOURCE3 1 + angle_coeff @angle:ca-na-s6 harmonic 61.55 120.69 # SOURCE3 1 + angle_coeff @angle:ca-na-s harmonic 59.27 125.64 # SOURCE3 1 + angle_coeff @angle:ca-na-sh harmonic 60.55 125.44 # SOURCE3 1 + angle_coeff @angle:ca-na-ss harmonic 59.16 129.91 # SOURCE4 8 0.1449 + angle_coeff @angle:cc-na-cc harmonic 68.94 109.90 # SOURCE3 109 1.5547 + angle_coeff @angle:cc-na-cd harmonic 63.88 128.01 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-na-ce harmonic 63.05 126.61 # SOURCE4 8 0.5158 + angle_coeff @angle:cc-na-cl harmonic 53.10 124.61 # SOURCE3 3 0.5208 + angle_coeff @angle:cc-na-f harmonic 64.60 118.03 # SOURCE3 4 0.3081 + angle_coeff @angle:cc-na-hn harmonic 47.02 125.50 # CORR 861 + angle_coeff @angle:cc-na-i harmonic 54.34 125.70 # SOURCE3 6 0.7821 + angle_coeff @angle:cc-na-n2 harmonic 66.83 122.96 # SOURCE3 15 0.9350 + angle_coeff @angle:cc-na-n4 harmonic 65.90 120.31 # SOURCE3 10 3.4394 + angle_coeff @angle:cc-na-n harmonic 66.52 123.19 # SOURCE3 13 0.3010 + angle_coeff @angle:cc-na-na harmonic 65.91 123.43 # SOURCE3 23 0.2088 + angle_coeff @angle:cc-na-nc harmonic 70.18 113.02 # SOURCE3 38 2.2867 + angle_coeff @angle:cc-na-nd harmonic 66.41 126.22 # CORR 124 + angle_coeff @angle:cc-na-nh harmonic 66.23 122.25 # SOURCE3 19 0.2010 + angle_coeff @angle:cc-na-no harmonic 65.40 121.78 # SOURCE3 9 0.3521 + angle_coeff @angle:cc-na-o harmonic 69.01 125.21 # SOURCE3 10 0.0124 + angle_coeff @angle:cc-na-oh harmonic 66.67 122.38 # SOURCE3 10 0.1570 + angle_coeff @angle:cc-na-os harmonic 67.01 116.86 # CORR 48 + angle_coeff @angle:cc-na-p2 harmonic 75.29 125.86 # SOURCE3 14 2.2993 + angle_coeff @angle:cc-na-p3 harmonic 75.02 125.25 # SOURCE3 8 0.1998 + angle_coeff @angle:cc-na-p4 harmonic 81.11 127.73 # SOURCE3 7 3.6077 + angle_coeff @angle:cc-na-p5 harmonic 76.81 124.70 # SOURCE3 13 1.4225 + angle_coeff @angle:cc-na-s4 harmonic 59.45 121.03 # SOURCE3 10 0.5589 + angle_coeff @angle:cc-na-s6 harmonic 60.98 122.19 # SOURCE3 10 0.9634 + angle_coeff @angle:cc-na-s harmonic 59.10 125.66 # SOURCE3 8 0.1880 + angle_coeff @angle:cc-na-sh harmonic 60.71 123.96 # SOURCE3 10 0.3424 + angle_coeff @angle:cc-na-ss harmonic 61.34 120.10 # CORR 44 + angle_coeff @angle:cd-na-cd harmonic 68.94 109.90 # SOURCE3 109 1.5547 + angle_coeff @angle:cd-na-cl harmonic 53.10 124.61 # SOURCE3 3 same_as_cc-na-cl + angle_coeff @angle:cd-na-f harmonic 64.60 118.03 # SOURCE3 4 0.3081 + angle_coeff @angle:cd-na-hn harmonic 47.02 125.50 # CORR 861 + angle_coeff @angle:cd-na-i harmonic 54.34 125.70 # SOURCE3 6 0.7821 + angle_coeff @angle:cd-na-n2 harmonic 66.83 122.96 # SOURCE3 15 0.9350 + angle_coeff @angle:cd-na-n4 harmonic 65.90 120.31 # SOURCE3 10 3.4394 + angle_coeff @angle:cd-na-n harmonic 66.52 123.19 # SOURCE3 13 0.3010 + angle_coeff @angle:cd-na-na harmonic 65.91 123.43 # SOURCE3 23 0.2088 + angle_coeff @angle:cd-na-nc harmonic 66.41 126.22 # CORR 124 + angle_coeff @angle:cd-na-nd harmonic 70.18 113.02 # SOURCE3 38 2.2867 + angle_coeff @angle:cd-na-nh harmonic 66.23 122.25 # SOURCE3 19 0.2010 + angle_coeff @angle:cd-na-no harmonic 65.40 121.78 # SOURCE3 9 0.3521 + angle_coeff @angle:cd-na-o harmonic 69.01 125.21 # SOURCE3 10 0.0124 + angle_coeff @angle:cd-na-oh harmonic 66.67 122.38 # SOURCE3 10 0.1570 + angle_coeff @angle:cd-na-os harmonic 67.01 116.86 # CORR 48 + angle_coeff @angle:cd-na-p2 harmonic 75.29 125.86 # SOURCE3 14 2.2993 + angle_coeff @angle:cd-na-p3 harmonic 75.02 125.25 # SOURCE3 8 0.1998 + angle_coeff @angle:cd-na-p4 harmonic 81.11 127.73 # SOURCE3 7 same_as_cc-na-p4 + angle_coeff @angle:cd-na-p5 harmonic 76.81 124.70 # SOURCE3 13 1.4225 + angle_coeff @angle:cd-na-s4 harmonic 59.45 121.03 # SOURCE3 10 0.5589 + angle_coeff @angle:cd-na-s6 harmonic 60.98 122.19 # SOURCE3 10 0.9634 + angle_coeff @angle:cd-na-s harmonic 59.10 125.66 # SOURCE3 8 0.1880 + angle_coeff @angle:cd-na-sh harmonic 60.71 123.96 # SOURCE3 10 0.3424 + angle_coeff @angle:cd-na-ss harmonic 61.34 120.10 # CORR 44 + angle_coeff @angle:cl-na-cl harmonic 48.73 122.80 # SOURCE3 1 + angle_coeff @angle:cl-na-nc harmonic 55.70 119.36 # SOURCE3 4 1.7128 + angle_coeff @angle:cl-na-nd harmonic 55.70 119.36 # SOURCE3 4 same_as_cl-na-nc + angle_coeff @angle:cl-na-os harmonic 58.63 106.58 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-na-p2 harmonic 68.67 121.29 # SOURCE3 1 + angle_coeff @angle:cl-na-pc harmonic 69.19 120.51 # SOURCE3 3 2.1985 + angle_coeff @angle:cl-na-pd harmonic 69.19 120.51 # SOURCE3 3 same_as_cl-na-pc + angle_coeff @angle:cl-na-ss harmonic 56.71 111.91 # SOURCE3 1 0.0000 + angle_coeff @angle:f-na-f harmonic 62.22 120.20 # SOURCE3 1 + angle_coeff @angle:f-na-nc harmonic 66.64 118.05 # SOURCE3 4 1.7931 + angle_coeff @angle:f-na-nd harmonic 66.64 118.05 # SOURCE3 4 same_as_f-na-nc + angle_coeff @angle:f-na-os harmonic 69.15 103.86 # SOURCE3 1 0.0000 + angle_coeff @angle:f-na-p2 harmonic 75.54 119.95 # SOURCE3 1 + angle_coeff @angle:f-na-pc harmonic 76.37 119.10 # SOURCE3 3 2.3967 + angle_coeff @angle:f-na-pd harmonic 76.37 119.10 # SOURCE3 3 same_as_f-na-pc + angle_coeff @angle:f-na-ss harmonic 63.34 108.01 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-na-hn harmonic 39.83 116.80 # SOURCE3 1 + angle_coeff @angle:hn-na-n harmonic 50.90 111.26 # SOURCE4 5 1.1280 + angle_coeff @angle:hn-na-nc harmonic 50.00 119.61 # SOURCE3 16 1.8079 + angle_coeff @angle:hn-na-nd harmonic 50.00 119.61 # SOURCE3 16 1.8079 + angle_coeff @angle:hn-na-os harmonic 51.44 101.41 # SOURCE3 7 3.0814 + angle_coeff @angle:hn-na-p2 harmonic 51.02 122.52 # SOURCE3 1 + angle_coeff @angle:hn-na-pc harmonic 51.81 121.48 # SOURCE3 3 2.9355 + angle_coeff @angle:hn-na-pd harmonic 51.81 121.48 # SOURCE3 3 same_as_hn-na-pc + angle_coeff @angle:hn-na-ss harmonic 42.24 113.95 # SOURCE3 1 0.0000 + angle_coeff @angle:i-na-i harmonic 58.32 124.20 # SOURCE3 1 + angle_coeff @angle:i-na-nc harmonic 56.94 120.03 # SOURCE3 4 2.0032 + angle_coeff @angle:i-na-nd harmonic 56.94 120.03 # SOURCE3 4 same_as_i-na-nc + angle_coeff @angle:i-na-os harmonic 59.85 109.91 # SOURCE3 1 0.0000 + angle_coeff @angle:i-na-p2 harmonic 73.36 122.28 # SOURCE3 1 + angle_coeff @angle:i-na-pc harmonic 73.81 121.40 # SOURCE3 3 2.4763 + angle_coeff @angle:i-na-pd harmonic 73.81 121.40 # SOURCE3 3 same_as_i-na-pc + angle_coeff @angle:i-na-ss harmonic 59.04 118.40 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-na-n2 harmonic 70.35 116.71 # SOURCE3 1 + angle_coeff @angle:n2-na-nc harmonic 69.85 119.96 # SOURCE3 4 4.5041 + angle_coeff @angle:n2-na-nd harmonic 69.85 119.96 # SOURCE3 4 same_as_n2-na-nc + angle_coeff @angle:n2-na-os harmonic 70.33 111.53 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-na-p2 harmonic 77.46 124.88 # SOURCE3 1 + angle_coeff @angle:n2-na-pc harmonic 78.60 123.18 # SOURCE3 3 4.7947 + angle_coeff @angle:n2-na-pd harmonic 78.60 123.18 # SOURCE3 3 same_as_n2-na-pc + angle_coeff @angle:n2-na-ss harmonic 61.71 124.64 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-na-n3 harmonic 65.77 124.00 # SOURCE3 1 + angle_coeff @angle:n4-na-n4 harmonic 68.57 111.70 # SOURCE3 1 + angle_coeff @angle:n4-na-nc harmonic 69.09 116.44 # SOURCE3 4 3.6604 + angle_coeff @angle:n4-na-nd harmonic 69.09 116.44 # SOURCE3 4 same_as_n4-na-nc + angle_coeff @angle:n4-na-os harmonic 71.61 102.97 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-na-p2 harmonic 77.04 123.56 # SOURCE3 1 + angle_coeff @angle:n4-na-pc harmonic 78.10 121.98 # SOURCE3 3 4.4884 + angle_coeff @angle:n4-na-pd harmonic 78.10 121.98 # SOURCE3 3 same_as_n4-na-pc + angle_coeff @angle:na-na-na harmonic 66.77 123.60 # SOURCE3 1 + angle_coeff @angle:na-na-nc harmonic 69.08 119.64 # SOURCE3 4 1.6920 + angle_coeff @angle:na-na-nd harmonic 69.08 119.64 # SOURCE3 4 same_as_na-na-nc + angle_coeff @angle:na-na-os harmonic 70.25 109.47 # SOURCE3 1 0.0000 + angle_coeff @angle:na-na-p2 harmonic 78.07 121.72 # SOURCE3 1 + angle_coeff @angle:na-na-pc harmonic 78.92 120.91 # SOURCE3 3 2.3033 + angle_coeff @angle:na-na-pd harmonic 78.92 120.91 # SOURCE3 3 same_as_na-na-pc + angle_coeff @angle:na-na-ss harmonic 63.50 116.50 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-na-nc harmonic 71.20 117.08 # SOURCE3 31 1.8121 + angle_coeff @angle:nc-na-nd harmonic 69.53 122.77 # SOURCE4 5 0.1352 + angle_coeff @angle:nc-na-nh harmonic 68.82 120.55 # SOURCE3 8 1.1436 + angle_coeff @angle:nc-na-no harmonic 68.19 119.15 # SOURCE3 4 1.6049 + angle_coeff @angle:nc-na-o harmonic 72.04 122.79 # SOURCE3 6 1.3154 + angle_coeff @angle:nc-na-oh harmonic 69.71 119.22 # SOURCE3 4 1.7201 + angle_coeff @angle:nc-na-os harmonic 68.30 119.65 # SOURCE3 4 1.5019 + angle_coeff @angle:nc-na-p2 harmonic 79.23 119.99 # SOURCE3 4 3.6009 + angle_coeff @angle:nc-na-p3 harmonic 78.72 120.07 # SOURCE3 4 3.7188 + angle_coeff @angle:nc-na-p4 harmonic 86.25 119.77 # SOURCE3 3 0.3747 + angle_coeff @angle:nc-na-p5 harmonic 80.84 118.95 # SOURCE3 4 3.1194 + angle_coeff @angle:nc-na-pc harmonic 80.31 118.66 # SOURCE3 27 1.5082 + angle_coeff @angle:nc-na-s4 harmonic 61.52 119.20 # SOURCE3 4 2.3841 + angle_coeff @angle:nc-na-s6 harmonic 63.45 119.24 # SOURCE3 4 2.2262 + angle_coeff @angle:nc-na-s harmonic 61.55 122.26 # SOURCE3 4 0.9173 + angle_coeff @angle:nc-na-sh harmonic 63.29 120.50 # SOURCE3 4 1.5016 + angle_coeff @angle:nc-na-ss harmonic 62.94 120.50 # SOURCE3 4 1.5615 + angle_coeff @angle:nd-na-nd harmonic 71.20 117.08 # SOURCE3 31 1.8121 + angle_coeff @angle:nd-na-nh harmonic 68.82 120.55 # SOURCE3 8 same_as_nc-na-nh + angle_coeff @angle:nd-na-no harmonic 68.19 119.15 # SOURCE3 4 same_as_nc-na-no + angle_coeff @angle:nd-na-o harmonic 72.04 122.79 # SOURCE3 6 same_as_nc-na-o + angle_coeff @angle:nd-na-oh harmonic 69.71 119.22 # SOURCE3 4 same_as_nc-na-oh + angle_coeff @angle:nd-na-os harmonic 68.30 119.65 # SOURCE3 4 same_as_nc-na-os + angle_coeff @angle:nd-na-p2 harmonic 79.23 119.99 # SOURCE3 4 same_as_nc-na-p2 + angle_coeff @angle:nd-na-p3 harmonic 78.72 120.07 # SOURCE3 4 same_as_nc-na-p3 + angle_coeff @angle:nd-na-p4 harmonic 86.25 119.77 # SOURCE3 3 same_as_nc-na-p4 + angle_coeff @angle:nd-na-p5 harmonic 80.84 118.95 # SOURCE3 4 same_as_nc-na-p5 + angle_coeff @angle:nd-na-pd harmonic 80.31 118.66 # SOURCE3 27 same_as_nc-na-pc + angle_coeff @angle:nd-na-s4 harmonic 61.52 119.20 # SOURCE3 4 same_as_nc-na-s4 + angle_coeff @angle:nd-na-s6 harmonic 63.45 119.24 # SOURCE3 4 same_as_nc-na-s6 + angle_coeff @angle:nd-na-s harmonic 61.55 122.26 # SOURCE3 4 same_as_nc-na-s + angle_coeff @angle:nd-na-sh harmonic 63.29 120.50 # SOURCE3 4 same_as_nc-na-sh + angle_coeff @angle:nd-na-ss harmonic 62.94 120.50 # SOURCE3 4 same_as_nc-na-ss + angle_coeff @angle:nh-na-nh harmonic 66.77 123.60 # SOURCE3 1 + angle_coeff @angle:nh-na-os harmonic 69.65 111.37 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-na-p2 harmonic 78.35 120.86 # SOURCE3 1 + angle_coeff @angle:nh-na-pc harmonic 79.10 120.38 # SOURCE3 6 1.3513 + angle_coeff @angle:nh-na-pd harmonic 79.10 120.38 # SOURCE3 6 same_as_nh-na-pc + angle_coeff @angle:nh-na-ss harmonic 64.66 112.35 # SOURCE3 2 5.2951 + angle_coeff @angle:n-na-n harmonic 67.78 123.80 # SOURCE3 1 + angle_coeff @angle:n-na-nc harmonic 69.61 119.85 # SOURCE3 4 1.6156 + angle_coeff @angle:n-na-nd harmonic 69.61 119.85 # SOURCE3 4 same_as_n-na-nc + angle_coeff @angle:no-na-no harmonic 65.22 122.80 # SOURCE3 1 + angle_coeff @angle:no-na-os harmonic 70.30 106.55 # SOURCE3 1 0.0000 + angle_coeff @angle:no-na-pc harmonic 78.65 120.11 # SOURCE3 3 2.0821 + angle_coeff @angle:no-na-pd harmonic 78.65 120.11 # SOURCE3 3 same_as_no-na-pc + angle_coeff @angle:n-na-os harmonic 72.34 104.71 # SOURCE3 1 0.0000 + angle_coeff @angle:no-na-ss harmonic 63.49 114.95 # SOURCE3 1 0.0000 + angle_coeff @angle:n-na-p2 harmonic 78.46 121.35 # SOURCE3 1 + angle_coeff @angle:n-na-pc harmonic 79.30 120.64 # SOURCE3 3 2.0168 + angle_coeff @angle:n-na-pd harmonic 79.30 120.64 # SOURCE3 3 same_as_n-na-pc + angle_coeff @angle:n-na-ss harmonic 63.84 116.10 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-na-oh harmonic 68.13 122.20 # SOURCE3 1 + angle_coeff @angle:oh-na-p2 harmonic 78.88 120.76 # SOURCE3 1 + angle_coeff @angle:oh-na-pc harmonic 79.74 119.99 # SOURCE3 3 2.1734 + angle_coeff @angle:oh-na-pd harmonic 79.74 119.99 # SOURCE3 3 same_as_oh-na-pc + angle_coeff @angle:oh-na-ss harmonic 64.88 113.04 # SOURCE3 1 0.0000 + angle_coeff @angle:o-na-o harmonic 74.03 126.20 # SOURCE3 1 + angle_coeff @angle:o-na-os harmonic 70.76 118.39 # SOURCE3 1 0.0000 + angle_coeff @angle:o-na-p2 harmonic 79.51 122.80 # SOURCE3 1 + angle_coeff @angle:o-na-pc harmonic 80.36 122.34 # SOURCE3 3 1.2908 + angle_coeff @angle:o-na-pd harmonic 80.36 122.34 # SOURCE3 3 same_as_o-na-pc + angle_coeff @angle:os-na-os harmonic 71.29 104.45 # SOURCE3 2 0.0983 + angle_coeff @angle:os-na-p2 harmonic 79.21 117.86 # SOURCE3 1 0.0000 + angle_coeff @angle:os-na-p3 harmonic 83.58 104.70 # SOURCE3 1 0.0000 + angle_coeff @angle:os-na-p5 harmonic 82.64 111.41 # SOURCE3 1 0.0000 + angle_coeff @angle:os-na-pc harmonic 79.09 119.91 # SOURCE3 3 1.9002 + angle_coeff @angle:os-na-pd harmonic 79.09 119.91 # SOURCE3 3 same_as_os-na-pc + angle_coeff @angle:os-na-s4 harmonic 64.81 105.88 # SOURCE3 2 0.0000 + angle_coeff @angle:os-na-s6 harmonic 64.80 112.00 # SOURCE3 2 0.0000 + angle_coeff @angle:os-na-ss harmonic 65.33 109.64 # SOURCE3 3 4.1395 + angle_coeff @angle:p2-na-p2 harmonic 96.62 120.91 # SOURCE3 1 + angle_coeff @angle:p2-na-p3 harmonic 94.74 124.80 # SOURCE3 1 + angle_coeff @angle:p2-na-p5 harmonic 96.33 123.99 # SOURCE3 1 + angle_coeff @angle:p2-na-pc harmonic 97.16 120.72 # SOURCE3 3 0.2407 + angle_coeff @angle:p2-na-pd harmonic 97.16 120.72 # SOURCE3 3 same_as_p2-na-pc + angle_coeff @angle:p2-na-s4 harmonic 74.88 122.47 # SOURCE3 1 + angle_coeff @angle:p2-na-s6 harmonic 76.31 122.50 # SOURCE3 1 + angle_coeff @angle:p2-na-s harmonic 75.69 121.85 # SOURCE3 1 + angle_coeff @angle:p2-na-sh harmonic 76.68 121.75 # SOURCE3 1 + angle_coeff @angle:p2-na-ss harmonic 76.38 121.88 # SOURCE3 1 + angle_coeff @angle:p3-na-p3 harmonic 93.72 126.60 # SOURCE3 1 + angle_coeff @angle:p3-na-pc harmonic 95.76 123.32 # SOURCE3 3 4.1781 + angle_coeff @angle:p3-na-pd harmonic 95.76 123.32 # SOURCE3 3 same_as_p3-na-pc + angle_coeff @angle:p5-na-p5 harmonic 97.06 124.60 # SOURCE3 1 + angle_coeff @angle:p5-na-pc harmonic 97.33 122.69 # SOURCE3 3 3.6738 + angle_coeff @angle:p5-na-pd harmonic 97.33 122.69 # SOURCE3 3 same_as_p5-na-pc + angle_coeff @angle:p5-na-ss harmonic 78.22 118.52 # SOURCE3 1 0.0000 + angle_coeff @angle:pc-na-pc harmonic 97.62 120.78 # SOURCE3 27 1.6457 + angle_coeff @angle:pc-na-s4 harmonic 75.52 121.51 # SOURCE3 3 2.7242 + angle_coeff @angle:pc-na-s6 harmonic 76.99 121.55 # SOURCE3 3 2.7065 + angle_coeff @angle:pc-na-s harmonic 76.17 121.47 # SOURCE3 3 1.0668 + angle_coeff @angle:pc-na-sh harmonic 77.28 121.08 # SOURCE3 3 1.8942 + angle_coeff @angle:pc-na-ss harmonic 76.97 121.20 # SOURCE3 3 1.9295 + angle_coeff @angle:pd-na-pd harmonic 97.62 120.78 # SOURCE3 27 same_as_pc-na-pc + angle_coeff @angle:pd-na-s4 harmonic 75.52 121.51 # SOURCE3 3 same_as_pc-na-s4 + angle_coeff @angle:pd-na-s6 harmonic 76.99 121.55 # SOURCE3 3 same_as_pc-na-s6 + angle_coeff @angle:pd-na-s harmonic 76.17 121.47 # SOURCE3 3 same_as_pc-na-s + angle_coeff @angle:pd-na-sh harmonic 77.28 121.08 # SOURCE3 3 same_as_pc-na-sh + angle_coeff @angle:pd-na-ss harmonic 76.97 121.20 # SOURCE3 3 same_as_pc-na-ss + angle_coeff @angle:py-na-py harmonic 122.69 78.25 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-na-s4 harmonic 58.05 124.20 # SOURCE3 1 + angle_coeff @angle:s4-na-s6 harmonic 62.00 112.86 # SOURCE3 1 + angle_coeff @angle:s4-na-ss harmonic 62.16 111.92 # SOURCE3 1 0.0000 + angle_coeff @angle:s6-na-s6 harmonic 60.51 123.20 # SOURCE3 1 + angle_coeff @angle:s6-na-ss harmonic 61.44 119.10 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-na-sh harmonic 60.38 124.60 # SOURCE3 1 + angle_coeff @angle:sh-na-ss harmonic 61.63 118.79 # SOURCE3 1 0.0000 + angle_coeff @angle:s-na-s harmonic 58.55 126.00 # SOURCE3 1 + angle_coeff @angle:s-na-ss harmonic 62.52 112.49 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-na-ss harmonic 62.90 113.24 # SOURCE3 2 6.6084 + angle_coeff @angle:sy-na-sy harmonic 60.51 123.20 # SOURCE3 1 + angle_coeff @angle:ca-nb-ca harmonic 68.59 115.86 # SOURCE3 46 1.1645 + angle_coeff @angle:ca-nb-cp harmonic 68.01 118.04 # SOURCE4 58 0.7819 + angle_coeff @angle:ca-nb-cq harmonic 68.01 118.04 # SOURCE4 58 same as ca-nb-cp + angle_coeff @angle:ca-nb-nb harmonic 69.37 118.89 # SOURCE3 10 0.6031 + angle_coeff @angle:cp-nb-nb harmonic 68.79 121.11 # SOURCE4 12 0.4315 + angle_coeff @angle:nb-nb-nb harmonic 70.44 121.04 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n-br harmonic 66.59 116.20 # SOURCE3 1 0.0000 + angle_coeff @angle:br-n-c harmonic 61.85 120.77 # SOURCE3 5 2.6390 + angle_coeff @angle:br-n-ca harmonic 62.07 118.19 # SOURCE3 1 + angle_coeff @angle:br-n-cc harmonic 62.34 118.19 # SOURCE3 1 same_as_br-n-cd + angle_coeff @angle:br-n-cd harmonic 62.34 118.19 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-n-c1 harmonic 73.52 102.69 # SOURCE3 1 + angle_coeff @angle:c1-n-ca harmonic 65.90 118.88 # SOURCE3 1 + angle_coeff @angle:c1-n-cc harmonic 67.02 118.88 # SOURCE3 1 same_as_c1-n-cd + angle_coeff @angle:c1-n-cd harmonic 67.02 118.88 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n-c2 harmonic 65.18 116.75 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n-c3 harmonic 63.06 119.98 # SOURCE4 23 2.3373 + angle_coeff @angle:c2-n-ca harmonic 64.88 116.54 # SOURCE3 1 + angle_coeff @angle:c2-n-cc harmonic 65.85 116.54 # SOURCE3 1 same_as_c2-n-cd + angle_coeff @angle:c2-n-cd harmonic 65.85 116.54 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-n-hn harmonic 47.33 118.36 # SOURCE4 40 1.8005 + angle_coeff @angle:c3-n-c3 harmonic 63.13 115.56 # SOURCE4 392 2.0191 + angle_coeff @angle:c3-n-ca harmonic 62.76 119.96 # SOURCE4 165 2.0808 + angle_coeff @angle:c3-n-cc harmonic 63.33 121.00 # CORR 267 + angle_coeff @angle:c3-n-cd harmonic 63.33 121.00 # CORR 267 + angle_coeff @angle:c3-n-cy harmonic 62.51 117.11 # SOURCE4 49 1.0344 + angle_coeff @angle:c3-n-hn harmonic 46.04 116.78 # SOURCE3 39 2.1985 + angle_coeff @angle:c3-n-n2 harmonic 64.89 121.68 # SOURCE4 52 1.3175 + angle_coeff @angle:c3-n-n harmonic 66.40 114.82 # SOURCE4 9 0.7008 + angle_coeff @angle:c3-n-nc harmonic 66.97 115.21 # CORR 48 + angle_coeff @angle:c3-n-nd harmonic 66.97 115.21 # CORR 48 + angle_coeff @angle:c3-n-oh harmonic 66.88 113.05 # SOURCE4 31 0.8144 + angle_coeff @angle:c3-n-os harmonic 66.99 112.65 # SOURCE4 16 1.5399 + angle_coeff @angle:c3-n-sy harmonic 60.53 121.27 # SOURCE4 5 1.1298 + angle_coeff @angle:ca-n-ca harmonic 64.31 117.39 # SOURCE4 39 1.6465 + angle_coeff @angle:ca-n-cc harmonic 66.19 114.06 # CORR 34 + angle_coeff @angle:ca-n-cd harmonic 66.19 114.06 # CORR 34 + angle_coeff @angle:ca-n-cl harmonic 57.24 117.72 # SOURCE3 1 + angle_coeff @angle:ca-n-f harmonic 64.62 114.92 # SOURCE3 1 + angle_coeff @angle:ca-n-hn harmonic 47.36 115.94 # SOURCE4 537 1.8890 + angle_coeff @angle:ca-n-i harmonic 56.58 119.30 # SOURCE3 1 + angle_coeff @angle:ca-n-n2 harmonic 65.72 122.17 # SOURCE4 5 0.2545 + angle_coeff @angle:ca-n-n4 harmonic 64.15 122.98 # SOURCE3 1 + angle_coeff @angle:ca-n-n harmonic 66.30 118.54 # SOURCE4 21 0.3399 + angle_coeff @angle:ca-n-na harmonic 66.33 119.31 # SOURCE4 16 0.3168 + angle_coeff @angle:ca-n-nc harmonic 68.25 114.36 # CORR 6 + angle_coeff @angle:ca-n-nd harmonic 68.25 114.36 # CORR 6 + angle_coeff @angle:ca-n-nh harmonic 66.60 116.45 # SOURCE3 1 + angle_coeff @angle:ca-n-p2 harmonic 79.60 112.32 # SOURCE3 1 + angle_coeff @angle:ca-n-p3 harmonic 74.22 125.11 # SOURCE3 1 + angle_coeff @angle:ca-n-s4 harmonic 59.97 118.40 # SOURCE3 1 + angle_coeff @angle:ca-n-s6 harmonic 62.01 117.32 # SOURCE3 1 + angle_coeff @angle:ca-n-ss harmonic 62.15 116.60 # SOURCE3 1 + angle_coeff @angle:c-n-c1 harmonic 68.47 117.04 # SOURCE3 1 0.0000 + angle_coeff @angle:c-n-c2 harmonic 65.09 122.15 # SOURCE3 9 5.1016 + angle_coeff @angle:c-n-c3 harmonic 63.92 121.35 # SOURCE3 54 2.3808 + angle_coeff @angle:c3-nc-cd harmonic 67.60 109.51 # SOURCE3 9 5.4142 + angle_coeff @angle:c-n-c harmonic 65.33 127.14 # SOURCE4 514 2.0111 + angle_coeff @angle:c-n-ca harmonic 64.29 123.71 # SOURCE3 10 3.8159 + angle_coeff @angle:ca-nc-ca harmonic 70.73 109.95 # SOURCE3 1 + angle_coeff @angle:ca-nc-cd harmonic 72.43 104.94 # CORR 437 + angle_coeff @angle:ca-nc-n harmonic 73.68 104.69 # CORR 2 + angle_coeff @angle:ca-nc-na harmonic 74.57 102.74 # CORR 14 + angle_coeff @angle:ca-nc-os harmonic 73.08 104.48 # CORR 10 + angle_coeff @angle:ca-nc-ss harmonic 67.84 116.29 # SOURCE3 1 + angle_coeff @angle:c-n-cc harmonic 65.24 124.19 # SOURCE3 57 2.2262 + angle_coeff @angle:c-nc-ca harmonic 66.11 120.66 # CORR 2 + angle_coeff @angle:cc-n-cc harmonic 68.80 108.92 # SOURCE3 11 0.3167 + angle_coeff @angle:cc-nc-cc harmonic 70.50 104.34 # CORR 6 + angle_coeff @angle:cc-nc-cd harmonic 71.08 105.67 # CORR 1240 + angle_coeff @angle:c-nc-cd harmonic 66.18 120.48 # CORR 138 + angle_coeff @angle:cc-n-cl harmonic 57.67 117.72 # SOURCE3 1 same_as_cd-n-cl + angle_coeff @angle:cc-nc-na harmonic 73.38 102.97 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-nc-nd harmonic 72.54 107.94 # SOURCE3 6 1.4052 + angle_coeff @angle:c-n-cd harmonic 65.24 124.19 # SOURCE3 57 2.2262 + angle_coeff @angle:cd-nc-cd harmonic 68.53 117.28 # CORR 17 + angle_coeff @angle:cd-nc-n harmonic 69.66 117.19 # CORR 64 + angle_coeff @angle:cd-nc-na harmonic 74.24 103.73 # SOURCE3 122 2.3292 + angle_coeff @angle:cd-nc-nc harmonic 71.99 107.88 # CORR 355 + angle_coeff @angle:cd-nc-os harmonic 73.04 104.66 # CORR 116 + angle_coeff @angle:cd-nc-ss harmonic 70.36 108.15 # CORR 45 + angle_coeff @angle:c-n-ce harmonic 62.21 131.83 # SOURCE4 146 1.3048 + angle_coeff @angle:cc-n-f harmonic 65.61 114.92 # SOURCE3 1 same_as_cd-n-f + angle_coeff @angle:cc-n-hn harmonic 47.99 119.14 # CORR 276 + angle_coeff @angle:cc-n-i harmonic 56.61 119.30 # SOURCE3 1 same_as_cd-n-i + angle_coeff @angle:c-n-cl harmonic 58.34 116.35 # SOURCE4 11 0.6829 + angle_coeff @angle:cc-n-n2 harmonic 70.09 110.87 # SOURCE3 1 same_as_cd-n-n2 + angle_coeff @angle:cc-n-n harmonic 66.53 121.37 # SOURCE3 1 same_as_cd-n-n + angle_coeff @angle:cc-n-na harmonic 67.87 117.57 # SOURCE3 1 same_as_cd-n-na + angle_coeff @angle:cc-n-nc harmonic 70.08 112.03 # CORR 14 + angle_coeff @angle:cc-n-nh harmonic 67.30 117.52 # SOURCE3 1 same_as_cd-n-nh + angle_coeff @angle:cc-n-no harmonic 66.40 115.92 # SOURCE3 1 same_as_cd-n-no + angle_coeff @angle:cc-n-o harmonic 70.07 120.54 # SOURCE3 1 same_as_cd-n-o + angle_coeff @angle:cc-n-oh harmonic 67.32 118.15 # SOURCE3 1 same_as_cd-n-oh + angle_coeff @angle:cc-n-os harmonic 68.06 115.56 # SOURCE3 1 same_as_cd-n-os + angle_coeff @angle:cc-n-p2 harmonic 80.17 112.32 # SOURCE3 1 same_as_cd-n-p2 + angle_coeff @angle:cc-n-p3 harmonic 74.70 125.11 # SOURCE3 1 same_as_cd-n-p3 + angle_coeff @angle:cc-n-p5 harmonic 78.11 121.00 # SOURCE3 1 same_as_cd-n-p5 + angle_coeff @angle:cc-n-s4 harmonic 60.34 118.40 # SOURCE3 1 same_as_cd-n-s4 + angle_coeff @angle:cc-n-s6 harmonic 62.48 117.32 # SOURCE3 1 same_as_cd-n-s6 + angle_coeff @angle:cc-n-s harmonic 60.78 118.29 # SOURCE3 1 same_as_cd-n-s + angle_coeff @angle:cc-n-sh harmonic 61.64 119.13 # SOURCE3 1 same_as_cd-n-sh + angle_coeff @angle:cc-n-ss harmonic 62.62 116.60 # SOURCE3 2 same_as_cd-n-ss + angle_coeff @angle:c-n-cx harmonic 64.22 122.07 # SOURCE4 11 1.9478 + angle_coeff @angle:c-n-cy harmonic 72.26 94.23 # SOURCE4 270 1.3777 + angle_coeff @angle:cd-n-cd harmonic 68.80 108.92 # SOURCE3 11 same_as_cc-n-cc + angle_coeff @angle:cd-n-cl harmonic 57.67 117.72 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-f harmonic 65.61 114.92 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-hn harmonic 47.99 119.14 # CORR 276 + angle_coeff @angle:cd-n-i harmonic 56.61 119.30 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-n2 harmonic 70.09 110.87 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-n harmonic 66.53 121.37 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-na harmonic 67.87 117.57 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-nd harmonic 70.08 112.03 # CORR 14 + angle_coeff @angle:cd-n-nh harmonic 67.30 117.52 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-no harmonic 66.40 115.92 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-o harmonic 70.07 120.54 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-oh harmonic 67.32 118.15 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-os harmonic 68.06 115.56 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-p2 harmonic 80.17 112.32 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-p3 harmonic 74.70 125.11 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-p5 harmonic 78.11 121.00 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-s4 harmonic 60.34 118.40 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-s6 harmonic 62.48 117.32 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-s harmonic 60.78 118.29 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-sh harmonic 61.64 119.13 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-n-ss harmonic 62.62 116.60 # SOURCE3 2 1.8318 + angle_coeff @angle:ce-n-cy harmonic 64.70 111.89 # CORR 152 + angle_coeff @angle:c-n-f harmonic 68.30 108.63 # SOURCE3 3 4.6785 + angle_coeff @angle:cf-n-cy harmonic 64.70 111.89 # CORR 152 + angle_coeff @angle:c-n-hn harmonic 49.21 118.46 # SOURCE3 157 2.4094 + angle_coeff @angle:c-n-i harmonic 56.34 120.38 # SOURCE3 5 2.1600 + angle_coeff @angle:cl-n-cl harmonic 54.70 111.69 # SOURCE3 1 0.0000 + angle_coeff @angle:c-n-n2 harmonic 68.06 120.59 # SOURCE3 9 3.2410 + angle_coeff @angle:c-n-n3 harmonic 67.13 120.43 # SOURCE3 5 0.9481 + angle_coeff @angle:c-n-n4 harmonic 68.85 112.32 # SOURCE3 5 1.2622 + angle_coeff @angle:c-n-n harmonic 68.18 118.42 # SOURCE3 10 2.8922 + angle_coeff @angle:c-n-na harmonic 68.25 119.20 # SOURCE3 11 2.3032 + angle_coeff @angle:na-nc-nd harmonic 75.97 105.47 # SOURCE3 6 0.6349 + angle_coeff @angle:c-n-nc harmonic 67.16 125.19 # CORR 84 + angle_coeff @angle:nc-nc-nd harmonic 73.11 111.29 # CORR 61 + angle_coeff @angle:c-n-nd harmonic 67.16 125.19 # CORR 84 + angle_coeff @angle:nd-nc-os harmonic 74.42 107.22 # SOURCE3 3 0.4707 + angle_coeff @angle:c-n-nh harmonic 68.02 117.81 # SOURCE4 21 1.5935 + angle_coeff @angle:c-n-no harmonic 66.47 118.16 # SOURCE3 4 5.4870 + angle_coeff @angle:c-n-o harmonic 71.64 118.90 # SOURCE3 9 5.4085 + angle_coeff @angle:c-n-oh harmonic 69.53 113.39 # SOURCE3 6 1.3345 + angle_coeff @angle:c-n-os harmonic 69.60 113.14 # SOURCE3 7 3.0839 + angle_coeff @angle:c-n-p2 harmonic 76.53 124.56 # SOURCE3 8 3.6907 + angle_coeff @angle:c-n-p3 harmonic 75.82 122.54 # SOURCE3 9 4.4802 + angle_coeff @angle:c-n-p4 harmonic 76.84 123.44 # SOURCE3 1 0.0000 + angle_coeff @angle:c-n-p5 harmonic 76.23 128.50 # SOURCE4 6 0.5353 + angle_coeff @angle:c-n-pc harmonic 77.00 122.23 # SOURCE3 3 2.8787 + angle_coeff @angle:c-n-pd harmonic 77.00 122.23 # SOURCE3 3 same_as_c-n-pc + angle_coeff @angle:c-n-s4 harmonic 60.09 120.41 # SOURCE3 4 3.1760 + angle_coeff @angle:c-n-s6 harmonic 60.86 125.01 # SOURCE4 13 1.6314 + angle_coeff @angle:c-n-s harmonic 59.04 126.55 # SOURCE3 3 4.3365 + angle_coeff @angle:c-n-sh harmonic 61.87 119.54 # SOURCE3 4 1.7681 + angle_coeff @angle:c-n-ss harmonic 61.97 120.37 # SOURCE3 7 1.4450 + angle_coeff @angle:c-n-sy harmonic 60.91 124.81 # SOURCE4 51 1.0517 + angle_coeff @angle:cx-n-hn harmonic 46.26 118.58 # SOURCE4 5 0.3288 + angle_coeff @angle:cx-n-os harmonic 97.40 54.04 # SOURCE3 1 0.0000 + angle_coeff @angle:cy-n-hn harmonic 45.34 119.00 # SOURCE4 65 1.3840 + angle_coeff @angle:c3-nd-cc harmonic 67.60 109.51 # SOURCE3 9 same_as_c3-nc-cd + angle_coeff @angle:ca-nd-ca harmonic 70.73 109.95 # SOURCE3 1 same_as_ca-nc-ca + angle_coeff @angle:ca-nd-cc harmonic 72.43 104.94 # CORR 437 + angle_coeff @angle:ca-nd-n harmonic 73.68 104.69 # CORR 2 + angle_coeff @angle:ca-nd-na harmonic 74.57 102.74 # CORR 14 + angle_coeff @angle:ca-nd-nc harmonic 73.55 108.41 # SOURCE4 9 0.1575 + angle_coeff @angle:ca-nd-os harmonic 73.08 104.48 # CORR 10 + angle_coeff @angle:ca-nd-ss harmonic 67.84 116.29 # SOURCE3 1 same_as_ca-nc-ss + angle_coeff @angle:c-nd-ca harmonic 66.11 120.66 # CORR 2 + angle_coeff @angle:c-nd-cc harmonic 66.18 120.48 # CORR 138 + angle_coeff @angle:cc-nd-cc harmonic 68.53 117.28 # CORR 17 + angle_coeff @angle:cc-nd-cd harmonic 71.08 105.67 # CORR 1240 + angle_coeff @angle:cc-nd-n harmonic 69.66 117.19 # CORR 64 + angle_coeff @angle:cc-nd-na harmonic 74.24 103.73 # SOURCE3 122 2.3292 + angle_coeff @angle:cc-nd-nd harmonic 71.99 107.88 # CORR 355 + angle_coeff @angle:cc-nd-os harmonic 73.04 104.66 # CORR 116 + angle_coeff @angle:cc-nd-ss harmonic 70.36 108.15 # CORR 45 + angle_coeff @angle:cd-nd-cd harmonic 70.50 104.34 # CORR 6 + angle_coeff @angle:cd-nd-na harmonic 73.38 102.97 # SOURCE3 1 same_as_cc-nc-na + angle_coeff @angle:cd-nd-nc harmonic 72.54 107.94 # SOURCE3 6 1.4052 + angle_coeff @angle:na-nd-nc harmonic 75.97 105.47 # SOURCE3 6 0.6349 + angle_coeff @angle:nc-nd-nd harmonic 73.11 111.29 # CORR 61 + angle_coeff @angle:nc-nd-os harmonic 74.42 107.22 # SOURCE3 3 same_as_nd-nc-os + angle_coeff @angle:c1-ne-ca harmonic 60.41 150.84 # CORR 9 + angle_coeff @angle:c1-ne-cg harmonic 66.00 140.00 # SOURCE2 1 0.0000 + angle_coeff @angle:c2-ne-ca harmonic 66.09 120.84 # CORR 55 + angle_coeff @angle:c2-ne-ce harmonic 67.33 118.17 # SOURCE3 3 1.2374 + angle_coeff @angle:c2-ne-cg harmonic 68.36 123.58 # SOURCE4 12 0.8560 + angle_coeff @angle:c2-ne-n2 harmonic 74.56 113.31 # SOURCE3 1 + angle_coeff @angle:c2-ne-ne harmonic 69.17 110.86 # SOURCE3 7 4.5874 + angle_coeff @angle:c2-ne-p2 harmonic 80.83 134.03 # SOURCE3 1 + angle_coeff @angle:c2-ne-pe harmonic 79.24 120.52 # SOURCE3 8 8.1381 + angle_coeff @angle:c2-ne-px harmonic 80.57 117.75 # SOURCE3 5 0.8581 + angle_coeff @angle:c2-ne-py harmonic 84.33 117.04 # SOURCE3 3 1.4398 + angle_coeff @angle:c2-ne-sx harmonic 60.95 111.98 # SOURCE3 3 0.4090 + angle_coeff @angle:c2-ne-sy harmonic 61.78 118.92 # CORR 9 + angle_coeff @angle:ca-ne-cf harmonic 65.56 121.98 # CORR 15 + angle_coeff @angle:ca-ne-n2 harmonic 69.73 114.06 # CORR 11 + angle_coeff @angle:ca-ne-nf harmonic 69.69 115.12 # CORR 44 + angle_coeff @angle:ca-ne-o harmonic 71.10 113.96 # SOURCE3 3 1.1253 + angle_coeff @angle:ca-ne-p2 harmonic 83.08 118.09 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-ne-s harmonic 65.75 120.11 # SOURCE3 1 0.0000 + angle_coeff @angle:c-ne-c2 harmonic 67.85 118.53 # CORR 6 + angle_coeff @angle:ce-ne-n2 harmonic 71.16 111.19 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-ne-o harmonic 72.26 112.16 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-ne-p2 harmonic 83.85 117.02 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-ne-s harmonic 67.15 116.28 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-ne-n1 harmonic 71.71 120.20 # SOURCE2 1 0.0000 + angle_coeff @angle:cg-ne-n2 harmonic 73.16 113.39 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-ne-o harmonic 74.43 114.70 # SOURCE2 1 0.0000 + angle_coeff @angle:cg-ne-p2 harmonic 84.75 119.57 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-ne-s harmonic 68.28 117.70 # SOURCE3 1 0.0000 + angle_coeff @angle:c-ne-sy harmonic 61.66 116.05 # SOURCE4 6 1.2661 + angle_coeff @angle:n2-ne-n2 harmonic 78.59 107.22 # SOURCE3 1 + angle_coeff @angle:n2-ne-ne harmonic 70.94 110.72 # SOURCE3 9 6.1488 + angle_coeff @angle:n2-ne-o harmonic 78.09 114.10 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-ne-p2 harmonic 91.59 109.66 # SOURCE3 1 + angle_coeff @angle:n2-ne-pe harmonic 84.18 112.15 # SOURCE3 7 6.5273 + angle_coeff @angle:n2-ne-px harmonic 83.20 115.97 # SOURCE3 3 1.9854 + angle_coeff @angle:n2-ne-py harmonic 87.34 114.60 # SOURCE3 3 2.9261 + angle_coeff @angle:n2-ne-s harmonic 71.27 115.90 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-ne-sx harmonic 63.80 107.29 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-ne-sy harmonic 65.46 111.21 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-ne-o harmonic 72.28 110.45 # SOURCE3 10 1.8535 + angle_coeff @angle:ne-ne-p2 harmonic 85.32 114.39 # SOURCE3 6 4.0528 + angle_coeff @angle:ne-ne-s harmonic 67.59 115.95 # SOURCE3 6 3.4604 + angle_coeff @angle:o-ne-o harmonic 76.91 124.09 # SOURCE3 2 8.7534 + angle_coeff @angle:o-ne-pe harmonic 78.32 132.32 # SOURCE3 11 23.9559 + angle_coeff @angle:o-ne-px harmonic 86.11 110.62 # SOURCE3 1 0.0000 + angle_coeff @angle:o-ne-py harmonic 90.01 110.79 # SOURCE3 4 1.6818 + angle_coeff @angle:o-ne-s harmonic 71.99 117.19 # SOURCE3 2 0.0225 + angle_coeff @angle:o-ne-sx harmonic 63.79 108.92 # SOURCE3 1 0.0000 + angle_coeff @angle:o-ne-sy harmonic 66.05 111.34 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-ne-pe harmonic 104.56 116.81 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-ne-px harmonic 100.10 128.35 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-ne-py harmonic 105.15 123.47 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-ne-sx harmonic 80.48 112.12 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-ne-sy harmonic 81.80 115.73 # SOURCE3 1 0.0000 + angle_coeff @angle:pe-ne-s harmonic 83.52 115.73 # SOURCE3 1 0.0000 + angle_coeff @angle:px-ne-s harmonic 78.54 131.84 # SOURCE3 1 0.0000 + angle_coeff @angle:py-ne-s harmonic 86.30 116.18 # SOURCE3 4 3.7135 + angle_coeff @angle:s-ne-s harmonic 68.65 120.87 # SOURCE3 1 0.0000 + angle_coeff @angle:s-ne-sx harmonic 63.66 112.96 # SOURCE3 1 0.0000 + angle_coeff @angle:s-ne-sy harmonic 63.94 119.63 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-nf-ca harmonic 60.41 150.84 # CORR 9 + angle_coeff @angle:c1-nf-ch harmonic 66.00 140.00 # SOURCE2 1 same_as_c1-ne-cg + angle_coeff @angle:c2-nf-ca harmonic 66.09 120.84 # CORR 55 + angle_coeff @angle:c2-nf-cf harmonic 67.33 118.17 # SOURCE3 3 same_as_c2-ne-ce + angle_coeff @angle:c2-nf-n2 harmonic 74.56 113.31 # SOURCE3 1 same_as_c2-ne-n2 + angle_coeff @angle:c2-nf-nf harmonic 69.17 110.86 # SOURCE3 7 same_as_c2-ne-ne + angle_coeff @angle:c2-nf-p2 harmonic 80.83 134.03 # SOURCE3 1 same_as_c2-ne-p2 + angle_coeff @angle:c2-nf-pf harmonic 79.24 120.52 # SOURCE3 8 same_as_c2-ne-pe + angle_coeff @angle:c2-nf-px harmonic 80.57 117.75 # SOURCE3 5 same_as_c2-ne-px + angle_coeff @angle:c2-nf-py harmonic 84.33 117.04 # SOURCE3 3 same_as_c2-ne-py + angle_coeff @angle:c2-nf-sx harmonic 60.95 111.98 # SOURCE3 3 same_as_c2-ne-sx + angle_coeff @angle:c2-nf-sy harmonic 61.78 118.92 # CORR 9 + angle_coeff @angle:ca-nf-ce harmonic 65.56 121.98 # CORR 15 + angle_coeff @angle:ca-nf-n2 harmonic 69.73 114.06 # CORR 11 + angle_coeff @angle:ca-nf-ne harmonic 69.69 115.12 # CORR 44 + angle_coeff @angle:ca-nf-o harmonic 71.10 113.96 # SOURCE3 3 same_as_ca-ne-o + angle_coeff @angle:ca-nf-p2 harmonic 83.08 118.09 # SOURCE3 1 same_as_ca-ne-p2 + angle_coeff @angle:ca-nf-s harmonic 65.75 120.11 # SOURCE3 1 same_as_ca-ne-s + angle_coeff @angle:c-nf-c2 harmonic 67.85 118.53 # CORR 6 + angle_coeff @angle:cf-nf-n2 harmonic 71.16 111.19 # SOURCE3 1 same_as_ce-ne-n2 + angle_coeff @angle:cf-nf-o harmonic 72.26 112.16 # SOURCE3 1 same_as_ce-ne-o + angle_coeff @angle:cf-nf-p2 harmonic 83.85 117.02 # SOURCE3 1 same_as_ce-ne-p2 + angle_coeff @angle:cf-nf-s harmonic 67.15 116.28 # SOURCE3 1 same_as_ce-ne-s + angle_coeff @angle:ch-nf-n1 harmonic 71.71 120.20 # SOURCE2 1 same_as_cg-ne-n1 + angle_coeff @angle:ch-nf-n2 harmonic 73.16 113.39 # SOURCE3 1 same_as_cg-ne-n2 + angle_coeff @angle:ch-nf-o harmonic 74.43 114.70 # SOURCE2 1 same_as_cg-ne-o + angle_coeff @angle:ch-nf-p2 harmonic 84.75 119.57 # SOURCE3 1 same_as_cg-ne-p2 + angle_coeff @angle:ch-nf-s harmonic 68.28 117.70 # SOURCE3 1 same_as_cg-ne-s + angle_coeff @angle:f-n-f harmonic 67.90 102.98 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-nf-n2 harmonic 78.59 107.22 # SOURCE3 1 same_as_n2-ne-n2 + angle_coeff @angle:n2-nf-nf harmonic 70.94 110.72 # SOURCE3 9 same_as_n2-ne-ne + angle_coeff @angle:n2-nf-o harmonic 78.09 114.10 # SOURCE3 1 same_as_n2-ne-o + angle_coeff @angle:n2-nf-p2 harmonic 91.59 109.66 # SOURCE3 1 same_as_n2-ne-p2 + angle_coeff @angle:n2-nf-pf harmonic 84.18 112.15 # SOURCE3 7 same_as_n2-ne-pe + angle_coeff @angle:n2-nf-px harmonic 83.20 115.97 # SOURCE3 3 same_as_n2-ne-px + angle_coeff @angle:n2-nf-py harmonic 87.34 114.60 # SOURCE3 3 same_as_n2-ne-py + angle_coeff @angle:n2-nf-s harmonic 71.27 115.90 # SOURCE3 1 same_as_n2-ne-s + angle_coeff @angle:n2-nf-sx harmonic 63.80 107.29 # SOURCE3 1 same_as_n2-ne-sx + angle_coeff @angle:n2-nf-sy harmonic 65.46 111.21 # SOURCE3 1 same_as_n2-ne-sy + angle_coeff @angle:nf-nf-o harmonic 72.28 110.45 # SOURCE3 10 same_as_ne-ne-o + angle_coeff @angle:nf-nf-p2 harmonic 85.32 114.39 # SOURCE3 6 same_as_ne-ne-p2 + angle_coeff @angle:nf-nf-s harmonic 67.59 115.95 # SOURCE3 6 same_as_ne-ne-s + angle_coeff @angle:o-nf-o harmonic 76.91 124.09 # SOURCE3 2 same_as_o-ne-o + angle_coeff @angle:o-nf-pf harmonic 78.32 132.32 # SOURCE3 11 same_as_o-ne-pe + angle_coeff @angle:o-nf-px harmonic 86.11 110.62 # SOURCE3 1 same_as_o-ne-px + angle_coeff @angle:o-nf-py harmonic 90.01 110.79 # SOURCE3 4 same_as_o-ne-py + angle_coeff @angle:o-nf-s harmonic 71.99 117.19 # SOURCE3 2 same_as_o-ne-s + angle_coeff @angle:o-nf-sx harmonic 63.79 108.92 # SOURCE3 1 same_as_o-ne-sx + angle_coeff @angle:o-nf-sy harmonic 66.05 111.34 # SOURCE3 1 same_as_o-ne-sy + angle_coeff @angle:p2-nf-pf harmonic 104.56 116.81 # SOURCE3 1 same_as_p2-ne-pe + angle_coeff @angle:p2-nf-px harmonic 100.10 128.35 # SOURCE3 1 same_as_p2-ne-px + angle_coeff @angle:p2-nf-py harmonic 105.15 123.47 # SOURCE3 1 same_as_p2-ne-py + angle_coeff @angle:p2-nf-sx harmonic 80.48 112.12 # SOURCE3 1 same_as_p2-ne-sx + angle_coeff @angle:p2-nf-sy harmonic 81.80 115.73 # SOURCE3 1 same_as_p2-ne-sy + angle_coeff @angle:pf-nf-s harmonic 83.52 115.73 # SOURCE3 1 same_as_pe-ne-s + angle_coeff @angle:px-nf-s harmonic 78.54 131.84 # SOURCE3 1 same_as_px-ne-s + angle_coeff @angle:py-nf-s harmonic 86.30 116.18 # SOURCE3 4 same_as_py-ne-s + angle_coeff @angle:s-nf-s harmonic 68.65 120.87 # SOURCE3 1 same_as_s-ne-s + angle_coeff @angle:s-nf-sx harmonic 63.66 112.96 # SOURCE3 1 same_as_s-ne-sx + angle_coeff @angle:s-nf-sy harmonic 63.94 119.63 # SOURCE3 1 same_as_s-ne-sy + angle_coeff @angle:br-nh-br harmonic 67.09 106.27 # SOURCE3 1 + angle_coeff @angle:br-nh-ca harmonic 62.04 111.88 # SOURCE3 1 0.0000 + angle_coeff @angle:br-nh-hn harmonic 42.11 101.56 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-nh-c1 harmonic 68.33 116.98 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-nh-c2 harmonic 66.36 122.71 # SOURCE4 5 1.0077 + angle_coeff @angle:c1-nh-ca harmonic 66.22 122.36 # SOURCE3 3 1.2016 + angle_coeff @angle:c1-nh-hn harmonic 49.55 117.30 # SOURCE4 8 0.7120 + angle_coeff @angle:c2-nh-c2 harmonic 65.54 124.50 # SOURCE4 43 1.7515 + angle_coeff @angle:c2-nh-c3 harmonic 63.17 123.71 # SOURCE3 8 3.5348 + angle_coeff @angle:c2-nh-ca harmonic 64.59 127.34 # SOURCE4 97 2.4321 + angle_coeff @angle:c2-nh-cc harmonic 64.92 126.03 # CORR 11 + angle_coeff @angle:c2-nh-cd harmonic 64.92 126.03 # CORR 11 + angle_coeff @angle:c2-nh-cx harmonic 63.08 124.44 # SOURCE4 10 1.6817 + angle_coeff @angle:c2-nh-hn harmonic 49.62 114.89 # SOURCE4 1000 1.4571 + angle_coeff @angle:c2-nh-n2 harmonic 68.36 120.00 # SOURCE4 33 1.1823 + angle_coeff @angle:c2-nh-n3 harmonic 67.57 116.98 # SOURCE4 14 1.4183 + angle_coeff @angle:c2-nh-no harmonic 66.09 125.63 # SOURCE4 7 0.7554 + angle_coeff @angle:c2-nh-oh harmonic 69.45 112.51 # SOURCE4 12 1.1687 + angle_coeff @angle:c2-nh-os harmonic 69.27 112.93 # SOURCE4 6 0.3945 + angle_coeff @angle:c2-nh-sy harmonic 61.76 121.13 # SOURCE4 10 0.5133 + angle_coeff @angle:c3-nh-c3 harmonic 63.53 114.44 # SOURCE4 523 2.1428 + angle_coeff @angle:c3-nh-ca harmonic 64.56 117.77 # SOURCE3 8 1.7521 + angle_coeff @angle:c3-nh-cc harmonic 64.17 119.23 # CORR 163 + angle_coeff @angle:c3-nh-cd harmonic 64.17 119.23 # CORR 163 + angle_coeff @angle:c3-nh-cf harmonic 63.47 119.92 # SOURCE4 20 1.8571 + angle_coeff @angle:c3-nh-cz harmonic 63.01 125.51 # SOURCE4 12 0.5177 + angle_coeff @angle:c3-nh-hn harmonic 46.46 114.95 # SOURCE3 19 2.4787 + angle_coeff @angle:c3-nh-n2 harmonic 67.89 112.35 # SOURCE3 9 4.0058 + angle_coeff @angle:c3-nh-n harmonic 67.10 111.71 # SOURCE4 6 2.4251 + angle_coeff @angle:c3-nh-na harmonic 66.92 112.43 # SOURCE4 8 1.4219 + angle_coeff @angle:c3-nh-p2 harmonic 77.12 123.35 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-nh-sy harmonic 61.91 116.12 # SOURCE4 13 1.2830 + angle_coeff @angle:ca-nh-ca harmonic 64.34 127.46 # SOURCE3 2 0.0002 + angle_coeff @angle:ca-nh-cc harmonic 63.77 129.77 # CORR 38 + angle_coeff @angle:ca-nh-cd harmonic 63.77 129.77 # CORR 38 + angle_coeff @angle:ca-nh-cl harmonic 57.67 113.15 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-nh-cx harmonic 63.11 123.63 # SOURCE4 36 0.5899 + angle_coeff @angle:ca-nh-f harmonic 67.90 106.09 # SOURCE3 3 1.0660 + angle_coeff @angle:ca-nh-hn harmonic 49.08 116.13 # SOURCE4 1780 1.2853 + angle_coeff @angle:ca-nh-i harmonic 55.55 117.83 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-nh-n1 harmonic 69.37 117.13 # HF/6-31G* 1 + angle_coeff @angle:ca-nh-n2 harmonic 67.82 121.11 # SOURCE4 19 0.9700 + angle_coeff @angle:ca-nh-n3 harmonic 68.18 114.21 # SOURCE3 6 2.2412 + angle_coeff @angle:ca-nh-n4 harmonic 68.56 108.94 # SOURCE3 5 0.6562 + angle_coeff @angle:ca-nh-n harmonic 68.07 116.15 # SOURCE4 12 0.8135 + angle_coeff @angle:ca-nh-na harmonic 68.58 114.54 # SOURCE3 8 0.7807 + angle_coeff @angle:ca-nh-nh harmonic 68.49 114.87 # SOURCE3 6 2.1432 + angle_coeff @angle:ca-nh-no harmonic 69.19 113.92 # SOURCE3 4 2.9561 + angle_coeff @angle:ca-nh-o harmonic 69.64 121.92 # SOURCE3 2 3.9630 + angle_coeff @angle:ca-nh-oh harmonic 69.15 112.80 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-nh-os harmonic 69.93 110.17 # SOURCE3 3 0.6448 + angle_coeff @angle:ca-nh-p2 harmonic 77.99 125.27 # SOURCE3 8 5.1798 + angle_coeff @angle:ca-nh-p3 harmonic 76.07 125.70 # SOURCE3 3 5.7796 + angle_coeff @angle:ca-nh-p4 harmonic 77.43 124.01 # SOURCE3 3 2.5810 + angle_coeff @angle:ca-nh-p5 harmonic 78.16 125.61 # SOURCE3 3 0.5287 + angle_coeff @angle:ca-nh-s4 harmonic 62.13 115.62 # SOURCE3 3 0.3434 + angle_coeff @angle:ca-nh-s6 harmonic 61.56 123.53 # SOURCE4 33 2.0385 + angle_coeff @angle:ca-nh-s harmonic 59.38 122.54 # SOURCE3 3 2.7001 + angle_coeff @angle:ca-nh-sh harmonic 61.78 121.41 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-nh-ss harmonic 61.75 121.50 # SOURCE3 3 2.6255 + angle_coeff @angle:ca-nh-sy harmonic 60.64 125.26 # SOURCE4 41 1.7517 + angle_coeff @angle:cc-nh-cx harmonic 63.09 123.72 # CORR 58 + angle_coeff @angle:cc-nh-hn harmonic 48.86 117.16 # SOURCE3 11 2.6137 + angle_coeff @angle:cc-nh-n2 harmonic 68.23 119.66 # SOURCE4 5 1.3903 + angle_coeff @angle:cc-nh-sy harmonic 61.22 122.91 # SOURCE4 23 1.2029 + angle_coeff @angle:cd-nh-cx harmonic 63.09 123.72 # CORR 58 + angle_coeff @angle:cd-nh-hn harmonic 48.86 117.16 # SOURCE3 11 2.6137 + angle_coeff @angle:ce-nh-hn harmonic 48.38 115.62 # CORR 203 + angle_coeff @angle:ce-nh-o harmonic 66.85 129.43 # CORR 2 + angle_coeff @angle:ce-nh-sy harmonic 63.58 112.97 # SOURCE4 7 1.0636 + angle_coeff @angle:cf-nh-hn harmonic 48.38 115.62 # CORR 203 + angle_coeff @angle:cf-nh-o harmonic 66.85 129.43 # CORR 2 + angle_coeff @angle:cl-nh-cl harmonic 54.43 106.60 # SOURCE3 1 + angle_coeff @angle:cl-nh-hn harmonic 40.07 104.14 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-nh-cx harmonic 86.53 62.02 # SOURCE4 45 0.6189 + angle_coeff @angle:cx-nh-hn harmonic 45.79 118.89 # SOURCE4 8 0.1391 + angle_coeff @angle:cz-nh-hn harmonic 48.79 121.24 # SOURCE4 40 0.5682 + angle_coeff @angle:f-nh-f harmonic 66.93 101.70 # SOURCE3 1 0.0000 + angle_coeff @angle:f-nh-hn harmonic 49.80 101.23 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-nh-hn harmonic 40.05 114.85 # SOURCE4 1108 2.0811 + angle_coeff @angle:hn-nh-i harmonic 36.55 107.57 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-nh-n1 harmonic 52.31 110.57 # HF/6-31G* 1 + angle_coeff @angle:hn-nh-n2 harmonic 50.08 118.22 # SOURCE4 75 2.3319 + angle_coeff @angle:hn-nh-n3 harmonic 50.05 109.12 # SOURCE3 5 2.3680 + angle_coeff @angle:hn-nh-n4 harmonic 49.69 104.40 # SOURCE3 3 0.5056 + angle_coeff @angle:hn-nh-n harmonic 50.89 107.96 # SOURCE4 16 1.2025 + angle_coeff @angle:hn-nh-na harmonic 50.95 107.91 # SOURCE3 26 1.5528 + angle_coeff @angle:hn-nh-nh harmonic 50.32 110.64 # SOURCE4 8 1.3390 + angle_coeff @angle:hn-nh-no harmonic 50.99 109.93 # SOURCE4 7 0.2027 + angle_coeff @angle:hn-nh-o harmonic 52.99 116.45 # SOURCE3 2 0.6063 + angle_coeff @angle:hn-nh-oh harmonic 51.13 106.55 # SOURCE4 8 0.4590 + angle_coeff @angle:hn-nh-os harmonic 51.51 104.76 # SOURCE3 3 0.4883 + angle_coeff @angle:hn-nh-p2 harmonic 54.38 118.18 # SOURCE3 21 3.6927 + angle_coeff @angle:hn-nh-p3 harmonic 53.06 116.19 # SOURCE3 3 3.0539 + angle_coeff @angle:hn-nh-p4 harmonic 54.74 112.60 # SOURCE3 3 0.8237 + angle_coeff @angle:hn-nh-p5 harmonic 55.35 115.26 # SOURCE3 3 0.9168 + angle_coeff @angle:hn-nh-s4 harmonic 43.06 107.48 # SOURCE3 3 1.3960 + angle_coeff @angle:hn-nh-s harmonic 40.81 114.37 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-nh-s6 harmonic 44.04 109.98 # SOURCE4 29 0.7478 + angle_coeff @angle:hn-nh-sh harmonic 43.27 112.25 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-nh-ss harmonic 42.95 113.89 # SOURCE3 3 1.4030 + angle_coeff @angle:hn-nh-sy harmonic 43.28 111.23 # SOURCE4 62 1.1413 + angle_coeff @angle:i-nh-i harmonic 59.80 115.82 # SOURCE3 1 + angle_coeff @angle:n1-nh-n1 harmonic 75.13 106.71 # HF/6-31G* 1 + angle_coeff @angle:n2-nh-n2 harmonic 70.76 117.50 # SOURCE3 2 1.1907 + angle_coeff @angle:n2-nh-n3 harmonic 69.63 115.54 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-nh-o harmonic 70.40 126.06 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-nh-n3 harmonic 69.52 110.98 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-nh-n4 harmonic 68.15 108.36 # SOURCE3 1 0.0000 + angle_coeff @angle:na-nh-na harmonic 70.14 112.01 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-hn harmonic 39.73 117.85 # SOURCE3 15 2.3694 + angle_coeff @angle:nh-nh-nh harmonic 70.07 112.23 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-i harmonic 36.08 117.24 # SOURCE3 2 0.4435 + angle_coeff @angle:hn-n-n2 harmonic 49.62 118.33 # SOURCE3 5 2.2377 + angle_coeff @angle:hn-n-n3 harmonic 48.69 117.22 # SOURCE4 37 1.3737 + angle_coeff @angle:hn-n-n4 harmonic 48.90 112.68 # SOURCE3 3 1.9746 + angle_coeff @angle:hn-n-n harmonic 50.14 113.12 # SOURCE3 7 3.2954 + angle_coeff @angle:hn-n-na harmonic 50.40 113.55 # SOURCE3 8 1.9324 + angle_coeff @angle:hn-n-nc harmonic 50.74 115.24 # SOURCE4 10 0.4966 + angle_coeff @angle:hn-n-nh harmonic 49.74 113.13 # SOURCE4 12 1.2125 + angle_coeff @angle:hn-n-no harmonic 48.71 110.11 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-o harmonic 53.83 116.32 # SOURCE3 2 0.0175 + angle_coeff @angle:n-nh-o harmonic 72.07 115.63 # SOURCE3 1 + angle_coeff @angle:hn-n-oh harmonic 50.33 110.71 # SOURCE4 46 1.1278 + angle_coeff @angle:no-nh-no harmonic 72.07 108.55 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-os harmonic 50.52 109.82 # SOURCE4 12 0.6996 + angle_coeff @angle:hn-n-p2 harmonic 52.51 118.05 # SOURCE3 7 3.0564 + angle_coeff @angle:hn-n-p3 harmonic 50.93 119.63 # SOURCE3 2 0.0000 + angle_coeff @angle:hn-n-p4 harmonic 53.00 115.71 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-p5 harmonic 54.50 113.20 # SOURCE4 6 1.0341 + angle_coeff @angle:hn-n-s4 harmonic 41.18 112.46 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-s harmonic 41.14 114.92 # SOURCE3 2 0.0260 + angle_coeff @angle:hn-n-s6 harmonic 43.06 112.18 # SOURCE4 6 0.6101 + angle_coeff @angle:hn-n-sh harmonic 42.19 114.91 # SOURCE3 1 0.0000 + angle_coeff @angle:hn-n-ss harmonic 42.36 115.60 # SOURCE3 3 0.6414 + angle_coeff @angle:hn-n-sy harmonic 43.02 112.34 # SOURCE4 38 0.6039 + angle_coeff @angle:oh-nh-oh harmonic 72.15 106.27 # SOURCE3 1 + angle_coeff @angle:o-nh-o harmonic 72.24 128.06 # SOURCE3 1 + angle_coeff @angle:os-nh-os harmonic 72.41 105.27 # SOURCE3 1 + angle_coeff @angle:p2-nh-p2 harmonic 98.07 127.33 # SOURCE3 2 2.7857 + angle_coeff @angle:p3-nh-p3 harmonic 96.03 125.08 # SOURCE3 1 + angle_coeff @angle:p5-nh-p5 harmonic 104.72 112.76 # SOURCE3 1 + angle_coeff @angle:s4-nh-s4 harmonic 62.56 112.39 # SOURCE3 1 + angle_coeff @angle:s6-nh-s6 harmonic 62.35 120.27 # SOURCE3 1 + angle_coeff @angle:sh-nh-sh harmonic 62.26 119.00 # SOURCE3 1 + angle_coeff @angle:s-nh-s harmonic 59.67 118.73 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-nh-ss harmonic 62.19 119.25 # SOURCE3 1 + angle_coeff @angle:i-n-i harmonic 60.66 118.20 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-n-n2 harmonic 70.16 116.89 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-n-n3 harmonic 68.02 117.94 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-n-n4 harmonic 68.42 112.69 # SOURCE3 1 0.0000 + angle_coeff @angle:na-n-na harmonic 69.61 117.38 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-n-nc harmonic 71.04 116.41 # CORR 2 + angle_coeff @angle:nc-n-p2 harmonic 80.69 117.21 # CORR 2 + angle_coeff @angle:nc-n-pc harmonic 80.42 117.21 # CORR 2 + angle_coeff @angle:nd-n-nd harmonic 71.04 116.41 # CORR 2 + angle_coeff @angle:nd-n-p2 harmonic 80.69 117.21 # CORR 2 + angle_coeff @angle:nd-n-pd harmonic 80.42 117.21 # CORR 2 + angle_coeff @angle:nh-n-nh harmonic 69.10 115.18 # SOURCE3 1 0.0000 + angle_coeff @angle:n-n-n harmonic 69.89 114.62 # SOURCE3 1 0.0000 + angle_coeff @angle:no-n-no harmonic 68.52 108.66 # SOURCE3 1 0.0000 + angle_coeff @angle:br-no-o harmonic 58.48 113.19 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-no-o harmonic 71.34 116.63 # SOURCE3 6 0.0000 + angle_coeff @angle:c2-no-o harmonic 69.87 116.87 # SOURCE3 8 0.4200 + angle_coeff @angle:c3-no-o harmonic 66.96 116.56 # SOURCE3 6 0.3959 + angle_coeff @angle:ca-no-o harmonic 68.74 118.10 # SOURCE3 10 1.1524 + angle_coeff @angle:cc-no-o harmonic 70.34 117.52 # SOURCE4 198 0.6255 + angle_coeff @angle:cl-no-o harmonic 57.30 115.08 # SOURCE3 2 0.0000 + angle_coeff @angle:c-no-o harmonic 67.10 115.26 # SOURCE3 1 + angle_coeff @angle:hn-no-o harmonic 55.31 115.49 # SOURCE3 2 0.0000 + angle_coeff @angle:oh-n-oh harmonic 72.05 107.26 # SOURCE3 1 0.0000 + angle_coeff @angle:i-no-o harmonic 54.60 116.31 # SOURCE3 2 0.0000 + angle_coeff @angle:n1-no-o harmonic 73.78 115.00 # HF/6-31G* 1 + angle_coeff @angle:n2-no-o harmonic 65.79 115.10 # SOURCE2 2 2.4000 + angle_coeff @angle:n3-no-o harmonic 72.01 115.56 # SOURCE3 6 0.6427 + angle_coeff @angle:n4-no-o harmonic 72.87 109.00 # SOURCE3 2 0.0000 + angle_coeff @angle:na-no-o harmonic 72.24 115.49 # SOURCE3 18 0.5640 + angle_coeff @angle:nh-no-o harmonic 74.08 115.71 # SOURCE3 8 0.4811 + angle_coeff @angle:n-no-o harmonic 71.67 115.41 # SOURCE3 8 0.3748 + angle_coeff @angle:no-no-o harmonic 59.92 112.38 # SOURCE3 4 0.0000 + angle_coeff @angle:o-n-o harmonic 73.39 128.61 # SOURCE3 3 1.0626 + angle_coeff @angle:o-no-o harmonic 77.15 125.13 # SOURCE4 461 0.7605 + angle_coeff @angle:o-no-oh harmonic 74.09 114.70 # SOURCE3 2 0.0000 + angle_coeff @angle:o-no-os harmonic 73.71 114.01 # SOURCE3 8 0.9778 + angle_coeff @angle:o-no-p2 harmonic 82.07 117.38 # SOURCE3 20 0.8083 + angle_coeff @angle:o-no-p3 harmonic 77.73 116.78 # SOURCE3 6 0.4929 + angle_coeff @angle:o-no-p4 harmonic 76.69 116.64 # SOURCE3 6 0.0089 + angle_coeff @angle:o-no-p5 harmonic 78.18 116.69 # SOURCE3 8 0.4507 + angle_coeff @angle:o-no-s4 harmonic 57.15 114.49 # SOURCE3 6 0.5674 + angle_coeff @angle:o-no-s6 harmonic 57.79 114.39 # SOURCE3 6 0.8311 + angle_coeff @angle:o-no-s harmonic 64.05 119.81 # SOURCE3 4 0.0042 + angle_coeff @angle:o-no-sh harmonic 62.94 116.10 # SOURCE3 2 0.0000 + angle_coeff @angle:o-no-ss harmonic 62.27 115.58 # SOURCE3 6 0.5860 + angle_coeff @angle:os-n-os harmonic 72.28 106.53 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-n-p2 harmonic 98.03 119.62 # SOURCE3 1 + angle_coeff @angle:p3-n-p3 harmonic 100.67 108.73 # SOURCE3 3 0.2591 + angle_coeff @angle:p4-n-p4 harmonic 102.85 108.55 # SOURCE3 1 + angle_coeff @angle:p5-n-p5 harmonic 108.79 99.99 # SOURCE3 1 + angle_coeff @angle:pc-n-pc harmonic 97.64 119.62 # SOURCE3 1 0.0000 + angle_coeff @angle:pd-n-pd harmonic 97.64 119.62 # SOURCE3 1 same_as_pc-n-pc + angle_coeff @angle:s4-n-s4 harmonic 61.03 113.75 # SOURCE3 1 0.0000 + angle_coeff @angle:s6-n-s6 harmonic 61.82 119.68 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-n-sh harmonic 61.53 119.03 # SOURCE3 1 0.0000 + angle_coeff @angle:s-n-s harmonic 58.48 126.00 # SOURCE3 1 + angle_coeff @angle:ss-n-ss harmonic 62.06 118.49 # SOURCE3 1 0.0000 + angle_coeff @angle:br-oh-ho harmonic 42.15 101.60 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-oh-ho harmonic 50.20 108.76 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-oh-ho harmonic 49.91 108.98 # SOURCE3 6 2.2379 + angle_coeff @angle:c3-oh-ho harmonic 47.09 108.16 # SOURCE3 42 1.3034 + angle_coeff @angle:ca-oh-ho harmonic 48.85 109.47 # SOURCE3 7 1.0405 + angle_coeff @angle:cc-oh-ho harmonic 49.96 107.06 # CORR 117 + angle_coeff @angle:cd-oh-ho harmonic 49.96 107.06 # CORR 117 + angle_coeff @angle:ce-oh-ho harmonic 49.85 106.95 # CORR 34 + angle_coeff @angle:cf-oh-ho harmonic 49.85 106.95 # CORR 34 + angle_coeff @angle:c-oh-ho harmonic 51.19 107.37 # SOURCE3 34 1.6830 + angle_coeff @angle:cl-oh-ho harmonic 40.51 102.40 # SOURCE2 1 0.0000 + angle_coeff @angle:cx-oh-ho harmonic 49.64 106.17 # SOURCE3 3 0.0644 + angle_coeff @angle:cy-oh-ho harmonic 47.62 107.32 # SOURCE4 5 0.4955 + angle_coeff @angle:f-oh-ho harmonic 48.47 96.80 # SOURCE2 1 0.0000 + angle_coeff @angle:ho-oh-ho harmonic 41.93 104.80 # SOURCE2 1 0.0000 + angle_coeff @angle:ho-oh-i harmonic 35.67 107.98 # SOURCE3 2 0.0000 + angle_coeff @angle:ho-oh-n1 harmonic 52.55 107.81 # HF/6-31G* 1 + angle_coeff @angle:ho-oh-n2 harmonic 50.57 102.74 # SOURCE3 9 2.1286 + angle_coeff @angle:ho-oh-n3 harmonic 50.61 102.33 # SOURCE3 5 1.2591 + angle_coeff @angle:ho-oh-n4 harmonic 49.44 106.63 # SOURCE3 3 0.2770 + angle_coeff @angle:ho-oh-n harmonic 50.46 101.03 # SOURCE3 6 1.4086 + angle_coeff @angle:ho-oh-na harmonic 50.24 103.71 # SOURCE3 9 1.2590 + angle_coeff @angle:ho-oh-nh harmonic 49.97 102.42 # SOURCE4 15 0.6819 + angle_coeff @angle:ho-oh-no harmonic 50.31 102.17 # SOURCE3 1 0.0000 + angle_coeff @angle:ho-oh-o harmonic 47.26 100.87 # SOURCE3 1 + angle_coeff @angle:ho-oh-oh harmonic 49.34 98.72 # SOURCE3 2 0.0000 + angle_coeff @angle:ho-oh-os harmonic 49.58 99.69 # SOURCE4 18 0.3384 + angle_coeff @angle:ho-oh-p2 harmonic 55.87 109.45 # SOURCE3 8 3.3491 + angle_coeff @angle:ho-oh-p3 harmonic 53.84 110.64 # SOURCE3 3 0.5191 + angle_coeff @angle:ho-oh-p4 harmonic 55.27 110.19 # SOURCE3 4 0.2372 + angle_coeff @angle:ho-oh-p5 harmonic 55.88 110.14 # SOURCE3 92 3.8033 + angle_coeff @angle:ho-oh-py harmonic 56.18 110.73 # SOURCE3 79 1.7835 + angle_coeff @angle:ho-oh-s4 harmonic 42.77 106.76 # SOURCE4 9 0.4035 + angle_coeff @angle:ho-oh-s harmonic 40.86 100.15 # SOURCE3 2 0.0000 + angle_coeff @angle:ho-oh-s6 harmonic 45.46 109.20 # SOURCE3 13 0.1856 + angle_coeff @angle:ho-oh-sh harmonic 42.97 106.24 # SOURCE3 2 0.0661 + angle_coeff @angle:ho-oh-ss harmonic 43.10 107.06 # SOURCE3 4 0.9967 + angle_coeff @angle:ho-oh-sy harmonic 44.20 106.41 # SOURCE4 33 0.3729 + angle_coeff @angle:br-os-br harmonic 65.08 110.63 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-os-c1 harmonic 66.99 115.02 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-os-c3 harmonic 64.47 113.39 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-os-c2 harmonic 65.95 113.14 # SOURCE3 6 2.1932 + angle_coeff @angle:c2-os-c3 harmonic 64.21 112.09 # SOURCE3 7 4.1809 + angle_coeff @angle:c2-os-ca harmonic 65.43 113.59 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-os-n2 harmonic 64.91 118.13 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-os-na harmonic 68.21 103.85 # SOURCE3 4 0.6297 + angle_coeff @angle:c2-os-os harmonic 68.35 102.77 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-os-p5 harmonic 77.31 126.37 # SOURCE4 7 1.7939 + angle_coeff @angle:c2-os-ss harmonic 63.08 108.13 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-os-c3 harmonic 62.39 112.45 # SOURCE4 1293 1.6468 + angle_coeff @angle:c3-os-ca harmonic 62.27 117.97 # SOURCE4 2495 1.4576 + angle_coeff @angle:c3-os-cc harmonic 62.50 117.33 # CORR 248 + angle_coeff @angle:c3-os-cd harmonic 62.50 117.33 # CORR 248 + angle_coeff @angle:c3-os-ce harmonic 62.79 116.05 # CORR 37 + angle_coeff @angle:c3-os-cf harmonic 62.79 116.05 # CORR 37 + angle_coeff @angle:c3-os-cl harmonic 56.20 110.50 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-os-cy harmonic 61.67 115.65 # SOURCE4 5 0.2390 + angle_coeff @angle:c3-os-i harmonic 54.88 113.70 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-os-n1 harmonic 66.31 113.50 # HF/6-31G* 1 + angle_coeff @angle:c3-os-n2 harmonic 65.92 108.12 # SOURCE3 7 0.3048 + angle_coeff @angle:c3-os-n3 harmonic 64.52 110.28 # SOURCE4 14 1.9026 + angle_coeff @angle:c3-os-n4 harmonic 64.88 110.50 # SOURCE3 3 0.5426 + angle_coeff @angle:c3-os-n harmonic 65.40 109.52 # SOURCE4 14 0.6827 + angle_coeff @angle:c3-os-na harmonic 64.54 109.91 # SOURCE3 9 1.8268 + angle_coeff @angle:c3-os-nc harmonic 64.80 112.73 # SOURCE3 2 1.0358 + angle_coeff @angle:c3-os-nd harmonic 64.80 112.73 # SOURCE3 2 same_as_c3-os-nc + angle_coeff @angle:c3-os-nh harmonic 65.22 109.69 # SOURCE4 8 0.1662 + angle_coeff @angle:c3-os-no harmonic 63.89 113.80 # SOURCE4 42 0.2726 + angle_coeff @angle:c3-os-o harmonic 65.62 103.00 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-os-oh harmonic 65.24 107.97 # SOURCE4 11 0.4333 + angle_coeff @angle:c3-os-os harmonic 65.89 105.01 # SOURCE3 7 0.6328 + angle_coeff @angle:c3-os-p2 harmonic 80.24 115.47 # SOURCE3 8 2.6374 + angle_coeff @angle:c3-os-p3 harmonic 76.51 115.97 # SOURCE3 3 0.3597 + angle_coeff @angle:c3-os-p4 harmonic 77.59 117.48 # SOURCE3 4 0.3850 + angle_coeff @angle:c3-os-p5 harmonic 78.48 118.00 # SOURCE3 31 1.2882 + angle_coeff @angle:c3-os-py harmonic 78.07 117.80 # SOURCE3 16 0.9654 + angle_coeff @angle:c3-os-s4 harmonic 61.32 111.50 # SOURCE3 6 1.4240 + angle_coeff @angle:c3-os-s6 harmonic 63.21 115.79 # SOURCE4 60 1.2588 + angle_coeff @angle:c3-os-s harmonic 59.28 109.55 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-os-sh harmonic 61.67 112.82 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-os-ss harmonic 60.74 113.19 # SOURCE3 3 0.2455 + angle_coeff @angle:ca-os-ca harmonic 63.31 119.95 # SOURCE4 107 1.6535 + angle_coeff @angle:ca-os-cc harmonic 67.21 106.65 # CORR 62 + angle_coeff @angle:ca-os-cd harmonic 67.21 106.65 # CORR 62 + angle_coeff @angle:ca-os-n3 harmonic 65.39 112.19 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-os-na harmonic 66.47 108.24 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-os-nc harmonic 66.09 113.68 # SOURCE3 2 + angle_coeff @angle:ca-os-nd harmonic 66.09 113.68 # SOURCE3 2 + angle_coeff @angle:ca-os-p5 harmonic 77.96 123.42 # SOURCE4 54 1.1358 + angle_coeff @angle:ca-os-s6 harmonic 63.95 116.97 # SOURCE4 15 0.9514 + angle_coeff @angle:c-os-c2 harmonic 64.91 118.02 # SOURCE4 7 0.3666 + angle_coeff @angle:c-os-c3 harmonic 63.63 115.14 # SOURCE3 17 1.8967 + angle_coeff @angle:c-os-c harmonic 64.54 120.64 # SOURCE4 7 1.5114 + angle_coeff @angle:c-os-ca harmonic 63.75 120.87 # SOURCE4 257 1.7209 + angle_coeff @angle:c-os-cc harmonic 64.15 119.62 # SOURCE3 5 6.0675 + angle_coeff @angle:cc-os-cc harmonic 67.27 106.69 # CORR 252 + angle_coeff @angle:cc-os-cd harmonic 63.80 118.62 # SOURCE4 14 1.9764 + angle_coeff @angle:c-os-cd harmonic 64.15 119.62 # SOURCE3 5 6.0675 + angle_coeff @angle:cc-os-na harmonic 65.51 111.66 # SOURCE3 28 4.1343 + angle_coeff @angle:cc-os-nc harmonic 68.12 107.23 # SOURCE3 6 2.7507 + angle_coeff @angle:cc-os-os harmonic 66.27 108.47 # SOURCE3 2 0.0000 + angle_coeff @angle:cc-os-ss harmonic 59.85 119.59 # SOURCE3 1 0.0000 + angle_coeff @angle:c-os-cy harmonic 71.75 91.10 # SOURCE3 2 0.0155 + angle_coeff @angle:cd-os-cd harmonic 67.27 106.69 # CORR 252 + angle_coeff @angle:cd-os-na harmonic 65.51 111.66 # SOURCE3 28 4.1343 + angle_coeff @angle:cd-os-nd harmonic 68.12 107.23 # SOURCE3 6 2.7507 + angle_coeff @angle:cd-os-os harmonic 66.27 108.47 # SOURCE3 2 same_as_cc-os-os + angle_coeff @angle:cd-os-ss harmonic 59.85 119.59 # SOURCE3 1 same_as_cc-os-ss + angle_coeff @angle:cl-os-cl harmonic 52.29 110.76 # SOURCE3 2 0.0000 + angle_coeff @angle:c-os-n2 harmonic 66.95 112.08 # SOURCE4 6 0.1154 + angle_coeff @angle:c-os-n harmonic 66.83 112.10 # SOURCE4 6 0.6163 + angle_coeff @angle:c-os-oh harmonic 66.50 110.50 # SOURCE3 1 0.0000 + angle_coeff @angle:c-os-os harmonic 66.25 110.28 # SOURCE4 10 1.3612 + angle_coeff @angle:c-os-p5 harmonic 78.89 122.10 # SOURCE4 5 0.5870 + angle_coeff @angle:c-os-sy harmonic 61.85 113.49 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-os-cx harmonic 85.27 61.82 # SOURCE4 107 0.1793 + angle_coeff @angle:cx-os-n harmonic 88.98 59.99 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-os-os harmonic 90.38 56.52 # SOURCE3 2 0.0000 + angle_coeff @angle:cy-os-cy harmonic 68.81 93.40 # SOURCE2 2 1.4000 + angle_coeff @angle:f-os-f harmonic 63.94 103.30 # SOURCE2 1 0.0000 + angle_coeff @angle:f-os-os harmonic 63.94 109.50 # SOURCE2 1 0.0000 + angle_coeff @angle:i-os-i harmonic 58.06 115.67 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-os-n1 harmonic 70.28 117.79 # HF/6-31G* 1 + angle_coeff @angle:n2-os-n2 harmonic 68.76 106.83 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-os-s6 harmonic 66.63 111.30 # SOURCE4 7 0.5651 + angle_coeff @angle:n3-os-n3 harmonic 67.76 104.88 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-os-n4 harmonic 65.66 114.68 # SOURCE3 1 0.0000 + angle_coeff @angle:na-os-na harmonic 66.10 109.59 # SOURCE3 1 0.0000 + angle_coeff @angle:na-os-ss harmonic 64.75 104.34 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-os-nc harmonic 68.17 110.40 # SOURCE2 1 0.0000 + angle_coeff @angle:nc-os-ss harmonic 63.38 110.97 # SOURCE3 1 0.0000 + angle_coeff @angle:nd-os-nd harmonic 68.17 110.40 # SOURCE2 1 same_as_nc-os-nc + angle_coeff @angle:nd-os-ss harmonic 63.38 110.97 # SOURCE3 1 same_as_nc-os-ss + angle_coeff @angle:nh-os-nh harmonic 67.81 108.29 # SOURCE3 1 0.0000 + angle_coeff @angle:n-os-n harmonic 68.08 108.31 # SOURCE3 1 0.0000 + angle_coeff @angle:no-os-no harmonic 66.40 111.86 # SOURCE3 1 0.0000 + angle_coeff @angle:n-os-s6 harmonic 65.87 113.62 # SOURCE4 5 0.0928 + angle_coeff @angle:o-os-o harmonic 62.76 114.68 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-os-p2 harmonic 103.59 120.02 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-os-p5 harmonic 108.26 107.86 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-os-p3 harmonic 96.17 121.22 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-os-py harmonic 105.11 105.58 # SOURCE3 1 0.0000 + angle_coeff @angle:p5-os-p5 harmonic 99.18 126.25 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-os-s4 harmonic 62.09 111.63 # SOURCE3 1 0.0000 + angle_coeff @angle:s6-os-s6 harmonic 64.77 119.07 # SOURCE3 2 0.4318 + angle_coeff @angle:sh-os-sh harmonic 61.15 118.95 # SOURCE3 1 0.0000 + angle_coeff @angle:s-os-s harmonic 56.98 118.08 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-os-ss harmonic 60.82 115.64 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p2-br harmonic 40.68 108.60 # SOURCE3 1 + angle_coeff @angle:br-p2-c2 harmonic 39.43 102.32 # SOURCE3 2 0.0146 + angle_coeff @angle:br-p2-n2 harmonic 40.42 103.33 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p2-o harmonic 39.43 110.87 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p2-p2 harmonic 50.16 115.46 # SOURCE3 4 7.8622 + angle_coeff @angle:br-p2-s harmonic 40.59 110.52 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-p2-c1 harmonic 39.20 99.04 # SOURCE3 1 + angle_coeff @angle:c1-p2-c2 harmonic 39.82 101.29 # SOURCE3 1 + angle_coeff @angle:c1-p2-n2 harmonic 41.36 101.79 # SOURCE3 1 + angle_coeff @angle:c1-p2-o harmonic 41.32 107.62 # SOURCE3 1 + angle_coeff @angle:c1-p2-p2 harmonic 53.31 99.54 # SOURCE3 1 + angle_coeff @angle:c1-p2-s harmonic 41.00 105.90 # SOURCE3 1 + angle_coeff @angle:c2-p2-c2 harmonic 40.45 104.50 # SOURCE3 1 + angle_coeff @angle:c2-p2-c3 harmonic 38.60 101.90 # SOURCE3 4 0.1132 + angle_coeff @angle:c2-p2-ca harmonic 38.79 101.95 # SOURCE3 1 + angle_coeff @angle:c2-p2-cl harmonic 35.61 102.72 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-p2-f harmonic 41.60 103.47 # SOURCE3 2 0.0136 + angle_coeff @angle:c2-p2-hp harmonic 30.13 97.19 # SOURCE3 3 0.0216 + angle_coeff @angle:c2-p2-i harmonic 33.85 101.94 # SOURCE3 2 0.0368 + angle_coeff @angle:c2-p2-n2 harmonic 43.20 99.88 # SOURCE3 1 + angle_coeff @angle:c2-p2-n3 harmonic 41.99 101.80 # SOURCE3 1 + angle_coeff @angle:c2-p2-n4 harmonic 39.07 98.26 # SOURCE3 6 0.1522 + angle_coeff @angle:c2-p2-n harmonic 40.89 103.28 # SOURCE3 4 3.3113 + angle_coeff @angle:c2-p2-na harmonic 40.54 103.99 # SOURCE3 8 1.6834 + angle_coeff @angle:c2-p2-nh harmonic 41.20 105.17 # SOURCE3 8 0.8263 + angle_coeff @angle:c2-p2-no harmonic 41.91 97.97 # SOURCE3 3 0.4175 + angle_coeff @angle:c2-p2-o harmonic 41.51 115.16 # SOURCE3 1 + angle_coeff @angle:c2-p2-oh harmonic 42.50 102.89 # SOURCE3 3 0.8191 + angle_coeff @angle:c2-p2-os harmonic 43.35 102.12 # SOURCE3 4 0.8783 + angle_coeff @angle:c2-p2-p2 harmonic 54.72 99.56 # SOURCE3 1 + angle_coeff @angle:c2-p2-p3 harmonic 48.11 99.27 # SOURCE3 4 1.1590 + angle_coeff @angle:c2-p2-p4 harmonic 48.19 96.94 # SOURCE3 1 + angle_coeff @angle:c2-p2-p5 harmonic 48.01 97.61 # SOURCE3 1 + angle_coeff @angle:c2-p2-s4 harmonic 38.27 95.15 # SOURCE3 1 + angle_coeff @angle:c2-p2-s6 harmonic 38.35 95.51 # SOURCE3 1 + angle_coeff @angle:c2-p2-s harmonic 42.19 105.53 # SOURCE3 1 + angle_coeff @angle:c2-p2-sh harmonic 40.19 101.49 # SOURCE3 3 0.0057 + angle_coeff @angle:c2-p2-ss harmonic 40.19 101.81 # SOURCE3 4 0.5883 + angle_coeff @angle:c3-p2-c3 harmonic 37.36 99.30 # SOURCE3 1 + angle_coeff @angle:c3-p2-n2 harmonic 40.30 100.82 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p2-o harmonic 40.10 106.72 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p2-os harmonic 40.68 101.34 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p2-p2 harmonic 51.78 100.48 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p2-s harmonic 40.04 105.68 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-p2-ca harmonic 37.59 99.70 # SOURCE3 1 + angle_coeff @angle:ca-p2-n2 harmonic 40.53 100.82 # SOURCE3 1 + angle_coeff @angle:ca-p2-n harmonic 41.68 89.97 # SOURCE3 1 + angle_coeff @angle:ca-p2-na harmonic 41.69 89.21 # SOURCE3 1 + angle_coeff @angle:ca-p2-o harmonic 40.31 106.88 # SOURCE3 1 + angle_coeff @angle:ca-p2-s harmonic 39.79 107.93 # SOURCE3 1 + angle_coeff @angle:c-p2-c2 harmonic 38.89 97.30 # SOURCE3 1 + angle_coeff @angle:c-p2-c harmonic 38.29 90.10 # SOURCE3 1 + angle_coeff @angle:ce-p2-o harmonic 40.63 107.44 # SOURCE3 1 + angle_coeff @angle:ce-p2-s harmonic 40.55 105.54 # SOURCE3 1 + angle_coeff @angle:cf-p2-o harmonic 40.63 107.44 # SOURCE3 1 same_as_ce-p2-o + angle_coeff @angle:cf-p2-s harmonic 40.55 105.54 # SOURCE3 1 same_as_ce-p2-s + angle_coeff @angle:cl-p2-cl harmonic 32.00 108.70 # SOURCE3 1 + angle_coeff @angle:cl-p2-n2 harmonic 36.67 103.38 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-p2-o harmonic 36.00 110.57 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-p2-p2 harmonic 47.78 103.11 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-p2-s harmonic 36.62 110.11 # SOURCE3 1 0.0000 + angle_coeff @angle:f-p2-f harmonic 42.20 107.10 # SOURCE3 1 + angle_coeff @angle:f-p2-n2 harmonic 43.59 103.57 # SOURCE3 1 0.0000 + angle_coeff @angle:f-p2-o harmonic 43.81 110.61 # SOURCE3 1 0.0000 + angle_coeff @angle:f-p2-p2 harmonic 54.54 103.48 # SOURCE3 1 0.0000 + angle_coeff @angle:f-p2-s harmonic 41.15 114.71 # SOURCE3 2 5.2794 + angle_coeff @angle:hp-p2-hp harmonic 22.84 98.76 # SOURCE3 1 + angle_coeff @angle:hp-p2-n1 harmonic 31.08 95.18 # SOURCE3 2 1.5708 + angle_coeff @angle:hp-p2-n2 harmonic 32.08 95.54 # SOURCE3 19 4.7352 + angle_coeff @angle:hp-p2-ne harmonic 31.94 100.10 # SOURCE3 14 6.1290 + angle_coeff @angle:hp-p2-nf harmonic 31.94 100.10 # SOURCE3 14 same_as_hp-p2-ne + angle_coeff @angle:hp-p2-o harmonic 32.04 105.58 # SOURCE3 1 0.0000 + angle_coeff @angle:hp-p2-p2 harmonic 38.16 101.88 # SOURCE3 27 12.9535 + angle_coeff @angle:hp-p2-p4 harmonic 32.69 94.51 # SOURCE3 1 0.0000 + angle_coeff @angle:hp-p2-p5 harmonic 33.66 89.07 # SOURCE3 1 0.0000 + angle_coeff @angle:hp-p2-pe harmonic 37.56 97.25 # SOURCE3 16 8.8916 + angle_coeff @angle:hp-p2-pf harmonic 37.56 97.25 # SOURCE3 16 same_as_hp-p2-pe + angle_coeff @angle:hp-p2-s4 harmonic 26.33 89.99 # SOURCE3 1 0.0000 + angle_coeff @angle:hp-p2-s harmonic 30.26 102.52 # SOURCE3 1 0.0000 + angle_coeff @angle:hp-p2-s6 harmonic 26.74 88.13 # SOURCE3 1 0.0000 + angle_coeff @angle:i-p2-i harmonic 35.75 104.16 # SOURCE3 1 + angle_coeff @angle:i-p2-n2 harmonic 34.63 101.77 # SOURCE3 1 0.0000 + angle_coeff @angle:i-p2-o harmonic 33.34 109.51 # SOURCE3 1 0.0000 + angle_coeff @angle:i-p2-p2 harmonic 46.22 102.63 # SOURCE3 1 0.0000 + angle_coeff @angle:i-p2-s harmonic 35.18 110.60 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-p2-n1 harmonic 46.52 86.22 # HF/6-31G* 1 + angle_coeff @angle:n2-p2-n2 harmonic 45.62 98.00 # SOURCE3 1 + angle_coeff @angle:n2-p2-n3 harmonic 44.14 100.42 # SOURCE3 1 + angle_coeff @angle:n2-p2-n4 harmonic 41.53 93.42 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-na harmonic 42.63 102.03 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-nh harmonic 43.69 101.87 # SOURCE3 2 0.8491 + angle_coeff @angle:n2-p2-no harmonic 43.64 98.12 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-o harmonic 43.53 115.34 # SOURCE3 1 + angle_coeff @angle:n2-p2-oh harmonic 43.02 109.72 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-os harmonic 45.35 102.29 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-p3 harmonic 49.55 99.51 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-p4 harmonic 48.48 101.73 # SOURCE3 1 + angle_coeff @angle:n2-p2-p5 harmonic 50.50 93.68 # SOURCE3 1 + angle_coeff @angle:n2-p2-s4 harmonic 38.89 97.83 # SOURCE3 1 + angle_coeff @angle:n2-p2-s6 harmonic 38.99 98.14 # SOURCE3 1 + angle_coeff @angle:n2-p2-s harmonic 42.45 112.94 # SOURCE3 1 + angle_coeff @angle:n2-p2-sh harmonic 41.75 100.82 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-p2-ss harmonic 41.64 101.76 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-p2-n3 harmonic 42.10 106.30 # SOURCE3 1 + angle_coeff @angle:n3-p2-o harmonic 44.16 106.83 # SOURCE3 1 + angle_coeff @angle:n3-p2-p2 harmonic 55.78 100.58 # SOURCE3 1 + angle_coeff @angle:n3-p2-s harmonic 43.18 105.75 # SOURCE3 1 + angle_coeff @angle:n4-p2-n4 harmonic 39.61 88.80 # SOURCE3 1 + angle_coeff @angle:n4-p2-o harmonic 40.67 101.36 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-p2-p2 harmonic 52.72 96.53 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-p2-s harmonic 40.06 104.98 # SOURCE3 1 0.0000 + angle_coeff @angle:na-p2-na harmonic 40.23 106.10 # SOURCE3 1 + angle_coeff @angle:na-p2-o harmonic 42.71 107.46 # SOURCE3 1 0.0000 + angle_coeff @angle:na-p2-s harmonic 41.81 108.15 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-p2-o harmonic 45.72 107.71 # SOURCE3 1 + angle_coeff @angle:ne-p2-s harmonic 44.34 105.50 # SOURCE3 1 + angle_coeff @angle:nf-p2-o harmonic 45.72 107.71 # SOURCE3 1 same_as_ne-p2-o + angle_coeff @angle:nf-p2-s harmonic 44.34 105.50 # SOURCE3 1 same_as_ne-p2-s + angle_coeff @angle:nh-p2-nh harmonic 42.33 104.00 # SOURCE3 1 + angle_coeff @angle:nh-p2-o harmonic 43.75 108.11 # SOURCE3 2 0.6773 + angle_coeff @angle:nh-p2-p2 harmonic 53.77 107.73 # SOURCE3 3 3.1678 + angle_coeff @angle:nh-p2-s harmonic 42.31 109.62 # SOURCE3 2 1.7725 + angle_coeff @angle:n-p2-n2 harmonic 43.55 98.85 # SOURCE3 1 0.0000 + angle_coeff @angle:n-p2-o harmonic 43.46 105.08 # SOURCE3 1 0.0000 + angle_coeff @angle:no-p2-no harmonic 42.08 98.20 # SOURCE3 1 + angle_coeff @angle:no-p2-o harmonic 43.42 104.87 # SOURCE3 1 0.0000 + angle_coeff @angle:no-p2-p2 harmonic 52.75 108.57 # SOURCE3 3 8.2121 + angle_coeff @angle:no-p2-s harmonic 41.76 109.06 # SOURCE3 2 5.4074 + angle_coeff @angle:n-p2-p2 harmonic 54.46 102.12 # SOURCE3 1 0.0000 + angle_coeff @angle:n-p2-s harmonic 41.20 112.34 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-p2-oh harmonic 44.96 100.10 # SOURCE3 1 + angle_coeff @angle:oh-p2-p2 harmonic 54.71 107.82 # SOURCE3 2 2.6708 + angle_coeff @angle:oh-p2-s harmonic 43.05 109.75 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p2-o harmonic 44.39 119.96 # SOURCE3 1 + angle_coeff @angle:o-p2-oh harmonic 44.33 110.46 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p2-os harmonic 45.59 108.81 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p2-p2 harmonic 54.57 114.23 # SOURCE3 1 + angle_coeff @angle:o-p2-p3 harmonic 48.45 106.69 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p2-p4 harmonic 48.42 104.37 # SOURCE3 1 + angle_coeff @angle:o-p2-p5 harmonic 48.37 104.49 # SOURCE3 1 + angle_coeff @angle:o-p2-pe harmonic 46.73 145.96 # SOURCE3 1 + angle_coeff @angle:o-p2-pf harmonic 46.73 145.96 # SOURCE3 1 same_as_o-p2-pe + angle_coeff @angle:o-p2-s4 harmonic 37.68 106.59 # SOURCE3 1 + angle_coeff @angle:o-p2-s6 harmonic 38.12 105.04 # SOURCE3 1 + angle_coeff @angle:o-p2-s harmonic 42.77 117.42 # SOURCE3 1 + angle_coeff @angle:o-p2-sh harmonic 40.81 109.60 # SOURCE3 1 0.0000 + angle_coeff @angle:os-p2-os harmonic 47.01 98.30 # SOURCE3 1 + angle_coeff @angle:os-p2-p2 harmonic 57.14 101.46 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p2-ss harmonic 40.89 109.60 # SOURCE3 1 0.0000 + angle_coeff @angle:os-p2-s harmonic 43.89 108.47 # SOURCE3 3 1.7065 + angle_coeff @angle:p2-p2-n2 harmonic 57.57 97.40 # SOURCE3 1 + angle_coeff @angle:p2-p2-p3 harmonic 64.09 101.73 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-p2-p4 harmonic 63.42 101.98 # SOURCE3 1 + angle_coeff @angle:p2-p2-p5 harmonic 64.24 99.33 # SOURCE3 1 + angle_coeff @angle:p2-p2-s4 harmonic 51.53 95.73 # SOURCE3 1 + angle_coeff @angle:p2-p2-s6 harmonic 51.64 95.95 # SOURCE3 1 + angle_coeff @angle:p2-p2-s harmonic 54.52 111.28 # SOURCE3 1 + angle_coeff @angle:p2-p2-sh harmonic 50.78 113.94 # SOURCE3 3 8.5009 + angle_coeff @angle:p3-p2-p3 harmonic 59.88 101.00 # SOURCE3 1 + angle_coeff @angle:p3-p2-s harmonic 48.09 113.28 # SOURCE3 2 6.7035 + angle_coeff @angle:p4-p2-s harmonic 49.75 103.89 # SOURCE3 1 + angle_coeff @angle:p5-p2-p5 harmonic 62.82 89.40 # SOURCE3 1 + angle_coeff @angle:p5-p2-s harmonic 50.38 101.21 # SOURCE3 1 + angle_coeff @angle:pe-p2-s harmonic 54.45 106.35 # SOURCE3 1 + angle_coeff @angle:pf-p2-s harmonic 54.45 106.35 # SOURCE3 1 same_as_pe-p2-s + angle_coeff @angle:s4-p2-s4 harmonic 39.97 85.30 # SOURCE3 1 + angle_coeff @angle:s6-p2-s6 harmonic 37.42 98.20 # SOURCE3 1 + angle_coeff @angle:sh-p2-sh harmonic 41.33 98.50 # SOURCE3 1 + angle_coeff @angle:s-p2-s harmonic 44.19 106.60 # SOURCE3 1 + angle_coeff @angle:s-p2-s4 harmonic 38.90 105.29 # SOURCE3 1 + angle_coeff @angle:s-p2-s6 harmonic 38.73 106.93 # SOURCE3 1 + angle_coeff @angle:s-p2-sh harmonic 40.82 110.73 # SOURCE3 2 0.0232 + angle_coeff @angle:s-p2-ss harmonic 40.27 114.14 # SOURCE3 4 5.9223 + angle_coeff @angle:ss-p2-ss harmonic 41.56 97.90 # SOURCE3 1 + angle_coeff @angle:br-p3-br harmonic 41.27 103.54 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p3-hp harmonic 26.94 96.36 # SOURCE3 4 0.6701 + angle_coeff @angle:c1-p3-c1 harmonic 38.48 100.50 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-p3-f harmonic 40.73 96.90 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-p3-hp harmonic 28.14 97.67 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-p3-c2 harmonic 37.32 101.77 # SOURCE3 3 0.0000 + angle_coeff @angle:c2-p3-hp harmonic 27.57 97.85 # SOURCE3 4 0.0000 + angle_coeff @angle:c3-p3-c3 harmonic 37.51 99.66 # SOURCE3 40 0.9854 + angle_coeff @angle:c3-p3-ca harmonic 37.29 101.94 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-cl harmonic 35.74 99.89 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p3-f harmonic 39.74 97.80 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-p3-hp harmonic 27.47 97.66 # SOURCE3 9 0.4096 + angle_coeff @angle:c3-p3-n2 harmonic 39.87 96.55 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-n3 harmonic 39.28 101.18 # SOURCE3 10 2.2338 + angle_coeff @angle:c3-p3-n4 harmonic 38.58 96.94 # SOURCE3 6 0.4815 + angle_coeff @angle:c3-p3-n harmonic 38.78 101.77 # SOURCE3 12 2.4449 + angle_coeff @angle:c3-p3-na harmonic 39.16 100.17 # SOURCE3 4 0.0554 + angle_coeff @angle:c3-p3-nh harmonic 38.65 104.50 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-no harmonic 38.96 96.98 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-o harmonic 39.33 111.67 # SOURCE3 28 5.3387 + angle_coeff @angle:c3-p3-oh harmonic 40.60 98.21 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-os harmonic 40.25 99.53 # SOURCE3 3 1.7678 + angle_coeff @angle:c3-p3-p3 harmonic 45.77 100.31 # SOURCE3 18 2.1836 + angle_coeff @angle:c3-p3-p5 harmonic 45.65 100.90 # SOURCE3 10 2.7070 + angle_coeff @angle:c3-p3-s4 harmonic 37.94 98.88 # SOURCE3 8 6.2235 + angle_coeff @angle:c3-p3-s6 harmonic 37.62 101.18 # SOURCE3 12 6.4536 + angle_coeff @angle:c3-p3-sh harmonic 37.43 98.71 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-p3-ss harmonic 37.44 99.37 # SOURCE3 2 0.0000 + angle_coeff @angle:ca-p3-ca harmonic 37.89 99.86 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-p3-hp harmonic 27.74 97.50 # SOURCE3 2 0.0000 + angle_coeff @angle:c-p3-c3 harmonic 37.60 97.06 # SOURCE3 3 1.1490 + angle_coeff @angle:c-p3-c harmonic 36.51 100.90 # SOURCE3 1 0.0000 + angle_coeff @angle:c-p3-hp harmonic 27.15 96.55 # SOURCE3 6 0.5223 + angle_coeff @angle:cl-p3-cl harmonic 33.91 102.82 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-p3-f harmonic 37.03 99.20 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-p3-hp harmonic 25.67 96.30 # SOURCE3 3 0.6203 + angle_coeff @angle:c-p3-os harmonic 43.95 81.32 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-p3-hp harmonic 27.54 95.20 # SOURCE2 1 0.0000 + angle_coeff @angle:f-p3-f harmonic 43.08 97.40 # SOURCE2 8 1.6636 + angle_coeff @angle:f-p3-hp harmonic 30.56 96.41 # SOURCE3 2 0.0000 + angle_coeff @angle:f-p3-n3 harmonic 41.86 100.60 # SOURCE2 1 0.0000 + angle_coeff @angle:f-p3-os harmonic 42.42 102.20 # SOURCE2 1 0.0000 + angle_coeff @angle:f-p3-p3 harmonic 47.13 97.20 # SOURCE2 1 0.0000 + angle_coeff @angle:hp-p3-hp harmonic 22.02 95.52 # SOURCE3 44 2.4200 + angle_coeff @angle:hp-p3-i harmonic 23.42 96.19 # SOURCE3 4 0.6454 + angle_coeff @angle:hp-p3-n1 harmonic 31.27 92.98 # HF/6-31G* 1 + angle_coeff @angle:hp-p3-n2 harmonic 29.07 98.28 # SOURCE3 10 1.8860 + angle_coeff @angle:hp-p3-n3 harmonic 30.10 94.46 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-n4 harmonic 28.34 93.21 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-n harmonic 29.47 95.15 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-na harmonic 29.25 97.27 # SOURCE3 12 0.9318 + angle_coeff @angle:hp-p3-nh harmonic 30.16 94.10 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-no harmonic 28.83 93.06 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-o harmonic 32.01 101.02 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-oh harmonic 30.73 95.95 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-os harmonic 30.39 97.35 # SOURCE3 6 2.8326 + angle_coeff @angle:hp-p3-p2 harmonic 32.41 99.11 # SOURCE3 16 4.3022 + angle_coeff @angle:hp-p3-p3 harmonic 32.07 95.52 # SOURCE3 4 0.0844 + angle_coeff @angle:hp-p3-p4 harmonic 31.97 95.95 # SOURCE3 6 0.0489 + angle_coeff @angle:hp-p3-p5 harmonic 32.08 95.54 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-s4 harmonic 26.89 95.49 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-s6 harmonic 27.38 92.95 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-sh harmonic 26.51 94.21 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p3-ss harmonic 26.59 94.61 # SOURCE3 2 0.0000 + angle_coeff @angle:i-p3-i harmonic 36.63 105.25 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-p3-n1 harmonic 45.91 90.44 # HF/6-31G* 1 + angle_coeff @angle:n2-p3-n2 harmonic 40.40 103.46 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-p3-n3 harmonic 39.27 113.80 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-p3-o harmonic 43.04 107.10 # SOURCE3 4 0.0000 + angle_coeff @angle:n3-p3-oh harmonic 43.13 98.36 # SOURCE3 1 + angle_coeff @angle:n4-p3-n4 harmonic 38.45 100.53 # SOURCE3 1 0.0000 + angle_coeff @angle:na-p3-na harmonic 39.91 106.22 # SOURCE3 1 + angle_coeff @angle:nh-p3-nh harmonic 40.11 109.11 # SOURCE3 1 0.0000 + angle_coeff @angle:n-p3-n harmonic 40.04 104.58 # SOURCE3 1 + angle_coeff @angle:n-p3-o harmonic 42.80 104.99 # SOURCE3 4 0.0000 + angle_coeff @angle:no-p3-no harmonic 39.64 98.33 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-p3-oh harmonic 42.77 104.48 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p3-o harmonic 43.78 122.18 # SOURCE3 2 7.8556 + angle_coeff @angle:o-p3-p3 harmonic 45.09 116.74 # SOURCE3 14 0.7525 + angle_coeff @angle:o-p3-p5 harmonic 46.98 107.62 # SOURCE3 4 0.0000 + angle_coeff @angle:o-p3-s4 harmonic 38.63 110.70 # SOURCE3 4 0.7259 + angle_coeff @angle:o-p3-s6 harmonic 39.52 106.66 # SOURCE3 6 3.4017 + angle_coeff @angle:os-p3-os harmonic 42.11 106.65 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-p3-p2 harmonic 59.12 103.58 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-p3-p3 harmonic 57.00 105.31 # SOURCE3 4 3.5864 + angle_coeff @angle:p4-p3-p4 harmonic 58.70 99.09 # SOURCE3 1 + angle_coeff @angle:p5-p3-p5 harmonic 58.78 99.10 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-p3-s4 harmonic 39.08 98.26 # SOURCE3 1 0.0000 + angle_coeff @angle:s6-p3-s6 harmonic 39.36 97.78 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-p3-sh harmonic 36.56 107.58 # SOURCE3 1 0.0000 + angle_coeff @angle:s-p3-s harmonic 34.08 131.32 # SOURCE3 1 + angle_coeff @angle:ss-p3-ss harmonic 36.47 109.24 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p4-br harmonic 41.07 110.41 # SOURCE3 1 + angle_coeff @angle:br-p4-o harmonic 37.80 124.80 # SOURCE3 1 + angle_coeff @angle:c2-p4-c2 harmonic 37.13 104.21 # SOURCE3 1 + angle_coeff @angle:c2-p4-hp harmonic 27.68 99.50 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-p4-o harmonic 39.43 113.59 # SOURCE3 1 + angle_coeff @angle:c3-p4-c3 harmonic 37.20 102.55 # SOURCE3 4 0.0192 + angle_coeff @angle:c3-p4-n2 harmonic 39.09 103.17 # SOURCE3 1 + angle_coeff @angle:c3-p4-n3 harmonic 39.50 102.37 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p4-n4 harmonic 37.54 99.57 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p4-n harmonic 38.98 103.26 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p4-na harmonic 37.92 117.67 # SOURCE3 5 19.0404 + angle_coeff @angle:c3-p4-nh harmonic 39.33 102.79 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p4-no harmonic 38.24 99.80 # SOURCE3 3 0.2151 + angle_coeff @angle:c3-p4-o harmonic 38.77 116.44 # SOURCE3 25 2.6494 + angle_coeff @angle:c3-p4-oh harmonic 41.01 98.56 # SOURCE3 2 0.4558 + angle_coeff @angle:c3-p4-os harmonic 41.17 98.01 # SOURCE3 2 0.0931 + angle_coeff @angle:c3-p4-p2 harmonic 44.43 109.27 # SOURCE3 1 + angle_coeff @angle:c3-p4-p3 harmonic 45.09 103.53 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p4-p4 harmonic 48.14 102.12 # SOURCE3 1 + angle_coeff @angle:c3-p4-p5 harmonic 44.64 104.15 # SOURCE3 1 + angle_coeff @angle:c3-p4-sh harmonic 37.43 100.17 # SOURCE3 2 0.0815 + angle_coeff @angle:c3-p4-ss harmonic 37.38 101.19 # SOURCE3 1 + angle_coeff @angle:ca-p4-ca harmonic 36.83 107.77 # SOURCE3 1 + angle_coeff @angle:ca-p4-o harmonic 40.03 111.64 # SOURCE3 1 + angle_coeff @angle:cl-p4-cl harmonic 33.80 103.51 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-p4-o harmonic 36.03 116.53 # SOURCE3 2 0.0000 + angle_coeff @angle:hp-p4-hp harmonic 22.57 99.21 # SOURCE3 4 6.4572 + angle_coeff @angle:hp-p4-n1 harmonic 30.24 99.91 # HF/6-31G* 1 + angle_coeff @angle:hp-p4-o harmonic 31.44 109.35 # SOURCE3 6 10.8284 + angle_coeff @angle:hp-p4-p3 harmonic 31.40 98.96 # SOURCE3 4 0.0000 + angle_coeff @angle:hp-p4-s harmonic 24.32 110.24 # SOURCE3 4 4.1081 + angle_coeff @angle:i-p4-i harmonic 38.53 113.22 # SOURCE3 2 6.7916 + angle_coeff @angle:i-p4-o harmonic 37.71 110.22 # SOURCE3 4 9.7726 + angle_coeff @angle:n1-p4-n1 harmonic 43.01 100.61 # HF/6-31G* 1 + angle_coeff @angle:n1-p4-o harmonic 42.53 114.59 # HF/6-31G* 1 + angle_coeff @angle:n2-p4-n2 harmonic 41.52 102.54 # SOURCE3 1 + angle_coeff @angle:n2-p4-o harmonic 40.81 120.28 # SOURCE3 1 + angle_coeff @angle:n3-p4-o harmonic 42.50 113.27 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-p4-o harmonic 39.56 107.61 # SOURCE3 1 0.0000 + angle_coeff @angle:na-p4-o harmonic 45.17 110.60 # SOURCE3 5 1.3133 + angle_coeff @angle:nh-p4-nh harmonic 43.52 95.30 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-p4-o harmonic 41.87 115.86 # SOURCE3 3 3.2712 + angle_coeff @angle:n-p4-o harmonic 41.05 117.99 # SOURCE3 1 0.0000 + angle_coeff @angle:no-p4-o harmonic 39.42 114.69 # SOURCE3 3 0.1070 + angle_coeff @angle:oh-p4-oh harmonic 45.67 95.71 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p4-o harmonic 45.06 117.22 # SOURCE3 6 2.7792 + angle_coeff @angle:o-p4-oh harmonic 42.88 117.39 # SOURCE3 4 1.0083 + angle_coeff @angle:o-p4-os harmonic 43.10 116.67 # SOURCE3 4 0.6923 + angle_coeff @angle:o-p4-p2 harmonic 44.91 121.35 # SOURCE3 1 + angle_coeff @angle:o-p4-p3 harmonic 45.60 114.00 # SOURCE3 3 0.6663 + angle_coeff @angle:o-p4-p4 harmonic 48.81 116.43 # SOURCE3 1 + angle_coeff @angle:o-p4-p5 harmonic 46.05 109.76 # SOURCE3 1 + angle_coeff @angle:o-p4-s4 harmonic 35.77 112.19 # SOURCE3 1 + angle_coeff @angle:o-p4-s6 harmonic 35.22 113.89 # SOURCE3 1 + angle_coeff @angle:o-p4-s harmonic 37.34 112.78 # SOURCE3 2 0.0000 + angle_coeff @angle:o-p4-sh harmonic 36.99 118.09 # SOURCE3 1 + angle_coeff @angle:os-p4-os harmonic 44.74 100.34 # SOURCE3 1 0.0000 + angle_coeff @angle:o-p4-ss harmonic 37.47 116.14 # SOURCE3 4 1.0636 + angle_coeff @angle:p2-p4-p2 harmonic 56.48 110.71 # SOURCE3 1 + angle_coeff @angle:p3-p4-p3 harmonic 54.50 114.98 # SOURCE3 1 0.0000 + angle_coeff @angle:p4-p4-p4 harmonic 61.44 107.38 # SOURCE3 1 + angle_coeff @angle:p5-p4-p5 harmonic 55.76 107.78 # SOURCE3 1 + angle_coeff @angle:s4-p4-s4 harmonic 36.61 96.24 # SOURCE3 1 + angle_coeff @angle:s6-p4-s6 harmonic 35.22 102.36 # SOURCE3 1 + angle_coeff @angle:sh-p4-sh harmonic 38.45 98.81 # SOURCE3 1 0.0000 + angle_coeff @angle:s-p4-s harmonic 36.54 106.30 # SOURCE3 2 25.0119 + angle_coeff @angle:ss-p4-ss harmonic 37.60 104.41 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p5-br harmonic 41.96 103.38 # SOURCE3 1 0.0000 + angle_coeff @angle:br-p5-o harmonic 39.04 114.65 # SOURCE3 3 1.0910 + angle_coeff @angle:br-p5-oh harmonic 40.90 102.92 # SOURCE3 4 0.5468 + angle_coeff @angle:c1-p5-c1 harmonic 38.83 102.89 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-p5-o harmonic 40.32 115.77 # SOURCE3 2 0.0000 + angle_coeff @angle:c1-p5-oh harmonic 41.43 102.79 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-p5-c2 harmonic 35.85 106.56 # SOURCE3 1 + angle_coeff @angle:c2-p5-o harmonic 39.62 109.24 # SOURCE4 7 2.2628 + angle_coeff @angle:c2-p5-oh harmonic 40.04 101.69 # SOURCE3 1 + angle_coeff @angle:c2-p5-os harmonic 39.90 103.34 # SOURCE3 1 + angle_coeff @angle:c3-p5-c3 harmonic 36.95 106.23 # SOURCE3 14 2.6389 + angle_coeff @angle:c3-p5-hp harmonic 27.05 103.62 # SOURCE4 7 1.1616 + angle_coeff @angle:c3-p5-n3 harmonic 40.01 102.76 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-p5-o harmonic 39.91 112.50 # SOURCE3 23 4.4203 + angle_coeff @angle:c3-p5-oh harmonic 40.83 101.56 # SOURCE3 17 2.1803 + angle_coeff @angle:c3-p5-os harmonic 41.20 100.77 # SOURCE4 51 2.0928 + angle_coeff @angle:c3-p5-p4 harmonic 44.32 106.27 # SOURCE3 1 + angle_coeff @angle:c3-p5-s harmonic 37.51 113.40 # SOURCE3 4 2.0067 + angle_coeff @angle:c3-p5-ss harmonic 36.91 103.76 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-p5-ca harmonic 37.10 107.53 # SOURCE3 1 + angle_coeff @angle:ca-p5-o harmonic 39.95 113.98 # SOURCE3 1 + angle_coeff @angle:ca-p5-oh harmonic 41.04 101.77 # SOURCE3 1 + angle_coeff @angle:ca-p5-os harmonic 40.86 103.75 # SOURCE3 1 + angle_coeff @angle:c-p5-c harmonic 35.96 104.16 # SOURCE3 1 + angle_coeff @angle:cl-p5-cl harmonic 33.77 103.70 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-p5-o harmonic 36.29 115.32 # SOURCE3 2 0.0000 + angle_coeff @angle:cl-p5-oh harmonic 37.85 102.44 # SOURCE3 2 0.0000 + angle_coeff @angle:c-p5-o harmonic 39.74 107.19 # SOURCE4 16 0.5711 + angle_coeff @angle:c-p5-oh harmonic 39.73 102.12 # SOURCE3 1 + angle_coeff @angle:f-p5-f harmonic 42.49 99.96 # SOURCE2 4 0.9197 + angle_coeff @angle:f-p5-o harmonic 43.22 112.03 # SOURCE4 7 0.5178 + angle_coeff @angle:f-p5-oh harmonic 43.33 101.98 # SOURCE3 2 0.0000 + angle_coeff @angle:f-p5-os harmonic 43.51 102.70 # SOURCE4 5 0.1524 + angle_coeff @angle:f-p5-s harmonic 38.09 117.40 # SOURCE2 1 0.0000 + angle_coeff @angle:hp-p5-hp harmonic 21.44 101.09 # SOURCE3 4 1.3036 + angle_coeff @angle:hp-p5-n1 harmonic 31.09 101.32 # HF/6-31G* 1 + angle_coeff @angle:hp-p5-o harmonic 30.21 116.58 # SOURCE3 7 1.3282 + angle_coeff @angle:hp-p5-oh harmonic 30.57 101.45 # SOURCE3 5 0.9084 + angle_coeff @angle:hp-p5-s harmonic 25.97 119.20 # SOURCE2 1 0.0000 + angle_coeff @angle:i-p5-i harmonic 35.88 107.17 # SOURCE3 1 0.0000 + angle_coeff @angle:i-p5-o harmonic 32.99 115.93 # SOURCE3 3 0.0415 + angle_coeff @angle:i-p5-oh harmonic 35.44 102.26 # SOURCE3 4 1.9577 + angle_coeff @angle:n1-p5-n1 harmonic 45.78 101.55 # HF/6-31G* 1 + angle_coeff @angle:n1-p5-o harmonic 44.71 113.78 # HF/6-31G* 1 + angle_coeff @angle:n2-p5-n2 harmonic 43.96 106.34 # SOURCE3 1 + angle_coeff @angle:n2-p5-o harmonic 44.30 113.53 # SOURCE3 1 + angle_coeff @angle:n2-p5-oh harmonic 44.68 102.40 # SOURCE3 1 + angle_coeff @angle:n3-p5-n3 harmonic 42.87 103.37 # SOURCE4 47 2.1009 + angle_coeff @angle:n3-p5-nh harmonic 42.63 104.02 # SOURCE4 5 1.8740 + angle_coeff @angle:n3-p5-o harmonic 43.02 114.64 # SOURCE4 76 2.2728 + angle_coeff @angle:n3-p5-oh harmonic 43.43 104.18 # SOURCE3 6 0.4373 + angle_coeff @angle:n3-p5-os harmonic 44.20 101.94 # SOURCE4 34 2.3553 + angle_coeff @angle:n3-p5-s harmonic 39.05 117.12 # SOURCE4 7 0.7109 + angle_coeff @angle:n4-p5-n4 harmonic 39.18 102.20 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-p5-o harmonic 41.10 109.78 # SOURCE3 5 2.7519 + angle_coeff @angle:n4-p5-oh harmonic 42.23 98.48 # SOURCE3 6 0.4104 + angle_coeff @angle:n4-p5-os harmonic 43.31 94.55 # SOURCE3 2 0.0000 + angle_coeff @angle:na-p5-na harmonic 40.56 108.57 # SOURCE3 1 0.0000 + angle_coeff @angle:na-p5-o harmonic 42.38 113.43 # SOURCE3 11 0.8968 + angle_coeff @angle:na-p5-oh harmonic 43.14 102.07 # SOURCE3 16 1.4144 + angle_coeff @angle:na-p5-os harmonic 43.20 103.06 # SOURCE3 4 0.7463 + angle_coeff @angle:nh-p5-nh harmonic 43.48 99.51 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-p5-o harmonic 42.11 118.91 # SOURCE3 3 1.3237 + angle_coeff @angle:nh-p5-oh harmonic 43.40 103.81 # SOURCE3 2 0.0000 + angle_coeff @angle:nh-p5-os harmonic 44.39 100.51 # SOURCE3 2 0.0000 + angle_coeff @angle:n-p5-n3 harmonic 42.13 104.11 # SOURCE4 11 1.4088 + angle_coeff @angle:n-p5-n harmonic 41.80 103.09 # SOURCE3 1 0.0000 + angle_coeff @angle:n-p5-o harmonic 43.40 108.73 # SOURCE4 5 0.2571 + angle_coeff @angle:n-p5-oh harmonic 43.17 102.44 # SOURCE3 4 0.0999 + angle_coeff @angle:no-p5-no harmonic 40.40 95.68 # SOURCE3 1 0.0000 + angle_coeff @angle:no-p5-o harmonic 40.49 112.75 # SOURCE3 4 3.3684 + angle_coeff @angle:no-p5-oh harmonic 41.56 101.35 # SOURCE3 2 0.0000 + angle_coeff @angle:no-p5-os harmonic 41.69 101.70 # SOURCE3 4 0.0565 + angle_coeff @angle:n-p5-os harmonic 43.85 100.48 # SOURCE3 2 0.0000 + angle_coeff @angle:oh-p5-oh harmonic 44.58 102.45 # SOURCE3 39 2.4223 + angle_coeff @angle:oh-p5-os harmonic 44.91 102.37 # SOURCE3 8 1.5063 + angle_coeff @angle:oh-p5-p2 harmonic 48.24 103.53 # SOURCE3 1 + angle_coeff @angle:oh-p5-p3 harmonic 47.55 103.83 # SOURCE3 13 0.4303 + angle_coeff @angle:oh-p5-p4 harmonic 47.57 101.79 # SOURCE3 1 + angle_coeff @angle:oh-p5-p5 harmonic 51.43 100.45 # SOURCE3 1 + angle_coeff @angle:oh-p5-s4 harmonic 40.30 103.24 # SOURCE3 1 + angle_coeff @angle:oh-p5-s6 harmonic 40.65 101.48 # SOURCE3 1 + angle_coeff @angle:oh-p5-s harmonic 42.20 102.88 # SOURCE3 3 1.6044 + angle_coeff @angle:oh-p5-sh harmonic 40.01 101.41 # SOURCE3 2 0.0000 + angle_coeff @angle:oh-p5-ss harmonic 38.95 104.33 # SOURCE3 6 2.0112 + angle_coeff @angle:o-p5-o harmonic 46.01 115.80 # SOURCE3 17 5.7902 + angle_coeff @angle:o-p5-oh harmonic 43.79 115.26 # SOURCE4 740 1.3004 + angle_coeff @angle:o-p5-os harmonic 44.01 116.09 # SOURCE3 35 3.2062 + angle_coeff @angle:o-p5-p2 harmonic 46.23 114.60 # SOURCE3 1 + angle_coeff @angle:o-p5-p3 harmonic 45.38 115.48 # SOURCE3 9 2.1084 + angle_coeff @angle:o-p5-p4 harmonic 45.07 114.66 # SOURCE3 1 + angle_coeff @angle:o-p5-p5 harmonic 49.11 113.44 # SOURCE3 1 + angle_coeff @angle:o-p5-s4 harmonic 39.61 110.23 # SOURCE3 1 + angle_coeff @angle:o-p5-s6 harmonic 39.34 111.75 # SOURCE3 1 + angle_coeff @angle:o-p5-s harmonic 40.46 116.94 # SOURCE3 3 2.9506 + angle_coeff @angle:o-p5-sh harmonic 38.14 114.56 # SOURCE3 3 1.7645 + angle_coeff @angle:os-p5-os harmonic 45.37 101.77 # SOURCE4 243 2.0816 + angle_coeff @angle:os-p5-p3 harmonic 47.66 103.67 # SOURCE3 2 0.0000 + angle_coeff @angle:os-p5-p5 harmonic 50.58 104.48 # SOURCE3 1 + angle_coeff @angle:os-p5-s4 harmonic 40.57 102.52 # SOURCE3 1 + angle_coeff @angle:os-p5-s6 harmonic 40.69 101.89 # SOURCE3 1 + angle_coeff @angle:o-p5-ss harmonic 37.95 112.46 # SOURCE3 6 2.7392 + angle_coeff @angle:os-p5-s harmonic 39.69 117.28 # SOURCE4 74 0.7542 + angle_coeff @angle:os-p5-sh harmonic 39.51 104.59 # SOURCE3 2 0.0000 + angle_coeff @angle:os-p5-ss harmonic 39.36 102.65 # SOURCE4 25 1.8093 + angle_coeff @angle:p2-p5-p2 harmonic 57.39 107.14 # SOURCE3 1 + angle_coeff @angle:p3-p5-p3 harmonic 57.04 105.23 # SOURCE3 3 5.1024 + angle_coeff @angle:p4-p5-p4 harmonic 57.42 101.62 # SOURCE3 1 + angle_coeff @angle:p5-p5-p5 harmonic 59.38 112.72 # SOURCE3 1 + angle_coeff @angle:s6-p5-s6 harmonic 38.64 105.18 # SOURCE3 1 + angle_coeff @angle:sh-p5-sh harmonic 37.97 104.56 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-p5-ss harmonic 37.22 107.13 # SOURCE3 1 + angle_coeff @angle:s-p5-s harmonic 39.37 114.13 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-p5-ss harmonic 36.51 109.61 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-pc-n harmonic 42.75 90.80 # SOURCE3 3 2.3423 + angle_coeff @angle:cd-pc-na harmonic 43.00 90.18 # SOURCE3 81 2.7619 + angle_coeff @angle:cc-pd-n harmonic 42.75 90.80 # SOURCE3 3 same_as_cd-pc-n + angle_coeff @angle:cc-pd-na harmonic 43.00 90.18 # SOURCE3 81 same_as_cd-pc-na + angle_coeff @angle:c2-pe-ca harmonic 38.84 101.44 # SOURCE3 3 0.7177 + angle_coeff @angle:c2-pe-ce harmonic 38.68 103.01 # SOURCE3 4 1.4470 + angle_coeff @angle:c2-pe-cg harmonic 40.85 104.03 # SOURCE3 3 3.8740 + angle_coeff @angle:c2-pe-n2 harmonic 44.94 94.14 # SOURCE3 1 + angle_coeff @angle:c2-pe-ne harmonic 41.85 98.70 # SOURCE3 12 5.3383 + angle_coeff @angle:c2-pe-o harmonic 41.06 115.16 # SOURCE3 2 0.0149 + angle_coeff @angle:c2-pe-p2 harmonic 50.94 107.82 # SOURCE3 1 + angle_coeff @angle:c2-pe-pe harmonic 48.17 102.99 # SOURCE3 9 8.2860 + angle_coeff @angle:c2-pe-px harmonic 51.11 97.37 # SOURCE3 4 0.6655 + angle_coeff @angle:c2-pe-py harmonic 50.92 96.71 # SOURCE3 4 1.2755 + angle_coeff @angle:c2-pe-s harmonic 41.06 111.16 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-pe-sx harmonic 38.51 95.11 # SOURCE3 4 0.2676 + angle_coeff @angle:c2-pe-sy harmonic 37.78 95.56 # SOURCE3 2 0.0462 + angle_coeff @angle:ca-pe-n2 harmonic 40.97 102.03 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-pe-o harmonic 40.40 106.88 # SOURCE3 2 0.0018 + angle_coeff @angle:ca-pe-p2 harmonic 50.96 100.79 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-pe-pf harmonic 48.44 99.70 # SOURCE3 2 0.0000 + angle_coeff @angle:ca-pe-s harmonic 40.07 107.93 # SOURCE3 1 0.0000 + angle_coeff @angle:c-pe-c2 harmonic 38.58 97.30 # SOURCE3 3 0.0335 + angle_coeff @angle:ce-pe-n2 harmonic 41.45 100.55 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-pe-o harmonic 40.47 107.44 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-pe-p2 harmonic 51.42 99.56 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-pe-s harmonic 40.65 105.54 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-pe-n2 harmonic 44.31 101.79 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-pe-o harmonic 43.57 107.62 # SOURCE3 1 0.0000 + angle_coeff @angle:cg-pe-p2 harmonic 52.47 104.68 # SOURCE3 2 5.1435 + angle_coeff @angle:cg-pe-s harmonic 42.30 108.60 # SOURCE3 4 2.6981 + angle_coeff @angle:n2-pe-n2 harmonic 45.26 108.14 # SOURCE3 1 + angle_coeff @angle:n2-pe-ne harmonic 42.89 106.80 # SOURCE3 6 4.5981 + angle_coeff @angle:n2-pe-o harmonic 44.34 115.39 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-pe-p2 harmonic 52.85 111.60 # SOURCE3 1 + angle_coeff @angle:n2-pe-pe harmonic 48.70 109.40 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-pe-px harmonic 50.28 110.30 # SOURCE3 3 6.0548 + angle_coeff @angle:n2-pe-py harmonic 54.11 93.68 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-pe-s harmonic 42.94 114.84 # SOURCE3 3 3.6512 + angle_coeff @angle:n2-pe-sx harmonic 39.42 97.83 # SOURCE3 1 0.0000 + angle_coeff @angle:n2-pe-sy harmonic 38.61 98.14 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-pe-o harmonic 42.65 110.24 # SOURCE3 3 3.8478 + angle_coeff @angle:ne-pe-p2 harmonic 52.77 104.48 # SOURCE3 2 7.1207 + angle_coeff @angle:ne-pe-s harmonic 42.21 109.19 # SOURCE3 5 3.6708 + angle_coeff @angle:o-pe-o harmonic 44.01 119.96 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-p2 harmonic 52.71 114.23 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-pe harmonic 42.47 145.96 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-px harmonic 52.10 104.37 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-py harmonic 51.64 104.49 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-s harmonic 42.89 117.42 # SOURCE3 2 0.0426 + angle_coeff @angle:o-pe-sx harmonic 38.02 106.59 # SOURCE3 1 0.0000 + angle_coeff @angle:o-pe-sy harmonic 37.56 105.04 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-pe-pe harmonic 65.58 98.24 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-pe-px harmonic 64.12 108.28 # SOURCE3 2 6.2959 + angle_coeff @angle:p2-pe-py harmonic 62.99 110.87 # SOURCE3 3 8.1645 + angle_coeff @angle:p2-pe-s harmonic 53.42 111.28 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-pe-sx harmonic 51.26 95.73 # SOURCE3 1 0.0000 + angle_coeff @angle:p2-pe-sy harmonic 50.47 95.95 # SOURCE3 1 0.0000 + angle_coeff @angle:pe-pe-s harmonic 50.40 107.91 # SOURCE3 2 1.5577 + angle_coeff @angle:px-pe-s harmonic 51.97 107.62 # SOURCE3 2 3.7266 + angle_coeff @angle:py-pe-s harmonic 51.36 108.73 # SOURCE3 3 5.3201 + angle_coeff @angle:s-pe-s harmonic 34.43 178.44 # SOURCE3 1 0.0000 + angle_coeff @angle:s-pe-sx harmonic 38.72 108.32 # SOURCE3 2 3.0318 + angle_coeff @angle:s-pe-sy harmonic 38.35 106.93 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-pf-ca harmonic 38.84 101.44 # SOURCE3 3 same_as_c2-pe-ca + angle_coeff @angle:c2-pf-cf harmonic 38.68 103.01 # SOURCE3 4 same_as_c2-pe-ce + angle_coeff @angle:c2-pf-ch harmonic 40.85 104.03 # SOURCE3 3 same_as_c2-pe-cg + angle_coeff @angle:c2-pf-n2 harmonic 44.94 94.14 # SOURCE3 1 same_as_c2-pe-n2 + angle_coeff @angle:c2-pf-nf harmonic 41.85 98.70 # SOURCE3 12 same_as_c2-pe-ne + angle_coeff @angle:c2-pf-o harmonic 41.06 115.16 # SOURCE3 2 same_as_c2-pe-o + angle_coeff @angle:c2-pf-p2 harmonic 50.94 107.82 # SOURCE3 1 same_as_c2-pe-p2 + angle_coeff @angle:c2-pf-pf harmonic 48.17 102.99 # SOURCE3 9 same_as_c2-pe-pe + angle_coeff @angle:c2-pf-px harmonic 51.11 97.37 # SOURCE3 4 same_as_c2-pe-px + angle_coeff @angle:c2-pf-py harmonic 50.92 96.71 # SOURCE3 4 same_as_c2-pe-py + angle_coeff @angle:c2-pf-s harmonic 41.06 111.16 # SOURCE3 2 same_as_c2-pe-s + angle_coeff @angle:c2-pf-sx harmonic 38.51 95.11 # SOURCE3 4 same_as_c2-pe-sx + angle_coeff @angle:c2-pf-sy harmonic 37.78 95.56 # SOURCE3 2 same_as_c2-pe-sy + angle_coeff @angle:ca-pf-n2 harmonic 40.97 102.03 # SOURCE3 1 same_as_ca-pe-n2 + angle_coeff @angle:ca-pf-o harmonic 40.40 106.88 # SOURCE3 2 same_as_ca-pe-o + angle_coeff @angle:ca-pf-p2 harmonic 50.96 100.79 # SOURCE3 1 same_as_ca-pe-p2 + angle_coeff @angle:ca-pf-pe harmonic 48.44 99.70 # SOURCE3 2 0.0000 + angle_coeff @angle:ca-pf-s harmonic 40.07 107.93 # SOURCE3 1 same_as_ca-pe-s + angle_coeff @angle:c-pf-c2 harmonic 38.58 97.30 # SOURCE3 3 same_as_c-pe-c2 + angle_coeff @angle:cf-pf-n2 harmonic 41.45 100.55 # SOURCE3 1 same_as_ce-pe-n2 + angle_coeff @angle:cf-pf-o harmonic 40.47 107.44 # SOURCE3 1 same_as_ce-pe-o + angle_coeff @angle:cf-pf-p2 harmonic 51.42 99.56 # SOURCE3 1 same_as_ce-pe-p2 + angle_coeff @angle:cf-pf-s harmonic 40.65 105.54 # SOURCE3 1 same_as_ce-pe-s + angle_coeff @angle:ch-pf-n2 harmonic 44.31 101.79 # SOURCE3 1 same_as_cg-pe-n2 + angle_coeff @angle:ch-pf-o harmonic 43.57 107.62 # SOURCE3 1 same_as_cg-pe-o + angle_coeff @angle:ch-pf-p2 harmonic 52.47 104.68 # SOURCE3 2 same_as_cg-pe-p2 + angle_coeff @angle:ch-pf-s harmonic 42.30 108.60 # SOURCE3 4 same_as_cg-pe-s + angle_coeff @angle:n2-pf-n2 harmonic 45.26 108.14 # SOURCE3 1 same_as_n2-pe-n2 + angle_coeff @angle:n2-pf-nf harmonic 42.89 106.80 # SOURCE3 6 same_as_n2-pe-ne + angle_coeff @angle:n2-pf-o harmonic 44.34 115.39 # SOURCE3 1 same_as_n2-pe-o + angle_coeff @angle:n2-pf-p2 harmonic 52.85 111.60 # SOURCE3 1 same_as_n2-pe-p2 + angle_coeff @angle:n2-pf-pf harmonic 48.70 109.40 # SOURCE3 1 same_as_n2-pe-pe + angle_coeff @angle:n2-pf-px harmonic 50.28 110.30 # SOURCE3 3 same_as_n2-pe-px + angle_coeff @angle:n2-pf-py harmonic 54.11 93.68 # SOURCE3 1 same_as_n2-pe-py + angle_coeff @angle:n2-pf-s harmonic 42.94 114.84 # SOURCE3 3 same_as_n2-pe-s + angle_coeff @angle:n2-pf-sx harmonic 39.42 97.83 # SOURCE3 1 same_as_n2-pe-sx + angle_coeff @angle:n2-pf-sy harmonic 38.61 98.14 # SOURCE3 1 same_as_n2-pe-sy + angle_coeff @angle:nf-pf-o harmonic 42.65 110.24 # SOURCE3 3 same_as_ne-pe-o + angle_coeff @angle:nf-pf-p2 harmonic 52.77 104.48 # SOURCE3 2 same_as_ne-pe-p2 + angle_coeff @angle:nf-pf-s harmonic 42.21 109.19 # SOURCE3 5 same_as_ne-pe-s + angle_coeff @angle:o-pf-o harmonic 44.01 119.96 # SOURCE3 1 same_as_o-pe-o + angle_coeff @angle:o-pf-p2 harmonic 52.71 114.23 # SOURCE3 1 same_as_o-pe-p2 + angle_coeff @angle:o-pf-pf harmonic 42.47 145.96 # SOURCE3 1 same_as_o-pe-pe + angle_coeff @angle:o-pf-px harmonic 52.10 104.37 # SOURCE3 1 same_as_o-pe-px + angle_coeff @angle:o-pf-py harmonic 51.64 104.49 # SOURCE3 1 same_as_o-pe-py + angle_coeff @angle:o-pf-s harmonic 42.89 117.42 # SOURCE3 2 same_as_o-pe-s + angle_coeff @angle:o-pf-sx harmonic 38.02 106.59 # SOURCE3 1 same_as_o-pe-sx + angle_coeff @angle:o-pf-sy harmonic 37.56 105.04 # SOURCE3 1 same_as_o-pe-sy + angle_coeff @angle:p2-pf-pf harmonic 65.58 98.24 # SOURCE3 1 same_as_p2-pe-pe + angle_coeff @angle:p2-pf-px harmonic 64.12 108.28 # SOURCE3 2 same_as_p2-pe-px + angle_coeff @angle:p2-pf-py harmonic 62.99 110.87 # SOURCE3 3 same_as_p2-pe-py + angle_coeff @angle:p2-pf-s harmonic 53.42 111.28 # SOURCE3 1 same_as_p2-pe-s + angle_coeff @angle:p2-pf-sx harmonic 51.26 95.73 # SOURCE3 1 same_as_p2-pe-sx + angle_coeff @angle:p2-pf-sy harmonic 50.47 95.95 # SOURCE3 1 same_as_p2-pe-sy + angle_coeff @angle:pf-pf-s harmonic 50.40 107.91 # SOURCE3 2 same_as_pe-pe-s + angle_coeff @angle:px-pf-s harmonic 51.97 107.62 # SOURCE3 2 same_as_px-pe-s + angle_coeff @angle:py-pf-s harmonic 51.36 108.73 # SOURCE3 3 same_as_py-pe-s + angle_coeff @angle:s-pf-s harmonic 34.43 178.44 # SOURCE3 1 same_as_s-pe-s + angle_coeff @angle:s-pf-sx harmonic 38.72 108.32 # SOURCE3 2 same_as_s-pe-sx + angle_coeff @angle:s-pf-sy harmonic 38.35 106.93 # SOURCE3 1 same_as_s-pe-sy + angle_coeff @angle:c3-px-ca harmonic 36.97 104.79 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-px-ce harmonic 37.00 104.86 # SOURCE3 4 0.6354 + angle_coeff @angle:c3-px-cf harmonic 37.00 104.86 # SOURCE3 4 same_as_c3-px-ce + angle_coeff @angle:c3-px-ne harmonic 39.55 102.46 # SOURCE3 7 1.8685 + angle_coeff @angle:c3-px-nf harmonic 39.55 102.46 # SOURCE3 7 same_as_c3-px-ne + angle_coeff @angle:c3-px-o harmonic 39.39 113.68 # SOURCE3 28 4.8990 + angle_coeff @angle:c3-px-pe harmonic 47.82 105.73 # SOURCE3 10 4.4059 + angle_coeff @angle:c3-px-pf harmonic 47.82 105.73 # SOURCE3 10 same_as_c3-px-pe + angle_coeff @angle:c3-px-py harmonic 45.50 103.11 # SOURCE3 3 0.8680 + angle_coeff @angle:c3-px-sx harmonic 36.06 99.55 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-px-sy harmonic 35.30 103.41 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-px-ca harmonic 37.08 104.15 # SOURCE3 2 3.6168 + angle_coeff @angle:ca-px-o harmonic 40.49 107.50 # SOURCE3 5 5.7355 + angle_coeff @angle:c-px-c3 harmonic 36.70 101.72 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-px-ce harmonic 37.15 104.21 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-px-o harmonic 39.42 113.79 # SOURCE3 6 0.3877 + angle_coeff @angle:cf-px-cf harmonic 37.15 104.21 # SOURCE3 1 same_as_ce-px-ce + angle_coeff @angle:cf-px-o harmonic 39.42 113.79 # SOURCE3 6 same_as_ce-px-o + angle_coeff @angle:c-px-o harmonic 37.98 114.47 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-px-ne harmonic 41.92 103.22 # SOURCE3 2 0.6807 + angle_coeff @angle:ne-px-o harmonic 42.27 114.13 # SOURCE3 11 8.9737 + angle_coeff @angle:nf-px-nf harmonic 41.92 103.22 # SOURCE3 2 same_as_ne-px-ne + angle_coeff @angle:nf-px-o harmonic 42.27 114.13 # SOURCE3 11 same_as_ne-px-o + angle_coeff @angle:o-px-pe harmonic 49.41 116.50 # SOURCE3 12 8.2925 + angle_coeff @angle:o-px-pf harmonic 49.41 116.50 # SOURCE3 12 same_as_o-px-pe + angle_coeff @angle:o-px-py harmonic 45.90 114.20 # SOURCE3 5 1.7165 + angle_coeff @angle:o-px-sx harmonic 35.81 112.81 # SOURCE3 3 0.8799 + angle_coeff @angle:o-px-sy harmonic 35.59 113.54 # SOURCE3 3 0.5010 + angle_coeff @angle:pe-px-pe harmonic 61.38 110.71 # SOURCE3 1 0.0000 + angle_coeff @angle:pf-px-pf harmonic 61.38 110.71 # SOURCE3 1 same_as_pe-px-pe + angle_coeff @angle:py-px-py harmonic 56.72 107.78 # SOURCE3 1 0.0000 + angle_coeff @angle:sx-px-sx harmonic 36.76 96.24 # SOURCE3 1 0.0000 + angle_coeff @angle:sy-px-sy harmonic 35.53 102.36 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-py-n4 harmonic 37.34 103.83 # SOURCE3 4 0.0000 + angle_coeff @angle:c3-py-na harmonic 38.76 106.89 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-py-o harmonic 38.95 117.87 # SOURCE3 13 2.3554 + angle_coeff @angle:c3-py-oh harmonic 41.22 100.16 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-py-os harmonic 40.15 105.39 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-py-px harmonic 44.89 106.27 # SOURCE3 2 0.0000 + angle_coeff @angle:c3-py-py harmonic 43.54 113.97 # SOURCE3 10 1.6346 + angle_coeff @angle:c3-py-sx harmonic 34.74 106.36 # SOURCE3 4 0.0000 + angle_coeff @angle:ca-py-ca harmonic 36.99 107.55 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-py-o harmonic 39.82 113.98 # SOURCE3 3 0.5309 + angle_coeff @angle:ca-py-oh harmonic 40.90 102.68 # SOURCE4 5 1.2945 + angle_coeff @angle:ca-py-os harmonic 40.66 103.75 # SOURCE3 2 0.0000 + angle_coeff @angle:c-py-c3 harmonic 35.71 110.36 # SOURCE3 1 0.0000 + angle_coeff @angle:c-py-c harmonic 36.23 104.20 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-py-ce harmonic 37.29 106.54 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-py-o harmonic 40.24 112.16 # SOURCE3 5 3.2594 + angle_coeff @angle:ce-py-oh harmonic 40.58 104.77 # SOURCE3 6 2.1852 + angle_coeff @angle:ce-py-os harmonic 40.82 103.34 # SOURCE3 2 0.0000 + angle_coeff @angle:cf-py-cf harmonic 37.29 106.54 # SOURCE3 1 same_as_ce-py-ce + angle_coeff @angle:cf-py-o harmonic 40.24 112.16 # SOURCE3 5 same_as_ce-py-o + angle_coeff @angle:cf-py-oh harmonic 40.58 104.77 # SOURCE3 6 same_as_ce-py-oh + angle_coeff @angle:cf-py-os harmonic 40.82 103.34 # SOURCE3 2 same_as_ce-py-os + angle_coeff @angle:c-py-o harmonic 38.52 115.25 # SOURCE3 6 2.6519 + angle_coeff @angle:c-py-oh harmonic 40.03 102.14 # SOURCE3 6 1.0654 + angle_coeff @angle:c-py-os harmonic 41.32 95.74 # SOURCE3 3 9.0999 + angle_coeff @angle:n3-py-ne harmonic 41.93 108.44 # SOURCE4 12 0.9498 + angle_coeff @angle:n4-py-o harmonic 38.83 115.58 # SOURCE3 4 0.0000 + angle_coeff @angle:n4-py-py harmonic 63.24 55.10 # SOURCE3 4 0.0000 + angle_coeff @angle:na-py-o harmonic 40.78 122.40 # SOURCE3 2 0.0000 + angle_coeff @angle:na-py-py harmonic 67.66 50.88 # SOURCE3 2 0.0000 + angle_coeff @angle:ne-py-ne harmonic 43.51 106.29 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-py-o harmonic 44.00 113.21 # SOURCE3 15 3.8894 + angle_coeff @angle:ne-py-oh harmonic 44.13 104.70 # SOURCE3 26 2.7513 + angle_coeff @angle:ne-py-os harmonic 44.80 101.33 # SOURCE3 2 0.0000 + angle_coeff @angle:nf-py-nf harmonic 43.51 106.29 # SOURCE3 1 same_as_ne-py-ne + angle_coeff @angle:nf-py-o harmonic 44.00 113.21 # SOURCE3 15 same_as_ne-py-o + angle_coeff @angle:nf-py-oh harmonic 44.13 104.70 # SOURCE3 26 same_as_ne-py-oh + angle_coeff @angle:nf-py-os harmonic 44.80 101.33 # SOURCE3 2 same_as_ne-py-os + angle_coeff @angle:oh-py-oh harmonic 45.06 101.78 # SOURCE3 35 2.2937 + angle_coeff @angle:oh-py-pe harmonic 50.99 104.84 # SOURCE3 22 2.0337 + angle_coeff @angle:oh-py-pf harmonic 50.99 104.84 # SOURCE3 22 same_as_oh-py-pe + angle_coeff @angle:oh-py-px harmonic 47.75 104.30 # SOURCE3 8 1.2772 + angle_coeff @angle:oh-py-py harmonic 48.91 100.45 # SOURCE3 6 0.0000 + angle_coeff @angle:oh-py-sx harmonic 37.44 100.94 # SOURCE3 4 0.0000 + angle_coeff @angle:oh-py-sy harmonic 38.51 101.47 # SOURCE3 6 0.2490 + angle_coeff @angle:o-py-oh harmonic 43.74 116.14 # SOURCE3 79 2.1455 + angle_coeff @angle:o-py-os harmonic 43.55 116.79 # SOURCE3 17 1.3534 + angle_coeff @angle:o-py-pe harmonic 49.46 114.56 # SOURCE3 12 3.6114 + angle_coeff @angle:o-py-pf harmonic 49.46 114.56 # SOURCE3 12 same_as_o-py-pe + angle_coeff @angle:o-py-px harmonic 46.50 111.37 # SOURCE3 5 0.3803 + angle_coeff @angle:o-py-py harmonic 44.97 120.43 # SOURCE3 16 6.0629 + angle_coeff @angle:os-py-os harmonic 45.06 101.25 # SOURCE3 8 2.0860 + angle_coeff @angle:os-py-py harmonic 47.94 104.48 # SOURCE3 4 0.0000 + angle_coeff @angle:os-py-sx harmonic 36.90 103.86 # SOURCE3 2 0.0000 + angle_coeff @angle:os-py-sy harmonic 38.37 102.12 # SOURCE3 2 0.0000 + angle_coeff @angle:o-py-sx harmonic 34.68 118.56 # SOURCE3 7 6.2976 + angle_coeff @angle:o-py-sy harmonic 36.96 111.71 # SOURCE3 5 1.1937 + angle_coeff @angle:pe-py-pe harmonic 61.78 107.14 # SOURCE3 1 0.0000 + angle_coeff @angle:pf-py-pf harmonic 61.78 107.14 # SOURCE3 1 same_as_pe-py-pe + angle_coeff @angle:py-py-py harmonic 55.80 112.70 # SOURCE3 1 0.0000 + angle_coeff @angle:py-py-sx harmonic 58.65 61.54 # SOURCE3 4 0.0000 + angle_coeff @angle:sy-py-sy harmonic 36.13 105.17 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-s2-o harmonic 65.76 117.25 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-s2-n2 harmonic 68.67 110.84 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-s2-o harmonic 66.18 114.70 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-s2-n1 harmonic 53.42 117.70 # SOURCE2 1 0.0000 + angle_coeff @angle:f-s2-n1 harmonic 66.15 116.90 # SOURCE2 1 0.0000 + angle_coeff @angle:n1-s2-o harmonic 73.05 108.46 # HF/6-31G* 1 + angle_coeff @angle:n2-s2-o harmonic 67.93 121.20 # SOURCE2 2 0.8000 + angle_coeff @angle:o-s2-o harmonic 67.99 116.17 # SOURCE3 1 0.0000 + angle_coeff @angle:o-s2-s harmonic 63.79 118.30 # SOURCE2 1 0.0000 + angle_coeff @angle:s-s2-s harmonic 63.50 115.04 # SOURCE3 1 0.0000 + angle_coeff @angle:br-s4-br harmonic 64.61 98.02 # SOURCE3 1 + angle_coeff @angle:br-s4-c3 harmonic 62.19 92.98 # SOURCE3 1 0.0000 + angle_coeff @angle:br-s4-o harmonic 59.20 112.07 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-s4-c1 harmonic 65.35 93.55 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-s4-o harmonic 65.98 110.36 # SOURCE3 2 0.0000 + angle_coeff @angle:c2-s4-c2 harmonic 62.00 102.29 # SOURCE3 1 + angle_coeff @angle:c2-s4-c3 harmonic 63.48 94.95 # SOURCE3 1 + angle_coeff @angle:c2-s4-o harmonic 66.61 107.09 # SOURCE3 1 + angle_coeff @angle:c3-s4-c3 harmonic 62.07 96.82 # SOURCE3 11 1.5580 + angle_coeff @angle:c3-s4-ca harmonic 62.99 95.00 # SOURCE3 1 + angle_coeff @angle:c3-s4-f harmonic 66.32 91.70 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-hs harmonic 46.55 90.60 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-i harmonic 52.86 90.53 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-n2 harmonic 69.07 90.59 # SOURCE3 1 + angle_coeff @angle:c3-s4-n3 harmonic 65.18 94.49 # SOURCE3 4 1.5570 + angle_coeff @angle:c3-s4-n harmonic 64.28 96.07 # SOURCE3 4 1.0354 + angle_coeff @angle:c3-s4-n4 harmonic 61.99 92.47 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-na harmonic 65.11 93.07 # SOURCE3 10 1.8813 + angle_coeff @angle:c3-s4-nh harmonic 64.51 97.08 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-no harmonic 62.53 89.53 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-o harmonic 65.63 106.21 # SOURCE3 60 2.0426 + angle_coeff @angle:c3-s4-oh harmonic 68.22 90.25 # SOURCE4 8 0.3023 + angle_coeff @angle:c3-s4-os harmonic 68.23 90.06 # SOURCE3 4 0.4484 + angle_coeff @angle:c3-s4-p2 harmonic 76.43 94.37 # SOURCE3 1 + angle_coeff @angle:c3-s4-p3 harmonic 78.19 96.54 # SOURCE3 4 1.3634 + angle_coeff @angle:c3-s4-p4 harmonic 73.69 97.40 # SOURCE3 1 + angle_coeff @angle:c3-s4-p5 harmonic 78.32 99.18 # SOURCE3 1 + angle_coeff @angle:c3-s4-s4 harmonic 64.31 89.50 # SOURCE3 1 + angle_coeff @angle:c3-s4-s harmonic 61.31 98.72 # SOURCE3 2 0.0185 + angle_coeff @angle:c3-s4-s6 harmonic 61.62 97.48 # SOURCE3 1 + angle_coeff @angle:c3-s4-sh harmonic 60.74 94.66 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s4-ss harmonic 60.58 95.31 # SOURCE3 3 1.4101 + angle_coeff @angle:ca-s4-ca harmonic 63.26 95.21 # SOURCE3 1 + angle_coeff @angle:ca-s4-o harmonic 66.01 106.63 # SOURCE3 1 + angle_coeff @angle:c-s4-c3 harmonic 61.53 95.07 # SOURCE3 1 + angle_coeff @angle:c-s4-c harmonic 63.34 86.83 # SOURCE3 1 + angle_coeff @angle:cl-s4-cl harmonic 53.89 97.68 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-s4-o harmonic 58.13 108.34 # SOURCE3 2 0.0000 + angle_coeff @angle:c-s4-o harmonic 63.97 106.17 # SOURCE3 1 + angle_coeff @angle:cx-s4-cx harmonic 86.71 48.80 # SOURCE2 1 0.0000 + angle_coeff @angle:cx-s4-o harmonic 64.10 110.00 # SOURCE2 1 0.0000 + angle_coeff @angle:f-s4-f harmonic 69.99 92.71 # SOURCE2 3 0.1490 + angle_coeff @angle:f-s4-o harmonic 70.11 106.81 # SOURCE2 2 0.0100 + angle_coeff @angle:f-s4-s harmonic 59.78 107.50 # SOURCE2 1 0.0000 + angle_coeff @angle:hs-s4-hs harmonic 37.79 87.00 # SOURCE3 2 0.0202 + angle_coeff @angle:hs-s4-n1 harmonic 51.22 90.51 # HF/6-31G* 1 + angle_coeff @angle:hs-s4-o harmonic 49.80 110.27 # SOURCE3 5 0.1908 + angle_coeff @angle:i-s4-i harmonic 54.45 97.29 # SOURCE3 1 + angle_coeff @angle:i-s4-o harmonic 47.32 113.91 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-s4-n1 harmonic 72.41 94.02 # HF/6-31G* 1 + angle_coeff @angle:n1-s4-o harmonic 70.24 110.09 # HF/6-31G* 1 + angle_coeff @angle:n2-s4-n2 harmonic 75.77 90.17 # SOURCE3 1 + angle_coeff @angle:n2-s4-o harmonic 72.12 107.57 # SOURCE3 1 + angle_coeff @angle:n3-s4-n3 harmonic 68.89 91.19 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-s4-o harmonic 67.59 109.07 # SOURCE3 6 2.3605 + angle_coeff @angle:n4-s4-n4 harmonic 60.39 94.61 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-s4-o harmonic 63.17 104.91 # SOURCE3 3 0.4370 + angle_coeff @angle:na-s4-na harmonic 63.63 103.10 # SOURCE3 1 + angle_coeff @angle:na-s4-o harmonic 66.52 109.75 # SOURCE3 10 2.6919 + angle_coeff @angle:nh-s4-nh harmonic 68.96 92.24 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-s4-o harmonic 68.40 107.54 # SOURCE3 3 0.0401 + angle_coeff @angle:n-s4-n harmonic 68.03 91.30 # SOURCE3 1 + angle_coeff @angle:n-s4-o harmonic 68.09 105.70 # SOURCE3 4 1.6857 + angle_coeff @angle:no-s4-no harmonic 63.55 83.40 # SOURCE3 1 0.0000 + angle_coeff @angle:no-s4-o harmonic 62.93 103.58 # SOURCE3 3 1.5109 + angle_coeff @angle:oh-s4-oh harmonic 69.00 100.34 # SOURCE3 1 + angle_coeff @angle:o-s4-o harmonic 74.43 110.61 # SOURCE3 5 3.6413 + angle_coeff @angle:o-s4-oh harmonic 69.42 110.13 # SOURCE4 10 0.5760 + angle_coeff @angle:o-s4-os harmonic 69.67 109.02 # SOURCE3 8 1.5005 + angle_coeff @angle:o-s4-p2 harmonic 76.18 106.77 # SOURCE3 1 + angle_coeff @angle:o-s4-p3 harmonic 79.76 106.51 # SOURCE3 8 4.0943 + angle_coeff @angle:o-s4-p4 harmonic 75.38 103.36 # SOURCE3 1 + angle_coeff @angle:o-s4-p5 harmonic 85.32 96.95 # SOURCE3 1 + angle_coeff @angle:o-s4-s4 harmonic 63.80 104.55 # SOURCE3 1 + angle_coeff @angle:o-s4-s harmonic 61.69 112.22 # SOURCE3 4 2.8682 + angle_coeff @angle:o-s4-s6 harmonic 64.33 102.84 # SOURCE3 1 + angle_coeff @angle:o-s4-sh harmonic 60.56 107.51 # SOURCE3 3 0.7511 + angle_coeff @angle:os-s4-os harmonic 71.26 93.68 # SOURCE3 2 2.4166 + angle_coeff @angle:o-s4-ss harmonic 60.06 109.49 # SOURCE3 5 1.8509 + angle_coeff @angle:p2-s4-p2 harmonic 98.20 92.62 # SOURCE3 1 + angle_coeff @angle:p3-s4-p3 harmonic 101.37 95.71 # SOURCE3 2 1.2239 + angle_coeff @angle:p5-s4-p5 harmonic 104.72 93.86 # SOURCE3 1 + angle_coeff @angle:s4-s4-s4 harmonic 65.42 90.17 # SOURCE3 1 + angle_coeff @angle:s4-s4-s6 harmonic 65.42 90.17 # SOURCE3 1 + angle_coeff @angle:s6-s4-s6 harmonic 64.23 93.52 # SOURCE3 1 + angle_coeff @angle:sh-s4-sh harmonic 58.79 102.76 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-s4-ss harmonic 58.85 102.64 # SOURCE3 1 + angle_coeff @angle:s-s4-s harmonic 59.87 108.08 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-s4-ss harmonic 61.05 95.47 # SOURCE3 1 0.0000 + angle_coeff @angle:br-s6-br harmonic 67.11 101.57 # SOURCE3 1 0.0000 + angle_coeff @angle:br-s6-c3 harmonic 63.24 98.99 # SOURCE3 1 0.0000 + angle_coeff @angle:br-s6-f harmonic 63.06 100.60 # SOURCE2 1 0.0000 + angle_coeff @angle:br-s6-o harmonic 63.90 107.58 # SOURCE3 6 0.3000 + angle_coeff @angle:c1-s6-c1 harmonic 64.09 99.99 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-s6-o harmonic 68.10 108.23 # SOURCE3 4 0.0000 + angle_coeff @angle:c2-s6-c2 harmonic 61.86 102.75 # SOURCE3 1 + angle_coeff @angle:c2-s6-c3 harmonic 61.23 104.05 # SOURCE3 1 + angle_coeff @angle:c2-s6-o harmonic 67.53 106.58 # SOURCE3 1 + angle_coeff @angle:c3-s6-c3 harmonic 61.35 102.83 # SOURCE3 7 1.2531 + angle_coeff @angle:c3-s6-ca harmonic 61.51 103.17 # SOURCE3 1 + angle_coeff @angle:c3-s6-cy harmonic 62.55 94.57 # SOURCE4 8 0.4183 + angle_coeff @angle:c3-s6-f harmonic 65.73 97.11 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-hs harmonic 44.94 100.62 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-i harmonic 50.82 97.74 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-n2 harmonic 63.42 112.95 # SOURCE4 11 0.7920 + angle_coeff @angle:c3-s6-n3 harmonic 65.71 101.38 # SOURCE4 60 0.9507 + angle_coeff @angle:c3-s6-n harmonic 63.84 102.97 # SOURCE3 4 0.8785 + angle_coeff @angle:c3-s6-n4 harmonic 61.33 99.40 # SOURCE3 3 0.4695 + angle_coeff @angle:c3-s6-na harmonic 63.68 102.81 # SOURCE3 10 3.1256 + angle_coeff @angle:c3-s6-nh harmonic 63.74 104.31 # SOURCE4 34 1.5848 + angle_coeff @angle:c3-s6-no harmonic 60.08 99.57 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-o harmonic 66.59 108.32 # SOURCE3 112 1.8014 + angle_coeff @angle:c3-s6-oh harmonic 67.71 98.60 # SOURCE4 42 0.8366 + angle_coeff @angle:c3-s6-os harmonic 68.68 96.32 # SOURCE4 30 0.4539 + angle_coeff @angle:c3-s6-p2 harmonic 72.54 106.47 # SOURCE3 1 + angle_coeff @angle:c3-s6-p3 harmonic 76.24 103.40 # SOURCE3 3 0.8516 + angle_coeff @angle:c3-s6-p4 harmonic 71.10 104.12 # SOURCE3 1 + angle_coeff @angle:c3-s6-p5 harmonic 77.16 103.46 # SOURCE3 1 + angle_coeff @angle:c3-s6-s4 harmonic 61.78 98.10 # SOURCE3 1 + angle_coeff @angle:c3-s6-s harmonic 60.70 104.50 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-s6 harmonic 60.60 101.95 # SOURCE3 1 + angle_coeff @angle:c3-s6-sh harmonic 60.07 101.84 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-s6-ss harmonic 59.68 102.47 # SOURCE3 3 1.7451 + angle_coeff @angle:ca-s6-ca harmonic 61.80 103.08 # SOURCE3 1 + angle_coeff @angle:ca-s6-o harmonic 68.37 104.07 # SOURCE4 59 0.5636 + angle_coeff @angle:c-s6-c3 harmonic 60.12 101.24 # SOURCE3 1 + angle_coeff @angle:c-s6-c harmonic 59.07 99.82 # SOURCE3 1 + angle_coeff @angle:cc-s6-o harmonic 65.29 103.63 # SOURCE4 9 0.5934 + angle_coeff @angle:cl-s6-cl harmonic 52.93 101.25 # SOURCE3 1 0.0000 + angle_coeff @angle:cl-s6-f harmonic 57.88 99.00 # SOURCE2 1 0.0000 + angle_coeff @angle:cl-s6-o harmonic 58.51 107.66 # SOURCE3 4 0.0000 + angle_coeff @angle:c-s6-o harmonic 63.97 107.97 # SOURCE3 1 + angle_coeff @angle:c-s6-os harmonic 64.36 102.12 # SOURCE3 1 + angle_coeff @angle:cx-s6-cx harmonic 86.21 54.70 # SOURCE2 1 0.0000 + angle_coeff @angle:cy-s6-o harmonic 63.83 110.22 # SOURCE4 20 1.1009 + angle_coeff @angle:f-s6-f harmonic 70.81 94.70 # SOURCE2 3 0.9899 + angle_coeff @angle:f-s6-o harmonic 72.38 106.48 # SOURCE3 2 0.0000 + angle_coeff @angle:hs-s6-hs harmonic 35.84 99.02 # SOURCE3 2 0.0595 + angle_coeff @angle:hs-s6-n1 harmonic 54.71 97.27 # HF/6-31G* 1 + angle_coeff @angle:hs-s6-o harmonic 51.91 107.60 # SOURCE3 10 0.0343 + angle_coeff @angle:i-s6-i harmonic 53.90 99.25 # SOURCE3 1 + angle_coeff @angle:i-s6-o harmonic 47.73 109.74 # SOURCE3 2 0.0000 + angle_coeff @angle:n1-s6-n1 harmonic 83.71 95.52 # HF/6-31G* 1 + angle_coeff @angle:n1-s6-o harmonic 78.79 107.52 # HF/6-31G* 1 + angle_coeff @angle:n2-s6-n2 harmonic 75.20 98.61 # SOURCE3 1 + angle_coeff @angle:n2-s6-o harmonic 72.08 116.41 # SOURCE3 3 5.0830 + angle_coeff @angle:n2-s6-oh harmonic 71.75 106.96 # SOURCE3 2 0.0000 + angle_coeff @angle:n2-s6-os harmonic 73.30 103.25 # SOURCE3 1 + angle_coeff @angle:n3-s6-n3 harmonic 71.49 98.57 # SOURCE4 7 0.2690 + angle_coeff @angle:n3-s6-o harmonic 72.90 106.80 # SOURCE3 14 1.7908 + angle_coeff @angle:n3-s6-os harmonic 72.84 99.26 # SOURCE4 8 0.5141 + angle_coeff @angle:n4-s6-n4 harmonic 59.97 101.85 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-s6-o harmonic 65.83 102.92 # SOURCE3 10 1.5434 + angle_coeff @angle:na-s6-na harmonic 67.74 98.04 # SOURCE3 1 + angle_coeff @angle:na-s6-o harmonic 70.46 105.67 # SOURCE3 20 0.8019 + angle_coeff @angle:nh-s6-nh harmonic 70.22 94.56 # SOURCE3 1 0.0000 + angle_coeff @angle:nh-s6-o harmonic 70.23 109.12 # SOURCE3 6 0.9556 + angle_coeff @angle:n-s6-n harmonic 66.18 104.16 # SOURCE3 1 + angle_coeff @angle:n-s6-o harmonic 70.74 105.91 # SOURCE3 8 0.2953 + angle_coeff @angle:no-s6-no harmonic 61.24 91.63 # SOURCE3 1 0.0000 + angle_coeff @angle:no-s6-o harmonic 62.67 107.43 # SOURCE3 6 1.5494 + angle_coeff @angle:n-s6-os harmonic 70.81 99.23 # SOURCE4 5 0.9794 + angle_coeff @angle:oh-s6-oh harmonic 73.67 100.34 # SOURCE3 6 0.0076 + angle_coeff @angle:oh-s6-os harmonic 75.33 96.62 # SOURCE4 26 0.6688 + angle_coeff @angle:oh-s6-p2 harmonic 75.13 109.67 # SOURCE3 2 0.0000 + angle_coeff @angle:o-s6-o harmonic 74.58 119.73 # SOURCE4 324 2.0530 + angle_coeff @angle:o-s6-oh harmonic 74.13 108.21 # SOURCE3 18 0.7437 + angle_coeff @angle:o-s6-os harmonic 74.58 107.84 # SOURCE3 12 0.7025 + angle_coeff @angle:o-s6-p2 harmonic 76.65 106.61 # SOURCE3 1 + angle_coeff @angle:o-s6-p3 harmonic 80.16 107.07 # SOURCE3 22 1.0550 + angle_coeff @angle:o-s6-p4 harmonic 73.92 105.67 # SOURCE3 1 + angle_coeff @angle:o-s6-p5 harmonic 81.69 106.64 # SOURCE3 1 + angle_coeff @angle:o-s6-s4 harmonic 63.02 107.85 # SOURCE3 1 + angle_coeff @angle:o-s6-s harmonic 63.52 110.29 # SOURCE3 6 2.2405 + angle_coeff @angle:o-s6-s6 harmonic 63.55 106.07 # SOURCE3 1 + angle_coeff @angle:o-s6-sh harmonic 62.53 106.81 # SOURCE3 6 0.6292 + angle_coeff @angle:os-s6-os harmonic 74.80 98.70 # SOURCE3 1 0.0000 + angle_coeff @angle:o-s6-ss harmonic 62.06 107.43 # SOURCE3 10 1.1423 + angle_coeff @angle:p3-s6-p3 harmonic 94.93 110.17 # SOURCE3 4 5.3678 + angle_coeff @angle:p5-s6-p5 harmonic 99.25 104.49 # SOURCE3 1 + angle_coeff @angle:s4-s6-s4 harmonic 61.51 101.99 # SOURCE3 1 + angle_coeff @angle:s4-s6-s6 harmonic 65.42 90.17 # SOURCE3 1 + angle_coeff @angle:s6-s6-s6 harmonic 61.12 103.29 # SOURCE3 1 + angle_coeff @angle:sh-s6-sh harmonic 59.41 106.43 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-s6-ss harmonic 60.36 102.64 # SOURCE3 1 + angle_coeff @angle:s-s6-s harmonic 60.63 109.34 # SOURCE3 1 0.0000 + angle_coeff @angle:ss-s6-ss harmonic 60.46 101.82 # SOURCE3 1 0.0000 + angle_coeff @angle:br-sh-hs harmonic 43.54 95.64 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-sh-hs harmonic 48.23 95.99 # calculated_based_on_C#C-SH 0 + angle_coeff @angle:c2-sh-hs harmonic 45.81 97.08 # SOURCE4 5 0.3132 + angle_coeff @angle:c3-sh-hs harmonic 44.94 96.60 # SOURCE3 12 0.8009 + angle_coeff @angle:ca-sh-hs harmonic 46.32 94.84 # SOURCE4 13 0.4130 + angle_coeff @angle:cc-sh-hs harmonic 46.41 95.38 # SOURCE4 8 1.1410 + angle_coeff @angle:c-sh-hs harmonic 45.96 96.07 # SOURCE3 6 1.1164 + angle_coeff @angle:f-sh-hs harmonic 48.09 96.50 # SOURCE3 1 0.0000 + angle_coeff @angle:hs-sh-hs harmonic 37.45 93.72 # SOURCE3 3 0.4777 + angle_coeff @angle:hs-sh-i harmonic 37.09 96.44 # SOURCE3 1 0.0000 + angle_coeff @angle:hs-sh-n1 harmonic 51.69 93.51 # HF/6-31G* 1 + angle_coeff @angle:hs-sh-n2 harmonic 48.12 95.82 # SOURCE3 5 3.1495 + angle_coeff @angle:hs-sh-n harmonic 48.41 95.59 # SOURCE3 4 3.9065 + angle_coeff @angle:hs-sh-n3 harmonic 48.06 95.98 # SOURCE3 3 1.1735 + angle_coeff @angle:hs-sh-n4 harmonic 47.15 93.13 # SOURCE3 3 0.1675 + angle_coeff @angle:hs-sh-na harmonic 48.12 97.38 # SOURCE3 9 1.0223 + angle_coeff @angle:hs-sh-nh harmonic 47.52 101.11 # SOURCE3 1 0.0000 + angle_coeff @angle:hs-sh-no harmonic 47.35 92.93 # SOURCE3 1 0.0000 + angle_coeff @angle:hs-sh-o harmonic 48.22 109.23 # SOURCE3 2 0.0068 + angle_coeff @angle:hs-sh-oh harmonic 48.75 98.64 # SOURCE3 2 0.0605 + angle_coeff @angle:hs-sh-os harmonic 49.35 98.15 # SOURCE3 3 0.1661 + angle_coeff @angle:hs-sh-p2 harmonic 56.52 99.12 # SOURCE3 10 5.4110 + angle_coeff @angle:hs-sh-p3 harmonic 53.11 95.81 # SOURCE3 3 0.4396 + angle_coeff @angle:hs-sh-p4 harmonic 54.01 94.22 # SOURCE3 4 0.7605 + angle_coeff @angle:hs-sh-p5 harmonic 54.80 94.52 # SOURCE3 3 0.5589 + angle_coeff @angle:hs-sh-s harmonic 40.94 102.87 # SOURCE3 2 0.0000 + angle_coeff @angle:hs-sh-s4 harmonic 42.04 92.16 # SOURCE3 3 1.6519 + angle_coeff @angle:hs-sh-s6 harmonic 42.91 93.83 # SOURCE3 3 1.2561 + angle_coeff @angle:hs-sh-sh harmonic 42.80 99.07 # SOURCE3 2 0.0000 + angle_coeff @angle:hs-sh-ss harmonic 42.59 99.17 # SOURCE3 3 0.2457 + angle_coeff @angle:br-ss-br harmonic 67.00 102.92 # SOURCE3 1 0.0000 + angle_coeff @angle:br-ss-c3 harmonic 63.06 99.03 # SOURCE3 1 0.0000 + angle_coeff @angle:c1-ss-c1 harmonic 66.30 98.30 # SOURCE2 1 0.0000 + angle_coeff @angle:c1-ss-c3 harmonic 62.89 99.90 # SOURCE2 1 0.0000 + angle_coeff @angle:c2-ss-c2 harmonic 63.71 99.56 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-ss-c3 harmonic 61.87 100.37 # SOURCE4 100 2.3280 + angle_coeff @angle:c2-ss-cy harmonic 65.30 88.61 # SOURCE4 27 0.4481 + angle_coeff @angle:c2-ss-n2 harmonic 64.45 106.76 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-ss-na harmonic 65.02 100.51 # SOURCE3 6 6.9702 + angle_coeff @angle:c2-ss-os harmonic 69.78 89.76 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-ss-ss harmonic 64.78 92.26 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-c3 harmonic 60.63 99.92 # SOURCE3 14 2.0723 + angle_coeff @angle:c3-ss-ca harmonic 60.80 102.12 # SOURCE4 161 1.3084 + angle_coeff @angle:c3-ss-cc harmonic 61.74 100.75 # CORR 87 + angle_coeff @angle:c3-ss-cd harmonic 61.74 100.75 # CORR 87 + angle_coeff @angle:c3-ss-cl harmonic 56.40 99.40 # SOURCE2 1 0.0000 + angle_coeff @angle:c3-ss-cy harmonic 61.94 94.32 # SOURCE4 62 0.3646 + angle_coeff @angle:c3-ss-f harmonic 63.40 97.49 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-i harmonic 56.03 100.00 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-n1 harmonic 65.93 98.44 # HF/6-31G* 1 + angle_coeff @angle:c3-ss-n2 harmonic 65.94 96.42 # SOURCE3 5 1.3604 + angle_coeff @angle:c3-ss-n3 harmonic 64.10 98.83 # SOURCE3 3 0.2909 + angle_coeff @angle:c3-ss-n harmonic 63.71 100.30 # SOURCE3 4 0.6579 + angle_coeff @angle:c3-ss-n4 harmonic 62.94 97.79 # SOURCE3 3 0.2002 + angle_coeff @angle:c3-ss-na harmonic 63.51 100.14 # SOURCE3 12 1.7415 + angle_coeff @angle:c3-ss-nh harmonic 63.75 100.63 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-no harmonic 62.40 98.62 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-o harmonic 64.67 106.60 # SOURCE3 2 1.6714 + angle_coeff @angle:c3-ss-oh harmonic 65.29 98.28 # SOURCE3 2 1.4326 + angle_coeff @angle:c3-ss-os harmonic 64.97 98.21 # SOURCE3 4 1.7097 + angle_coeff @angle:c3-ss-p2 harmonic 80.22 98.41 # SOURCE3 8 0.9454 + angle_coeff @angle:c3-ss-p3 harmonic 76.29 98.70 # SOURCE3 3 0.0356 + angle_coeff @angle:c3-ss-p4 harmonic 76.93 98.16 # SOURCE3 4 0.1361 + angle_coeff @angle:c3-ss-p5 harmonic 75.86 100.22 # SOURCE4 23 1.1410 + angle_coeff @angle:c3-ss-s4 harmonic 60.11 96.37 # SOURCE3 3 0.0202 + angle_coeff @angle:c3-ss-s harmonic 59.94 101.90 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-s6 harmonic 60.94 96.76 # SOURCE3 3 1.5680 + angle_coeff @angle:c3-ss-sh harmonic 60.36 101.93 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-ss-ss harmonic 60.34 103.10 # SOURCE4 70 1.3377 + angle_coeff @angle:ca-ss-ca harmonic 62.76 98.71 # SOURCE4 97 1.2321 + angle_coeff @angle:ca-ss-cc harmonic 66.53 89.47 # CORR 134 + angle_coeff @angle:ca-ss-cd harmonic 66.53 89.47 # CORR 134 + angle_coeff @angle:ca-ss-cl harmonic 56.45 101.05 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-ss-n harmonic 65.76 97.16 # SOURCE3 1 + angle_coeff @angle:ca-ss-na harmonic 64.76 99.32 # SOURCE3 1 + angle_coeff @angle:ca-ss-nc harmonic 69.21 94.76 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-ss-nd harmonic 69.21 94.76 # SOURCE3 1 same_as_ca-ss-nc + angle_coeff @angle:ca-ss-ss harmonic 60.39 104.90 # SOURCE4 19 0.8743 + angle_coeff @angle:c-ss-c2 harmonic 65.63 92.43 # SOURCE3 1 0.0000 + angle_coeff @angle:c-ss-c3 harmonic 61.48 100.29 # SOURCE3 5 2.2127 + angle_coeff @angle:c-ss-c harmonic 62.20 101.40 # SOURCE3 1 0.0000 + angle_coeff @angle:c-ss-cc harmonic 65.61 92.43 # SOURCE4 14 2.3600 + angle_coeff @angle:cc-ss-cc harmonic 67.01 89.91 # SOURCE3 11 2.2164 + angle_coeff @angle:cc-ss-cd harmonic 67.07 89.74 # SOURCE4 49 0.7509 + angle_coeff @angle:cc-ss-n harmonic 66.42 97.16 # SOURCE3 1 same_as_cd-ss-n + angle_coeff @angle:cc-ss-na harmonic 65.39 99.33 # SOURCE3 18 same_as_cd-ss-na + angle_coeff @angle:cc-ss-nc harmonic 70.31 94.08 # CORR 13 + angle_coeff @angle:cc-ss-os harmonic 66.48 98.81 # SOURCE3 2 2.1583 + angle_coeff @angle:cc-ss-ss harmonic 63.91 94.76 # CORR 13 + angle_coeff @angle:cd-ss-cd harmonic 67.01 89.91 # SOURCE3 11 2.2164 + angle_coeff @angle:cd-ss-n harmonic 66.42 97.16 # SOURCE3 1 0.0000 + angle_coeff @angle:cd-ss-na harmonic 65.39 99.33 # SOURCE3 18 2.5847 + angle_coeff @angle:cd-ss-nd harmonic 70.31 94.08 # CORR 13 + angle_coeff @angle:cd-ss-os harmonic 66.48 98.81 # SOURCE3 2 same_as_cc-ss-os + angle_coeff @angle:cd-ss-ss harmonic 63.91 94.76 # CORR 13 + angle_coeff @angle:cl-ss-cl harmonic 52.39 103.37 # SOURCE3 1 0.0000 + angle_coeff @angle:cx-ss-cx harmonic 87.49 48.30 # SOURCE2 1 0.0000 + angle_coeff @angle:f-ss-f harmonic 66.18 98.30 # SOURCE2 1 0.0000 + angle_coeff @angle:f-ss-ss harmonic 59.85 108.30 # SOURCE2 1 0.0000 + angle_coeff @angle:i-ss-i harmonic 58.15 106.29 # SOURCE3 1 0.0000 + angle_coeff @angle:n1-ss-n1 harmonic 73.07 96.96 # HF/6-31G* 1 + angle_coeff @angle:n2-ss-n2 harmonic 71.12 96.75 # SOURCE3 1 0.0000 + angle_coeff @angle:n3-ss-n3 harmonic 66.50 102.34 # SOURCE3 1 0.0000 + angle_coeff @angle:n4-ss-n4 harmonic 63.55 101.19 # SOURCE3 1 0.0000 + angle_coeff @angle:na-ss-na harmonic 65.92 102.81 # SOURCE3 1 0.0000 + angle_coeff @angle:nc-ss-nc harmonic 75.03 97.94 # CORR 9 + angle_coeff @angle:nd-ss-nd harmonic 75.03 97.94 # CORR 9 + angle_coeff @angle:nh-ss-nh harmonic 65.30 107.89 # SOURCE3 1 0.0000 + angle_coeff @angle:n-ss-n harmonic 66.45 103.10 # SOURCE3 1 0.0000 + angle_coeff @angle:no-ss-no harmonic 61.43 106.43 # SOURCE3 1 0.0000 + angle_coeff @angle:oh-ss-oh harmonic 68.23 104.25 # SOURCE3 1 0.0000 + angle_coeff @angle:o-ss-o harmonic 69.80 119.30 # SOURCE2 1 0.0000 + angle_coeff @angle:o-ss-p5 harmonic 78.64 106.41 # SOURCE3 1 0.0000 + angle_coeff @angle:o-ss-s6 harmonic 62.35 105.39 # SOURCE3 1 + angle_coeff @angle:os-ss-os harmonic 67.76 102.99 # SOURCE3 1 0.0000 + angle_coeff @angle:o-ss-ss harmonic 62.04 112.70 # SOURCE2 1 0.0000 + angle_coeff @angle:p2-ss-p2 harmonic 105.52 99.52 # SOURCE3 1 0.0000 + angle_coeff @angle:p3-ss-p3 harmonic 96.77 101.67 # SOURCE3 1 + angle_coeff @angle:p5-ss-p5 harmonic 103.25 89.83 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-ss-s4 harmonic 60.86 96.08 # SOURCE3 1 0.0000 + angle_coeff @angle:s4-ss-s6 harmonic 59.93 101.26 # SOURCE3 1 + angle_coeff @angle:s6-ss-s6 harmonic 60.46 101.81 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-ss-sh harmonic 60.28 107.54 # SOURCE3 1 0.0000 + angle_coeff @angle:sh-ss-ss harmonic 60.81 106.53 # SOURCE3 1 + angle_coeff @angle:s-ss-s harmonic 57.67 115.04 # SOURCE3 1 + angle_coeff @angle:ss-ss-ss harmonic 60.44 108.76 # SOURCE4 8 0.2385 + angle_coeff @angle:c3-sx-ca harmonic 61.85 96.41 # SOURCE4 13 0.3130 + angle_coeff @angle:c3-sx-cc harmonic 62.52 95.11 # SOURCE4 17 0.6557 + angle_coeff @angle:c3-sx-ce harmonic 62.82 94.95 # SOURCE3 3 0.0007 + angle_coeff @angle:c3-sx-cf harmonic 62.82 94.95 # SOURCE3 3 same_as_c3-sx-ce + angle_coeff @angle:c3-sx-ne harmonic 65.33 90.06 # SOURCE3 5 1.9627 + angle_coeff @angle:c3-sx-nf harmonic 65.33 90.06 # SOURCE3 5 same_as_c3-sx-ne + angle_coeff @angle:c3-sx-o harmonic 64.94 107.88 # SOURCE3 30 0.8721 + angle_coeff @angle:c3-sx-pe harmonic 76.99 94.32 # SOURCE3 7 0.5547 + angle_coeff @angle:c3-sx-pf harmonic 76.99 94.32 # SOURCE3 7 same_as_c3-sx-pe + angle_coeff @angle:c3-sx-px harmonic 74.26 96.46 # SOURCE3 3 1.3351 + angle_coeff @angle:c3-sx-py harmonic 74.13 95.67 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-sx-sx harmonic 57.22 91.47 # SOURCE3 4 1.9919 + angle_coeff @angle:c3-sx-sy harmonic 58.71 95.47 # SOURCE3 3 2.8422 + angle_coeff @angle:ca-sx-ca harmonic 61.97 95.21 # SOURCE3 1 0.0000 + angle_coeff @angle:ca-sx-o harmonic 64.82 106.89 # SOURCE4 25 0.5562 + angle_coeff @angle:c-sx-c3 harmonic 62.01 92.71 # SOURCE3 3 0.3095 + angle_coeff @angle:c-sx-c harmonic 62.83 86.85 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-sx-o harmonic 65.92 104.49 # SOURCE4 17 1.7759 + angle_coeff @angle:ce-sx-ce harmonic 63.02 94.96 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-sx-o harmonic 65.38 107.47 # SOURCE3 5 0.3128 + angle_coeff @angle:cf-sx-cf harmonic 63.02 94.96 # SOURCE3 1 same_as_ce-sx-ce + angle_coeff @angle:cf-sx-o harmonic 65.38 107.47 # SOURCE3 5 same_as_ce-sx-o + angle_coeff @angle:c-sx-o harmonic 63.47 106.17 # SOURCE3 5 0.9477 + angle_coeff @angle:ne-sx-ne harmonic 66.37 90.17 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-sx-o harmonic 65.36 109.20 # SOURCE3 7 1.4542 + angle_coeff @angle:nf-sx-nf harmonic 66.37 90.17 # SOURCE3 1 same_as_ne-sx-ne + angle_coeff @angle:nf-sx-o harmonic 65.36 109.20 # SOURCE3 7 same_as_ne-sx-o + angle_coeff @angle:o-sx-pe harmonic 77.00 106.43 # SOURCE3 9 2.8345 + angle_coeff @angle:o-sx-pf harmonic 77.00 106.43 # SOURCE3 9 same_as_o-sx-pe + angle_coeff @angle:o-sx-px harmonic 75.16 104.77 # SOURCE3 3 1.9810 + angle_coeff @angle:o-sx-py harmonic 73.10 109.13 # SOURCE3 7 5.6840 + angle_coeff @angle:o-sx-sx harmonic 55.68 104.65 # SOURCE3 6 3.0524 + angle_coeff @angle:o-sx-sy harmonic 59.44 103.41 # SOURCE3 5 0.9618 + angle_coeff @angle:pe-sx-pe harmonic 99.19 92.62 # SOURCE3 1 0.0000 + angle_coeff @angle:pf-sx-pf harmonic 99.19 92.62 # SOURCE3 1 same_as_pe-sx-pe + angle_coeff @angle:py-sx-py harmonic 110.11 69.23 # SOURCE3 3 17.4143 + angle_coeff @angle:sx-sx-sx harmonic 58.65 84.90 # SOURCE3 1 0.0000 + angle_coeff @angle:sy-sx-sy harmonic 59.25 93.52 # SOURCE3 1 0.0000 + angle_coeff @angle:c3-sy-ca harmonic 60.74 103.86 # SOURCE4 54 0.3180 + angle_coeff @angle:c3-sy-cc harmonic 61.24 102.19 # SOURCE4 12 1.5324 + angle_coeff @angle:c3-sy-ce harmonic 60.79 103.81 # SOURCE3 3 0.3368 + angle_coeff @angle:c3-sy-cf harmonic 60.79 103.81 # SOURCE3 3 same_as_c3-sy-ce + angle_coeff @angle:c3-sy-ne harmonic 63.01 103.12 # SOURCE3 5 4.1882 + angle_coeff @angle:c3-sy-nf harmonic 63.01 103.12 # SOURCE3 5 same_as_c3-sy-ne + angle_coeff @angle:c3-sy-o harmonic 65.97 108.48 # SOURCE3 62 0.8576 + angle_coeff @angle:c3-sy-pe harmonic 71.79 106.03 # SOURCE3 6 2.6117 + angle_coeff @angle:c3-sy-pf harmonic 71.79 106.03 # SOURCE3 6 same_as_c3-sy-pe + angle_coeff @angle:c3-sy-px harmonic 71.71 103.62 # SOURCE3 3 0.7078 + angle_coeff @angle:c3-sy-py harmonic 73.48 103.39 # SOURCE3 3 0.4563 + angle_coeff @angle:c3-sy-sx harmonic 56.27 104.64 # SOURCE3 3 4.6276 + angle_coeff @angle:c3-sy-sy harmonic 57.43 100.78 # SOURCE3 4 1.1633 + angle_coeff @angle:ca-sy-ca harmonic 60.65 104.04 # SOURCE4 25 2.0762 + angle_coeff @angle:ca-sy-cc harmonic 60.36 105.09 # SOURCE4 5 0.3628 + angle_coeff @angle:ca-sy-n3 harmonic 64.10 102.48 # SOURCE4 180 1.0802 + angle_coeff @angle:ca-sy-n harmonic 62.89 105.45 # SOURCE4 51 1.1497 + angle_coeff @angle:ca-sy-ne harmonic 62.86 103.47 # SOURCE4 11 1.6071 + angle_coeff @angle:ca-sy-nh harmonic 62.86 105.59 # SOURCE4 78 1.5805 + angle_coeff @angle:ca-sy-o harmonic 65.84 108.73 # SOURCE3 26 1.2638 + angle_coeff @angle:ca-sy-oh harmonic 65.64 101.25 # SOURCE4 23 0.9100 + angle_coeff @angle:ca-sy-os harmonic 67.64 92.98 # SOURCE3 1 0.0000 + angle_coeff @angle:c-sy-c3 harmonic 60.09 101.25 # SOURCE3 3 1.1850 + angle_coeff @angle:c-sy-c harmonic 59.23 99.81 # SOURCE3 1 0.0000 + angle_coeff @angle:cc-sy-n3 harmonic 64.10 102.54 # CORR 30 + angle_coeff @angle:cc-sy-o harmonic 66.17 107.71 # CORR 100 + angle_coeff @angle:cd-sy-n3 harmonic 64.10 102.54 # CORR 30 + angle_coeff @angle:cd-sy-nh harmonic 65.53 97.20 # SOURCE4 6 0.2429 + angle_coeff @angle:cd-sy-o harmonic 66.17 107.71 # CORR 100 + angle_coeff @angle:ce-sy-ce harmonic 61.09 102.78 # SOURCE3 1 0.0000 + angle_coeff @angle:ce-sy-o harmonic 66.35 107.25 # SOURCE3 10 0.5477 + angle_coeff @angle:cf-sy-cf harmonic 61.09 102.78 # SOURCE3 1 same_as_ce-sy-ce + angle_coeff @angle:cf-sy-o harmonic 66.35 107.25 # SOURCE3 10 same_as_ce-sy-o + angle_coeff @angle:c-sy-o harmonic 64.07 107.23 # SOURCE3 10 0.8425 + angle_coeff @angle:f-sy-o harmonic 63.64 105.60 # SOURCE4 7 0.2000 + angle_coeff @angle:n2-sy-o harmonic 61.16 123.53 # SOURCE4 6 1.2388 + angle_coeff @angle:n3-sy-ne harmonic 66.36 102.40 # SOURCE4 5 1.3390 + angle_coeff @angle:n3-sy-o harmonic 70.45 107.11 # SOURCE4 375 1.1257 + angle_coeff @angle:na-sy-na harmonic 67.74 98.04 # SOURCE3 1 + angle_coeff @angle:nc-sy-nc harmonic 75.24 98.04 # SOURCE3 2 + angle_coeff @angle:nd-sy-nd harmonic 75.24 98.04 # SOURCE3 2 + angle_coeff @angle:ne-sy-ne harmonic 66.58 98.62 # SOURCE3 1 0.0000 + angle_coeff @angle:ne-sy-o harmonic 68.89 107.06 # SOURCE3 14 2.2705 + angle_coeff @angle:nf-sy-nf harmonic 66.58 98.62 # SOURCE3 1 same_as_ne-sy-ne + angle_coeff @angle:nf-sy-o harmonic 68.89 107.06 # SOURCE3 14 same_as_ne-sy-o + angle_coeff @angle:nh-sy-o harmonic 70.18 106.38 # SOURCE4 123 1.6517 + angle_coeff @angle:n-sy-o harmonic 69.79 107.50 # SOURCE4 61 1.8720 + angle_coeff @angle:o-sy-o harmonic 72.40 121.88 # SOURCE3 46 0.9495 + angle_coeff @angle:o-sy-oh harmonic 72.26 106.93 # SOURCE3 8 0.7424 + angle_coeff @angle:o-sy-os harmonic 70.39 108.31 # SOURCE4 7 0.1222 + angle_coeff @angle:o-sy-pe harmonic 75.40 106.90 # SOURCE3 12 1.4524 + angle_coeff @angle:o-sy-pf harmonic 75.40 106.90 # SOURCE3 12 same_as_o-sy-pe + angle_coeff @angle:o-sy-px harmonic 74.45 106.17 # SOURCE3 6 0.7059 + angle_coeff @angle:o-sy-py harmonic 76.54 106.67 # SOURCE3 10 0.6478 + angle_coeff @angle:o-sy-sx harmonic 58.62 106.33 # SOURCE3 10 2.0456 + angle_coeff @angle:o-sy-sy harmonic 58.79 106.19 # SOURCE3 12 0.1754 + angle_coeff @angle:py-sy-py harmonic 92.79 104.49 # SOURCE3 1 0.0000 + angle_coeff @angle:sx-sy-sx harmonic 56.74 101.99 # SOURCE3 1 0.0000 + angle_coeff @angle:sy-sy-sy harmonic 56.50 103.29 # SOURCE3 1 0.0000 + angle_coeff @angle:c2-c1-cf harmonic 58.18 179.01 # NEW 6 + angle_coeff @angle:c3-c1-ch harmonic 55.79 178.52 # NEW 39 + angle_coeff @angle:nf-c1-s harmonic 57.59 175.81 # NEW 8 + angle_coeff @angle:br-c2-cf harmonic 63.21 121.59 # NEW 7 + angle_coeff @angle:cd-c2-h4 harmonic 49.19 120.33 # NEW 7 + angle_coeff @angle:cd-c2-nh harmonic 69.46 122.96 # NEW 10 + angle_coeff @angle:cd-c2-o harmonic 72.80 123.59 # NEW 6 + angle_coeff @angle:cf-c2-cl harmonic 58.06 123.90 # NEW 11 + angle_coeff @angle:cf-c2-h4 harmonic 49.38 122.29 # NEW 75 + angle_coeff @angle:cf-c2-na harmonic 68.82 123.71 # NEW 6 + angle_coeff @angle:cf-c2-nh harmonic 70.64 120.72 # NEW 93 + angle_coeff @angle:cf-c2-no harmonic 68.45 119.65 # NEW 5 + angle_coeff @angle:cf-c2-o harmonic 73.66 123.08 # NEW 5 + angle_coeff @angle:cf-c2-oh harmonic 70.90 123.27 # NEW 42 + angle_coeff @angle:cf-c2-os harmonic 70.47 122.52 # NEW 51 + angle_coeff @angle:h4-c2-nf harmonic 52.87 119.63 # NEW 10 + angle_coeff @angle:h5-c2-nf harmonic 52.76 119.62 # NEW 17 + angle_coeff @angle:nf-c2-os harmonic 74.86 118.76 # NEW 5 + angle_coeff @angle:nf-c2-ss harmonic 65.41 120.06 # NEW 9 + angle_coeff @angle:n-c2-nf harmonic 70.89 125.38 # NEW 10 + angle_coeff @angle:ca-c3-cf harmonic 63.81 112.33 # NEW 51 + angle_coeff @angle:cd-c3-cx harmonic 63.85 112.55 # NEW 5 + angle_coeff @angle:c-c3-cf harmonic 64.02 111.98 # NEW 16 + angle_coeff @angle:cd-c3-hx harmonic 47.17 111.02 # NEW 9 + angle_coeff @angle:cd-c3-n2 harmonic 66.85 110.47 # NEW 11 + angle_coeff @angle:cd-c3-n4 harmonic 64.88 115.58 # NEW 6 + angle_coeff @angle:cd-c3-na harmonic 66.43 113.39 # NEW 8 + angle_coeff @angle:cd-c3-p5 harmonic 76.89 116.23 # NEW 6 + angle_coeff @angle:cf-c3-cf harmonic 64.24 111.44 # NEW 18 + angle_coeff @angle:cf-c3-n harmonic 67.09 110.41 # NEW 6 + angle_coeff @angle:cf-c3-oh harmonic 68.00 111.05 # NEW 17 + angle_coeff @angle:cf-c3-os harmonic 68.64 108.10 # NEW 16 + angle_coeff @angle:cf-c3-ss harmonic 61.87 111.10 # NEW 7 + angle_coeff @angle:cd-ca-cq harmonic 64.63 124.30 # NEW 10 + angle_coeff @angle:cf-ca-na harmonic 67.44 119.85 # NEW 9 + angle_coeff @angle:ch-ca-cq harmonic 65.26 121.53 # NEW 12 + angle_coeff @angle:cl-ca-cq harmonic 58.19 120.31 # NEW 18 + angle_coeff @angle:cq-ca-f harmonic 67.10 119.39 # NEW 16 + angle_coeff @angle:cq-ca-h4 harmonic 48.15 120.03 # NEW 27 + angle_coeff @angle:cq-ca-na harmonic 72.91 108.79 # NEW 165 + angle_coeff @angle:cq-ca-nb harmonic 68.56 123.72 # NEW 50 + angle_coeff @angle:cq-ca-nh harmonic 68.66 121.52 # NEW 11 + angle_coeff @angle:cq-ca-oh harmonic 69.26 120.96 # NEW 12 + angle_coeff @angle:cq-ca-ss harmonic 63.87 112.75 # NEW 8 + angle_coeff @angle:ca-c-nf harmonic 67.74 114.39 # NEW 5 + angle_coeff @angle:br-cd-c harmonic 63.98 115.68 # NEW 8 + angle_coeff @angle:br-cd-cd harmonic 61.82 124.89 # NEW 8 + angle_coeff @angle:br-cd-cc harmonic 62.26 124.56 # NEW 32 + angle_coeff @angle:br-cd-na harmonic 64.60 121.42 # NEW 6 + angle_coeff @angle:ca-cd-cf harmonic 62.51 127.87 # NEW 11 + angle_coeff @angle:ca-cd-nh harmonic 67.46 122.45 # NEW 9 + angle_coeff @angle:cd-c-cf harmonic 64.64 115.68 # NEW 6 + angle_coeff @angle:cd-cd-f harmonic 66.35 119.41 # NEW 7 + angle_coeff @angle:c-cd-ch harmonic 64.98 118.14 # NEW 7 + angle_coeff @angle:cd-cd-sy harmonic 59.22 128.36 # NEW 8 + angle_coeff @angle:cc-cd-f harmonic 67.42 121.08 # NEW 28 + angle_coeff @angle:cc-cd-no harmonic 65.78 128.95 # NEW 117 + angle_coeff @angle:c-cd-f harmonic 66.16 116.87 # NEW 16 + angle_coeff @angle:ch-cd-na harmonic 67.51 122.35 # NEW 5 + angle_coeff @angle:ch-cd-ss harmonic 62.33 120.70 # NEW 12 + angle_coeff @angle:cd-c-h4 harmonic 47.13 115.45 # NEW 5 + angle_coeff @angle:cl-cd-na harmonic 59.37 121.61 # NEW 12 + angle_coeff @angle:cl-cd-ss harmonic 58.09 119.85 # NEW 11 + angle_coeff @angle:c-cd-nf harmonic 67.11 119.88 # NEW 6 + angle_coeff @angle:cd-c-s harmonic 61.67 127.94 # NEW 12 + angle_coeff @angle:cd-c-ss harmonic 63.47 112.52 # NEW 10 + angle_coeff @angle:cx-cd-nc harmonic 65.61 127.75 # NEW 12 + angle_coeff @angle:cx-cd-os harmonic 67.94 118.08 # NEW 10 + angle_coeff @angle:cc-c-cx harmonic 63.88 117.46 # NEW 13 + angle_coeff @angle:cc-c-nc harmonic 68.65 113.75 # NEW 14 + angle_coeff @angle:cf-c-cx harmonic 63.95 116.25 # NEW 6 + angle_coeff @angle:cf-c-h4 harmonic 46.93 114.88 # NEW 19 + angle_coeff @angle:cf-c-ss harmonic 63.94 110.39 # NEW 5 + angle_coeff @angle:na-cd-no harmonic 68.48 124.90 # NEW 48 + angle_coeff @angle:na-cd-oh harmonic 73.25 117.26 # NEW 16 + angle_coeff @angle:na-cd-sx harmonic 63.25 117.04 # NEW 13 + angle_coeff @angle:na-cd-sy harmonic 63.13 120.55 # NEW 7 + angle_coeff @angle:nd-cd-no harmonic 69.31 121.54 # NEW 7 + angle_coeff @angle:nc-cd-nc harmonic 70.88 128.17 # NEW 7 + angle_coeff @angle:nc-cd-nf harmonic 69.29 129.66 # NEW 7 + angle_coeff @angle:nc-cd-no harmonic 69.90 122.68 # NEW 16 + angle_coeff @angle:nc-cd-sh harmonic 62.75 124.92 # NEW 5 + angle_coeff @angle:nc-cd-sx harmonic 60.81 127.60 # NEW 14 + angle_coeff @angle:nc-cd-sy harmonic 62.75 123.08 # NEW 13 + angle_coeff @angle:nf-cd-ss harmonic 65.39 116.99 # NEW 7 + angle_coeff @angle:n-cd-n2 harmonic 74.78 114.48 # NEW 15 + angle_coeff @angle:no-cd-os harmonic 71.01 117.59 # NEW 62 + angle_coeff @angle:no-cd-ss harmonic 63.76 121.10 # NEW 10 + angle_coeff @angle:ca-cc-cf harmonic 65.09 125.10 # NEW 9 + angle_coeff @angle:ca-cc-na harmonic 67.03 123.45 # NEW 39 + angle_coeff @angle:cd-cc-cg harmonic 64.92 126.05 # NEW 30 + angle_coeff @angle:cd-cc-cy harmonic 63.93 122.13 # NEW 10 + angle_coeff @angle:cd-cc-nd harmonic 69.42 123.82 # NEW 14 + angle_coeff @angle:cc-cc-cy harmonic 63.17 120.93 # NEW 6 + angle_coeff @angle:cf-cc-nc harmonic 68.22 124.90 # NEW 5 + angle_coeff @angle:c-cc-h4 harmonic 46.77 118.19 # NEW 8 + angle_coeff @angle:na-cc-nh harmonic 72.43 116.98 # NEW 46 + angle_coeff @angle:na-cc-ss harmonic 67.07 111.46 # NEW 20 + angle_coeff @angle:nc-cc-nc harmonic 69.47 125.58 # NEW 13 + angle_coeff @angle:oh-cc-os harmonic 75.54 111.61 # NEW 6 + angle_coeff @angle:c2-cf-cl harmonic 57.87 119.51 # NEW 24 + angle_coeff @angle:c2-cf-h4 harmonic 48.64 125.58 # NEW 11 + angle_coeff @angle:c2-cf-n1 harmonic 72.67 117.85 # NEW 7 + angle_coeff @angle:c2-cf-na harmonic 69.29 119.19 # NEW 5 + angle_coeff @angle:c2-cf-oh harmonic 70.32 123.78 # NEW 10 + angle_coeff @angle:c3-cf-ch harmonic 63.79 118.48 # NEW 8 + angle_coeff @angle:c3-cf-ne harmonic 67.26 120.75 # NEW 6 + angle_coeff @angle:c3-cf-nh harmonic 65.76 119.90 # NEW 5 + angle_coeff @angle:ca-cf-cf harmonic 63.84 119.62 # NEW 14 + angle_coeff @angle:ca-cf-cl harmonic 57.99 114.22 # NEW 6 + angle_coeff @angle:ca-cf-h4 harmonic 46.71 116.86 # NEW 74 + angle_coeff @angle:ca-cf-nh harmonic 67.87 115.51 # NEW 93 + angle_coeff @angle:ca-cf-os harmonic 68.60 115.58 # NEW 8 + angle_coeff @angle:ca-cf-ss harmonic 61.21 117.73 # NEW 5 + angle_coeff @angle:c-cf-ca harmonic 63.79 117.98 # NEW 8 + angle_coeff @angle:cd-cf-cc harmonic 63.28 130.36 # NEW 5 + angle_coeff @angle:c-cf-cf harmonic 63.46 120.89 # NEW 16 + angle_coeff @angle:c-cf-ch harmonic 64.57 118.32 # NEW 15 + angle_coeff @angle:cd-cf-h4 harmonic 47.52 115.40 # NEW 29 + angle_coeff @angle:c-cf-cl harmonic 57.67 115.40 # NEW 6 + angle_coeff @angle:cd-cf-nh harmonic 67.31 119.17 # NEW 8 + angle_coeff @angle:c-cf-cy harmonic 72.72 88.22 # NEW 19 + angle_coeff @angle:cf-cf-cl harmonic 57.29 117.93 # NEW 12 + angle_coeff @angle:cf-cf-oh harmonic 69.29 116.89 # NEW 11 + angle_coeff @angle:ce-cf-cy harmonic 60.53 137.74 # NEW 13 + angle_coeff @angle:ce-cf-h4 harmonic 49.02 123.76 # NEW 5 + angle_coeff @angle:ce-cf-n1 harmonic 72.03 120.03 # NEW 6 + angle_coeff @angle:ce-cf-nh harmonic 69.48 121.52 # NEW 12 + angle_coeff @angle:ch-cf-n2 harmonic 69.59 121.43 # NEW 6 + angle_coeff @angle:c-cf-oh harmonic 68.34 117.92 # NEW 5 + angle_coeff @angle:c-cf-os harmonic 69.09 113.78 # NEW 21 + angle_coeff @angle:h4-cf-n1 harmonic 52.58 116.36 # NEW 7 + angle_coeff @angle:h4-cf-nf harmonic 49.72 115.81 # NEW 7 + angle_coeff @angle:n2-cf-os harmonic 74.58 118.13 # NEW 6 + angle_coeff @angle:n2-cf-ss harmonic 64.40 117.23 # NEW 6 + angle_coeff @angle:nf-cf-nh harmonic 71.89 112.91 # NEW 12 + angle_coeff @angle:ne-cf-nh harmonic 73.31 118.13 # NEW 6 + angle_coeff @angle:ca-ce-cd harmonic 62.70 130.80 # NEW 12 + angle_coeff @angle:c-ce-cc harmonic 64.25 117.76 # NEW 10 + angle_coeff @angle:c-ce-n2 harmonic 70.16 114.88 # NEW 5 + angle_coeff @angle:h4-ce-nf harmonic 52.29 120.21 # NEW 6 + angle_coeff @angle:c1-ch-cd harmonic 56.97 178.60 # NEW 6 + angle_coeff @angle:ch-cg-cg harmonic 58.68 179.67 # NEW 7 + angle_coeff @angle:n-c-nf harmonic 74.43 110.37 # NEW 10 + angle_coeff @angle:ca-cq-na harmonic 68.78 119.43 # NEW 21 + angle_coeff @angle:nb-cq-nb harmonic 71.31 125.72 # NEW 5 + angle_coeff @angle:cd-cx-hc harmonic 47.37 113.84 # NEW 15 + angle_coeff @angle:cf-cy-h2 harmonic 45.50 117.25 # NEW 17 + angle_coeff @angle:cf-cy-n harmonic 74.69 88.02 # NEW 14 + angle_coeff @angle:cf-cy-ss harmonic 58.47 121.33 # NEW 13 + angle_coeff @angle:cd-n2-na harmonic 73.01 108.92 # NEW 9 + angle_coeff @angle:cd-n2-nh harmonic 70.37 118.47 # NEW 6 + angle_coeff @angle:c3-n4-cd harmonic 62.84 111.09 # NEW 7 + angle_coeff @angle:c3-na-cq harmonic 63.76 119.46 # NEW 7 + angle_coeff @angle:ca-na-cq harmonic 65.88 120.96 # NEW 20 + angle_coeff @angle:cd-na-cf harmonic 63.05 126.61 # NEW 8 + angle_coeff @angle:cq-nb-nb harmonic 68.79 121.11 # NEW 12 + angle_coeff @angle:c-n-cf harmonic 62.21 131.83 # NEW 146 + angle_coeff @angle:ca-nc-nd harmonic 73.55 108.41 # NEW 9 + angle_coeff @angle:c2-nf-ch harmonic 68.36 123.58 # NEW 12 + angle_coeff @angle:c-nf-sy harmonic 61.66 116.05 # NEW 6 + angle_coeff @angle:c3-nh-ce harmonic 63.47 119.92 # NEW 20 + angle_coeff @angle:cd-nh-n2 harmonic 68.23 119.66 # NEW 5 + angle_coeff @angle:cd-nh-sy harmonic 61.22 122.91 # NEW 23 + angle_coeff @angle:cf-nh-sy harmonic 63.58 112.97 # NEW 7 + angle_coeff @angle:hn-n-nd harmonic 50.74 115.24 # NEW 10 + angle_coeff @angle:cd-no-o harmonic 70.34 117.52 # NEW 198 + angle_coeff @angle:n3-py-nf harmonic 41.93 108.44 # NEW 12 + angle_coeff @angle:cd-s6-o harmonic 70.23 103.63 # NEW 9 + angle_coeff @angle:cd-sh-hs harmonic 46.41 95.38 # NEW 8 + angle_coeff @angle:c-ss-cd harmonic 65.61 92.43 # NEW 14 + angle_coeff @angle:c3-sx-cd harmonic 62.52 95.11 # NEW 17 + angle_coeff @angle:cd-sx-o harmonic 65.92 104.49 # NEW 17 + angle_coeff @angle:c3-sy-cd harmonic 61.24 102.19 # NEW 12 + angle_coeff @angle:ca-sy-cd harmonic 60.36 105.09 # NEW 5 + angle_coeff @angle:ca-sy-nf harmonic 62.86 103.47 # NEW 11 + angle_coeff @angle:cc-sy-nh harmonic 65.53 97.20 # NEW 6 + angle_coeff @angle:n3-sy-nf harmonic 66.36 102.40 # NEW 5 + } # (end of angle_coeffs) + + write_once("Data Angles By Type") { + @angle:hw-ow-hw @atom:hw @atom:ow @atom:hw + @angle:hw-hw-ow @atom:hw @atom:hw @atom:ow + @angle:br-c1-br @atom:br @atom:c1 @atom:br + @angle:br-c1-c1 @atom:br @atom:c1 @atom:c1 + @angle:c1-c1-c1 @atom:c1 @atom:c1 @atom:c1 + @angle:c1-c1-c2 @atom:c1 @atom:c1 @atom:c2 + @angle:c1-c1-c3 @atom:c1 @atom:c1 @atom:c3 + @angle:c1-c1-ca @atom:c1 @atom:c1 @atom:ca + @angle:c1-c1-cl @atom:c1 @atom:c1 @atom:cl + @angle:c1-c1-f @atom:c1 @atom:c1 @atom:f + @angle:c1-c1-ha @atom:c1 @atom:c1 @atom:ha + @angle:c1-c1-hc @atom:c1 @atom:c1 @atom:hc + @angle:c1-c1-i @atom:c1 @atom:c1 @atom:i + @angle:c1-c1-n1 @atom:c1 @atom:c1 @atom:n1 + @angle:c1-c1-n2 @atom:c1 @atom:c1 @atom:n2 + @angle:c1-c1-n3 @atom:c1 @atom:c1 @atom:n3 + @angle:c1-c1-n4 @atom:c1 @atom:c1 @atom:n4 + @angle:c1-c1-n @atom:c1 @atom:c1 @atom:n + @angle:c1-c1-na @atom:c1 @atom:c1 @atom:na + @angle:c1-c1-nh @atom:c1 @atom:c1 @atom:nh + @angle:c1-c1-no @atom:c1 @atom:c1 @atom:no + @angle:c1-c1-o @atom:c1 @atom:c1 @atom:o + @angle:c1-c1-oh @atom:c1 @atom:c1 @atom:oh + @angle:c1-c1-os @atom:c1 @atom:c1 @atom:os + @angle:c1-c1-p2 @atom:c1 @atom:c1 @atom:p2 + @angle:c1-c1-p3 @atom:c1 @atom:c1 @atom:p3 + @angle:c1-c1-p4 @atom:c1 @atom:c1 @atom:p4 + @angle:c1-c1-p5 @atom:c1 @atom:c1 @atom:p5 + @angle:c1-c1-s4 @atom:c1 @atom:c1 @atom:s4 + @angle:c1-c1-s6 @atom:c1 @atom:c1 @atom:s6 + @angle:c1-c1-s @atom:c1 @atom:c1 @atom:s + @angle:c1-c1-sh @atom:c1 @atom:c1 @atom:sh + @angle:c1-c1-ss @atom:c1 @atom:c1 @atom:ss + @angle:c2-c1-c2 @atom:c2 @atom:c1 @atom:c2 + @angle:c2-c1-ce @atom:c2 @atom:c1 @atom:ce + @angle:c2-c1-n1 @atom:c2 @atom:c1 @atom:n1 + @angle:c2-c1-o @atom:c2 @atom:c1 @atom:o + @angle:c2-c1-s2 @atom:c2 @atom:c1 @atom:s2 + @angle:c3-c1-c3 @atom:c3 @atom:c1 @atom:c3 + @angle:c3-c1-cg @atom:c3 @atom:c1 @atom:cg + @angle:c3-c1-n1 @atom:c3 @atom:c1 @atom:n1 + @angle:ca-c1-ca @atom:ca @atom:c1 @atom:ca + @angle:c-c1-c1 @atom:c @atom:c1 @atom:c1 + @angle:cg-c1-ha @atom:cg @atom:c1 @atom:ha + @angle:ch-c1-ha @atom:ch @atom:c1 @atom:ha + @angle:cl-c1-cl @atom:cl @atom:c1 @atom:cl + @angle:f-c1-f @atom:f @atom:c1 @atom:f + @angle:i-c1-i @atom:i @atom:c1 @atom:i + @angle:n1-c1-n1 @atom:n1 @atom:c1 @atom:n1 + @angle:n1-c1-n3 @atom:n1 @atom:c1 @atom:n3 + @angle:n1-c1-nh @atom:n1 @atom:c1 @atom:nh + @angle:n1-c1-os @atom:n1 @atom:c1 @atom:os + @angle:n1-c1-p3 @atom:n1 @atom:c1 @atom:p3 + @angle:n1-c1-ss @atom:n1 @atom:c1 @atom:ss + @angle:n2-c1-n2 @atom:n2 @atom:c1 @atom:n2 + @angle:n2-c1-o @atom:n2 @atom:c1 @atom:o + @angle:n2-c1-s @atom:n2 @atom:c1 @atom:s + @angle:n3-c1-n3 @atom:n3 @atom:c1 @atom:n3 + @angle:n4-c1-n4 @atom:n4 @atom:c1 @atom:n4 + @angle:na-c1-na @atom:na @atom:c1 @atom:na + @angle:ne-c1-o @atom:ne @atom:c1 @atom:o + @angle:ne-c1-s @atom:ne @atom:c1 @atom:s + @angle:nf-c1-o @atom:nf @atom:c1 @atom:o + @angle:nh-c1-nh @atom:nh @atom:c1 @atom:nh + @angle:n-c1-n @atom:n @atom:c1 @atom:n + @angle:no-c1-no @atom:no @atom:c1 @atom:no + @angle:oh-c1-oh @atom:oh @atom:c1 @atom:oh + @angle:o-c1-o @atom:o @atom:c1 @atom:o + @angle:os-c1-os @atom:os @atom:c1 @atom:os + @angle:p2-c1-p2 @atom:p2 @atom:c1 @atom:p2 + @angle:p3-c1-p3 @atom:p3 @atom:c1 @atom:p3 + @angle:p4-c1-p4 @atom:p4 @atom:c1 @atom:p4 + @angle:p5-c1-p5 @atom:p5 @atom:c1 @atom:p5 + @angle:s2-c1-s2 @atom:s2 @atom:c1 @atom:s2 + @angle:s4-c1-s4 @atom:s4 @atom:c1 @atom:s4 + @angle:s6-c1-s6 @atom:s6 @atom:c1 @atom:s6 + @angle:sh-c1-sh @atom:sh @atom:c1 @atom:sh + @angle:s-c1-s @atom:s @atom:c1 @atom:s + @angle:ss-c1-ss @atom:ss @atom:c1 @atom:ss + @angle:br-c2-br @atom:br @atom:c2 @atom:br + @angle:br-c2-c2 @atom:br @atom:c2 @atom:c2 + @angle:br-c2-c3 @atom:br @atom:c2 @atom:c3 + @angle:br-c2-ce @atom:br @atom:c2 @atom:ce + @angle:br-c2-h4 @atom:br @atom:c2 @atom:h4 + @angle:br-c2-ha @atom:br @atom:c2 @atom:ha + @angle:c1-c2-c1 @atom:c1 @atom:c2 @atom:c1 + @angle:c1-c2-c2 @atom:c1 @atom:c2 @atom:c2 + @angle:c1-c2-c3 @atom:c1 @atom:c2 @atom:c3 + @angle:c1-c2-f @atom:c1 @atom:c2 @atom:f + @angle:c1-c2-ha @atom:c1 @atom:c2 @atom:ha + @angle:c2-c2-c2 @atom:c2 @atom:c2 @atom:c2 + @angle:c2-c2-c3 @atom:c2 @atom:c2 @atom:c3 + @angle:c2-c2-ca @atom:c2 @atom:c2 @atom:ca + @angle:c2-c2-cc @atom:c2 @atom:c2 @atom:cc + @angle:c2-c2-cd @atom:c2 @atom:c2 @atom:cd + @angle:c2-c2-cl @atom:c2 @atom:c2 @atom:cl + @angle:c2-c2-cx @atom:c2 @atom:c2 @atom:cx + @angle:c2-c2-cy @atom:c2 @atom:c2 @atom:cy + @angle:c2-c2-f @atom:c2 @atom:c2 @atom:f + @angle:c2-c2-h4 @atom:c2 @atom:c2 @atom:h4 + @angle:c2-c2-ha @atom:c2 @atom:c2 @atom:ha + @angle:c2-c2-hc @atom:c2 @atom:c2 @atom:hc + @angle:c2-c2-hx @atom:c2 @atom:c2 @atom:hx + @angle:c2-c2-i @atom:c2 @atom:c2 @atom:i + @angle:c2-c2-n1 @atom:c2 @atom:c2 @atom:n1 + @angle:c2-c2-n2 @atom:c2 @atom:c2 @atom:n2 + @angle:c2-c2-n3 @atom:c2 @atom:c2 @atom:n3 + @angle:c2-c2-n4 @atom:c2 @atom:c2 @atom:n4 + @angle:c2-c2-n @atom:c2 @atom:c2 @atom:n + @angle:c2-c2-na @atom:c2 @atom:c2 @atom:na + @angle:c2-c2-nh @atom:c2 @atom:c2 @atom:nh + @angle:c2-c2-no @atom:c2 @atom:c2 @atom:no + @angle:c2-c2-o @atom:c2 @atom:c2 @atom:o + @angle:c2-c2-oh @atom:c2 @atom:c2 @atom:oh + @angle:c2-c2-os @atom:c2 @atom:c2 @atom:os + @angle:c2-c2-p2 @atom:c2 @atom:c2 @atom:p2 + @angle:c2-c2-p3 @atom:c2 @atom:c2 @atom:p3 + @angle:c2-c2-p4 @atom:c2 @atom:c2 @atom:p4 + @angle:c2-c2-p5 @atom:c2 @atom:c2 @atom:p5 + @angle:c2-c2-s4 @atom:c2 @atom:c2 @atom:s4 + @angle:c2-c2-s6 @atom:c2 @atom:c2 @atom:s6 + @angle:c2-c2-s @atom:c2 @atom:c2 @atom:s + @angle:c2-c2-sh @atom:c2 @atom:c2 @atom:sh + @angle:c2-c2-ss @atom:c2 @atom:c2 @atom:ss + @angle:c3-c2-c3 @atom:c3 @atom:c2 @atom:c3 + @angle:c3-c2-cc @atom:c3 @atom:c2 @atom:cc + @angle:c3-c2-cd @atom:c3 @atom:c2 @atom:cd + @angle:c3-c2-ce @atom:c3 @atom:c2 @atom:ce + @angle:c3-c2-cf @atom:c3 @atom:c2 @atom:cf + @angle:c3-c2-h4 @atom:c3 @atom:c2 @atom:h4 + @angle:c3-c2-ha @atom:c3 @atom:c2 @atom:ha + @angle:c3-c2-hc @atom:c3 @atom:c2 @atom:hc + @angle:c3-c2-n2 @atom:c3 @atom:c2 @atom:n2 + @angle:c3-c2-n @atom:c3 @atom:c2 @atom:n + @angle:c3-c2-na @atom:c3 @atom:c2 @atom:na + @angle:c3-c2-ne @atom:c3 @atom:c2 @atom:ne + @angle:c3-c2-nf @atom:c3 @atom:c2 @atom:nf + @angle:c3-c2-nh @atom:c3 @atom:c2 @atom:nh + @angle:c3-c2-o @atom:c3 @atom:c2 @atom:o + @angle:c3-c2-oh @atom:c3 @atom:c2 @atom:oh + @angle:c3-c2-os @atom:c3 @atom:c2 @atom:os + @angle:c3-c2-p2 @atom:c3 @atom:c2 @atom:p2 + @angle:c3-c2-s @atom:c3 @atom:c2 @atom:s + @angle:c3-c2-ss @atom:c3 @atom:c2 @atom:ss + @angle:ca-c2-ca @atom:ca @atom:c2 @atom:ca + @angle:ca-c2-hc @atom:ca @atom:c2 @atom:hc + @angle:c-c2-c2 @atom:c @atom:c2 @atom:c2 + @angle:c-c2-c3 @atom:c @atom:c2 @atom:c3 + @angle:c-c2-c @atom:c @atom:c2 @atom:c + @angle:cc-c2-h4 @atom:cc @atom:c2 @atom:h4 + @angle:cc-c2-ha @atom:cc @atom:c2 @atom:ha + @angle:cc-c2-nh @atom:cc @atom:c2 @atom:nh + @angle:cc-c2-o @atom:cc @atom:c2 @atom:o + @angle:cd-c2-ha @atom:cd @atom:c2 @atom:ha + @angle:ce-c2-cl @atom:ce @atom:c2 @atom:cl + @angle:ce-c2-h4 @atom:ce @atom:c2 @atom:h4 + @angle:ce-c2-ha @atom:ce @atom:c2 @atom:ha + @angle:ce-c2-na @atom:ce @atom:c2 @atom:na + @angle:ce-c2-nh @atom:ce @atom:c2 @atom:nh + @angle:ce-c2-no @atom:ce @atom:c2 @atom:no + @angle:ce-c2-o @atom:ce @atom:c2 @atom:o + @angle:ce-c2-oh @atom:ce @atom:c2 @atom:oh + @angle:ce-c2-os @atom:ce @atom:c2 @atom:os + @angle:cf-c2-ha @atom:cf @atom:c2 @atom:ha + @angle:c-c2-ha @atom:c @atom:c2 @atom:ha + @angle:c-c2-hc @atom:c @atom:c2 @atom:hc + @angle:cl-c2-cl @atom:cl @atom:c2 @atom:cl + @angle:cl-c2-h4 @atom:cl @atom:c2 @atom:h4 + @angle:cl-c2-ha @atom:cl @atom:c2 @atom:ha + @angle:cx-c2-ha @atom:cx @atom:c2 @atom:ha + @angle:f-c2-f @atom:f @atom:c2 @atom:f + @angle:f-c2-ha @atom:f @atom:c2 @atom:ha + @angle:h4-c2-n2 @atom:h4 @atom:c2 @atom:n2 + @angle:h4-c2-n @atom:h4 @atom:c2 @atom:n + @angle:h4-c2-na @atom:h4 @atom:c2 @atom:na + @angle:h4-c2-ne @atom:h4 @atom:c2 @atom:ne + @angle:h4-c2-nh @atom:h4 @atom:c2 @atom:nh + @angle:h4-c2-no @atom:h4 @atom:c2 @atom:no + @angle:h4-c2-os @atom:h4 @atom:c2 @atom:os + @angle:h4-c2-ss @atom:h4 @atom:c2 @atom:ss + @angle:h5-c2-n2 @atom:h5 @atom:c2 @atom:n2 + @angle:h5-c2-na @atom:h5 @atom:c2 @atom:na + @angle:h5-c2-ne @atom:h5 @atom:c2 @atom:ne + @angle:h5-c2-nh @atom:h5 @atom:c2 @atom:nh + @angle:ha-c2-ha @atom:ha @atom:c2 @atom:ha + @angle:ha-c2-n1 @atom:ha @atom:c2 @atom:n1 + @angle:ha-c2-n2 @atom:ha @atom:c2 @atom:n2 + @angle:ha-c2-n3 @atom:ha @atom:c2 @atom:n3 + @angle:ha-c2-n @atom:ha @atom:c2 @atom:n + @angle:ha-c2-na @atom:ha @atom:c2 @atom:na + @angle:ha-c2-ne @atom:ha @atom:c2 @atom:ne + @angle:ha-c2-nf @atom:ha @atom:c2 @atom:nf + @angle:ha-c2-nh @atom:ha @atom:c2 @atom:nh + @angle:ha-c2-no @atom:ha @atom:c2 @atom:no + @angle:ha-c2-o @atom:ha @atom:c2 @atom:o + @angle:ha-c2-oh @atom:ha @atom:c2 @atom:oh + @angle:ha-c2-os @atom:ha @atom:c2 @atom:os + @angle:ha-c2-p2 @atom:ha @atom:c2 @atom:p2 + @angle:ha-c2-p3 @atom:ha @atom:c2 @atom:p3 + @angle:ha-c2-p4 @atom:ha @atom:c2 @atom:p4 + @angle:ha-c2-p5 @atom:ha @atom:c2 @atom:p5 + @angle:ha-c2-pe @atom:ha @atom:c2 @atom:pe + @angle:ha-c2-pf @atom:ha @atom:c2 @atom:pf + @angle:ha-c2-s2 @atom:ha @atom:c2 @atom:s2 + @angle:ha-c2-s4 @atom:ha @atom:c2 @atom:s4 + @angle:ha-c2-s @atom:ha @atom:c2 @atom:s + @angle:ha-c2-s6 @atom:ha @atom:c2 @atom:s6 + @angle:ha-c2-sh @atom:ha @atom:c2 @atom:sh + @angle:ha-c2-ss @atom:ha @atom:c2 @atom:ss + @angle:hc-c2-hc @atom:hc @atom:c2 @atom:hc + @angle:hc-c2-n2 @atom:hc @atom:c2 @atom:n2 + @angle:hc-c2-n @atom:hc @atom:c2 @atom:n + @angle:hc-c2-na @atom:hc @atom:c2 @atom:na + @angle:hc-c2-nh @atom:hc @atom:c2 @atom:nh + @angle:hc-c2-no @atom:hc @atom:c2 @atom:no + @angle:hc-c2-oh @atom:hc @atom:c2 @atom:oh + @angle:hc-c2-os @atom:hc @atom:c2 @atom:os + @angle:hc-c2-p3 @atom:hc @atom:c2 @atom:p3 + @angle:hc-c2-p5 @atom:hc @atom:c2 @atom:p5 + @angle:hc-c2-s4 @atom:hc @atom:c2 @atom:s4 + @angle:hc-c2-s6 @atom:hc @atom:c2 @atom:s6 + @angle:hc-c2-sh @atom:hc @atom:c2 @atom:sh + @angle:hc-c2-ss @atom:hc @atom:c2 @atom:ss + @angle:hx-c2-n4 @atom:hx @atom:c2 @atom:n4 + @angle:i-c2-i @atom:i @atom:c2 @atom:i + @angle:n1-c2-n1 @atom:n1 @atom:c2 @atom:n1 + @angle:n2-c2-n2 @atom:n2 @atom:c2 @atom:n2 + @angle:n2-c2-n4 @atom:n2 @atom:c2 @atom:n4 + @angle:n2-c2-na @atom:n2 @atom:c2 @atom:na + @angle:n2-c2-nh @atom:n2 @atom:c2 @atom:nh + @angle:n2-c2-oh @atom:n2 @atom:c2 @atom:oh + @angle:n2-c2-os @atom:n2 @atom:c2 @atom:os + @angle:n2-c2-ss @atom:n2 @atom:c2 @atom:ss + @angle:n3-c2-n3 @atom:n3 @atom:c2 @atom:n3 + @angle:n4-c2-n4 @atom:n4 @atom:c2 @atom:n4 + @angle:n4-c2-ss @atom:n4 @atom:c2 @atom:ss + @angle:na-c2-na @atom:na @atom:c2 @atom:na + @angle:ne-c2-nh @atom:ne @atom:c2 @atom:nh + @angle:ne-c2-os @atom:ne @atom:c2 @atom:os + @angle:ne-c2-ss @atom:ne @atom:c2 @atom:ss + @angle:nf-c2-nh @atom:nf @atom:c2 @atom:nh + @angle:nh-c2-nh @atom:nh @atom:c2 @atom:nh + @angle:nh-c2-oh @atom:nh @atom:c2 @atom:oh + @angle:nh-c2-os @atom:nh @atom:c2 @atom:os + @angle:nh-c2-ss @atom:nh @atom:c2 @atom:ss + @angle:n-c2-n2 @atom:n @atom:c2 @atom:n2 + @angle:n-c2-n @atom:n @atom:c2 @atom:n + @angle:n-c2-na @atom:n @atom:c2 @atom:na + @angle:n-c2-ne @atom:n @atom:c2 @atom:ne + @angle:n-c2-nh @atom:n @atom:c2 @atom:nh + @angle:no-c2-no @atom:no @atom:c2 @atom:no + @angle:n-c2-ss @atom:n @atom:c2 @atom:ss + @angle:oh-c2-oh @atom:oh @atom:c2 @atom:oh + @angle:o-c2-o @atom:o @atom:c2 @atom:o + @angle:o-c2-oh @atom:o @atom:c2 @atom:oh + @angle:o-c2-s @atom:o @atom:c2 @atom:s + @angle:os-c2-os @atom:os @atom:c2 @atom:os + @angle:p2-c2-p2 @atom:p2 @atom:c2 @atom:p2 + @angle:p3-c2-p3 @atom:p3 @atom:c2 @atom:p3 + @angle:p5-c2-p5 @atom:p5 @atom:c2 @atom:p5 + @angle:s4-c2-s4 @atom:s4 @atom:c2 @atom:s4 + @angle:s4-c2-s6 @atom:s4 @atom:c2 @atom:s6 + @angle:s6-c2-s6 @atom:s6 @atom:c2 @atom:s6 + @angle:sh-c2-sh @atom:sh @atom:c2 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@atom:cf @atom:cf @atom:cl + @angle:cf-cf-oh @atom:cf @atom:cf @atom:oh + @angle:ce-cf-cy @atom:ce @atom:cf @atom:cy + @angle:ce-cf-h4 @atom:ce @atom:cf @atom:h4 + @angle:ce-cf-n1 @atom:ce @atom:cf @atom:n1 + @angle:ce-cf-nh @atom:ce @atom:cf @atom:nh + @angle:ch-cf-n2 @atom:ch @atom:cf @atom:n2 + @angle:c-cf-oh @atom:c @atom:cf @atom:oh + @angle:c-cf-os @atom:c @atom:cf @atom:os + @angle:h4-cf-n1 @atom:h4 @atom:cf @atom:n1 + @angle:h4-cf-nf @atom:h4 @atom:cf @atom:nf + @angle:n2-cf-os @atom:n2 @atom:cf @atom:os + @angle:n2-cf-ss @atom:n2 @atom:cf @atom:ss + @angle:nf-cf-nh @atom:nf @atom:cf @atom:nh + @angle:ne-cf-nh @atom:ne @atom:cf @atom:nh + @angle:ca-ce-cd @atom:ca @atom:ce @atom:cd + @angle:c-ce-cc @atom:c @atom:ce @atom:cc + @angle:c-ce-n2 @atom:c @atom:ce @atom:n2 + @angle:h4-ce-nf @atom:h4 @atom:ce @atom:nf + @angle:c1-ch-cd @atom:c1 @atom:ch @atom:cd + @angle:ch-cg-cg @atom:ch @atom:cg @atom:cg + @angle:n-c-nf @atom:n @atom:c @atom:nf + @angle:ca-cq-na @atom:ca @atom:cq @atom:na + @angle:nb-cq-nb @atom:nb @atom:cq @atom:nb + @angle:cd-cx-hc @atom:cd @atom:cx @atom:hc + @angle:cf-cy-h2 @atom:cf @atom:cy @atom:h2 + @angle:cf-cy-n @atom:cf @atom:cy @atom:n + @angle:cf-cy-ss @atom:cf @atom:cy @atom:ss + @angle:cd-n2-na @atom:cd @atom:n2 @atom:na + @angle:cd-n2-nh @atom:cd @atom:n2 @atom:nh + @angle:c3-n4-cd @atom:c3 @atom:n4 @atom:cd + @angle:c3-na-cq @atom:c3 @atom:na @atom:cq + @angle:ca-na-cq @atom:ca @atom:na @atom:cq + @angle:cd-na-cf @atom:cd @atom:na @atom:cf + @angle:cq-nb-nb @atom:cq @atom:nb @atom:nb + @angle:c-n-cf @atom:c @atom:n @atom:cf + @angle:ca-nc-nd @atom:ca @atom:nc @atom:nd + @angle:c2-nf-ch @atom:c2 @atom:nf @atom:ch + @angle:c-nf-sy @atom:c @atom:nf @atom:sy + @angle:c3-nh-ce @atom:c3 @atom:nh @atom:ce + @angle:cd-nh-n2 @atom:cd @atom:nh @atom:n2 + @angle:cd-nh-sy @atom:cd @atom:nh @atom:sy + @angle:cf-nh-sy @atom:cf @atom:nh @atom:sy + @angle:hn-n-nd @atom:hn @atom:n @atom:nd + @angle:cd-no-o @atom:cd @atom:no @atom:o + @angle:n3-py-nf @atom:n3 @atom:py @atom:nf + @angle:cd-s6-o @atom:cd @atom:s6 @atom:o + @angle:cd-sh-hs @atom:cd @atom:sh @atom:hs + @angle:c-ss-cd @atom:c @atom:ss @atom:cd + @angle:c3-sx-cd @atom:c3 @atom:sx @atom:cd + @angle:cd-sx-o @atom:cd @atom:sx @atom:o + @angle:c3-sy-cd @atom:c3 @atom:sy @atom:cd + @angle:ca-sy-cd @atom:ca @atom:sy @atom:cd + @angle:ca-sy-nf @atom:ca @atom:sy @atom:nf + @angle:cc-sy-nh @atom:cc @atom:sy @atom:nh + @angle:n3-sy-nf @atom:n3 @atom:sy @atom:nf + } # (end of Angles By Type) + + write_once("In Settings") { + dihedral_coeff @dihedral:X-c-c-X fourier 1 0.3 2 180.0 # + dihedral_coeff @dihedral:X-c-c1-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c-cg-X fourier 1 0.0 2 180.0 # same as X-c-c1-X + dihedral_coeff @dihedral:X-c-ch-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c-c2-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cu-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cv-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-ce-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cf-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-c3-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-cx-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-cy-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-ca-X fourier 1 1.0 2 180.0 # optimized by Junmei Wang, Jan-2013 + dihedral_coeff @dihedral:X-c-cc-X fourier 1 2.875 2 180.0 # statistic value + dihedral_coeff @dihedral:X-c-cd-X fourier 1 2.875 2 180.0 # statistic value + dihedral_coeff @dihedral:X-c-n-X fourier 1 2.5 2 180.0 # AA,NMA (no c-n3, c-n4, c-nh) + dihedral_coeff @dihedral:X-c-n2-X fourier 1 4.15 2 180.0 # double bond, same as X-c2-n2-X + dihedral_coeff @dihedral:X-c-nc-X fourier 1 4.0 2 180.0 # same as X-C-NC-X + dihedral_coeff @dihedral:X-c-nd-X fourier 1 4.0 2 180.0 # same as X-C-NC-X + dihedral_coeff @dihedral:X-c-ne-X fourier 1 0.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-nf-X fourier 1 0.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-na-X fourier 2 1.45 2 180.0 0.35 4 180.0 # + dihedral_coeff @dihedral:X-c-no-X fourier 1 0.45 2 180.0 # + dihedral_coeff @dihedral:X-c-oh-X fourier 1 2.3 2 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c-os-X fourier 1 2.7 2 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c-p2-X fourier 1 6.65 2 180.0 # double bond, same as X-c2-p2-X + dihedral_coeff @dihedral:X-c-pc-X fourier 1 2.0 2 180.0 # estimated + dihedral_coeff @dihedral:X-c-pd-X fourier 1 2.0 2 180.0 # estimated + dihedral_coeff @dihedral:X-c-pe-X fourier 1 0.0 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-pf-X fourier 1 0.0 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-p3-X fourier 1 1.55 2 180.0 # + dihedral_coeff @dihedral:X-c-p4-X fourier 1 1.35 2 180.0 # + dihedral_coeff @dihedral:X-c-px-X fourier 1 1.35 2 180.0 # + dihedral_coeff @dihedral:X-c-p5-X fourier 1 1.0 2 0.0 # + dihedral_coeff @dihedral:X-c-py-X fourier 1 1.0 2 0.0 # + dihedral_coeff @dihedral:X-c-sh-X fourier 1 2.25 2 180.0 # + dihedral_coeff @dihedral:X-c-ss-X fourier 1 3.1 2 180.0 # + dihedral_coeff @dihedral:X-c-s4-X fourier 1 0.2 2 180.0 # + dihedral_coeff @dihedral:X-c-sx-X fourier 1 0.2 2 180.0 # + dihedral_coeff @dihedral:X-c-s6-X fourier 1 0.5 2 0.0 # + dihedral_coeff @dihedral:X-c-sy-X fourier 1 0.5 2 0.0 # + dihedral_coeff @dihedral:X-c1-c1-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-cg-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-ch-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-cg-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-c2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-c3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-ca-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-ce-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cu-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cv-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cx-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-cy-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-n-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-n2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-n3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-n4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-na-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-nb-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-nc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-nd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-ne-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-nf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-nh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-no-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-oh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-os-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-p2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-pb-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-pc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-pd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-pe-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-pf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-p3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-p4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-px-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-p5-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-py-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-s2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-sh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-ss-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-s4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-sx-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-s6-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c1-sy-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-c2-c2-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c2-ce-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c2-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ce-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ce-ce-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 + dihedral_coeff @dihedral:X-cf-cf-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 + dihedral_coeff @dihedral:X-cc-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-cc-cc-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-cd-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-c2-c3-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c2-ca-X fourier 1 0.7 2 180.0 # optimized by Junmei Wang, March 2013 + dihedral_coeff @dihedral:X-c2-n-X fourier 1 0.65 2 180.0 # + dihedral_coeff @dihedral:X-c2-n2-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-c2-ne-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-c2-nf-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-ce-ne-X fourier 1 0.8 2 180.0 # single bond + dihedral_coeff @dihedral:X-cf-nf-X fourier 1 0.8 2 180.0 # single bond + dihedral_coeff @dihedral:X-c2-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-c2-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cc-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-nc-X fourier 1 4.75 2 180.0 # statistiv value from parm94 + dihedral_coeff @dihedral:X-cc-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-nd-X fourier 1 4.75 2 180.0 # statistiv value from parm94 + dihedral_coeff @dihedral:X-c2-n3-X fourier 1 0.3 2 180.0 # intrpol. + dihedral_coeff @dihedral:X-c2-n4-X fourier 1 0.0 3 180.0 # intrpol. + dihedral_coeff @dihedral:X-c2-na-X fourier 1 0.625 2 180.0 # + dihedral_coeff @dihedral:X-cc-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-c2-nh-X fourier 1 0.675 2 180.0 # + dihedral_coeff @dihedral:X-c2-no-X fourier 1 0.75 2 180.0 # + dihedral_coeff @dihedral:X-c2-oh-X fourier 1 1.05 2 180.0 # parm99 + dihedral_coeff @dihedral:X-c2-os-X fourier 1 1.05 2 180.0 # parm99 + dihedral_coeff @dihedral:X-c2-p2-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-c2-pe-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-c2-pf-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-ce-pf-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-ce-pe-X fourier 1 0.95 2 180.0 # single bond + dihedral_coeff @dihedral:X-cf-pf-X fourier 1 0.95 2 180.0 # single bond + dihedral_coeff @dihedral:X-c2-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-c2-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cc-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cc-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cd-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cd-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-c2-p3-X fourier 1 0.45 2 180.0 # + dihedral_coeff @dihedral:X-c2-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-ce-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-cf-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-c2-px-X fourier 1 0.325 2 0.0 # + dihedral_coeff @dihedral:X-ce-px-X fourier 1 0.325 2 0.0 # + dihedral_coeff @dihedral:X-cf-px-X fourier 1 0.325 2 0.0 # + dihedral_coeff @dihedral:X-c2-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-ce-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-cf-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-c2-py-X fourier 1 1.43333333333 2 180.0 # + dihedral_coeff @dihedral:X-ce-py-X fourier 1 1.43333333333 2 180.0 # + dihedral_coeff @dihedral:X-cf-py-X fourier 1 1.43333333333 2 180.0 # + dihedral_coeff @dihedral:X-c2-sh-X fourier 1 0.5 2 180.0 # + dihedral_coeff @dihedral:X-c2-ss-X fourier 1 1.1 2 180.0 # + dihedral_coeff @dihedral:X-c2-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-ce-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-cf-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-c2-sx-X fourier 1 0.6 2 0.0 # + dihedral_coeff @dihedral:X-ce-sx-X fourier 1 0.6 2 0.0 # + dihedral_coeff @dihedral:X-cf-sx-X fourier 1 0.6 2 0.0 # + dihedral_coeff @dihedral:X-c2-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-ce-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-cf-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-c2-sy-X fourier 1 1.26666666667 2 180.0 # + dihedral_coeff @dihedral:X-ce-sy-X fourier 1 1.26666666667 2 180.0 # + dihedral_coeff @dihedral:X-cf-sy-X fourier 1 1.26666666667 2 180.0 # + dihedral_coeff @dihedral:X-c3-c3-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-cx-cx-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X + dihedral_coeff @dihedral:X-cy-cy-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X + dihedral_coeff @dihedral:X-c3-ca-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-n-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-cx-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X + dihedral_coeff @dihedral:X-cy-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X + dihedral_coeff @dihedral:X-c3-n2-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-ne-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-nf-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-n3-X fourier 1 0.3 3 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c3-n4-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-na-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-nh-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-no-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-oh-X fourier 1 0.166666666667 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-os-X fourier 1 0.383333333333 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-p2-X fourier 1 0.266666666667 2 180.0 # + dihedral_coeff @dihedral:X-c3-pe-X fourier 1 0.266666666667 2 180.0 # + dihedral_coeff @dihedral:X-c3-pf-X fourier 1 0.266666666667 2 180.0 # + dihedral_coeff @dihedral:X-c3-p3-X fourier 1 0.133333333333 3 0.0 # + dihedral_coeff @dihedral:X-c3-p4-X fourier 1 0.133333333333 3 0.0 # + dihedral_coeff @dihedral:X-c3-px-X fourier 1 0.133333333333 3 0.0 # + dihedral_coeff @dihedral:X-c3-p5-X fourier 1 0.0222222222222 3 0.0 # + dihedral_coeff @dihedral:X-c3-py-X fourier 1 0.0222222222222 3 0.0 # + dihedral_coeff @dihedral:X-c3-sh-X fourier 1 0.25 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-ss-X fourier 1 0.333333333333 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-s4-X fourier 1 0.2 3 0.0 # + dihedral_coeff @dihedral:X-c3-sx-X fourier 1 0.2 3 0.0 # + dihedral_coeff @dihedral:X-c3-s6-X fourier 1 0.144444444444 3 0.0 # + dihedral_coeff @dihedral:X-c3-sy-X fourier 1 0.144444444444 3 0.0 # + dihedral_coeff @dihedral:X-c3-cc-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X + dihedral_coeff @dihedral:X-c3-cd-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X + dihedral_coeff @dihedral:X-ca-ca-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ca-cp-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ca-cq-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-cp-cp-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-cq-cq-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ca-n-X fourier 1 0.45 2 180.0 # + dihedral_coeff @dihedral:X-ca-n2-X fourier 1 0.0 3 180.0 # + dihedral_coeff @dihedral:X-ca-ne-X fourier 1 0.0 3 180.0 # + dihedral_coeff @dihedral:X-ca-nf-X fourier 1 0.0 3 180.0 # + dihedral_coeff @dihedral:X-ca-n4-X fourier 1 1.75 2 0.0 # + dihedral_coeff @dihedral:X-ca-na-X fourier 1 0.3 2 180.0 # + dihedral_coeff @dihedral:X-ca-nb-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nc-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nd-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nh-X fourier 1 1.05 2 180.0 # + dihedral_coeff @dihedral:X-cc-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X + dihedral_coeff @dihedral:X-cd-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X + dihedral_coeff @dihedral:X-ca-no-X fourier 1 0.6 2 180.0 # + dihedral_coeff @dihedral:X-ca-oh-X fourier 1 0.9 2 180.0 # Junmei et al, 99 + dihedral_coeff @dihedral:X-ca-os-X fourier 1 0.9 2 180.0 # same as X-ca-oh-X + dihedral_coeff @dihedral:X-ca-p2-X fourier 1 0.6 2 180.0 # + dihedral_coeff @dihedral:X-ca-pe-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X + dihedral_coeff @dihedral:X-ca-pf-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X + dihedral_coeff @dihedral:X-ca-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-ca-pd-X fourier 1 4.8 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-ca-p3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-ca-p4-X fourier 1 0.525 2 180.0 # + dihedral_coeff @dihedral:X-ca-px-X fourier 1 0.525 2 180.0 # estimated, same as X-ca-p4-X + dihedral_coeff @dihedral:X-ca-p5-X fourier 1 1.46666666667 2 180.0 # + dihedral_coeff @dihedral:X-ca-py-X fourier 1 1.46666666667 2 180.0 # estimated, same as X-ca-p5-X + dihedral_coeff @dihedral:X-ca-sh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-ca-ss-X fourier 1 0.4 2 180.0 # + dihedral_coeff @dihedral:X-ca-s4-X fourier 1 0.3 2 0.0 # + dihedral_coeff @dihedral:X-ca-sx-X fourier 1 0.3 2 0.0 # estimated, same as X-ca-s4-X + dihedral_coeff @dihedral:X-ca-s6-X fourier 1 1.3 2 180.0 # + dihedral_coeff @dihedral:X-ca-sy-X fourier 1 1.3 2 180.0 # estimated, same as X-ca-s6-X + dihedral_coeff @dihedral:X-n-cc-X fourier 1 1.65 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-n-cd-X fourier 1 1.65 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-n-n-X fourier 1 1.15 2 0.0 # + dihedral_coeff @dihedral:X-n-n2-X fourier 1 0.4 2 0.0 # + dihedral_coeff @dihedral:X-n-ne-X fourier 1 0.4 2 0.0 # + dihedral_coeff @dihedral:X-n-nf-X fourier 1 0.4 2 0.0 # + dihedral_coeff @dihedral:X-n-n3-X fourier 1 1.075 2 0.0 # + dihedral_coeff @dihedral:X-n-n4-X fourier 1 0.95 2 0.0 # + dihedral_coeff @dihedral:X-n-na-X fourier 1 0.7 2 0.0 # + dihedral_coeff @dihedral:X-n-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-nh-X fourier 1 1.1 2 0.0 # + dihedral_coeff @dihedral:X-n-no-X fourier 1 1.375 2 180.0 # + dihedral_coeff @dihedral:X-n-oh-X fourier 1 1.5 2 0.0 # + dihedral_coeff @dihedral:X-n-os-X fourier 1 1.1 2 0.0 # + dihedral_coeff @dihedral:X-n-p2-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-n-pe-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-n-pf-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-pd-X fourier 1 4.8 2 180.0 # + dihedral_coeff @dihedral:X-n-p3-X fourier 1 2.25 2 0.0 # + dihedral_coeff @dihedral:X-n-p4-X fourier 1 0.325 2 0.0 # + dihedral_coeff @dihedral:X-n-px-X fourier 1 0.325 2 0.0 # + dihedral_coeff @dihedral:X-n-p5-X fourier 1 2.2 2 180.0 # + dihedral_coeff @dihedral:X-n-py-X fourier 1 2.2 2 180.0 # + dihedral_coeff @dihedral:X-n-sh-X fourier 1 1.1 2 0.0 # + dihedral_coeff @dihedral:X-n-ss-X fourier 1 1.5 2 0.0 # + dihedral_coeff @dihedral:X-n-s4-X fourier 1 1.5 3 0.0 # + dihedral_coeff @dihedral:X-n-sx-X fourier 1 1.5 3 0.0 # + dihedral_coeff @dihedral:X-n-s6-X fourier 1 1.1 2 180.0 # + dihedral_coeff @dihedral:X-n-sy-X fourier 1 1.1 2 180.0 # + dihedral_coeff @dihedral:X-n1-c2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-c3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-ca-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-ce-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cu-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cv-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cx-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-cy-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-n-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-n1-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-n2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-n3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-n4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-na-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-nb-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-nc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-nd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-ne-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-nf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-nh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-no-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-oh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-os-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-p2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-pb-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-pc-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-pd-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-pe-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-pf-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-p3-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-p4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-px-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-p5-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-py-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-s2-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-sh-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-ss-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-s4-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-sx-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-s6-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n1-sy-X fourier 1 0.0 2 180.0 # + dihedral_coeff @dihedral:X-n2-n2-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-n2-ne-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-n2-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-ne-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-ne-ne-X fourier 1 1.2 2 180.0 # single bond, intrpol + dihedral_coeff @dihedral:X-nf-nf-X fourier 1 1.2 2 180.0 # single bond, intrpol + dihedral_coeff @dihedral:X-nc-nc-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-nd-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-nc-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-n2-nc-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X + dihedral_coeff @dihedral:X-n2-nd-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X + dihedral_coeff @dihedral:X-n2-n3-X fourier 1 6.1 2 180.0 # + dihedral_coeff @dihedral:X-ne-n3-X fourier 1 6.1 2 180.0 # + dihedral_coeff @dihedral:X-nf-n3-X fourier 1 6.1 2 180.0 # + dihedral_coeff @dihedral:X-n2-n4-X fourier 1 8.0 2 180.0 # + dihedral_coeff @dihedral:X-ne-n4-X fourier 1 8.0 2 180.0 # + dihedral_coeff @dihedral:X-nf-n4-X fourier 1 8.0 2 180.0 # + dihedral_coeff @dihedral:X-n2-na-X fourier 1 1.7 2 180.0 # + dihedral_coeff @dihedral:X-ne-na-X fourier 1 1.7 2 180.0 # + dihedral_coeff @dihedral:X-nf-na-X fourier 1 1.7 2 180.0 # + dihedral_coeff @dihedral:X-na-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-na-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-nh-X fourier 1 2.8 2 180.0 # + dihedral_coeff @dihedral:X-ne-nh-X fourier 1 2.8 2 180.0 # + dihedral_coeff @dihedral:X-nf-nh-X fourier 1 2.8 2 180.0 # + dihedral_coeff @dihedral:X-n2-no-X fourier 1 0.75 2 180.0 # + dihedral_coeff @dihedral:X-ne-no-X fourier 1 0.75 2 180.0 # + dihedral_coeff @dihedral:X-nf-no-X fourier 1 0.75 2 180.0 # + dihedral_coeff @dihedral:X-n2-oh-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-ne-oh-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-nf-oh-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-n2-os-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-ne-os-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-nf-os-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-nc-os-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-ss-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pe-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ne-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pc-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pd-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ne-pe-X fourier 1 0.6 1 0.0 # single bond + dihedral_coeff @dihedral:X-nf-pf-X fourier 1 0.6 1 0.0 # single bond + dihedral_coeff @dihedral:X-n2-p3-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-n2-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-nf-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-n2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-p5-X fourier 1 1.0 3 180.0 # + dihedral_coeff @dihedral:X-nf-p5-X fourier 1 1.0 3 180.0 # + dihedral_coeff @dihedral:X-ne-px-X fourier 1 1.0 3 180.0 # + dihedral_coeff @dihedral:X-nf-px-X fourier 1 1.0 3 180.0 # + dihedral_coeff @dihedral:X-n2-sh-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-ne-sh-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-nf-sh-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-n2-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 # + dihedral_coeff @dihedral:X-ne-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 # + dihedral_coeff @dihedral:X-nf-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 # + dihedral_coeff @dihedral:X-n2-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-sx-X fourier 1 1.5 3 180.0 # + dihedral_coeff @dihedral:X-nf-sx-X fourier 1 1.5 3 180.0 # + dihedral_coeff @dihedral:X-n2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 # + dihedral_coeff @dihedral:X-nf-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 # + dihedral_coeff @dihedral:X-n3-n3-X fourier 1 2.25 2 0.0 # + dihedral_coeff @dihedral:X-n3-n4-X fourier 1 0.25 3 0.0 # + dihedral_coeff @dihedral:X-n3-na-X fourier 1 1.6 2 0.0 # + dihedral_coeff @dihedral:X-n3-nh-X fourier 1 1.9 2 0.0 # + dihedral_coeff @dihedral:X-n3-no-X fourier 1 4.0 2 180.0 # + dihedral_coeff @dihedral:X-n3-oh-X fourier 1 2.2 2 0.0 # + dihedral_coeff @dihedral:X-n3-os-X fourier 1 1.8 2 0.0 # + dihedral_coeff @dihedral:X-n3-p2-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-n3-pe-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-n3-pf-X fourier 1 3.2 2 180.0 # + dihedral_coeff @dihedral:X-n3-p3-X fourier 1 2.35 2 0.0 # + dihedral_coeff @dihedral:X-n3-p4-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-n3-px-X fourier 1 2.1 2 180.0 # + dihedral_coeff @dihedral:X-n3-p5-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-n3-py-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-n3-sh-X fourier 1 3.1 2 0.0 # + dihedral_coeff @dihedral:X-n3-ss-X fourier 1 2.6 2 0.0 # + dihedral_coeff @dihedral:X-n3-s4-X fourier 1 3.75 2 0.0 # + dihedral_coeff @dihedral:X-n3-sx-X fourier 1 3.75 2 0.0 # + dihedral_coeff @dihedral:X-n3-s6-X fourier 1 3.13333333333 2 0.0 # + dihedral_coeff @dihedral:X-n3-sy-X fourier 1 3.13333333333 2 0.0 # + dihedral_coeff @dihedral:X-n4-n4-X fourier 1 0.188888888889 3 0.0 # + dihedral_coeff @dihedral:X-n4-na-X fourier 1 0.233333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-nh-X fourier 1 0.183333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-no-X fourier 1 0.0833333333333 3 180.0 # + dihedral_coeff @dihedral:X-n4-oh-X fourier 1 0.333333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-os-X fourier 1 0.566666666667 3 0.0 # + dihedral_coeff @dihedral:X-n4-p2-X fourier 1 0.166666666667 3 180.0 # + dihedral_coeff @dihedral:X-n4-pe-X fourier 1 0.166666666667 3 180.0 # + dihedral_coeff @dihedral:X-n4-pf-X fourier 1 0.166666666667 3 180.0 # + dihedral_coeff @dihedral:X-n4-p3-X fourier 1 0.15 3 0.0 # + dihedral_coeff @dihedral:X-n4-p4-X fourier 1 0.05 3 0.0 # + dihedral_coeff @dihedral:X-n4-px-X fourier 1 0.05 3 0.0 # + dihedral_coeff @dihedral:X-n4-p5-X fourier 1 0.0888888888889 3 0.0 # + dihedral_coeff @dihedral:X-n4-py-X fourier 1 0.0888888888889 3 0.0 # + dihedral_coeff @dihedral:X-n4-sh-X fourier 1 0.666666666667 3 0.0 # + dihedral_coeff @dihedral:X-n4-ss-X fourier 1 0.333333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-s4-X fourier 1 0.283333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-sx-X fourier 1 0.283333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-s6-X fourier 1 0.133333333333 3 0.0 # + dihedral_coeff @dihedral:X-n4-sy-X fourier 1 0.133333333333 3 0.0 # + dihedral_coeff @dihedral:X-na-na-X fourier 1 0.9 2 0.0 # + dihedral_coeff @dihedral:X-na-nh-X fourier 1 1.2 2 0.0 # + dihedral_coeff @dihedral:X-na-no-X fourier 1 6.0 2 180.0 # + dihedral_coeff @dihedral:X-na-oh-X fourier 1 1.0 2 0.0 # + dihedral_coeff @dihedral:X-na-os-X fourier 1 0.65 2 0.0 # + dihedral_coeff @dihedral:X-na-p2-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-na-pe-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-na-pf-X fourier 1 1.0 2 180.0 # + dihedral_coeff @dihedral:X-na-p3-X fourier 1 1.45 2 0.0 # + dihedral_coeff @dihedral:X-na-p4-X fourier 1 1.1 3 0.0 # + dihedral_coeff @dihedral:X-na-px-X fourier 1 1.1 3 0.0 # + dihedral_coeff @dihedral:X-na-p5-X fourier 1 0.833333333333 2 180.0 # + dihedral_coeff @dihedral:X-na-py-X fourier 1 0.833333333333 2 180.0 # + dihedral_coeff @dihedral:X-na-sh-X fourier 1 1.8 2 0.0 # + dihedral_coeff @dihedral:X-na-ss-X fourier 1 7.8 2 0.0 # + dihedral_coeff @dihedral:X-na-s4-X fourier 1 1.05 2 0.0 # + dihedral_coeff @dihedral:X-na-sx-X fourier 1 1.05 2 0.0 # + dihedral_coeff @dihedral:X-na-s6-X fourier 1 3.66666666667 2 180.0 # + dihedral_coeff @dihedral:X-na-sy-X fourier 1 3.66666666667 2 180.0 # + dihedral_coeff @dihedral:X-nh-nh-X fourier 1 1.8 3 180.0 # + dihedral_coeff @dihedral:X-nh-no-X fourier 1 2.55 2 180.0 # + dihedral_coeff @dihedral:X-nh-oh-X fourier 1 1.5 2 0.0 # + dihedral_coeff @dihedral:X-nh-os-X fourier 1 1.5 1 0.0 # + dihedral_coeff @dihedral:X-nh-p2-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-nh-pe-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-nh-pf-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-nh-p3-X fourier 1 2.35 2 0.0 # + dihedral_coeff @dihedral:X-nh-p4-X fourier 1 1.175 3 0.0 # + dihedral_coeff @dihedral:X-nh-px-X fourier 1 1.175 3 0.0 # + dihedral_coeff @dihedral:X-nh-p5-X fourier 1 0.8 2 0.0 # + dihedral_coeff @dihedral:X-nh-py-X fourier 1 0.8 2 0.0 # + dihedral_coeff @dihedral:X-nh-sh-X fourier 1 1.6 2 0.0 # + dihedral_coeff @dihedral:X-nh-ss-X fourier 1 2.1 2 0.0 # + dihedral_coeff @dihedral:X-nh-s4-X fourier 2 0.75 2 0.0 0.1 3 180.0 # + dihedral_coeff @dihedral:X-nh-sx-X fourier 2 0.75 2 0.0 0.1 3 180.0 # + dihedral_coeff @dihedral:X-nh-s6-X fourier 1 0.1 2 180.0 # + dihedral_coeff @dihedral:X-nh-sy-X fourier 1 0.1 2 180.0 # + dihedral_coeff @dihedral:X-no-no-X fourier 2 0.4 4 180.0 1.8 2 180.0 # + dihedral_coeff @dihedral:X-no-oh-X fourier 1 3.9 2 180.0 # + dihedral_coeff @dihedral:X-no-os-X fourier 1 3.0 2 180.0 # + dihedral_coeff @dihedral:X-no-p2-X fourier 1 0.3 2 180.0 # + dihedral_coeff @dihedral:X-no-pe-X fourier 1 0.3 2 180.0 # + dihedral_coeff @dihedral:X-no-pf-X fourier 1 0.3 2 180.0 # + dihedral_coeff @dihedral:X-no-p3-X fourier 1 1.9 2 180.0 # + dihedral_coeff @dihedral:X-no-p4-X fourier 1 0.575 2 180.0 # + dihedral_coeff @dihedral:X-no-px-X fourier 1 0.575 2 180.0 # + dihedral_coeff @dihedral:X-no-p5-X fourier 2 2.4 2 0.0 0.4 3 0.0 # + dihedral_coeff @dihedral:X-no-py-X fourier 2 2.4 2 0.0 0.4 3 0.0 # + dihedral_coeff @dihedral:X-no-sh-X fourier 1 2.3 2 180.0 # + dihedral_coeff @dihedral:X-no-ss-X fourier 1 2.7 2 180.0 # + dihedral_coeff @dihedral:X-no-s4-X fourier 1 2.6 2 180.0 # + dihedral_coeff @dihedral:X-no-sx-X fourier 1 2.6 2 180.0 # + dihedral_coeff @dihedral:X-no-s6-X fourier 1 0.333333333333 2 0.0 # + dihedral_coeff @dihedral:X-no-sy-X fourier 1 0.333333333333 2 0.0 # + dihedral_coeff @dihedral:X-oh-oh-X fourier 1 1.6 2 0.0 # + dihedral_coeff @dihedral:X-oh-os-X fourier 1 1.6 2 0.0 # + dihedral_coeff @dihedral:X-oh-p2-X fourier 1 1.5 2 180.0 # + dihedral_coeff @dihedral:X-oh-pe-X fourier 1 1.5 2 180.0 # + dihedral_coeff @dihedral:X-oh-pf-X fourier 1 1.5 2 180.0 # + dihedral_coeff @dihedral:X-oh-p3-X fourier 1 0.4 3 180.0 # + dihedral_coeff @dihedral:X-oh-p4-X fourier 1 0.7 1 0.0 # + dihedral_coeff @dihedral:X-oh-px-X fourier 1 0.7 1 0.0 # + dihedral_coeff @dihedral:X-oh-p5-X fourier 1 0.533333333333 3 0.0 # + dihedral_coeff @dihedral:X-oh-py-X fourier 1 0.533333333333 3 0.0 # + dihedral_coeff @dihedral:X-oh-sh-X fourier 1 2.4 2 0.0 # + dihedral_coeff @dihedral:X-oh-ss-X fourier 1 2.4 2 0.0 # + dihedral_coeff @dihedral:X-oh-s4-X fourier 1 5.0 1 0.0 # + dihedral_coeff @dihedral:X-oh-sx-X fourier 1 5.0 1 0.0 # + dihedral_coeff @dihedral:X-oh-s6-X fourier 1 9.5 1 180.0 # + dihedral_coeff @dihedral:X-oh-sy-X fourier 1 9.5 1 180.0 # + dihedral_coeff @dihedral:X-os-os-X fourier 1 1.0 1 0.0 # + dihedral_coeff @dihedral:X-os-ss-X fourier 1 2.2 2 0.0 # + dihedral_coeff @dihedral:X-os-sh-X fourier 1 1.8 2 0.0 # + dihedral_coeff @dihedral:X-os-s4-X fourier 1 1.65 3 0.0 # + dihedral_coeff @dihedral:X-os-sx-X fourier 1 1.65 3 0.0 # + dihedral_coeff @dihedral:X-os-s6-X fourier 1 1.2 2 180.0 # + dihedral_coeff @dihedral:X-os-sy-X fourier 1 1.2 2 180.0 # + dihedral_coeff @dihedral:X-os-p2-X fourier 2 3.0 2 180.0 2.0 1 180.0 # + dihedral_coeff @dihedral:X-os-pe-X fourier 2 3.0 2 180.0 2.0 1 180.0 # + dihedral_coeff @dihedral:X-os-pf-X fourier 2 3.0 2 180.0 2.0 1 180.0 # + dihedral_coeff @dihedral:X-os-p3-X fourier 1 2.2 2 0.0 # + dihedral_coeff @dihedral:X-os-p4-X fourier 1 1.05 2 180.0 # + dihedral_coeff @dihedral:X-os-px-X fourier 1 1.05 2 180.0 # + dihedral_coeff @dihedral:X-os-p5-X fourier 1 0.8 2 0.0 # + dihedral_coeff @dihedral:X-os-py-X fourier 1 0.8 2 0.0 # + dihedral_coeff @dihedral:X-p2-p2-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pe-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pf-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pe-pe-X fourier 1 1.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-pf-pf-X fourier 1 1.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-pc-pc-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pd-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pc-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-p3-X fourier 1 1.2 1 0.0 # + dihedral_coeff @dihedral:X-pe-p3-X fourier 1 1.2 1 0.0 # + dihedral_coeff @dihedral:X-pf-p3-X fourier 1 1.2 1 0.0 # + dihedral_coeff @dihedral:X-p2-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-px-X fourier 1 2.45 2 0.0 # + dihedral_coeff @dihedral:X-pf-px-X fourier 1 2.45 2 0.0 # + dihedral_coeff @dihedral:X-p2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-py-X fourier 1 1.9 1 0.0 # + dihedral_coeff @dihedral:X-pf-py-X fourier 1 1.9 1 0.0 # + dihedral_coeff @dihedral:X-p2-sh-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-pe-sh-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-pf-sh-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-p2-ss-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-pe-ss-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-pf-ss-X fourier 1 1.4 2 180.0 # + dihedral_coeff @dihedral:X-p2-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-sx-X fourier 1 1.5 2 0.0 # + dihedral_coeff @dihedral:X-pf-sx-X fourier 1 1.5 2 0.0 # + dihedral_coeff @dihedral:X-p2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-sy-X fourier 1 0.4 3 180.0 # + dihedral_coeff @dihedral:X-pf-sy-X fourier 1 0.4 3 180.0 # + dihedral_coeff @dihedral:X-p3-p3-X fourier 1 0.5 3 0.0 # + dihedral_coeff @dihedral:X-p3-p4-X fourier 1 0.9 1 0.0 # + dihedral_coeff @dihedral:X-p3-px-X fourier 1 0.9 1 0.0 # + dihedral_coeff @dihedral:X-p3-p5-X fourier 1 1.83333333333 2 180.0 # + dihedral_coeff @dihedral:X-p3-py-X fourier 1 1.83333333333 2 180.0 # + dihedral_coeff @dihedral:X-p3-sh-X fourier 1 4.6 2 0.0 # + dihedral_coeff @dihedral:X-p3-ss-X fourier 1 1.15 3 0.0 # + dihedral_coeff @dihedral:X-p3-s4-X fourier 1 3.85 2 0.0 # + dihedral_coeff @dihedral:X-p3-sx-X fourier 1 3.85 2 0.0 # + dihedral_coeff @dihedral:X-p3-s6-X fourier 1 0.266666666667 3 0.0 # + dihedral_coeff @dihedral:X-p3-sy-X fourier 1 0.266666666667 3 0.0 # + dihedral_coeff @dihedral:X-p4-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-px-X fourier 1 1.45 2 180.0 # + dihedral_coeff @dihedral:X-p4-p5-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-py-X fourier 1 0.316666666667 2 180.0 # + dihedral_coeff @dihedral:X-p4-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-sx-X fourier 1 0.85 1 0.0 # + dihedral_coeff @dihedral:X-p4-s6-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-sy-X fourier 1 0.116666666667 3 0.0 # + dihedral_coeff @dihedral:X-p4-sh-X fourier 1 0.25 1 180.0 # + dihedral_coeff @dihedral:X-px-sh-X fourier 1 0.25 1 180.0 # + dihedral_coeff @dihedral:X-p4-ss-X fourier 1 0.6 2 180.0 # + dihedral_coeff @dihedral:X-px-ss-X fourier 1 0.6 2 180.0 # + dihedral_coeff @dihedral:X-p5-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-py-X fourier 1 0.6 2 0.0 # + dihedral_coeff @dihedral:X-p5-sh-X fourier 1 0.3 3 0.0 # + dihedral_coeff @dihedral:X-py-sh-X fourier 1 0.3 3 0.0 # + dihedral_coeff @dihedral:X-p5-ss-X fourier 1 3.8 2 180.0 # + dihedral_coeff @dihedral:X-py-ss-X fourier 1 3.8 2 180.0 # + dihedral_coeff @dihedral:X-p5-s4-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-sx-X fourier 1 0.266666666667 3 0.0 # + dihedral_coeff @dihedral:X-p5-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-sy-X fourier 1 0.277777777778 3 0.0 # + dihedral_coeff @dihedral:X-sh-sh-X fourier 1 5.6 3 0.0 # + dihedral_coeff @dihedral:X-sh-ss-X fourier 1 5.3 3 0.0 # + dihedral_coeff @dihedral:X-sh-s4-X fourier 1 0.7 3 0.0 # + dihedral_coeff @dihedral:X-sh-sx-X fourier 1 0.7 3 0.0 # + dihedral_coeff @dihedral:X-sh-s6-X fourier 1 4.66666666667 2 180.0 # + dihedral_coeff @dihedral:X-sh-sy-X fourier 1 4.66666666667 2 180.0 # + dihedral_coeff @dihedral:X-ss-ss-X fourier 1 0.0 3 0.0 # + dihedral_coeff @dihedral:X-ss-s4-X fourier 1 0.3 3 0.0 # + dihedral_coeff @dihedral:X-ss-sx-X fourier 1 0.3 3 0.0 # + dihedral_coeff @dihedral:X-ss-s6-X fourier 1 3.06666666667 2 180.0 # + dihedral_coeff @dihedral:X-ss-sy-X fourier 1 3.06666666667 2 180.0 # + dihedral_coeff @dihedral:X-s4-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sx-sx-X fourier 1 0.625 3 0.0 # + dihedral_coeff @dihedral:X-s4-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sx-sy-X fourier 1 4.33333333333 2 180.0 # + dihedral_coeff @dihedral:X-s6-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sy-sy-X fourier 1 0.155555555556 2 180.0 # + dihedral_coeff @dihedral:X-cf-pe-X fourier 1 6.65 2 180.0 # NEW + dihedral_coeff @dihedral:X-nd-os-X fourier 1 4.8 2 180.0 # NEW + dihedral_coeff @dihedral:X-nd-ss-X fourier 1 4.8 2 180.0 # NEW + dihedral_coeff @dihedral:X-nf-pe-X fourier 1 5.4 2 180.0 # NEW + dihedral_coeff @dihedral:c3-c-sh-hs fourier 2 2.25 2 180.0 1.3 1 180.0 # + dihedral_coeff @dihedral:c2-c2-ss-c3 fourier 2 1.1 2 180.0 0.7 3 180.0 # + dihedral_coeff @dihedral:c2-c2-n-c fourier 2 0.65 2 180.0 1.2 1 180.0 # + dihedral_coeff @dihedral:c-n-p2-c2 fourier 2 1.0 2 180.0 1.9 1 180.0 # + dihedral_coeff @dihedral:n-c3-c-n fourier 2 1.7 1 180.0 2.0 2 180.0 # + dihedral_coeff @dihedral:c-n-c3-c fourier 2 0.85 2 180.0 0.8 1 0.0 # + dihedral_coeff @dihedral:c3-c3-n-c fourier 3 0.5 4 180.0 0.15 3 180.0 0.53 1 0.0 # phi,psi,parm94 + dihedral_coeff @dihedral:c3-c3-c-n fourier 2 0.1 4 0.0 0.07 2 0.0 # phi,psi,parm94 + dihedral_coeff @dihedral:c2-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:c2-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:ce-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:ce-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:cf-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:cf-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # + dihedral_coeff @dihedral:hn-n-c-o fourier 2 2.5 2 180.0 2.0 1 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:c3-ss-ss-c3 fourier 2 3.5 2 0.0 0.6 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:c3-n3-nh-ca fourier 2 1.9 2 0.0 1.9 3 0.0 # + dihedral_coeff @dihedral:c3-n3-p5-o fourier 2 3.0 2 180.0 2.3 3 0.0 # + dihedral_coeff @dihedral:ca-nh-oh-ho fourier 2 1.2 1 0.0 1.5 2 0.0 # + dihedral_coeff @dihedral:oh-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:os-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:h1-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-hc fourier 1 0.15 3 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-c3 fourier 1 0.16 3 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c2-c2 fourier 2 0.38 3 180.0 1.15 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:ho-oh-c3-c3 fourier 2 0.16 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:ho-oh-c-o fourier 2 2.3 2 180.0 1.9 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c2-c2-c-o fourier 2 2.175 2 180.0 0.3 3 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-c2-c2-c3 fourier 2 6.65 2 180.0 1.9 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-c3-c3-c3 fourier 3 0.18 3 0.0 0.25 2 180.0 0.2 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-c3-n3-c3 fourier 2 0.3 3 0.0 0.48 2 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-c3-os-c3 fourier 2 0.383 3 0.0 0.1 2 180.0 # + dihedral_coeff @dihedral:c3-c3-os-c fourier 2 0.383 3 0.0 0.8 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-os-c3-os fourier 3 0.1 3 0.0 0.85 2 180.0 1.35 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:c3-os-c3-na fourier 2 0.383 3 0.0 0.65 2 0.0 # parm98.dat, TC,PC,PAK + dihedral_coeff @dihedral:o-c-os-c3 fourier 2 2.7 2 180.0 1.4 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:os-c3-na-c2 fourier 2 0.0 2 0.0 2.5 1 0.0 # parm98, TC,PC,PAK + dihedral_coeff @dihedral:os-c3-c3-os fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK + dihedral_coeff @dihedral:os-c3-c3-oh fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK + dihedral_coeff @dihedral:oh-c3-c3-oh fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK + dihedral_coeff @dihedral:f-c3-c3-f fourier 2 0.0 3 0.0 1.2 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:cl-c3-c3-cl fourier 2 0.0 3 0.0 0.45 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:br-c3-c3-br fourier 2 0.0 3 0.0 0.0 1 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:h1-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:h1-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:h1-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:h1-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:h1-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:hc-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999 + } # (end of dihedral_coeffs) + + write_once("Data Dihedrals By Type") { + @dihedral:X-c-c-X @atom:* @atom:c @atom:c @atom:* + @dihedral:X-c-c1-X @atom:* @atom:c @atom:c1 @atom:* + @dihedral:X-c-cg-X @atom:* @atom:c @atom:cg @atom:* + @dihedral:X-c-ch-X @atom:* @atom:c @atom:ch @atom:* + @dihedral:X-c-c2-X @atom:* @atom:c @atom:c2 @atom:* + @dihedral:X-c-cu-X @atom:* @atom:c @atom:cu @atom:* + @dihedral:X-c-cv-X @atom:* @atom:c @atom:cv @atom:* + @dihedral:X-c-ce-X @atom:* @atom:c @atom:ce @atom:* + @dihedral:X-c-cf-X @atom:* @atom:c @atom:cf @atom:* + @dihedral:X-c-c3-X @atom:* @atom:c @atom:c3 @atom:* + @dihedral:X-c-cx-X @atom:* @atom:c @atom:cx @atom:* + @dihedral:X-c-cy-X @atom:* @atom:c @atom:cy @atom:* + @dihedral:X-c-ca-X @atom:* @atom:c @atom:ca @atom:* + @dihedral:X-c-cc-X @atom:* @atom:c @atom:cc @atom:* + @dihedral:X-c-cd-X @atom:* @atom:c @atom:cd @atom:* + @dihedral:X-c-n-X @atom:* @atom:c @atom:n @atom:* + @dihedral:X-c-n2-X @atom:* @atom:c @atom:n2 @atom:* + @dihedral:X-c-nc-X @atom:* @atom:c @atom:nc @atom:* + @dihedral:X-c-nd-X @atom:* @atom:c @atom:nd @atom:* + @dihedral:X-c-ne-X @atom:* @atom:c @atom:ne @atom:* + @dihedral:X-c-nf-X @atom:* @atom:c @atom:nf @atom:* + @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* + @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* + @dihedral:X-c-no-X @atom:* @atom:c @atom:no @atom:* + @dihedral:X-c-oh-X @atom:* @atom:c @atom:oh @atom:* + @dihedral:X-c-os-X @atom:* @atom:c @atom:os @atom:* + @dihedral:X-c-p2-X @atom:* @atom:c @atom:p2 @atom:* + @dihedral:X-c-pc-X @atom:* @atom:c @atom:pc @atom:* + @dihedral:X-c-pd-X @atom:* @atom:c @atom:pd @atom:* + @dihedral:X-c-pe-X @atom:* @atom:c @atom:pe @atom:* + @dihedral:X-c-pf-X @atom:* @atom:c @atom:pf @atom:* + @dihedral:X-c-p3-X @atom:* @atom:c @atom:p3 @atom:* + @dihedral:X-c-p4-X @atom:* @atom:c @atom:p4 @atom:* + @dihedral:X-c-px-X @atom:* @atom:c @atom:px @atom:* + @dihedral:X-c-p5-X @atom:* @atom:c @atom:p5 @atom:* + @dihedral:X-c-py-X @atom:* @atom:c @atom:py @atom:* + @dihedral:X-c-sh-X @atom:* @atom:c @atom:sh @atom:* + @dihedral:X-c-ss-X @atom:* @atom:c @atom:ss @atom:* + @dihedral:X-c-s4-X @atom:* @atom:c @atom:s4 @atom:* + @dihedral:X-c-sx-X @atom:* @atom:c @atom:sx @atom:* + @dihedral:X-c-s6-X @atom:* @atom:c @atom:s6 @atom:* + @dihedral:X-c-sy-X @atom:* @atom:c @atom:sy @atom:* + @dihedral:X-c1-c1-X @atom:* @atom:c1 @atom:c1 @atom:* + @dihedral:X-c1-cg-X @atom:* @atom:c1 @atom:cg @atom:* + @dihedral:X-c1-ch-X @atom:* @atom:c1 @atom:ch @atom:* + @dihedral:X-cg-cg-X @atom:* @atom:cg @atom:cg @atom:* + @dihedral:X-ch-ch-X @atom:* @atom:ch @atom:ch @atom:* + @dihedral:X-cg-ch-X @atom:* @atom:cg @atom:ch @atom:* + @dihedral:X-c1-c2-X @atom:* @atom:c1 @atom:c2 @atom:* + @dihedral:X-c1-c3-X @atom:* @atom:c1 @atom:c3 @atom:* + @dihedral:X-c1-ca-X @atom:* @atom:c1 @atom:ca @atom:* + @dihedral:X-c1-cc-X @atom:* @atom:c1 @atom:cc @atom:* + @dihedral:X-c1-cd-X @atom:* @atom:c1 @atom:cd @atom:* + @dihedral:X-c1-ce-X @atom:* @atom:c1 @atom:ce @atom:* + @dihedral:X-c1-cf-X @atom:* @atom:c1 @atom:cf @atom:* + @dihedral:X-c1-cu-X @atom:* @atom:c1 @atom:cu @atom:* + @dihedral:X-c1-cv-X @atom:* @atom:c1 @atom:cv @atom:* + @dihedral:X-c1-cx-X @atom:* @atom:c1 @atom:cx @atom:* + @dihedral:X-c1-cy-X @atom:* @atom:c1 @atom:cy @atom:* + @dihedral:X-c1-n-X @atom:* @atom:c1 @atom:n @atom:* + @dihedral:X-c1-n2-X @atom:* @atom:c1 @atom:n2 @atom:* + @dihedral:X-c1-n3-X @atom:* @atom:c1 @atom:n3 @atom:* + @dihedral:X-c1-n4-X @atom:* @atom:c1 @atom:n4 @atom:* + @dihedral:X-c1-na-X @atom:* @atom:c1 @atom:na @atom:* + @dihedral:X-c1-nb-X @atom:* @atom:c1 @atom:nb @atom:* + @dihedral:X-c1-nc-X @atom:* @atom:c1 @atom:nc @atom:* + @dihedral:X-c1-nd-X @atom:* @atom:c1 @atom:nd @atom:* + @dihedral:X-c1-ne-X @atom:* @atom:c1 @atom:ne @atom:* + @dihedral:X-c1-nf-X @atom:* @atom:c1 @atom:nf @atom:* + @dihedral:X-c1-nh-X @atom:* @atom:c1 @atom:nh @atom:* + @dihedral:X-c1-no-X @atom:* @atom:c1 @atom:no @atom:* + @dihedral:X-c1-oh-X @atom:* @atom:c1 @atom:oh @atom:* + @dihedral:X-c1-os-X @atom:* @atom:c1 @atom:os @atom:* + @dihedral:X-c1-p2-X @atom:* @atom:c1 @atom:p2 @atom:* + @dihedral:X-c1-pb-X @atom:* @atom:c1 @atom:pb @atom:* + @dihedral:X-c1-pc-X @atom:* @atom:c1 @atom:pc @atom:* + @dihedral:X-c1-pd-X @atom:* @atom:c1 @atom:pd @atom:* + @dihedral:X-c1-pe-X @atom:* @atom:c1 @atom:pe @atom:* + @dihedral:X-c1-pf-X @atom:* @atom:c1 @atom:pf @atom:* + @dihedral:X-c1-p3-X @atom:* @atom:c1 @atom:p3 @atom:* + @dihedral:X-c1-p4-X @atom:* @atom:c1 @atom:p4 @atom:* + @dihedral:X-c1-px-X @atom:* @atom:c1 @atom:px @atom:* + @dihedral:X-c1-p5-X @atom:* @atom:c1 @atom:p5 @atom:* + @dihedral:X-c1-py-X @atom:* @atom:c1 @atom:py @atom:* + @dihedral:X-c1-s2-X @atom:* @atom:c1 @atom:s2 @atom:* + @dihedral:X-c1-sh-X @atom:* @atom:c1 @atom:sh @atom:* + @dihedral:X-c1-ss-X @atom:* @atom:c1 @atom:ss @atom:* + @dihedral:X-c1-s4-X @atom:* @atom:c1 @atom:s4 @atom:* + @dihedral:X-c1-sx-X @atom:* @atom:c1 @atom:sx @atom:* + @dihedral:X-c1-s6-X @atom:* @atom:c1 @atom:s6 @atom:* + @dihedral:X-c1-sy-X @atom:* @atom:c1 @atom:sy @atom:* + @dihedral:X-c2-c2-X @atom:* @atom:c2 @atom:c2 @atom:* + @dihedral:X-c2-ce-X @atom:* @atom:c2 @atom:ce @atom:* + @dihedral:X-c2-cf-X @atom:* @atom:c2 @atom:cf @atom:* + @dihedral:X-ce-cf-X @atom:* @atom:ce @atom:cf @atom:* + @dihedral:X-ce-ce-X @atom:* @atom:ce @atom:ce @atom:* + @dihedral:X-cf-cf-X @atom:* @atom:cf @atom:cf @atom:* + @dihedral:X-cc-cd-X @atom:* @atom:cc @atom:cd @atom:* + @dihedral:X-cc-cc-X @atom:* @atom:cc @atom:cc @atom:* + @dihedral:X-cd-cd-X @atom:* @atom:cd @atom:cd @atom:* + @dihedral:X-c2-c3-X @atom:* @atom:c2 @atom:c3 @atom:* + @dihedral:X-c2-ca-X @atom:* @atom:c2 @atom:ca @atom:* + @dihedral:X-c2-n-X @atom:* @atom:c2 @atom:n @atom:* + @dihedral:X-c2-n2-X @atom:* @atom:c2 @atom:n2 @atom:* + @dihedral:X-c2-ne-X @atom:* @atom:c2 @atom:ne @atom:* + @dihedral:X-c2-nf-X @atom:* @atom:c2 @atom:nf @atom:* + @dihedral:X-ce-ne-X @atom:* @atom:ce @atom:ne @atom:* + @dihedral:X-cf-nf-X @atom:* @atom:cf @atom:nf @atom:* + @dihedral:X-c2-nc-X @atom:* @atom:c2 @atom:nc @atom:* + @dihedral:X-c2-nd-X @atom:* @atom:c2 @atom:nd @atom:* + @dihedral:X-cc-nd-X @atom:* @atom:cc @atom:nd @atom:* + @dihedral:X-cd-nc-X @atom:* @atom:cd @atom:nc @atom:* + @dihedral:X-cc-nc-X @atom:* @atom:cc @atom:nc @atom:* + @dihedral:X-cd-nd-X @atom:* @atom:cd @atom:nd @atom:* + @dihedral:X-c2-n3-X @atom:* @atom:c2 @atom:n3 @atom:* + @dihedral:X-c2-n4-X @atom:* @atom:c2 @atom:n4 @atom:* + @dihedral:X-c2-na-X @atom:* @atom:c2 @atom:na @atom:* + @dihedral:X-cc-na-X @atom:* @atom:cc @atom:na @atom:* + @dihedral:X-cd-na-X @atom:* @atom:cd @atom:na @atom:* + @dihedral:X-c2-nh-X @atom:* @atom:c2 @atom:nh @atom:* + @dihedral:X-c2-no-X @atom:* @atom:c2 @atom:no @atom:* + @dihedral:X-c2-oh-X @atom:* @atom:c2 @atom:oh @atom:* + @dihedral:X-c2-os-X @atom:* @atom:c2 @atom:os @atom:* + @dihedral:X-c2-p2-X @atom:* @atom:c2 @atom:p2 @atom:* + @dihedral:X-c2-pe-X @atom:* @atom:c2 @atom:pe @atom:* + @dihedral:X-c2-pf-X @atom:* @atom:c2 @atom:pf @atom:* + @dihedral:X-ce-pf-X @atom:* @atom:ce @atom:pf @atom:* + @dihedral:X-ce-pe-X @atom:* @atom:ce @atom:pe @atom:* + @dihedral:X-cf-pf-X @atom:* @atom:cf @atom:pf @atom:* + @dihedral:X-c2-pc-X @atom:* @atom:c2 @atom:pc @atom:* + @dihedral:X-c2-pd-X @atom:* @atom:c2 @atom:pd @atom:* + @dihedral:X-cc-pc-X @atom:* @atom:cc @atom:pc @atom:* + @dihedral:X-cc-pd-X @atom:* @atom:cc @atom:pd @atom:* + @dihedral:X-cd-pc-X @atom:* @atom:cd @atom:pc @atom:* + @dihedral:X-cd-pd-X @atom:* @atom:cd @atom:pd @atom:* + @dihedral:X-c2-p3-X @atom:* @atom:c2 @atom:p3 @atom:* + @dihedral:X-c2-p4-X @atom:* @atom:c2 @atom:p4 @atom:* + @dihedral:X-ce-p4-X @atom:* @atom:ce @atom:p4 @atom:* + @dihedral:X-cf-p4-X @atom:* @atom:cf @atom:p4 @atom:* + @dihedral:X-c2-px-X @atom:* @atom:c2 @atom:px @atom:* + @dihedral:X-ce-px-X @atom:* @atom:ce @atom:px @atom:* + @dihedral:X-cf-px-X @atom:* @atom:cf @atom:px @atom:* + @dihedral:X-c2-p5-X @atom:* @atom:c2 @atom:p5 @atom:* + @dihedral:X-ce-p5-X @atom:* @atom:ce @atom:p5 @atom:* + @dihedral:X-cf-p5-X @atom:* @atom:cf @atom:p5 @atom:* + @dihedral:X-c2-py-X @atom:* @atom:c2 @atom:py @atom:* + @dihedral:X-ce-py-X @atom:* @atom:ce @atom:py @atom:* + @dihedral:X-cf-py-X @atom:* @atom:cf @atom:py @atom:* + @dihedral:X-c2-sh-X @atom:* @atom:c2 @atom:sh @atom:* + @dihedral:X-c2-ss-X @atom:* @atom:c2 @atom:ss @atom:* + @dihedral:X-c2-s4-X @atom:* @atom:c2 @atom:s4 @atom:* + @dihedral:X-ce-s4-X @atom:* @atom:ce @atom:s4 @atom:* + @dihedral:X-cf-s4-X @atom:* @atom:cf @atom:s4 @atom:* + @dihedral:X-c2-sx-X @atom:* @atom:c2 @atom:sx @atom:* + @dihedral:X-ce-sx-X @atom:* @atom:ce @atom:sx @atom:* + @dihedral:X-cf-sx-X @atom:* @atom:cf @atom:sx @atom:* + @dihedral:X-c2-s6-X @atom:* @atom:c2 @atom:s6 @atom:* + @dihedral:X-ce-s6-X @atom:* @atom:ce @atom:s6 @atom:* + @dihedral:X-cf-s6-X @atom:* @atom:cf @atom:s6 @atom:* + @dihedral:X-c2-sy-X @atom:* @atom:c2 @atom:sy @atom:* + @dihedral:X-ce-sy-X @atom:* @atom:ce @atom:sy @atom:* + @dihedral:X-cf-sy-X @atom:* @atom:cf @atom:sy @atom:* + @dihedral:X-c3-c3-X @atom:* @atom:c3 @atom:c3 @atom:* + @dihedral:X-cx-cx-X @atom:* @atom:cx @atom:cx @atom:* + @dihedral:X-cy-cy-X @atom:* @atom:cy @atom:cy @atom:* + @dihedral:X-c3-ca-X @atom:* @atom:c3 @atom:ca @atom:* + @dihedral:X-c3-n-X @atom:* @atom:c3 @atom:n @atom:* + @dihedral:X-cx-n-X @atom:* @atom:cx @atom:n @atom:* + @dihedral:X-cy-n-X @atom:* @atom:cy @atom:n @atom:* + @dihedral:X-c3-n2-X @atom:* @atom:c3 @atom:n2 @atom:* + @dihedral:X-c3-ne-X @atom:* @atom:c3 @atom:ne @atom:* + @dihedral:X-c3-nf-X @atom:* @atom:c3 @atom:nf @atom:* + @dihedral:X-c3-n3-X @atom:* @atom:c3 @atom:n3 @atom:* + @dihedral:X-c3-n4-X @atom:* @atom:c3 @atom:n4 @atom:* + @dihedral:X-c3-na-X @atom:* @atom:c3 @atom:na @atom:* + @dihedral:X-c3-nh-X @atom:* @atom:c3 @atom:nh @atom:* + @dihedral:X-c3-no-X @atom:* @atom:c3 @atom:no @atom:* + @dihedral:X-c3-oh-X @atom:* @atom:c3 @atom:oh @atom:* + @dihedral:X-c3-os-X @atom:* @atom:c3 @atom:os @atom:* + @dihedral:X-c3-p2-X @atom:* @atom:c3 @atom:p2 @atom:* + @dihedral:X-c3-pe-X @atom:* @atom:c3 @atom:pe @atom:* + @dihedral:X-c3-pf-X @atom:* @atom:c3 @atom:pf @atom:* + @dihedral:X-c3-p3-X @atom:* @atom:c3 @atom:p3 @atom:* + @dihedral:X-c3-p4-X @atom:* @atom:c3 @atom:p4 @atom:* + @dihedral:X-c3-px-X @atom:* @atom:c3 @atom:px @atom:* + @dihedral:X-c3-p5-X @atom:* 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@dihedral:c3-c2-c2-c3 @atom:c3 @atom:c2 @atom:c2 @atom:c3 + @dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3 + @dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3 + @dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3 + @dihedral:c3-c3-n3-c3 @atom:c3 @atom:c3 @atom:n3 @atom:c3 + @dihedral:c3-c3-n3-c3 @atom:c3 @atom:c3 @atom:n3 @atom:c3 + @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 + @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 + @dihedral:c3-c3-os-c @atom:c3 @atom:c3 @atom:os @atom:c + @dihedral:c3-c3-os-c @atom:c3 @atom:c3 @atom:os @atom:c + @dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os + @dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os + @dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os + @dihedral:c3-os-c3-na @atom:c3 @atom:os @atom:c3 @atom:na + @dihedral:c3-os-c3-na @atom:c3 @atom:os @atom:c3 @atom:na + @dihedral:o-c-os-c3 @atom:o @atom:c @atom:os @atom:c3 + @dihedral:o-c-os-c3 @atom:o @atom:c @atom:os @atom:c3 + @dihedral:os-c3-na-c2 @atom:os @atom:c3 @atom:na @atom:c2 + @dihedral:os-c3-na-c2 @atom:os @atom:c3 @atom:na @atom:c2 + @dihedral:os-c3-c3-os @atom:os @atom:c3 @atom:c3 @atom:os + @dihedral:os-c3-c3-os @atom:os @atom:c3 @atom:c3 @atom:os + @dihedral:os-c3-c3-oh @atom:os @atom:c3 @atom:c3 @atom:oh + @dihedral:os-c3-c3-oh @atom:os @atom:c3 @atom:c3 @atom:oh + @dihedral:oh-c3-c3-oh @atom:oh @atom:c3 @atom:c3 @atom:oh + @dihedral:oh-c3-c3-oh @atom:oh @atom:c3 @atom:c3 @atom:oh + @dihedral:f-c3-c3-f @atom:f @atom:c3 @atom:c3 @atom:f + @dihedral:f-c3-c3-f @atom:f @atom:c3 @atom:c3 @atom:f + @dihedral:cl-c3-c3-cl @atom:cl @atom:c3 @atom:c3 @atom:cl + @dihedral:cl-c3-c3-cl @atom:cl @atom:c3 @atom:c3 @atom:cl + @dihedral:br-c3-c3-br @atom:br @atom:c3 @atom:c3 @atom:br + @dihedral:br-c3-c3-br @atom:br @atom:c3 @atom:c3 @atom:br + @dihedral:h1-c3-c3-os @atom:h1 @atom:c3 @atom:c3 @atom:os + @dihedral:h1-c3-c3-os @atom:h1 @atom:c3 @atom:c3 @atom:os + @dihedral:h1-c3-c3-oh @atom:h1 @atom:c3 @atom:c3 @atom:oh + @dihedral:h1-c3-c3-oh @atom:h1 @atom:c3 @atom:c3 @atom:oh + @dihedral:h1-c3-c3-f @atom:h1 @atom:c3 @atom:c3 @atom:f + @dihedral:h1-c3-c3-f @atom:h1 @atom:c3 @atom:c3 @atom:f + @dihedral:h1-c3-c3-cl @atom:h1 @atom:c3 @atom:c3 @atom:cl + @dihedral:h1-c3-c3-cl @atom:h1 @atom:c3 @atom:c3 @atom:cl + @dihedral:h1-c3-c3-br @atom:h1 @atom:c3 @atom:c3 @atom:br + @dihedral:h1-c3-c3-br @atom:h1 @atom:c3 @atom:c3 @atom:br + @dihedral:hc-c3-c3-os @atom:hc @atom:c3 @atom:c3 @atom:os + @dihedral:hc-c3-c3-os @atom:hc @atom:c3 @atom:c3 @atom:os + @dihedral:hc-c3-c3-oh @atom:hc @atom:c3 @atom:c3 @atom:oh + @dihedral:hc-c3-c3-oh @atom:hc @atom:c3 @atom:c3 @atom:oh + @dihedral:hc-c3-c3-f @atom:hc @atom:c3 @atom:c3 @atom:f + @dihedral:hc-c3-c3-f @atom:hc @atom:c3 @atom:c3 @atom:f + @dihedral:hc-c3-c3-cl @atom:hc @atom:c3 @atom:c3 @atom:cl + @dihedral:hc-c3-c3-cl @atom:hc @atom:c3 @atom:c3 @atom:cl + @dihedral:hc-c3-c3-br @atom:hc @atom:c3 @atom:c3 @atom:br + @dihedral:hc-c3-c3-br @atom:hc @atom:c3 @atom:c3 @atom:br + } # (end of Dihedrals By Type) + + write_once("In Settings") { + improper_coeff @improper:c-X-X-o cvff 10.5 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:c-X-o-o cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:ca-X-X-ha cvff 1.1 -1 2 # bsd.on C6H6 nmodes + improper_coeff @improper:n-X-X-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:n2-X-X-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:na-X-X-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:n-X-c3-c3 cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:ca-X-n2-n2 cvff 10.5 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:c2-c-c2-c3 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:ca-c-ca-c3 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:n-c-c3-hn cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:n-c-c3-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:na-c2-c2-c3 cvff 1.1 -1 2 # + improper_coeff @improper:c2-c2-c-c3 cvff 1.1 -1 2 # + improper_coeff @improper:c2-c2-c3-hc cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-c2-c3-hc cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c-c2-hc-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c-c3-o-oh cvff 1.1 -1 2 # + improper_coeff @improper:c2-c3-c2-n2 cvff 1.1 -1 2 # + improper_coeff @improper:c2-c3-c2-na cvff 1.1 -1 2 # + improper_coeff @improper:ca-c3-ca-n2 cvff 1.1 -1 2 # + improper_coeff @improper:ca-c3-ca-na cvff 1.1 -1 2 # + improper_coeff @improper:ca-ca-ca-c2 cvff 1.1 -1 2 # + improper_coeff @improper:ca-ca-ca-c3 cvff 1.1 -1 2 # + improper_coeff @improper:ca-ca-ca-f cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-cl cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-br cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-i cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c-ca-ca-oh cvff 1.1 -1 2 # (not used in tyr!) + improper_coeff @improper:na-ca-ca-c3 cvff 1.1 -1 2 # + improper_coeff @improper:ca-ca-c-c3 cvff 1.1 -1 2 # + improper_coeff @improper:c-ca-hc-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-n2-n2 cvff 1.1 -1 2 # dac, 10/94 + improper_coeff @improper:c-hc-o-oh cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c-hc-o-os cvff 1.1 -1 2 # + improper_coeff @improper:ca-n2-c2-n2 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:ca-n2-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:ca-na-n2-n2 cvff 1.1 -1 2 # dac, 10/94 + } # (end of improper_coeffs) + + write_once("Data Impropers By Type") { + @improper:c-X-X-o @atom:c @atom:* @atom:* @atom:o + @improper:c-X-o-o @atom:c @atom:* @atom:o @atom:o + @improper:ca-X-X-ha @atom:ca @atom:* @atom:* @atom:ha + @improper:n-X-X-hn @atom:n @atom:* @atom:* @atom:hn + @improper:n2-X-X-hn @atom:n2 @atom:* @atom:* @atom:hn + @improper:na-X-X-hn @atom:na @atom:* @atom:* @atom:hn + @improper:n-X-c3-c3 @atom:n @atom:* @atom:c3 @atom:c3 + @improper:ca-X-n2-n2 @atom:ca @atom:* @atom:n2 @atom:n2 + @improper:c2-c-c2-c3 @atom:c2 @atom:c @atom:c2 @atom:c3 + @improper:ca-c-ca-c3 @atom:ca @atom:c @atom:ca @atom:c3 + @improper:n-c-c3-hn @atom:n @atom:c @atom:c3 @atom:hn + @improper:n-c-c3-o @atom:n @atom:c @atom:c3 @atom:o + @improper:na-c2-c2-c3 @atom:na @atom:c2 @atom:c2 @atom:c3 + @improper:c2-c2-c-c3 @atom:c2 @atom:c2 @atom:c @atom:c3 + @improper:c2-c2-c3-hc @atom:c2 @atom:c2 @atom:c3 @atom:hc + @improper:ca-c2-c3-hc @atom:ca @atom:c2 @atom:c3 @atom:hc + @improper:c-c2-hc-o @atom:c @atom:c2 @atom:hc @atom:o + @improper:c-c3-o-oh @atom:c @atom:c3 @atom:o @atom:oh + @improper:c2-c3-c2-n2 @atom:c2 @atom:c3 @atom:c2 @atom:n2 + @improper:c2-c3-c2-na @atom:c2 @atom:c3 @atom:c2 @atom:na + @improper:ca-c3-ca-n2 @atom:ca @atom:c3 @atom:ca @atom:n2 + @improper:ca-c3-ca-na @atom:ca @atom:c3 @atom:ca @atom:na + @improper:ca-ca-ca-c2 @atom:ca @atom:ca @atom:ca @atom:c2 + @improper:ca-ca-ca-c3 @atom:ca @atom:ca @atom:ca @atom:c3 + @improper:ca-ca-ca-f @atom:ca @atom:ca @atom:ca @atom:f + @improper:ca-ca-ca-cl @atom:ca @atom:ca @atom:ca @atom:cl + @improper:ca-ca-ca-br @atom:ca @atom:ca @atom:ca @atom:br + @improper:ca-ca-ca-i @atom:ca @atom:ca @atom:ca @atom:i + @improper:c-ca-ca-oh @atom:c @atom:ca @atom:ca @atom:oh + @improper:na-ca-ca-c3 @atom:na @atom:ca @atom:ca @atom:c3 + @improper:ca-ca-c-c3 @atom:ca @atom:ca @atom:c @atom:c3 + @improper:c-ca-hc-o @atom:c @atom:ca @atom:hc @atom:o + @improper:ca-ca-n2-n2 @atom:ca @atom:ca @atom:n2 @atom:n2 + @improper:c-hc-o-oh @atom:c @atom:hc @atom:o @atom:oh + @improper:c-hc-o-os @atom:c @atom:hc @atom:o @atom:os + @improper:ca-n2-c2-n2 @atom:ca @atom:n2 @atom:c2 @atom:n2 + @improper:ca-n2-ca-n2 @atom:ca @atom:n2 @atom:ca @atom:n2 + @improper:ca-na-n2-n2 @atom:ca @atom:na @atom:n2 @atom:n2 + } # (end of Impropers By Type) + + + write_once("In Init") { + # Default styles and settings for AMBER based force-fields: + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + improper_style hybrid cvff + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + kspace_style pppm 0.0001 + + # NOTE: If you do not want to use long-range coulombic forces, + # comment out the two lines above and uncomment this line: + # pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 + + pair_modify mix arithmetic + special_bonds amber + } + +} + + diff --git a/tools/moltemplate/common/graphene.lt b/tools/moltemplate/common/graphene.lt new file mode 100644 index 0000000000..4a17862fc3 --- /dev/null +++ b/tools/moltemplate/common/graphene.lt @@ -0,0 +1,106 @@ +# This file contains a unit cell for building graphene and nanotubes +# +# +# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any +# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg") +# Surfaces constructed with this unit cell can be flat or curved into tubes. +# The distance between nearest-neighbor carbon atoms (ie the length of a +# carbon-carbon bond) is equal to "d" which I set to 1.420 Angstroms. +# +# d = length of each hexagon's side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms +# +# Consequently, the Lattice-cell vectors for singe-layer graphene are: +# (2.4595121467478, 0, 0) (aligned with X axis) +# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d) +# So, to build a sheet of graphite, you could use: +# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) + + + + +Graphene { + + 2AtomCellAlignX + { + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 + $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 + } + } + + # Now define properties of the Carbon graphene atom + + write_once("In Init") { + pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 + } + + write_once("Data Masses") { + @atom:C 12.0 + } + + write_once("In Settings") { + # i j epsilon sigma + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407 + + # These Lennard-Jones parameters come from + # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, + # Chem Phys Lett, 348:187 (2001) + + # Define a group consisting of only carbon atoms in graphene molecules + group Cgraphene type @atom:C + } + + # Notice that the two atoms in the unit-cell above lie in the XY plane. + # (Their z-coordinate is zero). It's also useful to have a version of + # this object which lies in the XZ plan. So we define this below: + + 2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0) + +} # Graphene + + + + + + + + + + +# ------------ Graphite ----------- +# +# Note: For graphite: sheets stacked in the Z direction are separated by a +# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction +# by a distance of d (1.42 Angstroms). To add additional graphene layers +# you could use: +# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet2[*][*].move(0, 1.42, 3.35) +# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet3[*][*].move(0, -1.42, 6.70) +# etc... +# However, to build a thick sheet of graphite, it would +# be more efficient to use a 4-atom unit cell: +# +#Graphene { +# GraphiteCell { +# # atomID molID atomType charge x y z +# write("Data Atoms") { +# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 +# $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 +# $atom:C3 $mol:... @atom:../C 0.0 -0.61487803668695 1.065 3.35 +# $atom:C4 $mol:... @atom:../C 0.0 0.61487803668695 1.775 3.35 +# } +# } # GraphiteCell +#} +# +# Then you could create a thick sheet of graphite this way: +# +# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# [5].move(0,0,6.70) diff --git a/tools/moltemplate/common/images/graphene_unit_cell.jpg b/tools/moltemplate/common/images/graphene_unit_cell.jpg new file mode 100644 index 0000000000..12dbf8fca2 Binary files /dev/null and b/tools/moltemplate/common/images/graphene_unit_cell.jpg differ diff --git a/tools/moltemplate/common/images/ice_rect8_unitcell.png b/tools/moltemplate/common/images/ice_rect8_unitcell.png new file mode 100644 index 0000000000..5bd6057e1e Binary files /dev/null and b/tools/moltemplate/common/images/ice_rect8_unitcell.png differ diff --git a/tools/moltemplate/common/images/spce_ball_and_stick.jpg b/tools/moltemplate/common/images/spce_ball_and_stick.jpg new file mode 100644 index 0000000000..60aaf90b95 Binary files /dev/null and b/tools/moltemplate/common/images/spce_ball_and_stick.jpg differ diff --git a/tools/moltemplate/common/oplsaa/AUTHOR.TXT b/tools/moltemplate/common/oplsaa/AUTHOR.TXT new file mode 100644 index 0000000000..d5e469af37 --- /dev/null +++ b/tools/moltemplate/common/oplsaa/AUTHOR.TXT @@ -0,0 +1,3 @@ + +OPLSAA force-field conversion tools provided by Jason Lambert. + diff --git a/tools/moltemplate/common/oplsaa/README.TXT b/tools/moltemplate/common/oplsaa/README.TXT new file mode 100644 index 0000000000..e90ca955b4 --- /dev/null +++ b/tools/moltemplate/common/oplsaa/README.TXT @@ -0,0 +1,118 @@ +Unfortunately, moltemplate does not come with a file containing OPLSAA +paramters which is ready to use. You must build it yourself. +This directory has tools and instructions to explain how to do this. + +----------------------------- + +When you want to run a new simulation, you must download the full +"oplsaa.prm" force-field file (from the TINKER web site) and manually +delete all the atom types which you do not need. (See below.) +Then you must use the "oplsaa_moltemplate.py" script to create +"oplsaa.lt" file which moltemplate.sh needs. Then you must run moltemplate.sh. +You must do this for each new simulation you plan to run which uses OPLSAA. + +---- Details: ---- + + Download the original "oplsaa.prm" file here: +http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm + or here: +http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm + +and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE +so that it only contains atom types you plan to have in your simulation +(see below). Finally, you must run the opls_moltemplate.py script this way: + + +python oplsaa_moltemplate.py oplsaa_subset.prm + + +This will create a file named "oplsaa.lt" +Look over the newly created "oplsaa.lt" file. +Then, if necessary, move this file to wherever you plan to run moltemplate. + +There is a directory containing an example how to use this code located here: +examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/README.TXT + +----- DETAILS: Editing the "oplsaa_subset.prm" file ------- + +Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm" +file (or "oplsaa_subset.prm file) and eliminate atom types which do not +correspond to any of the atoms in your simulation. This means you must +look for lines near the beginning of this file which begin with the word "atom" +and refer to atom types which appear in the simulation you plan to run. All +other lines (beginning with the word "atom") must be deleted or commented out. +(Leave the rest of the file alone.) + +For example: +If you were working with ethylene and benzene you would delete every line +beginning with the word "atom", except for these four lines: + +# for ethylene: +atom 88 47 CM "Alkene H2-C=" 6 12.011 3 +atom 89 46 HC "Alkene H-C=" 1 1.008 1 +# for benzene: +atom 90 48 CA "Aromatic C" 6 12.011 3 +atom 91 49 HA "Aromatic H-C" 1 1.008 1 + +Then you are ready to run oplsaa_moltemplate.py on this file. + +(You can try to delete more irrelevant information, but be careful. + It is not necessary, and it is easy to make mistakes.) + + +----- Using the "oplsaa.lt" file ----- + +Once you have created the "oplsaa.lt" file, you can create files (like +ethylene.lt) which define molecules that refer to these atom types. +Here is an excerpt from "ethyelene.lt": + +Ethylene inherits OPLSAA { + write('Data Atoms') { + list of atoms goes here ... + } + write('Data Bond List') { + list of bonds goes here ... + } +} + +And then run moltemplate. + + +----------- CHARGE: ----------- + +By default, the OPLSAA force-field assigns atom charge according to atom type. +When you run moltemplate, it will create a file named "system.in.charges", +containing commands like: + +set type 2 charge -0.42 +set type 3 charge 0.21 + +(This assumes your main moltemplate file is named "system.lt". If it was +named something else, eg "polymer.lt", then the file created by moltemplate +will be named "polymer.in.charges".) + +Include these commands somewhere in your LAMMPS input script +(or use the LAMMPS "include" command to load the commands in system.in.charges) + +Note that the atom numbers (eg "2", "3") in this file will not match the +OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file, +created by moltemplate, to see a table of "@atom" type numbers translated +from OPLSAA into LAMMPS.) + +----------- CREDIT ----------- + +If you use these tools and you publish a paper using OPLSAA, please also cite +the TINKER program. (Because the original "oplsaa.prm" file which we depend on +is distributed with TINKER.) I think these are the relevant citations: + +1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newtonâ€like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024. + +2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/ + +------------------------------- + +Jason Lambert and Andrew Jewett +April, 2014 + +Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com + diff --git a/tools/moltemplate/common/oplsaa/alternate_oplsaa_file/README_alternate_atom_numbers.txt b/tools/moltemplate/common/oplsaa/alternate_oplsaa_file/README_alternate_atom_numbers.txt new file mode 100644 index 0000000000..a5ce2304aa --- /dev/null +++ b/tools/moltemplate/common/oplsaa/alternate_oplsaa_file/README_alternate_atom_numbers.txt @@ -0,0 +1,52 @@ +MOST USERS CAN IGNORE THIS DIRECTORY. + +This is the original version of oplsaa.txt released with +moltemplate version 1.20. Later on I decided to direct +users to the (hopefully current) version of the "oplsaa.prm" +file distributed with TINKER's force-field-explorer program. + +http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm +http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm + +The original oplsaa.txt from moltemplate version 1.20 file is located here. +Feel free to pick whichever one works well for your application, but +if you publish a paper using these parameters please cite TINKER, +since that appears to be the source of all of these files. +I think these are the relevant citations: + +Ponder, J. W., & Richards, F. M. (1987). "An efficient newtonâ€like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024. + +Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/ + + +Here is a discussion of a difference between these two files: + +>> On Fri, Apr 11, 2014 at 6:44 PM, Andrew Jewett wrote: +>> Jason +>> Lambert graciously wrote the "oplsaa_moltemplate.py" script and +>> provided the "oplsaa.txt" file which it reads as an input file (after +>> some minor manual editing on the part of the user). I did some +>> googling, and I noticed that this file is very similar to the +>> "oplsaa.prm" file located at this web site: +>> +>> http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm +>> +>> I suspect it uses the same parameter conventions. +>> +>> However I just realized that the two files are not identical. (I am +>> emailing Jason now to ask about the difference.) +>> +>> Where did you get the data for the "oplsaa.txt" file? More +>> specifically, where do the atom numbers come from? + +>On Tue, Apr 15, 2014 at 6:06 PM, jason Lambert wrote: +>To be honest I do not know the original source of the OPLSA force +> field file. The file was provided by a graduate student from a group +> I worked with and I did not question it other than spot checking with +> values that were published. I am surprised that the files are different. +> Anyways, I am not aware of any logic to the observed switches in +> the parameters. I did a diff -y on the two files and the difference is +> primarily atom switching. The code works with either one though +> so it is not a problem. We can provide a link to the prm file as well. +> I know I added some dihedrals explicitly but the ones I added were +> already encompassed by the dihedrals containing wild cards. diff --git a/tools/moltemplate/common/oplsaa/alternate_oplsaa_file/oplsaa.txt b/tools/moltemplate/common/oplsaa/alternate_oplsaa_file/oplsaa.txt new file mode 100644 index 0000000000..d39a40030f --- /dev/null +++ b/tools/moltemplate/common/oplsaa/alternate_oplsaa_file/oplsaa.txt @@ -0,0 +1,5971 @@ +# This text is similar but not identical to this file: +# http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm +# The difference appears to be the atom numbering and switching. +# If you can help us figure out which numbering convention we should use +# please email us at jewett.aij@gmail.com and jlamber9@gmail.com + + ############################## + ## ## + ## Force Field Definition ## + ## ## + ############################## + + +#forcefield OPLS-AA +#vdwindex TYPE +#vdwtype LENNARD-JONES +#radiusrule GEOMETRIC +#radiustype SIGMA +#radiussize DIAMETER +#epsilonrule GEOMETRIC +#torsionunit 0.5 +#imptorunit 0.5 +#vdw-14-scale 2.0 +#chg-14-scale 2.0 +#electric 332.06 +#dielectric 1.0 + + + ############################# + ## ## + ## Literature References ## + ## ## + ############################# + + +#The parameters supplied with TINKER are from "OPLS All-Atom Parameters +#for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as +#provided by W. L. Jorgensen, Yale University during June 2009. These +#parameters are taken from those distributed with BOSS Version 4.8. + +#Note that "atom type" numbers and not "atom class" numbers are used +#to index van der Waals parameters, see the "vdwindex" keyword above + +#The atom types with (UA) in the description are "united atom" values, +#ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their +#attached atoms. All other parameters are "all-atom", OPLS-AA, including +#explicit hydrogen atoms. + + + ############################# + ## ## + ## Atom Type Definitions ## + ## ## + ############################# + + +atom 1 1 F "Fluoride -CH2-F (UA)" 9 18.998 1 +atom 2 2 C2 "Fluoride -CH2-F (UA)" 6 14.027 2 +atom 3 3 C "Acetic Acid -COOH (UA)" 6 12.011 3 +atom 4 4 O "Acetic Acid >C=O (UA)" 8 15.999 1 +atom 5 5 OH "Acetic Acid -OH (UA)" 8 15.999 2 +atom 6 6 C3 "Acetic Acid CH3- (UA)" 6 15.035 1 +atom 7 7 HO "Acetic Acid -OH (UA)" 1 1.008 1 +atom 8 8 C4 "Methane CH4 (UA)" 6 16.043 0 +atom 9 6 C3 "Ethane CH3- (UA)" 6 15.035 1 +atom 10 6 C3 "N-Alkane CH3- (UA)" 6 15.035 1 +atom 11 6 C3 "Isobutane CH3- (UA)" 6 15.035 1 +atom 12 6 C3 "Neopentane CH3- (UA)" 6 15.035 1 +atom 13 2 C2 "Alkanes -CH2- (UA)" 6 14.027 2 +atom 14 9 C9 "1-Alkene CH2= (UA)" 6 14.027 1 +atom 15 10 CH "Isobutane CH (UA)" 6 13.019 3 +atom 16 11 C8 "2-Alkene -CH= (UA)" 6 13.019 2 +atom 17 12 CD "Aromatic CH (UA)" 6 13.019 2 +atom 18 13 CT "Neopentane C (UA)" 6 12.011 4 +atom 19 14 C7 "Isobutene >C= (UA)" 6 12.011 3 +atom 20 5 OH "Alcohol OH (UA)" 8 15.999 2 +atom 21 7 HO "Alcohol OH (UA)" 1 1.008 1 +atom 22 6 C3 "Methanol CH3- (UA)" 6 15.035 1 +atom 23 2 C2 "Ethanol -CH2OH (UA)" 6 14.027 2 +atom 24 15 SH "Hydrogen Sulfide H2S" 16 32.060 2 +atom 25 15 SH "Alkyl Sulfide RSH (UA)" 16 32.060 2 +atom 26 16 S "Thioether RSR (UA)" 16 32.060 2 +atom 27 16 S "Disulfide RSSR (UA)" 16 32.060 2 +atom 28 17 HS "Hydrogen Sulfide H2S" 1 1.008 1 +atom 29 17 HS "Alkyl Sulfide RSH (UA)" 1 1.008 1 +atom 30 6 C3 "Methyl Sulfide CH3 (UA)" 6 15.035 1 +atom 31 2 C2 "Alkyl Sulfide CH2 (UA)" 6 14.027 2 +atom 32 6 C3 "Thioether CH3 (UA)" 6 15.035 1 +atom 33 2 C2 "Thioether CH2 (UA)" 6 14.027 2 +atom 34 6 C3 "Disulfide CH3 (UA)" 6 15.035 1 +atom 35 2 C2 "Disulfide CH2 (UA)" 6 14.027 2 +atom 36 18 NZ "Acetonitrile -CN (UA)" 7 14.007 1 +atom 37 19 CZ "Acetonitrile -CN (UA)" 6 12.011 2 +atom 38 6 C3 "Acetonitrile CH3 (UA)" 6 15.035 1 +atom 39 20 OW "TIP5P Water O" 8 15.999 4 +atom 40 21 HW "TIP5P Water H" 1 1.008 1 +atom 41 22 LP "TIP5P Water M" 99 0.000 1 +atom 42 23 DM "Dummy Atom" 99 0.000 0 +atom 43 24 He "Helium Atom" 2 4.003 0 +atom 44 25 Ne "Neon Atom" 10 20.179 0 +atom 45 26 Ar "Argon Atom" 18 39.948 0 +atom 46 27 Kr "Krypton Atom" 36 83.800 0 +atom 47 28 Xe "Xenon Atom" 54 131.300 0 +atom 48 10 CH "Isopropanol >CHOH (UA)" 6 13.019 3 +atom 49 13 CT "t-Butanol COH (UA)" 6 12.011 4 +atom 50 29 OS "Ether ROR (UA)" 8 15.999 2 +atom 51 6 C3 "Ether CH3-OR (UA)" 6 15.035 1 +atom 52 2 C2 "Ether -CH2-OR (UA)" 6 14.027 2 +atom 53 20 OW "TIP3P Water O" 8 15.999 2 +atom 54 21 HW "TIP3P Water H" 1 1.008 1 +atom 55 20 OW "TIP4P Water O" 8 15.999 3 +atom 56 21 HW "TIP4P Water H" 1 1.008 1 +atom 57 22 LP "TIP4P Water M" 99 0.000 1 +atom 58 20 OW "TIP3F Water O" 8 15.999 2 +atom 59 21 HW "TIP3F Water H" 1 1.008 1 +atom 60 2 C2 "Methylene Chloride (UA)" 6 14.027 2 +atom 61 30 Cl "Methylene Chloride (UA)" 17 35.453 1 +atom 62 10 CH "Chloroform CHCl3 (UA)" 6 12.011 3 +atom 63 30 Cl "Chloroform CHCl3 (UA)" 17 35.453 1 +atom 64 13 CT "Carbon Tetrachloride" 6 12.011 4 +atom 65 30 Cl "Carbon Tetrachloride" 17 35.453 1 +atom 66 31 SZ "DMSO >S=O (UA)" 16 32.060 3 +atom 67 32 OY "DMSO >S=O (UA)" 8 15.999 1 +atom 68 6 C3 "DMSO CH3- (UA)" 6 15.035 1 +atom 69 33 NT "Ammonia NH3" 7 14.007 3 +atom 70 34 H "Ammonia NH3" 1 1.008 1 +atom 71 4 O "DMF C=O (UA)" 8 15.999 1 +atom 72 35 N "DMF CON< (UA)" 7 14.007 3 +atom 73 3 C "DMF C=O (UA)" 6 12.011 3 +atom 74 6 C3 "DMF CH3- (UA)" 6 15.035 1 +atom 75 20 OW "SPC Water O" 8 15.999 2 +atom 76 21 HW "SPC Water H" 1 1.008 1 +atom 77 13 CT "Alkane CH3-" 6 12.011 4 +atom 78 13 CT "Alkane -CH2-" 6 12.011 4 +atom 79 13 CT "Alkane >CH-" 6 12.011 4 +atom 80 13 CT "Methane CH4" 6 12.011 4 +atom 81 13 CT "Alkane >C<" 6 12.011 4 +atom 82 36 HC "Alkane H-C" 1 1.008 1 +atom 83 37 CM "Alkene R2-C=" 6 12.011 3 +atom 84 37 CM "Alkene RH-C=" 6 12.011 3 +atom 85 37 CM "Alkene H2-C=" 6 12.011 3 +atom 86 36 HC "Alkene H-C=" 1 1.008 1 +atom 87 38 CA "Aromatic C" 6 12.011 3 +atom 88 39 HA "Aromatic H-C" 1 1.008 1 +atom 89 38 CA "Naphthalene Fusion C" 6 12.011 3 +atom 90 13 CT "Ethyl Benzene CH3-" 6 12.011 4 +atom 91 13 CT "Ethyl Benzene -CH2-" 6 12.011 4 +atom 92 40 C= "Diene =CH-CH=" 6 12.011 3 +atom 93 5 OH "Alcohol -OH" 8 15.999 2 +atom 94 7 HO "Alcohol -OH" 1 1.008 1 +atom 95 36 HC "Methanol CH3-" 1 1.008 1 +atom 96 13 CT "Alcohol CH3OH & RCH2OH" 6 12.011 4 +atom 97 13 CT "Alcohol R2CHOH" 6 12.011 4 +atom 98 13 CT "Alcohol R3COH" 6 12.011 4 +atom 99 13 CT "Trifluoroethanol -CH2-" 6 12.011 4 +atom 100 13 CT "Trifluoroethanol CF3-" 6 12.011 4 +atom 101 5 OH "Trifluoroethanol -OH" 8 15.999 2 +atom 102 7 HO "Trifluoroethanol -OH" 1 1.008 1 +atom 103 1 F "Trifluoroethanol F" 9 18.998 1 +atom 104 36 HC "Trifluoroethanol -CH2-" 1 1.008 1 +atom 105 38 CA "Phenol C-OH" 6 12.011 3 +atom 106 5 OH "Phenol -OH" 8 15.999 2 +atom 107 7 HO "Phenol -OH" 1 1.008 1 +atom 108 5 OH "Diol -OH" 8 15.999 2 +atom 109 7 HO "Diol -OH" 1 1.008 1 +atom 110 5 OH "Triol -OH" 8 15.999 2 +atom 111 7 HO "Triol -OH" 1 1.008 1 +atom 112 13 CT "Diol & Triol -CH2OH" 6 12.011 4 +atom 113 13 CT "Diol & Triol -CHROH" 6 12.011 4 +atom 114 13 CT "Diol & Triol -CR2OH" 6 12.011 4 +atom 115 36 HC "Diol & Triol H-COH" 1 1.008 1 +atom 116 29 OS "Diphenyl Ether" 8 15.999 2 +atom 117 40 C= "Diene =CR-CR=" 6 12.011 3 +atom 118 29 OS "Anisole -OCH3" 8 15.999 1 +atom 119 29 OS "Dialkyl Ether -O-" 8 15.999 2 +atom 120 13 CT "Methyl Ether CH3OR" 6 12.011 4 +atom 121 13 CT "Ethyl Ether -CH2OR" 6 12.011 4 +atom 122 13 CT "Isopropyl Ether >CHOR" 6 12.011 4 +atom 123 13 CT "t-Butyl Ether COR" 6 12.011 4 +atom 124 36 HC "Alkyl Ether H-COR" 1 1.008 1 +atom 125 29 OS "Acetal RO-CR2OX" 8 15.999 4 +atom 126 5 OH "Hemiacetal -OH" 8 15.999 2 +atom 127 7 HO "Hemiacetal -OH" 1 1.008 1 +atom 128 41 CO "Acetal RO-CH2-OR" 6 12.011 4 +atom 129 36 HC "Acetal RO-CH2-OR" 1 1.008 1 +atom 130 41 CO "Hemiacetal RO-CH2-OH" 6 12.011 4 +atom 131 36 HC "Hemiacetal RO-CH2-OH" 1 1.008 1 +atom 132 41 CO "Acetal RO-CHR-OR" 6 12.011 4 +atom 133 36 HC "Acetal RO-CHR-OR" 1 1.008 1 +atom 134 41 CO "Hemiacetal RO-CHR-OH" 6 12.011 4 +atom 135 36 HC "Hemiacetal RO-CHR-OH" 1 1.008 1 +atom 136 41 CO "Acetal RO-CR2-OR" 6 12.011 4 +atom 137 41 CO "Hemiacetal RO-CR2-OH" 6 12.011 4 +atom 138 38 CA "Anisole C-OCH3" 6 12.011 4 +atom 139 15 SH "Thiol -SH" 16 32.060 2 +atom 140 15 SH "Hydrogen Sulfide H2S" 16 32.060 2 +atom 141 16 S "Sulfide -S-" 16 32.060 2 +atom 142 16 S "Disulfide -S-S-" 16 32.060 2 +atom 143 17 HS "Thiol -SH" 1 1.008 1 +atom 144 17 HS "Hydrogen Sulfide H2S" 1 1.008 1 +atom 145 13 CT "Thiol -CH2-SH" 6 12.011 4 +atom 146 13 CT "Thiol >CH-SH" 6 12.011 4 +atom 147 13 CT "Thiol C-SH" 6 12.011 4 +atom 148 13 CT "Methyl Sulfide CH3-SR" 6 12.011 4 +atom 149 13 CT "Sulfide RCH2-SR" 6 12.011 4 +atom 150 13 CT "Sulfide R2CH-SR" 6 12.011 4 +atom 151 13 CT "Sulfide R3C-SR" 6 12.011 4 +atom 152 13 CT "Disulfide CH3-S-SR" 6 12.011 4 +atom 153 13 CT "Disulfide RCH2-S-SR" 6 12.011 4 +atom 154 13 CT "Disulfide R2CH-S-SR" 6 12.011 4 +atom 155 13 CT "Disulfide R3C-S-SR" 6 12.011 4 +atom 156 13 CT "Methanethiol CH3-SH" 6 12.011 4 +atom 157 13 CT "Benzyl Alcohol -CH2OH" 6 12.011 4 +atom 158 13 CT "Benzyl Alcohol -CHROH" 6 12.011 4 +atom 159 13 CT "Benzyl Alcohol -CR2OH" 6 12.011 4 +atom 160 38 CA "Benzyl Alcohol/Nitrile" 6 12.011 3 +atom 161 16 S "Thioanisole -SCH3" 16 32.060 2 +atom 162 13 CT "RCH2-NH2 & GLY CA" 6 12.011 4 +atom 163 13 CT "RCHR-NH2 & ALA CA" 6 12.011 4 +atom 164 13 CT "R3C-NH2 & AIB CA" 6 12.011 4 +atom 165 30 Cl "Chloroalkene Cl-CH=" 17 35.453 1 +atom 166 37 CM "Chloroalkene Cl-CH=" 6 12.011 3 +atom 167 38 CA "Thioanisole C-SCH3" 6 12.011 3 +atom 168 13 CT "Amide -NH-CHR2" 6 12.011 4 +atom 169 13 CT "Amide -NH-CR3" 6 12.011 4 +atom 170 3 C "Benzophenone C=O" 6 12.011 3 +atom 171 3 C "Benzaldehyde C=O" 6 12.011 3 +atom 172 3 C "Acetophenone C=O" 6 12.011 3 +atom 173 3 C "Benzamide C=O" 6 12.011 3 +atom 174 3 C "Amide C=O" 6 12.011 3 +atom 175 4 O "Amide C=O" 8 15.999 1 +atom 176 35 N "Amide -CO-NH2" 7 14.007 3 +atom 177 35 N "Amide -CO-NHR" 7 14.007 3 +atom 178 35 N "Amide -CO-NR2" 7 14.007 3 +atom 179 34 H "Amide -CO-NH2" 1 1.008 1 +atom 180 34 H "Amide -CO-NHR" 1 1.008 1 +atom 181 13 CT "Amide -NH-CH3" 6 12.011 4 +atom 182 13 CT "Amide -NR-CH3" 6 12.011 4 +atom 183 13 CT "Amide -NH-CH2R" 6 12.011 4 +atom 184 13 CT "Amide -NR-CH2R & PRO CD" 6 12.011 4 +atom 185 13 CT "Amide -NR-CHR2 & PRO CA" 6 12.011 4 +atom 186 3 C "Urea C=O" 6 12.011 3 +atom 187 4 O "Urea C=O" 8 15.999 1 +atom 188 35 N "Urea -NH2" 7 14.007 3 +atom 189 34 H "Urea -NH2" 1 1.008 1 +atom 190 35 N "Imide -NH-" 7 14.007 3 +atom 191 3 C "Imide C=O" 6 12.011 3 +atom 192 4 O "Imide C=O" 8 15.999 1 +atom 193 34 H "Imide -NH-" 1 1.008 1 +atom 194 36 HC "Formimide H-C=O" 1 1.008 1 +atom 195 13 CT "Imide CH3-CONHCO-" 6 12.011 4 +atom 196 13 CT "Imide -CH2-CONHCO-" 6 12.011 4 +atom 197 13 CT "Imide >CH-CONHCO-" 6 12.011 4 +atom 198 13 CT "Imide C-CONHCO-" 6 12.011 4 +atom 199 38 CA "Benzonitrile C-CN" 6 12.011 3 +atom 200 19 CZ "Benzonitrile -CN" 6 12.011 2 +atom 201 18 NZ "Benzonitrile -CN" 7 14.007 1 +atom 202 38 CA "Chlorobenzene C-Cl" 6 12.011 3 +atom 203 30 Cl "Chlorobenzene C-Cl" 17 35.453 1 +atom 204 35 N "N-Phenylacetamide N" 7 14.007 3 +atom 205 38 CA "N-Phenylacetamide N-CA" 6 12.011 3 +atom 206 3 C "Carboxylic Acid -COOH" 6 12.011 3 +atom 207 5 OH "Carboxylic Acid C=O" 8 15.999 1 +atom 208 4 O "Carboxylic Acid -OH" 8 15.999 2 +atom 209 7 HO "Carboxylic Acid -COOH" 1 1.008 1 +atom 210 3 C "Carboxylate COO-" 6 12.011 3 +atom 211 42 O2 "Carboxylate COO-" 8 15.999 1 +atom 212 13 CT "Carboxylate CH3-COO-" 6 12.011 4 +atom 213 13 CT "Carboxylate RCH2-COO-" 6 12.011 4 +atom 214 13 CT "Carboxylate R2CH-COO-" 6 12.011 4 +atom 215 13 CT "Carboxylate R3C-COO-" 6 12.011 4 +atom 216 3 C "Aldehyde/Acyl Halide C=O" 6 12.011 3 +atom 217 4 O "Aldyhyde/Acyl Halide C=O" 8 15.999 1 +atom 218 36 HC "Aldehyde/Formamide HCO-" 1 1.008 1 +atom 219 3 C "Ketone C=O" 6 12.011 3 +atom 220 4 O "Ketone C=O" 8 15.999 1 +atom 221 36 HC "Acyl H-C-COX" 1 1.008 1 +atom 222 13 CT "C-Terminal ALA CA" 6 12.011 4 +atom 223 13 CT "C-Terminal GLY CA" 6 12.011 4 +atom 224 13 CT "C-Terminal AIB CA" 6 12.011 4 +atom 225 13 CT "C-Terminal PRO CA" 6 12.011 4 +atom 226 43 N3 "Ammonium NH4+" 7 14.007 4 +atom 227 43 N3 "Ammonium RNH3+" 7 14.007 4 +atom 228 43 N3 "Ammonium R4N+" 7 14.007 4 +atom 229 44 H3 "Ammonium NH4+" 1 1.008 1 +atom 230 44 H3 "Ammonium RNH3+" 1 1.008 1 +atom 231 13 CT "Ammonium CH3-NH3+" 6 12.011 4 +atom 232 13 CT "CH3NH3+/N-Term GLY CA" 6 12.011 4 +atom 233 13 CT "RCH2NH3+/N-Term ALA CA" 6 12.011 4 +atom 234 13 CT "R3C-NH3+/N-Term AIB CA" 6 12.011 4 +atom 235 13 CT "N-Terminal PRO CA" 6 12.011 4 +atom 236 13 CT "N-Terminal PRO CD" 6 12.011 4 +atom 237 13 CT "Ammonium CH3-NH2R+" 6 12.011 4 +atom 238 13 CT "GLY Zwitterion CA" 6 12.011 4 +atom 239 13 CT "ALA Zwitterion CA" 6 12.011 4 +atom 240 45 N2 "Guanidinium -NH2" 7 14.007 3 +atom 241 44 H3 "Guanidinium -NH2" 1 1.008 1 +atom 242 38 CA "Guanidinium C+" 6 12.011 3 +atom 243 45 N2 "Guanidinium -NHR" 7 14.007 3 +atom 244 44 H3 "Guanidinium -NHR" 1 1.008 1 +atom 245 13 CT "Me Guanidinium CH3-" 6 12.011 4 +atom 246 13 CT "Et Guanidinium CH3-" 6 12.011 4 +atom 247 13 CT "Et Guan -CH2- & ARG CD" 6 12.011 4 +atom 248 13 CT "Pr Guan -CH2- & ARG CG" 6 12.011 4 +atom 249 43 N3 "Ammonium R2NH2+" 7 14.007 4 +atom 250 44 H3 "Ammonium R2NH2+" 1 1.008 1 +atom 251 46 NC "Diaminopyridine N1" 7 14.007 2 +atom 252 38 CA "Diaminopyridine C2" 6 12.011 3 +atom 253 45 N2 "Diaminopyridine -NH2" 7 14.007 3 +atom 254 34 H "Diaminopyridine -NH2" 1 1.008 3 +atom 255 38 CA "Diaminopyridine C3" 6 12.011 3 +atom 256 39 HA "Diaminopyridine H3" 1 1.008 1 +atom 257 38 CA "Diaminopyridine C4" 6 12.011 3 +atom 258 39 HA "Diaminopyridine H4" 1 1.008 1 +atom 259 47 NA "Uracil & Thymine N1" 7 14.007 3 +atom 260 3 C "Uracil & Thymine C2" 6 12.011 3 +atom 261 47 NA "Uracil & Thymine N3" 7 14.007 3 +atom 262 3 C "Uracil & Thymine C4" 6 12.011 3 +atom 263 37 CM "Uracil & Thymine C5" 6 12.011 3 +atom 264 37 CM "Uracil & Thymine C6" 6 12.011 3 +atom 265 34 H "Uracil & Thymine HN1" 1 1.008 1 +atom 266 4 O "Uracil & Thymine O2" 8 15.999 1 +atom 267 34 H "Uracil & Thymine HN3" 1 1.008 1 +atom 268 4 O "Uracil & Thymine O4" 8 15.999 1 +atom 269 36 HC "Uracil & Thymine HC5" 1 1.008 1 +atom 270 36 HC "Uracil & Thymine HC6" 1 1.008 1 +atom 271 13 CT "Thymine CH3-" 6 12.011 4 +atom 272 36 HC "Thymine CH3-" 1 1.008 1 +atom 273 47 NA "Cytosine N1" 7 14.007 3 +atom 274 3 C "Cytosine C2" 6 12.011 3 +atom 275 46 NC "Cytosine N3" 7 14.007 2 +atom 276 38 CA "Cytosine C4" 6 12.011 3 +atom 277 37 CM "Cytosine C5" 6 12.011 3 +atom 278 37 CM "Cytosine C6" 6 12.011 3 +atom 279 34 H "Cytosine HN1" 1 1.008 1 +atom 280 4 O "Cytosine O2" 8 15.999 1 +atom 281 45 N2 "Cytosine NH2-" 7 14.007 3 +atom 282 34 H "Cytosine NH2- (N3)" 1 1.008 1 +atom 283 34 H "Cytosine NH2- (C5)" 1 1.008 1 +atom 284 36 HC "Cytosine HC5" 1 1.008 1 +atom 285 48 H4 "Cytosine HC6" 1 1.008 1 +atom 286 46 NC "Adenine N1" 7 14.007 2 +atom 287 49 CQ "Adenine C2" 6 12.011 3 +atom 288 46 NC "Adenine N3" 7 14.007 2 +atom 289 50 CB "Adenine C4" 6 12.011 3 +atom 290 50 CB "Adenine C5" 6 12.011 3 +atom 291 38 CA "Adenine C6" 6 12.011 3 +atom 292 51 NB "Adenine & Guanine N7" 7 14.007 2 +atom 293 52 CK "Adenine & Guanine C8" 6 12.011 3 +atom 294 47 NA "Adenine & Guanine N9" 7 14.007 2 +atom 295 53 H5 "Adenine HC2" 1 1.008 1 +atom 296 45 N2 "Adenine NH2-" 7 14.007 3 +atom 297 34 H "Adenine NH2- (N1)" 1 1.008 1 +atom 298 34 H "Adenine NH2- (C5)" 1 1.008 1 +atom 299 53 H5 "Adenine & Guanine HC8" 1 1.008 1 +atom 300 34 H "Adenine & Guanine HN9" 1 1.008 1 +atom 301 47 NA "Guanine N1" 7 14.007 3 +atom 302 38 CA "Guanine C2" 6 12.011 3 +atom 303 46 NC "Guanine N3" 7 14.007 2 +atom 304 50 CB "Guanine C4" 6 12.011 3 +atom 305 50 CB "Guanine C5" 6 12.011 3 +atom 306 3 C "Guanine C6" 6 12.011 3 +atom 307 34 H "Guanine HN1" 1 1.008 1 +atom 308 45 N2 "Guanine NH2-" 7 14.007 3 +atom 309 34 H "Guanine NH2-" 1 1.008 1 +atom 310 4 O "Guanine O6" 8 15.999 1 +atom 311 13 CT "9-Me A & 9-Me-G CH3-" 6 12.011 4 +atom 312 36 HC "9-Me-A & 9-Me-G CH3-" 1 1.008 1 +atom 313 13 CT "1-Me-U & 1-Me-T CH3-" 6 12.011 4 +atom 314 36 HC "1-Me-U & 1-Me-T CH3-" 1 1.008 1 +atom 315 13 CT "1-Me-Cytosine CH3-" 6 12.011 4 +atom 316 36 HC "1-Me-Cytosine CH3-" 1 1.008 1 +atom 317 47 NA "CytosineH+ N1" 7 14.007 3 +atom 318 3 C "CytosineH+ C2" 6 12.011 3 +atom 319 47 NA "CytosineH+ N3" 7 14.007 3 +atom 320 38 CA "CytosineH+ C4" 6 12.011 3 +atom 321 37 CM "CytosineH+ C5" 6 12.011 3 +atom 322 37 CM "CytosineH+ C6" 6 12.011 3 +atom 323 34 H "CytosineH+ HN1" 1 1.008 1 +atom 324 4 O "CytosineH+ O2" 8 15.999 1 +atom 325 34 H "CytosineH+ HN3" 1 1.008 1 +atom 326 45 N2 "CytosineH+ NH2-" 7 14.007 3 +atom 327 34 H "CytosineH+ NH2- (N3)" 1 1.008 1 +atom 328 34 H "CytosineH+ NH2- (C5)" 1 1.008 1 +atom 329 39 HA "CytosineH+ HC5" 1 1.008 1 +atom 330 48 H4 "CytosineH+ HC6" 1 1.008 1 +atom 331 13 CT "1-Me-CytosineH+ CH3-" 6 12.011 4 +atom 332 36 HC "1-Me-CytosineH+ CH3-" 1 1.008 1 +atom 333 54 P "DiMePhosphate P (UA)" 15 30.974 4 +atom 334 42 O2 "DiMePhosphate O=P-O (UA)" 8 15.999 1 +atom 335 29 OS "DiMePhosphate CH3-O (UA)" 8 15.999 2 +atom 336 13 CT "DiMePhosphate CH3-O (UA)" 6 15.035 1 +atom 337 37 CM "Trifluorothymine CF3-" 6 12.011 4 +atom 338 30 Cl "Chloroalkene Cl2-C=" 17 35.453 1 +atom 339 37 CM "Chloroalkene Cl2-C=" 6 12.011 3 +atom 340 1 F "Fluoride Ion F-" 9 18.998 0 +atom 341 30 Cl "Chloride Ion Cl-" 17 35.453 0 +atom 342 55 Br "Bromide Ion Br-" 35 79.904 0 +atom 343 56 I "Iodide Ion I-" 53 126.905 0 +atom 344 57 N4 "Ammonium Ion NH4+ (UA)" 7 18.039 0 +atom 345 58 Li "Lithium Ion Li+" 3 6.941 0 +atom 346 59 Na "Sodium Ion Na+" 11 22.990 0 +atom 347 60 K "Potassium Ion K+" 19 39.098 0 +atom 348 61 Rb "Rubidium Ion Rb+" 37 85.468 0 +atom 349 62 Cs "Cesium Ion Cs+" 55 132.905 0 +atom 350 63 Mg "Magnesium Ion Mg+2" 12 24.305 0 +atom 351 64 Ca "Calcium Ion Ca+2" 20 40.080 0 +atom 352 65 Sr "Strontium Ion Sr+2" 38 87.620 0 +atom 353 66 Ba "Barium Ion Ba+2" 56 137.330 0 +atom 354 6 C3 "Methyl Thiolate CH3S-" 6 12.011 4 +atom 355 36 HC "Methyl Thiolate CH3S-" 1 1.008 1 +atom 356 15 SH "Methyl Thiolate CH3S-" 16 32.060 1 +atom 357 6 C3 "Methoxide CH3O-" 6 12.011 4 +atom 358 36 HC "Methoxide CH3O-" 1 1.008 1 +atom 359 5 OH "Methoxide CH3O-" 8 15.999 1 +atom 360 13 CT "Nitrile Anion CNCH2-" 6 12.011 3 +atom 361 36 HC "Nitrile Anion CNCH2-" 1 1.008 1 +atom 362 19 CZ "Nitrile Anion CNCH2-" 6 12.011 2 +atom 363 18 NZ "Nitrile Anion CNCH2-" 7 14.007 1 +atom 364 6 C3 "Me Amine Anion CH3NH-" 6 12.011 4 +atom 365 36 HC "Me Amine Anion CH3NH-" 1 1.008 1 +atom 366 43 N3 "Me Amine Anion CH3NH-" 7 14.007 2 +atom 367 34 H "Methyl Amine Anion" 1 1.008 1 +atom 368 6 C3 "Ethyl Anion CH3-CH2-" 6 12.011 4 +atom 369 36 HC "Ethyl Anion CH3-CH2-" 1 1.008 1 +atom 370 13 CT "Ethyl Anion CH3-CH2-" 6 12.011 4 +atom 371 36 HC "Ethyl Anion CH3-CH2-" 1 1.008 1 +atom 372 22 LP "Ethyl Anion CH3-CH2-" 99 0.000 1 +atom 373 5 OH "Hydroxide Ion OH-" 8 15.999 1 +atom 374 7 HO "Hydroxide Ion OH-" 1 1.008 1 +atom 375 67 U "Uranyl Ion UO2+" 92 238.029 2 +atom 376 68 OU "Uranyl Ion UO2+" 8 15.999 1 +atom 377 29 OS "GTP O-(POn)2" 8 15.999 2 +atom 378 54 P "DiMe Phosphate P" 15 30.974 4 +atom 379 42 O2 "DiMe Phosphate O=P-O" 8 15.999 1 +atom 380 29 OS "DiMe Phosphate CH3-O" 8 15.999 1 +atom 381 13 CT "DiMe Phosphate CH3-O" 6 12.011 4 +atom 382 36 HC "DiMe Phosphate CH3-O" 1 1.008 1 +atom 383 54 P "Me Phosphate P" 15 30.974 4 +atom 384 42 O2 "Me Phosphate O=PO2" 8 15.999 1 +atom 385 29 OS "Me Phosphate CH3-O" 8 15.999 1 +atom 386 13 CT "Me Phosphate CH3-O" 6 12.011 4 +atom 387 36 HC "Me Phosphate CH3-O" 1 1.008 1 +atom 388 54 P "Me MePhosphonate P" 15 30.974 4 +atom 389 42 O2 "Me MePhosphonate O=P-O" 8 15.999 1 +atom 390 29 OS "Me MePhosphonate CH3-O" 8 15.999 1 +atom 391 13 CT "Me MePhosphonate CH3-O" 6 12.011 4 +atom 392 36 HC "Me MePhosphonate CH3-O" 1 1.008 1 +atom 393 13 CT "Me MePhosphonate CH3-P" 6 12.011 4 +atom 394 36 HC "Me MePhosphonate CH3-P" 1 1.008 1 +atom 395 38 CA "Bz MePhosphonate Cipso" 6 12.011 3 +atom 396 13 CT "Bz MePhosphonate CH3-O" 6 12.011 4 +atom 397 36 HC "Bz MePhosphonate CH3-O" 1 1.008 1 +atom 398 38 CA "Me BzPhosphonate Cipso" 6 12.011 3 +atom 399 13 CT "Me BzPhosphonate CH3-P" 6 12.011 4 +atom 400 36 HC "Me BzPhosphonate CH3-P" 1 1.008 1 +atom 401 38 CA "Ph Phosphate Cipso" 6 12.011 3 +atom 402 13 CT "Barbiturate C6(R2)" 6 12.011 4 +atom 403 3 C "Ester -COOR" 6 12.011 3 +atom 404 4 O "Ester C=O" 8 15.999 1 +atom 405 29 OS "Ester CO-O-R" 8 15.999 2 +atom 406 13 CT "Methyl Ester -OCH3" 6 12.011 4 +atom 407 36 HC "Methyl Ester -OCH3" 1 1.008 1 +atom 408 3 C "Benzoic Acid -COOH" 6 12.011 3 +atom 409 3 C "Aryl Ester -COOR" 6 12.011 3 +atom 410 38 CA "Phenyl Ester Cipso" 6 12.011 3 +atom 411 29 OS "Phenyl Ester -OPh" 8 15.999 2 +atom 412 69 SY "Sulfonamide -SO2N<" 16 32.060 4 +atom 413 32 OY "Sulfonamide -SO2N<" 8 15.999 1 +atom 414 13 CT "Sulfonamide CH3-S" 6 12.011 4 +atom 415 36 HC "Sulfonamide CH3-S" 1 1.008 1 +atom 416 35 N "Sulfonamide -SO2NH2" 7 14.007 3 +atom 417 34 H "Sulfonamide -SO2NH2" 1 1.008 1 +atom 418 35 N "Sulfonamide -SO2NHR" 7 14.007 3 +atom 419 34 H "Sulfonamide -SO2NHR" 1 1.008 1 +atom 420 13 CT "N-Me Sulfonamide CH3-" 6 12.011 4 +atom 421 36 HC "N-Me Sulfonamide CH3-" 1 1.008 1 +atom 422 13 CT "Sulfonamide N-CH2-R" 6 12.011 4 +atom 423 36 HC "Sulfonamide N-CH2-R" 1 1.008 1 +atom 424 13 CT "N-Et Sulfonamide CH3-" 6 12.011 4 +atom 425 36 HC "N-Et Sulfonamide CH3-" 1 1.008 1 +atom 426 38 CA "Aryl Sulfonamide C-SO2N" 6 12.011 3 +atom 427 38 CA "Aryl Sulfoxide C-S=O" 6 12.011 3 +atom 428 13 CT "Et Ester -OCH2R" 6 12.011 4 +atom 429 13 CT "i-Pr Ester -OCHR2" 6 12.011 4 +atom 430 13 CT "t-Bu Ester -OCR3" 6 12.011 4 +atom 431 69 SY "Sulfone R-SO2-R" 16 32.060 4 +atom 432 32 OY "Sulfone R-SO2-R" 8 15.999 1 +atom 433 31 SZ "Alkyl Aryl Sulfoxide" 16 32.060 3 +atom 434 31 SZ "Dialkyl Sulfoxide" 16 32.060 3 +atom 435 32 OY "Sulfoxide R-SO-R" 8 15.999 1 +atom 436 13 CT "Sulfoxide CH3-SO-R" 6 12.011 4 +atom 437 13 CT "Sulfoxide -CH2-SO-R" 6 12.011 4 +atom 438 70 C* "TRP CG" 6 12.011 3 +atom 439 50 CB "TRP CD" 6 12.011 3 +atom 440 71 CN "TRP CE" 6 12.011 3 +atom 441 47 NA "TRP NE, HID ND & HIE NE" 7 14.007 3 +atom 442 34 H "TRP HNE & HID/HIE HN" 1 1.008 1 +atom 443 13 CT "HIS CB" 6 12.011 4 +atom 444 72 CR "HID & HIE CE1" 6 12.011 3 +atom 445 73 CV "HID CD2 & HIE CG" 6 12.011 3 +atom 446 74 CW "HID CG & HIE CD2" 6 12.011 3 +atom 447 72 CR "HIP CE1" 6 12.011 3 +atom 448 75 CX "HIP CG & CD2" 6 12.011 3 +atom 449 51 NB "HID NE & HIE ND" 7 14.007 2 +atom 450 47 NA "HIP ND & NE" 7 14.007 3 +atom 451 34 H "HIP HND & HNE" 1 1.008 1 +atom 452 74 CW "TRP CD1" 6 12.011 3 +atom 453 13 CT "i-Pr Benzene -CHMe2" 6 12.011 4 +atom 454 13 CT "t-Bu Benzene -CMe3" 6 12.011 4 +atom 455 37 CM "Vinyl Ether =CH-OR" 6 12.011 3 +atom 456 37 CM "Vinyl Ether =CR-OR" 6 12.011 3 +atom 457 76 C! "Biphenyl C1" 6 12.011 3 +atom 458 46 NC "Pyridine N" 7 14.007 2 +atom 459 38 CA "Pyridine C1" 6 12.011 3 +atom 460 38 CA "Pyridine C2" 6 12.011 3 +atom 461 38 CA "Pyridine C3" 6 12.011 3 +atom 462 39 HA "Pyridine H1" 1 1.008 1 +atom 463 39 HA "Pyridine H2" 1 1.008 1 +atom 464 39 HA "Pyridine H3" 1 1.008 1 +atom 465 46 NC "Pyrazine N" 7 14.007 2 +atom 466 38 CA "Pyrazine CH" 6 12.011 3 +atom 467 39 HA "Pyrazine CH" 1 1.008 1 +atom 468 46 NC "Pyrimidine N" 7 14.007 2 +atom 469 49 CQ "Pyrimidine C2" 6 12.011 3 +atom 470 38 CA "Pyrimidine C4" 6 12.011 3 +atom 471 38 CA "Pyrimidine C5" 6 12.011 3 +atom 472 39 HA "Pyrimidine HC2" 1 1.008 1 +atom 473 39 HA "Pyrimidine HC4" 1 1.008 1 +atom 474 39 HA "Pyrimidine HC5" 1 1.008 1 +atom 475 46 NC "Pyridazine N" 7 14.007 2 +atom 476 38 CA "Pyridazine C3" 6 12.011 3 +atom 477 38 CA "Pyridazine C4" 6 12.011 3 +atom 478 39 HA "Pyridazine HC3" 1 1.008 1 +atom 479 39 HA "Pyridazine HC4" 1 1.008 1 +atom 480 47 NA "Pyrrole N" 7 14.007 3 +atom 481 74 CW "Pyrrole C2" 6 12.011 3 +atom 482 77 CS "Pyrrole C3" 6 12.011 3 +atom 483 34 H "Pyrrole HN" 1 1.008 1 +atom 484 39 HA "Pyrrole HC2" 1 1.008 1 +atom 485 39 HA "Pyrrole HC3" 1 1.008 1 +atom 486 47 NA "Pyrazole N1" 7 14.007 3 +atom 487 51 NB "Pyrazole N2" 7 14.007 2 +atom 488 78 CU "Pyrazole C3" 6 12.011 3 +atom 489 77 CS "Pyrazole C4" 6 12.011 3 +atom 490 74 CW "Pyrazole C5" 6 12.011 3 +atom 491 34 H "Pyrazole HN1" 1 1.008 1 +atom 492 39 HA "Pyrazole HC3" 1 1.008 1 +atom 493 39 HA "Pyrazole HC4" 1 1.008 1 +atom 494 39 HA "Pyrazole HC5" 1 1.008 1 +atom 495 47 NA "Imidazole N1" 7 14.007 3 +atom 496 72 CR "Imidazole C2" 6 12.011 3 +atom 497 51 NB "Imidazole N3" 7 14.007 2 +atom 498 73 CV "Imidazole C4" 6 12.011 3 +atom 499 74 CW "Imidazole C5" 6 12.011 3 +atom 500 34 H "Imidazole HN1" 1 1.008 1 +atom 501 39 HA "Imidazole HC2" 1 1.008 1 +atom 502 39 HA "Imidazole HC4" 1 1.008 1 +atom 503 39 HA "Imidazole HC5" 1 1.008 1 +atom 504 29 OS "Furan O" 8 15.999 2 +atom 505 74 CW "Furan C2" 6 12.011 3 +atom 506 77 CS "Furan C3" 6 12.011 3 +atom 507 39 HA "Furan HC2" 1 1.008 1 +atom 508 39 HA "Furan HC3" 1 1.008 1 +atom 509 29 OS "Oxazole O" 8 15.999 2 +atom 510 72 CR "Oxazole C2" 6 12.011 3 +atom 511 51 NB "Oxazole N" 7 14.007 2 +atom 512 73 CV "Oxazole C4" 6 12.011 3 +atom 513 74 CW "Oxazole C5" 6 12.011 3 +atom 514 39 HA "Oxazole HC2" 1 1.008 1 +atom 515 39 HA "Oxazole HC4" 1 1.008 1 +atom 516 39 HA "Oxazole HC5" 1 1.008 1 +atom 517 29 OS "Isoxazole O" 8 15.999 2 +atom 518 51 NB "Isoxazole N" 7 14.007 2 +atom 519 78 CU "Isoxazole C3" 6 12.011 3 +atom 520 77 CS "Isoxazole C4" 6 12.011 3 +atom 521 74 CW "Isoxazole C5" 6 12.011 3 +atom 522 39 HA "Isoxazole HC3" 1 1.008 1 +atom 523 39 HA "Isoxazole HC4" 1 1.008 1 +atom 524 39 HA "Isoxazole HC5" 1 1.008 1 +atom 525 47 NA "Indole N1" 7 14.007 3 +atom 526 74 CW "Indole C2" 6 12.011 3 +atom 527 77 CS "Indole C3" 6 12.011 3 +atom 528 38 CA "Indole C4" 6 12.011 3 +atom 529 38 CA "Indole C5" 6 12.011 3 +atom 530 38 CA "Indole C6" 6 12.011 3 +atom 531 38 CA "Indole C7" 6 12.011 3 +atom 532 71 CN "Indole C8" 6 12.011 3 +atom 533 50 CB "Indole C9" 6 12.011 3 +atom 534 34 H "Indole HN1" 1 1.008 1 +atom 535 39 HA "Indole HC2" 1 1.008 1 +atom 536 39 HA "Indole HC3" 1 1.008 1 +atom 537 39 HA "Indole HC4" 1 1.008 1 +atom 538 39 HA "Indole HC5" 1 1.008 1 +atom 539 39 HA "Indole HC6" 1 1.008 1 +atom 540 39 HA "Indole HC7" 1 1.008 1 +atom 541 46 NC "Quinoline N1" 7 14.007 2 +atom 542 38 CA "Quinoline C2" 6 12.011 3 +atom 543 38 CA "Quinoline C3" 6 12.011 3 +atom 544 38 CA "Quinoline C4" 6 12.011 3 +atom 545 38 CA "Quinoline C5" 6 12.011 3 +atom 546 38 CA "Quinoline C6" 6 12.011 3 +atom 547 38 CA "Quinoline C7" 6 12.011 3 +atom 548 38 CA "Quinoline C8" 6 12.011 3 +atom 549 38 CA "Quinoline C9" 6 12.011 3 +atom 550 38 CA "Quinoline C10" 6 12.011 3 +atom 551 39 HA "Quinoline HC2" 1 1.008 1 +atom 552 39 HA "Quinoline HC3" 1 1.008 1 +atom 553 39 HA "Quinoline HC4" 1 1.008 1 +atom 554 39 HA "Quinoline HC5" 1 1.008 1 +atom 555 39 HA "Quinoline HC6" 1 1.008 1 +atom 556 39 HA "Quinoline HC7" 1 1.008 1 +atom 557 39 HA "Quinoline HC8" 1 1.008 1 +atom 558 46 NC "Purine N1" 7 14.007 2 +atom 559 49 CQ "Purine C2" 6 12.011 3 +atom 560 46 NC "Purine N3" 7 14.007 2 +atom 561 50 CB "Purine C4" 6 12.011 3 +atom 562 50 CB "Purine C5" 6 12.011 3 +atom 563 38 CA "Purine C6" 6 12.011 3 +atom 564 51 NB "Purine N7" 7 14.007 2 +atom 565 52 CK "Purine C8" 6 12.011 3 +atom 566 47 NA "Purine N9" 7 14.007 3 +atom 567 39 HA "Purine HC2" 1 1.008 1 +atom 568 39 HA "Purine HC6" 1 1.008 1 +atom 569 39 HA "Purine HC8" 1 1.008 1 +atom 570 34 H "Purine HN9" 1 1.008 1 +atom 571 16 S "Thiazole S" 16 32.060 2 +atom 572 72 CR "Thiazole C2" 6 12.011 3 +atom 573 51 NB "Thiazole N" 7 14.007 2 +atom 574 73 CV "Thiazole C4" 6 12.011 3 +atom 575 74 CW "Thiazole C5" 6 12.011 3 +atom 576 39 HA "Thiazole HC2" 1 1.008 1 +atom 577 39 HA "Thiazole HC4" 1 1.008 1 +atom 578 39 HA "Thiazole HC5" 1 1.008 1 +atom 579 46 NC "1,3,5-Triazine N" 7 14.007 2 +atom 580 49 CQ "1,3,5-Triazine CH" 6 12.011 3 +atom 581 39 HA "1,3,5-Triazine CH" 1 1.008 1 +atom 582 38 CA "Serotonin C5-OH" 6 12.011 3 +atom 583 13 CT "Serotonin CH2 on C3" 6 12.011 4 +atom 584 46 NC "1,10-Phenanthroline N" 7 14.007 2 +atom 585 38 CA "1,10-Phenanthroline C2" 6 12.011 3 +atom 586 38 CA "1,10-Phenanthroline C3" 6 12.011 3 +atom 587 38 CA "1,10-Phenanthroline C4" 6 12.011 3 +atom 588 38 CA "1,10-Phenanthroline C12" 6 12.011 3 +atom 589 38 CA "1,10-Phenanthroline C11" 6 12.011 3 +atom 590 38 CA "1,10-Phenanthroline C5" 6 12.011 3 +atom 591 39 HA "1,10-Phenanthroline HC2" 1 1.008 1 +atom 592 39 HA "1,10-Phenanthroline HC3" 1 1.008 1 +atom 593 39 HA "1,10-Phenanthroline HC4" 1 1.008 1 +atom 594 39 HA "1,10-Phenanthroline HC5" 1 1.008 1 +atom 595 47 NA "1-Methylimidazole N1" 7 14.007 3 +atom 596 72 CR "1-Methylimidazole C2" 6 12.011 3 +atom 597 51 NB "1-Methylimidazole N3" 7 14.007 2 +atom 598 73 CV "1-Methylimidazole C4" 6 12.011 3 +atom 599 74 CW "1-Methylimidazole C5" 6 12.011 3 +atom 600 13 CT "1-Methylimidazole CH3-" 6 12.011 4 +atom 601 39 HA "1-Methylimidazole HC2" 1 1.008 1 +atom 602 39 HA "1-Methylimidazole HC4" 1 1.008 1 +atom 603 39 HA "1-Methylimidazole HC5" 1 1.008 1 +atom 604 36 HC "1-Methylimidazole CH3-" 1 1.008 1 +atom 605 13 CT "1-Et Imidazole RCH2-" 6 12.011 4 +atom 606 13 CT "1-iPr Imidazole R2CH-" 6 12.011 4 +atom 607 13 CT "1-MeO-Me-Imidazole CH2" 6 12.011 4 +atom 608 13 CT "2-Me Pyridine CH3" 6 12.011 4 +atom 609 13 CT "2-Et Pyridine CH2" 6 12.011 4 +atom 610 13 CT "3-Me Pyridazine CH3" 6 12.011 4 +atom 611 13 CT "3-Et Pyridazine CH2" 6 12.011 4 +atom 612 13 CT "4-Me Pyrimidine CH3" 6 12.011 4 +atom 613 13 CT "4-Et Pyrimidine CH2" 6 12.011 4 +atom 614 13 CT "2-Me Pyrazine CH3" 6 12.011 4 +atom 615 13 CT "2-Et Pyrazine CH2" 6 12.011 4 +atom 616 13 CT "2-Me Pyrrole CH3" 6 12.011 4 +atom 617 13 CT "2-Et Pyrrole CH2" 6 12.011 4 +atom 618 13 CT "2-Me Furan CH3" 6 12.011 4 +atom 619 13 CT "2-Et Furan CH2" 6 12.011 4 +atom 620 15 SH "6-Mercaptopurine SH" 16 32.060 2 +atom 621 17 HS "6-Mercaptopurine SH" 1 1.008 1 +atom 622 38 CA "6-Mercaptopurine C6" 6 12.011 3 +atom 623 79 C$ "Beta-Lactam N-C=O" 6 12.011 3 +atom 624 80 N$ "Beta-Lactam N-C=O" 7 14.007 4 +atom 625 81 CY "Penicillin CH-N" 6 12.011 4 +atom 626 81 CY "Penicillin CH-CO" 6 12.011 4 +atom 627 13 CT "3-Me Indole CH3" 6 12.011 4 +atom 628 76 C! "2-Phenyl Pyridine C2" 6 12.011 3 +atom 629 76 C! "2-Phenyl Pyridine C2'" 6 12.011 3 +atom 630 76 C! "2-Phenyl Pyridine C3" 6 12.011 3 +atom 631 76 C! "2-Phenyl Pyridine C3'" 6 12.011 3 +atom 632 76 C! "2-Phenyl Pyridine C4" 6 12.011 3 +atom 633 76 C! "2-Phenyl Pyridine C4'" 6 12.011 3 +atom 634 16 S "Diphenyl Thioether S" 16 32.060 2 +atom 635 82 Ac "Actinium Ion Ac+3" 89 227.000 0 +atom 636 83 Th "Thorium Ion Th+4" 90 232.038 0 +atom 637 84 Am "Americium Ion Am+3" 95 243.000 0 +atom 638 85 C+ "t-Butyl Cation C+" 6 12.011 3 +atom 639 13 CT "t-Butyl Cation CH3-" 6 12.011 4 +atom 640 36 HC "t-Butyl Cation CH3-" 1 1.008 1 +atom 641 86 La "Lanthanum Ion La+3" 57 138.906 0 +atom 642 87 Nd "Neodymium Ion Nd+3" 60 144.240 0 +atom 643 88 Eu "Europium Ion Eu+3" 63 151.960 0 +atom 644 89 Gd "Gadolinium Ion Gd+3" 64 157.250 0 +atom 645 90 Yb "Ytterbium Ion Yb+3" 70 173.040 0 +atom 646 37 CM "Cl..CH3..Cl- Sn2 TS" 6 12.011 5 +atom 647 30 Cl "Cl..CH3..Cl- Sn2 TS" 17 35.453 1 +atom 648 36 HC "Cl..CH3..Cl- Sn2 TS" 1 1.008 1 +atom 649 81 CY "Cyclopropane -CH2-" 6 12.011 4 +atom 650 81 CY "Cyclopropane -CHR-" 6 12.011 4 +atom 651 81 CY "Cyclopropane -CR2-" 6 12.011 4 +atom 652 38 CA "Cyclopentadienyl Anion" 6 12.011 3 +atom 653 39 HA "Cyclopentadienyl Anion" 1 1.008 1 +atom 654 38 CA "Cyclopentadienyl Radical" 6 12.011 3 +atom 655 39 HA "Cyclopentadienyl Radical" 1 1.008 1 +atom 656 38 CA "Fluorobenzene CF" 6 12.011 3 +atom 657 1 F "Fluorobenzene CF" 9 18.998 1 +atom 658 38 CA "Hexafluorobenzene CF" 6 12.011 3 +atom 659 1 F "Hexafluorobenzene CF" 9 18.998 1 +atom 660 55 Br "Bromide -CH2-Br (UA)" 35 79.904 1 +atom 661 2 C2 "Bromide -CH2-Br (UA)" 6 14.027 0 +atom 662 38 CA "TrifluoroMeBenzene C-CF3" 6 12.011 3 +atom 663 13 CT "TrifluoroMeBenzene CF3-" 6 12.011 4 +atom 664 1 F "TrifluoroMeBenzene CF3-" 9 18.998 1 +atom 665 38 CA "Difluorobenzene CF" 6 12.011 3 +atom 666 1 F "Difluorobenzene CF" 9 18.998 1 +atom 667 38 CA "Bromobenzene CBr" 6 12.011 3 +atom 668 55 Br "Bromobenzene CBr" 35 79.904 1 +atom 669 38 CA "Iodobenzene CI" 6 12.011 3 +atom 670 56 I "Iodobenzene CI" 53 126.905 1 +atom 671 81 CY "cProp/cBut Benzene C-Ar" 6 12.011 4 +atom 672 15 SH "Thiophenol SH" 16 32.060 2 +atom 673 38 CA "Thiophenol C-SH" 6 12.011 3 +atom 674 38 CA "Benzamidine CG" 6 12.011 3 +atom 675 38 CA "Benzamidine CD" 6 12.011 3 +atom 676 38 CA "Benzamidine CE" 6 12.011 3 +atom 677 38 CA "Benzamidine CZ" 6 12.011 3 +atom 678 39 HA "Benzamidine HCD" 1 1.008 1 +atom 679 39 HA "Benzamidine HCE" 1 1.008 1 +atom 680 38 CA "Benzamidine C+" 6 12.011 3 +atom 681 45 N2 "Benzamidine -NH2" 7 14.007 3 +atom 682 34 H "Benzamidine H1-N" 1 1.008 1 +atom 683 34 H "Benzamidine H2-N" 1 1.008 1 +atom 684 39 HA "Benzamidine HCG" 1 1.008 1 +atom 685 13 CT "Neutral MeGdn CH3-" 6 12.011 4 +atom 686 13 CT "Neutral ARG CD" 6 12.011 4 +atom 687 91 NY "Neutral ARG NE" 7 14.007 3 +atom 688 46 NC "Neutral ARG N1 (HN=C)" 7 14.007 2 +atom 689 91 NY "Neutral ARG N2 (H2N-C)" 7 14.007 3 +atom 690 38 CA "Neutral ARG CZ (>C=)" 6 12.011 3 +atom 691 18 NZ "Alkyl Nitrile -CN" 7 14.007 1 +atom 692 19 CZ "Alkyl Nitrile -CN" 6 12.011 2 +atom 693 13 CT "Acetonitrile CH3-CN" 6 12.011 4 +atom 694 13 CT "Alkyl Nitrile RCH2-CN" 6 12.011 4 +atom 695 13 CT "Alkyl Nitrile R2CH-CN" 6 12.011 4 +atom 696 13 CT "Alkyl Nitrile R3C-CN" 6 12.011 4 +atom 697 36 HC "Alkyl Nitrile H-C-CN" 1 1.008 1 +atom 698 92 NO "Nitroalkane -NO2" 7 14.007 3 +atom 699 93 ON "Nitroalkane -NO2" 8 15.999 1 +atom 700 13 CT "Nitromethane CH3-NO2" 6 12.011 4 +atom 701 36 HC "Nitroalkane H-C-NO2" 1 1.008 1 +atom 702 13 CT "Nitroalkane RCH2-NO2" 6 12.011 4 +atom 703 13 CT "Nitroalkane R2CH-NO2" 6 12.011 4 +atom 704 13 CT "Nitroalkane R3C-NO2" 6 12.011 4 +atom 705 92 NO "Nitrobenzene -NO2" 7 14.007 3 +atom 706 38 CA "Nitrobenzene C-NO2" 6 12.011 3 +atom 707 13 CT "Benzonitrile -CH2-" 6 12.011 0 +atom 708 46 NC "Neutral Benzamidine N" 7 14.007 2 +atom 709 4 O "Propylene Carbonate C=O" 8 15.999 1 +atom 710 3 C "Propylene Carbonate C=O" 6 12.011 3 +atom 711 29 OS "Propylene Carbonate C-O" 8 15.999 2 +atom 712 13 CT "Propylene Carbonate CH2" 6 12.011 4 +atom 713 13 CT "Propylene Carbonate CH" 6 12.011 4 +atom 714 13 CT "Propylene Carbonate CH3" 6 12.011 4 +atom 715 36 HC "Propylene Carbonate CH2" 1 1.008 1 +atom 716 36 HC "Propylene Carbonate CH" 1 1.008 1 +atom 717 36 HC "Propylene Carbonate CH3" 1 1.008 1 +atom 718 29 OS "GTP O-(POn)2" 8 15.999 2 +atom 719 94 P+ "Phosphonium R4P+" 15 30.974 4 +atom 720 13 CT "Phosphonium CH3-PR3+" 6 12.011 4 +atom 721 13 CT "Phosphonium RCH2-PR3+" 6 12.011 4 +atom 722 36 HC "Phosphonium CH3-PR3+" 1 1.008 1 +atom 723 54 P "Hexafluorophosphate Ion" 15 30.974 6 +atom 724 1 F "Hexafluorophosphate Ion" 9 18.998 1 +atom 725 35 N "Nitrate Ion NO3-" 7 14.007 3 +atom 726 4 O "Nitrate Ion NO3-" 8 15.999 1 +atom 727 20 OW "TIP4F Water O" 8 15.999 3 +atom 728 21 HW "TIP4F Water H" 1 1.008 1 +atom 729 22 LP "TIP4F Water M" 99 0.000 1 +atom 730 33 NT "Amine RNH2" 7 14.007 3 +atom 731 33 NT "Amine R2NH" 7 14.007 3 +atom 732 33 NT "Amine R3N" 7 14.007 3 +atom 733 13 CT "Amine CH3-NH2" 6 12.011 4 +atom 734 13 CT "Amine CH3-NHR" 6 12.011 4 +atom 735 13 CT "Amine CH3-NR2" 6 12.011 4 +atom 736 13 CT "Amine RCH2-NH2" 6 12.011 4 +atom 737 13 CT "Amine RCH2-NHR" 6 12.011 4 +atom 738 13 CT "Amine RCH2-NR2" 6 12.011 4 +atom 739 34 H "Amine RNH2" 1 1.008 1 +atom 740 34 H "Amine R2NH" 1 1.008 1 +atom 741 36 HC "Amine H-C-N" 1 1.008 1 +atom 742 13 CT "Amine R2CH-NH2" 6 12.011 4 +atom 743 13 CT "Amine R3C-NH2" 6 12.011 4 +atom 744 13 CT "Amine R2CH-NHR" 6 12.011 4 +atom 745 13 CT "Amine R2CH-NR2" 6 12.011 4 +atom 746 38 CA "Aniline C-NH2" 6 12.011 3 +atom 747 38 CA "N-Me Aniline C-NHR" 6 12.011 3 +atom 748 38 CA "N-DiMe Aniline C-NR2" 6 12.011 3 +atom 749 13 CT "Benzyl Amine -CH2NH2" 6 12.011 4 +atom 750 13 CT "Benzyl Amine -CHRNH2" 6 12.011 4 +atom 751 13 CT "Benzyl Amine -CR2NH2" 6 12.011 4 +atom 752 13 CT "Benzyl Ether -CH2OR" 6 12.011 4 +atom 753 13 CT "Benzyl Sulfide -CH2SH" 6 12.011 4 +atom 754 13 CT "Benzyl Amine -CH2NHR" 6 12.011 4 +atom 755 19 CZ "Alkyne HCC-" 6 12.011 2 +atom 756 36 HC "Alkyne HCC-" 1 1.008 1 +atom 757 19 CZ "Alkyne RCCH R w/ 2/3 H" 6 12.011 2 +atom 758 19 CZ "Alkyne RCCH R w/ 1 H" 6 12.011 2 +atom 759 19 CZ "Alkyne RCCH R w/ O H/Ph" 6 12.011 2 +atom 760 36 HC "Alkyne H-C-CC-" 1 1.008 1 +atom 761 41 CO "A & G Sugar C1'" 6 12.011 4 +atom 762 41 CO "C Sugar C1'" 6 12.011 4 +atom 763 41 CO "U & T Sugar C1'" 6 12.011 4 +atom 764 5 OH "Sugar O5'" 8 15.999 5 +atom 765 7 HO "Sugar H3' (-OH)" 1 1.008 1 +atom 766 95 N* "A & G Nucleoside N9" 7 14.007 3 +atom 767 95 N* "C Nucleoside N1" 7 14.007 3 +atom 768 95 N* "U & T Nucleoside N1" 7 14.007 3 +atom 769 19 CZ "Alkyne RCCR" 6 12.011 2 +atom 770 43 N3 "Ammonium R3NH+" 7 14.007 4 +atom 771 44 H3 "Ammonium R3NH+" 1 1.008 1 +atom 772 13 CT "Ammonium CH3-NHR2+" 6 12.011 4 +atom 773 13 CT "Ammonium RCH2-NHR2+" 6 12.011 4 +atom 774 13 CT "Ammonium R2CH-NHR2+" 6 12.011 4 +atom 775 13 CT "Ammonium R3C-NHR2+" 6 12.011 4 +atom 776 74 CW "2-Phenyl Furan C2" 6 12.011 3 +atom 777 77 CS "2-Phenyl Furan C3" 6 12.011 3 +atom 778 76 C! "2-Phenyl Furan C2'" 6 12.011 3 +atom 779 76 C! "2-Phenyl Furan C3'" 6 12.011 3 +atom 780 36 HC "GLY Zwitterion HA" 1 1.008 1 +atom 781 13 CT "GLY Zwitterion CA" 6 12.011 4 +atom 782 3 C "GLY Zwitterion C" 6 12.011 3 +atom 783 43 N3 "GLY Zwitterion N" 7 14.007 4 +atom 784 42 O2 "GLY Zwitterion O" 8 15.999 1 +atom 785 44 H3 "GLY Zwitterion HN" 1 1.008 1 +atom 786 1 F "Alkyl Fluoride C-F" 9 18.998 1 +atom 787 13 CT "Alkyl Fluoride RCH2-F" 6 12.011 4 +atom 788 36 HC "Alkyl Fluoride H-C-F" 1 1.008 1 +atom 789 13 CT "Alkyl Fluoride R2CH-F" 6 12.011 4 +atom 790 13 CT "Alkyl Fluoride R3C-F" 6 12.011 4 +atom 791 13 CT "Perfluoroalkane CF3-" 6 12.011 4 +atom 792 13 CT "Perfluoroalkane -CF2-" 6 12.011 4 +atom 793 13 CT "Perfluoroalkane >CF-" 6 12.011 4 +atom 794 13 CT "Tetrafluoromethane CF4" 6 12.011 4 +atom 795 1 F "Perfluoroalkane C-F" 9 18.998 1 +atom 796 13 CT "DifluoroMeBenzene -CHF2" 6 12.011 4 +atom 797 36 HC "DifluoroMeBenzene -CHF2" 1 1.008 1 +atom 798 13 CT "Fluoroacetate FCH2-COO-" 6 12.011 4 +atom 799 13 CT "Chloroacetate ClCH2-COO-" 6 12.011 4 +atom 800 30 Cl "Alkyl Chloride C-Cl" 17 35.453 1 +atom 801 13 CT "Alkyl Chloride RCH2-Cl" 6 12.011 4 +atom 802 36 HC "Alkyl Chloride H-C-Cl" 1 1.008 1 +atom 803 13 CT "Alkyl Chloride R2CH-Cl" 6 12.011 4 +atom 804 13 CT "Alkyl Chloride R3C-Cl" 6 12.011 4 +atom 805 55 Br "Alkyl Bromide C-Br" 35 79.904 1 +atom 806 13 CT "Alkyl Bromide RCH2-Br" 6 12.011 4 +atom 807 36 HC "Alkyl Bromide H-C-Br" 1 1.008 1 +atom 808 13 CT "Alkyl Bromide R2CH-Br" 6 12.011 4 +atom 809 13 CT "Alkyl Bromide R3C-Br" 6 12.011 4 +atom 810 1 F "Acyl Fluoride F-C=O" 9 18.998 1 +atom 811 30 Cl "Acyl Chloride Cl-C=O" 17 35.453 1 +atom 812 55 Br "Acyl Bromide Br-C=O" 35 79.904 1 +atom 813 38 CA "Trifluoroanisole C-OCF3" 6 12.011 3 +atom 814 29 OS "Trifluoroanisole -OCF3" 8 15.999 2 +atom 815 13 CT "Trifluoroanisole -OCF3" 6 12.011 4 +atom 816 1 F "Trifluoroanisole -OCF3" 9 18.998 1 +atom 817 35 N "N-Me,N-PhAcetamide N" 7 14.007 3 +atom 818 38 CA "N-Me,N-PhAcetamide Cipso" 6 12.011 3 +atom 819 13 CT "Benzyl Amine -CH2NR2" 6 12.011 4 +atom 820 3 C "Alkyl Hydroxamic Acid C" 6 12.011 3 +atom 821 3 C "Aryl Hydroxamic Acid C" 6 12.011 3 +atom 822 4 O "Hydroxamic Acid C=O" 8 15.999 1 +atom 823 35 N "Hydroxamic Acid N" 7 14.007 3 +atom 824 34 H "Hydroxamic Acid HN" 1 1.008 1 +atom 825 5 OH "Hydroxamic Acid OH" 8 15.999 2 +atom 826 7 HO "Hydroxamic Acid OH" 1 1.008 1 +atom 827 13 CT "Benzyl Ether -CHROR" 6 12.011 4 +atom 828 13 CT "Benzyl Ether -CR2OR" 6 12.011 4 +atom 829 76 C! "3-Phenyl Pyrrole C3" 6 12.011 3 +atom 830 76 C! "3-Phenyl Pyrrole C3'" 6 12.011 3 +atom 831 76 C! "4-Phenyl Imidazole C4" 6 12.011 3 +atom 832 76 C! "4-Phenyl Imidazole C4'" 6 12.011 3 +atom 833 38 CA "Diphenylmethane Cipso" 6 12.011 3 +atom 834 96 Zn "Zinc Ion Zn+2" 30 0.000 0 +atom 835 13 CT "Alkyl Iodide RCH2-I" 6 12.011 4 +atom 836 13 CT "Alkyl Iodide R2CH-I" 6 12.011 4 +atom 837 13 CT "Alkyl Iodide R3C-I" 6 12.011 4 +atom 838 56 I "Alkyl Iodide C-I" 53 126.905 1 +atom 839 36 HC "Alkyl Iodide H-C-I" 1 1.008 1 +atom 840 35 N "N-Ph Sulfonamide -NHPh" 7 14.007 3 +atom 841 38 CA "N-Ph Sulfonamide Cipso" 6 12.011 3 +atom 842 38 CA "Benzoate C-COO-" 6 12.011 3 +atom 843 35 N "N-Phenyl Urea N" 7 14.007 3 +atom 844 38 CA "N-Phenyl Urea Cipso" 6 12.011 3 +atom 845 3 C "Tertiary Amide -CO-NR2" 6 12.011 3 +atom 846 4 O "Tertiary Amide -CO-NR2" 8 15.999 1 +atom 847 97 NM "Tertiary Amide -CO-NR2" 7 14.007 3 +atom 848 13 CT "Tertiary Amide -NRCH3" 6 12.011 4 +atom 849 13 CT "Tertiary Amide -NRCH2R" 6 12.011 4 +atom 850 13 CT "Tertiary Amide -NRCHR2" 6 12.011 4 +atom 851 13 CT "Tertiary Amide -NRCR3" 6 12.011 4 +atom 852 36 HC "Tertiary Amide H-C-N" 1 1.008 2 +atom 853 3 C "Tertiary Formamide C=O" 6 12.011 3 +atom 854 4 O "Tertiary Formamide C=O" 8 15.999 1 +atom 855 36 HC "Tertiary Formamide H-C=O" 1 1.008 1 +atom 856 13 CT "B2-Peptide CA" 6 12.011 4 +atom 857 13 CT "B3-Peptide CA Main/N-Ter" 6 12.011 4 +atom 858 13 CT "B3-Pep CB GLY Main/C-Ter" 6 12.011 4 +atom 859 13 CT "B3-Pep CB ALA Main/C-Ter" 6 12.011 4 +atom 860 13 CT "B3-Pep CB PRO Main/C-Ter" 6 12.011 4 +atom 861 13 CT "B3-Peptide CA C-Ter" 6 12.011 4 +atom 862 13 CT "B3-Peptide CB ALA N-Ter" 6 12.011 4 +atom 863 13 CT "B3-Peptide CB GLY N-Ter" 6 12.011 4 +atom 864 13 CT "B3-Peptide CB PRO N-Ter" 6 12.011 4 +atom 865 13 CT "B3-Peptide CE PRO N-Ter" 6 12.011 4 +atom 866 98 Si "Alkyl Silane R4Si" 14 28.086 4 +atom 867 98 Si "Alkyl Silane R3SiH" 14 28.086 4 +atom 868 98 Si "Alkyl Silane R2SiH2" 14 28.086 4 +atom 869 98 Si "Alkyl Silane RSiH3" 14 28.086 4 +atom 870 34 H "Alkyl Silane H-C-Si" 1 1.008 1 +atom 871 13 CT "Methyl Silane CH3-Si" 6 12.011 4 +atom 872 13 CT "Alkyl Silane RCH2-Si" 6 12.011 4 +atom 873 13 CT "Alkyl Silane R2CH-Si" 6 12.011 4 +atom 874 13 CT "Alkyl Silane R3C-Si" 6 12.011 4 +atom 875 1 F "Fluoride Ion (GBSA)" 9 18.998 0 +atom 876 30 Cl "Chloride Ion (GBSA)" 17 35.453 0 +atom 877 55 Br "Bromide Ion (GBSA)" 35 79.904 0 +atom 878 56 I "Iodide Ion (GBSA)" 53 126.905 0 +atom 879 58 Li "Lithium Ion (GBSA)" 3 6.941 0 +atom 880 59 Na "Sodium Ion (GBSA)" 11 22.990 0 +atom 881 60 K "Potassium Ion (GBSA)" 19 39.098 0 +atom 882 61 Rb "Rubidium Ion (GBSA)" 37 85.468 0 +atom 883 62 Cs "Cesium Ion (GBSA)" 55 132.905 0 +atom 884 63 Mg "Magnesium Ion (GBSA)" 12 24.305 0 +atom 885 64 Ca "Calcium Ion (GBSA)" 20 40.080 0 +atom 886 65 Sr "Strontium Ion (GBSA)" 38 87.620 0 +atom 887 66 Ba "Barium Ion (GBSA)" 56 137.330 0 +atom 888 13 CT "Ammonium CH3-NR3+" 6 12.011 4 +atom 889 13 CT "Ammonium RCH2-NR3+" 6 12.011 4 +atom 890 13 CT "Ammonium R2CH-NR3+" 6 12.011 4 +atom 891 13 CT "Ammonium R3C-NR3+" 6 12.011 4 +atom 892 36 HC "Ammonium CH3-NR3+" 1 1.008 1 +atom 893 43 N3 "Anilinium Ar-NR3+" 7 14.007 4 +atom 894 38 CA "Anilinium C-NR3+" 6 12.011 3 +atom 895 43 N3 "Anilinium Ar-NHR2+" 7 14.007 4 +atom 896 38 CA "Anilinium C-NHR2+" 6 12.011 3 +atom 897 99 Ctr "Triene R2-C= (mid C=C)" 6 12.011 3 +atom 898 99 Ctr "Triene RH-C= (mid C=C)" 6 12.011 3 +atom 899 36 HC "Allene/Ketene H-C=C=X" 1 1.008 1 +atom 900 37 CM "Allene/Ketene H2C=C=X" 6 12.011 3 +atom 901 37 CM "Allene/Ketene HRC=C=X" 6 12.011 3 +atom 902 37 CM "Allene/Ketene R2C=C=X" 6 12.011 3 +atom 903 100 C: "Allene =C=" 6 12.011 2 +atom 904 100 C: "Ketene =C=" 6 12.011 2 +atom 905 4 O "Ketene C=O" 8 15.999 1 +atom 906 13 CT "N-Me-HIS CB" 6 12.011 4 + + + ################################ + ## ## + ## Van der Waals Parameters ## + ## ## + ################################ + + +vdw 1 2.9400 0.0610 +vdw 2 3.9050 0.1180 +vdw 3 3.7500 0.1050 +vdw 4 2.9600 0.2100 +vdw 5 3.0000 0.1700 +vdw 6 3.9100 0.1600 +vdw 7 0.0000 0.0000 +vdw 8 3.7300 0.2940 +vdw 9 3.7750 0.2070 +vdw 10 3.9050 0.1750 +vdw 11 3.9100 0.1600 +vdw 12 3.9600 0.1450 +vdw 13 3.9050 0.1180 +vdw 14 3.8500 0.1400 +vdw 15 3.8500 0.0800 +vdw 16 3.8000 0.1150 +vdw 17 3.7500 0.1100 +vdw 18 3.8000 0.0500 +vdw 19 3.7500 0.1050 +vdw 20 3.0700 0.1700 +vdw 21 0.0000 0.0000 +vdw 22 3.7750 0.2070 +vdw 23 3.9050 0.1180 +vdw 24 3.7000 0.2500 +vdw 25 3.5500 0.2500 +vdw 26 3.5500 0.2500 +vdw 27 3.5500 0.2500 +vdw 28 0.0000 0.0000 +vdw 29 0.0000 0.0000 +vdw 30 3.7750 0.2070 +vdw 31 3.9050 0.1180 +vdw 32 3.8000 0.1700 +vdw 33 3.8000 0.1180 +vdw 34 3.8000 0.1700 +vdw 35 3.8000 0.1180 +vdw 36 3.2000 0.1700 +vdw 37 3.6500 0.1500 +vdw 38 3.7750 0.2070 +vdw 39 3.1200 0.1600 +vdw 40 0.0000 0.0000 +vdw 41 0.0000 0.0000 +vdw 42 0.0000 0.0000 +vdw 43 2.5560 0.0200 +vdw 44 2.7800 0.0690 +vdw 45 3.4010 0.2339 +vdw 46 3.6240 0.3170 +vdw 47 3.9350 0.4330 +vdw 48 3.8500 0.0800 +vdw 49 3.8000 0.0500 +vdw 50 3.0000 0.1700 +vdw 51 3.8000 0.1700 +vdw 52 3.8000 0.1180 +vdw 53 3.15061 0.1521 +vdw 54 0.0000 0.0000 +vdw 55 3.15365 0.1550 +vdw 56 0.0000 0.0000 +vdw 57 0.0000 0.0000 +vdw 58 3.1760 0.1500 +vdw 59 0.0000 0.0000 +vdw 60 3.8000 0.1180 +vdw 61 3.4000 0.3000 +vdw 62 3.8000 0.0800 +vdw 63 3.4700 0.3000 +vdw 64 3.8000 0.0500 +vdw 65 3.4700 0.2660 +vdw 66 3.5600 0.3950 +vdw 67 2.9300 0.2800 +vdw 68 3.8100 0.1600 +vdw 69 3.4200 0.1700 +vdw 70 0.0000 0.0000 +vdw 71 2.9600 0.2100 +vdw 72 3.2500 0.1700 +vdw 73 3.8000 0.1150 +vdw 74 3.8000 0.1700 +vdw 75 3.16557 0.1554 +vdw 76 0.0000 0.0000 +vdw 77 3.5000 0.0660 +vdw 78 3.5000 0.0660 +vdw 79 3.5000 0.0660 +vdw 80 3.5000 0.0660 +vdw 81 3.5000 0.0660 +vdw 82 2.5000 0.0300 +vdw 83 3.5500 0.0760 +vdw 84 3.5500 0.0760 +vdw 85 3.5500 0.0760 +vdw 86 2.4200 0.0300 +vdw 87 3.5500 0.0700 +vdw 88 2.4200 0.0300 +vdw 89 3.5500 0.0700 +vdw 90 3.5000 0.0660 +vdw 91 3.5000 0.0660 +vdw 92 3.5500 0.0760 +vdw 93 3.1200 0.1700 +vdw 94 0.0000 0.0000 +vdw 95 2.5000 0.0300 +vdw 96 3.5000 0.0660 +vdw 97 3.5000 0.0660 +vdw 98 3.5000 0.0660 +vdw 99 3.5000 0.0660 +vdw 100 3.2500 0.0620 +vdw 101 3.0700 0.1700 +vdw 102 0.0000 0.0000 +vdw 103 2.9400 0.0610 +vdw 104 2.5000 0.0300 +vdw 105 3.5500 0.0700 +vdw 106 3.0700 0.1700 +vdw 107 0.0000 0.0000 +vdw 108 3.0700 0.1700 +vdw 109 0.0000 0.0000 +vdw 110 3.0700 0.1700 +vdw 111 0.0000 0.0000 +vdw 112 3.5000 0.0660 +vdw 113 3.5000 0.0660 +vdw 114 3.5000 0.0660 +vdw 115 2.5000 0.0300 +vdw 116 2.9000 0.1400 +vdw 117 3.5500 0.0760 +vdw 118 2.9000 0.1400 +vdw 119 2.9000 0.1400 +vdw 120 3.5000 0.0660 +vdw 121 3.5000 0.0660 +vdw 122 3.5000 0.0660 +vdw 123 3.5000 0.0660 +vdw 124 2.5000 0.0300 +vdw 125 2.9000 0.1400 +vdw 126 3.0700 0.1700 +vdw 127 0.0000 0.0000 +vdw 128 3.5000 0.0660 +vdw 129 2.5000 0.0300 +vdw 130 3.5000 0.0660 +vdw 131 2.5000 0.0300 +vdw 132 3.5000 0.0660 +vdw 133 2.5000 0.0300 +vdw 134 3.5000 0.0660 +vdw 135 2.5000 0.0300 +vdw 136 3.5000 0.0660 +vdw 137 3.5000 0.0660 +vdw 138 3.5500 0.0700 +vdw 139 3.5500 0.2500 +vdw 140 3.7000 0.2500 +vdw 141 3.5500 0.2500 +vdw 142 3.5500 0.2500 +vdw 143 0.0000 0.0000 +vdw 144 0.0000 0.0000 +vdw 145 3.5000 0.0660 +vdw 146 3.5000 0.0660 +vdw 147 3.5000 0.0660 +vdw 148 3.5000 0.0660 +vdw 149 3.5000 0.0660 +vdw 150 3.5000 0.0660 +vdw 151 3.5000 0.0660 +vdw 152 3.5000 0.0660 +vdw 153 3.5000 0.0660 +vdw 154 3.5000 0.0660 +vdw 155 3.5000 0.0660 +vdw 156 3.5000 0.0660 +vdw 157 3.5000 0.0660 +vdw 158 3.5000 0.0660 +vdw 159 3.5000 0.0660 +vdw 160 3.5500 0.0700 +vdw 161 3.5500 0.2500 +vdw 162 3.5000 0.0660 +vdw 163 3.5000 0.0660 +vdw 164 3.5000 0.0660 +vdw 165 3.4000 0.3000 +vdw 166 3.5500 0.0760 +vdw 167 3.5500 0.0700 +vdw 168 3.5000 0.0660 +vdw 169 3.5000 0.0660 +vdw 170 3.7500 0.1050 +vdw 171 3.7500 0.1050 +vdw 172 3.7500 0.1050 +vdw 173 3.7500 0.1050 +vdw 174 3.7500 0.1050 +vdw 175 2.9600 0.2100 +vdw 176 3.2500 0.1700 +vdw 177 3.2500 0.1700 +vdw 178 3.2500 0.1700 +vdw 179 0.0000 0.0000 +vdw 180 0.0000 0.0000 +vdw 181 3.5000 0.0660 +vdw 182 3.5000 0.0660 +vdw 183 3.5000 0.0660 +vdw 184 3.5000 0.0660 +vdw 185 3.5000 0.0660 +vdw 186 3.7500 0.1050 +vdw 187 2.9600 0.2100 +vdw 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0.000171 +vdw 883 4.8200 0.000081 +vdw 884 2.9100 0.875044 +vdw 885 3.4700 0.449657 +vdw 886 3.8200 0.118226 +vdw 887 4.1800 0.047096 +vdw 888 3.5000 0.0660 +vdw 889 3.5000 0.0660 +vdw 890 3.5000 0.0660 +vdw 891 3.5000 0.0660 +vdw 892 2.5000 0.0300 +vdw 893 3.2500 0.1700 +vdw 894 3.5500 0.0700 +vdw 895 3.2500 0.1700 +vdw 896 3.5500 0.0700 +vdw 897 3.5500 0.0760 +vdw 898 3.5500 0.0760 +vdw 899 2.4200 0.0300 +vdw 900 3.3000 0.0860 +vdw 901 3.3000 0.0860 +vdw 902 3.3000 0.0860 +vdw 903 3.3000 0.0860 +vdw 904 3.3000 0.0860 +vdw 905 2.9600 0.2100 +vdw 906 3.5000 0.0660 + + + ################################## + ## ## + ## Bond Stretching Parameters ## + ## ## + ################################## + + +bond 1 2 367.00 1.3800 +bond 1 3 420.00 1.3570 +bond 1 13 367.00 1.3600 +bond 1 19 450.00 1.2790 +bond 1 23 300.00 0.3000 +bond 1 37 420.00 1.3400 +bond 1 38 420.00 1.3540 +bond 1 72 420.00 1.3540 +bond 1 73 420.00 1.3540 +bond 1 74 420.00 1.3540 +bond 1 77 420.00 1.3540 +bond 1 78 420.00 1.3540 +bond 1 98 461.00 1.5700 +bond 2 2 260.00 1.5260 +bond 2 3 317.00 1.5220 +bond 2 5 386.00 1.4250 +bond 2 6 260.00 1.5260 +bond 2 10 260.00 1.5260 +bond 2 11 317.00 1.5000 +bond 2 12 317.00 1.5100 +bond 2 13 260.00 1.5260 +bond 2 14 317.00 1.5000 +bond 2 15 222.00 1.8100 +bond 2 16 222.00 1.8100 +bond 2 29 320.00 1.4250 +bond 2 33 382.00 1.4480 +bond 2 35 337.00 1.4490 +bond 2 38 317.00 1.5100 +bond 2 41 260.00 1.5260 +bond 2 43 367.00 1.4710 +bond 2 45 337.00 1.4630 +bond 2 70 317.00 1.4950 +bond 3 3 350.00 1.5100 +bond 3 4 570.00 1.2290 +bond 3 5 450.00 1.3640 +bond 3 6 317.00 1.5220 +bond 3 10 317.00 1.5220 +bond 3 12 469.00 1.4000 +bond 3 13 317.00 1.5220 +bond 3 19 400.00 1.4440 +bond 3 29 214.00 1.3270 +bond 3 30 300.00 1.7900 +bond 3 33 317.00 1.5220 +bond 3 35 490.00 1.3350 +bond 3 36 340.00 1.0900 +bond 3 37 410.00 1.4440 +bond 3 38 400.00 1.4900 +bond 3 40 385.00 1.4600 +bond 3 42 656.00 1.2500 +bond 3 46 457.00 1.3580 +bond 3 47 418.00 1.3880 +bond 3 50 447.00 1.4190 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1.4630 +bond 13 46 337.00 1.4490 +bond 13 47 337.00 1.4750 +bond 13 50 317.00 1.5100 +bond 13 54 212.00 1.8430 +bond 13 55 245.00 1.9450 +bond 13 56 200.00 2.1900 +bond 13 69 340.00 1.7700 +bond 13 70 317.00 1.4950 +bond 13 73 317.00 1.5040 +bond 13 74 317.00 1.5040 +bond 13 75 317.00 1.5040 +bond 13 77 317.00 1.4950 +bond 13 80 337.00 1.4490 +bond 13 81 280.00 1.5100 +bond 13 85 532.80 1.4600 +bond 13 91 382.00 1.4480 +bond 13 92 375.00 1.4900 +bond 13 94 212.00 1.8200 +bond 13 95 337.00 1.4750 +bond 13 97 337.00 1.4490 +bond 13 98 187.00 1.8600 +bond 13 99 317.00 1.5100 +bond 14 14 530.00 1.3400 +bond 15 17 274.00 1.3360 +bond 15 38 250.00 1.7400 +bond 16 16 166.00 2.0380 +bond 16 19 300.00 1.6850 +bond 16 23 340.00 0.5000 +bond 16 35 250.00 1.7300 +bond 16 37 250.00 1.7600 +bond 16 38 250.00 1.7600 +bond 16 51 250.00 1.7300 +bond 16 72 250.00 1.7600 +bond 16 74 250.00 1.7400 +bond 16 81 222.00 1.8100 +bond 16 98 144.00 2.1500 +bond 17 23 340.00 0.1000 +bond 18 18 550.00 1.1200 +bond 18 19 650.00 1.1570 +bond 18 38 400.00 1.4100 +bond 18 46 550.00 1.2400 +bond 19 19 1150.00 1.2100 +bond 19 30 330.00 1.6370 +bond 19 36 420.00 1.0800 +bond 19 37 400.00 1.4260 +bond 19 38 400.00 1.4510 +bond 19 40 400.00 1.4260 +bond 19 55 330.00 1.7840 +bond 19 78 400.00 1.4510 +bond 19 81 400.00 1.4510 +bond 20 21 600.00 0.9572 +bond 20 22 900.00 0.1750 +bond 20 96 40.00 2.0500 +bond 23 23 340.00 0.3000 +bond 23 29 340.00 0.3000 +bond 23 30 300.00 0.3000 +bond 23 31 340.00 0.5000 +bond 23 32 340.00 0.3000 +bond 23 33 340.00 0.3000 +bond 23 34 340.00 0.1000 +bond 23 35 367.00 0.3000 +bond 23 36 340.00 0.3000 +bond 23 37 340.00 0.3000 +bond 23 38 367.00 0.3000 +bond 23 39 340.00 0.3000 +bond 23 43 340.00 0.3000 +bond 23 46 367.00 0.3000 +bond 23 51 367.00 0.3000 +bond 23 55 300.00 0.3000 +bond 23 93 340.00 0.1000 +bond 29 29 250.00 1.4700 +bond 29 30 200.00 1.6900 +bond 29 33 320.00 1.4500 +bond 29 35 320.00 1.4500 +bond 29 37 450.00 1.3700 +bond 29 38 450.00 1.3640 +bond 29 41 320.00 1.3800 +bond 29 50 340.00 1.3600 +bond 29 51 462.00 1.3990 +bond 29 54 230.00 1.6100 +bond 29 72 462.00 1.3570 +bond 29 74 340.00 1.3600 +bond 29 98 374.00 1.6400 +bond 30 37 300.00 1.7250 +bond 30 38 300.00 1.7250 +bond 30 72 300.00 1.7250 +bond 30 73 300.00 1.7250 +bond 30 74 300.00 1.7250 +bond 30 77 300.00 1.7250 +bond 30 78 300.00 1.7250 +bond 30 98 223.00 2.0200 +bond 31 32 700.00 1.5300 +bond 32 69 700.00 1.4400 +bond 33 33 350.00 1.4450 +bond 33 34 434.00 1.0100 +bond 33 38 481.00 1.3400 +bond 33 69 340.00 1.7700 +bond 33 81 382.00 1.4480 +bond 33 98 266.00 1.7400 +bond 34 35 434.00 1.0100 +bond 34 43 434.00 1.0100 +bond 34 45 434.00 1.0100 +bond 34 46 434.00 1.0100 +bond 34 47 434.00 1.0100 +bond 34 91 434.00 1.0100 +bond 34 95 434.00 1.0100 +bond 34 98 166.00 1.4800 +bond 35 38 427.00 1.3810 +bond 35 49 427.00 1.3810 +bond 35 69 434.00 1.6700 +bond 35 74 427.00 1.3810 +bond 35 78 427.00 1.3810 +bond 35 81 337.00 1.4490 +bond 35 93 500.00 1.2700 +bond 35 96 40.00 2.0500 +bond 36 37 340.00 1.0800 +bond 36 40 340.00 1.0800 +bond 36 41 340.00 1.0900 +bond 36 70 340.00 1.0800 +bond 36 81 340.00 1.0880 +bond 36 85 532.80 1.0840 +bond 36 98 166.00 1.4800 +bond 36 99 340.00 1.0800 +bond 37 37 549.00 1.3400 +bond 37 38 427.00 1.4330 +bond 37 40 549.00 1.3400 +bond 37 47 448.00 1.3650 +bond 37 48 367.00 1.0800 +bond 37 55 300.00 1.9000 +bond 37 56 250.00 2.0800 +bond 37 76 385.00 1.4600 +bond 37 81 317.00 1.5100 +bond 37 95 448.00 1.3650 +bond 37 100 700.00 1.3050 +bond 38 38 469.00 1.4000 +bond 38 39 367.00 1.0800 +bond 38 40 427.00 1.4330 +bond 38 43 400.00 1.4500 +bond 38 45 481.00 1.3400 +bond 38 46 483.00 1.3390 +bond 38 47 427.00 1.3810 +bond 38 50 469.00 1.4040 +bond 38 51 414.00 1.3910 +bond 38 54 220.00 1.7800 +bond 38 55 300.00 1.8700 +bond 38 56 250.00 2.0800 +bond 38 69 340.00 1.7700 +bond 38 71 469.00 1.4000 +bond 38 74 546.00 1.3670 +bond 38 76 469.00 1.4000 +bond 38 78 469.00 1.4210 +bond 38 81 317.00 1.4900 +bond 38 91 382.00 1.3850 +bond 38 92 400.00 1.4600 +bond 38 99 427.00 1.4330 +bond 39 49 367.00 1.0800 +bond 39 52 340.00 1.0800 +bond 39 72 367.00 1.0800 +bond 39 73 367.00 1.0800 +bond 39 74 367.00 1.0800 +bond 39 75 367.00 1.0800 +bond 39 77 367.00 1.0800 +bond 39 78 367.00 1.0800 +bond 40 40 385.00 1.4600 +bond 40 46 457.00 1.2900 +bond 40 74 549.00 1.3650 +bond 40 99 385.00 1.4600 +bond 41 95 337.00 1.4750 +bond 42 54 525.00 1.4800 +bond 43 44 434.00 1.0100 +bond 44 45 434.00 1.0100 +bond 45 49 481.00 1.3400 +bond 45 72 481.00 1.3400 +bond 46 46 500.00 1.3200 +bond 46 49 502.00 1.3240 +bond 46 50 461.00 1.3540 +bond 46 72 461.00 1.3540 +bond 46 76 483.00 1.3390 +bond 46 93 550.00 1.2100 +bond 46 99 457.00 1.2900 +bond 47 50 436.00 1.3740 +bond 47 51 400.00 1.3490 +bond 47 52 440.00 1.3710 +bond 47 71 428.00 1.3800 +bond 47 72 477.00 1.3430 +bond 47 74 427.00 1.3810 +bond 47 75 427.00 1.3810 +bond 47 76 385.00 1.4400 +bond 48 73 367.00 1.0800 +bond 48 74 367.00 1.0800 +bond 49 53 367.00 1.0800 +bond 50 50 520.00 1.3700 +bond 50 51 414.00 1.3910 +bond 50 70 388.00 1.4590 +bond 50 71 447.00 1.4190 +bond 50 77 469.00 1.4240 +bond 50 95 436.00 1.3740 +bond 51 51 400.00 1.2800 +bond 51 52 529.00 1.3040 +bond 51 72 488.00 1.3350 +bond 51 73 410.00 1.3940 +bond 51 74 410.00 1.3940 +bond 51 78 410.00 1.3200 +bond 52 53 367.00 1.0800 +bond 52 95 440.00 1.3710 +bond 53 72 367.00 1.0800 +bond 54 98 108.00 2.2500 +bond 55 72 300.00 1.8700 +bond 55 73 300.00 1.8700 +bond 55 74 300.00 1.8700 +bond 55 77 300.00 1.8700 +bond 55 78 300.00 1.8700 +bond 55 98 151.00 2.1900 +bond 56 72 250.00 2.0800 +bond 56 73 250.00 2.0800 +bond 56 74 250.00 2.0800 +bond 56 77 250.00 2.0800 +bond 56 78 250.00 2.0800 +bond 56 98 108.00 2.4400 +bond 67 68 500.00 1.8000 +bond 70 74 546.00 1.3520 +bond 72 76 385.00 1.4600 +bond 72 77 520.00 1.3700 +bond 73 74 520.00 1.3700 +bond 73 76 385.00 1.4600 +bond 74 74 512.00 1.3750 +bond 74 76 385.00 1.4600 +bond 74 77 546.00 1.3670 +bond 74 78 520.00 1.3700 +bond 75 75 520.00 1.3700 +bond 76 76 385.00 1.4600 +bond 76 77 385.00 1.4600 +bond 76 78 385.00 1.4600 +bond 77 77 469.00 1.4240 +bond 77 78 469.00 1.4240 +bond 79 80 490.00 1.3350 +bond 79 81 317.00 1.5220 +bond 80 81 337.00 1.4490 +bond 81 81 260.00 1.5200 +bond 92 93 550.00 1.2250 +bond 98 98 94.00 2.3200 +bond 99 99 549.00 1.3450 + + + ################################ + ## ## + ## Angle Bending Parameters ## + ## ## + ################################ + + +angle 23 1 23 33.00 109.47 +angle 1 2 2 50.00 109.50 +angle 2 2 2 63.00 112.40 +angle 2 2 3 63.00 112.40 +angle 2 2 5 80.00 109.50 +angle 2 2 6 63.00 112.40 +angle 2 2 10 63.00 112.40 +angle 2 2 16 50.00 114.70 +angle 2 2 29 80.00 109.50 +angle 2 2 33 56.20 109.47 +angle 2 2 35 80.00 111.20 +angle 2 2 38 63.00 112.40 +angle 2 2 41 63.00 112.40 +angle 2 2 43 80.00 111.20 +angle 2 2 45 80.00 111.20 +angle 3 2 10 63.00 112.40 +angle 3 2 33 80.00 111.20 +angle 3 2 35 80.00 110.30 +angle 5 2 6 80.00 109.50 +angle 5 2 10 80.00 109.50 +angle 6 2 6 63.00 112.40 +angle 6 2 10 63.00 112.40 +angle 6 2 13 63.00 112.40 +angle 6 2 29 80.00 109.50 +angle 6 2 33 56.20 109.47 +angle 6 2 41 63.00 112.40 +angle 10 2 10 63.00 112.40 +angle 10 2 12 63.00 114.00 +angle 10 2 15 50.00 108.60 +angle 10 2 16 50.00 114.70 +angle 10 2 29 80.00 109.50 +angle 10 2 33 56.20 109.47 +angle 10 2 38 63.00 114.00 +angle 10 2 70 63.00 115.60 +angle 13 2 33 56.20 109.47 +angle 1 3 4 80.00 121.00 +angle 1 3 13 80.00 111.00 +angle 2 3 4 80.00 120.40 +angle 2 3 35 70.00 116.60 +angle 2 3 42 70.00 117.00 +angle 3 3 4 80.00 121.40 +angle 3 3 13 80.00 117.20 +angle 3 3 35 70.00 116.60 +angle 4 3 4 80.00 126.00 +angle 4 3 5 80.00 121.00 +angle 4 3 6 80.00 120.40 +angle 4 3 10 80.00 120.40 +angle 4 3 13 80.00 120.40 +angle 4 3 29 83.00 123.40 +angle 4 3 30 75.00 119.00 +angle 4 3 33 80.00 120.40 +angle 4 3 35 80.00 122.90 +angle 4 3 36 35.00 123.00 +angle 4 3 37 80.00 125.30 +angle 4 3 38 80.00 120.40 +angle 4 3 40 80.00 124.00 +angle 4 3 42 80.00 126.00 +angle 4 3 46 80.00 122.50 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35 3 38 70.00 115.50 +angle 35 3 50 70.00 111.30 +angle 36 3 36 35.00 115.00 +angle 36 3 38 35.00 115.00 +angle 36 3 40 80.00 116.00 +angle 36 3 46 35.00 116.00 +angle 36 3 46 35.00 122.00 +angle 37 3 47 70.00 114.10 +angle 38 3 38 85.00 120.00 +angle 38 3 42 70.00 117.00 +angle 42 3 42 80.00 126.00 +angle 46 3 47 70.00 118.60 +angle 46 3 95 70.00 118.60 +angle 47 3 47 70.00 118.60 +angle 47 3 50 70.00 111.30 +angle 47 3 95 70.00 115.40 +angle 3 4 23 35.00 113.00 +angle 23 4 23 10.00 117.00 +angle 2 5 7 55.00 108.50 +angle 3 5 7 35.00 113.00 +angle 6 5 7 55.00 108.50 +angle 7 5 10 55.00 108.50 +angle 7 5 13 55.00 108.50 +angle 7 5 23 10.00 109.47 +angle 7 5 35 49.00 105.40 +angle 7 5 37 35.00 109.00 +angle 7 5 38 35.00 113.00 +angle 7 5 41 55.00 108.50 +angle 7 5 54 55.00 108.50 +angle 7 5 69 74.00 110.00 +angle 7 5 96 100.00 126.00 +angle 13 5 23 10.00 109.47 +angle 13 5 54 100.00 120.50 +angle 23 5 23 5.00 109.47 +angle 23 5 38 10.00 109.47 +angle 5 7 23 10.00 109.47 +angle 23 7 23 33.00 109.47 +angle 2 10 2 63.00 112.40 +angle 2 10 3 63.00 111.10 +angle 2 10 5 80.00 109.50 +angle 2 10 6 63.00 112.40 +angle 2 10 10 63.00 111.50 +angle 2 10 29 80.00 109.50 +angle 2 10 33 56.20 109.47 +angle 2 10 35 80.00 109.70 +angle 2 10 38 63.00 112.40 +angle 2 10 95 80.00 109.50 +angle 3 10 6 63.00 111.10 +angle 3 10 10 63.00 111.10 +angle 3 10 33 80.00 109.70 +angle 3 10 35 63.00 110.10 +angle 5 10 6 80.00 109.50 +angle 5 10 10 80.00 109.50 +angle 6 10 6 63.00 111.50 +angle 6 10 10 63.00 111.50 +angle 6 10 29 80.00 109.50 +angle 6 10 33 56.20 109.47 +angle 6 10 35 80.00 109.50 +angle 10 10 10 63.00 111.50 +angle 10 10 29 80.00 109.50 +angle 10 10 33 56.20 109.47 +angle 10 10 35 80.00 109.70 +angle 10 10 95 80.00 109.50 +angle 13 10 33 56.20 109.47 +angle 29 10 38 80.00 109.50 +angle 29 10 95 80.00 109.50 +angle 2 11 2 70.00 124.00 +angle 2 11 6 70.00 124.00 +angle 2 11 9 70.00 118.00 +angle 2 11 10 70.00 124.00 +angle 2 11 11 70.00 118.00 +angle 2 11 13 70.00 124.00 +angle 6 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75 70.00 130.70 +angle 39 75 47 35.00 120.00 +angle 39 75 75 35.00 130.70 +angle 47 75 75 70.00 106.30 +angle 38 76 38 63.00 120.00 +angle 38 76 46 70.00 124.00 +angle 38 76 72 63.00 120.00 +angle 38 76 73 63.00 120.00 +angle 38 76 74 63.00 120.00 +angle 38 76 76 63.00 120.00 +angle 38 76 77 63.00 120.00 +angle 38 76 78 63.00 120.00 +angle 46 76 76 70.00 124.00 +angle 2 77 74 70.00 125.00 +angle 3 77 74 70.00 130.00 +angle 13 77 50 70.00 128.60 +angle 13 77 74 70.00 125.00 +angle 36 77 50 35.00 126.80 +angle 36 77 74 35.00 126.80 +angle 39 77 50 35.00 120.00 +angle 39 77 74 35.00 125.70 +angle 39 77 77 35.00 127.50 +angle 50 77 74 85.00 106.40 +angle 50 77 77 70.00 107.30 +angle 72 77 74 70.00 110.40 +angle 74 77 74 70.00 103.80 +angle 74 77 76 70.00 125.70 +angle 74 77 77 70.00 107.30 +angle 74 77 78 70.00 103.80 +angle 76 77 77 70.00 127.50 +angle 13 78 51 70.00 118.90 +angle 19 78 51 70.00 118.90 +angle 38 78 39 35.00 128.60 +angle 39 78 51 35.00 118.90 +angle 51 78 77 70.00 111.90 +angle 4 79 80 80.00 134.00 +angle 4 79 81 80.00 134.00 +angle 80 79 81 70.00 91.00 +angle 13 80 79 55.00 127.00 +angle 13 80 81 50.00 126.00 +angle 79 80 81 50.00 94.00 +angle 13 81 36 35.00 114.30 +angle 13 81 81 37.50 117.20 +angle 16 81 36 37.50 108.00 +angle 16 81 80 55.00 109.00 +angle 16 81 81 55.00 128.00 +angle 33 81 36 35.00 114.30 +angle 33 81 81 37.50 117.20 +angle 35 81 36 35.00 108.00 +angle 35 81 79 70.00 117.00 +angle 35 81 81 37.50 126.00 +angle 36 81 36 35.00 114.30 +angle 36 81 37 35.00 109.50 +angle 36 81 79 37.50 110.00 +angle 36 81 80 35.00 111.00 +angle 36 81 81 37.50 117.20 +angle 37 81 81 63.00 114.00 +angle 79 81 81 63.00 85.00 +angle 80 81 81 80.00 89.00 +angle 81 81 81 30.00 79.20 +angle 13 85 13 172.80 120.00 +angle 13 85 36 144.00 120.00 +angle 13 91 34 35.00 109.50 +angle 13 91 38 50.00 120.50 +angle 34 91 34 43.60 106.40 +angle 34 91 38 50.00 112.50 +angle 13 92 93 80.00 117.50 +angle 38 92 93 80.00 117.50 +angle 93 92 93 80.00 125.00 +angle 23 93 23 10.00 109.50 +angle 23 93 92 10.00 109.50 +angle 13 94 13 45.00 109.50 +angle 3 95 10 70.00 117.60 +angle 3 95 13 70.00 117.60 +angle 3 95 34 35.00 119.20 +angle 3 95 37 70.00 121.60 +angle 3 95 41 70.00 117.60 +angle 6 95 50 70.00 125.80 +angle 6 95 52 70.00 128.80 +angle 10 95 50 70.00 125.80 +angle 10 95 52 70.00 128.80 +angle 13 95 37 70.00 121.20 +angle 13 95 50 70.00 125.80 +angle 13 95 52 70.00 128.80 +angle 34 95 37 35.00 119.20 +angle 34 95 50 30.00 125.80 +angle 34 95 52 30.00 128.80 +angle 37 95 41 70.00 121.20 +angle 41 95 50 70.00 125.80 +angle 41 95 52 70.00 128.80 +angle 50 95 52 70.00 105.40 +angle 4 96 35 20.00 109.50 +angle 35 96 35 20.00 109.50 +angle 3 97 13 50.00 121.90 +angle 13 97 13 50.00 118.00 +angle 1 98 13 35.00 110.50 +angle 13 98 13 60.00 110.00 +angle 13 98 29 60.00 100.00 +angle 13 98 30 35.00 110.50 +angle 13 98 34 35.00 110.50 +angle 13 98 36 35.00 110.50 +angle 13 98 55 35.00 110.50 +angle 13 98 56 35.00 110.50 +angle 13 98 98 50.00 112.00 +angle 29 98 29 60.00 110.00 +angle 34 98 34 35.00 109.50 +angle 36 98 36 35.00 109.50 +angle 13 99 40 70.00 124.00 +angle 13 99 99 70.00 124.00 +angle 36 99 38 35.00 123.30 +angle 36 99 40 35.00 120.00 +angle 36 99 99 35.00 120.00 +angle 38 99 99 85.00 117.00 +angle 40 99 99 70.00 124.00 +angle 4 100 37 160.00 180.00 +angle 37 100 37 160.00 180.00 + + + ##################################### + ## ## + ## Improper Torsional Parameters ## + ## ## + ##################################### + + +imptors 0 0 3 4 21.000 180.0 2 +imptors 0 0 3 42 21.000 180.0 2 +imptors 0 0 35 0 5.000 180.0 2 +imptors 0 0 37 0 30.000 180.0 2 +imptors 0 0 38 0 5.000 180.0 2 + + + ############################ + ## ## + ## Torsional Parameters ## + ## ## + ############################ + + + ################################################################### + ## ## + ## Alternative Torsional Parameter Values for Use with OPLS-AA ## + ## ## + ## For some torsions, OPLS-AA has multiple possible parameter ## + ## values; the list below shows functional groups for which ## + ## these alternate (commented) values should be preferred; the ## + ## values are in the same order as in the full parameter list ## + ## ## + ## 4 3 3 36 generic (default) ## + ## 4 3 3 36 dicarbonyls ## + ## 36 3 3 36 hydrocarbon (default) ## + ## 36 3 3 36 dicarbonyls ## + ## 13 3 5 7 carboxylic acid (default) ## + ## 13 3 5 7 1,2-diacid monoanion ## + ## 4 3 13 13 peptide (default) ## + ## 4 3 13 13 propanamide ## + ## 4 3 13 13 carboxylic acid ## + ## 4 3 13 13 dicarboxylic acid ## + ## 4 3 13 13 aldyhyde, ketone, acyl halide ## + ## 4 3 13 13 1,2-diacid monoanion ## + ## 5 3 13 13 carboxylic acid (default) ## + ## 5 3 13 13 dicarboxylic acid ## + ## 35 3 13 13 peptide psi' (default) ## + ## 35 3 13 13 propanamide ## + ## 35 3 13 13 beta-3-peptide, last psi ## + ## 4 3 29 13 esters (default) ## + ## 4 3 29 13 benzoic esters ## + ## 7 5 13 13 alcohols (default) ## + ## 7 5 13 13 trifluoroethanol ## + ## 7 5 13 13 hexopyranoses ## + ## 7 5 13 36 alcohols (default) ## + ## 7 5 13 36 axial cyclohexanol ## + ## 7 5 13 36 trifluoroethanol ## + ## 0 13 13 13 alcohols, ethers (default) ## + ## 0 13 13 13 hexopyranoses ## + ## 3 13 13 3 dicarboxylic acid (default) ## + ## 3 13 13 3 1,2-diacid monoanion ## + ## 3 13 13 13 butanamide (default) ## + ## 3 13 13 13 carboxylate ion ## + ## 3 13 13 13 aldyhyde, ketone, acyl halide ## + ## 3 13 13 36 all carbonyls (default) ## + ## 3 13 13 36 dicarboxylic acid ## + ## 3 13 13 36 aldehyde, ketone, acyl halide ## + ## 5 13 13 5 diols only (default) ## + ## 5 13 13 5 triols only ## + ## 5 13 13 5 hexopyranoses ## + ## 13 13 13 13 hydrocarbon (default) ## + ## 13 13 13 13 perfluoroalkane ## + ## 13 13 13 35 peptide chi-1 (default) ## + ## 13 13 13 35 N-propylformamide ## + ## 36 13 13 69 generic (default) ## + ## 36 13 13 69 sulfone ## + ## 13 13 33 13 amine (default) ## + ## 13 13 33 13 exocyclic amine ## + ## 13 13 33 13 exocyclic 1,4-diamine ## + ## 13 13 33 34 amine (default) ## + ## 13 13 33 34 azetidine, 4-ring ## + ## 13 13 33 34 pyrrolidine, 5-ring ## + ## 13 13 33 34 cyclic amine ## + ## 13 13 33 34 cyclic 1,4-diamine ## + ## 13 13 35 3 peptide phi' (default) ## + ## 13 13 35 3 N-ethylformamide ## + ## 13 13 35 3 beta-3-peptide, first theta tors ## + ## 13 13 35 13 proline, CD-N-CA-CB (default) ## + ## 13 13 35 13 proline, CG-CD-N-CA ## + ## 36 13 35 3 peptide phi'' (default) ## + ## 36 13 35 3 N-methylformamide ## + ## 13 13 47 0 imidazole, indole, purine (default) ## + ## 13 13 47 0 nucleoside chi ## + ## 13 13 47 52 nucleoside (default) ## + ## 13 13 47 52 imidazole, indole, purine ## + ## 29 13 47 0 imidazole, indole, purine (default) ## + ## 29 13 47 0 nucleoside chi ## + ## 29 13 95 52 nucleoside (default) ## + ## 29 13 95 52 imidazole, indole, purine ## + ## 13 13 97 13 generic (default) ## + ## 13 13 97 13 generic ## + ## 17 15 38 0 aromatic thiol (default) ## + ## 17 15 38 0 aromatic thiol, N-C-S-H ## + ## 13 29 54 42 phosphonates (default) ## + ## 13 29 54 42 dimethyl phosphate ## + ## 34 35 72 16 diaryl amine (default) ## + ## 34 35 72 16 aniline-like ## + ## 34 35 72 29 diaryl amine (default) ## + ## 34 35 72 29 aniline-like ## + ## 13 40 40 37 diene (default) ## + ## 13 40 40 37 2-methyl-1,3-butadiene ## + ## 0 46 72 0 generic (default) ## + ## 0 46 72 0 generic ## + ## 0 47 72 0 generic (default) ## + ## 0 47 72 0 generic ## + ## 0 47 74 0 generic (default) ## + ## 0 47 74 0 generic ## + ## 0 47 74 0 generic ## + ## 0 51 72 0 generic (default) ## + ## 0 51 72 0 HA-CR-NB-?? or N?-CR-NB-?? ## + ## 0 72 77 0 generic (default) ## + ## 0 72 77 0 biphenyl-like, N-C-C-C ## + ## ## + ################################################################### + + +torsion 0 2 2 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 0 2 2 6 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 1 2 2 2 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 +torsion 1 2 2 6 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 +torsion 2 2 2 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 13 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 55 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 +torsion 6 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 6 2 2 55 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 +torsion 10 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 +torsion 6 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 +torsion 10 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 +torsion 0 2 10 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 10 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 13 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 6 2 29 2 -7.400 0.0 1 3.000 180.0 2 1.800 0.0 3 +torsion 6 2 29 6 -8.400 0.0 1 3.000 180.0 2 1.800 0.0 3 +torsion 4 3 3 4 1.600 0.0 1 3.200 180.0 2 0.000 0.0 3 +torsion 4 3 3 13 0.000 0.0 1 0.500 180.0 2 0.000 0.0 3 +torsion 4 3 3 35 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 3 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +#torsion 4 3 3 36 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 +torsion 13 3 3 13 0.700 0.0 1 -1.500 180.0 2 0.000 0.0 3 +torsion 13 3 3 35 -0.500 0.0 1 0.200 180.0 2 0.000 0.0 3 +torsion 13 3 3 36 0.800 0.0 1 -0.760 180.0 2 0.000 0.0 3 +torsion 35 3 3 36 -0.900 0.0 1 0.300 180.0 2 0.000 0.0 3 +torsion 36 3 3 36 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +#torsion 36 3 3 36 0.800 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 3 3 5 7 3.000 0.0 1 5.500 180.0 2 0.000 0.0 3 +torsion 4 3 5 7 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 13 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 +#torsion 13 3 5 7 3.200 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 35 3 5 7 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 36 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 +torsion 38 3 5 7 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 1 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 3 13 36 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 +torsion 3 3 13 36 0.000 0.0 1 0.000 180.0 2 0.085 0.0 3 +torsion 4 3 13 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +#torsion 4 3 13 13 0.000 0.0 1 1.166 180.0 2 0.000 0.0 3 +#torsion 4 3 13 13 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 +#torsion 4 3 13 13 -0.750 0.0 1 -0.550 180.0 2 -0.250 0.0 3 +#torsion 4 3 13 13 -0.277 0.0 1 1.228 180.0 2 -0.694 0.0 3 +#torsion 4 3 13 13 -1.000 0.0 1 -1.900 180.0 2 -0.900 0.0 3 +torsion 4 3 13 30 -0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 33 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 +torsion 4 3 13 35 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 38 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 +torsion 5 3 13 13 0.000 0.0 1 1.412 180.0 2 0.000 0.0 3 +#torsion 5 3 13 13 1.000 0.0 1 0.546 180.0 2 0.450 0.0 3 +torsion 5 3 13 33 5.260 0.0 1 0.820 180.0 2 0.000 0.0 3 +torsion 5 3 13 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 3 13 13 1.454 0.0 1 -0.144 180.0 2 -0.775 0.0 3 +torsion 13 3 13 36 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3 +torsion 29 3 13 13 0.000 0.0 1 0.000 180.0 2 -0.553 0.0 3 +torsion 29 3 13 36 0.000 0.0 1 0.000 180.0 2 0.132 0.0 3 +torsion 30 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 30 3 13 36 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 +torsion 35 3 13 13 1.173 0.0 1 0.189 180.0 2 -1.200 0.0 3 +#torsion 35 3 13 13 3.250 0.0 1 -0.402 180.0 2 -0.136 0.0 3 +#torsion 35 3 13 13 3.260 0.0 1 0.440 180.0 2 0.600 0.0 3 +torsion 35 3 13 30 0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 35 3 13 35 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3 +torsion 35 3 13 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 36 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 36 3 13 36 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 +torsion 38 3 13 36 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3 +torsion 42 3 13 13 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 +torsion 42 3 13 33 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 +torsion 42 3 13 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 55 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 55 3 13 36 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 +torsion 97 3 13 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 29 13 0.000 0.0 1 5.124 180.0 2 0.000 0.0 3 +#torsion 4 3 29 13 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 4 3 29 38 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 13 3 29 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3 +torsion 13 3 29 38 1.500 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 35 3 29 13 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 36 3 29 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3 +torsion 38 3 29 13 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 3 3 35 13 0.400 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 3 3 35 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 4 3 35 5 0.000 0.0 1 6.603 180.0 2 0.000 0.0 3 +torsion 4 3 35 13 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 4 3 35 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 4 3 35 37 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 4 3 35 38 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 4 3 35 81 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 5 3 35 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 5 3 35 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 13 3 35 5 4.542 0.0 1 6.603 180.0 2 1.045 0.0 3 +torsion 13 3 35 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 13 3 35 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 13 3 35 38 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 29 3 35 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 29 3 35 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 35 3 35 3 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 35 3 35 13 4.600 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 35 3 35 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 36 3 35 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 36 3 35 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 37 3 35 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 38 3 35 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 38 3 35 38 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 38 3 35 74 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 38 3 35 77 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 74 3 35 38 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 74 3 35 74 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 74 3 35 77 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 77 3 35 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 77 3 35 38 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 77 3 35 74 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 77 3 35 77 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 0 3 37 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3 +torsion 4 3 37 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 37 37 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 +torsion 5 3 37 37 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3 +torsion 35 3 37 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 35 3 37 37 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 97 3 37 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 97 3 37 37 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 38 38 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 +torsion 5 3 38 38 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 +torsion 13 3 38 38 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 +torsion 29 3 38 38 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 +torsion 35 3 38 38 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 +torsion 36 3 38 38 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 +torsion 0 3 40 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3 +torsion 4 3 40 37 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 +torsion 5 3 40 37 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3 +torsion 13 3 40 37 0.800 0.0 1 -3.000 180.0 2 0.000 0.0 3 +torsion 13 3 46 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 13 3 46 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 36 3 46 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 36 3 46 34 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 0 3 50 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3 +torsion 4 3 50 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3 +torsion 4 3 72 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 72 47 2.000 0.0 1 1.000 180.0 2 0.000 0.0 3 +torsion 4 3 72 51 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3 +torsion 72 3 72 47 -2.000 0.0 1 1.000 180.0 2 0.000 0.0 3 +torsion 72 3 72 51 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3 +torsion 4 3 74 29 -0.750 0.0 1 1.500 180.0 2 0.000 0.0 3 +torsion 4 3 74 77 0.750 0.0 1 1.500 180.0 2 0.000 0.0 3 +torsion 74 3 74 29 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3 +torsion 74 3 74 77 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3 +torsion 38 3 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 0 3 77 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 4 3 77 74 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 +torsion 4 3 77 77 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 +torsion 35 3 77 74 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 +torsion 35 3 77 77 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 +torsion 4 3 97 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 13 3 97 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 4 3 99 99 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 +torsion 5 3 99 99 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3 +torsion 0 4 96 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 7 5 10 2 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3 +torsion 7 5 10 6 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3 +torsion 7 5 13 2 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3 +torsion 7 5 13 6 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3 +torsion 7 5 13 13 -0.356 0.0 1 -0.174 180.0 2 0.492 0.0 3 +#torsion 7 5 13 13 4.478 0.0 1 -2.175 180.0 2 0.000 0.0 3 +#torsion 7 5 13 13 2.674 0.0 1 -2.883 180.0 2 1.026 0.0 3 +torsion 7 5 13 36 0.000 0.0 1 0.000 180.0 2 0.352 0.0 3 +#torsion 7 5 13 36 -2.589 0.0 1 -1.123 180.0 2 0.270 0.0 3 +#torsion 7 5 13 36 0.000 0.0 1 0.000 180.0 2 0.476 0.0 3 +torsion 7 5 13 37 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 7 5 13 38 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 7 5 13 40 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 7 5 33 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 7 5 33 34 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 7 5 35 3 5.519 0.0 1 -6.700 180.0 2 0.581 0.0 3 +torsion 7 5 35 34 2.722 0.0 1 -5.154 180.0 2 0.000 0.0 3 +torsion 7 5 37 37 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3 +torsion 7 5 38 38 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3 +torsion 7 5 41 29 -1.257 0.0 1 -1.806 180.0 2 0.003 0.0 3 +torsion 7 5 46 3 3.000 0.0 1 3.000 180.0 2 0.000 0.0 3 +torsion 7 5 54 4 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 7 5 54 5 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 7 5 69 13 -0.750 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 7 5 69 32 0.750 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 7 5 69 38 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 13 13 3 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 +torsion 0 13 13 13 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3 +#torsion 0 13 13 13 -1.336 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 13 13 35 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 +torsion 1 13 13 1 -2.500 0.0 1 0.000 180.0 2 0.250 0.0 3 +torsion 1 13 13 5 0.000 0.0 1 0.000 180.0 2 0.540 0.0 3 +torsion 1 13 13 13 0.300 0.0 1 -0.400 180.0 2 0.400 0.0 3 +torsion 1 13 13 36 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 3 13 13 3 -0.550 0.0 1 0.000 180.0 2 1.000 0.0 3 +#torsion 3 13 13 3 0.800 0.0 1 0.000 180.0 2 0.900 0.0 3 +torsion 3 13 13 5 -6.180 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 3 13 13 13 -2.060 0.0 1 -0.313 180.0 2 0.315 0.0 3 +#torsion 3 13 13 13 -3.185 0.0 1 -0.825 180.0 2 0.493 0.0 3 +#torsion 3 13 13 13 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 +torsion 3 13 13 15 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 +torsion 3 13 13 16 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 +torsion 3 13 13 35 -9.000 0.0 1 2.000 180.0 2 0.800 0.0 3 +torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 -0.100 0.0 3 +#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 0.074 0.0 3 +#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 -0.076 0.0 3 +torsion 3 13 13 38 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 +torsion 3 13 13 70 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 +torsion 5 13 13 5 9.508 0.0 1 0.000 180.0 2 0.000 0.0 3 +#torsion 5 13 13 5 12.234 0.0 1 0.000 180.0 2 0.000 0.0 3 +#torsion 5 13 13 5 9.066 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 13 13 13 -1.552 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 13 13 29 4.319 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 13 13 33 8.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 13 13 35 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3 +torsion 5 13 13 36 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3 +torsion 13 13 13 13 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 +#torsion 13 13 13 13 6.622 0. 1 0.948 180. 2 -1.388 0. 3 -2.118 180. 4 +torsion 13 13 13 15 1.262 0.0 1 -0.198 180.0 2 0.465 0.0 3 +torsion 13 13 13 16 2.619 0.0 1 -0.620 180.0 2 0.258 0.0 3 +torsion 13 13 13 19 0.000 0.0 1 -0.650 180.0 2 0.000 0.0 3 +torsion 13 13 13 30 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 13 13 13 33 2.392 0.0 1 -0.674 180.0 2 0.550 0.0 3 +torsion 13 13 13 35 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 +#torsion 13 13 13 35 1.964 0.0 1 0.000 180.0 2 0.659 0.0 3 +torsion 13 13 13 36 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +#the parameter was added because it did not exist. +torsion 13 13 13 37 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3 +torsion 13 13 13 41 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 +torsion 13 13 13 43 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3 +torsion 13 13 13 55 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 13 13 13 56 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 13 13 13 69 1.262 0.0 1 -0.198 180.0 2 0.465 0.0 3 +torsion 13 13 13 97 1.964 0.0 1 0.000 180.0 2 0.659 0.0 3 +torsion 13 13 13 98 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 15 13 13 36 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 +torsion 16 13 13 36 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 +torsion 19 13 13 36 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 +torsion 29 13 13 29 -0.550 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 29 13 13 36 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3 +torsion 30 13 13 30 -0.250 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 30 13 13 33 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 30 13 13 36 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 33 13 13 33 11.035 0.0 1 -0.968 180.0 2 0.270 0.0 3 +torsion 33 13 13 36 -1.013 0.0 1 -0.709 180.0 2 0.473 0.0 3 +torsion 33 13 13 38 -0.800 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 35 13 13 36 0.000 0.0 1 0.000 180.0 2 0.464 0.0 3 +torsion 35 13 13 38 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 +torsion 35 13 13 70 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 +torsion 36 13 13 36 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 36 13 13 37 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 +torsion 36 13 13 38 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 +torsion 36 13 13 41 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 36 13 13 43 0.000 0.0 1 0.000 180.0 2 0.384 0.0 3 +torsion 36 13 13 45 0.000 0.0 1 0.000 180.0 2 -0.582 0.0 3 +torsion 36 13 13 49 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 +torsion 36 13 13 52 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 +torsion 36 13 13 55 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 36 13 13 56 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 36 13 13 69 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 +#torsion 36 13 13 69 0.000 0.0 1 0.000 180.0 2 0.350 0.0 3 +torsion 36 13 13 70 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 +torsion 36 13 13 72 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 +torsion 36 13 13 73 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 +torsion 36 13 13 74 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 +torsion 36 13 13 77 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 +torsion 36 13 13 78 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 +torsion 36 13 13 92 0.000 0.0 1 0.000 180.0 2 -0.225 0.0 3 +torsion 36 13 13 94 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 36 13 13 97 0.000 0.0 1 0.000 180.0 2 0.464 0.0 3 +torsion 36 13 13 98 0.000 0.0 1 0.000 180.0 2 0.450 0.0 3 +torsion 36 13 13 99 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 +torsion 38 13 13 43 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 98 13 13 98 5.200 0.0 1 -0.500 180.0 2 0.000 0.0 3 +torsion 13 13 15 17 -0.759 0.0 1 -0.282 180.0 2 0.680 0.0 3 +torsion 36 13 15 17 0.000 0.0 1 0.000 180.0 2 0.480 0.0 3 +torsion 13 13 16 13 0.925 0.0 1 -0.576 180.0 2 0.677 0.0 3 +torsion 13 13 16 16 1.941 0.0 1 -0.836 180.0 2 0.935 0.0 3 +torsion 36 13 16 13 0.000 0.0 1 0.000 180.0 2 0.647 0.0 3 +torsion 36 13 16 16 0.000 0.0 1 0.000 180.0 2 0.558 0.0 3 +torsion 36 13 16 38 0.000 0.0 1 0.000 180.0 2 0.647 0.0 3 +torsion 0 13 18 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 36 13 18 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 13 19 18 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 36 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 13 29 13 -0.521 0.0 1 -2.018 180.0 2 1.996 0.0 3 +torsion 46 13 29 13 -0.500 0.0 1 -1.500 180.0 2 1.000 0.0 3 +torsion 47 13 29 13 -0.500 0.0 1 -1.500 180.0 2 1.000 0.0 3 +torsion 13 13 29 3 -1.220 0.0 1 -0.126 180.0 2 0.422 0.0 3 +torsion 13 13 29 13 0.650 0.0 1 -0.250 180.0 2 0.670 0.0 3 +torsion 13 13 29 54 -1.420 0.0 1 -0.620 180.0 2 0.100 0.0 3 +torsion 36 13 29 0 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 +torsion 36 13 29 3 0.000 0.0 1 0.000 180.0 2 0.198 0.0 3 +torsion 36 13 29 37 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 +torsion 36 13 29 38 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 +torsion 36 13 29 41 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 +torsion 36 13 29 54 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 13 13 33 13 0.416 0.0 1 -0.128 180.0 2 0.695 0.0 3 +#torsion 13 13 33 13 1.536 0.0 1 -0.128 180.0 2 0.695 0.0 3 +#torsion 13 13 33 13 1.464 0.0 1 -0.128 180.0 2 0.695 0.0 3 +torsion 13 13 33 34 -0.190 0.0 1 -0.417 180.0 2 0.418 0.0 3 +#torsion 13 13 33 34 0.000 0.0 1 4.000 180.0 2 0.000 0.0 3 +#torsion 13 13 33 34 0.200 0.0 1 -0.417 180.0 2 0.418 0.0 3 +#torsion 13 13 33 34 0.819 0.0 1 -0.417 180.0 2 0.418 0.0 3 +#torsion 13 13 33 34 1.522 0.0 1 -0.417 180.0 2 0.418 0.0 3 +torsion 36 13 33 13 0.000 0.0 1 0.000 180.0 2 0.560 0.0 3 +torsion 36 13 33 34 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 36 13 33 38 0.000 0.0 1 0.000 180.0 2 0.560 0.0 3 +torsion 0 13 35 34 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 3 13 35 3 -2.365 0.0 1 0.912 180.0 2 -0.850 0.0 3 +torsion 3 13 35 13 -1.737 0.0 1 1.251 180.0 2 -3.501 0.0 3 +torsion 3 13 35 34 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 35 3 0.000 0.0 1 0.462 180.0 2 0.000 0.0 3 +#torsion 13 13 35 3 -1.396 0.0 1 -0.427 180.0 2 0.000 0.0 3 +#torsion 13 13 35 3 1.130 0.0 1 -1.420 180.0 2 0.440 0.0 3 +torsion 13 13 35 13 4.753 0.0 1 -0.734 180.0 2 0.000 0.0 3 +#torsion 13 13 35 13 2.859 0.0 1 2.058 180.0 2 -11.266 0.0 3 +torsion 13 13 35 34 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 35 49 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 35 69 2.929 0.0 1 -2.533 180.0 2 0.497 0.0 3 +torsion 13 13 35 81 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 36 13 35 3 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +#torsion 36 13 35 3 0.000 0.0 1 0.000 180.0 2 -0.139 0.0 3 +torsion 36 13 35 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 36 13 35 34 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 36 13 35 38 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 36 13 35 69 1.362 0.0 1 -1.457 180.0 2 0.149 0.0 3 +torsion 38 13 35 49 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 13 37 13 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3 +torsion 0 13 37 36 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3 +torsion 0 13 37 37 0.500 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 13 37 40 0.500 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 13 37 37 0.500 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 37 13 2.817 0.0 1 -0.169 180.0 2 0.543 0.0 3 +torsion 13 13 37 37 0.346 0.0 1 0.405 180.0 2 -0.904 0.0 3 +torsion 13 13 37 40 0.346 0.0 1 0.405 180.0 2 -0.904 0.0 3 +torsion 36 13 37 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 36 13 37 36 0.000 0.0 1 0.000 180.0 2 0.318 0.0 3 +torsion 36 13 37 37 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 36 13 37 40 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 36 13 37 100 0.000 0.0 1 0.000 180.0 2 -0.250 0.0 3 +torsion 37 13 37 13 0.000 0.0 1 -8.000 180.0 2 0.000 0.0 3 +torsion 37 13 37 36 0.000 0.0 1 -8.000 180.0 2 0.000 0.0 3 +torsion 0 13 38 38 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 13 38 38 0.000 0.0 1 0.450 180.0 2 0.000 0.0 3 +torsion 13 13 38 38 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 38 46 -0.500 0.0 1 0.500 180.0 2 -0.500 0.0 3 +torsion 30 13 38 38 0.000 0.0 1 -0.400 180.0 2 0.000 0.0 3 +torsion 36 13 38 38 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 54 13 38 38 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 55 13 38 38 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 0 13 40 37 0.500 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 40 40 0.346 0.0 1 0.405 180.0 2 -0.904 0.0 3 +torsion 36 13 40 37 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 36 13 40 40 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 36 13 40 99 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 13 13 41 0 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3 +torsion 13 13 41 36 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 36 13 41 29 0.000 0.0 1 0.000 180.0 2 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0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 38 38 55 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 38 38 56 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 38 38 76 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 38 38 99 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 46 38 38 76 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 38 38 40 36 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 38 38 40 37 1.241 0.0 1 3.353 180.0 2 -0.286 0.0 3 +torsion 46 38 40 36 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 46 38 40 37 1.241 0.0 1 3.353 180.0 2 -0.286 0.0 3 +torsion 38 38 43 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 38 38 43 44 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 38 45 34 0.000 0.0 1 2.030 180.0 2 0.000 0.0 3 +torsion 38 38 45 34 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3 +torsion 45 38 45 13 0.000 0.0 1 7.936 180.0 2 0.000 0.0 3 +torsion 45 38 45 34 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3 +torsion 50 38 45 34 0.000 0.0 1 2.030 180.0 2 0.000 0.0 3 +torsion 0 38 46 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 38 38 46 38 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 38 46 38 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 38 50 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3 +torsion 0 38 69 32 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 38 38 69 13 0.000 0.0 1 -0.900 180.0 2 0.000 0.0 3 +torsion 38 38 69 35 1.656 0.0 1 -0.768 180.0 2 -0.117 0.0 3 +torsion 38 38 76 38 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 38 38 76 46 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 38 38 76 76 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 38 76 38 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 38 76 46 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 38 76 76 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 46 38 76 38 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 46 38 76 76 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 38 78 39 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 46 38 91 13 0.000 0.0 1 3.651 180.0 2 0.000 0.0 3 +torsion 38 38 92 93 0.000 0.0 1 1.150 180.0 2 0.000 0.0 3 +torsion 38 38 99 13 0.205 0.0 1 -0.531 180.0 2 0.000 0.0 3 +torsion 38 38 99 36 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 38 38 99 99 1.241 0.0 1 3.353 180.0 2 -0.286 0.0 3 +torsion 0 40 40 39 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 3 40 40 3 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 13 40 40 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 13 40 40 36 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 13 40 40 37 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +#torsion 13 40 40 37 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3 +torsion 36 40 40 36 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 36 40 40 37 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 37 40 40 37 1.423 0.0 1 4.055 180.0 2 0.858 0.0 3 +torsion 13 40 99 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 13 40 99 99 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 36 40 99 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 36 40 99 36 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 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+torsion 38 46 76 76 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 47 50 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 34 47 50 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 0 47 51 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 0 47 52 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 0 47 71 0 0.000 0.0 1 3.050 180.0 2 0.000 0.0 3 +torsion 0 47 72 0 0.000 0.0 1 4.650 180.0 2 0.000 0.0 3 +#torsion 0 47 72 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 0 47 72 39 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 34 47 72 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 0 47 74 0 0.000 0.0 1 2.800 180.0 2 0.000 0.0 3 +#torsion 0 47 74 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +#torsion 0 47 74 0 0.000 0.0 1 3.000 180.0 2 0.000 0.0 3 +torsion 34 47 74 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 51 47 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 74 47 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 0 50 50 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 50 51 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 50 70 0 0.000 0.0 1 3.350 180.0 2 0.000 0.0 3 +torsion 0 50 71 0 0.000 0.0 1 6.000 180.0 2 0.000 0.0 3 +torsion 0 50 77 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 38 50 77 74 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 50 50 77 74 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 51 51 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 0 51 52 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 0 51 72 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +#torsion 0 51 72 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 0 51 72 39 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 73 51 72 16 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 78 51 72 16 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 78 51 72 29 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 51 73 0 0.000 0.0 1 4.800 180.0 2 0.000 0.0 3 +torsion 72 51 73 39 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 72 51 73 74 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 51 74 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 0 51 78 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 72 51 78 74 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 70 74 0 0.000 0.0 1 13.050 180.0 2 0.000 0.0 3 +torsion 0 72 74 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 16 72 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 29 72 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 47 72 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 51 72 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 0 72 77 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +#torsion 0 72 77 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 0 73 74 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 +torsion 0 73 74 39 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 +torsion 39 73 74 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 +torsion 39 73 74 16 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 +torsion 39 73 74 39 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 +torsion 51 73 74 16 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 51 73 74 29 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 51 73 74 39 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 73 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 51 73 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 51 73 77 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 74 73 77 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 0 74 74 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 +torsion 0 74 74 39 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 +torsion 16 74 74 39 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 +torsion 39 74 74 39 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 +torsion 0 74 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 16 74 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 29 74 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 47 74 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 0 74 77 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 74 77 39 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 74 77 39 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 74 78 39 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 16 74 78 39 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 +torsion 16 74 78 51 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 29 74 78 51 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 74 78 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 39 74 78 51 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 38 76 76 38 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 38 76 76 46 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 38 76 77 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 38 76 78 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 38 76 78 51 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 46 76 78 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 0 77 77 29 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 0 77 77 47 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 0 77 77 77 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 +torsion 39 77 77 39 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 4 79 80 13 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 4 79 80 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 4 79 80 38 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 4 79 80 81 0.000 0.0 1 20.000 180.0 2 0.000 0.0 3 +torsion 81 79 80 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 81 79 80 34 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 81 79 80 38 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 81 79 80 81 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 +torsion 0 79 81 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 79 81 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 79 81 81 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 80 79 81 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 80 79 81 81 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 80 81 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 80 81 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 80 81 81 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 81 81 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 81 81 35 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 81 81 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 81 81 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 36 81 81 36 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 36 81 81 81 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 81 81 81 81 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 0 99 99 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 13 99 99 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 13 99 99 36 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 13 99 99 38 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 13 99 99 40 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 13 99 99 99 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 36 99 99 36 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 36 99 99 38 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 36 99 99 40 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 36 99 99 99 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 38 99 99 38 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 38 99 99 40 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 38 99 99 99 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 40 99 99 40 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 40 99 99 99 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 99 99 99 99 1.423 0.0 1 4.055 180.0 2 0.858 0.0 3 + + + ################################################################ + ## ## + ## Additional Torsional Parameter Values Used with OPLS-AA ## + ## ## + ## The torsions listed below were added to official OPLS-AA ## + ## to complete the set needed for proteins; the values were ## + ## obtained by analogy from the closest OPLS-AA torsions; ## + ## most of the added values are for HIP or N-terminal AAs ## + ## ## + ################################################################ + + +torsion 35 3 13 43 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3 +torsion 42 3 13 35 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 +torsion 3 13 13 43 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 3 13 13 73 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 +torsion 3 13 13 74 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 +torsion 3 13 13 75 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 +torsion 5 13 13 43 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3 +torsion 15 13 13 43 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 +torsion 16 13 13 43 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 +torsion 13 13 13 45 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3 +torsion 35 13 13 73 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 +torsion 43 13 13 73 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 35 13 13 74 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 +torsion 43 13 13 74 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 35 13 13 75 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 +torsion 36 13 13 75 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 +torsion 43 13 13 75 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 3 13 43 13 1.438 0.0 1 -0.124 180.0 2 0.264 0.0 3 +torsion 3 13 43 44 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3 +torsion 13 13 43 44 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3 +torsion 36 13 45 44 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 75 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 75 47 1.700 0.0 1 -0.600 180.0 2 0.000 0.0 3 +torsion 36 13 75 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 45 38 45 44 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3 +torsion 0 38 71 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 47 75 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 0 75 75 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 + + + ######################################## + ## ## + ## Atomic Partial Charge Parameters ## + ## ## + ######################################## + + +charge 1 -0.2200 +charge 2 0.2200 +charge 3 0.5500 +charge 4 -0.5000 +charge 5 -0.5800 +charge 6 0.0800 +charge 7 0.4500 +charge 8 0.0000 +charge 9 0.0000 +charge 10 0.0000 +charge 11 0.0000 +charge 12 0.0000 +charge 13 0.0000 +charge 14 0.0000 +charge 15 0.0000 +charge 16 0.0000 +charge 17 0.0000 +charge 18 0.0000 +charge 19 0.0000 +charge 20 -0.7000 +charge 21 0.4350 +charge 22 0.2650 +charge 23 0.2650 +charge 24 -0.4700 +charge 25 -0.4500 +charge 26 -0.4700 +charge 27 -0.3000 +charge 28 0.2350 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######################################## + ## ## + ## Biopolymer Atom Type Conversions ## + ## ## + ######################################## + + +biotype 1 N "Glycine" 177 +biotype 2 CA "Glycine" 162 +biotype 3 C "Glycine" 174 +biotype 4 HN "Glycine" 180 +biotype 5 O "Glycine" 175 +biotype 6 HA "Glycine" 82 +biotype 7 N "Alanine" 177 +biotype 8 CA "Alanine" 163 +biotype 9 C "Alanine" 174 +biotype 10 HN "Alanine" 180 +biotype 11 O "Alanine" 175 +biotype 12 HA "Alanine" 82 +biotype 13 CB "Alanine" 77 +biotype 14 HB "Alanine" 82 +biotype 15 N "Valine" 177 +biotype 16 CA "Valine" 163 +biotype 17 C "Valine" 174 +biotype 18 HN "Valine" 180 +biotype 19 O "Valine" 175 +biotype 20 HA "Valine" 82 +biotype 21 CB "Valine" 79 +biotype 22 HB "Valine" 82 +biotype 23 CG1 "Valine" 77 +biotype 24 HG1 "Valine" 82 +biotype 25 CG2 "Valine" 77 +biotype 26 HG2 "Valine" 82 +biotype 27 N "Leucine" 177 +biotype 28 CA "Leucine" 163 +biotype 29 C "Leucine" 174 +biotype 30 HN "Leucine" 180 +biotype 31 O "Leucine" 175 +biotype 32 HA "Leucine" 82 +biotype 33 CB "Leucine" 78 +biotype 34 HB "Leucine" 82 +biotype 35 CG "Leucine" 79 +biotype 36 HG "Leucine" 82 +biotype 37 CD1 "Leucine" 77 +biotype 38 HD1 "Leucine" 82 +biotype 39 CD2 "Leucine" 77 +biotype 40 HD2 "Leucine" 82 +biotype 41 N "Isoleucine" 177 +biotype 42 CA "Isoleucine" 163 +biotype 43 C "Isoleucine" 174 +biotype 44 HN "Isoleucine" 180 +biotype 45 O "Isoleucine" 175 +biotype 46 HA "Isoleucine" 82 +biotype 47 CB "Isoleucine" 79 +biotype 48 HB "Isoleucine" 82 +biotype 49 CG1 "Isoleucine" 77 +biotype 50 HG1 "Isoleucine" 82 +biotype 51 CG2 "Isoleucine" 78 +biotype 52 HG2 "Isoleucine" 82 +biotype 53 CD "Isoleucine" 77 +biotype 54 HD "Isoleucine" 82 +biotype 55 N "Serine" 177 +biotype 56 CA "Serine" 163 +biotype 57 C "Serine" 174 +biotype 58 HN "Serine" 180 +biotype 59 O "Serine" 175 +biotype 60 HA "Serine" 82 +biotype 61 CB "Serine" 96 +biotype 62 HB "Serine" 82 +biotype 63 OG "Serine" 93 +biotype 64 HG "Serine" 94 +biotype 65 N "Threonine" 177 +biotype 66 CA "Threonine" 163 +biotype 67 C "Threonine" 174 +biotype 68 HN "Threonine" 180 +biotype 69 O "Threonine" 175 +biotype 70 HA "Threonine" 82 +biotype 71 CB "Threonine" 97 +biotype 72 HB "Threonine" 82 +biotype 73 OG1 "Threonine" 93 +biotype 74 HG1 "Threonine" 94 +biotype 75 CG2 "Threonine" 77 +biotype 76 HG2 "Threonine" 82 +biotype 77 N "Cysteine (SH)" 177 +biotype 78 CA "Cysteine (SH)" 163 +biotype 79 C "Cysteine (SH)" 174 +biotype 80 HN "Cysteine (SH)" 180 +biotype 81 O "Cysteine (SH)" 175 +biotype 82 HA "Cysteine (SH)" 82 +biotype 83 CB "Cysteine (SH)" 145 +biotype 84 HB "Cysteine (SH)" 82 +biotype 85 SG "Cysteine (SH)" 139 +biotype 86 HG "Cysteine (SH)" 143 +biotype 87 N "Cystine (SS)" 177 +biotype 88 CA "Cystine (SS)" 163 +biotype 89 C "Cystine (SS)" 174 +biotype 90 HN "Cystine (SS)" 180 +biotype 91 O "Cystine (SS)" 175 +biotype 92 HA "Cystine (SS)" 82 +biotype 93 CB "Cystine (SS)" 153 +biotype 94 HB "Cystine (SS)" 82 +biotype 95 SG "Cystine (SS)" 142 +biotype 96 N "Cysteine (S-)" -1 +biotype 97 CA "Cysteine (S-)" -1 +biotype 98 C "Cysteine (S-)" -1 +biotype 99 HN "Cysteine (S-)" -1 +biotype 100 O "Cysteine (S-)" -1 +biotype 101 HA "Cysteine (S-)" -1 +biotype 102 CB "Cysteine (S-)" -1 +biotype 103 HB "Cysteine (S-)" -1 +biotype 104 SG "Cysteine (S-)" -1 +biotype 105 N "Proline" 178 +biotype 106 CA "Proline" 185 +biotype 107 C "Proline" 174 +biotype 108 O "Proline" 175 +biotype 109 HA "Proline" 82 +biotype 110 CB "Proline" 78 +biotype 111 HB "Proline" 82 +biotype 112 CG "Proline" 78 +biotype 113 HG "Proline" 82 +biotype 114 CD "Proline" 184 +biotype 115 HD "Proline" 82 +biotype 116 N "Phenylalanine" 177 +biotype 117 CA "Phenylalanine" 163 +biotype 118 C "Phenylalanine" 174 +biotype 119 HN "Phenylalanine" 180 +biotype 120 O "Phenylalanine" 175 +biotype 121 HA "Phenylalanine" 82 +biotype 122 CB "Phenylalanine" 91 +biotype 123 HB "Phenylalanine" 82 +biotype 124 CG "Phenylalanine" 87 +biotype 125 CD "Phenylalanine" 87 +biotype 126 HD "Phenylalanine" 88 +biotype 127 CE "Phenylalanine" 87 +biotype 128 HE "Phenylalanine" 88 +biotype 129 CZ "Phenylalanine" 87 +biotype 130 HZ "Phenylalanine" 88 +biotype 131 N "Tyrosine" 177 +biotype 132 CA "Tyrosine" 163 +biotype 133 C "Tyrosine" 174 +biotype 134 HN "Tyrosine" 180 +biotype 135 O "Tyrosine" 175 +biotype 136 HA "Tyrosine" 82 +biotype 137 CB "Tyrosine" 91 +biotype 138 HB "Tyrosine" 82 +biotype 139 CG "Tyrosine" 87 +biotype 140 CD "Tyrosine" 87 +biotype 141 HD "Tyrosine" 88 +biotype 142 CE "Tyrosine" 87 +biotype 143 HE "Tyrosine" 88 +biotype 144 CZ "Tyrosine" 105 +biotype 145 OH "Tyrosine" 106 +biotype 146 HH "Tyrosine" 107 +biotype 147 N "Tyrosine (O-)" -1 +biotype 148 CA "Tyrosine (O-)" -1 +biotype 149 C "Tyrosine (O-)" -1 +biotype 150 HN "Tyrosine (O-)" -1 +biotype 151 O "Tyrosine (O-)" -1 +biotype 152 HA "Tyrosine (O-)" -1 +biotype 153 CB "Tyrosine (O-)" -1 +biotype 154 HB "Tyrosine (O-)" -1 +biotype 155 CG "Tyrosine (O-)" -1 +biotype 156 CD "Tyrosine (O-)" -1 +biotype 157 HD "Tyrosine (O-)" -1 +biotype 158 CE "Tyrosine (O-)" -1 +biotype 159 HE "Tyrosine (O-)" -1 +biotype 160 CZ "Tyrosine (O-)" -1 +biotype 161 OH "Tyrosine (O-)" -1 +biotype 162 N "Tryptophan" 177 +biotype 163 CA "Tryptophan" 163 +biotype 164 C "Tryptophan" 174 +biotype 165 HN "Tryptophan" 180 +biotype 166 O "Tryptophan" 175 +biotype 167 HA "Tryptophan" 82 +biotype 168 CB "Tryptophan" 78 +biotype 169 HB "Tryptophan" 82 +biotype 170 CG "Tryptophan" 438 +biotype 171 CD1 "Tryptophan" 452 +biotype 172 HD1 "Tryptophan" 88 +biotype 173 CD2 "Tryptophan" 439 +biotype 174 NE1 "Tryptophan" 441 +biotype 175 HE1 "Tryptophan" 442 +biotype 176 CE2 "Tryptophan" 440 +biotype 177 CE3 "Tryptophan" 87 +biotype 178 HE3 "Tryptophan" 88 +biotype 179 CZ2 "Tryptophan" 87 +biotype 180 HZ2 "Tryptophan" 88 +biotype 181 CZ3 "Tryptophan" 87 +biotype 182 HZ3 "Tryptophan" 88 +biotype 183 CH2 "Tryptophan" 87 +biotype 184 HH2 "Tryptophan" 88 +biotype 185 N "Histidine (+)" 177 +biotype 186 CA "Histidine (+)" 163 +biotype 187 C "Histidine (+)" 174 +biotype 188 HN "Histidine (+)" 180 +biotype 189 O "Histidine (+)" 175 +biotype 190 HA "Histidine (+)" 82 +biotype 191 CB "Histidine (+)" 443 +biotype 192 HB "Histidine (+)" 82 +biotype 193 CG "Histidine (+)" 448 +biotype 194 ND1 "Histidine (+)" 450 +biotype 195 HD1 "Histidine (+)" 451 +biotype 196 CD2 "Histidine (+)" 448 +biotype 197 HD2 "Histidine (+)" 88 +biotype 198 CE1 "Histidine (+)" 447 +biotype 199 HE1 "Histidine (+)" 88 +biotype 200 NE2 "Histidine (+)" 450 +biotype 201 HE2 "Histidine (+)" 451 +biotype 202 N "Histidine (HD)" 177 +biotype 203 CA "Histidine (HD)" 163 +biotype 204 C "Histidine (HD)" 174 +biotype 205 HN "Histidine (HD)" 180 +biotype 206 O "Histidine (HD)" 175 +biotype 207 HA "Histidine (HD)" 82 +biotype 208 CB "Histidine (HD)" 443 +biotype 209 HB "Histidine (HD)" 82 +biotype 210 CG "Histidine (HD)" 446 +biotype 211 ND1 "Histidine (HD)" 441 +biotype 212 HD1 "Histidine (HD)" 442 +biotype 213 CD2 "Histidine (HD)" 445 +biotype 214 HD2 "Histidine (HD)" 88 +biotype 215 CE1 "Histidine (HD)" 444 +biotype 216 HE1 "Histidine (HD)" 88 +biotype 217 NE2 "Histidine (HD)" 449 +biotype 218 N "Histidine (HE)" 177 +biotype 219 CA "Histidine (HE)" 163 +biotype 220 C "Histidine (HE)" 174 +biotype 221 HN "Histidine (HE)" 180 +biotype 222 O "Histidine (HE)" 175 +biotype 223 HA "Histidine (HE)" 82 +biotype 224 CB "Histidine (HE)" 443 +biotype 225 HB "Histidine (HE)" 82 +biotype 226 CG "Histidine (HE)" 445 +biotype 227 ND1 "Histidine (HE)" 449 +biotype 228 CD2 "Histidine (HE)" 446 +biotype 229 HD2 "Histidine (HE)" 88 +biotype 230 CE1 "Histidine (HE)" 444 +biotype 231 HE1 "Histidine (HE)" 88 +biotype 232 NE2 "Histidine (HE)" 441 +biotype 233 HE2 "Histidine (HE)" 442 +biotype 234 N "Aspartic Acid" 177 +biotype 235 CA "Aspartic Acid" 163 +biotype 236 C "Aspartic Acid" 174 +biotype 237 HN "Aspartic Acid" 180 +biotype 238 O "Aspartic Acid" 175 +biotype 239 HA "Aspartic Acid" 82 +biotype 240 CB "Aspartic Acid" 213 +biotype 241 HB "Aspartic Acid" 82 +biotype 242 CG "Aspartic Acid" 210 +biotype 243 OD "Aspartic Acid" 211 +biotype 244 N "Aspartic Acid (COOH)" -1 +biotype 245 CA "Aspartic Acid (COOH)" -1 +biotype 246 C "Aspartic Acid (COOH)" -1 +biotype 247 HN "Aspartic Acid (COOH)" -1 +biotype 248 O "Aspartic Acid (COOH)" -1 +biotype 249 HA "Aspartic Acid (COOH)" -1 +biotype 250 CB "Aspartic Acid (COOH)" -1 +biotype 251 HB "Aspartic Acid (COOH)" -1 +biotype 252 CG "Aspartic Acid (COOH)" -1 +biotype 253 OD1 "Aspartic Acid (COOH)" -1 +biotype 254 OD2 "Aspartic Acid (COOH)" -1 +biotype 255 HD2 "Aspartic Acid (COOH)" -1 +biotype 256 N "Asparagine" 177 +biotype 257 CA "Asparagine" 163 +biotype 258 C "Asparagine" 174 +biotype 259 HN "Asparagine" 180 +biotype 260 O "Asparagine" 175 +biotype 261 HA "Asparagine" 82 +biotype 262 CB "Asparagine" 78 +biotype 263 HB "Asparagine" 82 +biotype 264 CG "Asparagine" 174 +biotype 265 OD1 "Asparagine" 175 +biotype 266 ND2 "Asparagine" 176 +biotype 267 HD2 "Asparagine" 179 +biotype 268 N "Glutamic Acid" 177 +biotype 269 CA "Glutamic Acid" 163 +biotype 270 C "Glutamic Acid" 174 +biotype 271 HN "Glutamic Acid" 180 +biotype 272 O "Glutamic Acid" 175 +biotype 273 HA "Glutamic Acid" 82 +biotype 274 CB "Glutamic Acid" 78 +biotype 275 HB "Glutamic Acid" 82 +biotype 276 CG "Glutamic Acid" 213 +biotype 277 HG "Glutamic Acid" 82 +biotype 278 CD "Glutamic Acid" 210 +biotype 279 OE "Glutamic Acid" 211 +biotype 280 N "Glutamic Acid (COOH)" -1 +biotype 281 CA "Glutamic Acid (COOH)" -1 +biotype 282 C "Glutamic Acid (COOH)" -1 +biotype 283 HN "Glutamic Acid (COOH)" -1 +biotype 284 O "Glutamic Acid (COOH)" -1 +biotype 285 HA "Glutamic Acid (COOH)" -1 +biotype 286 CB "Glutamic Acid (COOH)" -1 +biotype 287 HB "Glutamic Acid (COOH)" -1 +biotype 288 CG "Glutamic Acid (COOH)" -1 +biotype 289 HG "Glutamic Acid (COOH)" -1 +biotype 290 CD "Glutamic Acid (COOH)" -1 +biotype 291 OE1 "Glutamic Acid (COOH)" -1 +biotype 292 OE2 "Glutamic Acid (COOH)" -1 +biotype 293 HE2 "Glutamic Acid (COOH)" -1 +biotype 294 N "Glutamine" 177 +biotype 295 CA "Glutamine" 163 +biotype 296 C "Glutamine" 174 +biotype 297 HN "Glutamine" 180 +biotype 298 O "Glutamine" 175 +biotype 299 HA "Glutamine" 82 +biotype 300 CB "Glutamine" 78 +biotype 301 HB "Glutamine" 82 +biotype 302 CG "Glutamine" 78 +biotype 303 HG "Glutamine" 82 +biotype 304 CD "Glutamine" 174 +biotype 305 OE1 "Glutamine" 175 +biotype 306 NE2 "Glutamine" 176 +biotype 307 HE2 "Glutamine" 179 +biotype 308 N "Methionine" 177 +biotype 309 CA "Methionine" 163 +biotype 310 C "Methionine" 174 +biotype 311 HN "Methionine" 180 +biotype 312 O "Methionine" 175 +biotype 313 HA "Methionine" 82 +biotype 314 CB "Methionine" 78 +biotype 315 HB "Methionine" 82 +biotype 316 CG "Methionine" 149 +biotype 317 HG "Methionine" 82 +biotype 318 SD "Methionine" 141 +biotype 319 CE "Methionine" 148 +biotype 320 HE "Methionine" 82 +biotype 321 N "Lysine" 177 +biotype 322 CA "Lysine" 163 +biotype 323 C "Lysine" 174 +biotype 324 HN "Lysine" 180 +biotype 325 O "Lysine" 175 +biotype 326 HA "Lysine" 82 +biotype 327 CB "Lysine" 78 +biotype 328 HB "Lysine" 82 +biotype 329 CG "Lysine" 78 +biotype 330 HG "Lysine" 82 +biotype 331 CD "Lysine" 78 +biotype 332 HD "Lysine" 82 +biotype 333 CE "Lysine" 232 +biotype 334 HE "Lysine" 82 +biotype 335 NZ "Lysine" 227 +biotype 336 HZ "Lysine" 230 +biotype 337 N "Lysine (NH2)" -1 +biotype 338 CA "Lysine (NH2)" -1 +biotype 339 C "Lysine (NH2)" -1 +biotype 340 HN "Lysine (NH2)" -1 +biotype 341 O "Lysine (NH2)" -1 +biotype 342 HA "Lysine (NH2)" -1 +biotype 343 CB "Lysine (NH2)" -1 +biotype 344 HB "Lysine (NH2)" -1 +biotype 345 CG "Lysine (NH2)" -1 +biotype 346 HG "Lysine (NH2)" -1 +biotype 347 CD "Lysine (NH2)" -1 +biotype 348 HD "Lysine (NH2)" -1 +biotype 349 CE "Lysine (NH2)" -1 +biotype 350 HE "Lysine (NH2)" -1 +biotype 351 NZ "Lysine (NH2)" -1 +biotype 352 HZ "Lysine (NH2)" -1 +biotype 353 N "Arginine" 177 +biotype 354 CA "Arginine" 163 +biotype 355 C "Arginine" 174 +biotype 356 HN "Arginine" 180 +biotype 357 O "Arginine" 175 +biotype 358 HA "Arginine" 82 +biotype 359 CB "Arginine" 78 +biotype 360 HB "Arginine" 82 +biotype 361 CG "Arginine" 248 +biotype 362 HG "Arginine" 82 +biotype 363 CD "Arginine" 247 +biotype 364 HD "Arginine" 82 +biotype 365 NE "Arginine" 243 +biotype 366 HE "Arginine" 244 +biotype 367 CZ "Arginine" 242 +biotype 368 NH "Arginine" 240 +biotype 369 HH "Arginine" 241 +biotype 370 N "Ornithine" 177 +biotype 371 CA "Ornithine" 163 +biotype 372 C "Ornithine" 174 +biotype 373 HN "Ornithine" 180 +biotype 374 O "Ornithine" 175 +biotype 375 HA "Ornithine" 82 +biotype 376 CB "Ornithine" 78 +biotype 377 HB "Ornithine" 82 +biotype 378 CG "Ornithine" 78 +biotype 379 HG "Ornithine" 82 +biotype 380 CD "Ornithine" 232 +biotype 381 HD "Ornithine" 82 +biotype 382 NE "Ornithine" 227 +biotype 383 HE "Ornithine" 230 +biotype 384 N "MethylAlanine (AIB)" 177 +biotype 385 CA "MethylAlanine (AIB)" 164 +biotype 386 C "MethylAlanine (AIB)" 174 +biotype 387 HN "MethylAlanine (AIB)" 180 +biotype 388 O "MethylAlanine (AIB)" 175 +biotype 389 CB "MethylAlanine (AIB)" 77 +biotype 390 HB "MethylAlanine (AIB)" 82 +biotype 391 N "Pyroglutamic Acid" 177 +biotype 392 CA "Pyroglutamic Acid" 163 +biotype 393 C "Pyroglutamic Acid" 174 +biotype 394 HN "Pyroglutamic Acid" 180 +biotype 395 O "Pyroglutamic Acid" 175 +biotype 396 HA "Pyroglutamic Acid" 82 +biotype 397 CB "Pyroglutamic Acid" 78 +biotype 398 HB "Pyroglutamic Acid" 82 +biotype 399 CG "Pyroglutamic Acid" 213 +biotype 400 HG "Pyroglutamic Acid" 82 +biotype 401 CD "Pyroglutamic Acid" 174 +biotype 402 OE "Pyroglutamic Acid" 175 +biotype 403 C "Formyl N-Terminus" 174 +biotype 404 H "Formyl N-Terminus" 218 +biotype 405 O "Formyl N-Terminus" 175 +biotype 406 CH3 "Acetyl N-Terminus" 77 +biotype 407 H "Acetyl N-Terminus" 82 +biotype 408 C "Acetyl N-Terminus" 174 +biotype 409 O "Acetyl N-Terminus" 175 +biotype 410 N "Amide C-Terminus" 176 +biotype 411 HN "Amide C-Terminus" 179 +biotype 412 N "N-MeAmide C-Terminus" 177 +biotype 413 HN "N-MeAmide C-Terminus" 180 +biotype 414 CH3 "N-MeAmide C-Terminus" 181 +biotype 415 H "N-MeAmide C-Terminus" 82 +biotype 416 N "N-Terminal GLY" 227 +biotype 417 CA "N-Terminal GLY" 232 +biotype 418 C "N-Terminal GLY" 174 +biotype 419 HN "N-Terminal GLY" 230 +biotype 420 O "N-Terminal GLY" 175 +biotype 421 HA "N-Terminal GLY" 82 +biotype 422 N "N-Terminal ALA" 227 +biotype 423 CA "N-Terminal ALA" 233 +biotype 424 C "N-Terminal ALA" 174 +biotype 425 HN "N-Terminal ALA" 230 +biotype 426 O "N-Terminal ALA" 175 +biotype 427 HA "N-Terminal ALA" 82 +biotype 428 N "N-Terminal VAL" 227 +biotype 429 CA "N-Terminal VAL" 233 +biotype 430 C "N-Terminal VAL" 174 +biotype 431 HN "N-Terminal VAL" 230 +biotype 432 O "N-Terminal VAL" 175 +biotype 433 HA "N-Terminal VAL" 82 +biotype 434 N "N-Terminal LEU" 227 +biotype 435 CA "N-Terminal LEU" 233 +biotype 436 C "N-Terminal LEU" 174 +biotype 437 HN "N-Terminal LEU" 230 +biotype 438 O "N-Terminal LEU" 175 +biotype 439 HA "N-Terminal LEU" 82 +biotype 440 N "N-Terminal ILE" 227 +biotype 441 CA "N-Terminal ILE" 233 +biotype 442 C "N-Terminal ILE" 174 +biotype 443 HN "N-Terminal ILE" 230 +biotype 444 O "N-Terminal ILE" 175 +biotype 445 HA "N-Terminal ILE" 82 +biotype 446 N "N-Terminal SER" 227 +biotype 447 CA "N-Terminal SER" 233 +biotype 448 C "N-Terminal SER" 174 +biotype 449 HN "N-Terminal SER" 230 +biotype 450 O "N-Terminal SER" 175 +biotype 451 HA "N-Terminal SER" 82 +biotype 452 N "N-Terminal THR" 227 +biotype 453 CA "N-Terminal THR" 233 +biotype 454 C "N-Terminal THR" 174 +biotype 455 HN "N-Terminal THR" 230 +biotype 456 O "N-Terminal THR" 175 +biotype 457 HA "N-Terminal THR" 82 +biotype 458 N "N-Terminal CYS (SH)" 227 +biotype 459 CA "N-Terminal CYS (SH)" 233 +biotype 460 C "N-Terminal CYS (SH)" 174 +biotype 461 HN "N-Terminal CYS (SH)" 230 +biotype 462 O "N-Terminal CYS (SH)" 175 +biotype 463 HA "N-Terminal CYS (SH)" 82 +biotype 464 N "N-Terminal CYX (SS)" 227 +biotype 465 CA "N-Terminal CYX (SS)" 233 +biotype 466 C "N-Terminal CYX (SS)" 174 +biotype 467 HN "N-Terminal CYX (SS)" 230 +biotype 468 O "N-Terminal CYX (SS)" 175 +biotype 469 HA "N-Terminal CYX (SS)" 82 +biotype 470 N "N-Terminal CYD (S-)" -1 +biotype 471 CA "N-Terminal CYD (S-)" -1 +biotype 472 C "N-Terminal CYD (S-)" -1 +biotype 473 HN "N-Terminal CYD (S-)" -1 +biotype 474 O "N-Terminal CYD (S-)" -1 +biotype 475 HA "N-Terminal CYD (S-)" -1 +biotype 476 N "N-Terminal PRO" 249 +biotype 477 CA "N-Terminal PRO" 235 +biotype 478 C "N-Terminal PRO" 174 +biotype 479 HN "N-Terminal PRO" 250 +biotype 480 O "N-Terminal PRO" 175 +biotype 481 HA "N-Terminal PRO" 82 +biotype 482 CD "N-Terminal PRO" 236 +biotype 483 HD "N-Terminal PRO" 82 +biotype 484 N "N-Terminal PHE" 227 +biotype 485 CA "N-Terminal PHE" 233 +biotype 486 C "N-Terminal PHE" 174 +biotype 487 HN "N-Terminal PHE" 230 +biotype 488 O "N-Terminal PHE" 175 +biotype 489 HA "N-Terminal PHE" 82 +biotype 490 N "N-Terminal TYR" 227 +biotype 491 CA "N-Terminal TYR" 233 +biotype 492 C "N-Terminal TYR" 174 +biotype 493 HN "N-Terminal TYR" 230 +biotype 494 O "N-Terminal TYR" 175 +biotype 495 HA "N-Terminal TYR" 82 +biotype 496 N "N-Terminal TYD (O-)" -1 +biotype 497 CA "N-Terminal TYD (O-)" -1 +biotype 498 C "N-Terminal TYD (O-)" -1 +biotype 499 HN "N-Terminal TYD (O-)" -1 +biotype 500 O "N-Terminal TYD (O-)" -1 +biotype 501 HA "N-Terminal TYD (O-)" -1 +biotype 502 N "N-Terminal TRP" 227 +biotype 503 CA "N-Terminal TRP" 233 +biotype 504 C "N-Terminal TRP" 174 +biotype 505 HN "N-Terminal TRP" 230 +biotype 506 O "N-Terminal TRP" 175 +biotype 507 HA "N-Terminal TRP" 82 +biotype 508 N "N-Terminal HIS (+)" 227 +biotype 509 CA "N-Terminal HIS (+)" 233 +biotype 510 C "N-Terminal HIS (+)" 174 +biotype 511 HN "N-Terminal HIS (+)" 230 +biotype 512 O "N-Terminal HIS (+)" 175 +biotype 513 HA "N-Terminal HIS (+)" 82 +biotype 514 N "N-Terminal HIS (HD)" 227 +biotype 515 CA "N-Terminal HIS (HD)" 233 +biotype 516 C "N-Terminal HIS (HD)" 174 +biotype 517 HN "N-Terminal HIS (HD)" 230 +biotype 518 O "N-Terminal HIS (HD)" 175 +biotype 519 HA "N-Terminal HIS (HD)" 82 +biotype 520 N "N-Terminal HIS (HE)" 227 +biotype 521 CA "N-Terminal HIS (HE)" 233 +biotype 522 C "N-Terminal HIS (HE)" 174 +biotype 523 HN "N-Terminal HIS (HE)" 230 +biotype 524 O "N-Terminal HIS (HE)" 175 +biotype 525 HA "N-Terminal HIS (HE)" 82 +biotype 526 N "N-Terminal ASP" 227 +biotype 527 CA "N-Terminal ASP" 233 +biotype 528 C "N-Terminal ASP" 174 +biotype 529 HN "N-Terminal ASP" 230 +biotype 530 O "N-Terminal ASP" 175 +biotype 531 HA "N-Terminal ASP" 82 +biotype 532 N "N-Terminal ASH (COOH)" -1 +biotype 533 CA "N-Terminal ASH (COOH)" -1 +biotype 534 C "N-Terminal ASH (COOH)" -1 +biotype 535 HN "N-Terminal ASH (COOH)" -1 +biotype 536 O "N-Terminal ASH (COOH)" -1 +biotype 537 HA "N-Terminal ASH (COOH)" -1 +biotype 538 N "N-Terminal ASN" 227 +biotype 539 CA "N-Terminal ASN" 233 +biotype 540 C "N-Terminal ASN" 174 +biotype 541 HN "N-Terminal ASN" 230 +biotype 542 O "N-Terminal ASN" 175 +biotype 543 HA "N-Terminal ASN" 82 +biotype 544 N "N-Terminal GLU" 227 +biotype 545 CA "N-Terminal GLU" 233 +biotype 546 C "N-Terminal GLU" 174 +biotype 547 HN "N-Terminal GLU" 230 +biotype 548 O "N-Terminal GLU" 175 +biotype 549 HA "N-Terminal GLU" 82 +biotype 550 N "N-Terminal GLH (COOH)" -1 +biotype 551 CA "N-Terminal GLH (COOH)" -1 +biotype 552 C "N-Terminal GLH (COOH)" -1 +biotype 553 HN "N-Terminal GLH (COOH)" -1 +biotype 554 O "N-Terminal GLH (COOH)" -1 +biotype 555 HA "N-Terminal GLH (COOH)" -1 +biotype 556 N "N-Terminal GLN" 227 +biotype 557 CA "N-Terminal GLN" 233 +biotype 558 C "N-Terminal GLN" 174 +biotype 559 HN "N-Terminal GLN" 230 +biotype 560 O "N-Terminal GLN" 175 +biotype 561 HA "N-Terminal GLN" 82 +biotype 562 N "N-Terminal MET" 227 +biotype 563 CA "N-Terminal MET" 233 +biotype 564 C "N-Terminal MET" 174 +biotype 565 HN "N-Terminal MET" 230 +biotype 566 O "N-Terminal MET" 175 +biotype 567 HA "N-Terminal MET" 82 +biotype 568 N "N-Terminal LYS" 227 +biotype 569 CA "N-Terminal LYS" 233 +biotype 570 C "N-Terminal LYS" 174 +biotype 571 HN "N-Terminal LYS" 230 +biotype 572 O "N-Terminal LYS" 175 +biotype 573 HA "N-Terminal LYS" 82 +biotype 574 N "N-Terminal LYD (NH2)" -1 +biotype 575 CA "N-Terminal LYD (NH2)" -1 +biotype 576 C "N-Terminal LYD (NH2)" -1 +biotype 577 HN "N-Terminal LYD (NH2)" -1 +biotype 578 O "N-Terminal LYD (NH2)" -1 +biotype 579 HA "N-Terminal LYD (NH2)" -1 +biotype 580 N "N-Terminal ARG" 227 +biotype 581 CA "N-Terminal ARG" 233 +biotype 582 C "N-Terminal ARG" 174 +biotype 583 HN "N-Terminal ARG" 230 +biotype 584 O "N-Terminal ARG" 175 +biotype 585 HA "N-Terminal ARG" 82 +biotype 586 N "N-Terminal ORN" 227 +biotype 587 CA "N-Terminal ORN" 233 +biotype 588 C "N-Terminal ORN" 174 +biotype 589 HN "N-Terminal ORN" 230 +biotype 590 O "N-Terminal ORN" 175 +biotype 591 HA "N-Terminal ORN" 82 +biotype 592 N "N-Terminal AIB" 227 +biotype 593 CA "N-Terminal AIB" 234 +biotype 594 C "N-Terminal AIB" 174 +biotype 595 HN "N-Terminal AIB" 230 +biotype 596 O "N-Terminal AIB" 175 +biotype 597 N "C-Terminal GLY" 177 +biotype 598 CA "C-Terminal GLY" 223 +biotype 599 C "C-Terminal GLY" 210 +biotype 600 HN "C-Terminal GLY" 180 +biotype 601 OXT "C-Terminal GLY" 211 +biotype 602 HA "C-Terminal GLY" 82 +biotype 603 N "C-Terminal ALA" 177 +biotype 604 CA "C-Terminal ALA" 222 +biotype 605 C "C-Terminal ALA" 210 +biotype 606 HN "C-Terminal ALA" 180 +biotype 607 OXT "C-Terminal ALA" 211 +biotype 608 HA "C-Terminal ALA" 82 +biotype 609 N "C-Terminal VAL" 177 +biotype 610 CA "C-Terminal VAL" 222 +biotype 611 C "C-Terminal VAL" 210 +biotype 612 HN "C-Terminal VAL" 180 +biotype 613 OXT "C-Terminal VAL" 211 +biotype 614 HA "C-Terminal VAL" 82 +biotype 615 N "C-Terminal LEU" 177 +biotype 616 CA "C-Terminal LEU" 222 +biotype 617 C "C-Terminal LEU" 210 +biotype 618 HN "C-Terminal LEU" 180 +biotype 619 OXT "C-Terminal LEU" 211 +biotype 620 HA "C-Terminal LEU" 82 +biotype 621 N "C-Terminal ILE" 177 +biotype 622 CA "C-Terminal ILE" 222 +biotype 623 C "C-Terminal ILE" 210 +biotype 624 HN "C-Terminal ILE" 180 +biotype 625 OXT "C-Terminal ILE" 211 +biotype 626 HA "C-Terminal ILE" 82 +biotype 627 N "C-Terminal SER" 177 +biotype 628 CA "C-Terminal SER" 222 +biotype 629 C "C-Terminal SER" 210 +biotype 630 HN "C-Terminal SER" 180 +biotype 631 OXT "C-Terminal SER" 211 +biotype 632 HA "C-Terminal SER" 82 +biotype 633 N "C-Terminal THR" 177 +biotype 634 CA "C-Terminal THR" 222 +biotype 635 C "C-Terminal THR" 210 +biotype 636 HN "C-Terminal THR" 180 +biotype 637 OXT "C-Terminal THR" 211 +biotype 638 HA "C-Terminal THR" 82 +biotype 639 N "C-Terminal CYS (SH)" 177 +biotype 640 CA "C-Terminal CYS (SH)" 222 +biotype 641 C "C-Terminal CYS (SH)" 210 +biotype 642 HN "C-Terminal CYS (SH)" 180 +biotype 643 OXT "C-Terminal CYS (SH)" 211 +biotype 644 HA "C-Terminal CYS (SH)" 82 +biotype 645 N "C-Terminal CYX (SS)" 177 +biotype 646 CA "C-Terminal CYX (SS)" 222 +biotype 647 C "C-Terminal CYX (SS)" 210 +biotype 648 HN "C-Terminal CYX (SS)" 180 +biotype 649 OXT "C-Terminal CYX (SS)" 211 +biotype 650 HA "C-Terminal CYX (SS)" 82 +biotype 651 N "C-Terminal CYD (S-)" -1 +biotype 652 CA "C-Terminal CYD (S-)" -1 +biotype 653 C "C-Terminal CYD (S-)" -1 +biotype 654 HN "C-Terminal CYD (S-)" -1 +biotype 655 OXT "C-Terminal CYD (S-)" -1 +biotype 656 HA "C-Terminal CYD (S-)" -1 +biotype 657 N "C-Terminal PRO" 178 +biotype 658 CA "C-Terminal PRO" 225 +biotype 659 C "C-Terminal PRO" 210 +biotype 660 OXT "C-Terminal PRO" 211 +biotype 661 HA "C-Terminal PRO" 82 +biotype 662 N "C-Terminal PHE" 177 +biotype 663 CA "C-Terminal PHE" 222 +biotype 664 C "C-Terminal PHE" 210 +biotype 665 HN "C-Terminal PHE" 180 +biotype 666 OXT "C-Terminal PHE" 211 +biotype 667 HA "C-Terminal PHE" 82 +biotype 668 N "C-Terminal TYR" 177 +biotype 669 CA "C-Terminal TYR" 222 +biotype 670 C "C-Terminal TYR" 210 +biotype 671 HN "C-Terminal TYR" 180 +biotype 672 OXT "C-Terminal TYR" 211 +biotype 673 HA "C-Terminal TYR" 82 +biotype 674 N "C-Terminal TYD (O-)" -1 +biotype 675 CA "C-Terminal TYD (O-)" -1 +biotype 676 C "C-Terminal TYD (O-)" -1 +biotype 677 HN "C-Terminal TYD (O-)" -1 +biotype 678 OXT "C-Terminal TYD (O-)" -1 +biotype 679 HA "C-Terminal TYD (O-)" -1 +biotype 680 N "C-Terminal TRP" 177 +biotype 681 CA "C-Terminal TRP" 222 +biotype 682 C "C-Terminal TRP" 210 +biotype 683 HN "C-Terminal TRP" 180 +biotype 684 OXT "C-Terminal TRP" 211 +biotype 685 HA "C-Terminal TRP" 82 +biotype 686 N "C-Terminal HIS (+)" 177 +biotype 687 CA "C-Terminal HIS (+)" 222 +biotype 688 C "C-Terminal HIS (+)" 210 +biotype 689 HN "C-Terminal HIS (+)" 180 +biotype 690 OXT "C-Terminal HIS (+)" 211 +biotype 691 HA "C-Terminal HIS (+)" 82 +biotype 692 N "C-Terminal HIS (HD)" 177 +biotype 693 CA "C-Terminal HIS (HD)" 222 +biotype 694 C "C-Terminal HIS (HD)" 210 +biotype 695 HN "C-Terminal HIS (HD)" 180 +biotype 696 OXT "C-Terminal HIS (HD)" 211 +biotype 697 HA "C-Terminal HIS (HD)" 82 +biotype 698 N "C-Terminal HIS (HE)" 177 +biotype 699 CA "C-Terminal HIS (HE)" 222 +biotype 700 C "C-Terminal HIS (HE)" 210 +biotype 701 HN "C-Terminal HIS (HE)" 180 +biotype 702 OXT "C-Terminal HIS (HE)" 211 +biotype 703 HA "C-Terminal HIS (HE)" 82 +biotype 704 N "C-Terminal ASP" 177 +biotype 705 CA "C-Terminal ASP" 222 +biotype 706 C "C-Terminal ASP" 210 +biotype 707 HN "C-Terminal ASP" 180 +biotype 708 OXT "C-Terminal ASP" 211 +biotype 709 HA "C-Terminal ASP" 82 +biotype 710 N "C-Terminal ASH (COOH)" -1 +biotype 711 CA "C-Terminal ASH (COOH)" -1 +biotype 712 C "C-Terminal ASH (COOH)" -1 +biotype 713 HN "C-Terminal ASH (COOH)" -1 +biotype 714 OXT "C-Terminal ASH (COOH)" -1 +biotype 715 HA "C-Terminal ASH (COOH)" -1 +biotype 716 N "C-Terminal ASN" 177 +biotype 717 CA "C-Terminal ASN" 222 +biotype 718 C "C-Terminal ASN" 210 +biotype 719 HN "C-Terminal ASN" 180 +biotype 720 OXT "C-Terminal ASN" 211 +biotype 721 HA "C-Terminal ASN" 82 +biotype 722 N "C-Terminal GLU" 177 +biotype 723 CA "C-Terminal GLU" 222 +biotype 724 C "C-Terminal GLU" 210 +biotype 725 HN "C-Terminal GLU" 180 +biotype 726 OXT "C-Terminal GLU" 211 +biotype 727 HA "C-Terminal GLU" 82 +biotype 728 N "C-Terminal GLH (COOH)" -1 +biotype 729 CA "C-Terminal GLH (COOH)" -1 +biotype 730 C "C-Terminal GLH (COOH)" -1 +biotype 731 HN "C-Terminal GLH (COOH)" -1 +biotype 732 OXT "C-Terminal GLH (COOH)" -1 +biotype 733 HA "C-Terminal GLH (COOH)" -1 +biotype 734 N "C-Terminal GLN" 177 +biotype 735 CA "C-Terminal GLN" 222 +biotype 736 C "C-Terminal GLN" 210 +biotype 737 HN "C-Terminal GLN" 180 +biotype 738 OXT "C-Terminal GLN" 211 +biotype 739 HA "C-Terminal GLN" 82 +biotype 740 N "C-Terminal MET" 177 +biotype 741 CA "C-Terminal MET" 222 +biotype 742 C "C-Terminal MET" 210 +biotype 743 HN "C-Terminal MET" 180 +biotype 744 OXT "C-Terminal MET" 211 +biotype 745 HA "C-Terminal MET" 82 +biotype 746 N "C-Terminal LYS" 177 +biotype 747 CA "C-Terminal LYS" 222 +biotype 748 C "C-Terminal LYS" 210 +biotype 749 HN "C-Terminal LYS" 180 +biotype 750 OXT "C-Terminal LYS" 211 +biotype 751 HA "C-Terminal LYS" 82 +biotype 752 N "C-Terminal LYD (NH2)" -1 +biotype 753 CA "C-Terminal LYD (NH2)" -1 +biotype 754 C "C-Terminal LYD (NH2)" -1 +biotype 755 HN "C-Terminal LYD (NH2)" -1 +biotype 756 OXT "C-Terminal LYD (NH2)" -1 +biotype 757 HA "C-Terminal LYD (NH2)" -1 +biotype 758 N "C-Terminal ARG" 177 +biotype 759 CA "C-Terminal ARG" 222 +biotype 760 C "C-Terminal ARG" 210 +biotype 761 HN "C-Terminal ARG" 180 +biotype 762 OXT "C-Terminal ARG" 211 +biotype 763 HA "C-Terminal ARG" 82 +biotype 764 N "C-Terminal ORN" 177 +biotype 765 CA "C-Terminal ORN" 222 +biotype 766 C "C-Terminal ORN" 210 +biotype 767 HN "C-Terminal ORN" 180 +biotype 768 OXT "C-Terminal ORN" 211 +biotype 769 HA "C-Terminal ORN" 82 +biotype 770 N "C-Terminal AIB" 177 +biotype 771 CA "C-Terminal AIB" 224 +biotype 772 C "C-Terminal AIB" 210 +biotype 773 HN "C-Terminal AIB" 180 +biotype 774 OXT "C-Terminal AIB" 211 diff --git a/tools/moltemplate/common/oplsaa/oplsaa_moltemplate.py b/tools/moltemplate/common/oplsaa/oplsaa_moltemplate.py new file mode 100755 index 0000000000..49cef1aff1 --- /dev/null +++ b/tools/moltemplate/common/oplsaa/oplsaa_moltemplate.py @@ -0,0 +1,386 @@ +#! /usr/bin/env python +#The purpose of this script is to create a moltemplate lt file for the opls-aa forcefield. +#This will assist researchers in building complex simulations using this OPLS-UA and the OPLS-AA forcefields. +__author__="Jason Lambert" +__version__="0.15" + +import sys +import os +from operator import itemgetter + +print(""" + +Warning: + Run this program on a SUBSET of the OPLS atoms which are relevant + to your problem. If not, this program (and moltemplate) may crash + your computer and/or generate enormous files that you do not need. +""") +# To do that, first make a copy of the \"oplsaa.prm\" file +# (which can be downloaded from the TINKER web site). +# The lines in this file beginning with the word \"atoms\" should +# define the atoms which you plan to put in your simulation. All other +# lines beginning with the word \"atoms\" should be deleted. +# (Leave the other sections of this file alone.) +#""") + + + +#input data from file containing opls aa force field parameters. +try: + f=open(sys.argv[1],"r") +except: + print("need to specify file name as an input argument:") + print("python oplsaa_moltemplate.py ") + print("or file name is specified incorrectly") + sys.exit() +#output lt file +g=open("oplsaa.lt","w") + + + +lines = f.readlines() + + + +# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. + +for i in range(0, len(lines)): + if (lines[i].find("## Atom Type Definitions ##") != -1): + break + else: + lines[i] = '# ' + lines[i] + + +# As of 2014-4-19, there appear to be 906 atom types, but we don't assume this. +# First try to infer out how many atom types there were in the original +# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. +# (Keep track of the maximum value of the first column in the "atom" section.) +max_atomType = 0 +for line in lines: + # skip over text after a # comment character + ic = line.find('#') + if ic != -1: + line = (line[:ic]).strip() + else: + line = line.strip() + # now look for lines beginning with the word "atom" + tokens = line.split() + if ((len(tokens)>2) and + (tokens[0] == "atom") and + (int(tokens[1]) > max_atomType)): + max_atomType = int(tokens[1]) + + +#temporary storage file +h=open("temp.txt","w+") +atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key +#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms +atom=[[-10000,-10000] for i in range(0,max_atomType+1)] +#charge_by_type={} # lookup charge by atom type +#vdw_by_type={} # lookup epsilon & sigma paramters by atom type +charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom +vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma + + + +#atom is declared this way so for sorting purposes. +#atom contains the following data upon allocation +#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) +#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) +#atom[][2]=atom_mass +#atom[][3]=partial charge +#atom[][4]=non_bonding sigma +#atom[][5]=non_bonding epsilon +#atom[][6]=atom comment +bond=[] +#bond contains the following data +#bond[0]=atom 1 ffid +#bond[1]=atom 2 ffid +#bond[2]=bond spring constant(OPLS-aa compatible) +#bond[3]=equilibrium bond distance(Angstrom) +angle=[] +#angle contains the following data +#angle[0]=atom 1 ffid +#angle[1]=atom 2 ffid +#angle[2]=atom 3 ffid +#angle[3]=spring constant +#angle[4]=equilibrium angle (degrees) +dihedral=[] +#dihedral contains the following data +#dihedral[0]=atom 1 ffid +#dihedral[1]=atom 2 ffid +#dihedral[2]=atom 3 ffid +#dihedral[3]=atom 4 ffid +#dihedral[4]=v1 +#dihedral[5]=v2 +#dihedral[6]=v3 +#dihedral[7]=v4 +improper=[] +#improper[0]=atom 1 ffid +#improper[1]=atom 2 ffid(central atom) +#improper[2]=atom 3 ffid +#improper[3]=atom 4 ffid +#improper[4]=spring coefficient +#improper[5]=equilibrium angle + + +#This section gets all the parameters from the force field file +for line in lines: + + # skip over text after a # comment character + ic = line.find('#') + if ic != -1: + line = (line[:ic]).strip() + else: + line = line.strip() + + if line.find("atom") == 0: + line=line.split() + atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), + 0.0,0.0,0.0," ".join(line[3:-2])] + elif line.find("vdw") == 0: + line=line.split() + #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) + if (int(line[1]) <= max_atomType): + vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) + elif line.find("bond") == 0: + line=line.split() + bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) + elif line.find("angle") == 0: + line=line.split() + angle.append([int(line[1]),int(line[2]),int(line[3]), + float(line[4]),float(line[5])]) + elif line.find("torsion") == 0: + line=line.split() + dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), + float(line[5]),float(line[8]), float(line[11]), 0.0]) + elif line.find("charge") == 0: + line=line.split() + #charge_temp.append([int(line[1]),float(line[2])]) + if (int(line[1]) <= max_atomType): + charge_by_type[int(line[1])] = float(line[2]) + elif line.find("imptors") == 0: + line=line.split() + improper.append([int(line[1]), int(line[2]), + int(line[3]), int(line[4]), float(line[5]), float(line[6])]) + +if len(atom) > 600: + sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" + " (You were supposed to edit out the atoms you don't need.\n" + " Not doing this may crash your computer.)\n" + "\n" + " Proceed? (Y/N): ") + reply = sys.stdin.readline() + if find(reply.strip().lower(), 'y') != 0: + exit(0) + +#adding the charge and Lennard Jones parameters to +#to each atom type. +#----------------------------------------------# +for i in range(0,len(atom)): + atom_type_num = atom[i][0] + #q = charge_by_type.get(atomTypeNum) + #if q: + # atom[i][3] = q + if atom_type_num != -10000: + q = charge_by_type[atom_type_num] + atom[i][3] = q + +for i in range(0,len(atom)): + atom_type_num = atom[i][0] + #vdw_params = vdw_by_type.get(atomTypeNum) + #if vdw_params: + # atom[i][4] = vdw_params[0] + # atom[i][5] = vdw_params[1] + if atom_type_num != -10000: + vdw_params = vdw_by_type[atom_type_num] + atom[i][4] = vdw_params[0] + atom[i][5] = vdw_params[1] + +del(charge_by_type) +del(vdw_by_type) + +#----------------------------------------------------------# +#begin writing content to lt file +g.write("OPLSAA {\n\n" ) + +#write out the atom masses +#----------------------------------------------------------# +g.write(" write_once(\"Data Masses\"){\n")#checked with gaff +for i,x in enumerate(atom): + if x[0] != -10000: + g.write(" @atom:{} {} #{} partial charge={}\n".format( + x[0],x[2],x[6],x[3])) +g.write(" } #(end of atom masses)\n\n") +#----------------------------------------------------------# + + +#write out the pair coefficients +#----------------------------------------------------------# +g.write(" write_once(\"In Settings\"){\n")#checked with gaff +for i,x in enumerate(atom): + if x[0] != -10000: + g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4])) +g.write(" } #(end of pair coeffs)\n\n") + +g.write(" write_once(\"In Charges\"){\n")#checked with gaff +for i,x in enumerate(atom): + if x[0] != -10000: + g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) +g.write(" } #(end of atom charges)\n\n") + +#-----------------------------------------------------------# + +# This part of the code creates a lookup dictionary +# that allows you to find every type of atom by its +# force field id. force field id is the id number +# relevant to bonds, angles, dihedrals, and impropers. +# This greatly increases the speed of angle, bond, dihedral +# and improper assignment. +#------------------------------------------------------------# +atom=sorted(atom,key=itemgetter(1)) +atom_ffid=0 +for x in atom: + if x[1]==atom_ffid: + atom_lookup[x[1]].append(x[0]) + elif x[1]>atom_ffid: + atom_lookup[x[1]]=[x[0]] + atom_ffid=x[1] +atom_lookup[0]=["*"] +#-------------------------------------------------------------# + + +#writing out the bond coefficients and bond parameters# +#-------------------------------------------------------------# +g.write(" write_once(\"In Settings\") {\n") +index1=0 +for x in bond: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) + h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) +g.write(" } #(end of bond_coeffs)\n\n") +h.seek(0,0) +g.write(" write_once(\"Data Bonds By Type\") {\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of bonds by type)\n\n") +del(bond) +h.close() +#-----------------------------------------------------------# +h=open("temp.txt","w+") + +#writing out angle coefficients and angles by type.---------# +#-----------------------------------------------------------# +g.write(" write_once(\"Data Angles By Type\"){\n") +for x in angle: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + #print(y,z,u,x) + h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u, + x[3]/2.0,x[4])) + g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format( + y,z,u)) + + +g.write(" } #(end of angles by type)\n\n") +h.seek(0,0) +g.write(" write_once(\"In Settings\" ){\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of angle_coeffs)\n\n") +del(angle) +h.close() +#----------------------------------------------------------# + +#writing dihedrals by type and dihedral coefficients-------# +h=h=open("temp.txt","w+") +g.write(" write_once(\"Data Dihedrals By Type\") {\n") +#print(atom_lookup) +for x in dihedral: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + for v in atom_lookup.get(x[3],[]): + if x[0]!=0 and x[3]!=0: + g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( + y,z,u,v)) + h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( + y,z,u,v,x[4],x[5],x[6],x[7])) + elif x[0]==0 and x[3]!=0: + g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( + y,z,u,v)) + h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( + z,u,v,x[4],x[5],x[6],x[7])) + elif x[0]==0 and x[3]==0: + g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( + y,z,u,v)) + #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( + h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( + z,u,x[4],x[5],x[6],x[7])) + +del(dihedral) +g.write(" } #(end of Dihedrals by type)\n\n") +h.seek(0,0) +g.write(" write_once(\"In Settings\") {\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of dihedral_coeffs)\n\n") +h.close() +#-----------------------------------------------------------------------# + +#----writing out improper coefficients and impropers by type------------# +h=open("temp.txt","w+") +g.write(" write_once(\"Data Impropers By Type\") {\n") +for x in improper: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + for v in atom_lookup.get(x[3],[]): + if x[0]==0 and x[1]==0 and x[3]==0: + g.write(" @improper:{2}-0-0-0 @atom:{2} @atom:{0} @atom:{1} @atom:{3}\n".format( + y,z,u,v)) + h.write(" improper_coeff @improper:{2}-0-0-0 harmonic {4} {5} \n".format( + y,z,u,v,x[4]/2,0)) + else: + g.write(" @improper:{2}-0-0-{3} @atom:{2} @atom:{0} @atom:{1} @atom:{3}\n".format( + y,z,u,v)) + h.write(" improper_coeff @improper:{2}-0-0-{3} harmonic {4} {5} \n".format( + y,z,u,v,x[4]/2,0)) + + +g.write(" } #(end of impropers by type)\n\n") +h.seek(0,0) +g.write(" write_once(\"In Settings\") {\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of improp_coeffs)\n\n") +#-----------------------------------------------------------------------# + +#This section writes out the input parameters required for an opls-aa simulation +# lammps. +g.write(" write_once(\"In Init\") {\n") +g.write(" units real\n") +g.write(" atom_style full\n") +g.write(" bond_style hybrid harmonic\n") +g.write(" angle_style hybrid harmonic\n") +g.write(" dihedral_style hybrid opls\n") +g.write(" improper_style hybrid harmonic\n") +#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n") +g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n") +g.write(" pair_modify mix arithmetic\n") +g.write(" special_bonds lj 0.0 0.0 0.5\n") +g.write(" kspace_style pppm 0.0001\n") +g.write(" } #end of init parameters\n\n") +g.write("} # OPLSAA\n") +f.close() +g.close() +h.close() +os.remove("temp.txt") + + + + + + diff --git a/tools/moltemplate/common/spce.lt b/tools/moltemplate/common/spce.lt new file mode 100644 index 0000000000..019911c19b --- /dev/null +++ b/tools/moltemplate/common/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeSPCE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/common/spce_ice_rect8.lt b/tools/moltemplate/common/spce_ice_rect8.lt new file mode 100644 index 0000000000..ccfd2f18c6 --- /dev/null +++ b/tools/moltemplate/common/spce_ice_rect8.lt @@ -0,0 +1,57 @@ +# This ice (1h) unit cell is rectangular and contains 8 water molecules. +# (Coordinates and cell dimensions converted were from a PDB file.) +# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362 + + +import "spce.lt" # <-- define the "SPCE" molecule + +SpceIceRect8 { + + # Create a 3-dimensional array of 8 water molecules + + wat = new SPCE[2][2][2] + + # Array indices will be correlated with position [xindex][yindex][zindex] + + # You can overwrite coordinates of atoms after they were created this way: + # (Order is not important) + # atom-ID molecule-ID atomType charge newX newY newZ + + write("Data Atoms") { + $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 + $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710 + $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710 + $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 + $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970 + $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652 + $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 + $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289 + $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971 + $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 + $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391 + $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391 + $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 + $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710 + $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710 + $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 + $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970 + $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652 + $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 + $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289 + $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971 + $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 + $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391 + $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391 + } +} # IceRect8 + +# Credit goes to Martin Chaplin. +# These coordinates were orignally downloaded from Martin Chaplin's +# website: http://www.btinternet.com/~martin.chaplin/ice1h.html +# ... and then they were stretched independently in the xy and z +# directions in order to match the lattice parameters measured by +# Rottger et al., +# "Lattice constants and thermal expansion of H2O and D2O ice Ih" +# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 +# I am using the lattice constants measured at temperature 265K +# (and pressure=100Torr). diff --git a/tools/moltemplate/common/tip3p_1983.lt b/tools/moltemplate/common/tip3p_1983.lt new file mode 100644 index 0000000000..45dc4ee9da --- /dev/null +++ b/tools/moltemplate/common/tip3p_1983.lt @@ -0,0 +1,123 @@ +############################################################# +# WARNING: THIS FILE HAS NOT BEEN TESTED! +# (If you use this file in a simulation, please email me to let me know +# if it worked. -Andrew 2012-10, (jewett dot aij at gmail dot com)) +######################################################### +# There are two different versions of TIP3P: +# +# tip3p_1983.lt # The implementation of TIP3P used by CHARMM (I think). +# tip3p_2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model +# # which uses long-range coulombics +######################################################### + +# file "tip3p_1983.lt" +# +# H1 H2 +# \ / +# O +# +# I think this is the TIP3P water model used by CHARMM (and AMBER?). See: +# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983) + + +TIP3P_1983 { + + write_once("In Init") { + # -- Default styles (for solo "TIP3P_1983" water) -- + units real + atom_style full + + # I'm not sure exactly which cutoffs distances are traditionally used in + # in the 1983 "TIP3P" model by Jorgensen model, (used by CHARMM). + # (See the Price JCP 2004 paper for a review.) + # My first guess was this: + # pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5 + # However, in the LAMMPS "peptide" example, they use these parameters: + + pair_style hybrid lj/charmm/coul/long 8.0 10.0 10.0 + + # ...alternately, if this does not work, try this: + # pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.0 10.5 + + bond_style hybrid harmonic + angle_style hybrid harmonic + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.834 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.417 0.756950327 0.00000 0.5858822766 + $atom:H2 $mol:. @atom:H 0.417 -0.756950327 0.00000 0.5858822766 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 450.0 0.9572 + angle_coeff @angle:HOH harmonic 55.0 104.52 + + ######################################################################### + #### There are two choices for for the O-O interactions + ######################################################################### + #### O-O nonbonded interactions + # For the 1983 Jorgensen version of TIP3P use: + + pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507 + + # For the 2004 Price & Brooks version of TIP3P use: + # pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.102 3.188 + ######################################################################### + #### There are three choices for for the O-H and H-H interactions + ######################################################################### + #### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter + + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 + pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic + + ######################################################################### + #### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, + #### If you want to use this, uncomment the following two lines: + # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 + # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric + ######################################################################### + #### 3) The original Jorgensen 1983 parameterization has no OH or HH + # lennard-jones interactions. (?? I think ??) + # For this behavior, uncomment these lines: + # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000 + # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753 + ######################################################################### + + # Define a group for the tip3p water molecules: + group tip3p type @atom:O @atom:H + + # Optional: Constrain the angles and distances. + # (Most implementations use this, but it is optional.) + fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeTIP3P during minimization.) + } + +} # "TIP3P_1983" water molecule type + + + + +# (note to self:) +# In the LAMMPS "peptide" example, these (nearly identical) parameters were used +# and they left the O-H parameters to be determined by the default mixing rules +#pair_style lj/charmm/coul/long 8.0 10.0 10.0 +#pair_coeff @atom:H @atom:H 0.046 0.400014 0.046 0.400014 +#pair_coeff @atom:O @atom:O 0.1521 3.15057 0.1521 3.15057 +#angle_style charmm +#angle_coeff @angle:HOH 55.0 104.52 0.0 0.0 diff --git a/tools/moltemplate/common/tip3p_2004.lt b/tools/moltemplate/common/tip3p_2004.lt new file mode 100644 index 0000000000..06964c7b63 --- /dev/null +++ b/tools/moltemplate/common/tip3p_2004.lt @@ -0,0 +1,97 @@ +######################################################### +# Warning: This file has not been carefully tested. +######################################################### +# There are two different versions of TIP3P: +# +# tip3p_1983.lt # The implementation of TIP3P used by CHARMM (I think). +# tip3p_2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model +# # which uses long-range coulombics +######################################################### + +# file "tip3p_2004.lt" +# +# H1 H2 +# \ / +# O +# +# I think this is the TIP3P water described in the paper by +# Daniel J. Price and Charles L. Brooks III +# J. Chem. Phys., 121(20): 10096 (2004) +# Specifically I think it refers to the "Model B" version of long-range TIP3P +# described in the 3rd-to-last column of "Table I", on p.10099. + +TIP3P_2004 { + + write_once("In Init") { + # -- Default styles (for solo "TIP3P_2004" water) -- + units real + atom_style full + + pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:ow -0.830 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:hw 0.415 0.756950327 0.00000 0.5858822766 + $atom:H2 $mol:. @atom:hw 0.415 -0.756950327 0.00000 0.5858822766 + } + + write_once("Data Masses") { + @atom:ow 15.9994 + @atom:hw 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 450.0 0.9572 + angle_coeff @angle:HOH harmonic 55.0 104.52 + + ######################################################################### + #### There are two choices for for the O-O interactions + ######################################################################### + #### O-O nonbonded interactions + # For the 1983 Jorgensen version of TIP3P use: + # pair_coeff @atom:ow @atom:ow lj/charmm/coul/charmm 0.1521 3.1507 + # For the 2004 Price & Brooks version of TIP3P use: + pair_coeff @atom:ow @atom:ow lj/charmm/coul/long 0.102 3.188 + ######################################################################### + #### There are three choices for for the O-H and H-H interactions + ######################################################################### + #### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter + pair_coeff @atom:hw @atom:hw lj/charmm/coul/long 0.0460 0.4000 + pair_coeff @atom:ow @atom:hw lj/charmm/coul/long 0.0836 1.7753 #arithmetic + ######################################################################### + #### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, + #### If you want to use this, uncomment the following two lines: + # pair_coeff @atom:hw @atom:hw lj/charmm/coul/charmm 0.0460 0.4000 + # pair_coeff @atom:ow @atom:hw lj/charmm/coul/charmm 0.0836 1.1226 #geometric + ######################################################################### + #### 3) The original Jorgensen 1983 parameterization has no OH or HH + # lennard-jones interactions. For this behavior, uncomment these lines: + # pair_coeff @atom:hw @atom:hw lj/charmm/coul/charmm 0.00 0.4000 + # pair_coeff @atom:ow @atom:hw lj/charmm/coul/charmm 0.00 1.7753 + ######################################################################### + + # Define a group for the tip3p water molecules: + group tip3p type @atom:ow @atom:hw + + # Optional: Constrain the angles and distances. + # (Most implementations use this, but it is optional.) + fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeTIP3P during minimization.) + } + +} # "TIP3P_2004" water molecule type + diff --git a/tools/moltemplate/common/trappe1998.lt b/tools/moltemplate/common/trappe1998.lt new file mode 100644 index 0000000000..1227b2aeba --- /dev/null +++ b/tools/moltemplate/common/trappe1998.lt @@ -0,0 +1,53 @@ +# This file stores complete LAMMPS data for the TraPPE model of saturated +# hydrocarbon chains. In this "united-atom" model, each methyl group is +# represented by a single atom. Forces between "atoms" are taken from the +# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577) + +TraPPE { + + write_once("Data Masses") { + @atom:CH2 14.1707 + @atom:CH3 15.2507 + @atom:CH4 16.3307 + } + + write_once("Data Angles By Type") { + @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated + } + + write_once("Data Dihedrals By Type") { + @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated + } + + write_once("In Settings") { + pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 + pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 + pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73 + bond_coeff @bond:saturated harmonic 120.0 1.54 + angle_coeff @angle:backbone harmonic 62.0022 114 + dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0 + } + + # Optional: Create a group corresponding to atoms used by the TraPPE force- + # field. (This is useful if you mix force-fields together.) + + write_once("In Settings") { + group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 + } + + write_once("In Init") { + # -- Default styles for "TraPPE" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid opls + improper_style none + pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + +} # class TraPPE + diff --git a/tools/moltemplate/common/watmw.lt b/tools/moltemplate/common/watmw.lt new file mode 100644 index 0000000000..c7aaecebbc --- /dev/null +++ b/tools/moltemplate/common/watmw.lt @@ -0,0 +1,54 @@ +# This file stores LAMMPS data for the "mW" water model. +# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) +# +# In this model, each water molecule is represented by a single "mW" particle. +# These particles interact with their neighbors via 3-body Stillinger-Weber +# forces whose parameters are tuned to mimic directional hydrogen-bonding +# in liquid water (as well as hexagonal ice, type II ice, and +# low-density super-cooled liquid/amorphous water phases). + +WatMW { + write("Data Atoms") { + $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:mW 18.02 + } + + write_once("system.in.sw") { + mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 + } + + write_once("In Init") { + # -- Default styles for "WatMW" -- + units real + pair_style sw + } + + write_once("In Settings") { + # --Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # -- Note: For this to work, you should probably run moltemplate this way: + # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt + # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) + } + + # -- optional -- + + write_once("In Settings") { + group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) + } + +} # WatMW diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT new file mode 100644 index 0000000000..09abbc4b2a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT @@ -0,0 +1,70 @@ + This example shows how to put a protein (inclusion) in a + lipid bilayer mixture composed of two different lipids (DPPC and DLPC). + The DPPC lipid model is described here: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) + (The DLPC model is a truncated version of DPPC. Modifications discussed below.) + The protein model is described here: + G. Bellesia, AI Jewett, and J-E Shea, + Protein Science, Vol19 141-154 (2010) + +--- PREREQUISITES: --- + +1) This example requires the "dihedral_style fourier", which is currently +in the USER-MISC package. Build LAMMPS with this package enabled using + make yes-user-misc +before compiling LAMMPS. +(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.) + +2) This example may require additional features to be added to LAMMPS. +If LAMMPS complains about an "Invalid pair_style", then + a) download the "additional_lammps_code" from + http://moltemplate.org (upper-left corner menu) + b) unpack it + c) copy the .cpp and .h files to the src folding of your lammps installation. + d) (re)compile LAMMPS. + + +----- Details -------- + +This example contains a coarse-grained model of a 4-helix bundle protein +inserted into a lipid bilayer (made from a mixture of DPPC and DLPC). + + -- Protein Model: -- + +The coarse-grained protein is described in: + G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +Here we use the "AUF2" model described in that paper. +(The hydrophobic beads face outwards.) + + -- Memebrane Model: -- + +The DPPC lipid bilayer described in: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) +and: + M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown + J. Chem. Phys. 135, 244701 (2011) + +As in Watson(JCP 2011), rigid bond-length constraints +have been replaced by harmonic bonds. + +A truncated version of this lipid (named "DLPC") has also been added. +The bending stiffness of each lipid has been increased to compensate +for the additional disorder resulting from mixing two different types +of lipids together. (Otherwise pores appear.) +Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models +have not been carefully parameterized to reproduce the correct behavior in +a lipid bilayer mixture. + + +------------- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh new file mode 100755 index 0000000000..9598e3b08d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data, and table_int.dat +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension) + +#or + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh new file mode 100755 index 0000000000..abf2fce64b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh @@ -0,0 +1,28 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # The "table_int.dat" file contains tabular data for the lipid INT-INT atom + # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, + # so I might look for a way to get rid of it later.) + cp -f table_int.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg new file mode 100644 index 0000000000..246ee54625 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg new file mode 100644 index 0000000000..fdbb446eed Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg new file mode 100644 index 0000000000..142f3f706f Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg new file mode 100644 index 0000000000..5d4b15b291 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg new file mode 100644 index 0000000000..285389039d Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt new file mode 100644 index 0000000000..a5df81056d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt @@ -0,0 +1,254 @@ +# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle (or a 4-strand beta-barrel). +# This approach is optional. If your protein has helices which are not +# identical, you should probably just include all 4 helices in a single +# "Data Atoms" section and don't try to subdivide the protein into pieces.) + + + +1beadProtSci2010 { # <-- enclose definitions in a namespace for portability + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0 + $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6 + $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2 + $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8 + $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4 + $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0 + $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6 + $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2 + $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8 + $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4 + $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0 + $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6 + $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2 + $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8 + $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4 + $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0 + $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44 + $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + + # ----- Now build a larger molecule using A16 and T3 ------- + + # Create a 4-Helix bundle. + # In this version, the hydrophobic beads are poing outward. + # I oriented them this way because I want to place this protein in a membrane. + # (There is another file in this directory containing alternate version + # of this same molecule with the hydrophobic beads pointing inward.) + + 4HelixInsideOut { + helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6) + + turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9) + turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0) + turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOut + + + # -------- Minor coordinates adjustment: ----------- + + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4HelixInsideOut.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + + + # -------------- Force-Field Parameters ------------ + + # Units and force-field styles for this protein model + # (These can be overridden later.) + + write_once("In Init") { + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + # --- Distance Units --- + # In this version of the model, sigma (the bond-length + # and particle diameter) is rounded to 5.5 Angstroms. + # + # --- Energy & Temperature Units --- + # In this protein model, "epsilon" represents the free energy + # bonus for bringing two hydrophobic amino acids together. + # Here I choose to set epsilon to 1.806551818181818 kCal/mole. + # This value was chosen so that a temperature of 300 Kelvin lies at + # 0.33 epsilon, which is the unfolding temperature of the marginally stable + # "ASF1" protein model from the Bellesia et al 2010 paper. + # This choice insures that both the "ASF1" model from that paper, + # as well as the much more stable "AUF2" protein we use here (which + # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin, + # in the bulk at least. (However it's not clear that these energy + # parameters will work well for a protein in membrane. Perhaps I'll + # run some tests and fine tune these parameters for this scenario.) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + } + + # The exact value of the bond_coeff does not matter too much as long as + # it is "stiff enough". Here I use a softer bond spring than the one + # used in the paper so that I can increase the time step. + # I also use a relatively soft spring to constrain the bond angles. + + # bond_coeff bondType bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 5.5 + } + + + + # We use the same bond-angle forces whenever + # there are 3 consecutively-bonded atoms: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # angle_coeff angleType anglestylename k theta0 + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 100.0 105.0 + } + + + + + # Dihedral interactions are also determined by atom-type name in this case. + # I chose atoms whose type-names begin with "t" to be "turn" atoms. + # Atoms whose type-names begin with "s" could be either helices or sheets. + # (In this case, helices. In this example, we use the @dihedral:delta65_0 + # parameters. This corresponds to the "AUF2" model from the + # Bellesia et. al 2010 paper.) + + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + write_once("Data Dihedrals By Type") { + @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * + + # If "tN" (turn) atoms are present, use the @dihedral:turn parameters + + @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * + } + + + # From the Bellesia et al 2010 paper: + # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta)) + # for turns: U_{dih}(\phi) = 0.2*cos(3\phi) + # + # General formula used for "dihedral_style fourier": + # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ] + # + # Syntax: + # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ... + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 + dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5 + dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 + dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 + # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. + } + + + # --- Mass Units --- + # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down): + write_once("Data Masses") { + @atom:1beadProtSci2010/sH 100.0 + @atom:1beadProtSci2010/sL 100.0 + @atom:1beadProtSci2010/tN 100.0 + } + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt new file mode 100644 index 0000000000..e6e6bced70 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt @@ -0,0 +1,225 @@ +### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ## +### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE## +# +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) + +import "1beadProtSci2010.lt" + +# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. + + +1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier + # This way we don't have to start from scratch. We can + # use all the atom types and angle settings defined earlier + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0 + $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8 + $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6 + $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4 + $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2 + $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0 + $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8 + $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6 + $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4 + $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2 + $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0 + $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8 + $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6 + $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4 + $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2 + $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + # ----- Now build larger molecules using B16 and T3 ------- + + + 4SheetBarrel { + sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0) + sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0) + sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0) + sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # Below I define several alternate conformations of the"4HelixBundleInsideOut" + # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however. + + 4HelixBundle { + helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + + turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2) + turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9) + turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4) + + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixBundle + + + + + # --- alternate conformations (same molecule) ---- + + # In the following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixBundleLoose { + + helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # In following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixInsideOutLoose { + helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8) + turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2) + turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOutLoose + + + + + # In the following version, the 4 helices are arranged next to each other, + # side-by-side, in a planar conformation (instead of a compact bundle). + + 4HelixPlanar { + helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0) + helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0) + helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0) + helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8) + turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8) + turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixPlanar + + + # -------- Minor coordinates adjustment: ----------- + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4SheetBarrel.scale(0.9166666666666666) + 4HelixBundle.scale(0.9166666666666666) + 4HelixBundleLoose.scale(0.9166666666666666) + 4HelixInsideOutLoose.scale(0.9166666666666666) + 4HelixPlanar.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt new file mode 100644 index 0000000000..3b39048f7e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt @@ -0,0 +1,198 @@ +# Note: +# +# This example may require additional features to be added to LAMMPS. If +# LAMMPS complains about an "Invalid pair_style", then download copy the +# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS +# "src" directory and recompile LAMMPS. +# +# -------- Description -------- +# +# This example contains an implementation of the DPPC lipid bilayer described in +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# and: +# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown +# J. Chem. Phys. 135, 244701 (2011) +# +# As in Watson(JCP 2011), rigid bond-length constraints have been replaced +# by harmonic bonds. +# +# A truncated version of this lipid (named "DLPC") has also been added. +# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +# parameterized to reproduce the correct behavior in a lipid bilayer mixture. +# +# Units: +# +# The "epsilon" parameter in their model is approximately 2.75 kJ/mole +# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) +# The "sigma" parameter corresponds to 7.5 angstroms. + + +CGLipidBr2005 { + + + write_once("In Init") { + # -- Default styles for "CGLipidBr2005" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + + #angle_style hybrid cosine/delta # <- used in the original article + angle_style hybrid harmonic # <- prevents unphysical acute angle turns + # Explanation: + # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + # angle_style harmonic: U(theta) = k*(theta-theta0)^2 + + dihedral_style none + improper_style none + pair_style hybrid table linear 1130 & + lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + + neighbor 2.0 multi # <- perhaps unnecessary + communicate multi # <- perhaps unnecessary + } + + + DPPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 + $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + $bond:b4 @bond:../backbone $atom:t2 $atom:t3 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 + } + + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + + } #DPPC + + + DLPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + } + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + } #DLPC + + + # Particles and properties shared by all lipid types: + + write_once("Data Masses") { + @atom:int 200.0 + @atom:tail 200.0 + @atom:head 200.0 #<- Default head type. We may override it later. + } + + write_once("In Settings") { + # -- Default settings/parameters for "CGLipidBr2005" -- + # (Hybrid bond & angle styles were used for portability.) + + # As in Watson(JCP 2011), rigid bond-length constraints + # have been replaced by harmonic bonds. + # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. + bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 + } + + write_once("In Settings") { + # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps + # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 + angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps + } + # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper + # to attempt to compensate for the fact that here we are using a lipid + # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal + # of disorder into the bilayer which would not be present in a DPPC bilayer. + # This causes pores to form. Increasing the angle stiffness prevents this.) + + write_once("In Settings") { + + # The interaction of "atom:int" with other "atom:int" atoms is given by + # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at + # r=3*sigma. This was implemented using pair_style table. + # Unfortunately, mixing lj/charmm and "table" pair styles in the same + # simulation is very inneficient. + + pair_coeff @atom:int @atom:int table table_int.dat INT + + # The interaction of tail beads with eachother is given by the formula below + # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: + # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), + pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # The interaction of head beads which all other beads is given by: + # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), + + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + } # write_once("In Settings") + + # Note: I divided epsilon by 4 to get "0.1643" because we are using the + # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) + # (The "es4k4l" coeffstyle is the default.) Using this convention makes it + # easier to mix this coarse-grained lipid model with other molecular models. + + + +} # CGLipidBr2005 + + + + + + + + +# Note: This example has not been optimized for speed. +# +# Unfortunately, using both lj/charmm and "table" pair styles in the same +# simulation seems to be very inneficient. (The simulation is twice as slow +# as using only the "lj/charmm" pair styles for every pairwise interaction, +# ...and about 25% slower than using "table" for every pairwise interaction. +# However the lennard-jones pair styles support mixing, so we use them to +# make it easier to run these molecules with other molecules which don't use +# pair_table. I felt that portability was worth the extra 25% slow down.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py new file mode 100755 index 0000000000..0d09e4d02e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py @@ -0,0 +1,29 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +rcut = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) + F_r = F(r, epsilon, sigma) + if r > rcut: + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py new file mode 100755 index 0000000000..32147e444a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# I realized later this is not what we want because although energy is conserved +# all enrgies are shifted with respect to energies used in the Brannigan paper +# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). +# (So don't use this.) + +# Calculate and print a + +def S(r, rc1, rc2, derivative=False): + """ + Calculate the switching function S(r) which decays continuously + between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): + S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 + I'm using the same smoothing/switching cutoff function used by the CHARMM + force-fields. (I'm even using the same code to implement it, taken + from lammps charmm/coul/charmm pair style, rewritten in python.) + + """ + assert(rc2>rc1) + rsq = r*r + rc1sq = rc1*rc1 + rc2sq = rc2*rc2 + denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* + (rc2sq-rc1sq)* + (rc2sq-rc1sq))) + if rsq > rc2sq: + return 0.0 + elif rsq < rc1sq: + if derivative: + return 0.0 + else: + return 1.0 + else: + rc2sq_minus_rsq = (rc2sq - rsq) + rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq + if derivative: + return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) + else: + return (rc2sq_minus_rsq_sq * + (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) + + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) + +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +Rc1 = 22.0 +Rc2 = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) + F_r = F(r, epsilon, sigma) + # Multiply U(r) & F(r) by the smoothing/switch function + U_r = U_r * S(r, Rc1, Rc2) + F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt new file mode 100644 index 0000000000..82a5c6eae4 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt @@ -0,0 +1,207 @@ +# Description: + +# This example shows how to put a protein (inclusion) in a +# lipid bilayer mixture composed of two different lipids (DPPC and DLPC). +# The DPPC lipid model is described here: +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# The protein model is described here: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# The new DLPC model is a truncated version of DPPC, +# (Its behaviour has not been rigorously tested.) +# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to +# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 + +# Note: +# This example may require additional features to be added to LAMMPS. +# If LAMMPS complains about an "Invalid pair_style", then copy the code +# in the "additional_lammps_code" directory into your LAMMPS "src" directory +# and recompile LAMMPS. + + + +import "CGLipidBr2005.lt" + +using namespace CGLipidBr2005 + +# The "= new random" syntax chooses one of several molecules at random + +lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) #"1234"=random_seed + [13].move(7.5, 0, 0) + [15].move(3.75, 6.49519, 0) # <-- hexagonal lattice + [2].rot(180, 1, 0, 0) # <-- 2 monolayers + +# Move all the lipds up to the center of the box + +lipids[*][*][*].move(0,0,75.0) + + + + +# Although this patch of lipids is not square or rectangular, (it looks +# like a parallelogram), this is no longer the case after rectangular +# periodic boundary conditions are applied. (Check by visualising in VMD.) + + +write_once("Data Boundary") { + 0 97.5 xlo xhi + 0 97.42785792 ylo yhi + 0 150.0 zlo zhi +} + + +# A note on geometry: +# We want to create a bilayer arranged in a hexagonal lattice consisting of +# 13 rows (each row is aligned with the x-axis) +# 15 columns (aligned at a 60 degree angle from the x axis) +# The lattice spacing is 7.5 Angstroms. +# When wrapped onto a rectangular box, the dimensions of the system are: +# 13 * 7.5 Angstroms in the X direction +# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction + + + + + + + +# ------------------- protein inclusion --------------------- + +import "1beadProtSci2010.lt" + +using namespace 1beadProtSci2010 + +protein = new 4HelixInsideOut + +protein.move(45.0, 25.98076211, 75.0) + + +# Delete a hole in the membrane to create space for the protein. + +delete lipids[4][2][*] +delete lipids[6][2][*] +delete lipids[3-6][3][*] +delete lipids[3-5][4][*] +delete lipids[2-5][5][*] +delete lipids[2][6][*] +delete lipids[4][6][*] + +# Note: All atom types must include the full path (the name of +# the namespace which defined them as well as the atom type name). +# (This is because we are no longer inside that namespace.) + + +write_once("In Settings") { + + # ----------------------------------------------------------- + # -------- interactions between protein and lipids ---------- + # ----------------------------------------------------------- + + # Interactions between the protein and lipid atoms are usually + # determined by mixing rules. (However this is not possible some + # for atoms, such as the "int" atoms in the lipid model which + # interact using -1/r^2 attraction.) Mixing rules do not make + # sense for these atoms so we must explicitly define their + # interaction with all other atoms. + + # We want the hydrophobic interactions between hydrophobic residues in + # the protein and beads the interior of the lipid to be energetically + # similar to the attractive interactions between the lipid tails. + # + # Note: I made the width of the outward-facing protein beads slightly larger + # ("12.5") whenever they interact with the "tail" beads in each lipid + # (in order to make the protein wider there). + # This hopefully relieves some of the internal negative pressure in the center + # of the bilayer which can otherwise rip apart the protein or suck it into + # the bilaer. (This is a hack, and I'm not sure if it is necessary. + # For different protein or lipid models, you probably don't need this.) + # + # i j pairstylename eps sig K L + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # To help keep the protein from tilting 90 degrees and burying itself + # within the lipid bilayer, we make the turn regions at either + # end of the protein (strongly) attracted to the head groups + # of the lipid. (In reality, they would probably be attracted + # to the water as well.) + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # All other interactions between proteins and lipids are steric. + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + # ----------------------------------------------------------- + # -------- Modifications to the protein model: -------------- + # ----------------------------------------------------------- + # + # Turn off attraction between the hydrophobic "@atom:sH" beads: + # (These beads are located in the outside of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + + # (Why: These beads are only attracted to + # each other in an aqueous environment) + + # ... and + # Turn ON attraction between the hydrophilic "@atom:sL" beads. + # (These beads are located in the interior of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # Why? + # In reality, polar groups in the interior of trans-membrane + # proteins do form hydrogen bonds with each other. This was + # absent from the original protein model because, in an aqueous + # environment, these groups preferentially interact with the water. + # + # Why is this necessary? + # Shouldn't attraction between lipid tails and the protein create + # an effective force which brings the hydrophilic beads together? + # (similar to the hydrophobic effect, but in reverse?). + # Answer: + # Unlike an aqueous environment (~zero pressure, or +1atm), there is + # a large negative pressure in the interior of some bilayer membrane + # models (such as this one). Without some kind of direct attraction + # between interior residues, the protein will get pulled apart. + # (Perhaps the attractive force I am using is too strong?) + +} + + + + +# Finally, we must combine the two force-field styles which were used for +# the coarse-grained lipid and protein. To do that, we write one last time +# to the "In Init" section. When reading the "Init" section LAMMPS will +# read these commands last and this will override any earlier settings. + +write_once("In Init") { + # -- These styles override earlier settings -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid cosine/delta harmonic + dihedral_style hybrid fourier + improper_style none + pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" +} + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat new file mode 100644 index 0000000000..b0d651d67f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat @@ -0,0 +1,1139 @@ +# Table for the INT-INT interaction from +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# This table contains +# i r_i U(r_i) -dU/dr|r_i +# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) + +INT +N 1130 + +1 0.02 2.0331818401e+30 1.21990910406e+33 +2 0.04 4.9638228518e+26 1.48914685554e+29 +3 0.06 3.82579033251e+24 7.65158066501e+26 +4 0.08 1.21187081343e+23 1.81780622014e+25 +5 0.1 8.32791281704e+21 9.99349538045e+23 +6 0.12 9.34030842897e+20 9.34030842897e+22 +7 0.14 1.46892540453e+20 1.25907891817e+22 +8 0.16 2.95866897809e+19 2.21900173357e+21 +9 0.18 7.19889946863e+18 4.79926631242e+20 +10 0.2 2.0331818401e+18 1.21990910406e+20 +11 0.22 6.47834392264e+17 3.53364213962e+19 +12 0.24 2.28034873754e+17 1.14017436877e+19 +13 0.26 8.72681951932e+16 4.02776285507e+18 +14 0.28 3.58624366341e+16 1.53696157003e+18 +15 0.3 1.56704372019e+16 6.26817488078e+17 +16 0.32 7.2233129348e+15 2.70874235055e+17 +17 0.34 3.48970861422e+15 1.23166186384e+17 +18 0.36 1.75754381558e+15 5.85847938527e+16 +19 0.38 9.18613895646e+14 2.90088598625e+16 +20 0.4 4.96382285179e+14 1.48914685554e+16 +21 0.42 2.76404230108e+14 7.89726371739e+15 +22 0.44 1.58162693423e+14 4.31352800247e+15 +23 0.46 9.27773983256e+13 2.42027995633e+15 +24 0.48 5.56725765996e+13 1.391814415e+15 +25 0.5 3.41111308981e+13 8.18667141564e+14 +26 0.52 2.13057117167e+13 4.91670270393e+14 +27 0.54 1.35459994024e+13 3.0102220895e+14 +28 0.56 8.75547769351e+12 1.87617379153e+14 +29 0.58 5.74645813711e+12 1.18892237325e+14 +30 0.6 3.8257903322e+12 7.65158066491e+13 +31 0.62 2.58128463312e+12 4.99603477424e+13 +32 0.64 1.7635041342e+12 3.30657025205e+13 +33 0.66 1.21901470178e+12 2.21639036726e+13 +34 0.68 8.51979641904e+11 1.50349348607e+13 +35 0.7 6.0167184547e+11 1.0314374497e+13 +36 0.72 4.29087845387e+11 7.15146409276e+12 +37 0.74 3.08855637556e+11 5.00846980094e+12 +38 0.76 2.24270970425e+11 3.54112058818e+12 +39 0.78 1.64210505205e+11 2.52631546702e+12 +40 0.8 1.2118708117e+11 1.81780621971e+12 +41 0.82 90109367359.1 1.31867367068e+12 +42 0.84 67481501334.4 9.64021449503e+11 +43 0.86 50880896383.4 7.09965997788e+11 +44 0.88 38613938681.2 5.26553710913e+11 +45 0.9 29486692086.8 3.93155896009e+11 +46 0.92 22650731882.4 2.95444330322e+11 +47 0.94 17498544395.3 2.23385674464e+11 +48 0.96 13591937526.4 1.69899220331e+11 +49 0.98 10612635712.6 1.29950642555e+11 +50 1.0 8327912706.34 99934953582.6 +51 1.02 6566502316.69 77252969474.2 +52 1.04 5201589672.36 60018343356.8 +53 1.06 4138717434.11 46853405843.3 +54 1.08 3307128665.58 36745874940.0 +55 1.1 2653529579.27 28947596241.1 +56 1.12 2137567708.15 22902511945.9 +57 1.14 1728534024.3 18195095739.0 +58 1.16 1402943799.0 14513212422.1 +59 1.18 1142752163.37 11621209113.9 +60 1.2 934030766.093 9340308300.6 +61 1.22 765981286.774 7534242773.65 +62 1.24 630196371.787 6098675145.29 +63 1.26 520103253.414 4953364870.6 +64 1.28 430542934.103 4036340534.04 +65 1.3 357450462.101 3299543229.91 +66 1.32 297610947.802 2705554551.18 +67 1.34 248472587.186 2225128105.44 +68 1.36 208002782.573 1835319108.76 +69 1.38 174576985.011 1518061159.35 +70 1.4 146892484.084 1259078837.33 +71 1.42 123901294.937 1047053582.16 +72 1.44 104757721.536 872981382.419 +73 1.46 88777241.639 729676313.267 +74 1.48 75404158.02 611385405.387 +75 1.5 64186061.7033 513488820.507 +76 1.52 54753607.1486 432265633.695 +77 1.54 46804443.7318 364710253.134 +78 1.56 40090410.0598 308388060.159 +79 1.58 34407297.9713 261321529.95 +80 1.6 29586646.6744 221900119.2 +81 1.62 25489145.661 188808745.634 +82 1.64 21999316.2868 160970856.824 +83 1.66 19021212.5921 137502982.517 +84 1.68 16474936.8715 117678352.86 +85 1.7 14293808.3245 100897694.735 +86 1.72 12422056.6082 86665727.6626 +87 1.74 10812938.3788 74572197.8496 +88 1.76 9427195.57103 64276535.39 +89 1.78 8231790.46096 55495411.7777 +90 1.8 7198865.45512 47992625.088 +91 1.82 6304885.77339 41570857.9644 +92 1.84 5529931.32911 36064946.1544 +93 1.86 4857110.59557 31336368.341 +94 1.88 4272074.43377 27268725.7382 +95 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-0.00354788564052 -0.0199492167196 +1117 22.34 -0.0031494369093 -0.0198956883597 +1118 22.36 -0.00275205683071 -0.0198423513132 +1119 22.38 -0.00235574158704 -0.0197892047262 +1120 22.4 -0.00196048737759 -0.0197362477497 +1121 22.42 -0.00156629041861 -0.0196834795391 +1122 22.44 -0.00117314694319 -0.0196308992543 +1123 22.46 -0.000781053201174 -0.0195785060596 +1124 22.48 -0.000390005459079 -0.019526299124 +1125 22.5 0.0 -0.0194742776206 +1126 22.52 0.0 0.0 +1127 22.54 0.0 0.0 +1128 22.56 0.0 0.0 +1129 22.58 0.0 0.0 +1130 22.6 0.0 0.0 diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min new file mode 100644 index 0000000000..fb2d3ddd87 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min @@ -0,0 +1,35 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. + + + +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt new file mode 100644 index 0000000000..2dc4bbe035 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt @@ -0,0 +1,65 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. +# + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + +#minimize 1.0e-5 1.0e-7 500 2000 + +timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy + + +# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon +# (for the "epsilon" used by the coarse-grained lipid), and +# to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein) +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. +# Note: We maintain the system system at constant (zero) tention +# using a barostat damping parameter Pdamp=1000 ("0 0 1000") + + +# optional (not sure if this helps): +# balance x uniform y uniform + + +run 100000 + +write_data system_after_npt.data diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt new file mode 100644 index 0000000000..c9195b4e62 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt @@ -0,0 +1,71 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) +# +# -------- LAMMPS REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. +# +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 10000 traj_nvt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. +# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. + +#restart 500000 + +run 10000000 + + +write_data system_after_nvt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT new file mode 100644 index 0000000000..1bf9d00b99 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT @@ -0,0 +1,33 @@ +Note: + This example may require additional features to be added to LAMMPS. +If LAMMPS complains about an "Invalid pair_style", then copy the code +in the "additional_lammps_code" directory into your LAMMPS "src" directory +and recompile LAMMPS. + +----- Description -------- + +This example contains an implementation of the DPPC lipid bilayer described in: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) +and: + M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown + J. Chem. Phys. 135, 244701 (2011) + +As in Watson(JCP 2011), rigid bond-length constraints +have been replaced by harmonic bonds. + +A truncated version of this lipid (named "DLPC") has also been added. +Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +parameterized to reproduce the correct behavior in a lipid bilayer. + + +------------- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh new file mode 100755 index 0000000000..9598e3b08d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data, and table_int.dat +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension) + +#or + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh new file mode 100755 index 0000000000..abf2fce64b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh @@ -0,0 +1,28 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # The "table_int.dat" file contains tabular data for the lipid INT-INT atom + # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, + # so I might look for a way to get rid of it later.) + cp -f table_int.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg new file mode 100644 index 0000000000..637f2f1c7a Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg new file mode 100644 index 0000000000..14f1a1ed2c Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg new file mode 100644 index 0000000000..757abe2684 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg new file mode 100644 index 0000000000..2322449c1d Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg new file mode 100644 index 0000000000..57e093023d Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt new file mode 100644 index 0000000000..242ec243dd --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt @@ -0,0 +1,191 @@ +# Note: +# +# This example may require additional features to be added to LAMMPS. If +# LAMMPS complains about an "Invalid pair_style", then download copy the +# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS +# "src" directory and recompile LAMMPS. +# +# -------- Description -------- +# +# This example contains an implementation of the DPPC lipid bilayer described in +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# and: +# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown +# J. Chem. Phys. 135, 244701 (2011) +# +# As in Watson(JCP 2011), rigid bond-length constraints have been replaced +# by harmonic bonds. +# +# --- DLPC lipids --- +# A truncated version of the DPPC lipid (named "DLPC") has also been added. +# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +# parameterized to reproduce the correct behavior in a lipid bilayer/mixture. +# (You may need to stiffen the bond-angle forces to make it behave correctly, +# but I did not do this here.) +# +# Units: +# +# The "epsilon" parameter in their model is approximately 2.75 kJ/mole +# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) +# The "sigma" parameter corresponds to 7.5 angstroms. +# +# +# The new DLPC model is a truncated version of DPPC, +# (Its behaviour has not been rigorously tested.) + + +CGLipidBr2005 { + + + write_once("In Init") { + # -- Default styles for "CGLipidBr2005" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid cosine/delta + dihedral_style none + improper_style none + pair_style hybrid table linear 1130 & + lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + + neighbor 2.0 multi # <- perhaps unnecessary + communicate multi # <- perhaps unnecessary + } + + + DPPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 + $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + $bond:b4 @bond:../backbone $atom:t2 $atom:t3 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 + } + + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + + } #DPPC + + + DLPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + } + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + } #DLPC + + + # Particles shared by all lipid types + write_once("Data Masses") { + @atom:int 200.0 + @atom:tail 200.0 + @atom:head 200.0 #<- Default head type. We may override it later. + } + + write_once("In Settings") { + # -- Default settings/parameters for "CGLipidBr2005" -- + # (Hybrid bond & angle styles were used for portability.) + + # As in Watson(JCP 2011), rigid bond-length constraints + # have been replaced by harmonic bonds. + # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. + bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 + } + + write_once("In Settings") { + angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps + #angle_coeff @angle:backbone cosine/delta 6.57265774 180 #<-- 10*eps + } + + write_once("In Settings") { + + # The interaction of "atom:int" with other "atom:int" atoms is given by + # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at + # r=3*sigma. This was implemented using pair_style table. + # Unfortunately, mixing lj/charmm and "table" pair styles in the same + # simulation is very inneficient. + + pair_coeff @atom:int @atom:int table table_int.dat INT + + # The interaction of tail beads with eachother is given by the formula below + # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: + # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), + pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # The interaction of head beads which all other beads is given by: + # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), + + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + } # write_once("In Settings") + + # Note: I divided epsilon by 4 to get "0.1643" because we are using the + # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) + # (The "es4k4l" coeffstyle is the default.) Using this convention makes it + # easier to mix this coarse-grained lipid model with other molecular models. + + + +} # CGLipidBr2005 + + + + + + + + +# Note: This example has not been optimized for speed. +# +# Unfortunately, using both lj/charmm and "table" pair styles in the same +# simulation seems to be very inneficient. (The simulation is twice as slow +# as using only the "lj/charmm" pair styles for every pairwise interaction, +# ...and about 25% slower than using "table" for every pairwise interaction. +# However the lennard-jones pair styles support mixing, so we use them to +# make it easier to run these molecules with other molecules which don't use +# pair_table. I felt that portability was worth the extra 25% slow down.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py new file mode 100755 index 0000000000..0d09e4d02e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py @@ -0,0 +1,29 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +rcut = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) + F_r = F(r, epsilon, sigma) + if r > rcut: + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py new file mode 100755 index 0000000000..32147e444a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# I realized later this is not what we want because although energy is conserved +# all enrgies are shifted with respect to energies used in the Brannigan paper +# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). +# (So don't use this.) + +# Calculate and print a + +def S(r, rc1, rc2, derivative=False): + """ + Calculate the switching function S(r) which decays continuously + between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): + S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 + I'm using the same smoothing/switching cutoff function used by the CHARMM + force-fields. (I'm even using the same code to implement it, taken + from lammps charmm/coul/charmm pair style, rewritten in python.) + + """ + assert(rc2>rc1) + rsq = r*r + rc1sq = rc1*rc1 + rc2sq = rc2*rc2 + denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* + (rc2sq-rc1sq)* + (rc2sq-rc1sq))) + if rsq > rc2sq: + return 0.0 + elif rsq < rc1sq: + if derivative: + return 0.0 + else: + return 1.0 + else: + rc2sq_minus_rsq = (rc2sq - rsq) + rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq + if derivative: + return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) + else: + return (rc2sq_minus_rsq_sq * + (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) + + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) + +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +Rc1 = 22.0 +Rc2 = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) + F_r = F(r, epsilon, sigma) + # Multiply U(r) & F(r) by the smoothing/switch function + U_r = U_r * S(r, Rc1, Rc2) + F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt new file mode 100644 index 0000000000..c556233c0d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt @@ -0,0 +1,94 @@ +# Description: + +# This constructs a bilayer constructed from coarse-grained DPPC lipids +# (implicit solvent). The DPPC lipid model is described here: +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# +# NOTE: There is an example of a 50%/50% DPPC & DLPC mixture +# in the "membrane+protein" and "vesicle" examples. + + + + + + +import "CGLipidBr2005Orig.lt" + +using namespace CGLipidBr2005 + +lipids = new DPPC [32].move(7.5, 0, 0) + [37].move(3.75, 6.49519, 0) + [2].rot(180, 1, 0, 0) + + +# Move the lipds up to the center of the box +lipids[*][*][*].move(0,0,75.0) + + +# Although this patch of lipids is not square or rectangular, (it looks +# like a parallelogram), this is no longer the case after rectangular +# periodic boundary conditions are applied. We apply them below: +# width: 240 = 32*7.5 +# height: 240.322 = 37*6.49519 + +write_once("Data Boundary") { + 0 240 xlo xhi + 0 240.322 ylo yhi + 0 150.0 zlo zhi +} + + + + + + + + +# -------------- File ends here. Only comments below.------------------- + +# ------------------------------------ +# ------------- COMMENTS: ------------ +# ------------------------------------ +# +# A note on geometry: +# We want to create a bilayer arranged in a hexagonal lattice consisting of +# 32 rows (each row is aligned with the x-axis) +# 37 columns (aligned at a 60 degree angle from the x axis) +# The lattice spacing is 8.0 Angstroms ( ~= 0.95*sigma*2^(1/6), where sigma=7.5) +# When wrapped onto a rectangular box, the dimensions of the system are: +# 32 * 7.5 Angstroms in the X direction +# 37 * 7.5*sqrt(3)/2 Angstroms in the Y direction +# ------------------------------------ +# +# Below I show simple ways to create a lipid bilayer: +# +# 1) If you just want to make lipid bilayer out of DPPC, +# without specifying the location of each lipid, you could use this syntax: +# lipids = new DPPC [32][37][2] # 3-D array +# Later you can load in the coordinates of the lipds from a PDB file. +# Alternately you could also use a 1-dimensional array: +# lipids = new DPPC [2368] # 1-D array. Note: 2368 = 32 x 37 x 2 +# It does not matter as long as the number of lipids is correct. +# Multidimensional arrays are only useful if you plan to apply independent +# coordinate transformations to each row and column and monolayer. See below: +# +# 2) Instead of loading a PDB file later, we can directly specify the location +# of each DPPC lipid in the LT file itself. For lipid bilayers, this is +# easy, because the bilayer structure resembles 2 planar lattices. +# We can use "move" commands to place each lipid, and the "rot" command +# to turn the lipids in one of the monolayers upside down. +# +# lipids = new DPPC [32].move(7.5, 0, 0) +# [37].move(3.75, 6.49519, 0) +# [2].rot(180, 1, 0, 0) +# +# 3) If you want to create a bilayer from a mixture of DPPC and DLPC, you must +# replace "DPPC" in the command above with random([DPPC,DLPC],[0.5,0.5],12345) +# Here "0.5,0.5" are the probabilities for each molecule type, and "12345" +# is an optional random seed. +# lipids = new random([DPPC,DLPC], [0.5,0.5], 12345) +# [32].move(7.5, 0, 0) +# [37].move(3.75, 6.49519, 0) +# [2].rot(180, 1, 0, 0) +# diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat new file mode 100644 index 0000000000..b0d651d67f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat @@ -0,0 +1,1139 @@ +# Table for the INT-INT interaction from +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# This table contains +# i r_i U(r_i) -dU/dr|r_i +# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) + +INT +N 1130 + +1 0.02 2.0331818401e+30 1.21990910406e+33 +2 0.04 4.9638228518e+26 1.48914685554e+29 +3 0.06 3.82579033251e+24 7.65158066501e+26 +4 0.08 1.21187081343e+23 1.81780622014e+25 +5 0.1 8.32791281704e+21 9.99349538045e+23 +6 0.12 9.34030842897e+20 9.34030842897e+22 +7 0.14 1.46892540453e+20 1.25907891817e+22 +8 0.16 2.95866897809e+19 2.21900173357e+21 +9 0.18 7.19889946863e+18 4.79926631242e+20 +10 0.2 2.0331818401e+18 1.21990910406e+20 +11 0.22 6.47834392264e+17 3.53364213962e+19 +12 0.24 2.28034873754e+17 1.14017436877e+19 +13 0.26 8.72681951932e+16 4.02776285507e+18 +14 0.28 3.58624366341e+16 1.53696157003e+18 +15 0.3 1.56704372019e+16 6.26817488078e+17 +16 0.32 7.2233129348e+15 2.70874235055e+17 +17 0.34 3.48970861422e+15 1.23166186384e+17 +18 0.36 1.75754381558e+15 5.85847938527e+16 +19 0.38 9.18613895646e+14 2.90088598625e+16 +20 0.4 4.96382285179e+14 1.48914685554e+16 +21 0.42 2.76404230108e+14 7.89726371739e+15 +22 0.44 1.58162693423e+14 4.31352800247e+15 +23 0.46 9.27773983256e+13 2.42027995633e+15 +24 0.48 5.56725765996e+13 1.391814415e+15 +25 0.5 3.41111308981e+13 8.18667141564e+14 +26 0.52 2.13057117167e+13 4.91670270393e+14 +27 0.54 1.35459994024e+13 3.0102220895e+14 +28 0.56 8.75547769351e+12 1.87617379153e+14 +29 0.58 5.74645813711e+12 1.18892237325e+14 +30 0.6 3.8257903322e+12 7.65158066491e+13 +31 0.62 2.58128463312e+12 4.99603477424e+13 +32 0.64 1.7635041342e+12 3.30657025205e+13 +33 0.66 1.21901470178e+12 2.21639036726e+13 +34 0.68 8.51979641904e+11 1.50349348607e+13 +35 0.7 6.0167184547e+11 1.0314374497e+13 +36 0.72 4.29087845387e+11 7.15146409276e+12 +37 0.74 3.08855637556e+11 5.00846980094e+12 +38 0.76 2.24270970425e+11 3.54112058818e+12 +39 0.78 1.64210505205e+11 2.52631546702e+12 +40 0.8 1.2118708117e+11 1.81780621971e+12 +41 0.82 90109367359.1 1.31867367068e+12 +42 0.84 67481501334.4 9.64021449503e+11 +43 0.86 50880896383.4 7.09965997788e+11 +44 0.88 38613938681.2 5.26553710913e+11 +45 0.9 29486692086.8 3.93155896009e+11 +46 0.92 22650731882.4 2.95444330322e+11 +47 0.94 17498544395.3 2.23385674464e+11 +48 0.96 13591937526.4 1.69899220331e+11 +49 0.98 10612635712.6 1.29950642555e+11 +50 1.0 8327912706.34 99934953582.6 +51 1.02 6566502316.69 77252969474.2 +52 1.04 5201589672.36 60018343356.8 +53 1.06 4138717434.11 46853405843.3 +54 1.08 3307128665.58 36745874940.0 +55 1.1 2653529579.27 28947596241.1 +56 1.12 2137567708.15 22902511945.9 +57 1.14 1728534024.3 18195095739.0 +58 1.16 1402943799.0 14513212422.1 +59 1.18 1142752163.37 11621209113.9 +60 1.2 934030766.093 9340308300.6 +61 1.22 765981286.774 7534242773.65 +62 1.24 630196371.787 6098675145.29 +63 1.26 520103253.414 4953364870.6 +64 1.28 430542934.103 4036340534.04 +65 1.3 357450462.101 3299543229.91 +66 1.32 297610947.802 2705554551.18 +67 1.34 248472587.186 2225128105.44 +68 1.36 208002782.573 1835319108.76 +69 1.38 174576985.011 1518061159.35 +70 1.4 146892484.084 1259078837.33 +71 1.42 123901294.937 1047053582.16 +72 1.44 104757721.536 872981382.419 +73 1.46 88777241.639 729676313.267 +74 1.48 75404158.02 611385405.387 +75 1.5 64186061.7033 513488820.507 +76 1.52 54753607.1486 432265633.695 +77 1.54 46804443.7318 364710253.134 +78 1.56 40090410.0598 308388060.159 +79 1.58 34407297.9713 261321529.95 +80 1.6 29586646.6744 221900119.2 +81 1.62 25489145.661 188808745.634 +82 1.64 21999316.2868 160970856.824 +83 1.66 19021212.5921 137502982.517 +84 1.68 16474936.8715 117678352.86 +85 1.7 14293808.3245 100897694.735 +86 1.72 12422056.6082 86665727.6626 +87 1.74 10812938.3788 74572197.8496 +88 1.76 9427195.57103 64276535.39 +89 1.78 8231790.46096 55495411.7777 +90 1.8 7198865.45512 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308970.999537 1584552.10475 +118 2.36 278972.551763 1418587.76828 +119 2.38 252103.765513 1271192.59046 +120 2.4 228015.837009 1140158.32224 +121 2.42 206401.282366 1023554.60663 +122 2.44 186988.75765 919692.114521 +123 2.46 169538.563484 827090.818108 +124 2.48 153838.739168 744452.651831 +125 2.5 139701.665073 670637.92543 +126 2.52 126961.103835 604644.949624 +127 2.54 115469.620781 545592.416037 +128 2.56 105096.332511 492704.141327 +129 2.58 95724.9397832 445295.843157 +130 2.6 87252.0069441 402763.664479 +131 2.62 79585.4554502 364574.203947 +132 2.64 72643.2434671 330255.845328 +133 2.66 66352.2073932 299391.208536 +134 2.68 60647.0444312 271610.570248 +135 2.7 55469.4181565 246586.123584 +136 2.72 50767.1714483 224026.964698 +137 2.74 46493.633237 203674.709811 +138 2.76 42607.0073083 185299.659567 +139 2.78 39069.8329526 168697.439095 +140 2.8 35848.5085794 153686.051901 +141 2.82 32912.8705664 140103.294183 +142 2.84 30235.8206098 127804.483324 +143 2.86 27792.9956998 116660.460548 +144 2.88 25562.4755962 106555.833042 +145 2.9 23524.5233195 97387.4254387 +146 2.92 21661.3547409 89062.9145204 +147 2.94 19956.9338374 81499.6244039 +148 2.96 18396.7906059 74623.4624292 +149 2.98 16967.8589974 68367.9785194 +150 3.0 15658.3325568 62673.5329856 +151 3.02 14457.5357325 57486.5596649 +152 3.04 13355.809067 52758.912937 +153 3.06 12344.4066925 48447.2886046 +154 3.08 11415.4047444 44512.7098736 +155 3.1 10561.6194689 40920.0707567 +156 3.12 9776.5339459 37637.7301715 +157 3.14 9054.23247117 34637.1508274 +158 3.16 8389.34175838 31892.5777179 +159 3.18 7776.97821258 29380.7516608 +160 3.2 7212.7006167 27080.6538766 +161 3.22 6692.4676457 24973.2780793 +162 3.24 6212.59969004 23041.4269669 +163 3.26 5769.74452856 21269.5303734 +164 3.28 5360.84644195 19643.4826615 +165 3.3 4983.1184041 18150.4972204 +166 3.32 4634.01702836 16778.97618 +167 3.34 4311.21998136 15518.393672 +168 3.36 4012.60560869 14359.191159 +169 3.38 3736.23454428 13292.6835236 +170 3.4 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b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.min @@ -0,0 +1,28 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# Optional: Make sure the pairwise energies look reasonable: +#pair_write 2 2 1001 r 2.6 16.0 test_tail-tail.dat t-t 0 0 +#pair_write 2 3 1001 r 2.6 16.0 test_tail-head.dat t-h 0 0 +#pair_write 1 2 1001 r 2.6 16.0 test_int-tail.dat i-t 0 0 +#pair_write 1 1 2573 r 2.6 16.0 test_int-int.dat i-i 0 0 +#pair_write 1 3 1001 r 2.6 16.0 test_int-head.dat i-h 0 0 +#pair_write 3 3 1001 r 2.6 16.0 test_head-head.dat h-h 0 0 + + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt new file mode 100644 index 0000000000..bd86869ab7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt @@ -0,0 +1,57 @@ +# -------- REQUIREMENTS: --------- +# 1) This example may require additional features and bug fixes for LAMMPS. +# Be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 2) Unpack it +# 3) copy the .cpp and .h files to the src folding of your lammps installation. +# 4) Compile LAMMPS. +# +# (If LAMMPS complains about an "Invalid pair_style" +# then you made a mistake in the instructions above.) +# + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy + + +# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon +# for the "epsilon" used by the coarse-grained lipid. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. +# Note: We maintain the system system at constant (zero) tention +# using a barostat damping parameter Pdamp=1000 ("0 0 1000") + + +# optional (not sure if this helps): +# balance x uniform y uniform + + +#restart 1000000 + +run 2000000 + +write_restart system_after_npt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt new file mode 100644 index 0000000000..775c074c21 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt @@ -0,0 +1,53 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Normally, I would minimize the system and equilibrate the system at constant +# pressure and temperature beforehand. If you run lammps with "run.in.npt", +# it will generate a restart file "system_after_npt.rst" with reasonable +# coordinates at that temperature and pressure. Then we could load it now: +# +#read_restart system_after_npt.rst +# +# Unfortunately the LAMMPS "read_restart" command has been undependable over +# the past year (2012), and I feel it is safer to remove it from the examples. +# Instead, for this example, I just read the raw coordinates generated by +# moltemplate (and the default volume). (I get fewer questions this way.) +# However you should never run any liquid simulations at constant volume without +# pressure equilibration first. Hopefully in the future "read_restart" will +# work. Until then, try "read_dump", "dump2data.py", or "restart2data". + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. +# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. + +#restart 1000000 + +run 1000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_FIRST.txt b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_FIRST.txt new file mode 100644 index 0000000000..b711a93c31 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_FIRST.txt @@ -0,0 +1,47 @@ +This is an implementation of the "two-stage" model used by Maxim Imakaev +in the Naumova et Al 2013 Science paper on metaphase chromatin. +(Download the supplemental materials section and scroll down to the section: + "Two-stage process: linear compaction - axial compression") + +---- SMALL MODIFICATION ---- + +Unlike that study, I did not use "softened" Lennard-Jones potentials +(which allow the chains to pass through each other). + +--- Why use moltemplate? --- + +Honestly, you don't need to use moltemplate to build this polymer. +It is almost counter-productive to use moltemplate to build this kind of +polymer because it is so simple. (The polymer has only 1 bead per atom. +It just makes it more complicated to introduce all these extra +files including monomer.lt, condensin.lt and system.lt, especially considering +that system.lt is a complex file which is generated by a separate script.) + +However building the sytem using moltemplate may pay off if you +replace each point-like monomer with a multi-atom molecule later on. +(Right now, using moltemplate to build this system is sort of overkill. + I'll post an example of building more complex models of chromatin eventually.) + +---- 30-nm fiber model: ---- + +Anyway, the two-stage model at the end of Naumova et al Science 2013 uses the "30nm-fiber" model, whose details are (somewhat vaguely) described in the supplemental materials section. + +For the 10nm model, + n=128000, + L=200, + U(alpha)=5*(1 - cos(alpha)) + bond_length=1.0 (=10nm) + sigma=1.0 (particle radius = 10nm) + +30nm-fiber model details: +"The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level." + +I interpret this to mean that, for the 30nm model, + n=128000/4.25~=30117 (however I rounded up to 32768=2^15) + L=200/4.25~=47 (however I rounded up to 51) + U(alpha)=1.17647*(1 - cos(alpha)) (5/4.25=1.17647) + +To increase the volume by a factor o 4.25, I increase both the diameter of each +bead (the "sigma" parameter), and the bond-lengths connecting them from +1.0 (corresponding to 10nm) to 4.25^(1/3)~=1.6198 (corresponding to 16.198nm). + diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt new file mode 100644 index 0000000000..38ad9c1c06 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt @@ -0,0 +1,29 @@ +--------------- +The average diameter of a mammalian cell nucleus is is 6 micrometers (μm), +which occupies about 10% of the total cell volume. + +(See "Molecular Biology of the Cell, Chapter 4, pages 191–234 (4th ed.)", by + Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, 2002) + +... of that, 25% of it is occupied by the nucleolus +http://en.wikipedia.org/wiki/Nucleolus +("citation needed") +--------------- + +From the supplemental material for the original HiC paper +(Lieberman-Aiden et al., Science 2009) + +Appendix 1. + Estimate of the Volume Fraction of Chromatin in Human Cells +In the simulations we sought to obtain an ensemble of structures that, in their statistical properties, resemble some of the features of chromatin arrangement in the cell. Below we demonstrate that chromatin occupies a significant fraction of cell volume, a property that we reproduced in simulations. Taking the nuclear diameter of a tissue culture cell to be 5-10um, and assuming close to a spherical shape we obtain the volume in the range 50-500 um^3, with a (geometric) mean of ~160 um^3. If we assume that the chromatin is built of DNA wrapped around nucleosomes, then we have 6x10^9bp/200bp=3x10^7 nucleosomes. Each may be approximated as a cylinder ~10nm in diameter and ~5nm in height, suggesting a volume of about 500nm3 each. The linker DNA after each nucleosome is about 50bps long, suggesting a volume of about 50*0.34nm*3.14*1nm^2=50nm^3. Thus the total volume of chromatin = 550x3x10^7 =16 um^3, or ~10% (3-23%) of the nuclear volume. This strikingly large volume fraction is itself a significant underestimate, since we ignored, among other things, all other DNA-bound proteins. Note that any further packing or localization of chromatin inside the nucleus will increase local density. +---- This next section mostly only justifies why they ---- +---- they did not stop the simulation when the globules ---- +---- were fully crumpled (ie with uniform density) ---- + In our simulations, the radius of the final crumpled globule was R≈12.5 and the volume V≈8000 cubic units. The total volume of the 4000 monomers, 1 unit in diameters each, is V≈2000. This implies a volume fraction of about 25%, which is consistent with the volume fraction estimated above. + ---- ---- + +Appendix 2. + Monomer length in base pairs +Each monomer of the chain corresponds to a fragment of chromatin that equals the Kuhn length of the chromatin fiber, i.e. approximately twice the persistence length of the fiber. Although the persistence length of the chromatin fiber is unknown it can be estimated using the following arguments. DNA is packed into nucleosomes, where 150 bps are wrapped around the histone core and do not contribute to flexibility of the fiber. The linker DNA of about 50 bps that connects consecutive nucleosomes is bendable, and is the source of flexibility in the fiber. Since the persistence length of double-stranded DNA is 150 bps, an equally flexible region of the nucleosomal DNA should contain 3 linkers, i.e. 3 consecutive nucleosomes packing about 600 bps of DNA. The excluded volume of the nucleosomes, nucleosome interactions, and other DNA-bound proteins can make the fiber less flexible or prohibit certain conformation and may tend to increase the persistence length of the fiber. Using this estimated lower bound estimate for the persistence length, we obtain the Kuhn length of the equivalent freely-jointed chain to be 6 nucleosomes, or ~ 1200bp. A simulated chain of 4000 monomers corresponds to 4.8Mb of packed DNA. The size of each monomer was chosen such that its volume is equal to (or slightly above) that of 6 nucleosomes (V=6 x 600 nm^3); thus the radius of the spherical monomer is R=10nm. The diameter of each globule shown in Figure 4 is about 200 nm. + + diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_run.sh new file mode 100755 index 0000000000..2ed2e747d2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_run.sh @@ -0,0 +1,7 @@ +# Run lammps using the following 3 commands: +# (assuming "lmp_linux" is the name of your LAMMPS binary) + +lmp_linux -i run.in.min +lmp_linux -i run.in.stage1 +lmp_linux -i run.in.stage2 + diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_setup.sh new file mode 100755 index 0000000000..14700a29cd --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_setup.sh @@ -0,0 +1,58 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # First, rescale and interpolate the positions + # where the monomers will be located. (This step is + # not needed if the coords_orig.raw file already has correct coordinates.) + + ./interpolate_coords.py 32768 1.6198059 < coords_orig.raw > coords.raw + + # Then, build the "system.lt" file + + ./generate_system_lt.py 32768 51 < coords.raw > system.lt + + # 32768 is the number of monomers in the polymer + # (which may be different from the number of coordinates + # in the "coords_orig.raw" file) This number will vary + # depending on how long you want the polymer to be. + # The second argument "51" is the average interval between + # condensin anchors (IE the "loop size" in monomers.) + + + # Run moltemplate + + moltemplate.sh system.lt -a "@bond:stage1 1" \ + -a "@bond:stage2 2" \ + -a "@atom:Monomer/A 1" + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + # + # We used the "-a" command to set the variable @bond:condensin to "2" + # because we will refer to it later in the "run.in" LAMMPS input script. + # (Of coarse, LAMMPS knows nothing about moltemplate variables, + # so in that file we refer to it as dihedral type "1") + + mv -f system.in* system.data ../ + + # We also need the table of bond forces used during "stage 2". + # (Like the system.data and the various input scripts, this file is needed by + # LAMMPS, so we need to copy it to the directory where we will run the sim.) + cp -f table_bonds_stage2.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + + # Optional: + # Remove the "system.lt" file created by "generate_system_lt.py" + #rm -f system.lt + +cd ../ + diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_visualize.txt new file mode 100644 index 0000000000..a5b46dc8a5 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/README_visualize.txt @@ -0,0 +1,131 @@ +NOTE: VMD DOES NOT ALLOW YOU TO VISUALIZE SYSTEMS WITH MANY BONDS ATTACHED + TO EACH ATOM. (IF IT DID, THE RESULTS WOULD BE UGLY ANWAY.) + +HOWEVER THIS MODEL ATTACHES APPROXIMATELY 60 BONDS TO EACH CONDENSIN ATOM. +IN ORDER TO PULL THE CONDENSIN MONOMERS TOGETHER. YOU MUST DELETE THOSE +BONDS (of type "1" or "2") FROM THE "system.data" FILE BEFORE YOU CARRY +OUT THE COMMANDS BELOW. (...And backup your "system.data" file. You'll need +all the bonds when you run the simulations.) + +-------------- COLORS --------------- +In order to show how the polymer is distributed along the length of the +cylinder, I recommend to select the +Graphics->Graphical Representations +menu option, and select "Index" from the "Coloring Method" pull-down menu. + +After doing this, you can switch from a red-white-blue scheme, to a +rainbow ("jet") scheme, by selecting the Extensions->Tk Console menu option +and loading the "vmd_colorscale_jet.tcl" file located in the "images" directory. +------------------------------------------- + +First, if you have not done so, download and install VMD: + +http://www.ks.uiuc.edu/Research/vmd/ +http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD + + + ------- To view a lammps trajectory in VMD -------- + +The system coordinates are initialy stored in a LAMMPS' ".data" file. +(If that file was built with moltemplate, it will be named "system.data".) + +The first step is to view that file. +Then you should create a ".psf" file +(The .psf file is necessary after you run the simulation + for viewing trajectories.) + +1) Build a PSF file for use in viewing with VMD + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +You will see a snapshot of the system on the screen. +(presumably the initial conformation at t=0) + +2) + +Later once you have run a simulation, +to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file + (It usually has names like "traj.lammpstrj". It depends on how you saved it.) + If necessary, for "file type" select: "LAMMPS Trajectory". + (However VMD should recognize the file type by the file extension.) + Load it. + + + + + +##################### PERIODIC BOUNDARY CONDITIONS ##################### + If you are only simulating a single molecule and you are not + using periodic boundary conditions, then ignore everything below. +######################################################################## + + ---- A note on trajectory format: ----- +If the trajectory is the standard LAMMPS format, (aka a "DUMP" file with +a ".lammpstrj" extension), then it's a good idea when you run the simulation +to tell LAMMPS you want to store the information needed for showing periodic +boundary conditions. (Even if you are not using periodic boundaries. +It never hurts to include a tiny bit of extra information.) To do that, +I've been using this command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 traj.lammpstrj id mol type x y z ix iy iz + +(Also: it's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. I think this is needed +to wrap atom coordinates visually without breaking molecules in half. Again +you don't need to worry about this if you are not using periodic boundaries.) + + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.5 -0.5 -0.5} + pbc box -shiftcenterrel {-0.5 -0.5 -0.5} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/stage2_interior.jpg b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/stage2_interior.jpg new file mode 100644 index 0000000000..8765cec85e Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/stage2_interior.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/stage2_interior_rotated.jpg b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/stage2_interior_rotated.jpg new file mode 100644 index 0000000000..2d46cc6a43 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/stage2_interior_rotated.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/t=0_before_minimizaion.jpg b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/t=0_before_minimizaion.jpg new file mode 100644 index 0000000000..06600ecc99 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/t=0_before_minimizaion.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/vmd_colorscale_jet.tcl b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/vmd_colorscale_jet.tcl new file mode 100644 index 0000000000..7434eca99e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/images/vmd_colorscale_jet.tcl @@ -0,0 +1,87 @@ + +proc lerpcolor { col1 col2 alpha } { + set dc [vecsub $col2 $col1] + set nc [vecadd $col1 [vecscale $dc $alpha]] + return $nc +} + +proc coltogs { col } { + foreach {r g b} $col {} + set gray [expr ($r + $g + $b) / 3.0] + return [list $gray $gray $gray] +} + +proc jet_tricolor_scale {} { + display update off + set mincolorid [expr [colorinfo num] - 1] + set maxcolorid [expr [colorinfo max] - 1] + set colrange [expr $maxcolorid - $mincolorid] + set colhalf [expr $colrange / 2] + for {set i $mincolorid} {$i < $maxcolorid} {incr i} { + set colpcnt [expr ($i - $mincolorid) / double($colrange)] + + # The following color definitions for "jet" sort-of came from: + #http://stackoverflow.com/questions/7706339/grayscale-to-red-green-blue-matlab-jet-color-scale + # but it was missing "green", so I inserted a green somewhere in the middle. + + # darkblue/violet 0.0 + set color0 { 0.08 0.0 0.77 } + + # blue 0.19 + set color1 { 0.0 0.0 1.0 } + + # cyan 0.34 + set color2 { 0.0 1.0 1.0 } + + # turquoise 0.4001 + set color3 { 0.0 1.0 0.78 } + + # green 0.445 + set color4 { 0.0 1.0 0.0 } + + # chartreuse 0.535 + set color5 { 0.875 1.0 0.0 } + + # yellow 0.69 + set color6 { 1.0 1.0 0.0 } + + # orange 0.73 + set color7 { 1.0 0.25 0.0 } + + # red 0.755 + set color8 { 1.0 0.0 0.0 } + + # darkred 1.0 + set color9 { 0.93 0.0 0.0 } + + if { $colpcnt < 0.19 } { + set nc [lerpcolor $color0 $color1 [expr $colpcnt/(0.19-0.0)]] + } elseif { $colpcnt < 0.34 } { + set nc [lerpcolor $color1 $color2 [expr ($colpcnt-0.19)/(0.34-0.19)]] + } elseif { $colpcnt < 0.4001 } { + set nc [lerpcolor $color2 $color3 [expr ($colpcnt-0.34)/(0.4001-0.34)]] + } elseif { $colpcnt < 0.445 } { + set nc [lerpcolor $color2 $color3 [expr ($colpcnt-0.4001)/(0.445-0.4001)]] + } elseif { $colpcnt < 0.535 } { + set nc [lerpcolor $color3 $color4 [expr ($colpcnt-0.445)/(0.535-0.445)]] + } elseif { $colpcnt < 0.69 } { + set nc [lerpcolor $color4 $color5 [expr ($colpcnt-0.535)/(0.69-0.535)]] + } elseif { $colpcnt < 0.73} { + set nc [lerpcolor $color5 $color6 [expr ($colpcnt-0.69)/(0.73-0.69)]] + } elseif { $colpcnt < 0.755} { + set nc [lerpcolor $color6 $color7 [expr ($colpcnt-0.73)/(0.755-0.73)]] + } else { + set nc [lerpcolor $color7 $color8 [expr ($colpcnt-0.755)/(1.0-0.755)]] + } + + # set nc [coltogs $nc] + foreach {r g b} $nc {} + puts "index: $i $r $g $b -- $colpcnt" + display update ui + color change rgb $i $r $g $b + } + display update on +} + +jet_tricolor_scale + diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/README_how_to_generate_system_lt.sh b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/README_how_to_generate_system_lt.sh new file mode 100755 index 0000000000..c23b222fa1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/README_how_to_generate_system_lt.sh @@ -0,0 +1,19 @@ + # First, rescale and interpolate the positions + # where the monomers will be located. (This step is not needed + # if the coords_orig.raw file already has correct coordinates.) + # The first argument, 32768 is the number of atoms in the desired file. + # The second argument, 1.6198059 = 4.25^(1/3), tells interpolate_coords.py + # to multiply all the coordinates (scale them up) by 1.6198059. + + ./interpolate_coords.py 32768 1.6198059 < coords_orig.raw > coords.raw + + # Then, build the "system.lt" file + + ./generate_system_lt.py 32768 51 < coords.raw > system.lt + + # 32768 is the number of monomers in the polymer + # (which may be different from the number of coordinates + # in the "coords_orig.raw" file) This number will vary + # depending on how long you want the polymer to be. + # The second argument "51" is the average interval between + # condensin anchors (IE the "loop size" in monomers.) diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/README_length_flexibility_details.txt b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/README_length_flexibility_details.txt new file mode 100644 index 0000000000..1d30ceb170 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/README_length_flexibility_details.txt @@ -0,0 +1,57 @@ +---- Andrew's comments ---- + +The two-stage model at the end of Naumova et al Science 2013 uses the "30nm-fiber" model, whose details are (somewhat vaguely) described in the supplemental materials section. + +For the 10nm model, + n=128000, + L=200, + U(alpha)=5*(1 - cos(alpha)) + bond_length=1.0 (=10nm) + sigma=1.0 (particle radius = 10nm) + +30nm-fiber model details: +"The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level." + +I interpret this to mean that, for the 30nm model, + n=128000/4.25~=30117 + L=200/4.25~=47 + U(alpha)=1.17647*(1 - cos(alpha)) (5/4.25=1.17647) +To increase the volume by a factor o 4.25, originally I thought I should increase the "sigma" parameter from 1.0 to 4.25^(1/3)~=1.6198. But I suspect that the bond-lengths between monomers should be fixed at 1.0. If that is the case, then, perhaps I should increase "sigma" from 1.0 to 4.25^(1/2)~=2.061552, and keep the bond-length fixed at 1.0 (which in the units used by thsi paper, corresponds to 10nm). (That would increase the volume of a cylinder of radius "sigma" and length="bond-length" by a factor of 4.25) + bond_length=1.0 (10nm again) + sigma=2.061552 (Yes, this is less than 3.0<-->30nm. See below.) + + + + +--- Excerpts from the Supplemental section of Naumova et al Science 2013 --- + +From p. 18 of the supplemental materials section of Naumova et al Science 2013. + + (This section was probably written by Maxim Imakaev.) + + In vivo, the structure of the chromatin fiber can be complicated and many details remain unknown, particularly in metaphase. Given this uncertainty, we simulated chromatin as a homogeneous “beads-on-a-string†polymer fiber. We consider a 10nm fiber, as the pervasiveness of the 30nm fiber in vivo has become increasingly contested. In our simulations, 77Mb is represented by a densely-packed 10nm fiber of 128,000 monomers. Each monomer represents a 10nm-sized DNA-histone complex containing 3 nucleosomes (around 600bp). The fiber has a persistence length of 4 monomers (~2.4Kb), which is based on earlier estimates of 5-10 nucleosomes for interphase (14). Those estimates arise from the assumption that 5-10 linker DNA fragments, each of 20-40bp, can collectively provide flexibility equal to that of the 150bp persistence length of DNA. Binding of proteins to the linker DNA (e.g. histone H1) and interactions between neighboring nucleosomes can further constrain dynamics, requiring more linkers to provide the persistence length. Due to the tight packing of nucleosomes in metaphase, we use the upper limit of this range, i.e. 12 nucleosomes. + For the consecutive loops on a scaffold model (the final folded state model with the best agreement with Hi-C data), we also performed simulations with a more flexible 10nm fiber, or with a 30nm fiber, and found similar results. The more flexible 10nm fiber was modeled by decreasing persistence length to 1.8 monomers. The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level. We note that a classic model of a 30nm fiber is much less dense than a compact metaphase chromosome. A textbook model of a 30nm fiber assumes packing of about 6 nucleosomes per 10nm of fiber length. This model predicts that only 28% of the volume of the fiber (a 30nm-diameter cylinder) is occupied by nucleosomes, assuming a nucleosome shell volume of 328 nm^3. This is much less than the estimated 30-50% density of nucleosomes in a metaphase chromosome, assuming a diameter of 600nm, a packing density of 50-70 Mb/um, and the same nucleosome volume. (See also (15), which gives an estimate of 0.14-0.18 pg/μm for DNA only, and would give about twice the density if DNA is counted with nucleosomes). As follows, these fibers would have to interdigitate, and fill in gaps within each other. We account for this overlap by assuming the effective diameter of the fiber to be less than 30nm. The effective diameter was chosen to make the volume of the fiber equal the total volume of all the nucleosomes. + + We accounted for topoisomerase II activity by allowing chromatin fibers to pass through each other, while still having excluded volume interactions. This was achieved by using a soft-core Lennard-Jones potential with 1kT energy cost for monomer overlap (see below). This allows for changes in the topological state of a chromosome that are known to occur during compaction in vivo. + +Our simulations of a two-step folding process show that Hi-C data for mitotic chromosomes is consistent with a linearly compressed array of consecutive chromatin loops. Whereas mechanisms for formation of consecutive chromatin loops have been proposed, the process of axial compression is less understood. Chromatid compression cannot be accomplished by increased chromatin-chromatin affinity alone, as this would lead to condensation into a globular geometry (14, 16, 17). However, mechanisms which locally compress the fiber of loop bases naturally allow for anisotropic compression into a shorter and thicker fiber, with the same width regardless of chromosome length (18). Differences in the duration or efficiency of the first and second stages of chromosomal condensation provide a natural mechanism for condensation-related proteins to separately affect mitotic chromosome length and width (19). We also note that the axis of loop-bases in our two-stage model does not necessarily form a continuous and rigid scaffold (Figure S26). As follows, we remain agnostic about the molecular details of the chromosomal scaffold, which might for example be formed by a network consisting of protein-protein and/or protein-DNA interactions (20). + + 1. Polymer simulations + + To perform Langevin dynamics polymer simulations we used OpenMM, a high-performance GPU-assisted molecular dynamics API (21, 22). To represent chromatin fibers as polymers, we used a sequence of spherical monomers of 1 unit of length in diameter. Here and below all distances are measured in monomer sizes, set to be 10nm unless specified otherwise. Neighboring monomers are connected by harmonic bonds, with a potential U = 100*(r - 1)^2 (here and below in units of kT). Polymer stiffness is modeled with a three point interaction term, with the potential U = 5*(1 - cos(alpha)), where alpha is the angle between neighboring bonds. All monomers interact via either a shifted Lennard-Jones (LJ) repulsive potential, or an attractive Lennard-Jones potential. At high densities in a confined volume, the details of the inter-monomer interactions become negligible due to screening (23), and we therefore used the computationally efficient shifted LJ potential. The shifted LJ potential allows for a short-range repulsion by truncating the LJ potential at its minimum and shifting the minimum to zero: U = 4 * (1/r^12 - 1/r^6) + 1, for r<2^(1/6); U=0 for r > 2^(1/6). The shifted LJ potential is one of the most computationally efficient repulsive potentials due to a very short cutoff radius. + + To allow chain passing, which represents activity of topoisomerase II, we softened the shifted LJ potential by truncating the interaction energy at Ecutoff = 1 kT. At energies more than 0.5 Ecutoff, the LJ potential was softened via: Usoftened = 0.5 * Ecutoff * (1 + tanh(2*U/Ecutoff - 1)). To avoid numerical 19instabilities in the calculation of U at r ~ 0, the interaction radius r was truncated at r=0.3 via: rtruncated = (r^10 + (0.3)^10)^0.1, which introduced negligible shift in a final softened potential. For an attractive LJ potential, we used: U = 4 * e * (1/r^12 - 1/r^6), with e = 0.46 kT, slightly below the theta-temperature. The attractive potential was similarly softened at 2 kT and cut off at r=2.5. Unless noted, we used a softened shifted LJ repulsive potential. + + Polymer models were visualized using Pymol and Rasmol. For images with loop bases highlighted, a base of each loop and 3 monomers surrounding it in each direction were labeled in red. + + SECTIONS 2-5 SKIPPED + +6. Two-stage process: linear compaction - axial compression + +To simulate the two-stage process of metaphase chromosome folding, we used the 30nm fiber representation described above for its computational efficiency. Simulations were initialized from 30000 monomer fractal globule conformations; fractal globule is a model for interphase chromatin organization. First, random consecutive loops with L=100 monomers (see above) were introduced, and anchors of neighboring loops were brought together using harmonic springs with a potential U = k * (r – r0)2; r0=0.5. To avoid abrupt motion of the loop anchors, the force was gradually turned on over the first +300000 timesteps, with k linearly increasing in time from 0 to 10 kT. We used softened shifted repulsive LJ potential for inter-monomer interaction. + +Upon completion of linear compaction, axial compression was initiated. This involves following changes: the repulsive LJ force is replaced with an attractive LJ force for all monomers, and the chromosomal core of loop anchors is homogeneously compressed. To achieve the latter, all anchor pairs separated by less than 30 anchors were attracted via a potential U = step(d-3) * abs(d-3) * 10 kT, which implements a constant attractive force between two anchors if they are separated by a distance larger than 3. The interactions between neighboring loop anchors were kept throughout this process. + +To obtain the contact map from this simulation, 50 independent runs of 1.5e7 timesteps were performed, and 250 conformations were collected from the second half of each run. The contact map was calculated from all conformations of all runs at a 30-monomer resolution, and was further averaged over three 10000-monomer blocks along the diagonal of the heatmap. The latter was done to show contact map at a relevant length scale (0 to 25 Mb), and to achieve a better averaging of the contact map. + diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/calc_table.sh b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/calc_table.sh new file mode 100755 index 0000000000..aed66719f0 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/calc_table.sh @@ -0,0 +1,8 @@ + + +for ((i=0; i<60; i++)); do echo "$((i+1)) " `echo "$i*0.05" | bc` 0 0; done + +echo 61 3.0 0 -5 + +for ((i=61; i<=4000; i++)); do echo "$((i+1)) " `echo "$i*0.05" | bc` `echo "($i-60)*0.5"|bc` -10; done + diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/condensin.lt b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/condensin.lt new file mode 100644 index 0000000000..f8dfea089b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/condensin.lt @@ -0,0 +1,47 @@ +# This file contains the definition of a molecule named "CondensinMonomer". +# (This particular molecule contain only one atom, but that is up to you.) +# Later, multiple CondensinMonomers can be connected together to build a molecule. + + + +CondensinMonomer { + + # atom-id mol-id(ignore) atom-type q x y z + + write("Data Atoms") { + $atom:a $mol @atom:A 0.000 0.00000 0.00000 0.00000 + } + + # (The x y z positions will be changed later with move commands + # You can spedify charge and other properties by changing the atom_style.) + + + + # atom-type mass + + write_once("Data Masses") { + @atom:A 1.0 + } + + # pairwise interactions (between non-bonded atoms): + # + # U(r) = 4*eps*((r/sig)^12 - (r/sig)^6) + # + # Note: when sigma=0.8908987181403393=2^(1/6), the minimia is at r=1.0 + # + # atom-type atom-type pair_style epsilon sigma + + write_once("In Settings") { + # I usually use sigma = 2^(-(1/6)), with a cutoff of 1 + #pair_coeff @atom:A @atom:A lj/cut 1.0 0.8908987181403393 1.0 + # In the 2013 Science (metaphase) paper, Imakaev used sigma=1.0 + # with a cutoff of 2^(1/6). Here we are trying to reproduce his results. + # 10nm fiber + #pair_coeff @atom:A @atom:A lj/cut 1.0 1.0 1.122462048309373 + # 30nm fiber (4.25^(1/2)=2.0615528128088303) + #pair_coeff @atom:A @atom:A lj/cut 1.0 2.0615528128088303 2.314014792963349 + # 30nm fiber (4.25^(1/3)=1.6198059006387417) + pair_coeff @atom:A @atom:A lj/cut 1.0 1.6198059006387417 1.8181706490945708 + } + +} # CondensinMonomer diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/coords_orig.raw b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/coords_orig.raw new file mode 100644 index 0000000000..9137c70616 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/coords_orig.raw @@ -0,0 +1,32768 @@ +-25.8563 0.5868639 -10.5686 +-26.7104 0.5123159 -10.988 +-26.6472 -0.3489721 -10.3989 +-27.477 0.09032793 -9.96323 +-27.5656 0.5432849 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b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/generate_system_lt.py new file mode 100755 index 0000000000..796347bb0b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/generate_system_lt.py @@ -0,0 +1,301 @@ +#!/usr/bin/env python + +err_msg = """ +Usage: + + generate_system_lt.py n < monomer_coords.raw > system.lt + +Example: + + generate_system_lt.py 30118 47 < coords.raw > system.lt + +Explanation: + ARGUMENTS: + n = total length of the polymer (in monomers) + L = the (average) length of each condensin interval (Poisson- + distributed) This is also 1/probability that each monomer + is a "condensin monomer". + + (Note: 30117 ~= 128000/4.25, but using 30118 makes interpolation cleaner, + and 47 = 200/4.25. Note that 128000 and 200 are for the 10nm model. + See the supplemental section of Naumova et al Science 2013, p 18.) + +""" + + +import sys +import random +from math import * + +# Parse the argument list: +if len(sys.argv) <= 2: + sys.stderr.write("Error:\n\nTypical Usage:\n\n"+err_msg+"\n") + exit(1) +N=int(sys.argv[1]) +L=float(sys.argv[2]) +if len(sys.argv) > 3: + delta_x = float(sys.argv[3]) +else: + delta_x = 2.0 +if len(sys.argv) > 4: + x_offset = float(sys.argv[4]) +else: + x_offset = -((N-1.0)/2) * delta_x + + +coords = [[0.0, 0.0, 0.0] for i in range(0,N)] +lines = sys.stdin.readlines() +if len(lines) != N: + sys.stderr.write("Error: Number of lines in input file ("+str(len(lines))+")\n" + " does not match first argument ("+str(N)+")\n") + exit(1) +for i in range(0, N): + coords[i] = map(float, lines[i].split()) + +# Now calculate the box_boundaries: +box_bounds_min = [0.0, 0.0, 0.0] +box_bounds_max = [0.0, 0.0, 0.0] +for i in range(0, N): + for d in range(0, 3): + if i == 0: + box_bounds_min[d] = coords[i][d] + box_bounds_max[d] = coords[i][d] + else: + if coords[i][d] > box_bounds_max[d]: + box_bounds_max[d] = coords[i][d] + if coords[i][d] < box_bounds_min[d]: + box_bounds_min[d] = coords[i][d] + +# Now scale the box boundaries outward by 50% +box_scale = 1.5 +for d in range(0,3): + box_bounds_cen = 0.5*(box_bounds_max[d] + box_bounds_min[d]) + box_bounds_width = box_bounds_max[d] - box_bounds_min[d] + box_bounds_min[d] = box_bounds_cen - 0.5*box_scale*box_bounds_width + box_bounds_max[d] = box_bounds_cen + 0.5*box_scale*box_bounds_width + +# Now calculate the direction each molecule should be pointing at: +direction_vects = [[0.0, 0.0, 0.0] for i in range(0,N)] +for d in range(0, 3): + direction_vects[0][d] = coords[1][d] - coords[0][d] + direction_vects[N-1][d] = coords[N-1][d] - coords[N-2][d] +for i in range(1, N-1): + for d in range(0, 3): + direction_vects[i][d] = coords[i+1][d] - coords[i-1][d] + +# Optional: normalize the direction vectors +for i in range(1, N-1): + direction_len = 0.0 + for d in range(0, 3): + direction_len += (direction_vects[i][d])**2 + direction_len = sqrt(direction_len) + for d in range(0, 3): + direction_vects[i][d] /= direction_len + +# Now, begin writing the text for the system.lt file: + +sys.stdout.write( +""" +import "monomer.lt" # <-- defines "Monomer" +import "condensin.lt" # <-- defines "CondensinMonomer" + + +""" +) + + + +# Figure out which monomers are "Monomers" and which monomers are +# "CondensinMonomers" + +ic = 0 # count the number of condensins added so far +condensin_is_here = [False for i in range(0, N)] +for i in range(0, N): + #add_condensin_here = random.random() < (1.0 / L) + add_condensin_here = random.random() < (1.0 / (L-2.0)) + + # We do not allow condensin at successive sites separated by less than 2 + # subunits (the "L-2.0" above is to compensate for this) + if (((i > 0) and condensin_is_here[i-1]) or + ((i > 1) and condensin_is_here[i-2])): + add_condensin_here = False + + if add_condensin_here: + condensin_is_here[i] = True + ic += 1 +Nc = ic + + +ic = 0 +for i in range(0, N): + if condensin_is_here[i]: + sys.stdout.write("condensins["+str(ic)+"] = new CondensinMonomer.scale(0.5,0.8,0.8).rotvv(1,0,0,") + ic+=1 + else: + sys.stdout.write("monomers["+str(i)+"] = new Monomer.scale(0.5,0.8,0.8).rotvv(1,0,0,") + sys.stdout.write(str(direction_vects[i][0])+"," + +str(direction_vects[i][1])+"," + +str(direction_vects[i][2])+ + ").move(" + +str(coords[i][0])+"," + +str(coords[i][1])+"," + +str(coords[i][2])+")\n") + + #if condensin_is_here[i]: + # if i < N-1: + # sys.stdout.write("\n" + # "#(override the dihedral angle for this monomer)\n" + # "write(\"Data Dihedrals\") {\n" + # " $dihedral:twistor"+str(i+1)+" @dihedral:CondensinMonomer/TWISTOR $atom:monomers["+str(i)+"]/t $atom:monomers["+str(i)+"]/c $atom:monomers["+str(i+1)+"]/c $atom:monomers["+str(i+1)+"]/t\n" + # "}\n" + # "\n") + + + +sys.stdout.write( +""" + +# ---------------- simulation box ----------------- + +# Now define a box big enough to hold a polymer with this (initial) shape + +""" +) + + +sys.stdout.write("write_once(\"Data Boundary\") {\n" + +str(box_bounds_min[0])+" "+str(box_bounds_max[0])+" xlo xhi\n" + +str(box_bounds_min[1])+" "+str(box_bounds_max[1])+" ylo yhi\n" + +str(box_bounds_min[2])+" "+str(box_bounds_max[2])+" zlo zhi\n" + "}\n\n\n") + + +sys.stdout.write( +""" +# What kind of boundary conditions are we using? + +write_once("In Init") { + boundary s s s # <-- boundary conditions in x y z directions + #boundary p p p # <-- boundary conditions in x y z directions +} +# "p" stands for "periodic" +# "s" stands for "shrink-wrapped" (non-periodic) + + +# ---- Bonds ---- + + +write_once("In Settings") { + # 10nm model: + #bond_coeff @bond:backbone harmonic 100.0 1.0 + # 30nm fiber (4.25^(1/3)=1.6198059006387417) + bond_coeff @bond:backbone harmonic 100.0 1.6198059006387417 +} + + +""" +) + + +sys.stdout.write("write(\"Data Bonds\") {\n") + +# Old bond-loop was simple: +#for i in range(0, N-1): +# sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:monomers["+str(i)+"]/a $atom:monomers["+str(i+1)+"]/a\n") + +ic = 0 +for i in range(0, N-1): + #sys.stderr.write("i="+str(i)+", ic="+str(ic)+", Nc="+str(Nc)+"\n") + + # Figure out if the first atom in the bond pair + # belongs to a regular Monomer or a CondensinMonomer + if condensin_is_here[i]: + sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:condensins["+str(ic)+"]/a") + ic+=1 + else: + sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:monomers["+str(i)+"]/a") + + # Do the same thing for the second atom in the bond pair + if condensin_is_here[i+1]: + assert(ic coords.raw + +Example: + + interpolate_coords.py 30118 3.0 < coords_orig.raw > coords.raw + + # (Note: 30117 ~= 128000/4.25, but using 30118 makes interpolation cleaner. + # See the supplemental section of Naumova et al Science 2013, p 18.) + +""" + + +import sys +from math import * + +# Parse the argument list: +if len(sys.argv) <= 1: + sys.stderr.write("Error:\n\nTypical Usage:\n\n"+err_msg+"\n") + exit(1) + +n_new = int(sys.argv[1]) + +if len(sys.argv) > 2: + scale = float(sys.argv[2]) +else: + scale = 1.0 + +coords_orig = [] + +lines = sys.stdin.readlines() + +for line in lines: + tokens = line.split() + if (len(tokens) > 0): + coords_orig.append(map(float, tokens)) + g_dim = len(tokens) + +n_orig = len(coords_orig) + +if n_orig < 2: + sys.stderr.write("Error:\n\nInput file contains less than two lines of coordinates\n") + exit(1) + +if n_new < 2: + sys.stderr.write("Error:\n\nOutput file will contain less than two lines of coordinates\n") + exit(1) + +coords_new = [[0.0 for d in range(0, g_dim)] for i in range(0, n_new)] + +for i_new in range(0, n_new): + I_orig = (i_new) * (float(n_orig-1) / float(n_new-1)) + i_orig = int(floor(I_orig)) + i_remainder = I_orig - i_orig + + if (i_new < n_new-1): + for d in range(0, g_dim): + coords_new[i_new][d] = scale*(coords_orig[i_orig][d] + + + i_remainder*(coords_orig[i_orig+1][d]- + coords_orig[i_orig][d])) + else: + for d in range(0, g_dim): + coords_new[i_new][d] = scale*coords_orig[n_orig-1][d] + + # print the coordates + for d in range(0, g_dim-1): + sys.stdout.write(str(coords_new[i_new][d]) + ' ') + sys.stdout.write(str(coords_new[i_new][g_dim-1]) + "\n") diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/monomer.lt b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/monomer.lt new file mode 100644 index 0000000000..9ef2b03984 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/monomer.lt @@ -0,0 +1,84 @@ +# This file contains the definition of a molecule named "Monomer". +# (This particular molecule contain only one atom, but that is up to you.) +# Later, multiple monomers can be connected together to build a molecule. + + + +Monomer { + + # atom-id mol-id(ignore) atom-type q x y z + + write("Data Atoms") { + $atom:a $mol @atom:A 0.000 0.00000 0.00000 0.00000 + } + + # (The x y z positions will be changed later with move commands + # You can spedify charge and other properties by changing the atom_style.) + + + + # atom-type mass + + write_once("Data Masses") { + @atom:A 1.0 + } + + # pairwise interactions (between non-bonded atoms): + # + # U(r) = 4*eps*((r/sig)^12 - (r/sig)^6) + # + # Note: when sigma=0.8908987181403393=2^(1/6), the minimia is at r=1.0 + # + # atom-type atom-type pair_style epsilon sigma rcutoff + + write_once("In Settings") { + # I usually use sigma = 2^(-(1/6)), with a cutoff of 1 + #pair_coeff @atom:A @atom:A lj/cut 1.0 0.8908987181403393 1.0 + # In the 2013 Science (metaphase) paper, Imakaev used sigma=1.0 + # with a cutoff of 2^(1/6). Here we are trying to reproduce his results. + # 10nm fiber + #pair_coeff @atom:A @atom:A lj/cut 1.0 1.0 1.122462048309373 + # 30nm fiber (4.25^(1/2)=2.0615528128088303) + #pair_coeff @atom:A @atom:A lj/cut 1.0 2.0615528128088303 2.314014792963349 + # 30nm fiber (4.25^(1/3)=1.6198059006387417) + pair_coeff @atom:A @atom:A lj/cut 1.0 1.6198059006387417 1.8181706490945708 + } + +} # Monomer + + + + +# -------------------------------------------------------------------- +# +# At some point we need to specify which force-field styles we want. +# LAMMPS also allows you to customize the kinds of properties you want +# each atom to have (the "atom_style"), such as charge, molecule-id, dipole etc. +# I typically specify this here. Doing it this way means that all systems built +# from "Monomers" (ie which import "monomer.lt") share these atom-styles +# and force-field styles by default. You can override these settings later. + + +write_once("In Init") { + # Default styles for molecules built out of "Monomers" + units lj + atom_style full + + bond_style hybrid harmonic table linear 4001 + angle_style hybrid cosine + dihedral_style none + + # If you need angles, dihedrals and impropers, uncomment or replace: + # angle_style hybrid harmonic + # dihedral_style hybrid fourier + + pair_style hybrid lj/cut 2.5 + + # If you are using gpu acceleration uncomment these lines: + # package gpu force/neigh 0 0 1.0 + # pair_style hybrid lj/cut/gpu 4.0 + + pair_modify mix arithmetic + special_bonds lj/coul 1 1 1 +} + diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/table_bonds_stage2.dat b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/table_bonds_stage2.dat new file mode 100644 index 0000000000..1bfb911c09 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/moltemplate_files/table_bonds_stage2.dat @@ -0,0 +1,4011 @@ +# This table contains the bond potential between condensin-anchors +# used by Imakaev in the Science 2013 (metaphase chromatin HiC) paper, +# two-stage model, during stage 2. +# +# i r_i U(r_i) -dU/dr|r_i +# where U(r) = step(d-3) * abs(d-3) * 10 + +STAGE2 +N 4001 FP 0 0 EQ 0 + +1 0 0 0 +2 .05 0 0 +3 .10 0 0 +4 .15 0 0 +5 .20 0 0 +6 .25 0 0 +7 .30 0 0 +8 .35 0 0 +9 .40 0 0 +10 .45 0 0 +11 .50 0 0 +12 .55 0 0 +13 .60 0 0 +14 .65 0 0 +15 .70 0 0 +16 .75 0 0 +17 .80 0 0 +18 .85 0 0 +19 .90 0 0 +20 .95 0 0 +21 1.00 0 0 +22 1.05 0 0 +23 1.10 0 0 +24 1.15 0 0 +25 1.20 0 0 +26 1.25 0 0 +27 1.30 0 0 +28 1.35 0 0 +29 1.40 0 0 +30 1.45 0 0 +31 1.50 0 0 +32 1.55 0 0 +33 1.60 0 0 +34 1.65 0 0 +35 1.70 0 0 +36 1.75 0 0 +37 1.80 0 0 +38 1.85 0 0 +39 1.90 0 0 +40 1.95 0 0 +41 2.00 0 0 +42 2.05 0 0 +43 2.10 0 0 +44 2.15 0 0 +45 2.20 0 0 +46 2.25 0 0 +47 2.30 0 0 +48 2.35 0 0 +49 2.40 0 0 +50 2.45 0 0 +51 2.50 0 0 +52 2.55 0 0 +53 2.60 0 0 +54 2.65 0 0 +55 2.70 0 0 +56 2.75 0 0 +57 2.80 0 0 +58 2.85 0 0 +59 2.90 0 0 +60 2.95 0 0 +61 3.0 0 -5 +62 3.05 .5 -10 +63 3.10 1.0 -10 +64 3.15 1.5 -10 +65 3.20 2.0 -10 +66 3.25 2.5 -10 +67 3.30 3.0 -10 +68 3.35 3.5 -10 +69 3.40 4.0 -10 +70 3.45 4.5 -10 +71 3.50 5.0 -10 +72 3.55 5.5 -10 +73 3.60 6.0 -10 +74 3.65 6.5 -10 +75 3.70 7.0 -10 +76 3.75 7.5 -10 +77 3.80 8.0 -10 +78 3.85 8.5 -10 +79 3.90 9.0 -10 +80 3.95 9.5 -10 +81 4.00 10.0 -10 +82 4.05 10.5 -10 +83 4.10 11.0 -10 +84 4.15 11.5 -10 +85 4.20 12.0 -10 +86 4.25 12.5 -10 +87 4.30 13.0 -10 +88 4.35 13.5 -10 +89 4.40 14.0 -10 +90 4.45 14.5 -10 +91 4.50 15.0 -10 +92 4.55 15.5 -10 +93 4.60 16.0 -10 +94 4.65 16.5 -10 +95 4.70 17.0 -10 +96 4.75 17.5 -10 +97 4.80 18.0 -10 +98 4.85 18.5 -10 +99 4.90 19.0 -10 +100 4.95 19.5 -10 +101 5.00 20.0 -10 +102 5.05 20.5 -10 +103 5.10 21.0 -10 +104 5.15 21.5 -10 +105 5.20 22.0 -10 +106 5.25 22.5 -10 +107 5.30 23.0 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196.75 1937.5 -10 +3937 196.80 1938.0 -10 +3938 196.85 1938.5 -10 +3939 196.90 1939.0 -10 +3940 196.95 1939.5 -10 +3941 197.00 1940.0 -10 +3942 197.05 1940.5 -10 +3943 197.10 1941.0 -10 +3944 197.15 1941.5 -10 +3945 197.20 1942.0 -10 +3946 197.25 1942.5 -10 +3947 197.30 1943.0 -10 +3948 197.35 1943.5 -10 +3949 197.40 1944.0 -10 +3950 197.45 1944.5 -10 +3951 197.50 1945.0 -10 +3952 197.55 1945.5 -10 +3953 197.60 1946.0 -10 +3954 197.65 1946.5 -10 +3955 197.70 1947.0 -10 +3956 197.75 1947.5 -10 +3957 197.80 1948.0 -10 +3958 197.85 1948.5 -10 +3959 197.90 1949.0 -10 +3960 197.95 1949.5 -10 +3961 198.00 1950.0 -10 +3962 198.05 1950.5 -10 +3963 198.10 1951.0 -10 +3964 198.15 1951.5 -10 +3965 198.20 1952.0 -10 +3966 198.25 1952.5 -10 +3967 198.30 1953.0 -10 +3968 198.35 1953.5 -10 +3969 198.40 1954.0 -10 +3970 198.45 1954.5 -10 +3971 198.50 1955.0 -10 +3972 198.55 1955.5 -10 +3973 198.60 1956.0 -10 +3974 198.65 1956.5 -10 +3975 198.70 1957.0 -10 +3976 198.75 1957.5 -10 +3977 198.80 1958.0 -10 +3978 198.85 1958.5 -10 +3979 198.90 1959.0 -10 +3980 198.95 1959.5 -10 +3981 199.00 1960.0 -10 +3982 199.05 1960.5 -10 +3983 199.10 1961.0 -10 +3984 199.15 1961.5 -10 +3985 199.20 1962.0 -10 +3986 199.25 1962.5 -10 +3987 199.30 1963.0 -10 +3988 199.35 1963.5 -10 +3989 199.40 1964.0 -10 +3990 199.45 1964.5 -10 +3991 199.50 1965.0 -10 +3992 199.55 1965.5 -10 +3993 199.60 1966.0 -10 +3994 199.65 1966.5 -10 +3995 199.70 1967.0 -10 +3996 199.75 1967.5 -10 +3997 199.80 1968.0 -10 +3998 199.85 1968.5 -10 +3999 199.90 1969.0 -10 +4000 199.95 1969.5 -10 +4001 200.00 1970.0 -10 diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/run.in.min b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/run.in.min new file mode 100644 index 0000000000..c8c28cd7a1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/run.in.min @@ -0,0 +1,41 @@ +######################################################### +# Example how to run this file: +# +# 1) Choose a ransom seed (in this case 141203) +# (or use `bash -c 'echo $RANDOM'`) +# +# 2) Then, from the shell, invoke LAMMPS to collapse the polymer: +# +# lmp_ubuntu_parallel -i run.in -var seed 141203 +# +######################################################### +# eg: +# time mpirun -np 2 lmp_ubuntu_parallel -i run.in.min +######################################################### + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + +dump 1 all custom 10000 traj_min.lammpstrj id mol type x y z ix iy iz +thermo_style custom step pe etotal vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 100 #(time interval for printing out "thermo" data) + +# Now minimize the system: + +min_style quickmin +min_modify dmax 0.05 +minimize 1.0e-7 1.0e-8 30000 100000000 + +write_data system_after_min.data diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/run.in.stage1 b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/run.in.stage1 new file mode 100644 index 0000000000..bf129df04f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/run.in.stage1 @@ -0,0 +1,110 @@ +# PREREQUISITES: You must run LAMMPS using "run.in.min" beforehand. +# (This will create the "system_after_min0.data" file needed below.) +######################################################### +# Run using: +# +# lmp_ubuntu_parallel -i run.in.stage1 +# +######################################################### +# GPUs: +# To enable gpu acceleration, make sure settings.in.init includes this line: +# package gpu force/neigh 0 0 1.0 (make sure it is not commented out.) +# ...and replace "lj/cut" in the "settings.in.init" and "settings.in.settings" +# files with "lj/cut/gpu" + + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +#read_data system.data +read_data system_after_min.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + +# DON'T MINIMIZE FIRST UNLESS YOU CHOOSE THE CORRECT INITIAL KbondC FORMULA +#thermo_style custom step pe etotal vol epair ebond eangle edihed +#thermo_modify norm no #(report total energy not energy / num_atoms) +#thermo 20 #(time interval for printing out "thermo" data) +#min_style sd +#min_modify dmax 0.05 +#minimize 1.0e-7 1.0e-8 20000 1000000 +#write_data system_after_min_t=0.data + + +mass * 1.0 +timestep 0.005 # "dt" +dump 1 all custom 25000 traj_stage1.lammpstrj id mol type x y z ix iy iz +reset_timestep 0 + + +# --- run the simulation --- + + +# set the velocity to zero +velocity all create 0.0 123456 + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve" +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Tstart Tstop tdamp randomseed + +fix fxlan all langevin 1.0 1.0 10.0 123456 + +# pstart pstop pdamp(time-units, 2000 iters usually) +#fix fxnph all nph x -0.000 -0.000 1.0 +fix fxnve all nve +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + +fix fxcenter all recenter 0.0 0.0 0.0 + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 1000 #(time interval for printing out "thermo" data) + +#balance dynamic x 20 1.0 -out tmp.balance +#balance x uniform + + +variable nloop1 loop 300 + + label loop1 + + print "############### LOOP ${nloop1} ###############" + + # Now, change the bond-strength between condensin monomers. + # From the Naumova et al Science 2013 paper (supp materials) + # "Two-stage model: linear compaction + axial compression" + # "First, random consecutive loops with L=100 monomers (see above) were + # introduced, and anchors of neighboring loops were brought together + # using harmonic springs with a potential U = k * (r – r0)2; r0=0.5. + # To avoid abrupt motion of the loop anchors, the force was gradually + # turned on over the first 300000 timesteps, with k linearly increasing + # in time from 0 to 10 kT." + # Do this by changing the parameters in the force-field for these + # bonds. + # + # Formula used for "bond_style harmonic": + # Ubond(r) = k*(r-r0)^2 + # bondType style + #bond_coeff 1 harmonic 0.1 0.5 + + variable time equal step + variable KbondC equal $((v_time+1)*(10.0/300000.0)) + print "timestep = ${time}, KbondC = ${KbondC}" file KbondC_vs_time.dat + + #bond_coeff 1 harmonic ${KbondC} 0.5 + bond_coeff 1 harmonic ${KbondC} 0.5 + run 1000 + + next nloop1 + jump SELF loop1 + +write_data system_after_stage1.data + diff --git a/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/run.in.stage2 b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/run.in.stage2 new file mode 100644 index 0000000000..e429fc8825 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/metaphase_chromatin_Naumova+Imakaev2013/run.in.stage2 @@ -0,0 +1,90 @@ +# PREREQUISITES: You must run LAMMPS using "run.in.stage1" beforehand. +# (This will create the "system_after_stage1.data" file.) +######################################################### +# Run using: +# +# lmp_ubuntu_parallel -i run.in.stage2 +# +######################################################### +# eg: +# time mpirun -np 2 lmp_ubuntu_parallel -i run.in -var seed 1 +######################################################### +# GPUs: +# To enable gpu acceleration, make sure settings.in.init includes this line: +# package gpu force/neigh 0 0 1.0 (make sure it is not commented out.) +# ...and replace "lj/cut" in the "settings.in.init" and "settings.in.settings" +# files with "lj/cut/gpu" + + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +#read_data system.data +read_data system_after_stage1.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +mass * 1.0 +timestep 0.005 # "dt" +dump 1 all custom 50000 traj_stage2.lammpstrj id mol type x y z ix iy iz +reset_timestep 300000 + + +# --- run the simulation --- + +# set the velocity to zero +velocity all create 0.0 123456 + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve" +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Tstart Tstop tdamp randomseed + +fix fxlan all langevin 1.0 1.0 10.0 123456 + +# pstart pstop pdamp(time-units, 2000 iters usually) +fix fxnve all nve +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + +fix fxcenter all recenter 0.0 0.0 0.0 + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 1000 #(time interval for printing out "thermo" data) + +#balance dynamic x 20 1.0 -out tmp.balance +#balance x uniform + +# atomTypes pairStyle epsilon sigma rcutoff +# 10nm-fiber +#pair_coeff 1 1 lj/cut 1.0 1.0 2.5 +#pair_coeff 2 2 lj/cut 1.0 1.0 2.5 +# 30nm fiber (4.25^(1/3)=1.6198059006387417) +pair_coeff 1 1 lj/cut 1.0 1.6198059006387417 4.049514751596854 +pair_coeff 2 2 lj/cut 1.0 1.6198059006387417 4.049514751596854 + + +# During stage 2, add attractive forces between all pairs of non-consecutive +# condensin anchors. These forces are stored in the table file below: +# bondType bondStyle filename label +bond_coeff 2 table table_bonds_stage2.dat STAGE2 + +# During stage 2, I assume the stage-1 bonds remain in place +# (They have length 0.5. +# After 300000 timesteps during stage 1, the "k" value should be 10.0.) + +# bondType bondStyle k r0 +bond_coeff 1 harmonic 10.0 0.5 + +timestep 0.005 +run 1700000 + +write_data system_after_stage2.data diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT new file mode 100644 index 0000000000..31abcd66ef --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT @@ -0,0 +1,33 @@ +# This directory contains examples of how to run a short simulation of a +# coarse-grained protein-like polymer, folding in the presence and absence of +# a chaperone (modeled as an attractive or repulsie spherical shell). +# +# The protein models and the chaperone models are described and used here: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# ...and also here: +# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006) +# +# (In the "frustrated+minichaperone" directory, the protein is +# placed outside the chaperone sphere, as opposed to inside.) +# +# -------- REQUIREMENTS: --------- +# 1) These examples require the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) They also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files in each directory. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT new file mode 100644 index 0000000000..a52f73ff7b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT @@ -0,0 +1,32 @@ +# This directory demonstrates how to run a long simulation of +# the "frustrated" coarse-grained protein confined in a frustrated +# coarse-grained chaperonin (R=6, h=0.475) as described in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# Note: If you want to use a "hydrophilic" chaperone (with h=0.0 +# instead of h=0.475), then replace the word "CHAP_INTERIOR_H0.475" +# (at the end of "system.lt") with "CHAP_INTERIOR_H0" +# +# Because this process takes a long time (even with the help of the chaperone) +# I save the data relatively infrequently. +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh new file mode 100755 index 0000000000..45bd2d451d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh new file mode 100755 index 0000000000..f2462426f1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..9e34246f8e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,86 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 28 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 1 1 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 2 2 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 1 1 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 2 2 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 27 1 2 2 0.000000 1.0000 0 + 28 2 4 4 0.000000 100.0000 0 + + 26 !NBOND: bonds + 1 2 2 3 3 4 4 5 + 5 6 6 7 7 8 8 9 + 9 10 10 11 11 12 12 13 + 13 14 14 15 15 16 16 17 + 17 18 18 19 19 20 20 21 + 21 22 22 23 23 24 24 25 + 25 26 26 27 + + 25 !NTHETA: angles + 13 14 15 7 8 9 6 7 8 + 16 17 18 15 16 17 2 3 4 + 4 5 6 9 10 11 11 12 13 + 14 15 16 1 2 3 3 4 5 + 10 11 12 12 13 14 25 26 27 + 5 6 7 8 9 10 17 18 19 + 18 19 20 22 23 24 21 22 23 + 19 20 21 20 21 22 23 24 25 + 24 25 26 + + 19 !NPHI: dihedrals + 1 2 3 4 2 3 4 5 + 3 4 5 6 4 5 6 7 + 8 9 10 11 9 10 11 12 + 10 11 12 13 11 12 13 14 + 12 13 14 15 15 16 17 18 + 16 17 18 19 17 18 19 20 + 18 19 20 21 19 20 21 22 + 20 21 22 23 21 22 23 24 + 22 23 24 25 23 24 25 26 + 24 25 26 27 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg new file mode 100644 index 0000000000..31853cd5ad Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg new file mode 100644 index 0000000000..fdc5c890b1 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt new file mode 100644 index 0000000000..e43026ba9f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt @@ -0,0 +1,216 @@ +# This file defines the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadFrustrated { + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 + $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 + $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 + $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 + $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 + $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 + $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 + $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 + $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 + $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 + $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 + $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 + $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 + $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 + $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 + $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 + $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 + $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 + $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 + $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 + $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 + $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 + $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 + $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 + $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 + $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 + $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 + } + + # bond-ID bond-Type atom-ID atom-ID + + write('Data Bonds') { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write('Data Dihedrals') { + + $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 + # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 + # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 + + $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 + # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 + + $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once('Data Angles By Type') { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadFrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + + # We use tabular dihedral potentials to implement the dihedral forces. + # (Actually there is a way to use Fourier series, using multiple charmm + # style dihedral interactions, but it's slower and messier.) + + write_once("In Settings") { + # style file keyword + dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA + dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA + # No need to specify dihedral interactions in the turn regions. (none exist) + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadFrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadFrustrated + + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt new file mode 100644 index 0000000000..54e2de4376 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt @@ -0,0 +1,85 @@ +import "1beadFrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadMisfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated". + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 + $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 + $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 + $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 + $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 + $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 + $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 + $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 + $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 + $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 + $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 + $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 + $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 + $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 + $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 + $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 + $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 + $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 + $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 + $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 + $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 + $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 + $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 + $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 + $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 + $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 + $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 + } + +} # 1beadMisfolded + + +1beadUnfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt new file mode 100644 index 0000000000..8266d2a898 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt @@ -0,0 +1,41 @@ +# Here we define a trivial molecule containing only one particle. + +Chaperonin { + + # atomID molID atomType charge x y z + + write("Data Atoms") { + $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:C 100.0 + } + + write_once("In Settings") { + # If for some reason there are multiple chaperones present, + # I assume that they interact repulsively (hence, L=0) + # i j epsilon sigma K L + + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0 + + # Optional: define the atoms in the "chaperonins" group: + # (Defining a group for the chaperone makes it easy to immobilize it later.) + + group chaperonins type @atom:C + } + + + # Specify which pair_styles, and atom styles work well with + # this model. (Again this can be overridden later.) + + write_once("In Init") { + units lj + atom_style full + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0 + } + +} # Chaperonin + +# We have not specified how this particle interacts with other particles +# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py new file mode 100755 index 0000000000..9b86809cc3 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between atoms in the +# protein and a chaperone provided in the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# This is stored in a tabulated force field with a singularity at a distance R. +# +# To calculate the table for interaction between +# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 +# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 +# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True +# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True + +from math import * +import sys + +def U(r, eps, sigma, R, h): + #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) + - h*pow((sigma/R), 6.0)) + xp = sigma/(r+R) + xm = sigma/(r-R) + term10 = pow(xm, 10.0) - pow(xp, 10.0) + term4 = pow(xm, 4.0) - pow(xp, 4.0) + return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) + +def F(r, eps, sigma, R, h): + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 0.0 + product_term_a = U(r, eps, sigma, R, h) / r + ixp = (r+R)/sigma + ixm = (r-R)/sigma + dix_dr = 1.0/sigma + term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) + term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) + product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) + return product_term_a + product_term_b + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + + """ + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + def __repr__(self): + return str(self) + +if len(sys.argv) < 8: + sys.stderr.write("Error: expected 7 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") + sys.exit(-1) + +epsilon = float(sys.argv[1]) +sigma = float(sys.argv[2]) +R = float(sys.argv[3]) +h = float(sys.argv[4]) +rmin = float(sys.argv[5]) +rmax = float(sys.argv[6]) +N = int(sys.argv[7]) + +subtract_Urcut = False +if len(sys.argv) == 9: + subtract_Urcut = True +rcut = rmax + +for i in range(0,N): + r = rmin + i*(rmax-rmin)/(N-1) + U_r = U(r, epsilon, sigma, R, h) + F_r = F(r, epsilon, sigma, R, h) + if subtract_Urcut: + U_r -= U(rcut, epsilon, sigma, R, h) + if (r >= rcut) or (i==N-1): + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py new file mode 100755 index 0000000000..34c66418a8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +# Calculate a table of dihedral angle interactions used in the alpha-helix +# and beta-sheet regions of the frustrated protein model described in +# provided in figure 8 of the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# Note that the "A" and "B" parameters were incorrectly reported to be +# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. +# The phiA and phiB values were 57.29577951308232 degrees (1 rad) +# and 180 degrees, respectively. Both expA and expB were 6.0. +# +# To generate the table used for the alpha-helix (1 degree resolution) use this: +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 +# To generate the table used for the beta-sheets (1 degree resolution) use this: +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 +# +# (If you're curious as to why I set the location of the minima at phi_alpha +# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. +# I think the correct value turns out to be something closer to 50 degrees.) + + +from math import * +import sys + + +# The previous version included the repulsive core term +def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) + termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) + return -A*termA - B*termB + +# The previous version included the repulsive core term +def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * + expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) + termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * + expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) + return -conv_units*(A*termA + B*termB) + +if len(sys.argv) != 10: + sys.stderr.write("Error: expected 9 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") + sys.exit(-1) + +A = float(sys.argv[1]) +phiA = float(sys.argv[2]) +expA = float(sys.argv[3]) +B = float(sys.argv[4]) +phiB = float(sys.argv[5]) +expB = float(sys.argv[6]) +phi_min = float(sys.argv[7]) +phi_max = float(sys.argv[8]) +N = int(sys.argv[9]) + +for i in range(0,N): + phi = phi_min + i*(phi_max - phi_min)/(N-1) + U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt new file mode 100644 index 0000000000..d70ea9b1f2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt @@ -0,0 +1,45 @@ +write_once("Data Boundary") { + 0.0 20.0 xlo xhi + 0.0 20.0 ylo yhi + 0.0 20.0 zlo zhi +} + + +import "1beadFrustrated_variants.lt" +import "chaperonin.lt" + + +protein = new 1beadMisfolded # (frustrated protein, misfolded conformation) +chaperinin = new Chaperonin # (hollow chaperonin cavity. usually immobile) + + + +# ---- Now define interactions between the atoms in the protein ---- +# ---- (named "B", "L", "N") and the atom which represents the ---- +# ---- chaperone ("C"). These interactions are tabulated. ---- + +write_once("In Settings") { + pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475 + pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/L table table_chaperonin_h=0.dat CH_H0 + pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/N table table_chaperonin_h=0.dat CH_H0 +} + +# Note: If you want to use a "hydrophilic" chaperone (with h=0, not h=0.475) +# then replace "table_chaperonin_h=0_475.dat CH_H0.475" +# with "table_chaperonin_h=0.dat CH_H0" + +# LAMMPS has many available force field styles (and atom styles). Here we +# select the ones which work well for the full combine system. (This should +# override any settings made in "1beadFrustrated.lt" or "chaperonin.lt") + + +write_once("In Init") { + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat new file mode 100644 index 0000000000..675d228a90 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat @@ -0,0 +1,1188 @@ +# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475). +# LAMMPS would crash unless I set the minimum radius to a positive value (not 0) + +CH_H0.475 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 -0.018422088583 0.0 +2 0.005 -0.0184221525389 2.55824082873e-05 +3 0.01 -0.0184223444081 5.11654127471e-05 +4 0.015 -0.018422664195 7.67496107175e-05 +5 0.02 -0.0184231119071 0.000102335598797 +6 0.025 -0.018423687555 0.000127923973785 +7 0.03 -0.0184243911519 0.000153515332637 +8 0.035 -0.0184252227143 0.000179110272379 +9 0.04 -0.0184261822615 0.000204709390236 +10 0.045 -0.0184272698161 0.000230313283607 +11 0.05 -0.0184284854033 0.000255922550119 +12 0.055 -0.0184298290516 0.000281537787625 +13 0.06 -0.0184313007922 0.000307159594253 +14 0.065 -0.0184329006595 0.000332788568419 +15 0.07 -0.0184346286908 0.000358425308862 +16 0.075 -0.0184364849265 0.000384070414671 +17 0.08 -0.0184384694099 0.000409724485298 +18 0.085 -0.0184405821873 0.000435388120601 +19 0.09 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5.855 626872755.056 -43125823862.6 +1173 5.86 889629660.718 -63393502739.0 +1174 5.865 1278740106.83 -94503868935.1 +1175 5.87 1863446791.23 -1.43025101229e+11 +1176 5.875 2756012237.96 -2.20012469835e+11 +1177 5.88 4141901662.1 -3.44454801129e+11 +1178 5.885 6333810219.82 -5.49690750348e+11 +1179 5.89 9870702215.02 -8.95661856872e+11 +1180 5.895 15704120493.1 -1.49296797827e+12 +1181 5.9 25558689542.6 -2.55153879404e+12 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat new file mode 100644 index 0000000000..2ad6d7b691 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat @@ -0,0 +1,1187 @@ +# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0) + +CH_H0 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 8.31299178857e-07 0.0 +2 0.005 8.31311879342e-07 -5.08022586688e-09 +3 0.01 8.31349981758e-07 -1.01608369733e-08 +4 0.015 8.31413488996e-07 -1.52422186449e-08 +5 0.02 8.31502405871e-07 -2.03247562721e-08 +6 0.025 8.31616739127e-07 -2.54088353865e-08 +7 0.03 8.31756497437e-07 -3.04948417048e-08 +8 0.035 8.319216914e-07 -3.55831611709e-08 +9 0.04 8.32112333547e-07 -4.06741800058e-08 +10 0.045 8.32328438343e-07 -4.57682847516e-08 +11 0.05 8.32570022183e-07 -5.08658623183e-08 +12 0.055 8.328371034e-07 -5.59673000292e-08 +13 0.06 8.33129702263e-07 -6.10729856679e-08 +14 0.065 8.33447840983e-07 -6.61833075238e-08 +15 0.07 8.33791543713e-07 -7.12986544391e-08 +16 0.075 8.34160836552e-07 -7.64194158551e-08 +17 0.08 8.34555747546e-07 -8.15459818584e-08 +18 0.085 8.34976306696e-07 -8.66787432278e-08 +19 0.09 8.35422545957e-07 -9.18180914814e-08 +20 0.095 8.35894499243e-07 -9.69644189231e-08 +21 0.1 8.36392202433e-07 -1.0211811869e-07 +22 0.105 8.36915693374e-07 -1.07279584798e-07 +23 0.11 8.37465011883e-07 -1.12449212192e-07 +24 0.115 8.38040199757e-07 -1.17627396792e-07 +25 0.12 8.38641300774e-07 -1.22814535539e-07 +26 0.125 8.392683607e-07 -1.28011026445e-07 +27 0.13 8.39921427291e-07 -1.33217268641e-07 +28 0.135 8.40600550305e-07 -1.38433662423e-07 +29 0.14 8.41305781504e-07 -1.43660609303e-07 +30 0.145 8.42037174658e-07 -1.48898512057e-07 +31 0.15 8.42794785557e-07 -1.54147774771e-07 +32 0.155 8.43578672015e-07 -1.59408802894e-07 +33 0.16 8.44388893873e-07 -1.64682003285e-07 +34 0.165 8.45225513015e-07 -1.69967784262e-07 +35 0.17 8.46088593367e-07 -1.75266555654e-07 +36 0.175 8.46978200908e-07 -1.80578728847e-07 +37 0.18 8.4789440368e-07 -1.85904716839e-07 +38 0.185 8.48837271792e-07 -1.91244934288e-07 +39 0.19 8.49806877432e-07 -1.96599797561e-07 +40 0.195 8.50803294874e-07 -2.01969724788e-07 +41 0.2 8.51826600486e-07 -2.07355135913e-07 +42 0.205 8.52876872743e-07 -2.12756452745e-07 +43 0.21 8.5395419223e-07 -2.18174099007e-07 +44 0.215 8.55058641658e-07 -2.23608500394e-07 +45 0.22 8.56190305871e-07 -2.29060084623e-07 +46 0.225 8.57349271858e-07 -2.34529281482e-07 +47 0.23 8.5853562876e-07 -2.40016522891e-07 +48 0.235 8.59749467885e-07 -2.4552224295e-07 +49 0.24 8.60990882715e-07 -2.51046877993e-07 +50 0.245 8.62259968921e-07 -2.56590866647e-07 +51 0.25 8.63556824372e-07 -2.62154649881e-07 +52 0.255 8.64881549149e-07 -2.67738671065e-07 +53 0.26 8.66234245555e-07 -2.73343376025e-07 +54 0.265 8.67615018129e-07 -2.78969213098e-07 +55 0.27 8.69023973658e-07 -2.84616633187e-07 +56 0.275 8.70461221189e-07 -2.90286089823e-07 +57 0.28 8.71926872044e-07 -2.95978039217e-07 +58 0.285 8.73421039834e-07 -3.0169294032e-07 +59 0.29 8.74943840469e-07 -3.07431254881e-07 +60 0.295 8.76495392179e-07 -3.13193447505e-07 +61 0.3 8.7807581552e-07 -3.18979985713e-07 +62 0.305 8.79685233396e-07 -3.24791340003e-07 +63 0.31 8.8132377107e-07 -3.30627983906e-07 +64 0.315 8.82991556179e-07 -3.36490394052e-07 +65 0.32 8.84688718753e-07 -3.42379050225e-07 +66 0.325 8.86415391229e-07 -3.48294435432e-07 +67 0.33 8.88171708466e-07 -3.54237035959e-07 +68 0.335 8.89957807764e-07 -3.60207341438e-07 +69 0.34 8.91773828877e-07 -3.66205844906e-07 +70 0.345 8.93619914037e-07 -3.72233042875e-07 +71 0.35 8.95496207963e-07 -3.78289435392e-07 +72 0.355 8.97402857887e-07 -3.84375526106e-07 +73 0.36 8.99340013567e-07 -3.90491822333e-07 +74 0.365 9.01307827305e-07 -3.96638835124e-07 +75 0.37 9.0330645397e-07 -4.02817079329e-07 +76 0.375 9.05336051015e-07 -4.09027073668e-07 +77 0.38 9.07396778494e-07 -4.152693408e-07 +78 0.385 9.09488799088e-07 -4.21544407387e-07 +79 0.39 9.11612278118e-07 -4.2785280417e-07 +80 0.395 9.13767383571e-07 -4.34195066035e-07 +81 0.4 9.15954286119e-07 -4.40571732086e-07 +82 0.405 9.18173159138e-07 -4.46983345718e-07 +83 0.41 9.20424178735e-07 -4.53430454687e-07 +84 0.415 9.22707523764e-07 -4.59913611186e-07 +85 0.42 9.25023375853e-07 -4.66433371919e-07 +86 0.425 9.27371919425e-07 -4.72990298174e-07 +87 0.43 9.29753341721e-07 -4.795849559e-07 +88 0.435 9.32167832821e-07 -4.86217915785e-07 +89 0.44 9.34615585674e-07 -4.9288975333e-07 +90 0.445 9.37096796117e-07 -4.99601048932e-07 +91 0.45 9.39611662902e-07 -5.0635238796e-07 +92 0.455 9.4216038772e-07 -5.13144360835e-07 +93 0.46 9.44743175226e-07 -5.19977563112e-07 +94 0.465 9.47360233068e-07 -5.26852595561e-07 +95 0.47 9.50011771908e-07 -5.33770064252e-07 +96 0.475 9.52698005456e-07 -5.40730580635e-07 +97 0.48 9.55419150489e-07 -5.47734761627e-07 +98 0.485 9.58175426884e-07 -5.54783229699e-07 +99 0.49 9.60967057644e-07 -5.61876612959e-07 +100 0.495 9.63794268928e-07 -5.69015545241e-07 +101 0.5 9.66657290077e-07 -5.76200666196e-07 +102 0.505 9.69556353647e-07 -5.83432621378e-07 +103 0.51 9.72491695434e-07 -5.90712062337e-07 +104 0.515 9.75463554509e-07 -5.9803964671e-07 +105 0.52 9.78472173246e-07 -6.05416038315e-07 +106 0.525 9.81517797354e-07 -6.12841907243e-07 +107 0.53 9.84600675908e-07 -6.20317929954e-07 +108 0.535 9.87721061381e-07 -6.27844789373e-07 +109 0.54 9.90879209678e-07 -6.3542317499e-07 +110 0.545 9.94075380168e-07 -6.43053782955e-07 +111 0.55 9.97309835716e-07 -6.50737316177e-07 +112 0.555 1.00058284272e-06 -6.58474484431e-07 +113 0.56 1.00389467115e-06 -6.66266004455e-07 +114 0.565 1.00724559456e-06 -6.74112600053e-07 +115 0.57 1.01063589016e-06 -6.82015002204e-07 +116 0.575 1.01406583882e-06 -6.89973949166e-07 +117 0.58 1.01753572513e-06 -6.97990186581e-07 +118 0.585 1.02104583743e-06 -7.06064467589e-07 +119 0.59 1.02459646782e-06 -7.14197552934e-07 +120 0.595 1.02818791224e-06 -7.22390211075e-07 +121 0.6 1.03182047051e-06 -7.30643218304e-07 +122 0.605 1.03549444631e-06 -7.38957358854e-07 +123 0.61 1.0392101473e-06 -7.47333425021e-07 +124 0.615 1.04296788511e-06 -7.55772217275e-07 +125 0.62 1.04676797537e-06 -7.64274544386e-07 +126 0.625 1.0506107378e-06 -7.72841223537e-07 +127 0.63 1.05449649623e-06 -7.81473080451e-07 +128 0.635 1.05842557863e-06 -7.90170949513e-07 +129 0.64 1.06239831715e-06 -7.98935673896e-07 +130 0.645 1.06641504821e-06 -8.07768105686e-07 +131 0.65 1.07047611249e-06 -8.1666910601e-07 +132 0.655 1.074581855e-06 -8.25639545171e-07 +133 0.66 1.07873262514e-06 -8.34680302772e-07 +134 0.665 1.08292877671e-06 -8.43792267857e-07 +135 0.67 1.08717066799e-06 -8.52976339042e-07 +136 0.675 1.09145866179e-06 -8.62233424653e-07 +137 0.68 1.09579312546e-06 -8.71564442867e-07 +138 0.685 1.10017443099e-06 -8.80970321849e-07 +139 0.69 1.10460295501e-06 -8.90451999898e-07 +140 0.695 1.1090790789e-06 -9.0001042559e-07 +141 0.7 1.11360318878e-06 -9.09646557926e-07 +142 0.705 1.1181756756e-06 -9.19361366479e-07 +143 0.71 1.1227969352e-06 -9.29155831544e-07 +144 0.715 1.12746736833e-06 -9.39030944294e-07 +145 0.72 1.13218738073e-06 -9.48987706931e-07 +146 0.725 1.13695738317e-06 -9.59027132844e-07 +147 0.73 1.14177779154e-06 -9.6915024677e-07 +148 0.735 1.14664902685e-06 -9.79358084952e-07 +149 0.74 1.15157151534e-06 -9.89651695304e-07 +150 0.745 1.15654568852e-06 -1.00003213758e-06 +151 0.75 1.16157198322e-06 -1.01050048352e-06 +152 0.755 1.16665084166e-06 -1.02105781707e-06 +153 0.76 1.17178271153e-06 -1.0317052345e-06 +154 0.765 1.176968046e-06 -1.0424438446e-06 +155 0.77 1.18220730383e-06 -1.05327476888e-06 +156 0.775 1.18750094943e-06 -1.0641991417e-06 +157 0.78 1.19284945291e-06 -1.07521811051e-06 +158 0.785 1.19825329013e-06 -1.08633283599e-06 +159 0.79 1.20371294282e-06 -1.09754449225e-06 +160 0.795 1.20922889858e-06 -1.10885426703e-06 +161 0.8 1.21480165102e-06 -1.12026336191e-06 +162 0.805 1.22043169976e-06 -1.13177299243e-06 +163 0.81 1.22611955055e-06 -1.14338438839e-06 +164 0.815 1.23186571533e-06 -1.15509879397e-06 +165 0.82 1.23767071227e-06 -1.16691746799e-06 +166 0.825 1.24353506591e-06 -1.17884168407e-06 +167 0.83 1.24945930716e-06 -1.19087273088e-06 +168 0.835 1.25544397344e-06 -1.20301191233e-06 +169 0.84 1.26148960871e-06 -1.21526054778e-06 +170 0.845 1.26759676357e-06 -1.22761997229e-06 +171 0.85 1.27376599533e-06 -1.2400915368e-06 +172 0.855 1.27999786811e-06 -1.2526766084e-06 +173 0.86 1.2862929529e-06 -1.26537657052e-06 +174 0.865 1.29265182763e-06 -1.27819282318e-06 +175 0.87 1.29907507731e-06 -1.29112678323e-06 +176 0.875 1.30556329404e-06 -1.30417988457e-06 +177 0.88 1.31211707714e-06 -1.31735357842e-06 +178 0.885 1.31873703325e-06 -1.33064933354e-06 +179 0.89 1.32542377639e-06 -1.34406863648e-06 +180 0.895 1.33217792804e-06 -1.35761299185e-06 +181 0.9 1.33900011726e-06 -1.37128392257e-06 +182 0.905 1.34589098079e-06 -1.38508297012e-06 +183 0.91 1.35285116309e-06 -1.39901169482e-06 +184 0.915 1.3598813165e-06 -1.41307167609e-06 +185 0.92 1.36698210128e-06 -1.42726451271e-06 +186 0.925 1.37415418575e-06 -1.44159182311e-06 +187 0.93 1.38139824636e-06 -1.45605524565e-06 +188 0.935 1.38871496782e-06 -1.47065643891e-06 +189 0.94 1.39610504317e-06 -1.48539708196e-06 +190 0.945 1.40356917389e-06 -1.50027887466e-06 +191 0.95 1.41110807003e-06 -1.51530353796e-06 +192 0.955 1.41872245029e-06 -1.5304728142e-06 +193 0.96 1.42641304213e-06 -1.54578846742e-06 +194 0.965 1.4341805819e-06 -1.56125228366e-06 +195 0.97 1.44202581492e-06 -1.57686607128e-06 +196 0.975 1.44994949562e-06 -1.59263166129e-06 +197 0.98 1.45795238763e-06 -1.60855090765e-06 +198 0.985 1.46603526391e-06 -1.62462568762e-06 +199 0.99 1.47419890689e-06 -1.64085790209e-06 +200 0.995 1.48244410853e-06 -1.65724947591e-06 +201 1.0 1.4907716705e-06 -1.67380235825e-06 +202 1.005 1.49918240425e-06 -1.69051852294e-06 +203 1.01 1.50767713119e-06 -1.70739996882e-06 +204 1.015 1.51625668278e-06 -1.72444872011e-06 +205 1.02 1.52492190065e-06 -1.74166682675e-06 +206 1.025 1.53367363676e-06 -1.75905636483e-06 +207 1.03 1.54251275352e-06 -1.77661943691e-06 +208 1.035 1.5514401239e-06 -1.7943581724e-06 +209 1.04 1.56045663161e-06 -1.81227472801e-06 +210 1.045 1.56956317119e-06 -1.83037128807e-06 +211 1.05 1.57876064818e-06 -1.84865006497e-06 +212 1.055 1.58804997927e-06 -1.86711329958e-06 +213 1.06 1.59743209239e-06 -1.88576326162e-06 +214 1.065 1.60690792693e-06 -1.90460225011e-06 +215 1.07 1.61647843382e-06 -1.92363259378e-06 +216 1.075 1.62614457572e-06 -1.94285665153e-06 +217 1.08 1.63590732717e-06 -1.9622768128e-06 +218 1.085 1.64576767472e-06 -1.98189549811e-06 +219 1.09 1.65572661711e-06 -2.00171515944e-06 +220 1.095 1.66578516541e-06 -2.02173828072e-06 +221 1.1 1.67594434321e-06 -2.04196737828e-06 +222 1.105 1.68620518674e-06 -2.06240500133e-06 +223 1.11 1.69656874507e-06 -2.08305373245e-06 +224 1.115 1.70703608027e-06 -2.10391618807e-06 +225 1.12 1.71760826757e-06 -2.12499501897e-06 +226 1.125 1.72828639555e-06 -2.14629291076e-06 +227 1.13 1.73907156631e-06 -2.16781258443e-06 +228 1.135 1.74996489563e-06 -2.18955679685e-06 +229 1.14 1.76096751317e-06 -2.21152834128e-06 +230 1.145 1.77208056264e-06 -2.23373004793e-06 +231 1.15 1.78330520203e-06 -2.2561647845e-06 +232 1.155 1.79464260371e-06 -2.27883545672e-06 +233 1.16 1.80609395472e-06 -2.30174500894e-06 +234 1.165 1.8176604569e-06 -2.32489642465e-06 +235 1.17 1.82934332711e-06 -2.34829272711e-06 +236 1.175 1.84114379742e-06 -2.3719369799e-06 +237 1.18 1.85306311533e-06 -2.39583228755e-06 +238 1.185 1.86510254397e-06 -2.41998179612e-06 +239 1.19 1.87726336227e-06 -2.44438869382e-06 +240 1.195 1.88954686527e-06 -2.46905621166e-06 +241 1.2 1.90195436421e-06 -2.49398762405e-06 +242 1.205 1.91448718686e-06 -2.51918624948e-06 +243 1.21 1.92714667767e-06 -2.54465545114e-06 +244 1.215 1.93993419801e-06 -2.57039863763e-06 +245 1.22 1.95285112644e-06 -2.59641926361e-06 +246 1.225 1.96589885888e-06 -2.62272083047e-06 +247 1.23 1.97907880889e-06 -2.64930688708e-06 +248 1.235 1.99239240789e-06 -2.67618103045e-06 +249 1.24 2.00584110541e-06 -2.7033469065e-06 +250 1.245 2.01942636933e-06 -2.73080821073e-06 +251 1.25 2.03314968614e-06 -2.75856868904e-06 +252 1.255 2.04701256117e-06 -2.78663213843e-06 +253 1.26 2.06101651889e-06 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0000000000..d660fee308 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat @@ -0,0 +1,735 @@ +# Table of the potential and its negative derivative for frustrated alpha helix +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 + +FRUSTRATED_ALPHA +N 360 DEGREES + +1 0.0 -2.74081145103 0.0783990792662 +2 1.0 -2.81950869101 0.0789852583442 +3 2.0 -2.89876136749 0.0795096391909 +4 3.0 -2.97850675562 0.0799703813963 +5 4.0 -3.05868032959 0.0803657243943 +6 5.0 -3.13921584545 0.0806939935737 +7 6.0 -3.22004543014 0.0809536062381 +8 7.0 -3.30109967628 0.0811430773977 +9 8.0 -3.38230774267 0.0812610253741 +10 9.0 -3.46359746038 0.0813061772009 +11 10.0 -3.54489544401 0.0812773738039 +12 11.0 -3.62612720812 0.0811735749433 +13 12.0 -3.70721728841 0.0809938639029 +14 13.0 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-1.53878331313 0.061018148454 +345 344.0 -1.60045794659 0.0623272072653 +346 345.0 -1.66342954101 0.0636117049668 +347 346.0 -1.72767243359 0.0648694329207 +348 347.0 -1.79315873807 0.0660981537565 +349 348.0 -1.85985831882 0.0672956071568 +350 349.0 -1.92773877092 0.0684595158069 +351 350.0 -1.99676540616 0.0695875914917 +352 351.0 -2.06690124527 0.0706775413231 +353 352.0 -2.13810701636 0.0717270740805 +354 353.0 -2.21034115987 0.0727339066469 +355 354.0 -2.28355983986 0.0736957705223 +356 355.0 -2.35771696194 0.0746104183955 +357 356.0 -2.43276419776 0.0754756307561 +358 357.0 -2.50865101613 0.0762892225281 +359 358.0 -2.58532472075 0.0770490497051 +360 359.0 -2.66273049463 0.0777530159679 + +# Table of the potential and its negative derivative for frustrated beta sheet +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 + +FRUSTRATED_BETA +N 360 DEGREES + +1 0.0 -2.55809068762 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0.0704439199439 +358 357.0 -2.3414076153 0.0712032738621 +359 358.0 -2.41296973939 0.0719124463259 +360 359.0 -2.48521512832 0.072569481568 diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min new file mode 100644 index 0000000000..321ba3c095 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min @@ -0,0 +1,25 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# Optional: Make sure the pairwise energies look reasonable: +pair_write 1 4 1001 r 0.00000000001 5.05 test_chap-B.dat C-B 0 0 +pair_write 2 4 1001 r 0.00000000001 5.05 test_chap-L.dat C-L 0 0 +pair_write 3 4 1001 r 0.00000000001 5.05 test_chap-N.dat C-N 0 0 + + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt new file mode 100644 index 0000000000..7c0855cb8d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt @@ -0,0 +1,48 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Keep the chaperonin fixed. Only let the protein move. + +fix fxlan proteins langevin 0.25 0.25 1.0 48279 +fix fxnve proteins nve + +# Notes: +# The temperature is in reduced units and is set to 0.25 +# which is the folding temperature for the frustrated protein +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50000 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 1000000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT new file mode 100644 index 0000000000..ecb9adad2e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT @@ -0,0 +1,38 @@ +# This directory demonstrates how to run a long simulation of +# the "frustrated" coarse-grained protein in the presence of one +# or more coarse-graine small ("mini") chaperones (R=3, h=0.6) as described in: +# +# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006) +# and earlier in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# +# Because this process takes a long time (even with the help of the chaperone) +# I save the data relatively infrequently. +# +# Note: In the 2006 paper, only one protein and one chaperone was simulated. +# In this example, 8 proteins and 8 chaperones were simulated. +# +# Note: In this case, the chaperones appear to catalyze aggregation. +# This is due to an artifact in the protein model. That model +# was not designed to study aggregation. However the simulation +# is suitable for making pretty pictures (to show off moltemplate). +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh new file mode 100755 index 0000000000..45bd2d451d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh new file mode 100755 index 0000000000..f2462426f1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..b0013ccc62 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,476 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 224 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 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and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt new file mode 100644 index 0000000000..e43026ba9f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt @@ -0,0 +1,216 @@ +# This file defines the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadFrustrated { + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 + $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 + $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 + $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 + $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 + $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 + $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 + $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 + $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 + $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 + $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 + $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 + $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 + $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 + $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 + $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 + $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 + $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 + $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 + $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 + $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 + $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 + $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 + $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 + $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 + $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 + $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 + } + + # bond-ID bond-Type atom-ID atom-ID + + write('Data Bonds') { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write('Data Dihedrals') { + + $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 + # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 + # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 + + $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 + # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 + + $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once('Data Angles By Type') { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadFrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + + # We use tabular dihedral potentials to implement the dihedral forces. + # (Actually there is a way to use Fourier series, using multiple charmm + # style dihedral interactions, but it's slower and messier.) + + write_once("In Settings") { + # style file keyword + dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA + dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA + # No need to specify dihedral interactions in the turn regions. (none exist) + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadFrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadFrustrated + + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt new file mode 100644 index 0000000000..54e2de4376 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt @@ -0,0 +1,85 @@ +import "1beadFrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadMisfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated". + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 + $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 + $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 + $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 + $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 + $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 + $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 + $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 + $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 + $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 + $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 + $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 + $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 + $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 + $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 + $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 + $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 + $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 + $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 + $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 + $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 + $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 + $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 + $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 + $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 + $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 + $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 + } + +} # 1beadMisfolded + + +1beadUnfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py new file mode 100755 index 0000000000..9b86809cc3 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between atoms in the +# protein and a chaperone provided in the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# This is stored in a tabulated force field with a singularity at a distance R. +# +# To calculate the table for interaction between +# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 +# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 +# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True +# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True + +from math import * +import sys + +def U(r, eps, sigma, R, h): + #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) + - h*pow((sigma/R), 6.0)) + xp = sigma/(r+R) + xm = sigma/(r-R) + term10 = pow(xm, 10.0) - pow(xp, 10.0) + term4 = pow(xm, 4.0) - pow(xp, 4.0) + return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) + +def F(r, eps, sigma, R, h): + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 0.0 + product_term_a = U(r, eps, sigma, R, h) / r + ixp = (r+R)/sigma + ixm = (r-R)/sigma + dix_dr = 1.0/sigma + term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) + term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) + product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) + return product_term_a + product_term_b + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + + """ + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + def __repr__(self): + return str(self) + +if len(sys.argv) < 8: + sys.stderr.write("Error: expected 7 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") + sys.exit(-1) + +epsilon = float(sys.argv[1]) +sigma = float(sys.argv[2]) +R = float(sys.argv[3]) +h = float(sys.argv[4]) +rmin = float(sys.argv[5]) +rmax = float(sys.argv[6]) +N = int(sys.argv[7]) + +subtract_Urcut = False +if len(sys.argv) == 9: + subtract_Urcut = True +rcut = rmax + +for i in range(0,N): + r = rmin + i*(rmax-rmin)/(N-1) + U_r = U(r, epsilon, sigma, R, h) + F_r = F(r, epsilon, sigma, R, h) + if subtract_Urcut: + U_r -= U(rcut, epsilon, sigma, R, h) + if (r >= rcut) or (i==N-1): + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py new file mode 100755 index 0000000000..34c66418a8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +# Calculate a table of dihedral angle interactions used in the alpha-helix +# and beta-sheet regions of the frustrated protein model described in +# provided in figure 8 of the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# Note that the "A" and "B" parameters were incorrectly reported to be +# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. +# The phiA and phiB values were 57.29577951308232 degrees (1 rad) +# and 180 degrees, respectively. Both expA and expB were 6.0. +# +# To generate the table used for the alpha-helix (1 degree resolution) use this: +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 +# To generate the table used for the beta-sheets (1 degree resolution) use this: +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 +# +# (If you're curious as to why I set the location of the minima at phi_alpha +# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. +# I think the correct value turns out to be something closer to 50 degrees.) + + +from math import * +import sys + + +# The previous version included the repulsive core term +def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) + termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) + return -A*termA - B*termB + +# The previous version included the repulsive core term +def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * + expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) + termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * + expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) + return -conv_units*(A*termA + B*termB) + +if len(sys.argv) != 10: + sys.stderr.write("Error: expected 9 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") + sys.exit(-1) + +A = float(sys.argv[1]) +phiA = float(sys.argv[2]) +expA = float(sys.argv[3]) +B = float(sys.argv[4]) +phiB = float(sys.argv[5]) +expB = float(sys.argv[6]) +phi_min = float(sys.argv[7]) +phi_max = float(sys.argv[8]) +N = int(sys.argv[9]) + +for i in range(0,N): + phi = phi_min + i*(phi_max - phi_min)/(N-1) + U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt new file mode 100644 index 0000000000..1d37823b7a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt @@ -0,0 +1,41 @@ +# Here we define a trivial molecule containing only one particle. + +Minichaperone { + + # atomID molID atomType charge x y z + + write("Data Atoms") { + $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:C 100.0 + } + + write_once("In Settings") { + # If for some reason there are multiple chaperones present, + # I assume that they interact repulsively (hence, L=0) + + # i j pairStyle eps sig K L + + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 3.0 1 0 + + # Optional: define the atoms in the "chaperonins" group: + # (Defining a group for the chaperone makes it easy to immobilize it later.) + + group chaperones type @atom:C + } + + # Specify which pair_styles, and atom styles work well with + # this model. (Again this can be overridden later.) + + write_once("In Init") { + units lj + atom_style full + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0 + } + +} # Minichaperone + +# We have not specified how this particle interacts with other particles +# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt new file mode 100644 index 0000000000..8f8c37d08b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt @@ -0,0 +1,72 @@ +write_once("Data Boundary") { + 0.0 80.0 xlo xhi + 0.0 80.0 ylo yhi + 0.0 80.0 zlo zhi +} + + +import "1beadFrustrated_variants.lt" +import "minichaperone.lt" + + +# Create 8 proteins and 8 chaperones (2x2x2 array): +# NOTE: Below I create multiple proteins and multiple chaperones +# to see what would happen. (I suspect nothing good. In the +# 2006 paper, only 1 protein and 1 chaperone were present.) + + +proteins = new 1beadUnfolded [2].move(40,0,0) + [2].move(0,40,0) + [2].move(0,0,40) + +chaperones = new Minichaperone [2].move(40,0,0) + [2].move(0,40,0) + [2].move(0,0,40) + +proteins[*][*][*].move(20,20,20) # to avoid overlap with the chaperones + + + +# If you only want 1 protein and 1 chaperone +# then replace the lines above with: +# +# protein = new 1beadMisfolded +# chaperone = new Minichaperone + + + + + +# ---- Now define interactions between the atoms in the protein ---- +# ---- (named "B", "L", "N") and the atom which represents the ---- +# ---- chaperone ("c"). These interactions are tabulated. ---- + +write_once("In Settings") { + pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/B table table_minichaperone_h=0.6.dat CH_H0.6 + pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/L table table_minichaperone_h=0.dat CH_H0 + pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/N table table_minichaperone_h=0.dat CH_H0 +} + +# Note: If you want purely repulsive spheres (crowding, h=0.0) +# instead of an attractive "hydrophobic" chaperone (h=0.6) +# then replace "table_minichaperone_h=0_6.dat CH_H0_6" +# with "table_minichaperone_h=0.dat CH_H0" +# (... or just use an ordinary Lennard-Jones interaction +# with sigma = 6.0 and epsilon near 0.0) + + +# LAMMPS has many available force field styles (and atom styles). Here we +# select the ones which work well for the full combine system. (This should +# override any settings made in "1beadFrustrated.lt" or "minichaperone.lt") + + +write_once("In Init") { + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 981 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat new file mode 100644 index 0000000000..d660fee308 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat @@ -0,0 +1,735 @@ +# Table of the potential and its negative derivative for frustrated alpha helix +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 + +FRUSTRATED_ALPHA +N 360 DEGREES + +1 0.0 -2.74081145103 0.0783990792662 +2 1.0 -2.81950869101 0.0789852583442 +3 2.0 -2.89876136749 0.0795096391909 +4 3.0 -2.97850675562 0.0799703813963 +5 4.0 -3.05868032959 0.0803657243943 +6 5.0 -3.13921584545 0.0806939935737 +7 6.0 -3.22004543014 0.0809536062381 +8 7.0 -3.30109967628 0.0811430773977 +9 8.0 -3.38230774267 0.0812610253741 +10 9.0 -3.46359746038 0.0813061772009 +11 10.0 -3.54489544401 0.0812773738039 +12 11.0 -3.62612720812 0.0811735749433 +13 12.0 -3.70721728841 0.0809938639029 +14 13.0 -3.78808936748 0.080737451911 +15 14.0 -3.86866640485 0.0804036822781 +16 15.0 -3.94887077101 0.0799920342374 +17 16.0 -4.02862438516 0.0795021264757 +18 17.0 -4.10784885622 0.0789337203415 +19 18.0 -4.18646562704 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-1.85985831882 0.0672956071568 +350 349.0 -1.92773877092 0.0684595158069 +351 350.0 -1.99676540616 0.0695875914917 +352 351.0 -2.06690124527 0.0706775413231 +353 352.0 -2.13810701636 0.0717270740805 +354 353.0 -2.21034115987 0.0727339066469 +355 354.0 -2.28355983986 0.0736957705223 +356 355.0 -2.35771696194 0.0746104183955 +357 356.0 -2.43276419776 0.0754756307561 +358 357.0 -2.50865101613 0.0762892225281 +359 358.0 -2.58532472075 0.0770490497051 +360 359.0 -2.66273049463 0.0777530159679 + +# Table of the potential and its negative derivative for frustrated beta sheet +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 + +FRUSTRATED_BETA +N 360 DEGREES + +1 0.0 -2.55809068762 0.0731724739818 +2 1.0 -2.63154144494 0.0737195744566 +3 2.0 -2.70551060968 0.0742089966437 +4 3.0 -2.77993963883 0.074639023134 +5 4.0 -2.85476830901 0.0750080115297 +6 5.0 -2.92993479441 0.0753144003899 +7 6.0 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a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat new file mode 100644 index 0000000000..d2b1ed3aaf --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat @@ -0,0 +1,988 @@ +# Interaction between a chaperone wall and hydrophobic ("B") beads (h=0.6) +# Generated using: +# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True + +CH_H0.6 +N 981 R 3.1 8.0 + +1 3.1 24321971157.7 2.4400451019e+12 +2 3.105 14907528428.0 1.42456746092e+12 +3 3.11 9347010266.92 8.52735030437e+11 +4 3.115 5983057175.03 5.22187648991e+11 +5 3.12 3902942155.05 3.26496996649e+11 +6 3.125 2590648415.38 2.0808159227e+11 +7 3.13 1747350825.1 1.34970444886e+11 +8 3.135 1196139798.89 88984974583.5 +9 3.14 830130182.341 59559787515.6 +10 3.145 583518174.975 40428507749.3 +11 3.15 415078797.287 27803974550.9 +12 3.155 298562827.719 19356989964.4 +13 3.16 217001769.743 13631486848.5 +14 3.165 159270305.159 9703243449.66 +15 3.17 117976881.962 6977184032.49 +16 3.175 88149161.6455 5064988683.98 +17 3.18 66402860.1298 3710042118.5 +18 3.185 50409022.6215 2740737360.59 +19 3.19 38548170.6708 2041021063.98 +20 3.195 29683036.1074 1531572773.33 +21 3.2 23007502.8905 1157631256.92 +22 3.205 17945109.6836 881028781.898 +23 3.21 14080149.2893 674921399.554 +24 3.215 11110438.2418 520266326.167 +25 3.22 8814639.75879 403443800.764 +26 3.225 7029455.47123 314636408.027 +27 3.23 5633571.16439 246714657.082 +28 3.235 4536265.59262 194464091.949 +29 3.24 3669265.83647 154044868.616 +30 3.245 2980881.1453 122610915.077 +31 3.25 2431748.15466 98039536.8272 +32 3.255 1991724.07297 78738058.3506 +33 3.26 1637603.46485 63504600.2322 +34 3.265 1351429.90872 51427172.534 +35 3.27 1119240.11293 41810074.9071 +36 3.275 930124.378436 34119886.2947 +37 3.28 775519.857832 27945597.578 +38 3.285 648676.115123 22969017.4933 +39 3.29 544248.919174 18942684.9889 +40 3.295 457989.984944 15673297.5619 +41 3.3 386508.875651 13009215.1485 +42 3.305 327089.446276 10830991.226 +43 3.31 277547.709074 9044163.93118 +44 3.315 236121.303553 7573742.76366 +45 3.32 201383.18845 6359973.47163 +46 3.325 172173.978278 5355070.91875 +47 3.33 147548.691578 4520688.28477 +48 3.335 126734.684289 3825948.80978 +49 3.34 109098.298235 3245909.11014 +50 3.345 94118.3261235 2760354.93052 +51 3.35 81364.827777 2352853.97713 +52 3.355 70482.1624146 2010008.31682 +53 3.36 61175.3541703 1720862.26897 +54 3.365 53199.1018261 1476431.88582 +55 3.37 46348.8930587 1269329.84244 +56 3.375 40453.7990113 1093465.44786 +57 3.38 35370.6146686 943803.998782 +58 3.385 30979.0803706 816173.162054 +59 3.39 27177.9744013 707106.743488 +60 3.395 23881.9094124 613718.268337 +61 3.4 21018.6991377 533598.403624 +62 3.405 18527.1884441 464731.50307 +63 3.41 16355.4608211 405427.532611 +64 3.415 14459.3541284 354266.400629 +65 3.42 12801.228731 310052.319542 +66 3.425 11348.9427887 271776.300627 +67 3.43 10074.9979765 238585.259865 +68 3.435 8955.82575185 209756.510836 +69 3.44 7971.18978782 184676.657916 +70 3.445 7103.68463562 162824.092297 +71 3.45 6338.31427303 143754.444665 +72 3.455 5662.13711315 127088.469763 +73 3.46 5063.9664184 112501.9356 +74 3.465 4534.11699728 99717.1686967 +75 3.47 4064.19064042 88495.970274 +76 3.475 3646.89404446 78633.6696895 +77 3.48 3275.88403311 69954.1231906 +78 3.485 2945.63575657 62305.4999784 +79 3.49 2651.33026883 55556.7252625 +80 3.495 2388.75847582 49594.4725913 +81 3.5 2154.23893796 44320.6162531 +82 3.505 1944.54741747 39650.0697323 +83 3.51 1756.8563988 35508.9486835 +84 3.515 1588.68309151 31833.0071751 +85 3.52 1437.84465949 28566.3044359 +86 3.525 1302.41961585 25660.0663588 +87 3.53 1180.71448694 23071.7118275 +88 3.535 1071.23498579 20764.0187577 +89 3.54 972.661050857 18704.4087568 +90 3.545 883.825202407 16864.3326446 +91 3.55 803.693750954 15218.7418698 +92 3.555 731.350460573 13745.6331832 +93 3.56 665.982328363 12425.6558809 +94 3.565 606.867190408 11241.7725673 +95 3.57 553.362906393 10178.9657593 +96 3.575 504.897910387 9223.98381086 +97 3.58 460.962945446 8365.12060921 +98 3.585 421.103825306 7592.02431669 +99 3.59 384.915088285 6895.53112553 +100 3.595 352.034427161 6267.5205811 +101 3.6 322.137794751 5700.78952663 +102 3.605 294.935098544 5188.94214534 +103 3.61 270.166409464 4726.29393494 +104 3.615 247.598619855 4307.78775517 +105 3.62 227.022494431 3928.92034957 +106 3.625 208.250065337 3585.67796495 +107 3.63 191.112328875 3274.47988201 +108 3.635 175.457206974 2992.12883298 +109 3.64 161.147741205 2735.76742147 +110 3.645 148.060491326 2502.83977901 +111 3.65 136.084113848 2291.05779528 +112 3.655 125.118099223 2098.37134728 +113 3.66 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-3.09346599767e-05 -0.00207982254527 +979 7.99 -2.05648617073e-05 -0.00206810960966 +980 7.995 -1.0253435891e-05 -0.00205647346771 +981 8.0 0.0 0.0 diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat new file mode 100644 index 0000000000..82eaa7e158 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat @@ -0,0 +1,989 @@ +# Interaction between a chaperone wall and hydrophilic ("L", "N") beads (h=0.0) +# Generated using: +# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.00 3.1 8.0 981 True + +CH_H0 +N 981 R 3.1 8.0 + +1 3.1 24322007640.7 2.44004657299e+12 +2 3.105 14907558394.3 1.42456861215e+12 +3 3.11 9347035105.18 8.52735941633e+11 +4 3.115 5983077933.86 5.22188377701e+11 +5 3.12 3902959636.31 3.26497584961e+11 +6 3.125 2590663239.27 2.08082071378e+11 +7 3.13 1747363476.38 1.34970838198e+11 +8 3.135 1196150660.14 88985299862.7 +9 3.14 830139558.184 59560058382.9 +10 3.145 583526310.01 40428734750.9 +11 3.15 415085889.414 27804165925.8 +12 3.155 298569038.21 19357152203.7 +13 3.16 217007230.904 13631625105.8 +14 3.165 159275126.218 9703361847.17 +15 3.17 117981153.625 6977285889.84 +16 3.175 88152959.6539 5065076691.93 +17 3.18 66406248.0614 3710118471.36 +18 3.185 50412054.1061 2740803858.1 +19 3.19 38550891.1571 2041079190.29 +20 3.195 29685484.2812 1531623758.63 +21 3.2 23009711.8183 1157676125.86 +22 3.205 17947107.7408 881068391.885 +23 3.21 14081960.9175 674956471.214 +24 3.215 11112084.5698 520297467.685 +25 3.22 8816139.11379 403471527.483 +26 3.225 7030823.80219 314661158.279 +27 3.23 5634822.39381 246736805.049 +28 3.235 4537411.91017 194483958.161 +29 3.24 3670317.94503 154062728.557 +30 3.245 2981848.4679 122627006.268 +31 3.25 2432639.00923 98054064.6797 +32 3.255 1992545.82032 78751201.0309 +33 3.26 1638362.63452 63516512.707 +34 3.265 1352132.30623 51437989.9558 +35 3.27 1119890.91156 41819915.4536 +36 3.275 930728.197936 34128853.5593 +37 3.28 776080.832192 27953782.5881 +38 3.285 649197.950984 22976500.4202 +39 3.29 544734.946388 18949536.6006 +40 3.295 458443.200409 15679580.461 +41 3.3 386931.981432 13014984.83 +42 3.305 327484.882814 10836296.983 +43 3.31 277917.684205 9049049.63384 +44 3.315 236467.817902 7578247.52911 +45 3.32 201708.057716 6364132.2427 +46 3.325 172478.852825 5358914.96458 +47 3.33 147835.073691 4524245.63494 +48 3.335 127003.943407 3829244.63171 +49 3.34 109351.684422 3248966.03768 +50 3.345 94356.982001 2763193.35086 +51 3.35 81589.7991199 2355492.28163 +52 3.355 70694.4075656 2012463.12085 +53 3.36 61375.7524283 1723148.60489 +54 3.365 53388.4609277 1478563.37272 +55 3.37 46527.9558627 1271318.83571 +56 3.375 40623.2494805 1095323.17118 +57 3.38 35531.0832305 945540.660872 +58 3.385 31131.1487289 817798.059995 +59 3.39 27322.1798598 708628.354433 +60 3.395 24018.7487675 615144.330958 +61 3.4 21148.6321858 534935.990585 +62 3.405 18650.6411473 465987.08561 +63 3.41 16472.8281676 406607.038172 +64 3.415 14571.00272 355375.264352 +65 3.42 12907.4991276 311095.530355 +66 3.425 11450.1516342 272758.442538 +67 3.43 10171.439929 239510.549012 +68 3.435 9047.7752383 210628.82877 +69 3.44 8058.90260095 185499.581541 +70 3.445 7187.39938846 163600.920836 +71 3.45 6418.25372556 144488.223969 +72 3.455 5738.50938334 127782.014261 +73 3.46 5136.9660889 113157.848128 +74 3.465 4603.92612777 100337.85845 +75 3.47 4130.97969454 89083.6690543 +76 3.475 3710.8227393 79190.4466465 +77 3.48 3337.10211855 70481.8981958 +78 3.485 3004.28373073 62806.0557792 +79 3.49 2707.54003568 56031.718535 +80 3.495 2442.65394998 50045.4440029 +81 3.5 2205.93660145 44748.9996316 +82 3.505 1994.15683268 40057.2004294 +83 3.51 1804.48068152 35896.0712099 +84 3.515 1634.41934741 32201.2821773 +85 3.52 1481.78438725 28916.8150767 +86 3.525 1344.64907977 25993.8241582 +87 3.53 1221.31506159 23389.6620133 +88 3.535 1110.28347503 21067.0451721 +89 3.54 1010.22998333 18993.3383579 +90 3.545 919.9831055 17139.9396418 +91 3.55 838.505404885 15481.7515237 +92 3.555 764.877134293 13996.7253013 +93 3.56 698.281998657 12665.4680354 +94 3.565 637.994745566 11470.9030593 +95 3.57 583.370335637 10397.9763514 +96 3.575 533.834480178 9433.40224818 +97 3.58 488.875363677 8565.44294671 +98 3.585 448.036394307 7783.71706925 +99 3.59 410.909847488 7079.03325566 +100 3.595 377.131286207 6443.24533767 +101 3.6 346.374657747 5869.126147 +102 3.605 318.34798013 5350.25743201 +103 3.61 292.789543287 4880.93371692 +104 3.615 269.464560006 4456.07824337 +105 3.62 248.162210353 4071.16939457 +106 3.625 228.693030668 3722.17622503 +107 3.63 210.886604667 3405.5019084 +108 3.635 194.589519671 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7.795 5.402401468e-08 3.33222289779e-07 +941 7.8 5.23679304898e-08 3.29220126433e-07 +942 7.805 5.07317266285e-08 3.25270035737e-07 +943 7.81 4.91151445613e-08 3.21371288087e-07 +944 7.815 4.75179293742e-08 3.17523164833e-07 +945 7.82 4.59398297194e-08 3.13724958102e-07 +946 7.825 4.43805977617e-08 3.09975970624e-07 +947 7.83 4.28399891263e-08 3.06275515564e-07 +948 7.835 4.13177628469e-08 3.02622916355e-07 +949 7.84 3.98136813144e-08 2.99017506534e-07 +950 7.845 3.83275102273e-08 2.95458629582e-07 +951 7.85 3.68590185422e-08 2.91945638765e-07 +952 7.855 3.54079784251e-08 2.8847789698e-07 +953 7.86 3.39741652039e-08 2.85054776599e-07 +954 7.865 3.25573573211e-08 2.81675659322e-07 +955 7.87 3.11573362879e-08 2.78339936025e-07 +956 7.875 2.97738866382e-08 2.7504700662e-07 +957 7.88 2.84067958844e-08 2.71796279909e-07 +958 7.885 2.70558544725e-08 2.68587173443e-07 +959 7.89 2.57208557397e-08 2.65419113385e-07 +960 7.895 2.44015958707e-08 2.62291534374e-07 +961 7.9 2.30978738564e-08 2.59203879393e-07 +962 7.905 2.18094914519e-08 2.56155599635e-07 +963 7.91 2.05362531363e-08 2.53146154374e-07 +964 7.915 1.92779660724e-08 2.50175010842e-07 +965 7.92 1.8034440067e-08 2.47241644098e-07 +966 7.925 1.68054875325e-08 2.44345536912e-07 +967 7.93 1.55909234484e-08 2.41486179638e-07 +968 7.935 1.43905653237e-08 2.38663070101e-07 +969 7.94 1.32042331597e-08 2.35875713474e-07 +970 7.945 1.20317494138e-08 2.33123622171e-07 +971 7.95 1.08729389636e-08 2.30406315726e-07 +972 7.955 9.72762907123e-09 2.27723320689e-07 +973 7.96 8.59564934896e-09 2.2507417051e-07 +974 7.965 7.47683172465e-09 2.2245840544e-07 +975 7.97 6.37101040818e-09 2.19875572416e-07 +976 7.975 5.27802185823e-09 2.17325224966e-07 +977 7.98 4.19770474957e-09 2.148069231e-07 +978 7.985 3.12989994095e-09 2.12320233213e-07 +979 7.99 2.07445044336e-09 2.09864727985e-07 +980 7.995 1.03120138888e-09 2.07439986287e-07 +981 8.0 0.0 0.0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min new file mode 100644 index 0000000000..e2d4a5cce4 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min @@ -0,0 +1,24 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# Optional: Make sure the pairwise energies look reasonable: +pair_write 1 4 1001 r 4.05 8 test_chap-B.dat C-B 0 0 +pair_write 2 4 1001 r 4.05 8 test_chap-L.dat C-L 0 0 +pair_write 3 4 1001 r 4.05 8 test_chap-N.dat C-N 0 0 + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt new file mode 100644 index 0000000000..523a16575a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt @@ -0,0 +1,46 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 0.25 0.25 1.0 48279 +fix fxnve all nve + +# Notes: +# The temperature is in reduced units and is set to 0.25 +# which is the folding temperature for the frustrated protein +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 5000 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 1000000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT new file mode 100644 index 0000000000..77af3de15a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT @@ -0,0 +1,29 @@ +# This directory demonstrates how to run a short simulation of +# the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# During this short simulation (run_short_sim.nvt.in) the protein evolves +# from an unfolded initial conformation to a misfolded conformation. +# (Visualize using VMD. Note: It can take hundreds of millions of +# timesteps to escape from this conformation and reach the folded state.) +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh new file mode 100755 index 0000000000..99338c7708 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh @@ -0,0 +1,21 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + +# ----------------------------------- + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run_short_sim.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh new file mode 100755 index 0000000000..f2462426f1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..c7f8572b29 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,85 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 27 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 1 1 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 2 2 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 1 1 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 2 2 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 27 1 2 2 0.000000 1.0000 0 + + 26 !NBOND: bonds + 1 2 2 3 3 4 4 5 + 5 6 6 7 7 8 8 9 + 9 10 10 11 11 12 12 13 + 13 14 14 15 15 16 16 17 + 17 18 18 19 19 20 20 21 + 21 22 22 23 23 24 24 25 + 25 26 26 27 + + 25 !NTHETA: angles + 13 14 15 7 8 9 6 7 8 + 16 17 18 15 16 17 2 3 4 + 4 5 6 9 10 11 11 12 13 + 14 15 16 1 2 3 3 4 5 + 10 11 12 12 13 14 25 26 27 + 5 6 7 8 9 10 17 18 19 + 18 19 20 22 23 24 21 22 23 + 19 20 21 20 21 22 23 24 25 + 24 25 26 + + 19 !NPHI: dihedrals + 1 2 3 4 2 3 4 5 + 3 4 5 6 4 5 6 7 + 8 9 10 11 9 10 11 12 + 10 11 12 13 11 12 13 14 + 12 13 14 15 15 16 17 18 + 16 17 18 19 17 18 19 20 + 18 19 20 21 19 20 21 22 + 20 21 22 23 21 22 23 24 + 22 23 24 25 23 24 25 26 + 24 25 26 27 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg new file mode 100644 index 0000000000..0869126bd0 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg new file mode 100644 index 0000000000..357bc780a2 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt new file mode 100644 index 0000000000..074b55c735 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt @@ -0,0 +1,216 @@ +# This file defines the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadFrustrated { + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 + $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 + $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 + $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 + $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 + $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 + $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 + $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 + $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 + $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 + $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 + $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 + $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 + $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 + $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 + $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 + $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 + $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 + $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 + $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 + $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 + $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 + $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 + $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 + $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 + $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 + $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 + } + + # bond-ID bond-Type atom-ID atom-ID + + write("Data Bonds") { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write("Data Dihedrals") { + + $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 + # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 + # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 + + $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 + # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 + + $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadFrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + + # We use tabular dihedral potentials to implement the dihedral forces. + # (Actually there is a way to use Fourier series, using multiple charmm + # style dihedral interactions, but it's slower and messier.) + + write_once("In Settings") { + # style file keyword + dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA + dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA + # No need to specify dihedral interactions in the turn regions. (none exist) + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadFrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadFrustrated + + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt new file mode 100644 index 0000000000..54e2de4376 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt @@ -0,0 +1,85 @@ +import "1beadFrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadMisfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated". + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 + $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 + $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 + $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 + $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 + $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 + $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 + $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 + $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 + $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 + $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 + $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 + $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 + $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 + $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 + $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 + $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 + $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 + $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 + $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 + $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 + $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 + $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 + $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 + $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 + $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 + $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 + } + +} # 1beadMisfolded + + +1beadUnfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py new file mode 100755 index 0000000000..34c66418a8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +# Calculate a table of dihedral angle interactions used in the alpha-helix +# and beta-sheet regions of the frustrated protein model described in +# provided in figure 8 of the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# Note that the "A" and "B" parameters were incorrectly reported to be +# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. +# The phiA and phiB values were 57.29577951308232 degrees (1 rad) +# and 180 degrees, respectively. Both expA and expB were 6.0. +# +# To generate the table used for the alpha-helix (1 degree resolution) use this: +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 +# To generate the table used for the beta-sheets (1 degree resolution) use this: +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 +# +# (If you're curious as to why I set the location of the minima at phi_alpha +# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. +# I think the correct value turns out to be something closer to 50 degrees.) + + +from math import * +import sys + + +# The previous version included the repulsive core term +def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) + termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) + return -A*termA - B*termB + +# The previous version included the repulsive core term +def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * + expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) + termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * + expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) + return -conv_units*(A*termA + B*termB) + +if len(sys.argv) != 10: + sys.stderr.write("Error: expected 9 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") + sys.exit(-1) + +A = float(sys.argv[1]) +phiA = float(sys.argv[2]) +expA = float(sys.argv[3]) +B = float(sys.argv[4]) +phiB = float(sys.argv[5]) +expB = float(sys.argv[6]) +phi_min = float(sys.argv[7]) +phi_max = float(sys.argv[8]) +N = int(sys.argv[9]) + +for i in range(0,N): + phi = phi_min + i*(phi_max - phi_min)/(N-1) + U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt new file mode 100644 index 0000000000..a27595559e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt @@ -0,0 +1,20 @@ +import "1beadFrustrated_variants.lt" + + +protein = new 1beadUnfolded + + + +# Note: The protein begins in an "Unfolded" conformation. If instead +# you want it to begin in the folded or misfolded conformations use: +# protein = new 1beadFrustrated # or +# protein = new 1beadMisfolded + + + +# ("27.0" is the length of the protein when maximally extended) +write_once("Data Boundary") { + 0.0 27.0 xlo xhi + 0.0 27.0 ylo yhi + 0.0 27.0 zlo zhi +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat new file mode 100644 index 0000000000..d660fee308 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat @@ -0,0 +1,735 @@ +# Table of the potential and its negative derivative for frustrated alpha helix +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 + +FRUSTRATED_ALPHA +N 360 DEGREES + +1 0.0 -2.74081145103 0.0783990792662 +2 1.0 -2.81950869101 0.0789852583442 +3 2.0 -2.89876136749 0.0795096391909 +4 3.0 -2.97850675562 0.0799703813963 +5 4.0 -3.05868032959 0.0803657243943 +6 5.0 -3.13921584545 0.0806939935737 +7 6.0 -3.22004543014 0.0809536062381 +8 7.0 -3.30109967628 0.0811430773977 +9 8.0 -3.38230774267 0.0812610253741 +10 9.0 -3.46359746038 0.0813061772009 +11 10.0 -3.54489544401 0.0812773738039 +12 11.0 -3.62612720812 0.0811735749433 +13 12.0 -3.70721728841 0.0809938639029 +14 13.0 -3.78808936748 0.080737451911 +15 14.0 -3.86866640485 0.0804036822781 +16 15.0 -3.94887077101 0.0799920342374 +17 16.0 -4.02862438516 0.0795021264757 +18 17.0 -4.10784885622 0.0789337203415 +19 18.0 -4.18646562704 0.0782867227197 +20 19.0 -4.26439612115 0.0775611885609 +21 20.0 -4.34156189202 0.0767573230567 +22 21.0 -4.41788477419 0.0758754834523 +23 22.0 -4.49328703609 0.0749161804868 +24 23.0 -4.56769153408 0.0738800794563 +25 24.0 -4.64102186743 0.0727680008923 +26 25.0 -4.71320253365 0.0715809208518 +27 26.0 -4.78415908407 0.0703199708131 +28 27.0 -4.85381827903 0.0689864371778 +29 28.0 -4.92210824234 0.067581760373 +30 29.0 -4.98895861476 0.0661075335571 +31 30.0 -5.05430070586 0.0645655009259 +32 31.0 -5.11806764409 0.0629575556235 +33 32.0 -5.18019452449 0.061285737258 +34 33.0 -5.24061855376 0.0595522290273 +35 34.0 -5.29927919225 0.0577593544584 +36 35.0 -5.3561182925 0.0559095737673 +37 36.0 -5.41108023395 0.0540054798439 +38 37.0 -5.46411205346 0.0520497938726 +39 38.0 -5.51516357127 0.0500453605949 +40 39.0 -5.56418751203 0.0479951432253 +41 40.0 -5.61113962059 0.0459022180302 +42 41.0 -5.65597877221 0.0437697685824 +43 42.0 -5.69866707689 0.0416010797029 +44 43.0 -5.7391699774 0.0393995311046 +45 44.0 -5.77745634094 0.0371685907508 +46 45.0 -5.81349854393 0.034911807945 +47 46.0 -5.84727254977 0.0326328061676 +48 47.0 -5.87875797937 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0.0706775413231 +353 352.0 -2.13810701636 0.0717270740805 +354 353.0 -2.21034115987 0.0727339066469 +355 354.0 -2.28355983986 0.0736957705223 +356 355.0 -2.35771696194 0.0746104183955 +357 356.0 -2.43276419776 0.0754756307561 +358 357.0 -2.50865101613 0.0762892225281 +359 358.0 -2.58532472075 0.0770490497051 +360 359.0 -2.66273049463 0.0777530159679 + +# Table of the potential and its negative derivative for frustrated beta sheet +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 + +FRUSTRATED_BETA +N 360 DEGREES + +1 0.0 -2.55809068762 0.0731724739818 +2 1.0 -2.63154144494 0.0737195744566 +3 2.0 -2.70551060968 0.0742089966437 +4 3.0 -2.77993963883 0.074639023134 +5 4.0 -2.85476830901 0.0750080115297 +6 5.0 -2.92993479441 0.0753144003899 +7 6.0 -3.00537575069 0.0755567150326 +8 7.0 -3.08102640456 0.0757335731758 +9 8.0 -3.15682064892 0.0758436903983 +10 9.0 -3.23269114341 0.075885885404 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0.0531611720525 +342 341.0 -1.32480451282 0.0544411134304 +343 342.0 -1.37987850417 0.055703842622 +344 343.0 -1.43620582346 0.0569474464963 +345 344.0 -1.49376636966 0.0581699665097 +346 345.0 -1.55253806258 0.05936940366 +347 346.0 -1.61249680493 0.0605437236497 +348 347.0 -1.67361644969 0.0616908622471 +349 348.0 -1.73586877296 0.0628087308273 +350 349.0 -1.79922345238 0.0638952220804 +351 350.0 -1.86364805137 0.0649482158688 +352 351.0 -1.92910800931 0.0659655852184 +353 352.0 -1.9955666377 0.066945202426 +354 353.0 -2.06298512258 0.0678849452658 +355 354.0 -2.13132253309 0.0687827032771 +356 355.0 -2.20053583647 0.0696363841147 +357 356.0 -2.27057991931 0.0704439199439 +358 357.0 -2.3414076153 0.0712032738621 +359 358.0 -2.41296973939 0.0719124463259 +360 359.0 -2.48521512832 0.072569481568 diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min new file mode 100644 index 0000000000..fce9843aa8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt new file mode 100644 index 0000000000..2974c12e8a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt @@ -0,0 +1,50 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Keep the chaperonin fixed. Only let the protein move. + +fix fxlan proteins langevin 0.25 0.25 1.0 48279 +fix fxnve proteins nve + +# Notes: +# The temperature is in reduced units and is set to 0.25 +# which is the folding temperature for the frustrated protein +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +# Just run it long enough for it to collapse (not fold) +# (If you need to run it longer, then dump trajectory data less frequently.) +run 50000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT new file mode 100644 index 0000000000..5da41b9a8b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT @@ -0,0 +1,32 @@ +# This directory demonstrates how to run a short simulation of +# the "unfrustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# In this example, the protein is placed inside a repulsive sphere +# of radius 6.0 sigma which confines its motion. +# (This sphere is sometimes called the "chaperonin", because +# we were using it to model the crude behavior of a chaperonin cavity.) +# +# During this short simulation (run.in.nvt) the protein evolves +# from an unfolded initial conformation to the folded state. +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh new file mode 100755 index 0000000000..45bd2d451d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh new file mode 100755 index 0000000000..f2462426f1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..7763505c0d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,98 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 28 !NATOM + 1 1 1 1 0.000000 100.0000 0 + 2 2 3 3 0.000000 1.0000 0 + 3 2 2 2 0.000000 1.0000 0 + 4 2 3 3 0.000000 1.0000 0 + 5 2 2 2 0.000000 1.0000 0 + 6 2 3 3 0.000000 1.0000 0 + 7 2 2 2 0.000000 1.0000 0 + 8 2 4 4 0.000000 1.0000 0 + 9 2 4 4 0.000000 1.0000 0 + 10 2 2 2 0.000000 1.0000 0 + 11 2 3 3 0.000000 1.0000 0 + 12 2 2 2 0.000000 1.0000 0 + 13 2 3 3 0.000000 1.0000 0 + 14 2 2 2 0.000000 1.0000 0 + 15 2 3 3 0.000000 1.0000 0 + 16 2 4 4 0.000000 1.0000 0 + 17 2 4 4 0.000000 1.0000 0 + 18 2 4 4 0.000000 1.0000 0 + 19 2 2 2 0.000000 1.0000 0 + 20 2 2 2 0.000000 1.0000 0 + 21 2 3 3 0.000000 1.0000 0 + 22 2 3 3 0.000000 1.0000 0 + 23 2 2 2 0.000000 1.0000 0 + 24 2 2 2 0.000000 1.0000 0 + 25 2 3 3 0.000000 1.0000 0 + 26 2 3 3 0.000000 1.0000 0 + 27 2 2 2 0.000000 1.0000 0 + 28 2 3 3 0.000000 1.0000 0 + + 26 !NBOND: bonds + 2 3 3 4 4 5 5 6 + 6 7 7 8 8 9 9 10 + 10 11 11 12 12 13 13 14 + 14 15 15 16 16 17 17 18 + 18 19 19 20 20 21 21 22 + 22 23 23 24 24 25 25 26 + 26 27 27 28 + + 25 !NTHETA: angles + 3 4 5 5 6 7 10 11 12 + 12 13 14 8 9 10 7 8 9 + 17 18 19 19 20 21 23 24 25 + 22 23 24 2 3 4 4 5 6 + 11 12 13 13 14 15 26 27 28 + 15 16 17 6 7 8 9 10 11 + 14 15 16 18 19 20 20 21 22 + 21 22 23 24 25 26 25 26 27 + 16 17 18 + + 43 !NPHI: dihedrals + 2 3 4 5 2 3 4 5 + 3 4 5 6 3 4 5 6 + 4 5 6 7 4 5 6 7 + 5 6 7 8 5 6 7 8 + 6 7 8 9 7 8 9 10 + 8 9 10 11 9 10 11 12 + 9 10 11 12 10 11 12 13 + 10 11 12 13 11 12 13 14 + 11 12 13 14 12 13 14 15 + 12 13 14 15 13 14 15 16 + 13 14 15 16 14 15 16 17 + 15 16 17 18 16 17 18 19 + 16 17 18 19 17 18 19 20 + 17 18 19 20 18 19 20 21 + 18 19 20 21 19 20 21 22 + 19 20 21 22 20 21 22 23 + 20 21 22 23 21 22 23 24 + 21 22 23 24 22 23 24 25 + 22 23 24 25 23 24 25 26 + 23 24 25 26 24 25 26 27 + 24 25 26 27 25 26 27 28 + 25 26 27 28 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg new file mode 100644 index 0000000000..a0da344db5 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg new file mode 100644 index 0000000000..a1aa5bd855 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt new file mode 100644 index 0000000000..0dc1f5dd05 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt @@ -0,0 +1,255 @@ +# This file defines a pair of coarse-grained protein models used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadUnfrustrated { + + # Note: the "unfrustrated" model is kind of funny looking. (My apologies.) + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118 + $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074 + $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456 + $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926 + $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356 + $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634 + $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503 + $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852 + $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528 + $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863 + $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636 + $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065 + $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921 + $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738 + $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232 + $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693 + $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841 + $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008 + $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678 + $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878 + $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001 + $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365 + $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748 + $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731 + $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442 + $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789 + $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241 + } + + # bond-ID bond-Type atom-ID atom-ID + + write("Data Bonds") { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + # + # Note that some quartets of atoms are listed because their + # potentials contain multiple terms in the Fourier expansion. + # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!) + # + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write("Data Dihedrals") { + $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8 + $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9 + $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10 + $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16 + $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17 + $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadUnfrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + # dihedral_coeff dihedralType dihedralstylename K n d w + # ("w" is the weight for 1-4 pair interactions, which we set to 0) + + # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d + # parameters. I'm hoping this will be fixed eventually. + + write_once("In Settings") { + # Correct version: + #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0 + # Correct version: + #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0 + dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0 + dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0 + dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0 + # Correct version: + # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0 + # Replacing with + dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0 + dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0 + dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0 + dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0 + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadUnfrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadUnfrustrated + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt new file mode 100644 index 0000000000..cbc8fe217c --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt @@ -0,0 +1,45 @@ +import "1beadUnfrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadUnfolded inherits 1beadUnfrustrated { + + # This molecule "inherits" all of its features from "1beadUnfrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt new file mode 100644 index 0000000000..8266d2a898 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt @@ -0,0 +1,41 @@ +# Here we define a trivial molecule containing only one particle. + +Chaperonin { + + # atomID molID atomType charge x y z + + write("Data Atoms") { + $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:C 100.0 + } + + write_once("In Settings") { + # If for some reason there are multiple chaperones present, + # I assume that they interact repulsively (hence, L=0) + # i j epsilon sigma K L + + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0 + + # Optional: define the atoms in the "chaperonins" group: + # (Defining a group for the chaperone makes it easy to immobilize it later.) + + group chaperonins type @atom:C + } + + + # Specify which pair_styles, and atom styles work well with + # this model. (Again this can be overridden later.) + + write_once("In Init") { + units lj + atom_style full + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0 + } + +} # Chaperonin + +# We have not specified how this particle interacts with other particles +# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py new file mode 100755 index 0000000000..9b86809cc3 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between atoms in the +# protein and a chaperone provided in the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# This is stored in a tabulated force field with a singularity at a distance R. +# +# To calculate the table for interaction between +# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 +# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 +# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True +# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True + +from math import * +import sys + +def U(r, eps, sigma, R, h): + #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) + - h*pow((sigma/R), 6.0)) + xp = sigma/(r+R) + xm = sigma/(r-R) + term10 = pow(xm, 10.0) - pow(xp, 10.0) + term4 = pow(xm, 4.0) - pow(xp, 4.0) + return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) + +def F(r, eps, sigma, R, h): + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 0.0 + product_term_a = U(r, eps, sigma, R, h) / r + ixp = (r+R)/sigma + ixm = (r-R)/sigma + dix_dr = 1.0/sigma + term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) + term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) + product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) + return product_term_a + product_term_b + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + + """ + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + def __repr__(self): + return str(self) + +if len(sys.argv) < 8: + sys.stderr.write("Error: expected 7 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") + sys.exit(-1) + +epsilon = float(sys.argv[1]) +sigma = float(sys.argv[2]) +R = float(sys.argv[3]) +h = float(sys.argv[4]) +rmin = float(sys.argv[5]) +rmax = float(sys.argv[6]) +N = int(sys.argv[7]) + +subtract_Urcut = False +if len(sys.argv) == 9: + subtract_Urcut = True +rcut = rmax + +for i in range(0,N): + r = rmin + i*(rmax-rmin)/(N-1) + U_r = U(r, epsilon, sigma, R, h) + F_r = F(r, epsilon, sigma, R, h) + if subtract_Urcut: + U_r -= U(rcut, epsilon, sigma, R, h) + if (r >= rcut) or (i==N-1): + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt new file mode 100644 index 0000000000..d8781c26f5 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt @@ -0,0 +1,45 @@ +write_once("Data Boundary") { + 0.0 20.0 xlo xhi + 0.0 20.0 ylo yhi + 0.0 20.0 zlo zhi +} + + +import "chaperonin.lt" +import "1beadUnfrustrated_variants.lt" + + +chaperinin = new Chaperonin # (hollow chaperonin, encloses protein) +protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein) + + + +# Now define interactions between the "c" atom in the +# chaperone and the "B", "L", "N" atoms in the protein: + +write_once("In Settings") { + pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.dat CH_H0 + pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/L table table_chaperonin_h=0.dat CH_H0 + pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/N table table_chaperonin_h=0.dat CH_H0 + # Note: In this example, the chaperone is playing the role of a repulsive wall + # (confinement). To use a sticky chaperonin, replace the first line with this: + # pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475 +} + + + +# LAMMPS has many available force field styles (and atom styles). +# Here, we pick the ones which work well for this molecular model: + +write_once("In Init") { + # --- Default options for the "1BeadUnfrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat new file mode 100644 index 0000000000..675d228a90 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat @@ -0,0 +1,1188 @@ +# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475). +# LAMMPS would crash unless I set the minimum radius to a positive value (not 0) + +CH_H0.475 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 -0.018422088583 0.0 +2 0.005 -0.0184221525389 2.55824082873e-05 +3 0.01 -0.0184223444081 5.11654127471e-05 +4 0.015 -0.018422664195 7.67496107175e-05 +5 0.02 -0.0184231119071 0.000102335598797 +6 0.025 -0.018423687555 0.000127923973785 +7 0.03 -0.0184243911519 0.000153515332637 +8 0.035 -0.0184252227143 0.000179110272379 +9 0.04 -0.0184261822615 0.000204709390236 +10 0.045 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b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat new file mode 100644 index 0000000000..2ad6d7b691 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat @@ -0,0 +1,1187 @@ +# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0) + +CH_H0 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 8.31299178857e-07 0.0 +2 0.005 8.31311879342e-07 -5.08022586688e-09 +3 0.01 8.31349981758e-07 -1.01608369733e-08 +4 0.015 8.31413488996e-07 -1.52422186449e-08 +5 0.02 8.31502405871e-07 -2.03247562721e-08 +6 0.025 8.31616739127e-07 -2.54088353865e-08 +7 0.03 8.31756497437e-07 -3.04948417048e-08 +8 0.035 8.319216914e-07 -3.55831611709e-08 +9 0.04 8.32112333547e-07 -4.06741800058e-08 +10 0.045 8.32328438343e-07 -4.57682847516e-08 +11 0.05 8.32570022183e-07 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-2.55154000294e+12 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min new file mode 100644 index 0000000000..fce9843aa8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt new file mode 100644 index 0000000000..5fb8d71b39 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt @@ -0,0 +1,48 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Keep the chaperonin fixed. Only let the protein move. + +fix fxlan proteins langevin 0.39 0.39 1.0 48279 +fix fxnve proteins nve + +# Notes: +# The temperature is in reduced units and is set to 0.39 +# which is the folding temperature for the unfrustrated protein. +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 5000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT new file mode 100644 index 0000000000..b2770e3e3d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT @@ -0,0 +1,27 @@ +# This directory demonstrates how to run a short simulation of +# the "unfrustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# During this short simulation (run.in.nvt) the protein evolves +# from an unfolded initial conformation to the folded state. +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh new file mode 100755 index 0000000000..45bd2d451d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh new file mode 100755 index 0000000000..cb3196cf8a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..1470af4bc1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,97 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 27 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 1 1 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 2 2 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 1 1 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 2 2 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 27 1 2 2 0.000000 1.0000 0 + + 26 !NBOND: bonds + 1 2 2 3 3 4 4 5 + 5 6 6 7 7 8 8 9 + 9 10 10 11 11 12 12 13 + 13 14 14 15 15 16 16 17 + 17 18 18 19 19 20 20 21 + 21 22 22 23 23 24 24 25 + 25 26 26 27 + + 25 !NTHETA: angles + 13 14 15 7 8 9 6 7 8 + 16 17 18 15 16 17 2 3 4 + 4 5 6 9 10 11 11 12 13 + 14 15 16 1 2 3 3 4 5 + 10 11 12 12 13 14 25 26 27 + 5 6 7 8 9 10 17 18 19 + 18 19 20 22 23 24 21 22 23 + 19 20 21 20 21 22 23 24 25 + 24 25 26 + + 43 !NPHI: dihedrals + 1 2 3 4 1 2 3 4 + 2 3 4 5 2 3 4 5 + 3 4 5 6 3 4 5 6 + 4 5 6 7 4 5 6 7 + 5 6 7 8 6 7 8 9 + 7 8 9 10 8 9 10 11 + 8 9 10 11 9 10 11 12 + 9 10 11 12 10 11 12 13 + 10 11 12 13 11 12 13 14 + 11 12 13 14 12 13 14 15 + 12 13 14 15 13 14 15 16 + 14 15 16 17 15 16 17 18 + 15 16 17 18 16 17 18 19 + 16 17 18 19 17 18 19 20 + 17 18 19 20 18 19 20 21 + 18 19 20 21 19 20 21 22 + 19 20 21 22 20 21 22 23 + 20 21 22 23 21 22 23 24 + 21 22 23 24 22 23 24 25 + 22 23 24 25 23 24 25 26 + 23 24 25 26 24 25 26 27 + 24 25 26 27 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg new file mode 100644 index 0000000000..152fa88ff9 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg new file mode 100644 index 0000000000..bb269f47f2 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt new file mode 100644 index 0000000000..0dc1f5dd05 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt @@ -0,0 +1,255 @@ +# This file defines a pair of coarse-grained protein models used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadUnfrustrated { + + # Note: the "unfrustrated" model is kind of funny looking. (My apologies.) + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118 + $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074 + $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456 + $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926 + $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356 + $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634 + $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503 + $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852 + $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528 + $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863 + $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636 + $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065 + $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921 + $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738 + $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232 + $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693 + $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841 + $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008 + $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678 + $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878 + $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001 + $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365 + $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748 + $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731 + $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442 + $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789 + $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241 + } + + # bond-ID bond-Type atom-ID atom-ID + + write("Data Bonds") { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + # + # Note that some quartets of atoms are listed because their + # potentials contain multiple terms in the Fourier expansion. + # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!) + # + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write("Data Dihedrals") { + $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8 + $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9 + $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10 + $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16 + $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17 + $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadUnfrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + # dihedral_coeff dihedralType dihedralstylename K n d w + # ("w" is the weight for 1-4 pair interactions, which we set to 0) + + # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d + # parameters. I'm hoping this will be fixed eventually. + + write_once("In Settings") { + # Correct version: + #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0 + # Correct version: + #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0 + dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0 + dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0 + dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0 + # Correct version: + # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0 + # Replacing with + dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0 + dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0 + dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0 + dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0 + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadUnfrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadUnfrustrated + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt new file mode 100644 index 0000000000..cbc8fe217c --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt @@ -0,0 +1,45 @@ +import "1beadUnfrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadUnfolded inherits 1beadUnfrustrated { + + # This molecule "inherits" all of its features from "1beadUnfrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt new file mode 100644 index 0000000000..5ebe6efb88 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt @@ -0,0 +1,11 @@ +import "1beadUnfrustrated_variants.lt" + + +protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein) + + +write_once("Data Boundary") { + 0.0 27.0 xlo xhi + 0.0 27.0 ylo yhi + 0.0 27.0 zlo zhi +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min new file mode 100644 index 0000000000..fce9843aa8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt new file mode 100644 index 0000000000..a831a97b4a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt @@ -0,0 +1,46 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 0.39 0.39 1.0 48279 +fix fxnve all nve + +# Notes: +# The temperature is in reduced units and is set to 0.39 +# which is the folding temperature for the unfrustrated protein. +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 8000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT new file mode 100644 index 0000000000..eda6a1ca22 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT @@ -0,0 +1,44 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +This is an example of a very simple coarse-grained protein. + +This example contains a 1-bead (C-alpha model) representation of the +"unfrustrated" 4-helix bundle model used in this paper: +G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) + +In this model, there are three atom-types (bead-types), H, L, and N +representing one amino-acid each. The "H" beads represent the hydrophobic +amino acids, and are attracted to eachother with a strength of "1.0" +(in dimensionless units of "epsilon"). The "L" and "N" atoms are +hydrophilic and purely repulsive, and only differ in their secondary-structure +propensity (ie their dihedral parameters). + +The dihedral-interaction is bi-stable with two deep local minima (corresponding +to helix-like and sheet-like secondary structure). You can adjust the bias +in favor of one minima or another by modifying the angle-shift parameter in +the appropriate "dihedral_coeff" command in the other .lt file. + +A definition for the 4-sheet beta-barell protein model is also included. +If you want to simulate that molecule instead, then edit the "system.lt" +file (in the "moltemplate_files" subdirectory), and replace this line: +prot = new 4HelixBundle + with +prot = new 4SheetBundle + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh new file mode 100755 index 0000000000..45bd2d451d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh new file mode 100755 index 0000000000..cb3196cf8a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg new file mode 100644 index 0000000000..b4d919f9e6 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg new file mode 100644 index 0000000000..cd65146ffa Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..de47509ed4 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,214 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 73 !NATOM + 1 1 1 1 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 2 2 0.000000 1.0000 0 + 5 1 1 1 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 2 2 0.000000 1.0000 0 + 8 1 2 2 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 1 1 0.000000 1.0000 0 + 11 1 2 2 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 1 1 0.000000 1.0000 0 + 15 1 2 2 0.000000 1.0000 0 + 16 1 2 2 0.000000 1.0000 0 + 17 1 1 1 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 2 2 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 1 1 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 2 2 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 1 1 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 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47 48 71 72 63 64 73 72 + 14 15 16 65 30 31 32 67 + 46 47 48 71 62 63 64 73 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt new file mode 100644 index 0000000000..9b4ff25354 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt @@ -0,0 +1,274 @@ +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. +# This approach is optional. If your protein has helices which are not +# identical, you should probably just include all 4 helices in a single +# "Data Atoms" section and don't try to subdivide the protein into pieces.) + + +1beadProtSci2010 { # <-- enclose definitions in a namespace for portability + + write_once("In Init") { + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 + $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 + $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 + $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 + $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 + $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 + $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 + $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 + $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 + $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 + $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 + $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 + $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 + $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 + $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 + $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 + $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 + $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 + $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 + $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 + $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 + $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 + $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 + $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 + $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 + $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 + $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 + $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 + $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 + $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 + $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 + $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 + $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + # ----- Now build larger molecules using A16, B16 and T3 ------- + + 4SheetBarrel { + + sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, -6) + sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, -6) + sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, -6) + sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, -6) + + turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,6.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-6.9) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,6.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + 4HelixBundle { + + helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, -4.5) + helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, -4.5) + helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, -4.5) + helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, -4.5) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,5.4) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-4.8) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,5.4) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + } + # Interactions between different atoms use "repulsive wins" mixing rules + + + # bond_coeff bondType bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 66.6 1.0 + } + + + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 66.6 105.0 + } + + # We use the same bond-angle forces whenever + # there are 3 consecutively-bonded atoms: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + + + # From the Bellesia et al 2010 paper: + # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta)) + # for turns: U_{dih}(\phi) = 0.2*cos(3\phi) + # + # General formula used for "dihedral_style fourier": + # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ] + # + # Syntax: + # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ... + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 + dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5 + dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 + dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 + # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. + } + + + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + write_once("Data Dihedrals By Type") { + @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * + @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * + @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * + } + # Note: This next rule is not needed: + # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * + # (By reflection symmetry, it's equivalent to the rule above.) + # + # Note: The example in ../../membrane+protein/moltemplate_files/ + # demonstrates how to define dihedral angles for this model + # in an alternate way which might be easier to understand. + + + # --- Mass Units --- + # There are 3 atom types (referred to above as ../H, ../L, and ../N) + # Define their masses (in reduced units): + + write_once("Data Masses") { + @atom:H 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh new file mode 100755 index 0000000000..852b9b76f2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh @@ -0,0 +1,13 @@ +# run moltemplate this way + +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data +# which are needed by LAMMPS. + +# ------ Other versions: -------- +# +# If you are using the "other_versions/charmm/1beadProtSci2010.lt" file, +# then you must run moltemplate this way: +# +# moltemplate.sh -overlay-dihdedrals system.lt diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT new file mode 100644 index 0000000000..82bc8c5c43 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT @@ -0,0 +1,13 @@ +This directory contains other versions of the same molecule +(with the same force-field), implemented in different ways. + +charmm/1beadProtSci2010.lt <-- This applies multiple "charmm" dihedral angle + forces to the same quartet of atoms to create + a Fourier series. (No packages needed.) + + NOTE: You must run moltemplate this way: + + moltemplate.sh -overlay-dihdedrals system.lt + +class2/1beadProtSci2010.lt <-- This uses the "class2" dihedral angles forces + (You must build LAMMPS with the CLASS2 package) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt new file mode 100644 index 0000000000..d57186bee7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt @@ -0,0 +1,411 @@ +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +# +# +# For portability, all definitions in this file are enclosed within +# the "1beadProtSci2010" namespace. To access them, put +# "using namespace 1beadProtSci2010" in your LT file. + +# Strategy: +# +#1) First I'll define some building blocks +# (short helices, sheets and turns of a predetermined length) +# +#2) Then I'll cut and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. +# +# Doing it this way is optional. It's simpler (but longer) to simply write +# out the entire sequence of all 73 atoms in a single "Data Atoms" section. +# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the +# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions +# manually (instead of inferring them from the atom type). If your protein +# has helices which are not identical, this would probably be easier. +# Use whichever style you prefer. +# +# +# Note that atom types, bond types, angle types, and dihedral types +# are shared between all molecules defined in the "1beadProtSci2010" family. +# (That's why there is a "../" in their path-names. Otherwise atom, bond, +# angle types, etc... are not shared between different molecules.) +# +# Confusing detail: +# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer). +# These are represented by the "$mol" variable written next to each atom. +# Our protein has multiple subunits (in this case: helices, sheets, turns). +# Because we want the subunits to share the same molecule-ID counter we use +# "$mol:..." instead of "$mol" which tells moltemplate to search for the +# parent molecule's ID. This is optional. If it bothers you, just use "$mol" + + + +1beadProtSci2010 { + + write_once("In Init") { + # -- Default styles for "1beadProtSci2010" -- + units lj + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style hybrid lj/cut/coul/debye 0.1 4.0 + # or (for short distances, below a couple nm) + #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + + # ---- Building blocks: A16, B16, Turn3 ---- + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 + $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 + $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 + $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 + $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 + $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 + $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 + $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 + $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 + $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 + $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 + $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 + $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 + $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 + $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 + $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 + $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 + $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 + $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 + $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 + $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 + $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 + $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 + $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 + $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 + $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 + $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 + $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 + $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 + $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 + $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 + $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 + $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) + # can be shared. The ".." in "@atom:../CA" tells moltemplate that + # atom type CA is defined in the parent's environment. (We are + # sharing the CA atom type between both the H and P residues. + # The same is true of the ".." in "@bond:../sidechain". + # + # + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # molecule's id number as it's own. + + + + # ----- Now build larger molecules using A16, B16 and T3 ------- + + 4HelixBundle { + + helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0) + helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0) + helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0) + helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0) + # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9) + + # Note: In the paper, this is described as the "UA2" conformation + # (I played around with the angles until it looked "okay". This is not + # the minimum energy conformation. Further minimization is necessary.) + + # Now bond the pieces together. + # (Note: angle & dihedral interactions will be generated automatically.) + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # <-- create a variable for the parent's Molecule-ID + } + + 4SheetBundle { + + sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0) + sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0) + sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0) + sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0) + # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2) + + turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # There are 3 atom types (referred to above as ../H, ../L, and ../N) + # Define their masses: + + write_once("Data Masses") { + @atom:H 1.0 + @atom:L 1.0 + @atom:N 1.0 + + } + + + + # -------------------------------------------------------------------- + # -- In this example, all force field parameters are stored in the -- + # -- file named "In Settings". They can also go in sections like -- + # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- + # -------------------------------------------------------------------- + + + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + } + # (Interactions between different atom types use "arithmetic" + # and "maxmax" ("repulsion-wins") mixing rules.) + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond_coeff bondType bondstylename k r0 + # + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 66.6 1.0 + } + + + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # The corresponding command is: + # + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 66.6 105.0 + } + + # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded + # together. We do this by to asking moltemplate to generate this + # 3-body interaction whenever 3 consecutively bonded atoms satisfy + # the following type requirement: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone * * * * * + } + + + + + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + # dihedral_coeff dihedralType dihedralstylename K n d w + # ("w" is the weight for 1-4 pair interactions, which we set to 0) + + write_once("In Settings") { + dihedral_coeff @dihedral:turn charmm 0.2 3 0 0 + dihedral_coeff @dihedral:term3 charmm 1.2 3 0 0 + + dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65 0 + dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62 0 + dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60 0 + dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57 0 + dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55 0 + } + + #write_once("In Settings") { + # dihedral_coeff @dihedral:turn charmm 0.2 3 0.0 0 + # dihedral_coeff @dihedral:term3 charmm 1.2 3 0.0 0 + # dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65.0 0 + # dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62.5 0 + # dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60.0 0 + # dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57.5 0 + # dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55.5 0 + #} + + # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy + # the following type requirements: + + write_once("Data Dihedrals By Type") { + # The dihedral interaction between backbone atoms in the helix or sheet-like + # regions is proportional to the sum of two terms: cos(phi+delta)+cos(3*phi) + # where delta is a constant used to control the bias between helices/sheets. + # As of 2013-4-07, the "fourier", "table", "class2", and "charmm", + " dihedral_styles can implement this potential. + # However dihedral_style "charmm" can only handle one cosine term at a time. + # So we use two commands to create two dihedral interactions for the same + # set of of four atoms ("cos3" and "delta60_0"). (To allow the + # superposition of multiple dihedral interactions on the same atoms, + # be sure to run moltemplate with the "-overlay-dihdedrals" argument.) + # + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + @dihedral:term3 @atom:H @atom:L @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * + + @dihedral:term3 @atom:H @atom:L @atom:L @atom:H * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * + + @dihedral:term3 @atom:L @atom:H @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * + + @dihedral:term3 @atom:H @atom:H @atom:L @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * + + # Comment out the next 4 lines: (They are redundant with the lines above) + #@dihedral:term3 @atom:L @atom:L @atom:H @atom:H * * * + #@dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * * + #@dihedral:term3 @atom:L @atom:H @atom:L @atom:H * * * + #@dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * * + # (Redundant: The LLHH pattern is identical to HHLL after order reversal) + # (Redundant: The LHLH pattern is identical to HLHL after order reversal) + + # Right now the dihedral-angle settings are "unfrustrated", meaning that the + # peptide backbone is equally happy to adopt helical or sheet-like secondary + # structure (See Table IV of Bellesia et. al, Prot Sci, 19, 141 (2010)). + # You can change that by changing "delta60_0" to one of the other choices. + + # Any dihedral interactions containing "N" atoms use the @dihedral:turn + # interaction (which is much weaker). + @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + # Comment out the next 4 lines: (They are redundant with the lines above) + # @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + # @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * * + # @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * * + # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * + } + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt new file mode 100644 index 0000000000..a0e305f844 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt @@ -0,0 +1,385 @@ +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +# +# +# For portability, all definitions in this file are enclosed within +# the "1beadProtSci2010" namespace. To access them, put +# "using namespace 1beadProtSci2010" in your LT file. + +# Strategy: +# +#1) First I'll define some building blocks +# (short helices, sheets and turns of a predetermined length) +# +#2) Then I'll cut and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. +# +# Doing it this way is optional. It's simpler (but longer) to simply write +# out the entire sequence of all 73 atoms in a single "Data Atoms" section. +# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the +# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions +# manually (instead of inferring them from the atom type). If your protein +# has helices which are not identical, this would probably be easier. +# Use whichever style you prefer. +# +# +# Note that atom types, bond types, angle types, and dihedral types +# are shared between all molecules defined in the "1beadProtSci2010" family. +# (That's why there is a "../" in their path-names. Otherwise atom, bond, +# angle types, etc... are not shared between different molecules.) +# +# Confusing detail: +# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer). +# These are represented by the "$mol" variable written next to each atom. +# Our protein has multiple subunits (in this case: helices, sheets, turns). +# Because we want the subunits to share the same molecule-ID counter we use +# "$mol:..." instead of "$mol" which tells moltemplate to search for the +# parent molecule's ID. This is optional. If it bothers you, just use "$mol" + + + +1beadProtSci2010 { + + write_once("In Init") { + # -- Default styles for "1beadProtSci2010" -- + units lj + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid class2 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 rsoftcore 1 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style hybrid lj/cut/coul/debye 0.1 4.0 + # or (for short distances, below a couple nm) + #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + + # ---- Building blocks: A16, B16, Turn3 ---- + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 + $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 + $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 + $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 + $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 + $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 + $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 + $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 + $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 + $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 + $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 + $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 + $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 + $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 + $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 + $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 + $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 + $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 + $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 + $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 + $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 + $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 + $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 + $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 + $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 + $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 + $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 + $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 + $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 + $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 + $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 + $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 + $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) + # can be shared. The ".." in "@atom:../CA" tells moltemplate that + # atom type CA is defined in the parent's environment. (We are + # sharing the CA atom type between both the H and P residues. + # The same is true of the ".." in "@bond:../sidechain". + # + # + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # molecule's id number as it's own. + + + + # ----- Now build larger molecules using A16, B16 and T3 ------- + + 4HelixBundle { + + helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0) + helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0) + helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0) + helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0) + # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9) + + # Note: In the paper, this is described as the "UA2" conformation + # (I played around with the angles until it looked "okay". This is not + # the minimum energy conformation. Further minimization is necessary.) + + # Now bond the pieces together. + # (Note: angle & dihedral interactions will be generated automatically.) + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # <-- create a variable for the parent's Molecule-ID + } + + 4SheetBundle { + + sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0) + sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0) + sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0) + sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0) + # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2) + + turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # There are 3 atom types (referred to above as ../H, ../L, and ../N) + # Define their masses: + + write_once("Data Masses") { + @atom:H 1.0 + @atom:L 1.0 + @atom:N 1.0 + + } + + + + # -------------------------------------------------------------------- + # -- In this example, all force field parameters are stored in the -- + # -- file named "In Settings". They can also go in sections like -- + # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- + # -------------------------------------------------------------------- + + + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 0 0 0 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0 + } + # (Interactions between different atom types use "arithmetic" + # and "maxmax" ("repulsion-wins") mixing rules.) + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond_coeff bondType bondstylename k r0 + # + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 66.6 1.0 + } + + + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # The corresponding command is: + # + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 66.6 105.0 + } + + # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded + # together. We do this by to asking moltemplate to generate this + # 3-body interaction whenever 3 consecutively bonded atoms satisfy + # the following type requirement: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone * * * * * + } + + + + + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + + # From the Bellesia et al paper: Udihedral(x) = 1.2*(cos(x+delta) + cos(3x)) (delta=60) + # (scratchwork: 1.2*cos(x+60) = -1.2*cos(x+60-180) = -1.2*cos(x-120)) + # and 1.2*cos(3x) = -1.2*cos(3x-180) + # and 0.2*cos(x) = -0.2*cos(x - 180) + # This way, the energies match exactly with the implementation using charmm dihedrals.) + # + # dihedralType dihedralstylename K1 phi1 K2 phi2 K3 phi3 + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 class2 1.2 120.0 0 0 1.2 180.0 + dihedral_coeff @dihedral:turn class2 0 0 0 0 0.2 180.0 + + # All of the cross-terms (for the class2 force-field) are zero (see docs): + dihedral_coeff @dihedral:delta60_0 class2 mbt 0 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 ebt 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 at 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 aat 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 bb13 0 0 0 + dihedral_coeff @dihedral:turn class2 mbt 0 0 0 0 + dihedral_coeff @dihedral:turn class2 ebt 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:turn class2 at 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:turn class2 aat 0 0 0 + dihedral_coeff @dihedral:turn class2 bb13 0 0 0 + } + + # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy + # the following type requirements: + + write_once("Data Dihedrals By Type") { + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * + @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * + + @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + + #### Comment out the next 6 lines: (They are redundant with the lines above) + ## @dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * * + ## @dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * * + ## @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + ## @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * * + ## @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * * + ## @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * + ################################################################### + } + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt new file mode 100644 index 0000000000..6300c4ce3f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt @@ -0,0 +1,12 @@ +import "1beadProtSci2010.lt" + +using namespace 1beadProtSci2010 + +prot = new 4HelixBundle + +write_once("Data Boundary") { + 0 100 xlo xhi + 0 100 ylo yhi + 0 100 zlo zhi +} + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min new file mode 100644 index 0000000000..fce9843aa8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt new file mode 100644 index 0000000000..f1a7aa6540 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt @@ -0,0 +1,44 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.008 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 0.4 0.4 1.0 48279 +fix fxnve all nve + +# Notes: +# The temperature is in reduced units and is set to 0.4. +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0. +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 500 #(time interval for printing out "thermo" data) + +restart 10000000 restart_nvt + +run 1000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README.TXT b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README.TXT new file mode 100644 index 0000000000..305d00d636 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README.TXT @@ -0,0 +1,114 @@ + This example shows how to build a multicomponent spherical vesicle. + The lipid bilayer is composed of two different lipids (DPPC and DLPC). + The vesicle also contains trans-membrane protein inclusions. + + The coordinates for the vesicle are constructed by PACKMOL (see below). + + The DPPC lipid model is described here: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) + (The DLPC model is a truncated version of DPPC. Modifications discussed below.) + The protein model is described here: + G. Bellesia, AI Jewett, and J-E Shea, + Protein Science, Vol19 141-154 (2010) + +--- PREREQUISITES: --- + +1) This example requires PACKMOL. You can download PACKMOL here: + + http://www.ime.unicamp.br/~martinez/packmol/ + + (Moltemplate does not come with an easy way to generate spherically-symmetric + structures, so I used the PACKMOL program to move the molecules into position.) + +2) This example requires the "dihedral_style fourier", which is currently +in the USER-MISC package. Build LAMMPS with this package enabled using + make yes-user-misc +before compiling LAMMPS. +(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.) + +3) This example may require additional features to be added to LAMMPS. +If LAMMPS complains about an "Invalid pair_style", then + a) download the "additional_lammps_code" from + http://moltemplate.org (upper-left corner menu) + b) unpack it + c) copy the .cpp and .h files to the src folding of your lammps installation. + d) (re)compile LAMMPS. + +------ Details ------- + +This example contains a coarse-grained model of a 4-helix bundle protein +inserted into a lipid bilayer (made from a mixture of DPPC and DLPC). + + -- Protein Model: -- + +The coarse-grained protein is described in: + G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +Here we use the "AUF2" model described in that paper. +(The hydrophobic beads face outwards.) + + -- Memebrane Model: -- + +The DPPC lipid bilayer described in: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) +and: + M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown + J. Chem. Phys. 135, 244701 (2011) + +As in Watson(JCP 2011), rigid bond-length constraints +have been replaced by harmonic bonds. + +A truncated version of this lipid (named "DLPC") has also been added. +The bending stiffness of each lipid has been increased to compensate +for the additional disorder resulting from mixing two different types +of lipids together. (Otherwise pores appear.) +Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models +have not been carefully parameterized to reproduce the correct behavior in +a lipid bilayer mixture. + + -- Interactions between the proteins and lipids -- + +This is discussed in the "system.lt" file. + +--- Building the files necessary to run a simulation in LAMMPS --- + +step 1) Run PACKMOL + + Type these commands into the shell. + (Each command could take several hours.) + +cd packmol_files + packmol < step1_proteins.inp # This step determines the protein's location + packmol < step2_innerlayer.inp # this step builds the inner monolayer + packmol < step3_outerlayer.inp # this step builds the outer monolayer +cd .. + +step 2) Run MOLTEMPLATE + Type these commands into the shell. + (This could take up to 10 minutes.) + +cd moltemplate_files + moltemplate.sh system.lt -xyz ../system.xyz + mv -f system.in* system.data ../ + cp -f table_int.dat ../ +cd .. + +--- Running LAMMPS --- + +step3) Run LAMMPS: + Type these commands into the shell. + (This could take days.) + +lmp_linux -i run.in.min # Minimize the system (important, and very slow) + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +If you have compiled the MPI version of lammps, you can run lammps in parallel: + +mpirun -np 4 lmp_linux -i run.in.min + or +mpirun -np 4 lmp_linux -i run.in.nvt + +(Assuming you have 4 cores, for example.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_run.sh new file mode 100755 index 0000000000..99f39891e4 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_run.sh @@ -0,0 +1,24 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with MOLTEMPLATE and PACKMOL: +# system.in.init, system.in.settings, system.in.coords, system.data, +# and table_int.dat +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + +lmp_linux -i run.in.min # Minimize the system (important, and very slow) + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.min +#or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_setup.sh new file mode 100755 index 0000000000..1ab21eb3ec --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_setup.sh @@ -0,0 +1,50 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + +# First, generate the coordinates (the "system.xyz" file) this way +# (This can be a very slow process.) +cd packmol_files + + # You must run each packmol commend one after the other + # NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding + # "inp" file. This should not happen. You can also usually interrupt + # packmol after 30 minutes, and the solution at that point should be good + # enough for use. + packmol < step1_proteins.inp # This step determines the protein's location + # It takes ~20 minutes (on an intel i7) + packmol < step2_innerlayer.inp # this step builds the inner monolayer + # It takes ~90 minutes + packmol < step3_outerlayer.inp # this step builds the outer monolayer + # It takes ~4 hours + + # Running these three commands will probably take about an hour. + # (It depends on how uniformly you need the packing to be.) + + mv -f step3_outerlayer.xyz ../system.xyz +cd .. + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -xyz ../system.xyz system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # The "table_int.dat" file contains tabular data for the lipid INT-INT atom + # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, + # so I might look for a way to get rid of it later.) + cp -f table_int.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg new file mode 100644 index 0000000000..c3ff599560 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt new file mode 100644 index 0000000000..d2aa805a5b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt @@ -0,0 +1,233 @@ +# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle (or a 4-strand beta-barrel). +# This approach is optional. If your protein has helices which are not +# identical, you should probably just include all 4 helices in a single +# "Data Atoms" section and don't try to subdivide the protein into pieces.) + + + +1beadProtSci2010 { # <-- enclose definitions in a namespace for portability + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0 + $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6 + $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2 + $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8 + $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4 + $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0 + $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6 + $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2 + $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8 + $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4 + $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0 + $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6 + $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2 + $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8 + $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4 + $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0 + $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44 + $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + + # ----- Now build a larger molecule using A16 and T3 ------- + + # Create a 4-Helix bundle. + # In this version, the hydrophobic beads are poing outward. + # I oriented them this way because I want to place this protein in a membrane. + # (There is another file in this directory containing alternate version + # of this same molecule with the hydrophobic beads pointing inward.) + + 4HelixInsideOut { + helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6) + + turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9) + turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0) + turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOut + + + # -------- Minor coordinates adjustment: ----------- + + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4HelixInsideOut.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + + + # -------------- Force-Field Parameters ------------ + + # Units and force-field styles for this protein model + # (These can be overridden later.) + + write_once("In Init") { + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + # --- Distance Units --- + # In this version of the model, sigma (the bond-length + # and particle diameter) is rounded to 5.5 Angstroms. + # + # --- Energy & Temperature Units --- + # In this protein model, "epsilon" represents the free energy + # bonus for bringing two hydrophobic amino acids together. + # Here I choose to set epsilon to 1.806551818181818 kCal/mole. + # This value was chosen so that a temperature of 300 Kelvin lies at + # 0.33 epsilon, which is the unfolding temperature of the marginally stable + # "ASF1" protein model from the Bellesia et al 2010 paper. + # This choice insures that both the "ASF1" model from that paper, + # as well as the much more stable "AUF2" protein we use here (which + # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin, + # in the bulk at least. (However it's not clear that these energy + # parameters will work well for a protein in membrane. Perhaps I'll + # run some tests and fine tune these parameters for this scenario.) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + } + + # The exact value of the bond_coeff does not matter too much as long as + # it is "stiff enough". Here I use a softer bond spring than the one + # used in the paper so that I can increase the time step. + # I also use a relatively soft spring to constrain the bond angles. + + # bond_coeff bondType bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 5.5 + } + + + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # angle_coeff angleType anglestylename k theta0 + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 100.0 105.0 + } + + + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + write_once("Data Dihedrals By Type") { + # For a chain of sH and sL atoms, use the @dihedral:delta65_0 + # parameters. (This corresponds to the "AUF2" model from the + # Bellesia et. al 2010 paper.) + + @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * + + # If "tN" (turn) atoms are present, use the @dihedral:turn parameters + + @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * + } + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 + dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 + dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 + # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. + } + + + # --- Mass Units --- + # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down): + write_once("Data Masses") { + @atom:1beadProtSci2010/sH 100.0 + @atom:1beadProtSci2010/sL 100.0 + @atom:1beadProtSci2010/tN 100.0 + } + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt new file mode 100644 index 0000000000..e6e6bced70 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt @@ -0,0 +1,225 @@ +### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ## +### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE## +# +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) + +import "1beadProtSci2010.lt" + +# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. + + +1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier + # This way we don't have to start from scratch. We can + # use all the atom types and angle settings defined earlier + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0 + $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8 + $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6 + $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4 + $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2 + $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0 + $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8 + $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6 + $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4 + $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2 + $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0 + $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8 + $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6 + $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4 + $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2 + $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + # ----- Now build larger molecules using B16 and T3 ------- + + + 4SheetBarrel { + sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0) + sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0) + sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0) + sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # Below I define several alternate conformations of the"4HelixBundleInsideOut" + # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however. + + 4HelixBundle { + helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + + turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2) + turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9) + turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4) + + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixBundle + + + + + # --- alternate conformations (same molecule) ---- + + # In the following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixBundleLoose { + + helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # In following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixInsideOutLoose { + helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8) + turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2) + turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOutLoose + + + + + # In the following version, the 4 helices are arranged next to each other, + # side-by-side, in a planar conformation (instead of a compact bundle). + + 4HelixPlanar { + helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0) + helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0) + helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0) + helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8) + turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8) + turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixPlanar + + + # -------- Minor coordinates adjustment: ----------- + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4SheetBarrel.scale(0.9166666666666666) + 4HelixBundle.scale(0.9166666666666666) + 4HelixBundleLoose.scale(0.9166666666666666) + 4HelixInsideOutLoose.scale(0.9166666666666666) + 4HelixPlanar.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt new file mode 100644 index 0000000000..3b39048f7e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt @@ -0,0 +1,198 @@ +# Note: +# +# This example may require additional features to be added to LAMMPS. If +# LAMMPS complains about an "Invalid pair_style", then download copy the +# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS +# "src" directory and recompile LAMMPS. +# +# -------- Description -------- +# +# This example contains an implementation of the DPPC lipid bilayer described in +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# and: +# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown +# J. Chem. Phys. 135, 244701 (2011) +# +# As in Watson(JCP 2011), rigid bond-length constraints have been replaced +# by harmonic bonds. +# +# A truncated version of this lipid (named "DLPC") has also been added. +# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +# parameterized to reproduce the correct behavior in a lipid bilayer mixture. +# +# Units: +# +# The "epsilon" parameter in their model is approximately 2.75 kJ/mole +# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) +# The "sigma" parameter corresponds to 7.5 angstroms. + + +CGLipidBr2005 { + + + write_once("In Init") { + # -- Default styles for "CGLipidBr2005" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + + #angle_style hybrid cosine/delta # <- used in the original article + angle_style hybrid harmonic # <- prevents unphysical acute angle turns + # Explanation: + # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + # angle_style harmonic: U(theta) = k*(theta-theta0)^2 + + dihedral_style none + improper_style none + pair_style hybrid table linear 1130 & + lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + + neighbor 2.0 multi # <- perhaps unnecessary + communicate multi # <- perhaps unnecessary + } + + + DPPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 + $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + $bond:b4 @bond:../backbone $atom:t2 $atom:t3 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 + } + + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + + } #DPPC + + + DLPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + } + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + } #DLPC + + + # Particles and properties shared by all lipid types: + + write_once("Data Masses") { + @atom:int 200.0 + @atom:tail 200.0 + @atom:head 200.0 #<- Default head type. We may override it later. + } + + write_once("In Settings") { + # -- Default settings/parameters for "CGLipidBr2005" -- + # (Hybrid bond & angle styles were used for portability.) + + # As in Watson(JCP 2011), rigid bond-length constraints + # have been replaced by harmonic bonds. + # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. + bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 + } + + write_once("In Settings") { + # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps + # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 + angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps + } + # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper + # to attempt to compensate for the fact that here we are using a lipid + # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal + # of disorder into the bilayer which would not be present in a DPPC bilayer. + # This causes pores to form. Increasing the angle stiffness prevents this.) + + write_once("In Settings") { + + # The interaction of "atom:int" with other "atom:int" atoms is given by + # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at + # r=3*sigma. This was implemented using pair_style table. + # Unfortunately, mixing lj/charmm and "table" pair styles in the same + # simulation is very inneficient. + + pair_coeff @atom:int @atom:int table table_int.dat INT + + # The interaction of tail beads with eachother is given by the formula below + # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: + # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), + pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # The interaction of head beads which all other beads is given by: + # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), + + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + } # write_once("In Settings") + + # Note: I divided epsilon by 4 to get "0.1643" because we are using the + # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) + # (The "es4k4l" coeffstyle is the default.) Using this convention makes it + # easier to mix this coarse-grained lipid model with other molecular models. + + + +} # CGLipidBr2005 + + + + + + + + +# Note: This example has not been optimized for speed. +# +# Unfortunately, using both lj/charmm and "table" pair styles in the same +# simulation seems to be very inneficient. (The simulation is twice as slow +# as using only the "lj/charmm" pair styles for every pairwise interaction, +# ...and about 25% slower than using "table" for every pairwise interaction. +# However the lennard-jones pair styles support mixing, so we use them to +# make it easier to run these molecules with other molecules which don't use +# pair_table. I felt that portability was worth the extra 25% slow down.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh new file mode 100755 index 0000000000..df70396a78 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh @@ -0,0 +1,22 @@ +# This example shows how to build a multicomponent spherical vesicle. +# The lipid bilayer is composed of two different lipids (DPPC and DLPC), +# The vesicle contains 120 trans-membrane protein inclusions. +# +# ---------------- Prerequisites: ------------------ +# You must run packmol to generate the coordinates beforehand. +# Afterwards, move and rename the final coordinate file to "../system.xyz" +# To do this, check the README.sh file in the ../packmol_files directory. +# (or follow these instructions below) +# +# cd ../packmol_files +# packmol < step1_proteins.inp +# packmol < step2_innerlayer.inp +# packmol < step3_outerlayer.inp +# cp step3_outerlayer.xyz ../system.xyz +# +# These steps could take a few hours. +# +# --- After you have done that, you can run moltemplate using this command: --- + +moltemplate.sh -xyz ../system.xyz system.lt + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py new file mode 100755 index 0000000000..0d09e4d02e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py @@ -0,0 +1,29 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +rcut = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) + F_r = F(r, epsilon, sigma) + if r > rcut: + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py new file mode 100755 index 0000000000..32147e444a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# I realized later this is not what we want because although energy is conserved +# all enrgies are shifted with respect to energies used in the Brannigan paper +# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). +# (So don't use this.) + +# Calculate and print a + +def S(r, rc1, rc2, derivative=False): + """ + Calculate the switching function S(r) which decays continuously + between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): + S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 + I'm using the same smoothing/switching cutoff function used by the CHARMM + force-fields. (I'm even using the same code to implement it, taken + from lammps charmm/coul/charmm pair style, rewritten in python.) + + """ + assert(rc2>rc1) + rsq = r*r + rc1sq = rc1*rc1 + rc2sq = rc2*rc2 + denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* + (rc2sq-rc1sq)* + (rc2sq-rc1sq))) + if rsq > rc2sq: + return 0.0 + elif rsq < rc1sq: + if derivative: + return 0.0 + else: + return 1.0 + else: + rc2sq_minus_rsq = (rc2sq - rsq) + rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq + if derivative: + return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) + else: + return (rc2sq_minus_rsq_sq * + (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) + + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) + +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +Rc1 = 22.0 +Rc2 = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) + F_r = F(r, epsilon, sigma) + # Multiply U(r) & F(r) by the smoothing/switch function + U_r = U_r * S(r, Rc1, Rc2) + F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt new file mode 100644 index 0000000000..98213116d8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt @@ -0,0 +1,192 @@ +# Description: +# +# This example shows how to build a multicomponent spherical vesicle. +# The lipid bilayer is composed of two different lipids (DPPC and DLPC), +# The vesicle contains 120 trans-membrane protein inclusions. +# +# The DPPC lipid model is described here: +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# The protein model is described here: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# The new DLPC model is a truncated version of DPPC, +# (Its behaviour has not been rigorously tested.) +# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to +# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 +# +# NOTE: THE COORDINATES FOR THESE MOLECULES ARE GENERATED BY PACKMOL (see below) +# +# NOTE: +# This example may require additional features to be added to LAMMPS. +# If LAMMPS complains about an "Invalid pair_style", then copy the code +# in the "additional_lammps_code" directory into your LAMMPS "src" directory +# and recompile LAMMPS. + +# First, load the definitions of the molecules we will need: + +import "CGLipidBr2005.lt" +using namespace CGLipidBr2005 + +import "1beadProtSci2010.lt" +using namespace 1beadProtSci2010 + +# PREREQUISITES: +# Coordinates for the molecules in this example are loaded from an .XYZ file +# created by PACKMOL. This must be done in advance. (See ../packmol_files/) +# +# The XYZ file was created by PACKMOL in 3 steps: +# (Add the proteins, then pack lipids in the inner & outer layers around them.) +# +# step1) Creae 120 proteins. Distribute them on the surface of the sphere. +# +# step2) Keeping the coordinates from step1 fixed, +# a) first we add 9500 DPPC lipids to the inner monolayer +# b) then we add 9500 DLPC lipids to the inner monolayer +# +# step3) Keeping the coordinates from steps 1 and 2 fixed, +# a) first we add 12500 DPPC lipids to the outer monolayer +# b) then we add 12500 DLPC lipids to the outer monolayer +# +# The order that molecules are created in moltemplate should match the order +# they appear in the final XYZ file created by PACKMOL. (See above.) +# Consequently I instantiate the molecules in the same order here: + + +# Step 1) ---- protein inclusions ---- + +proteins = new 4HelixInsideOut [120] + +# Step 2a) ---- inner monolayer ---- +dppc_in = new DPPC [9500] +# Step 2b) +dlpc_in = new DLPC [9500] + +# Step 3a) ---- outer monolayer ---- +dppc_out = new DPPC [12500] +# Step 3b) +dlpc_out = new DLPC [12500] + + + +# ------------------ boundary conditions -------------------- + +write_once("Data Boundary") { + -500.0 500.0 xlo xhi + -500.0 500.0 ylo yhi + -500.0 500.0 zlo zhi +} + + +write_once("In Settings") { + + # ----------------------------------------------------------- + # -------- interactions between protein and lipids ---------- + # ----------------------------------------------------------- + + # Interactions between the protein and lipid atoms are usually + # determined by mixing rules. (However this is not possible some + # for atoms, such as the "int" atoms in the lipid model which + # interact using -1/r^2 attraction.) Mixing rules do not make + # sense for these atoms so we must explicitly define their + # interaction with all other atoms. + + # We want the hydrophobic interactions between hydrophobic residues in + # the protein and beads the interior of the lipid to be energetically + # similar to the attractive interactions between the lipid tails. + # + # Note: I made the width of the outward-facing protein beads slightly larger + # ("12.5") whenever they interact with the "tail" beads in each lipid + # (in order to make the protein wider there). + # This hopefully relieves some of the internal negative pressure in the center + # of the bilayer which can otherwise rip apart the protein or suck it into + # the bilaer. (This is a hack, and I'm not sure if it is necessary. + # For different protein or lipid models, you probably don't need this.) + # + # i j pairstylename eps sig K L + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # To help keep the protein from tilting 90 degrees and burying itself + # within the lipid bilayer, we make the turn regions at either + # end of the protein (strongly) attracted to the head groups + # of the lipid. (In reality, they would probably be attracted + # to the water as well.) + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # All other interactions between proteins and lipids are steric. + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + # ----------------------------------------------------------- + # -------- Modifications to the protein model: -------------- + # ----------------------------------------------------------- + # + # Turn off attraction between the hydrophobic "@atom:sH" beads: + # (These beads are located in the outside of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + + # (Why: These beads are only attracted to + # each other in an aqueous environment) + + # ... and + # Turn ON attraction between the hydrophilic "@atom:sL" beads. + # (These beads are located in the interior of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # Why? + # In reality, polar groups in the interior of trans-membrane + # proteins do form hydrogen bonds with each other. This was + # absent from the original protein model because, in an aqueous + # environment, these groups preferentially interact with the water. + # + # Why is this necessary? + # Shouldn't attraction between lipid tails and the protein create + # an effective force which brings the hydrophilic beads together? + # (similar to the hydrophobic effect, but in reverse?). + # Answer: + # Unlike an aqueous environment (~zero pressure, or +1atm), there is + # a large negative pressure in the interior of some bilayer membrane + # models (such as this one). Without some kind of direct attraction + # between interior residues, the protein will get pulled apart. + # (Perhaps the attractive force I am using is too strong?) + +} + + +# Finally, we must combine the two force-field styles which were used for +# the coarse-grained lipid and protein. To do that, we write one last time +# to the "In Init" section. When reading the "Init" section LAMMPS will +# read these commands last and this will override any earlier settings. + +write_once("In Init") { + # -- These styles override earlier settings -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid cosine/delta harmonic + dihedral_style hybrid fourier + improper_style none + pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + communicate multi +} + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat new file mode 100644 index 0000000000..b0d651d67f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat @@ -0,0 +1,1139 @@ +# Table for the INT-INT interaction from +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# This table contains +# i r_i U(r_i) -dU/dr|r_i +# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) + +INT +N 1130 + +1 0.02 2.0331818401e+30 1.21990910406e+33 +2 0.04 4.9638228518e+26 1.48914685554e+29 +3 0.06 3.82579033251e+24 7.65158066501e+26 +4 0.08 1.21187081343e+23 1.81780622014e+25 +5 0.1 8.32791281704e+21 9.99349538045e+23 +6 0.12 9.34030842897e+20 9.34030842897e+22 +7 0.14 1.46892540453e+20 1.25907891817e+22 +8 0.16 2.95866897809e+19 2.21900173357e+21 +9 0.18 7.19889946863e+18 4.79926631242e+20 +10 0.2 2.0331818401e+18 1.21990910406e+20 +11 0.22 6.47834392264e+17 3.53364213962e+19 +12 0.24 2.28034873754e+17 1.14017436877e+19 +13 0.26 8.72681951932e+16 4.02776285507e+18 +14 0.28 3.58624366341e+16 1.53696157003e+18 +15 0.3 1.56704372019e+16 6.26817488078e+17 +16 0.32 7.2233129348e+15 2.70874235055e+17 +17 0.34 3.48970861422e+15 1.23166186384e+17 +18 0.36 1.75754381558e+15 5.85847938527e+16 +19 0.38 9.18613895646e+14 2.90088598625e+16 +20 0.4 4.96382285179e+14 1.48914685554e+16 +21 0.42 2.76404230108e+14 7.89726371739e+15 +22 0.44 1.58162693423e+14 4.31352800247e+15 +23 0.46 9.27773983256e+13 2.42027995633e+15 +24 0.48 5.56725765996e+13 1.391814415e+15 +25 0.5 3.41111308981e+13 8.18667141564e+14 +26 0.52 2.13057117167e+13 4.91670270393e+14 +27 0.54 1.35459994024e+13 3.0102220895e+14 +28 0.56 8.75547769351e+12 1.87617379153e+14 +29 0.58 5.74645813711e+12 1.18892237325e+14 +30 0.6 3.8257903322e+12 7.65158066491e+13 +31 0.62 2.58128463312e+12 4.99603477424e+13 +32 0.64 1.7635041342e+12 3.30657025205e+13 +33 0.66 1.21901470178e+12 2.21639036726e+13 +34 0.68 8.51979641904e+11 1.50349348607e+13 +35 0.7 6.0167184547e+11 1.0314374497e+13 +36 0.72 4.29087845387e+11 7.15146409276e+12 +37 0.74 3.08855637556e+11 5.00846980094e+12 +38 0.76 2.24270970425e+11 3.54112058818e+12 +39 0.78 1.64210505205e+11 2.52631546702e+12 +40 0.8 1.2118708117e+11 1.81780621971e+12 +41 0.82 90109367359.1 1.31867367068e+12 +42 0.84 67481501334.4 9.64021449503e+11 +43 0.86 50880896383.4 7.09965997788e+11 +44 0.88 38613938681.2 5.26553710913e+11 +45 0.9 29486692086.8 3.93155896009e+11 +46 0.92 22650731882.4 2.95444330322e+11 +47 0.94 17498544395.3 2.23385674464e+11 +48 0.96 13591937526.4 1.69899220331e+11 +49 0.98 10612635712.6 1.29950642555e+11 +50 1.0 8327912706.34 99934953582.6 +51 1.02 6566502316.69 77252969474.2 +52 1.04 5201589672.36 60018343356.8 +53 1.06 4138717434.11 46853405843.3 +54 1.08 3307128665.58 36745874940.0 +55 1.1 2653529579.27 28947596241.1 +56 1.12 2137567708.15 22902511945.9 +57 1.14 1728534024.3 18195095739.0 +58 1.16 1402943799.0 14513212422.1 +59 1.18 1142752163.37 11621209113.9 +60 1.2 934030766.093 9340308300.6 +61 1.22 765981286.774 7534242773.65 +62 1.24 630196371.787 6098675145.29 +63 1.26 520103253.414 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b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DLPC.xyz @@ -0,0 +1,6 @@ +4 + DLPC coarse-grained lipid + 4 0.000000 0.000000 30.000000 + 2 0.000000 0.000000 22.500000 + 3 0.000000 0.000000 15.000000 + 3 0.000000 0.000000 7.500000 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DPPC.xyz b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DPPC.xyz new file mode 100644 index 0000000000..c25a2dbd1a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DPPC.xyz @@ -0,0 +1,7 @@ +5 + DPPC coarse-grained lipid + 1 0.000000 0.000000 33.750000 + 2 0.000000 0.000000 26.250000 + 3 0.000000 0.000000 18.750000 + 3 0.000000 0.000000 11.250000 + 3 0.000000 0.000000 3.750000 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh new file mode 100755 index 0000000000..8df6285caf --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh @@ -0,0 +1,18 @@ +# Here we generate the starting coordinates of the simulation +# using PACKMOL + +# Running these three commands will probably take hours or even days. +# (It depends on how dense and how uniformly you need the packing to be.) +# NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding +# "inp" file. This should not happen. You can also usually interrupt +# packmol after 30 minutes, and the solution at that point should be good +# enough for use. + +packmol < step1_proteins.inp # This step determines the protein's location + # It takes ~20 minutes (on an intel i7) +packmol < step2_innerlayer.inp # This step builds the inner monolayer + # It takes ~90 minutes +packmol < step3_outerlayer.inp # This step builds the outer monolayer + # It takes ~4 hours + +# This should create a file named "system.xyz" (which moltemplate will read). diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/protein.xyz b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/protein.xyz new file mode 100644 index 0000000000..75557e6ffb --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/protein.xyz @@ -0,0 +1,75 @@ +73 + +6 -2.11383 -5.225 -29.7 +6 -5.225 -2.11383 -26.4 +7 -8.33617 -5.225 -23.1 +7 -5.225 -8.33617 -19.8 +6 -2.11383 -5.225 -16.5 +6 -5.225 -2.11383 -13.2 +7 -8.33617 -5.225 -9.9 +7 -5.225 -8.33617 -6.6 +6 -2.11383 -5.225 -3.3 +6 -5.225 -2.11383 0 +7 -8.33617 -5.225 3.3 +7 -5.225 -8.33617 6.6 +6 -2.11383 -5.225 9.9 +6 -5.225 -2.11383 13.2 +7 -8.33617 -5.225 16.5 +7 -5.225 -8.33617 19.8 +6 5.225 -2.11383 -26.4 +6 2.11383 -5.225 -23.1 +7 5.225 -8.33617 -19.8 +7 8.33617 -5.225 -16.5 +6 5.225 -2.11383 -13.2 +6 2.11383 -5.225 -9.9 +7 5.225 -8.33617 -6.6 +7 8.33617 -5.225 -3.3 +6 5.225 -2.11383 0 +6 2.11383 -5.225 3.3 +7 5.225 -8.33617 6.6 +7 8.33617 -5.225 9.9 +6 5.225 -2.11383 13.2 +6 2.11383 -5.225 16.5 +7 5.225 -8.33617 19.8 +7 8.33617 -5.225 23.1 +6 2.11383 5.225 -23.1 +6 5.225 2.11383 -19.8 +7 8.33617 5.225 -16.5 +7 5.225 8.33617 -13.2 +6 2.11383 5.225 -9.9 +6 5.225 2.11383 -6.6 +7 8.33617 5.225 -3.3 +7 5.225 8.33617 0 +6 2.11383 5.225 3.3 +6 5.225 2.11383 6.6 +7 8.33617 5.225 9.9 +7 5.225 8.33617 13.2 +6 2.11383 5.225 16.5 +6 5.225 2.11383 19.8 +7 8.33617 5.225 23.1 +7 5.225 8.33617 26.4 +6 -5.225 2.11383 -19.8 +6 -2.11383 5.225 -16.5 +7 -5.225 8.33617 -13.2 +7 -8.33617 5.225 -9.9 +6 -5.225 2.11383 -6.6 +6 -2.11383 5.225 -3.3 +7 -5.225 8.33617 0 +7 -8.33617 5.225 3.3 +6 -5.225 2.11383 6.6 +6 -2.11383 5.225 9.9 +7 -5.225 8.33617 13.2 +7 -8.33617 5.225 16.5 +6 -5.225 2.11383 19.8 +6 -2.11383 5.225 23.1 +7 -5.225 8.33617 26.4 +7 -8.33617 5.225 29.7 +8 -3.35683 -4.56775 24.0698 +8 0.795667 -6.90708 26.8152 +8 4.78683 -3.13225 27.0802 +8 2.75642 6.08575 -28.7448 +8 6.54133 3.72717 -31.9651 +8 5.58525 -1.68575 -31.7552 +8 3.35683 4.56775 29.8448 +8 -0.795667 6.90708 32.5903 +8 -4.78683 3.13225 32.8552 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp new file mode 100644 index 0000000000..abb48db7d6 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp @@ -0,0 +1,49 @@ +# Step 1: Create a sphere of proteins lying +# (In step 2 we will pack lipids around these proteins +# +# ----- Run using: ----- +# packmol < step1_proteins.inp +# (This takes about 30 minutes on an Intel i7 processor) + + +# ----- Settings: ----- + +# All the atoms from diferent proteins will be at least 50.0 Angstrons apart. +tolerance 50.0 +# (Setting "discale" to 2.0 increases the typical separation +# distance to approximately 2.0*50.0 = 100.0 Angstroms.) +discale 2.0 +# The other parameters below are optional: +nloop 10000 +maxit 20 +seed 12345 +sidemax 3000.0 +# What fraction of the molecules are moved during "large moves"? (default 0.05) +movefrac 0.05 + + +# The output file name + +output step1_proteins.xyz + + +# File types are in xyz format + +filetype xyz + + + +# First, specify the protein inclusions +# We will pack the lipids around these later + +structure protein.xyz + number 120 + atoms 68 69 70 + inside sphere 0. 0. 0. 273.75 + end atoms + atoms 65 66 67 71 72 73 + outside sphere 0. 0. 0. 325.0 + end atoms +end structure + + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp new file mode 100644 index 0000000000..9f61960f2e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp @@ -0,0 +1,70 @@ +# NOTE: YOU MUST COMPLETE STEP 1 BEFORE RUNNING PACKMOL ON THIS FILE + +# Step 2: Pack the lipids in the inner monolayer around the proteins from step1. +# +# ----- Run using: ----- +# packmol < step2_innerlayer.inp +# (This takes about 90 minutes on an Intel i7 processor) + + +# ----- Settings: ----- + +# All the atoms from diferent molecules will be at least 5.5 Angstrons apart +tolerance 5.5 +# (Setting "discale" to 1.4 increases the typical separation +# distance to approximately 1.4*5.5 = 7.7 Angstroms.) +discale 1.4 +# The other parameters below are optional: +nloop 10000 +maxit 20 +seed 12345 +sidemax 3000.0 +# What fraction of the molecules are moved during "large moves"? (default 0.05) +movefrac 0.05 + + +# The output file name + +output step2_innerlayer.xyz + +# File types are in xyz format + +filetype xyz + + +# The proteins whose position we determined earlier in step 1 +# will be frozen in place during this step. + +structure step1_proteins.xyz + number 1 + fixed 0. 0. 0. 0. 0. 0. +end structure + + +# 9500 DPPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing inwards, and their tails (atom 5) pointing outwards. + + +structure DPPC.xyz + number 9500 + atoms 1 + inside sphere 0. 0. 0. 270.0 + end atoms + atoms 5 + outside sphere 0. 0. 0. 295.0 + end atoms +end structure + +# 9500 DLPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing inwards, and their tails (atom 4) pointing outwards. + +structure DLPC.xyz + number 9500 + atoms 1 + inside sphere 0. 0. 0. 273.0 + end atoms + atoms 4 + outside sphere 0. 0. 0. 295.0 + end atoms +end structure + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp new file mode 100644 index 0000000000..bed1c04246 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp @@ -0,0 +1,70 @@ +# NOTE: YOU MUST COMPLETE STEPS 1 AND 2 BEFORE RUNNING PACKMOL ON THIS FILE + +# Step 3: Pack the lipids in the outer monolayer around the proteins from step1. +# +# ----- Run using: ----- +# packmol < step3_outerlayer.inp +# (This takes about 4 hours on an Intel i7 processor) + + +# ----- Settings: ----- + +# All the atoms from diferent molecules will be at least 5.5 Angstrons apart +tolerance 5.5 +# (Setting "discale" to 1.4 increases the typical separation +# distance to approximately 1.4*5.5 = 7.7 Angstroms.) +discale 1.4 +# The other parameters below are optional: +nloop 10000 +maxit 20 +seed 12345 +sidemax 3000.0 +# What fraction of the molecules are moved during "large moves"? (default 0.05) +movefrac 0.05 + + +# The output file name + +output step3_outerlayer.xyz + +# File types are in xyz format + +filetype xyz + + +# The proteins and lipids whose position we determined earlier in steps 1-2 +# will be frozen in place during this step. + +structure step2_innerlayer.xyz + number 1 + fixed 0. 0. 0. 0. 0. 0. +end structure + + +# 12500 DPPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing outwards, and their tails (atom 5) pointing inwards. + + +structure DPPC.xyz + number 12500 + atoms 5 + inside sphere 0. 0. 0. 310.0 + end atoms + atoms 1 + outside sphere 0. 0. 0. 336.0 + end atoms +end structure + +# 12500 DLPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing outwards, and their tails (atom 4) pointing inwards. + +structure DLPC.xyz + number 12500 + atoms 4 + inside sphere 0. 0. 0. 313.0 + end atoms + atoms 1 + outside sphere 0. 0. 0. 332.0 + end atoms +end structure + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min new file mode 100644 index 0000000000..9cb2d93003 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min @@ -0,0 +1,46 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. + + + +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +# minimize + +minimize 1.0e-5 1.0e-7 5000 20000 + +# If minimization crashes, then instead try Langevin dynamics +# with a small timestep and a fast damping parameter. For example: +# +# timestep 0.05 +# fix fxlan all langevin 300.0 300.0 100.0 48279 +# fix fxnve all nve +# +# run 10000 + +write_data system_after_min.data diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt new file mode 100644 index 0000000000..253c042670 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt @@ -0,0 +1,63 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. +# +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +# Commenting out: +# +# read_data system.data +# +# Instead read the data file created by "run.in.min". + +read_data system_after_min.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# Just in case the previous minimization failed, try again. +# (I don't know why this helps, but sometimes it does. Magic.) + +minimize 1.0e-5 1.0e-7 5000 20000 + +# Run main simulation + +timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 100 # time interval for printing out "thermo" data + + + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. +# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. + +run 1000000 + +write_data system_after_nvt.data + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT new file mode 100644 index 0000000000..c3173a1e19 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT @@ -0,0 +1,17 @@ + +This directory contains an example of a couarse-grained (vaguely protein-like) +heteropolymer consisting of 14 residues, each of which has 2 atoms +(one backbone atom, one residue atom.) + +There are two types of residues, H and P. +The R-atom for the H residue are attracted to eachother. +All other atoms are repulsive. + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh new file mode 100755 index 0000000000..1347aebbb4 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh @@ -0,0 +1,20 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh new file mode 100755 index 0000000000..acc5fbbaad --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt new file mode 100644 index 0000000000..5d97ea56ad --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt @@ -0,0 +1,86 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg new file mode 100644 index 0000000000..a57d0309c3 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg new file mode 100644 index 0000000000..c77d7ee9d9 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..8e82afaec3 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,1728 @@ +PSF + + 1 !NTITLE + REMARKS VMD-generated NAMD/X-Plor PSF structure file + + 756 !NATOM + 1 1 1 1 0.000000 13.0000 0 + 2 1 3 3 0.000000 50.0000 0 + 3 1 1 1 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b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt new file mode 100644 index 0000000000..853821471d --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt @@ -0,0 +1,128 @@ +# In this example, we define two types of molecules: "H" and "P", +# both containing two atoms, named "CA" and "R". +# +# @R +# | +# @CA +# +# Eventually, we will connect multiple "H" and "P" molecules +# together to form a polymer, as shown below: +# +# @R @R +# | | +# _@CA_ _@CA_ +# ... -.@CA-' `-@CA-' ` ... +# | | +# @R @R +# +# Suppose that the "H" and "P" molecules both use the same +# type of backbone atom ("CA"), but have their own custom "R" +# sidechain atoms with different properties: +# The "R" atoms belonging to "H" molecules are attracted to each other. +# The "R" atoms in "P" molecules are not. +# +# (Note: There is no reason the "H" and "P" molecules in this example need +# to contain the same number of atoms, or the same atom names. +# The point of this example is to illustrate how to share atom types +# and also the difference between local and global atom types.) +# +# By default, all counter variables are local. This means that whenever +# an atom type (or other counter variable) appears inside a molecule +# definition using the normal syntax "@atom:R", that atom type is a local +# property of the the "H" or "P" molecule in which it appears. +# Any properties assigned to the "R" atoms in either molecule are unique +# to that molecule. +# +# However in order to share "CA" atom types, we will override this behavior +# using the "@atom:../CA" syntax instead of "@atom:CA". This will define +# the "CA" atom in the outer (global) environment, and any properties +# (mass, radius, etc...) assigned to the "@atom:../CA" atom apply to +# "CA" atoms in both the the "H" and "P" molecules (and everywhere else). +# +# This might not be a desirable. "CA" is a popular name for carbon +# atoms in different types of molecules. We don't want to prevent other +# molecules from using this atom name. So we enclose the "CA" atom, +# (along with the definitions of the "H" and "P" molecules) within a +# namespace/environment object ("2bead"). This makes the definition +# of "H" and "P" more portable. Later on we can combine "H" and "P" +# molecules with other molecules without worrying whether they contain +# "CA" atoms with different properties. +# +# Note: In this example "2bead" is NOT a molecule. (Because it contains no +# "write("Data Atoms")" section of its own.) "2bead" is simply the +# name of an environment in which other molecules "H" and "P" are defined. + + + + +2bead { + + write_once("In Init") { + units real + atom_style full + } + + # Define H (the "hydrophobic" residue) + H { + # atom-id mol-id atom-type charge x y z + write("Data Atoms") { + $atom:CA $mol:... @atom:../CA 0.0 0.000 1.0000 0.0000000 + $atom:R $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 + } + + # Old Data Bonds style + # write("Data Bonds") { + # $bond:CR @bond:../sidechain $atom:CA $atom:R + # } + + # New Data Bond List style + write("Data Bond List") { + $bond:CR $atom:CA $atom:R + } + } + + + # Define P (the "polar" residue) + P { + # atom-id mol-id atom-type charge x y z + write("Data Atoms") { + $atom:CA $mol:... @atom:../CA 0.0 0.000 1.0000 0.0000000 + $atom:R $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 + } + + # Old Data Bonds style + # write("Data Bonds") { + # $bond:CR @bond:../sidechain $atom:CA $atom:R + # } + + # New Data Bond List style + write("Data Bond List") { + $bond:CR $atom:CA $atom:R + } + } + + + # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) + # can be shared. The ".." in "@atom:../CA" tells moltemplate that + # atom type CA is defined in the parent's environment. (We are + # sharing the CA atom type between both the H and P residues. + # The same is true of the ".." in "@bond:../sidechain". + # + # + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # molecule's id number as it's own. + + + + # There are 3 atom types: the R sidechain (belonging to the H and P residues) + # and the CA sidechain atom (shared by both residues) + + write_once("Data Masses") { + @atom:CA 13.0 + @atom:H/R 50.0 + @atom:P/R 50.0 + } + +} # 2bead + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_forcefield.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_forcefield.lt new file mode 100644 index 0000000000..84d82683ef --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_forcefield.lt @@ -0,0 +1,126 @@ + +# We define non-bonded and bonded (angular) interactions between atoms +# belonging to "2bead" molecules. +# We define the settings for angles or dihedrals which might be present +# later when we connect multiple "2bead/H" and "2bead/P" molecules together to +# build a polymer. + + +2bead { + + + # LAMMPS supports a large number of force-field styles. We must select + # which ones we need. This information belongs in the "In Init" section. + # (Hybrid styles used for portability. These choices can be overridden later.) + + write_once("In Init") { + # -- Default styles for "2bead" -- + # (Hybrid force fields were not necessary but are used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/cut 11.0 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style hybrid lj/cut/coul/debye 0.1 11.0 + # or (for short distances, below a couple nm) + #pair_style hybrid lj/charmm/coul/charmm/implicit 9.0 11.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + + + # OPTIONAL: Enclose these angle settings within the 2bead {...} environment. + # We do this for the same reason we enclosed "H" and "P" in "2bead". + # This does not overwrite the definition of 2bead. Here we are only + # augmenting "2bead" to include the following force field information. + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * ( (sig_ij/r)^12 - (sig_ij/r)^6 ) + # + # Hydrophobic side-chains are attractive (large epsilon parameter). + # Polar side-chains and backbone atoms are not attractive (small epsilon). + # + # i j pairstylename eps sig + # + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA lj/cut 0.10 2.0 + pair_coeff @atom:H/R @atom:H/R lj/cut 2.50 3.6 + pair_coeff @atom:P/R @atom:P/R lj/cut 0.10 3.6 + } + + # (Interactions between different atom types use "arithmetic" mixing rules.) + + write_once("Data Bonds By Type") { + @bond:backbone @atom:CA @atom:CA + @bond:sidechain @atom:CA @atom:*/R + } + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond_coeff bondType bondstylename k r0 + # + + write_once("In Settings") { + bond_coeff @bond:sidechain harmonic 30.0 3.4 + bond_coeff @bond:backbone harmonic 30.0 3.7 + } + + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 + + write_once("Data Angles By Type") { + @angle:backbone @atom:CA @atom:CA @atom:CA + @angle:sidechain @atom:CA @atom:CA @atom:*/R + } + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 + + write_once("Data Dihedrals By Type") { + @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA + @dihedral:RCCR @atom:*/R @atom:CA @atom:CA @atom:*/R + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # The corresponding command is: + # + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 30.00 114 + angle_coeff @angle:sidechain harmonic 30.00 123 + } + + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is + # dihedral_coeff dihedralType dihedralstylename K n d w + # "w" is the weight for 1-4 pair interactions, which we set to 0.0 + + write_once("In Settings") { + dihedral_coeff @dihedral:CCCC charmm -0.5 1 -180 0.0 + dihedral_coeff @dihedral:RCCR charmm -1.5 1 -180 0.0 + } # write_once("In Settings") + +} + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh new file mode 100755 index 0000000000..7604a672c6 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh @@ -0,0 +1,20 @@ +# The version of "2bead.lt" in this directory is defines two types of +# molecules (named "2bead/H" and "2bead/P"). +# +# However, there is another version of this file which is easier to understand. +# I recommend reading that file first. +# It is located at "simplified_version_one_residue/2bead.lt". +# It defines only one type of molecule (named "2bead") +# It is much simpler. + +# ------ + +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + +# run moltemplate + +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data. + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt new file mode 100644 index 0000000000..ae125b95fd --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt @@ -0,0 +1,50 @@ +import "2bead.lt" + +Peptide { + + # A polymer of alternating "H" and "P" beads: + + res1 = new 2bead/P + res2 = new 2bead/P.rot(180.0, 1,0,0).move(3.2,0,0) + res3 = new 2bead/H.rot( 0.0, 1,0,0).move(6.4,0,0) + res4 = new 2bead/H.rot(180.0, 1,0,0).move(9.6,0,0) + res5 = new 2bead/H.rot( 0.0, 1,0,0).move(12.8,0,0) + res6 = new 2bead/H.rot(180.0, 1,0,0).move(16.0,0,0) + res7 = new 2bead/P.rot( 0.0, 1,0,0).move(19.2,0,0) + res8 = new 2bead/P.rot(180.0, 1,0,0).move(22.4,0,0) + res9 = new 2bead/P.rot( 0.0, 1,0,0).move(25.6,0,0) + res10 = new 2bead/H.rot(180.0, 1,0,0).move(28.8,0,0) + res11 = new 2bead/H.rot( 0.0, 1,0,0).move(32.0,0,0) + res12 = new 2bead/H.rot(180.0, 1,0,0).move(35.2,0,0) + res13 = new 2bead/P.rot( 0.0, 1,0,0).move(38.4,0,0) + res14 = new 2bead/P.rot(180.0, 1,0,0).move(41.6,0,0) + + # Now, link the residues together this way: + write("Data Bond List") { + $bond:backbone1 $atom:res1/CA $atom:res2/CA + $bond:backbone2 $atom:res2/CA $atom:res3/CA + $bond:backbone3 $atom:res3/CA $atom:res4/CA + $bond:backbone4 $atom:res4/CA $atom:res5/CA + $bond:backbone5 $atom:res5/CA $atom:res6/CA + $bond:backbone6 $atom:res6/CA $atom:res7/CA + $bond:backbone7 $atom:res7/CA $atom:res8/CA + $bond:backbone8 $atom:res8/CA $atom:res9/CA + $bond:backbone9 $atom:res9/CA $atom:res10/CA + $bond:backbone10 $atom:res10/CA $atom:res11/CA + $bond:backbone11 $atom:res11/CA $atom:res12/CA + $bond:backbone12 $atom:res12/CA $atom:res13/CA + $bond:backbone13 $atom:res13/CA $atom:res14/CA + } + + create_var { $mol } # <--create a molecule ID number for this peptide + + # This causes res1,res2,res3,...,res14 to share the same molecule counter + # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks + # for a counter of that type in a parent molecule or earlier ancestor. + +} # Peptide + + + +# Angle, dihedral and improper interactions will be generated +# according to the instructions in "2bead_force_field.lt" diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt new file mode 100644 index 0000000000..2f0d4b5b96 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt @@ -0,0 +1,26 @@ +import "peptide.lt" +import "2bead_forcefield.lt" + + +# Specify the periodic boundary conditions: +write_once("Data Boundary") { + 0 180.0 xlo xhi + 0 180.0 ylo yhi + 0 180.0 zlo zhi +} + +# Create 27 peptides (=3x3x3) in a rectangular grid + +peptides = new Peptide [3].move(60.0, 0, 0) + [3].move(0, 60.0, 0) + [3].move(0, 0, 60.0) + +# Now (for fun) shift some of the peptides +# in the x direction by a distance of 20.0 +# Suppose we want to move the middle slice +# (which has constant Z). We do that this way: +peptides[1][*][*].move(0,0,20) +# more examples: +peptides[*][1][*].move(20,0,0) +peptides[*][*][1].move(0,20,0) + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt new file mode 100644 index 0000000000..eb864e049e --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt @@ -0,0 +1,38 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 2.0 +dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 300.0 300.0 5000.0 48279 +fix fxnve all nve + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 2500 # time interval for printing out "thermo" data + +restart 1000000 restart_nvt + +run 1000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT new file mode 100644 index 0000000000..1a077178e3 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT @@ -0,0 +1,36 @@ +This is a very crude attempt to create a polymer melt +consisting of 150 copies of the same polymer. + +THE FORCE FIELD PARAMETERS AND CONFORMATION FOR THIS SYSTEM ARE COMPLETELY WRONG + +The purpose of this example is to demonstrate one way to create a +large number of randomly generated polymers, and to use +an NPT simulation to pack them all into a small box. +(Smaller than their initial outstretched length.) + +Each polymer is a random heteropolymer of length 200 monomers. +This polymer is a polymoer of PVDF and PCTFE monomers +selected randomly in a 1:3 ratio. +Again, this is not a realistic simulation of PVDV or PCTFE polymers, + +Furthermore, even after the simulation is done, the arrangement of the +polymers in the box is not characteristic of a truly random polymer melt. + + +---- A note on size --- + +This is a large system with nearly 200000 atoms. +It takes several minutes to compile this example +and (currently requiring at least 4.0 Gb of memory). +(I'm working on reducing that requirement. -Andrew 2012-9-12) + +----------------------- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh new file mode 100755 index 0000000000..ac21c4c45e --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh @@ -0,0 +1,14 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh new file mode 100755 index 0000000000..acc5fbbaad --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg new file mode 100644 index 0000000000..f67da797f1 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg new file mode 100644 index 0000000000..15d7b29676 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..6915e27391 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,277 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 116 !NATOM + 1 1 3 3 0.000000 12.0000 0 + 2 1 4 4 0.000000 17.0000 0 + 3 1 4 4 0.000000 17.0000 0 + 4 1 3 3 0.000000 12.0000 0 + 5 1 4 4 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63 62 64 72 71 73 75 74 76 + 82 81 83 93 92 94 102 101 103 + 109 108 110 + + 47 !NPHI: dihedrals + 38 40 43 46 69 71 74 77 + 1 4 7 9 40 43 46 48 + 67 69 71 74 71 74 77 79 + 35 38 40 43 30 33 35 38 + 28 30 33 35 33 35 38 40 + 57 60 62 65 55 57 60 62 + 4 7 9 11 7 9 11 13 + 13 16 18 20 24 26 28 30 + 62 65 67 69 65 67 69 71 + 81 84 86 88 86 88 90 92 + 92 95 97 99 95 97 99 101 + 108 111 113 115 16 18 20 22 + 18 20 22 24 20 22 24 26 + 22 24 26 28 84 86 88 90 + 9 11 13 16 11 13 16 18 + 26 28 30 33 46 48 50 53 + 53 55 57 60 48 50 53 55 + 60 62 65 67 77 79 81 84 + 79 81 84 86 88 90 92 95 + 90 92 95 97 97 99 101 104 + 104 106 108 111 99 101 104 106 + 106 108 111 113 43 46 48 50 + 50 53 55 57 74 77 79 81 + 101 104 106 108 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg new file mode 100644 index 0000000000..cc6822e7b3 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg new file mode 100644 index 0000000000..efcaa76c06 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt new file mode 100644 index 0000000000..9a90c172ae --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt @@ -0,0 +1,115 @@ + # ---------------------------------------------------------------------- + # -- General comment: -- + # -- The write() and write_once() commands create and append text to -- + # -- files (replacing variables beginning with @ or $ with counters.) -- + # -- File names beginning with "In " or "Data " are special. -- + # -- They will be pasted into the LAMMPS input script and -- + # -- data files which are generated by moltemplate. The syntax -- + # -- of these files is exactly the same as the syntax from the -- + # -- corresponding sections of a LAMMPS input script or data file. -- + # ---------------------------------------------------------------------- + + +MonomerTypes { + + + 2bead { + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:CA $mol:... @atom:CA 0.0 0.000 1.000 0.0000 + $atom:R $mol:... @atom:R 0.0 0.000 4.400 0.0000 + } + + # bond-id bond-type atom-id1 atom-id2 + + write("Data Bonds") { + $bond:CR @bond:../sidechain $atom:CA $atom:R + } + + # atom-type mass + + write_once("Data Masses") { + @atom:CA 12.0 + @atom:R 17.0 + } + + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.10 2.0 + pair_coeff @atom:R @atom:R 0.50 3.0 + } + + } # 2bead + + + 3bead { + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:CA $mol:... @atom:CA 0.0 0.000 1.000 0.000 + $atom:R1 $mol:... @atom:R 0.0 0.000 2.700 2.950 + $atom:R2 $mol:... @atom:R 0.0 0.000 2.700 -2.950 + } + + # bond-id bond-type atom-id1 atom-id2 + + write("Data Bonds") { + $bond:CR1 @bond:../sidechain $atom:CA $atom:R1 + $bond:CR2 @bond:../sidechain $atom:CA $atom:R2 + } + + # atom-type mass + + write_once("Data Masses") { + @atom:CA 12.0 + @atom:R 17.0 + } + + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.10 2.0 + pair_coeff @atom:R @atom:R 0.50 3.0 + } + } # 3bead + + + write_once("In Settings") { + # bond-type k r0 + bond_coeff @bond:sidechain 20.0 3.4 + bond_coeff @bond:bb 20.0 3.4 # "bb" shorthand for "backbone" + } + + # Although there's no need to define angular interactions (because this + # "molecule" only contains two atoms), we define the settings for angles + # or dihedrals which might be present later when we build a polymer. + + write_once("In Settings") { + # angle-type k theta0 + angle_coeff @angle:backbone 10.00 160 + angle_coeff @angle:sidechain 10.00 120 + angle_coeff @angle:RCR 10.00 120 + # dihedral-type K1 K2 K3 K4 + dihedral_coeff @dihedral:backbn 0.10 -0.271016 3.145034 0.0 + } + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:*/CA @atom:*/CA @atom:*/CA @bond:* @bond:* + @angle:sidechain @atom:*/CA @atom:*/CA @atom:*/R @bond:* @bond:* + @angle:RCR @atom:*/R @atom:*/CA @atom:*/R @bond:* @bond:* + } + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 + + write_once("Data Dihedrals By Type") { + @dihedral:backbn @atom:*/CA @atom:*/CA @atom:*/CA @atom:*/CA * * * + } + +} # MonomerTypes + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt new file mode 100644 index 0000000000..9497dcc390 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt @@ -0,0 +1,82 @@ +import "monomers.lt" + +using namespace MonomerTypes + +RandomHeteropolymer { + + # Make a chain of monomers with random composition: + + monomers = new random([2bead,3bead], + [0.6,0.4], + 123456) # <-- optional random seed + [50].rot(180,1,0,0).move(2.95, 0, 0) + + # Now, link the monomers together this way: + + write("Data Bonds") { + $bond:bb1 @bond:MonomerTypes/bb $atom:monomers[0]/CA $atom:monomers[1]/CA + $bond:bb2 @bond:MonomerTypes/bb $atom:monomers[1]/CA $atom:monomers[2]/CA + $bond:bb3 @bond:MonomerTypes/bb $atom:monomers[2]/CA $atom:monomers[3]/CA + $bond:bb4 @bond:MonomerTypes/bb $atom:monomers[3]/CA $atom:monomers[4]/CA + $bond:bb5 @bond:MonomerTypes/bb $atom:monomers[4]/CA $atom:monomers[5]/CA + $bond:bb6 @bond:MonomerTypes/bb $atom:monomers[5]/CA $atom:monomers[6]/CA + $bond:bb7 @bond:MonomerTypes/bb $atom:monomers[6]/CA $atom:monomers[7]/CA + $bond:bb8 @bond:MonomerTypes/bb $atom:monomers[7]/CA $atom:monomers[8]/CA + $bond:bb9 @bond:MonomerTypes/bb $atom:monomers[8]/CA $atom:monomers[9]/CA + $bond:bb10 @bond:MonomerTypes/bb $atom:monomers[9]/CA $atom:monomers[10]/CA + $bond:bb11 @bond:MonomerTypes/bb $atom:monomers[10]/CA $atom:monomers[11]/CA + $bond:bb12 @bond:MonomerTypes/bb $atom:monomers[11]/CA $atom:monomers[12]/CA + $bond:bb13 @bond:MonomerTypes/bb $atom:monomers[12]/CA $atom:monomers[13]/CA + $bond:bb14 @bond:MonomerTypes/bb $atom:monomers[13]/CA $atom:monomers[14]/CA + $bond:bb15 @bond:MonomerTypes/bb $atom:monomers[14]/CA $atom:monomers[15]/CA + $bond:bb16 @bond:MonomerTypes/bb $atom:monomers[15]/CA $atom:monomers[16]/CA + $bond:bb17 @bond:MonomerTypes/bb $atom:monomers[16]/CA $atom:monomers[17]/CA + $bond:bb18 @bond:MonomerTypes/bb $atom:monomers[17]/CA $atom:monomers[18]/CA + $bond:bb19 @bond:MonomerTypes/bb $atom:monomers[18]/CA $atom:monomers[19]/CA + $bond:bb20 @bond:MonomerTypes/bb $atom:monomers[19]/CA $atom:monomers[20]/CA + $bond:bb21 @bond:MonomerTypes/bb $atom:monomers[20]/CA $atom:monomers[21]/CA + $bond:bb22 @bond:MonomerTypes/bb $atom:monomers[21]/CA $atom:monomers[22]/CA + $bond:bb23 @bond:MonomerTypes/bb $atom:monomers[22]/CA $atom:monomers[23]/CA + $bond:bb24 @bond:MonomerTypes/bb $atom:monomers[23]/CA $atom:monomers[24]/CA + $bond:bb25 @bond:MonomerTypes/bb $atom:monomers[24]/CA $atom:monomers[25]/CA + $bond:bb26 @bond:MonomerTypes/bb $atom:monomers[25]/CA $atom:monomers[26]/CA + $bond:bb27 @bond:MonomerTypes/bb $atom:monomers[26]/CA $atom:monomers[27]/CA + $bond:bb28 @bond:MonomerTypes/bb $atom:monomers[27]/CA $atom:monomers[28]/CA + $bond:bb29 @bond:MonomerTypes/bb $atom:monomers[28]/CA $atom:monomers[29]/CA + $bond:bb30 @bond:MonomerTypes/bb $atom:monomers[29]/CA $atom:monomers[30]/CA + $bond:bb31 @bond:MonomerTypes/bb $atom:monomers[30]/CA $atom:monomers[31]/CA + $bond:bb32 @bond:MonomerTypes/bb $atom:monomers[31]/CA $atom:monomers[32]/CA + $bond:bb33 @bond:MonomerTypes/bb $atom:monomers[32]/CA $atom:monomers[33]/CA + $bond:bb34 @bond:MonomerTypes/bb $atom:monomers[33]/CA $atom:monomers[34]/CA + $bond:bb35 @bond:MonomerTypes/bb $atom:monomers[34]/CA $atom:monomers[35]/CA + $bond:bb36 @bond:MonomerTypes/bb $atom:monomers[35]/CA $atom:monomers[36]/CA + $bond:bb37 @bond:MonomerTypes/bb $atom:monomers[36]/CA $atom:monomers[37]/CA + $bond:bb38 @bond:MonomerTypes/bb $atom:monomers[37]/CA $atom:monomers[38]/CA + $bond:bb39 @bond:MonomerTypes/bb $atom:monomers[38]/CA $atom:monomers[39]/CA + $bond:bb40 @bond:MonomerTypes/bb $atom:monomers[39]/CA $atom:monomers[40]/CA + $bond:bb41 @bond:MonomerTypes/bb $atom:monomers[40]/CA $atom:monomers[41]/CA + $bond:bb42 @bond:MonomerTypes/bb $atom:monomers[41]/CA $atom:monomers[42]/CA + $bond:bb43 @bond:MonomerTypes/bb $atom:monomers[42]/CA $atom:monomers[43]/CA + $bond:bb44 @bond:MonomerTypes/bb $atom:monomers[43]/CA $atom:monomers[44]/CA + $bond:bb45 @bond:MonomerTypes/bb $atom:monomers[44]/CA $atom:monomers[45]/CA + $bond:bb46 @bond:MonomerTypes/bb $atom:monomers[45]/CA $atom:monomers[46]/CA + $bond:bb47 @bond:MonomerTypes/bb $atom:monomers[46]/CA $atom:monomers[47]/CA + $bond:bb48 @bond:MonomerTypes/bb $atom:monomers[47]/CA $atom:monomers[48]/CA + $bond:bb49 @bond:MonomerTypes/bb $atom:monomers[48]/CA $atom:monomers[49]/CA + } + + # These lines of moltemplate script above were generated in python: + # for i in range(0,49): + # print(' $bond:bb'+str(i+1)+' @bond:MonomerTypes/bb $atom:monomers[' + # +str(i)+']/CA $atom:monomers['+str(i+1)+']/CA') + + # Finally, create a molecule ID number for this large polymer object + + create_var { $mol } + +} # RandomHeteropolymer + + + +# Angle, dihedral and improper interactions will be generated +# automatically according to the instructions in "monomers.lt" diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt new file mode 100644 index 0000000000..11f2d48fad --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt @@ -0,0 +1,33 @@ +# LAMMPS supports a large number of force-field styles. We must select +# which ones we need. This information belongs in the "In Init" section (and +# (you can specify it anywhere in your LT files, multiple times if you like). +# If different molecules use different force-field styles, you can use hybrid +# styles. (In this example the molecules share the same pair_style.) + +write_once("In Init") { + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style opls + pair_style lj/cut 9.0 + # If you have charged molecules immersed in a salty implicit + # solvent, you might try something like this this instead: + # pair_style lj/cut/coul/debye 0.1 9.0 + pair_modify mix arithmetic + dielectric 80.0 + special_bonds lj 0.0 0.0 0.0 +} + + +write_once("Data Boundary") { + 0.0 150.0 xlo xhi + 0.0 150.0 ylo yhi + 0.0 150.0 zlo zhi +} + + +import "polymer.lt" + +polymer = new RandomHeteropolymer + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt new file mode 100644 index 0000000000..5e08f03cb2 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt @@ -0,0 +1,29 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + +timestep 2.0 +dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Temperature = 500 degrees + +run 500000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_misc/translocation/README.TXT b/tools/moltemplate/examples/CG_misc/translocation/README.TXT new file mode 100644 index 0000000000..b9bac96d50 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README.TXT @@ -0,0 +1,23 @@ + +This example contains a (crude and somewhat simple) example of +the translocation of a (rather short) polymer through a hole in a wall, +surrounded by an explicit LJ solvent. + +(I used a short polymer because a longer polymer would require a larger box. + But this example looked more impressive visually when I used a smaller box.) +---- +Note: You must compile LAMMPS with the optional "RIGID" package installed. To + do this, go to the "src" directory of your lammps installation and type: + make yes-RIGID + make clean-all + make NAME_OF_TARGET #<--("make ubuntu", "make g++", "make linux".) +---- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_run.sh b/tools/moltemplate/examples/CG_misc/translocation/README_run.sh new file mode 100755 index 0000000000..7078918d5a --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README_run.sh @@ -0,0 +1,28 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +#or + +lmp_linux -i run.in.npt # Run a simulation at constant pressure + # (Note: Constant pressure conditions have not been + # well tested. The "run.in.npt" script may fail.) + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.nvt +#or +#mpirun -np 4 lmp_linux -i run.in.npt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh b/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh new file mode 100755 index 0000000000..acc5fbbaad --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt b/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/translocation/images/polymer_LR.jpg b/tools/moltemplate/examples/CG_misc/translocation/images/polymer_LR.jpg new file mode 100644 index 0000000000..5529fc74b9 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/translocation/images/polymer_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/translocation/images/solvent_LR.jpg b/tools/moltemplate/examples/CG_misc/translocation/images/solvent_LR.jpg new file mode 100644 index 0000000000..304693e2ac Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/translocation/images/solvent_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg b/tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg new file mode 100644 index 0000000000..c1dcc4c186 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/translocation/images/walls_LR.jpg b/tools/moltemplate/examples/CG_misc/translocation/images/walls_LR.jpg new file mode 100644 index 0000000000..319427ae61 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/translocation/images/walls_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt new file mode 100644 index 0000000000..a8a35339f5 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt @@ -0,0 +1,111 @@ + # ---------------------------------------------------------------------- + # -- General comment: -- + # -- The write() and write_once() commands create and append text to -- + # -- files (replacing variables beginning with @ or $ with counters.) -- + # -- File names beginning with "In " or "Data " are special. -- + # -- They will be pasted into the LAMMPS input script and -- + # -- data files which are generated by moltemplate. The syntax -- + # -- of these files is exactly the same as the syntax from the -- + # -- corresponding sections of a LAMMPS input script or data file. -- + # ---------------------------------------------------------------------- + + +Monomer { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:CA $mol:... @atom:CA 0.0 0.000 0.4000 0.00000 + $atom:R1 $mol:... @atom:R 0.0 0.000 1.000 1.000 + $atom:R2 $mol:... @atom:R 0.0 0.000 1.000 -1.000 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own + + + # atom-type mass + + write_once("Data Masses") { + @atom:CA 13.0 + @atom:R 50.0 + } + + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.05 2.0 + pair_coeff @atom:R @atom:R 0.50 2.0 + } + + # bond-id bond-type atom-id1 atom-id2 + + write("Data Bonds") { + $bond:CR1 @bond:sidechain $atom:CA $atom:R1 + $bond:CR2 @bond:sidechain $atom:CA $atom:R2 + } + + write_once("In Settings") { + # bond-type k r0 + bond_coeff @bond:sidechain 30.0 1.2 + bond_coeff @bond:bb 30.0 2.0 # "bb" shorthand for "backbone" + } + + # For a compound molecule consisting of smaller building blocks (such as a + # polymer built from monomers), it is tedious to explicitly list all of the + # angles, dihedrals in the entire molecule. Instead, you can define rules + # for automatically generating all the angular interactions between bonded + # atoms according to their connectivity and the atom/bond type. + # Later, when you connect multiple monomers together to form a polymer, + # appropriate bond-angle forces will be applied to these atoms automatically + # (as well as dihedral and improper forces, if defined). + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* + @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* + @angle:RCR @atom:R @atom:CA @atom:R @bond:* @bond:* + } + + # ("@angle:RCR" defines the angle between the R-C-R atoms within a monomer. + # The other angular interactions are between atoms in neighboring monomers.) + + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 + + write_once("Data Dihedrals By Type") { + @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* + } + + # Parameters for these new angular interactions must be defined. (I recommend + # putting all force-field parameters (coeffs) in the "In Settings" section.) + + write_once("In Settings") { + # angle-type k theta0 + angle_coeff @angle:backbone 50.00 160 + angle_coeff @angle:sidechain 50.00 120 + angle_coeff @angle:RCR 50.00 120 + # dihedral-type K1 K2 K3 K4 + dihedral_coeff @dihedral:backbn 1.411036 -0.271016 3.145034 0.0 + } + +} # Monomer + + + + + + +# ------------------------------------------------------------------------- +# Heteropolymers: +# +# There is a similar example for heteropolymers which is distributed online +# bundled with the moltemplate software. It is named "2bead_heteropolymer", +# and it demonstrates how to share backbone (CA) atoms, bonds and angles +# (so that you don't have to define them seperately for each type of monomer). +# ------------------------------------------------------------------------- + diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt new file mode 100644 index 0000000000..d7ab89dc36 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt @@ -0,0 +1,35 @@ +import "monomer.lt" + +Polymer { + + # Make a chain of monomers + monomers = new Monomer [12].rot(180, 1,0,0).move(2.0, 0, 0) + + + # Now, link the monomers together this way: + write("Data Bonds") { + $bond:bb1 @bond:Monomer/bb $atom:monomers[0]/CA $atom:monomers[1]/CA + $bond:bb2 @bond:Monomer/bb $atom:monomers[1]/CA $atom:monomers[2]/CA + $bond:bb3 @bond:Monomer/bb $atom:monomers[2]/CA $atom:monomers[3]/CA + $bond:bb4 @bond:Monomer/bb $atom:monomers[3]/CA $atom:monomers[4]/CA + $bond:bb5 @bond:Monomer/bb $atom:monomers[4]/CA $atom:monomers[5]/CA + $bond:bb6 @bond:Monomer/bb $atom:monomers[5]/CA $atom:monomers[6]/CA + $bond:bb7 @bond:Monomer/bb $atom:monomers[6]/CA $atom:monomers[7]/CA + $bond:bb8 @bond:Monomer/bb $atom:monomers[7]/CA $atom:monomers[8]/CA + $bond:bb9 @bond:Monomer/bb $atom:monomers[8]/CA $atom:monomers[9]/CA + $bond:bb10 @bond:Monomer/bb $atom:monomers[9]/CA $atom:monomers[10]/CA + $bond:bb11 @bond:Monomer/bb $atom:monomers[10]/CA $atom:monomers[11]/CA + } + + create_var { $mol } # Create a molecule ID number for this polymer + + # This causes monomer[0], monomer[1], ... to share the same molecule counter + # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks + # for a counter of that type in a parent molecule or earlier ancestor. + +} # Polymer + + + +# Angle, dihedral and improper interactions will be generated +# automatically according to the instructions in "monomer.lt" diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt new file mode 100644 index 0000000000..1073a58a14 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt @@ -0,0 +1,23 @@ +###################### SOLVENT ######################### + +import "solvent_single.lt" + +# Fill the simulation box with a solvent. +# In this example, the solvent is made of many +# copies of "MoleculeA" (which has only one atom). + +solvent = new MoleculeA [12].move(3.0,0,0) + [12].move(0,3.0,0) + [12].move(0,0,3.0) + +# To start with a reasonable conformation, it's a good idea to delete the +# solvent where the walls or the polymer is going to be. Here we do it manually: + +delete solvent[*][*][2] # <-- 1st wall will go here +delete solvent[*][*][8] # <-- 2nd wall will go here +delete solvent[6-7][0-8][5-6] # <-- polymer will go here + +# Alternate notation: +# [a:b] notation also works, however the "b" is a strict upper bound... +# ...hence the last line is equivalent to "delete solvent[6:8][0:9][5:7]" +# [a*b] notation also works, and is equivalent to [a-b] diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt new file mode 100644 index 0000000000..8057e3c6fc --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt @@ -0,0 +1,22 @@ +# The two files "solvent_single.lt" and "wall_single.lt" +# define two very simple molecules containing one atom each. +# Both atoms have a similar size (the have the same sigma parameter). + + +MoleculeA { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:a $mol:. @atom:a 0.0 0.0 0.0 0.0 + } + write_once("Data Masses") { + @atom:a 10.0 + } + write_once("In Settings") { + # i j epsilon sigma cutoff + pair_coeff @atom:a @atom:a 0.60 3.0 7.5 #<--attractive + group groupA type @atom:a #(Atoms of this type belong to the "A" group) + } + +} + diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt new file mode 100644 index 0000000000..90d60d3baa --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt @@ -0,0 +1,55 @@ + +# LAMMPS supports a large number of force-field styles. We must select +# which ones we need. This information belongs in the "In Init" section (and +# (you can specify it anywhere in your LT files, multiple times if you like). +# If different molecules use different force-field styles, you can use hybrid +# styles. (In this example the molecules share the same pair_style.) + +write_once("In Init") { + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style opls + pair_style lj/cut 9.0 + # If you have charged molecules immersed in a salty implicit + # solvent, you might try something like this this instead: + # pair_style lj/cut/coul/debye 0.1 9.0 + pair_modify mix arithmetic + dielectric 80.0 + special_bonds lj 0.0 0.0 0.0 +} + + +write_once("Data Boundary") { + 0.0 36.0 xlo xhi + 0.0 36.0 ylo yhi + 0.0 36.0 zlo zhi +} + + +import "solvent.lt" + +import "walls.lt" + +import "polymer.lt" + +polymer = new Polymer +polymer.rot(-90.0, 0,0,1) # rotate it -90 degrees around the Y axis +polymer.move(19.5,22.5,16.5) # move it near the openning of the hole + + + +####################### Notes: ######################### +# +# In this example we deleted solvent and wall molecule objects. +# You can also delete a monomer inside the polymer. To do that use: +# delete polymer/monomers[6] +# You can also delete individual atoms, bonds, angles, dihedrals, & impropers +# from existing molecules. For example to delete an atom in the middle +# of the polymer try this. (Bonds and other interactions will also be removed.) +# delete polymer/monomers[6]/CA +# To delete a bond, try this +# delete polymer/bb6 +# Note: This will not delete the angular interactions. Delete them manually +# Note: In both cases the two molecule fragments will keep the same mol counter. diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt new file mode 100644 index 0000000000..79275a06b4 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt @@ -0,0 +1,21 @@ +# The two files "solvent_single.lt" and "wall_single.lt" +# define two very simple molecules containing one atom each. +# Both atoms have a similar size (the have the same sigma parameter). + +MoleculeB { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:b $mol:. @atom:b 0.0 0.0 0.0 0.0 + } + write_once("Data Masses") { + @atom:b 10.0 + } + write_once("In Settings") { + # i j epsilon sigma cutoff + pair_coeff @atom:b @atom:b 0.05 3.0 7.5 #<--repulsive (approximately) + group groupB type @atom:b #(Atoms of this type belong to the "B" group) + } + +} + diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt new file mode 100644 index 0000000000..dcccac941e --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt @@ -0,0 +1,23 @@ +####################### WALLS ########################## + +import "wall_single.lt" + +# Create a wall at position z=6.0 (6.0 = 2*3.0) + +wall1 = new MoleculeB [12].move(3.0, 0, 0) + [12].move(0, 3.0, 0) + +wall1[*][*].move(0,0,6.0) + +# Create a second wall at position z=24.0 (24.0 = 8*3.0) + +wall2 = new MoleculeB [12].move(3.0, 0, 0) + [12].move(0, 3.0, 0) + +wall2[*][*].move(0,0,24.0) + +# Now delete some of the molecules in "wall2" to create a hole. + +delete wall2[6-7][6-9] +delete wall2[5-8][7-8] + diff --git a/tools/moltemplate/examples/CG_misc/translocation/run.in.npt b/tools/moltemplate/examples/CG_misc/translocation/run.in.npt new file mode 100644 index 0000000000..328378f061 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/run.in.npt @@ -0,0 +1,70 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 1.0 +dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + + +velocity groupB zero angular +velocity groupB zero linear +# (I'm not sure if the two lines above are necessary, but they don't hurt.) + +# Only the groupB atoms are immobile. + +group mobile subtract all groupB + +# ------------------------- NPT --------------------------- + +# Set temp=300K, pressure=500bar, and equilibrate volume only in the z direction + +fix fMoveStuff mobile npt temp 300 300 100 z 500 500 1000.0 dilate mobile + +# ------ QUESTIONABLE (see below): ------ + +fix Ffreezestuff groupB rigid/npt single temp 300 300 100 z 500 500 1000.0 force * off off off torque * off off off dilate mobile + +# -- Alternate npt rigid method -- +# I'm not sure which way is more correct, however +# this also seems to behave in a reasonable-looking way: +#fix Ffreezestuff groupB rigid single force * off off off torque * off off off dilate mobile +# +# The use of either "fix rigid" or "fix rigid/npt" to immobilize +# an object is somewhat controversial. Feel free to omit it. +#(Neither Trung or Steve Plimpton use rigid or rigid/npt for immobilizing +#molecules, but I noticed that at NPT, it does a better job of maintaining +# the correct volume. However "fix rigid" has changed since then (2011), +# so this may no longer be true. Please use this example with caution.) +# ---------------------------------------- + +# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the +# forces between immobilized atoms. +neigh_modify exclude group groupB groupB + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp +compute pressMobile all pressure tempMobile + +thermo_style custom step c_tempMobile c_pressMobile temp press vol + +fix_modify fMoveStuff temp tempMobile + +run 60000 + +write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt b/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt new file mode 100644 index 0000000000..c2e2e8de54 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt @@ -0,0 +1,49 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + + +# Optional: Improve efficiency by omitting the calcuation of interactions +# between immobile atoms. (Note: This is not optional under NPT conditions.) +neigh_modify exclude group groupB groupB + +# Only the groupB atoms are immobile. +group mobile subtract all groupB + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp + +# Integrate the equations of motion: +fix fMoveStuff mobile nvt temp 300.0 300.0 100.0 +fix_modify fMoveStuff temp tempMobile + + +run 100000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT new file mode 100644 index 0000000000..33eeddda6e --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT @@ -0,0 +1,28 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "MANYBODY" package. +# As of 2012-9, it is included by default, but this may change in the future. +# If lammps complains of a missing pair style enter "make yes-MANYBODY" +# into the shell before compiling lammps. For details see: +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +This is a relatively complex example containing two different types of +molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. + +The cyclododecane molecule uses the +TraPPE force field for hydrocarbon chains. +The parameters for the TraPPE force field are +in a file named "trappe1998.lt" which should be +located in the MOLTEMPLATE_PATH. +(See moltemplate installation instructions.) + +The water solvent is implemented using the 3-body single-particle +coarse-grained "mW" water model: +Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016 + +More detailed instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step 2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh new file mode 100755 index 0000000000..8220a755c4 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh @@ -0,0 +1,31 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data, system.in.sw +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh new file mode 100755 index 0000000000..cb4d908984 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh @@ -0,0 +1,25 @@ + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt + + # Here we just want to make sure that the "mW" atom type is assigned to + # number "1". It should be by default, so usually you can leave out + # -a "@atom:/WatMW/mW 1". + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg new file mode 100644 index 0000000000..5123dc7f60 Binary files /dev/null and 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b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg new file mode 100644 index 0000000000..6591b236a3 Binary files /dev/null and b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg differ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg new file mode 100644 index 0000000000..9b4ca06fb8 Binary files /dev/null and b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg differ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..97a19f0ffb --- /dev/null +++ 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a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh new file mode 100755 index 0000000000..97b9f577d9 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh @@ -0,0 +1,11 @@ +# Use this command to generate the LAMMPS input files: + +moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt + +# The -a argument insures that the "mW" atom type is assigned to "1". +# (This is necessary for the pair_coeff command to work. +# See system.lt for details.) + +# Note: To get rid of the annoying "atom_style unspecified warnings, +# use the "-atomstyle" command line argument, as in: +# moltemplate.sh -atomstyle full -a "@atom:/WatMW/mW 1" system.lt diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt new file mode 100644 index 0000000000..ceaa1c69d8 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt @@ -0,0 +1,55 @@ +import "trappe1998.lt" + +# The "trappe1998.lt" file is usually located in $MOLTEMPLATE_PATH (and is +# distributed with moltemplate. See the "Installation" section in the manual.) +# It contains definitions of the atoms "CH2", "CH3", and "CH4", as well +# as "saturated" bonds, and the parameters for (bonded/nonbonded) +# interactions between these atoms (all enclosed within the "TraPPE" namespace). + + +Cyclododecane { + + write('Data Atoms') { + $atom:C1 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.94118 0.0 + $atom:C2 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.54714 1.47059 + $atom:C3 $mol:. @atom:TraPPE/CH2 0.0 0.00000 1.47059 2.54714 + $atom:C4 $mol:. @atom:TraPPE/CH2 0.0 0.00000 0.0 2.94118 + $atom:C5 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -1.47059 2.54714 + $atom:C6 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.54714 1.47059 + $atom:C7 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.94118 0.0 + $atom:C8 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.54714 -1.47059 + $atom:C9 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -1.47059 -2.54714 + $atom:C10 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -0.0 -2.94118 + $atom:C11 $mol:. @atom:TraPPE/CH2 0.0 0.00000 1.47059 -2.54714 + $atom:C12 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.54714 -1.47059 + } + + # The "." in "$mol:." refers to the current object's molecule ID, + # and "@atom:TraPPE/CH2" refers to the "CH2" atom-type defined in TraPPE + + write('Data Bonds') { + $bond:bond1 @bond:TraPPE/saturated $atom:C1 $atom:C2 + $bond:bond2 @bond:TraPPE/saturated $atom:C2 $atom:C3 + $bond:bond3 @bond:TraPPE/saturated $atom:C3 $atom:C4 + $bond:bond4 @bond:TraPPE/saturated $atom:C4 $atom:C5 + $bond:bond5 @bond:TraPPE/saturated $atom:C5 $atom:C6 + $bond:bond6 @bond:TraPPE/saturated $atom:C6 $atom:C7 + $bond:bond7 @bond:TraPPE/saturated $atom:C7 $atom:C8 + $bond:bond8 @bond:TraPPE/saturated $atom:C8 $atom:C9 + $bond:bond9 @bond:TraPPE/saturated $atom:C9 $atom:C10 + $bond:bond10 @bond:TraPPE/saturated $atom:C10 $atom:C11 + $bond:bond11 @bond:TraPPE/saturated $atom:C11 $atom:C12 + $bond:bond12 @bond:TraPPE/saturated $atom:C12 $atom:C1 + } + +} # Cyclododecane + + +# coordinates in the "Data Atoms" section generated by this python code: +# from math import * +# bond_length=1.54 +# N=12 +# R=(N*bond_length)/(2*pi) +# for i in range(0,N): +# print('$atom:C'+str(i+1)+' $mol:... @atom:TraPPE/CH2 0.0 0.00000 '+ +# str(round(R*cos(i*2*pi/N),5))+' '+str(round(R*sin(i*2*pi/N),5))) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt new file mode 100644 index 0000000000..4a7063491b --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt @@ -0,0 +1,62 @@ +# This is a relatively complex example containing two different types of +# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. + +import "watmw.lt" +import "cyclododecane.lt" + +write_once("Data Boundary") { + 0.000000 48.000 xlo xhi + 0.000000 48.000 ylo yhi + 0.000000 48.000 zlo zhi +} + +wat = new WatMW [12].move(0, 0, 4.0) + [12].move(0, 4.0, 0) + [12].move(4.0, 0, 0) + +cyclododecane = new Cyclododecane [4].move(0, 0, 12.0) + [4].move(0, 12.0, 0) + [4].move(12.0, 0, 0) + +# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.) +cyclododecane[*][*][*].move(6.0,6.0,6.0) + +write_once("In Init") { + # -- Tell LAMMPS we want to use two different pair styles + # -- (This overrides earlier settings.) + pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 +} + + +write_once("In Settings") { + # -- Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # -- Note: For this to work, you should probably run moltemplate this way: + # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt + # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) +} + + + +# -- Somewhere we must eventually define interactions +# -- between atoms from different molecule types + +write_once("In Settings") { + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448 +} + + + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt new file mode 100644 index 0000000000..9bcc80cb1c --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt @@ -0,0 +1,50 @@ +# This file stores complete LAMMPS data for the TraPPE model of saturated +# hydrocarbon chains. In this "united-atom" model, each methyl group is +# represented by a single atom. Forces between "atoms" are taken from the +# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577) + +TraPPE { + + write_once("In Init") { + # -- Default styles for "TraPPE" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid opls + improper_style none + pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:CH2 14.1707 + @atom:CH3 15.2507 + @atom:CH4 16.3307 + } + + write_once("Data Angles By Type") { + @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated + } + + write_once("Data Dihedrals By Type") { + @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated + } + + write_once("In Settings") { + pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 + pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 + pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73 + bond_coeff @bond:saturated harmonic 120.0 1.54 + angle_coeff @angle:backbone harmonic 62.0022 114 + dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0 + } + + write_once("In Settings") { + group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 + } + +} # class TraPPE + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt new file mode 100644 index 0000000000..34bdfead77 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt @@ -0,0 +1,80 @@ +# This is a relatively complex example containing two different types of +# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. + +import "watmw.lt" +import "cyclododecane.lt" + +write_once("Data Boundary") { + 0.000000 48.000 xlo xhi + 0.000000 48.000 ylo yhi + 0.000000 48.000 zlo zhi +} + +wat = new WatMW [12].move(0, 0, 4.0) + [12].move(0, 4.0, 0) + [12].move(4.0, 0, 0) + +cyclododecane = new Cyclododecane [4].move(0, 0, 12.0) + [4].move(0, 12.0, 0) + [4].move(12.0, 0, 0) + +# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.) +cyclododecane[*][*][*].move(6.0,6.0,6.0) + +write_once("In Init") { + # -- Tell LAMMPS we want to use two different pair styles + # -- (This overrides earlier settings.) + pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 +} + + + +write_once("In Settings") { + # -- Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # + # For this to work, the first atom type (assigned to "1") + # must refer to the "mW" atom type (defined in watmw.lt). + # (This is why we included "watmw.lt" first, to insure that the + # atom counters in WatMW are assinged first, starting with 1.) + # Alternately we can further insure that this happens, it's + # a good idea to run moltemplate.sh using the "-a" argument: + # moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt + # This assigns the atom type named @atom:/WatMW/mW to 1 +} + + + + +# -- Somewhere we must eventually define interactions +# -- between atoms from different molecule types +# -- Now define interactions between DIFFERENT molecules +# Note: In the SPC/E model, the epsilon,sigma parameters for water is 0.1553 +# 3.166. As a crude guess, I chose the LJ parameters for the interaction +# between water & the CH2,CH3,CH4 atoms using Lorentz-Berthelot mixing rules + +write_once("In Settings") { + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448 +} + + + + + + + + + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt new file mode 100644 index 0000000000..c7aaecebbc --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt @@ -0,0 +1,54 @@ +# This file stores LAMMPS data for the "mW" water model. +# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) +# +# In this model, each water molecule is represented by a single "mW" particle. +# These particles interact with their neighbors via 3-body Stillinger-Weber +# forces whose parameters are tuned to mimic directional hydrogen-bonding +# in liquid water (as well as hexagonal ice, type II ice, and +# low-density super-cooled liquid/amorphous water phases). + +WatMW { + write("Data Atoms") { + $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:mW 18.02 + } + + write_once("system.in.sw") { + mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 + } + + write_once("In Init") { + # -- Default styles for "WatMW" -- + units real + pair_style sw + } + + write_once("In Settings") { + # --Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # -- Note: For this to work, you should probably run moltemplate this way: + # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt + # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) + } + + # -- optional -- + + write_once("In Settings") { + group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) + } + +} # WatMW diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt new file mode 100644 index 0000000000..544daee70d --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt @@ -0,0 +1,61 @@ +# run.in.npt +# +# -- Usage -- +# +# lmp_linux -i run.in.npt +# (assuming lmp_linux is the name of your lammps binary) +# +# -- Prerequisite Input Files: -- +# systen.data, system.in.init, system.in.settings, system.in.sw +# +# You can generate these files with this command: +# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt +# --------------------------------- + +# ----- Init Section ----- + + +include system.in.init + + +# ----- Atom Definition Section ----- + + +read_data system.data + + +# ----- Settings Section ----- + + +include system.in.settings + + +# ----- Run Section ----- + + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. + +minimize 1.0e-5 1.0e-7 100000 400000 + + +# -- simulation protocol -- + + +timestep 2.0 # <- This can be increased to 5.0 or 10.0 for bulk water +dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + +run 200000 + +write_data system_after_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also.) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt new file mode 100644 index 0000000000..66334249b3 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt @@ -0,0 +1,81 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# run.in.nvt +# +# -- Usage -- +# +# lmp_g++ -i run.in.nvt +# (assuming lmp_g++ is the name of your lammps binary) +# +# -- Prerequisite Input Files: -- +# systen.data, system.in.init, system.in.settings, system.in.sw +# system_after_npt.data +# +# You can generate these files using this procedure +# +# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt +# +# lmp_linux -i run.in.npt + +# --------------------------------- + + +# -- init section -- + + +include system.in.init + + + +# -- atom definition section -- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# -- settings section -- + + +include system.in.settings + + +# -- run section -- + + +timestep 2.0 +dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz +dump 2 TraPPE custom 1000 traj_alkane_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + +# The following commands are useful if you want to calculate the distribution +# of alkane-chain radius-of-gyration at a given temperature & pressure. +#compute cRg TraPPE gyration +#variable vRg equal c_cRg +#compute cPE all pe +#variable vPE equal c_cPE +#fix FprintPE all print 1000 "${vPE}" file U.dat +#fix FprintRg all print 1000 "${vRg}" file Rg.dat + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data +#thermo_modify flush yes + +restart 100000 restart_nvt + +run 1000000 + +write_data system_after_nvt.data + + diff --git a/tools/moltemplate/examples/README.TXT b/tools/moltemplate/examples/README.TXT new file mode 100644 index 0000000000..0ecddbbbd4 --- /dev/null +++ b/tools/moltemplate/examples/README.TXT @@ -0,0 +1,24 @@ +These are examples for the "moltemplate" molecule builder for LAMMPS. +http://www.moltemplate.org + +Each directory contains one or more examples. + +Each example directory contains: + + images/ This folder has pictures of the molecules in the system + moltemplate_files/ This folder contains LT files and other auxiliary files + README_setup.sh Instructions for how to use moltemplate (executable) + README_visualize.txt Instructions for viewing in DATA/DUMP files in VMD + + ...and one or more LAMMPS input scripts with names like + + run.in.min + run.in.npt + run.in.nvt + +You can run these scripts using + lmp_linux -i run.in.npt +(The name of your lammps binary, "lmp_linux" in this example, may vary. + Sometimes, these scripts must be run in a certain order. For example + it may be necessary to run run.in.min to minimize the system before + you can run the other scripts. These files have not been optimized.) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT new file mode 100644 index 0000000000..9d6d0e1b35 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT @@ -0,0 +1,54 @@ +# -------- WARNING: -------- + +This directory contains some examples of all-atom simulations using the GAFF +force field, prepared using moltemplate. + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that simulations +prepared using moltemplate will reproduce the behavior of AmberTools/AMBER. + +# -------- REQUEST FOR HELP: -------- + +If you notice a problem with these examples, please report it. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2013-12-01) + + +--- Charge --- + +Some force-fields (such as OPLSAA) can assign charge based on atom type. +But AMBER simulations, charge is usually assigned using AmberTools which +typically estimates partial charges using quantum chemistry. + +You must assign partial charges to each atom or LAMMPS will crash +when it discovers your system has no charged particles. +(To disable this, change the pair_style to lj/cut or something similar.) + +You have to assign charge manually, just as you would for an ordinary molecule. + +(For example, charges are explicitly assigned to each atom in these files: + waterTIP3P+isobutane/moltemplate_files/isobutane.lt + hexadecane/moltemplate_files/ch2group.lt + hexadecane/moltemplate_files/ch3group.lt) + +(How you do this is up to you. In these examples, I obtained +partial charges from the OPLSAA parameter file located here: +http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm) + +--- Improper angles --- + +I am also uncertain whether the improper angle interactions generated by +moltemplate are equivalent to those generated by AmberTools. (I think they are, +but I am worried that I might have listed the atom types in the wrong order.) + +--- Bloated lammps input scripts --- + +LAMMPS input scripts prepared using moltemplate contain the entire contents +of the GAFF force-field, even when simulating small systems with just a few +atom types. + +This is harmless, but if you want to get rid of this extra information, +follow the README instructions in the "optional_cleanup" directories. + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT new file mode 100644 index 0000000000..64ec594c6e --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT @@ -0,0 +1,44 @@ +This example is a simple simulation of 288 hexadecane molecules in a box at +room temperature and atmospheric pressure. Please read the WARNING.TXT file. + +-------- REQUIREMENTS: --------- +This example requires building LAMMPS with the "USER-MISC" package. +(because it uses dihedral_style fourier) +To do this, type "make yes-user-misc" before compiling LAMMPS. +http://lammps.sandia.gov/doc/Section_start.html#start_3 + +More detailed instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files: + +step 1) to setup the LAMMPS input files, run this file: +README_setup.sh + + (Currently there is a bug which makes this step slow. + I'll fix it later -Andrew 2013-10-15.) + +step 2) to run LAMMPS, follow the instructions in this file: +README_run.sh + +------------ NOTE: There are two versions of this example. ---------------- + +Both examples use the same force-field parameters. + +1) +In this version, the force-field parameters are loaded from the "gaff.lt" file +(located in the "common" subdirectory). +This frees the user from the drudgery of manually specifying all of these +force-field details for every molecule. (However, the user must be careful +to choose @atom-type names which match AMBER GAFF conventions, +such as the "c3" and "h1" atoms, in this example.) + +2) +Alternately, there is another "hexadecane" example in the "all_atom_examples" +directory. In that example, force-field parameters are loaded from a file +named "alkanes.lt" (instead of "gaff.lt"). The "alkanes.lt" file contains +only the excerpts from "gaff.lt" which are relevant to the hydrocarbon +molcules used in that example. ("gaff.lt" contains parameters for most +small organic molecules, not just hydrocarbons.) +In this way, by editing "alkanes.lt", the user can manually control all of the +force-field details in the simulation. (Without feeling as though they are +relying on some kind of mysterious "black box" to do it for them.) + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_run.sh new file mode 100755 index 0000000000..8b01ab92d7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_run.sh @@ -0,0 +1,39 @@ +# --- Running LAMMPS --- +# -------- REQUIREMENTS: --------- +# 1) This example requires building LAMMPS with the "USER-MISC" package. +# (because it makes use of "gaff.lt" which uses dihedral_style fourier) +# To do this, type "make yes-user-misc" before compiling LAMMPS. +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# -------- PREREQUISITES: -------- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh new file mode 100755 index 0000000000..87d19c11a2 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh @@ -0,0 +1,36 @@ +# -------- REQUIREMENTS: --------- +# You must define your MOLTEMPLATE_PATH environment variable +# and set it to the "common" subdirectory of your moltemplate distribution. +# (See the "Installation" section in the moltemplate manual.) + +# Create LAMMPS input files this way: + +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away + # rm -rf output_ttree/ + +cd ../ + + + + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in GAFF which you are not using in this simulation. This +# is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, follow the instructions in +# this script: "optional_cleanup/README_remove_irrelevant_info.sh" + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT new file mode 100644 index 0000000000..def26ba765 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT @@ -0,0 +1,16 @@ +# -------- WARNING: -------- + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that the simulation +will reproduce the behavior of real hexadecane molecules, +(or even of hexadecane molecules simulated using AMBER, which should + be using the same force-field). + +# -------- REQUEST FOR HELP: -------- + +However, if you notice a problem with this example, please report it. +I confess I do not have a lot of experience running all-atom simulations. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2013-10-16) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg new file mode 100644 index 0000000000..b0d31f8845 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg new file mode 100644 index 0000000000..f7c13d0989 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_LR.jpg new file mode 100644 index 0000000000..3ad353dbb4 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt new file mode 100644 index 0000000000..7ea5b67a60 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt @@ -0,0 +1,49 @@ + +import "gaff.lt" # <-- defines the "GAFF" force field + + +# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is +# distributed with moltemplate. See the "Installation" section in the manual.) +# It contains definitions of the atoms "c3", "h1", as well as the force-field +# parameters for bonded and non-bonded interactions between them +# (and many other atoms). + +# Atom charges were taken from the OPLSAA force field file: +# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm + + +CH2 inherits GAFF { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c3 -0.120 0.000 0.000 0.000 + $atom:H1 $mol:... @atom:h1 0.060 0.000 0.63104384422426 0.892430762954 + $atom:H2 $mol:... @atom:h1 0.060 0.000 0.63104384422426 -0.892430762954 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own. + # The CH2 group is part of the Hexadecane molecule. + + # Now specify which pairs of atoms are bonded: + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + } + +} # CH2 + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt new file mode 100644 index 0000000000..0ad7fa3ef3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt @@ -0,0 +1,55 @@ +import "gaff.lt" # <-- defines the "GAFF" force field + + +# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is +# distributed with moltemplate. See the "Installation" section in the manual.) +# It contains definitions of the atoms "c3", "h1", as well as the force-field +# parameters for bonded and non-bonded interactions between them +# (and many other atoms). +# +# Moltemplate is only a simple text manipulation tool. It cannot +# calculate atomic charge using quantom chemistry methods. +# Atom charges for this example were taken from the OPLSAA force field file: +# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm +# However, normally simulations in AMBER are assigned charges using the +# "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools. + + +CH3 inherits GAFF { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c3 -0.180 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.060 0.000000 0.6310438442242609 0.8924307629540046 + $atom:H2 $mol:... @atom:h1 0.060 0.000000 0.6310438442242609 -0.8924307629540046 + $atom:H3 $mol:... @atom:h1 0.060 -0.8924307629540046 -0.6310438442242609 0.000000 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own. + # The CH3 group is part of the Hexadecane molecule. + + # Now specify which pairs of atoms are bonded: + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + $bond:CH3 $atom:C $atom:H3 + } + +} # CH3 + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt new file mode 100644 index 0000000000..184bc7b1d4 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt @@ -0,0 +1,93 @@ +# This example looks complicated because I split the +# hexadecane molecule into individual CH2 and CH3 monomers. +# +# I defined it this way so that you can easily modify +# it to change the length of the alkane chain. + + +import "gaff.lt" # load the "GAFF" force-field information +import "ch2group.lt" # load the definition of the "CH2" object +import "ch3group.lt" # load the definition of the "CH3" object + + + +Hexadecane inherits GAFF { + + + # Create an array of 16 "CH2" objects distributed along the X axis + + monomers = new CH2.move(0,0.4431163,0) [16].rot(180,1,0,0).move(1.2533223,0,0) + + # Each CH2 monomer is initial moved in the +Y direction by 0.43116 + # angstroms. Then it is rotated 180 degrees with respect to the + # previous monomer, and moved 1.2533223 Angstroms down the X axis. + + # ---- Now, modify the ends: --- + # Delete the CH2 groups at the beginning and end, and replace them with CH3. + # (Note: Alternately, instead of deleting the CH2 groups at each end, you + # could modify them by adding an extra hydrogen atom to those carbons.) + + delete monomers[0] + delete monomers[15] + endcap1 = new CH3 + endcap2 = new CH3 + + # Move the CH3 groups to the correct location at either end of the chain: + + endcap1.move(0,0.4431163,0) + endcap2.move(0,0.4431163,0).rot(180,0,0,1).move(18.7998345,0,0) + + # Note: 18.7998345 = (16-1) * 1.2533223 + + + # Now add a list of bonds connecting the carbon atoms together: + + write('Data Bond List') { + $bond:b1 $atom:endcap1/C $atom:monomers[1]/C + $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C + $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C + $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C + $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C + $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C + $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C + $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C + $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C + $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C + $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C + $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C + $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C + $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C + $bond:b15 $atom:monomers[14]/C $atom:endcap2/C + } + + # OPTIONAL: + create_var { $mol } # Create a molecule ID number. This number will + # be shared by all of the atoms in this polymer. + # In ch2group.lt, "$mol:..." refers to this number. + +} # Hexadecane + + + + + + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# +# 1.2533223 = DeltaXc = how far each CH2 group is shifted along +# the X axis (in Angstoms). +# 0.4431163 = DeltaYc/2 = lateral displacement of carbons away +# from the central axis. (See below.) +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt new file mode 100644 index 0000000000..4e0cfaec69 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt @@ -0,0 +1,18 @@ +import "hexadecane.lt" # <- defines the "Hexadecane" molecule type. + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 62.4 xlo xhi + 0.0 62.4 ylo yhi + 0.0 62.4 zlo zhi +} + +molecules = new Hexadecane [12].move(0, 0, 5.2) + [12].move(0, 5.2, 0) + [2].move(31.2, 0, 0) + + +# NOTE: The spacing between molecules is large. There should be extra room to +# move during the initial stages of equilibration. However, you will have to +# run the simulation at NPT conditions later to compress the system to a +# more realistic density. diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh new file mode 100755 index 0000000000..d4494c4507 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh @@ -0,0 +1,52 @@ + # MOST USERS CAN IGNORE THIS FILE + # + # Unfortunately, as of 2014-4-19, the system.data and system.in.settings file + # which are created by moltemplate.sh contain a lot of irrelevant information, + # such as definition of parameters for atom types not present in the current + # system. This extra information takes up about 1 MB. + # + # This appears to be harmless. + # (Loading this extra information does not seem to slow down LAMMPS.) + # + # --------- OPTIONAL STEPS FOR STRIPPING OUT JUNK --------- + # + # However if you want to eliminate this junk from these files + # For now, we can strip this out using ltemplify.py to build a new .lt file. + # + # I suggest you do this in a temporary_directory + + mkdir new_lt_file + cd new_lt_file/ + + # now run ltemplify.py + + ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt + rm -rf ../system.data ../system.in* # these old lammps files no longer needed + + # This creates a new .LT file named "system.lt" in the local directory. + + # The ltemplify.py script also does not copy the boundary dimensions. + # We must do this manually. + # If you did NOT throw away the "Data Boundary" file usually located in + # "moltemplate_files/output_ttree/Data Boundary" + # then you can copy that information from this file into system.lt + + echo "write_once(\"Data Boundary\") {" >> system.lt + cat "../moltemplate_files/output_ttree/Data Boundary" >> system.lt + echo "}" >> system.lt + echo "" >> system.lt + # Now, run moltemplate on this new .LT file. + moltemplate.sh system.lt + # This will create: "system.data" "system.in.init" "system.in.settings." + + # That's it. The new "system.data" and system.in.* files should + # be ready to run in LAMMPS. + + # Now copy the system.data and system.in.* files to the place where + # you plan to run moltemplate + mv -f system.data system.in.* ../ + cd ../ + + # Now delete all of the temporary files we generated + rm -rf new_lt_file/ + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt new file mode 100644 index 0000000000..9793764643 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt @@ -0,0 +1,85 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# To avvoid explosions, I have a 4-step equilibraion process (expand, minimize, +# reorient, compress). The system (as defined in the "system.data" file) +# is already expanded. That means there are 3 steps left: + +dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz +thermo 50 + +# -- Equilibration: part 1: initial minimization -- + +# Note: In general, it's always a good idea to minimize the system at first. + +minimize 1.0e-5 1.0e-7 100000 400000 +undump dumpeq1 + +write_data system_after_eq1_min.data + +# -- Equilibration part 2: reorienting the molecules (NVT) -- + +timestep 1.0 +dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz + +# Run the system at high temperature (at constant volume) to reorient the +# the molecules (which would otherwise be pointing in the same direction). + +# To speed it up, I randomize the atomic positions for a few thousand steps +# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). +# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) + + +fix fxlan all langevin 900.0 900.0 120 48279 +fix fxnve all nve + +run 2000 + +unfix fxlan +unfix fxnve +# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). +fix fxnvt all nvt temp 900.0 900.0 100.0 + +run 5000 +undump dumpeq2 + + +write_data system_after_eq2_reorient.data + +unfix fxnvt + +# -- equilibration part 3: Equilibrating the density (NPT) -- + +# Originally, the simulation box (in "system.data" and "system.lt") was +# unrealistically large. The spacing between the molecules was large also. +# I did this to enable the molecules to move freely and reorient themselves. +# After doing that, we should run the simulation under NPT conditions to +# allow the simulation box to contract to it's natural size. We do that here: +# We begin the simulation at 100 barr (a relatively low pressure), and +# slowly decrease it to 1 barr, maintianing the temperature at 300K. + +dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0 + +timestep 1.0 +run 60000 + +write_data system_after_eq3_npt.data + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt new file mode 100644 index 0000000000..f8b2d31d09 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt @@ -0,0 +1,42 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_eq3_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1 +thermo 100 +#thermo_modify flush yes + +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README.TXT new file mode 100644 index 0000000000..2e8cef3078 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README.TXT @@ -0,0 +1,51 @@ +This is an example of how to use "canned" force-fields in like GAFF in LAMMPS. +In this example, we specify only the atom names, bond connectivity, +(and coordinates and charge), and use moltemplate to +load the GAFF parameters from an external file (gaff.lt) +(...instead of specifying them explicitly in the molecule definition). + +The simulation consists of a mixture of isobutane and water. +Over time (less than 1 ns), the two molecules phase-separate. + +The GAFF parameters are applied only to the isobutane molecule. +(The water molecule paramters are defined explicitly in common/tip3p_2004.lt) +For this to work, make sure you have defined the MOLTEMPLATE_PATH +environment variable and set it to "common". See manual for more details.) + +WARNING: THIS IS A PRELIMINARY EXAMPLE WHICH USES AMBER'S GAFF FORCE FIELD. + AS OF 2014-4-19, these features have not been tested. + THE ABILITY TO DETECT AND ASSIGN GAFF FORCE FIELD PARAMETERS + MOLECULES ACCORDING TO ATOM TYPE IS AN EXPERIMENTAL FEATURE + AND CURRENTLY PROBABLY HAS BUGS (IN THE DIHEDRALS AND IMPROPERS). + PLEASE REPORT BUGS AND/OR SEND CORRECTIONS. -A 2014-4-19 + +----------------- CHARGE ---------------------- + +NOTE: The GAFF force-field DOES NOT ASSIGN ATOM CHARGE. + In this example, atom charges were taken from the OPLSAA force field file: + http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm + This is not the charge in AMBER simunlations is typically assigned. + (As of 2014, it is assigned using the "HF/6-31G* RESP2" or "AM1-BCC3" + methods using AmberTools (which are not available in moltemplate). + http://ambermd.org/doc6/html/AMBER-sh-19.4.html + http://ambermd.org/tutorials/basic/tutorial4b/) + + +-------- REQUIREMENTS: --------- + +1) This example requires building LAMMPS with the "USER-MISC" package. + (because it makes use of "gaff.lt" which uses dihedral_style fourier) + To do this, type "make yes-user-misc" before compiling LAMMPS. + http://lammps.sandia.gov/doc/Section_start.html#start_3 + 2) You must define your MOLTEMPLATE_PATH environment variable + and set it to the "common" subdirectory of your moltemplate distribution. + (See the "Installation" section in the moltemplate manual.) + +More detailed instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step 2) +README_run.sh diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_run.sh new file mode 100755 index 0000000000..8b01ab92d7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_run.sh @@ -0,0 +1,39 @@ +# --- Running LAMMPS --- +# -------- REQUIREMENTS: --------- +# 1) This example requires building LAMMPS with the "USER-MISC" package. +# (because it makes use of "gaff.lt" which uses dihedral_style fourier) +# To do this, type "make yes-user-misc" before compiling LAMMPS. +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# -------- PREREQUISITES: -------- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh new file mode 100755 index 0000000000..ef5e35b672 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh @@ -0,0 +1,35 @@ +# -------- REQUIREMENTS: --------- +# You must define your MOLTEMPLATE_PATH environment variable +# and set it to the "common" subdirectory of your moltemplate distribution. +# (See the "Installation" section in the moltemplate manual.) + +# Create LAMMPS input files this way: + +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + #rm -rf output_ttree/ + +cd ../ + + + + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in GAFF which you are not using in this simulation. This +# is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, follow the instructions in +# this script: "optional_cleanup/README_remove_irrelevant_info.sh" diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/isobutane.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/isobutane.jpg new file mode 100644 index 0000000000..8c548fba84 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/isobutane.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg new file mode 100644 index 0000000000..fab496aa20 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg new file mode 100644 index 0000000000..aaa4abaf5e Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water.jpg new file mode 100644 index 0000000000..9d578b4ef8 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/isobutane.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/isobutane.lt new file mode 100644 index 0000000000..bdc79c22a9 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/isobutane.lt @@ -0,0 +1,56 @@ +import "gaff.lt" + +# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is +# distributed with moltemplate. See the "Installation" section in the manual.) +# It contains definitions of the atoms "c3", "h1", as well as the bonded +# and non-bonded interactions between them (and many other atoms). +# +# Moltemplate is only a simple text manipulation tool. It cannot +# calculate atomic charge using quantom chemistry methods. +# Atom charges for this example were taken from the OPLSAA force field file: +# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm +# However, normally simulations in AMBER are assigned charges using the +# "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools. + + +Isobutane inherits GAFF { + + # atomID molID atomTyle charge X Y Z + write('Data Atoms') { + $atom:C0 $mol:. @atom:c3 -0.0600 -0.001 -0.001 -0.439 + $atom:C1 $mol:. @atom:c3 -0.1800 -1.257 -0.726 0.078 + $atom:C2 $mol:. @atom:c3 -0.1800 1.258 -0.726 0.072 + $atom:C3 $mol:. @atom:c3 -0.1800 -0.001 1.453 0.069 + $atom:H0 $mol:. @atom:h1 0.0600 -0.003 -0.004 -1.439 + $atom:H11 $mol:. @atom:h1 0.0600 -2.075 -0.255 -0.254 + $atom:H12 $mol:. @atom:h1 0.0600 -1.256 -0.724 1.078 + $atom:H13 $mol:. @atom:h1 0.0600 -1.259 -1.669 -0.253 + $atom:H21 $mol:. @atom:h1 0.0600 2.074 -0.255 -0.264 + $atom:H22 $mol:. @atom:h1 0.0600 1.258 -1.669 -0.259 + $atom:H23 $mol:. @atom:h1 0.0600 1.261 -0.724 1.072 + $atom:H31 $mol:. @atom:h1 0.0600 -0.817 1.923 -0.263 + $atom:H32 $mol:. @atom:h1 0.0600 0.816 1.923 -0.268 + $atom:H33 $mol:. @atom:h1 0.0600 0.003 1.456 1.070 + } + + # The "." in "$mol:." refers to this molecule object's molecule ID + # (It means we do not expect this molecule to be a group or a subunit + # of a larger molecule. Otherwise we would use "$mol:..." instead.) + + write('Data Bond List') { + $bond:C01 $atom:C0 $atom:C1 + $bond:C02 $atom:C0 $atom:C2 + $bond:C03 $atom:C0 $atom:C3 + $bond:C0H $atom:C0 $atom:H0 + $bond:C1H1 $atom:C1 $atom:H11 + $bond:C1H2 $atom:C1 $atom:H12 + $bond:C1H3 $atom:C1 $atom:H13 + $bond:C2H1 $atom:C2 $atom:H21 + $bond:C2H2 $atom:C2 $atom:H22 + $bond:C2H3 $atom:C2 $atom:H23 + $bond:C3H1 $atom:C3 $atom:H31 + $bond:C3H2 $atom:C3 $atom:H32 + $bond:C3H3 $atom:C3 $atom:H33 + } + +} # Isobutane diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt new file mode 100644 index 0000000000..50c5392507 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt @@ -0,0 +1,32 @@ +import "tip3p_2004.lt" + # <- This defines the TIP3P water molecule. This file is + # located in the "common" directory. You can either copy it + # here, or (preferably), you can define a MOLTEMPLATE_PATH + # environment variable and point it to "common". + # (as explained in the installation section of the manual). + +import "isobutane.lt" # <- defines the "Isobutane" molecule type. + + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 41.50 xlo xhi + 0.0 41.50 ylo yhi + 0.0 41.50 zlo zhi +} + + +# The next command generates a (rather dense) cubic lattice with +# spacing 3.45 Angstroms. (The pressure must be equilibrated later.) + +wat = new TIP3P_2004 [12].move(0.00, 0.00, 3.45) + [12].move(0.00, 3.45, 0.00) + [12].move(3.45, 0.00, 0.00) + +isobutane = new Isobutane [4].move(0, 0, 10.35) + [4].move(0, 10.35, 0) + [4].move(10.35, 0, 0) + +# move the isobutane molecules slightly to reduce overlap with the water +isobutane[*][*][*].move(1.725, 1.725, 1.725) + diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh new file mode 100755 index 0000000000..829c20a93f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh @@ -0,0 +1,69 @@ + # MOST USERS CAN IGNORE THIS FILE + # + # Unfortunately, as of 2014-4-19, the system.data and system.in.settings file + # which are created by moltemplate.sh contain a lot of irrelevant information, + # such as definition of parameters for atom types not present in the current + # system. This extra information takes up about 1 MB. + # + # This appears to be harmless. + # (Loading this extra information does not seem to slow down LAMMPS.) + # + # --------- OPTIONAL STEPS FOR STRIPPING OUT JUNK --------- + # + # However if you want to eliminate this junk from these files + # For now, we can strip this out using ltemplify.py to build a new .lt file. + # + # I suggest you do this in a temporary_directory + + mkdir new_lt_file + cd new_lt_file/ + + # now run ltemplify.py + + ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt + rm -rf ../system.data ../system.in* # these old lammps files no longer needed + + # This creates a new .LT file named "system.lt" in the local directory. + # Unfortunately, it may be missing some information because ltemplify.py + # does not understand all the commands present in a LAMMPS input script. + # If you define groups or use constraints, you must define them again. In this + # case, we must add the SHAKE constraint for the "TIP3P_2004" water molecule. + # So we have to remember the original name of the bond types and angle types. + # (For this example, SHAKE is applied to the water molecule, which is defined + # in "tip3p_2004.lt" file in the "common/" directory. Check this file.) + + ATOMTYPENUM_ow=`awk '{if ($1 == "@/atom:TIP3P_2004/ow") print $2}' < ../moltemplate_files/output_ttree/ttree_assignments.txt` + ATOMTYPENUM_hw=`awk '{if ($1 == "@/atom:TIP3P_2004/hw") print $2}' < ../moltemplate_files/output_ttree/ttree_assignments.txt` + BONDTYPENUM=`awk '{if ($1 == "@/bond:TIP3P_2004/OH") print $2}' < ../moltemplate_files/output_ttree/ttree_assignments.txt` + ANGLETYPENUM=`awk '{if ($1 == "@/angle:TIP3P_2004/HOH") print $2}' < ../moltemplate_files/output_ttree/ttree_assignments.txt` + echo "" >> system.lt + echo "write_once(\"In Settings\") {" >> system.lt + echo " group tip3p type @atom:type$ATOMTYPENUM_ow @atom:type$ATOMTYPENUM_hw" >> system.lt + echo " fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:type$BONDTYPENUM a @angle:type$ANGLETYPENUM" >> system.lt + echo "}" >> system.lt + echo "" >> system.lt + + # The ltemplify.py script also does not copy the boundary dimensions. + # We must do this manually. + # If you did NOT throw away the "Data Boundary" file usually located in + # "moltemplate_files/output_ttree/Data Boundary" + # then you can copy that information from this file into system.lt + echo "write_once(\"Data Boundary\") {" >> system.lt + cat "../moltemplate_files/output_ttree/Data Boundary" >> system.lt + echo "}" >> system.lt + echo "" >> system.lt + + # Now, run moltemplate on this new .LT file. + moltemplate.sh system.lt + # This will create: "system.data" "system.in.init" "system.in.settings." + + # That's it. The new "system.data" and system.in.* files should + # be ready to run in LAMMPS. + + # Now copy the system.data and system.in.* files to the place where + # you plan to run moltemplate + mv -f system.data system.in.* ../ + cd ../ + + # Now delete all of the temporary files we generated + rm -rf new_lt_file/ diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt new file mode 100644 index 0000000000..0a829c52db --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt @@ -0,0 +1,44 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using +# ./README_setup.sh) +# +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fShakeTIP3P was defined in system.in.settings. It is incompatible with "minimize". +unfix fShakeTIP3P +minimize 1.0e-4 1.0e-6 100000 400000 +# Now read "system.in.settings" in order to redefine fShakeTIP3P again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 +thermo 100 +#thermo_modify flush yes + +run 40000 + +write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt new file mode 100644 index 0000000000..24dd41da3d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt @@ -0,0 +1,51 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# COMMENTING OUT MINIMIZATION STEPS: +# If you are reading the coordinates generated by the NPT run +# then you should not need to minimize the system beforehand. +# -- minimization protocol -- +## ("fix shake" is incompatible with "minimize".) +#unfix fShakeTIP3P +#minimize 1.0e-4 1.0e-6 100000 400000 +## Now read "system.in.settings" in order to redefine fShakeTIP3P again: +#include system.in.settings + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo 500 +#thermo_modify flush yes + +run 50000 + +write_restart system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/WARNING.TXT b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/WARNING.TXT new file mode 100644 index 0000000000..e95cac1925 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/WARNING.TXT @@ -0,0 +1,29 @@ +# -------- WARNING: -------- + +This directory contains some examples of all-atom simulations using the OPLSAA +force field, prepared using Jason Lambert's oplsaa_moltemplate.py conversion +tool, and moltemplate. + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that simulations +prepared using moltemplate will reproduce the behavior of other MD codes. + +# -------- REQUEST FOR HELP: -------- + +If you notice a problem with these examples, please report it. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2014-4-19) + +--- Improper angles --- + +I am also uncertain whether the improper angle interactions generated by +moltemplate are equivalent to those generated by BOSS or other molecule +builders. (I think they are, but I am worried that we might have listed +the atom types in the wrong order. Let us know if you see discrepancies +between what moltemplate and other molecule builders generates.) + +----------- +For more details how to use the OPLSAA force-field, read the "README.TXT" +file located in "ethylene/moltemplate_files/oplsaa_lt_generator/README.TXT" diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README.TXT b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README.TXT new file mode 100644 index 0000000000..32252bad09 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README.TXT @@ -0,0 +1,24 @@ + +This is an example of how to use the OPLSAA force-field in LAMMPS +(using moltemplate.sh and Jason Lambert's oplsaa_moltemplate.py conversion tool) + +This example also shows how to use moltemplate in combination with PACKMOL. +(PACKMOL is a useful program for generating atomic coordinates. In this example, + moltemplate.sh is only used to create the topology, force-field and charges, + and PACKMOL generates the coordinates, which moltemplate reads (in "step 1"). + Moltemplate can also be used for generating atomic coordinates, especially + for mixing many small molecules together, as we do in this example. However + I wanted to demonstrate how to combine PACKMOL with moltemplate.sh. + In some other scenarios, such as protein solvation, PACKMOL does a much + better job than moltemplate.) + +As of 2014-4-06, this code has not been tested for accuracy. +(See the WARNING.TXT file.) + +step 1) +To build the files which LAMMPS needs, follow the instructions in: +README_setup.sh + +step 2) +To run LAMMPS with these files, follow these instructions: +README_run.sh diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README_run.sh b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README_run.sh new file mode 100755 index 0000000000..8b01ab92d7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README_run.sh @@ -0,0 +1,39 @@ +# --- Running LAMMPS --- +# -------- REQUIREMENTS: --------- +# 1) This example requires building LAMMPS with the "USER-MISC" package. +# (because it makes use of "gaff.lt" which uses dihedral_style fourier) +# To do this, type "make yes-user-misc" before compiling LAMMPS. +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# -------- PREREQUISITES: -------- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README_setup.sh new file mode 100755 index 0000000000..33645bfc8c --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README_setup.sh @@ -0,0 +1,44 @@ +# -------- REQUIREMENTS: --------- +# You must define your MOLTEMPLATE_PATH environment variable +# and set it to the "common" subdirectory of your moltemplate distribution. +# (See the "Installation" section in the moltemplate manual.) + +# Create the coordinates of the atoms using PACKMOL +cd packmol_files + + packmol < mix_ethylene+benzene.inp + mv -f system.xyz ../moltemplate_files/ + +cd .. + + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # Create the "oplsaa.lt" file which moltemplate will need + + cd oplsaa_lt_generator/ + ./oplsaa_moltemplate.py oplsaa_subset.prm + mv -f oplsaa.lt .. + cd .. + + # run moltemplate + + moltemplate.sh -xyz system.xyz system.lt + + # This will generate various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + + # Optional: + # Delete the "oplsaa.lt" file: + rm -f oplsaa.lt + + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/benzene.jpg b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/benzene.jpg new file mode 100644 index 0000000000..356c784256 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/benzene.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg new file mode 100644 index 0000000000..00c82d3d9f Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/ethylene.jpg b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/ethylene.jpg new file mode 100644 index 0000000000..ab5bbbf49b Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/images/ethylene.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt new file mode 100644 index 0000000000..f240a091fe --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt @@ -0,0 +1,51 @@ +import "oplsaa.lt" + +# The "oplsaa.lt" file contains force-field definitions and masses for the +# atoms in your system. See oplsaa_lt_generator/README.TXT for details. + +# Note: +# Atom type @atom:90 corresponds to "Aromatic C" +# Atom type @atom:91 corresponds to "Aromatic H-C" + +Benzene inherits OPLSAA { + + # We just need a list of atom types and bonds. + # + # You don't have to specify the charge in this example because we are + # using the OPLSAA force-field assigns this by atom-type. + # + # You also don't have to specify the coordinates, because + # you are using PACKMOL to generate them for you. + # Just leave these numbers as 0.00 for now.. + + write('Data Atoms') { + $atom:C1 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" + $atom:C2 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" + $atom:C3 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" + $atom:C4 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" + $atom:C5 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" + $atom:C6 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" + $atom:H11 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" + $atom:H21 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" + $atom:H31 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" + $atom:H41 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" + $atom:H51 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" + $atom:H61 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" + } + + write('Data Bond List') { + $bond:C12 $atom:C1 $atom:C2 + $bond:C23 $atom:C2 $atom:C3 + $bond:C34 $atom:C3 $atom:C4 + $bond:C45 $atom:C4 $atom:C5 + $bond:C56 $atom:C5 $atom:C6 + $bond:C61 $atom:C6 $atom:C1 + $bond:C1H1 $atom:C1 $atom:H11 + $bond:C2H2 $atom:C2 $atom:H21 + $bond:C3H3 $atom:C3 $atom:H31 + $bond:C4H4 $atom:C4 $atom:H41 + $bond:C5H5 $atom:C5 $atom:H51 + $bond:C6H6 $atom:C6 $atom:H61 + } + +} # Benzene diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt new file mode 100644 index 0000000000..45adb1faef --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt @@ -0,0 +1,40 @@ +import "oplsaa.lt" + +# The "oplsaa.lt" file contains force-field definitions and masses for the +# atoms in your system. See oplsaa_lt_generator/README.TXT for details. + +# Note: +# Atom type 88 corresponds to "Alkene H2-C=" +# Atom type 89 corresponds to "Alkene H-C=" + + + +Ethylene inherits OPLSAA { + + # atom-id mol-id atom-type charge X Y Z + + write('Data Atoms') { + $atom:C1 $mol @atom:88 0.000 -0.6695 0.000000 0.000000 + $atom:C2 $mol @atom:88 0.000 0.6695 0.000000 0.000000 + $atom:H11 $mol @atom:89 0.000 -1.234217 -0.854458 0.000000 + $atom:H12 $mol @atom:89 0.000 -1.234217 0.854458 0.000000 + $atom:H21 $mol @atom:89 0.000 1.234217 -0.854458 0.000000 + $atom:H22 $mol @atom:89 0.000 1.234217 0.854458 0.000000 + } + + write('Data Bond List') { + $bond:C12 $atom:C1 $atom:C2 + $bond:C1H1 $atom:C1 $atom:H11 + $bond:C1H2 $atom:C1 $atom:H12 + $bond:C2H1 $atom:C2 $atom:H21 + $bond:C2H2 $atom:C2 $atom:H22 + } + +} # Ethylene + + + +# Note: You don't need to supply the partial partial charges of the atoms. +# If you like, just fill the fourth column with zeros ("0.000"). +# Moltemplate and LAMMPS will automatically assign the charge later + diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT new file mode 100644 index 0000000000..d5e469af37 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT @@ -0,0 +1,3 @@ + +OPLSAA force-field conversion tools provided by Jason Lambert. + diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT new file mode 100644 index 0000000000..cd38943338 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT @@ -0,0 +1,108 @@ +This directory contains instructions for creating a a moltemplate file +("oplsaa.lt") containing force-field definitions relevant to the +"ethylene+benzene" example. (However, these instructions should work +for other molecules too.) + +First, check and see if there is an "oplsaa_subset.prm" file present. +If not, then download this file: + +http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm + This file is also available here: +http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm + +and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE +so that it only contains atom types you plan to have in your simulation +(see below for details). Then run the opls_moltemplate.py script this way: + + +python oplsaa_moltemplate.py oplsaa_subset.prm + + +This will create a file named "oplsaa.lt" +Look over the newly created "oplsaa.lt" file. +Then move this file to wherever you plan to run moltemplate. For example: + +mv -f oplsaa.lt .. + +----- DETAILS: Editing the "oplsaa_subset.prm" file ------- + +Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm" +file (or "oplsaa_subset.prm file) and eliminate atom types which do not +correspond to any of the atoms in your simulation. This means you must +look for lines near the beginning of this file which begin with the word "atom" +and refer to atom types which appear in the simulation you plan to run. All +other lines (beginning with the word "atom") must be deleted or commented out. +(Leave the rest of the file alone.) + +For example: +If you were working with ethylene and benzene you would delete every line +beginning with the word "atom", except for these four lines: + +# for ethylene: +atom 88 47 CM "Alkene H2-C=" 6 12.011 3 +atom 89 46 HC "Alkene H-C=" 1 1.008 1 +# for benzene: +atom 90 48 CA "Aromatic C" 6 12.011 3 +atom 91 49 HA "Aromatic H-C" 1 1.008 1 + +Then you are ready to run oplsaa_moltemplate.py on this file. + +(You can try to delete more irrelevant information, but be careful. + It is not necessary, and it is easy to make mistakes.) + + +----- Using the "oplsaa.lt" file ----- + +Once you have created the "oplsaa.lt" file, you can create files (like +ethylene.lt) which define molecules that refer to these atom types. +Here is an excerpt from "ethyelene.lt": + +Ethylene inherits OPLSAA { + write('Data Atoms') { + list of atoms goes here ... + } + write('Data Bond List') { + list of bonds goes here ... + } +} + +And then run moltemplate. + + +----------- CHARGE: ----------- + +By default, the OPLSAA force-field assigns atom charge according to atom type. +When you run moltemplate, it will create a file named "system.in.charges", +containing commands like: + +set type 2 charge -0.42 +set type 3 charge 0.21 + +(This assumes your main moltemplate file is named "system.lt". If it was +named something else, eg "polymer.lt", then the file created by moltemplate +will be named "polymer.in.charges".) + +Include these commands somewhere in your LAMMPS input script +(or use the LAMMPS "include" command to load the commands in system.in.charges) + +Note that the atom numbers (eg "2", "3") in this file will not match the +OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file, +created by moltemplate, to see a table of "@atom" type numbers translated +from OPLSAA into LAMMPS.) + +----------- CREDIT ----------- + +If you use these tools and you publish a paper using OPLSAA, please also cite +the TINKER program. (Because these examples use the "oplsaa.prm" file which +is distributed with TINKER.) I think these are the relevant citations: + +1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newtonâ€like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024. + +2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/ + +------------------------------- + +Jason Lambert and Andrew Jewett +April, 2014 + +Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT new file mode 100644 index 0000000000..2fc1ea29ea --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT @@ -0,0 +1,16 @@ +MOST USERS SHOULD IGNORE THIS DIRECTORY. + +This directory contains versions of the oplsaa_subset.prm file +which nearly all of the OPLSAA force-field information removed. +However for the "ethylene+benzene" example, all of the essential +parameters are contained in these files. You can use oplsaa_moltemplate.py +with either of these files and the physics should be the same. + +However there is no reason to do this. +When you download the "oplsaa.prm" file from: +http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm +(also http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm) +...just remove the lines beginning with "atom" for atoms you don't need. +You don't have to delete all the other irrelevant interactions. +(In fact, it is hard to do that without making a mistake. + I recommend that you leave the rest of the oplsaa.prm file alone.) diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm new file mode 100644 index 0000000000..b4078f1214 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm @@ -0,0 +1,37 @@ + ############################# + ## Atom Type Definitions ## + ############################# + + +atom 88 47 CM "Alkene H2-C=" 6 12.011 3 +atom 89 46 HC "Alkene H-C=" 1 1.008 1 +atom 90 48 CA "Aromatic C" 6 12.011 3 +atom 91 49 HA "Aromatic H-C" 1 1.008 1 + +vdw 88 3.5500 0.0760 +vdw 89 2.4200 0.0300 +vdw 90 3.5500 0.0700 +vdw 91 2.4200 0.0300 + +bond 46 47 340.00 1.0800 +bond 47 47 549.00 1.3400 +bond 48 48 469.00 1.4000 +bond 48 49 367.00 1.0800 + +angle 46 47 46 35.00 117.00 +angle 46 47 47 35.00 120.00 +angle 48 48 48 63.00 120.00 +angle 48 48 49 35.00 120.00 + +torsion 46 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 48 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 49 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 48 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 + +imptors 0 0 47 0 30.000 180.0 2 +imptors 0 0 48 0 5.000 180.0 2 + +charge 88 -0.2300 +charge 89 0.1150 +charge 90 -0.1150 +charge 91 0.1150 diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm new file mode 100644 index 0000000000..6dbc6861ac --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm @@ -0,0 +1,49 @@ + ############################# + ## Atom Type Definitions ## + ############################# + +atom 88 47 CM "Alkene H2-C=" 6 12.011 3 +atom 89 46 HC "Alkene H-C=" 1 1.008 1 +atom 90 48 CA "Aromatic C" 6 12.011 3 +atom 91 49 HA "Aromatic H-C" 1 1.008 1 + +vdw 88 3.5500 0.0760 +vdw 89 2.4200 0.0300 +vdw 90 3.5500 0.0700 +vdw 91 2.4200 0.0300 + +bond 46 47 340.00 1.0800 +bond 47 47 549.00 1.3400 +bond 47 48 427.00 1.4330 +bond 48 48 469.00 1.4000 +bond 48 49 367.00 1.0800 + +angle 46 47 46 35.00 117.00 +angle 46 47 47 35.00 120.00 +angle 46 47 48 35.00 123.30 +angle 47 47 48 85.00 117.00 +angle 48 48 48 63.00 120.00 +angle 47 48 48 70.00 124.00 +angle 48 48 49 35.00 120.00 + +imptors 0 0 47 0 30.000 180.0 2 +imptors 0 0 48 0 5.000 180.0 2 + +torsion 47 46 47 46 0.000 0.0 1 -8.000 180.0 2 0.000 0.0 3 +torsion 0 47 47 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 46 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 46 47 47 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 46 47 48 48 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 +torsion 47 47 48 48 1.241 0.0 1 3.353 180.0 2 -0.286 0.0 3 +torsion 0 48 48 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 47 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 48 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 48 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 49 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 + +charge 88 -0.2300 +charge 89 0.1150 +charge 90 -0.1150 +charge 91 0.1150 diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py new file mode 100755 index 0000000000..49cef1aff1 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py @@ -0,0 +1,386 @@ +#! /usr/bin/env python +#The purpose of this script is to create a moltemplate lt file for the opls-aa forcefield. +#This will assist researchers in building complex simulations using this OPLS-UA and the OPLS-AA forcefields. +__author__="Jason Lambert" +__version__="0.15" + +import sys +import os +from operator import itemgetter + +print(""" + +Warning: + Run this program on a SUBSET of the OPLS atoms which are relevant + to your problem. If not, this program (and moltemplate) may crash + your computer and/or generate enormous files that you do not need. +""") +# To do that, first make a copy of the \"oplsaa.prm\" file +# (which can be downloaded from the TINKER web site). +# The lines in this file beginning with the word \"atoms\" should +# define the atoms which you plan to put in your simulation. All other +# lines beginning with the word \"atoms\" should be deleted. +# (Leave the other sections of this file alone.) +#""") + + + +#input data from file containing opls aa force field parameters. +try: + f=open(sys.argv[1],"r") +except: + print("need to specify file name as an input argument:") + print("python oplsaa_moltemplate.py ") + print("or file name is specified incorrectly") + sys.exit() +#output lt file +g=open("oplsaa.lt","w") + + + +lines = f.readlines() + + + +# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. + +for i in range(0, len(lines)): + if (lines[i].find("## Atom Type Definitions ##") != -1): + break + else: + lines[i] = '# ' + lines[i] + + +# As of 2014-4-19, there appear to be 906 atom types, but we don't assume this. +# First try to infer out how many atom types there were in the original +# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. +# (Keep track of the maximum value of the first column in the "atom" section.) +max_atomType = 0 +for line in lines: + # skip over text after a # comment character + ic = line.find('#') + if ic != -1: + line = (line[:ic]).strip() + else: + line = line.strip() + # now look for lines beginning with the word "atom" + tokens = line.split() + if ((len(tokens)>2) and + (tokens[0] == "atom") and + (int(tokens[1]) > max_atomType)): + max_atomType = int(tokens[1]) + + +#temporary storage file +h=open("temp.txt","w+") +atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key +#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms +atom=[[-10000,-10000] for i in range(0,max_atomType+1)] +#charge_by_type={} # lookup charge by atom type +#vdw_by_type={} # lookup epsilon & sigma paramters by atom type +charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom +vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma + + + +#atom is declared this way so for sorting purposes. +#atom contains the following data upon allocation +#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) +#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) +#atom[][2]=atom_mass +#atom[][3]=partial charge +#atom[][4]=non_bonding sigma +#atom[][5]=non_bonding epsilon +#atom[][6]=atom comment +bond=[] +#bond contains the following data +#bond[0]=atom 1 ffid +#bond[1]=atom 2 ffid +#bond[2]=bond spring constant(OPLS-aa compatible) +#bond[3]=equilibrium bond distance(Angstrom) +angle=[] +#angle contains the following data +#angle[0]=atom 1 ffid +#angle[1]=atom 2 ffid +#angle[2]=atom 3 ffid +#angle[3]=spring constant +#angle[4]=equilibrium angle (degrees) +dihedral=[] +#dihedral contains the following data +#dihedral[0]=atom 1 ffid +#dihedral[1]=atom 2 ffid +#dihedral[2]=atom 3 ffid +#dihedral[3]=atom 4 ffid +#dihedral[4]=v1 +#dihedral[5]=v2 +#dihedral[6]=v3 +#dihedral[7]=v4 +improper=[] +#improper[0]=atom 1 ffid +#improper[1]=atom 2 ffid(central atom) +#improper[2]=atom 3 ffid +#improper[3]=atom 4 ffid +#improper[4]=spring coefficient +#improper[5]=equilibrium angle + + +#This section gets all the parameters from the force field file +for line in lines: + + # skip over text after a # comment character + ic = line.find('#') + if ic != -1: + line = (line[:ic]).strip() + else: + line = line.strip() + + if line.find("atom") == 0: + line=line.split() + atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), + 0.0,0.0,0.0," ".join(line[3:-2])] + elif line.find("vdw") == 0: + line=line.split() + #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) + if (int(line[1]) <= max_atomType): + vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) + elif line.find("bond") == 0: + line=line.split() + bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) + elif line.find("angle") == 0: + line=line.split() + angle.append([int(line[1]),int(line[2]),int(line[3]), + float(line[4]),float(line[5])]) + elif line.find("torsion") == 0: + line=line.split() + dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), + float(line[5]),float(line[8]), float(line[11]), 0.0]) + elif line.find("charge") == 0: + line=line.split() + #charge_temp.append([int(line[1]),float(line[2])]) + if (int(line[1]) <= max_atomType): + charge_by_type[int(line[1])] = float(line[2]) + elif line.find("imptors") == 0: + line=line.split() + improper.append([int(line[1]), int(line[2]), + int(line[3]), int(line[4]), float(line[5]), float(line[6])]) + +if len(atom) > 600: + sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" + " (You were supposed to edit out the atoms you don't need.\n" + " Not doing this may crash your computer.)\n" + "\n" + " Proceed? (Y/N): ") + reply = sys.stdin.readline() + if find(reply.strip().lower(), 'y') != 0: + exit(0) + +#adding the charge and Lennard Jones parameters to +#to each atom type. +#----------------------------------------------# +for i in range(0,len(atom)): + atom_type_num = atom[i][0] + #q = charge_by_type.get(atomTypeNum) + #if q: + # atom[i][3] = q + if atom_type_num != -10000: + q = charge_by_type[atom_type_num] + atom[i][3] = q + +for i in range(0,len(atom)): + atom_type_num = atom[i][0] + #vdw_params = vdw_by_type.get(atomTypeNum) + #if vdw_params: + # atom[i][4] = vdw_params[0] + # atom[i][5] = vdw_params[1] + if atom_type_num != -10000: + vdw_params = vdw_by_type[atom_type_num] + atom[i][4] = vdw_params[0] + atom[i][5] = vdw_params[1] + +del(charge_by_type) +del(vdw_by_type) + +#----------------------------------------------------------# +#begin writing content to lt file +g.write("OPLSAA {\n\n" ) + +#write out the atom masses +#----------------------------------------------------------# +g.write(" write_once(\"Data Masses\"){\n")#checked with gaff +for i,x in enumerate(atom): + if x[0] != -10000: + g.write(" @atom:{} {} #{} partial charge={}\n".format( + x[0],x[2],x[6],x[3])) +g.write(" } #(end of atom masses)\n\n") +#----------------------------------------------------------# + + +#write out the pair coefficients +#----------------------------------------------------------# +g.write(" write_once(\"In Settings\"){\n")#checked with gaff +for i,x in enumerate(atom): + if x[0] != -10000: + g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4])) +g.write(" } #(end of pair coeffs)\n\n") + +g.write(" write_once(\"In Charges\"){\n")#checked with gaff +for i,x in enumerate(atom): + if x[0] != -10000: + g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) +g.write(" } #(end of atom charges)\n\n") + +#-----------------------------------------------------------# + +# This part of the code creates a lookup dictionary +# that allows you to find every type of atom by its +# force field id. force field id is the id number +# relevant to bonds, angles, dihedrals, and impropers. +# This greatly increases the speed of angle, bond, dihedral +# and improper assignment. +#------------------------------------------------------------# +atom=sorted(atom,key=itemgetter(1)) +atom_ffid=0 +for x in atom: + if x[1]==atom_ffid: + atom_lookup[x[1]].append(x[0]) + elif x[1]>atom_ffid: + atom_lookup[x[1]]=[x[0]] + atom_ffid=x[1] +atom_lookup[0]=["*"] +#-------------------------------------------------------------# + + +#writing out the bond coefficients and bond parameters# +#-------------------------------------------------------------# +g.write(" write_once(\"In Settings\") {\n") +index1=0 +for x in bond: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) + h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) +g.write(" } #(end of bond_coeffs)\n\n") +h.seek(0,0) +g.write(" write_once(\"Data Bonds By Type\") {\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of bonds by type)\n\n") +del(bond) +h.close() +#-----------------------------------------------------------# +h=open("temp.txt","w+") + +#writing out angle coefficients and angles by type.---------# +#-----------------------------------------------------------# +g.write(" write_once(\"Data Angles By Type\"){\n") +for x in angle: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + #print(y,z,u,x) + h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u, + x[3]/2.0,x[4])) + g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format( + y,z,u)) + + +g.write(" } #(end of angles by type)\n\n") +h.seek(0,0) +g.write(" write_once(\"In Settings\" ){\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of angle_coeffs)\n\n") +del(angle) +h.close() +#----------------------------------------------------------# + +#writing dihedrals by type and dihedral coefficients-------# +h=h=open("temp.txt","w+") +g.write(" write_once(\"Data Dihedrals By Type\") {\n") +#print(atom_lookup) +for x in dihedral: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + for v in atom_lookup.get(x[3],[]): + if x[0]!=0 and x[3]!=0: + g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( + y,z,u,v)) + h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( + y,z,u,v,x[4],x[5],x[6],x[7])) + elif x[0]==0 and x[3]!=0: + g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( + y,z,u,v)) + h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( + z,u,v,x[4],x[5],x[6],x[7])) + elif x[0]==0 and x[3]==0: + g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( + y,z,u,v)) + #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( + h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( + z,u,x[4],x[5],x[6],x[7])) + +del(dihedral) +g.write(" } #(end of Dihedrals by type)\n\n") +h.seek(0,0) +g.write(" write_once(\"In Settings\") {\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of dihedral_coeffs)\n\n") +h.close() +#-----------------------------------------------------------------------# + +#----writing out improper coefficients and impropers by type------------# +h=open("temp.txt","w+") +g.write(" write_once(\"Data Impropers By Type\") {\n") +for x in improper: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + for v in atom_lookup.get(x[3],[]): + if x[0]==0 and x[1]==0 and x[3]==0: + g.write(" @improper:{2}-0-0-0 @atom:{2} @atom:{0} @atom:{1} @atom:{3}\n".format( + y,z,u,v)) + h.write(" improper_coeff @improper:{2}-0-0-0 harmonic {4} {5} \n".format( + y,z,u,v,x[4]/2,0)) + else: + g.write(" @improper:{2}-0-0-{3} @atom:{2} @atom:{0} @atom:{1} @atom:{3}\n".format( + y,z,u,v)) + h.write(" improper_coeff @improper:{2}-0-0-{3} harmonic {4} {5} \n".format( + y,z,u,v,x[4]/2,0)) + + +g.write(" } #(end of impropers by type)\n\n") +h.seek(0,0) +g.write(" write_once(\"In Settings\") {\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of improp_coeffs)\n\n") +#-----------------------------------------------------------------------# + +#This section writes out the input parameters required for an opls-aa simulation +# lammps. +g.write(" write_once(\"In Init\") {\n") +g.write(" units real\n") +g.write(" atom_style full\n") +g.write(" bond_style hybrid harmonic\n") +g.write(" angle_style hybrid harmonic\n") +g.write(" dihedral_style hybrid opls\n") +g.write(" improper_style hybrid harmonic\n") +#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n") +g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n") +g.write(" pair_modify mix arithmetic\n") +g.write(" special_bonds lj 0.0 0.0 0.5\n") +g.write(" kspace_style pppm 0.0001\n") +g.write(" } #end of init parameters\n\n") +g.write("} # OPLSAA\n") +f.close() +g.close() +h.close() +os.remove("temp.txt") + + + + + + diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm new file mode 100644 index 0000000000..f226e55959 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm @@ -0,0 +1,5127 @@ +# This is a modified version of the file "oplsaa.prm" distributed with TINKER +# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm +# In this version, all of the lines beginning with "atom" have been deleted +# except for the atom types we will be using in this simulation +# +# If you use this file, please also cite the software this file comes from: +# +# Ponder, J. W., and Richards, F. M. J. Comput. Chem. (1987) 8(7), 1016-1024 +# "An efficient newtonâ€like method for molecular mechanics energy +# minimization of large molecules." +# +# Ponder, J. W, (2004) +# "TINKER: Software tools for molecular design" +# http://dasher.wustl.edu/tinker/ + + ############################## + ## ## + ## Force Field Definition ## + ## ## + ############################## + + +forcefield OPLS-AA + +vdwindex TYPE +vdwtype LENNARD-JONES +radiusrule GEOMETRIC +radiustype SIGMA +radiussize DIAMETER +epsilonrule GEOMETRIC +torsionunit 0.5 +imptorunit 0.5 +vdw-14-scale 2.0 +chg-14-scale 2.0 +electric 332.06 +dielectric 1.0 + + + ############################# + ## ## + ## Literature References ## + ## ## + ############################# + + +The parameters supplied with TINKER are from "OPLS All-Atom Parameters +for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as +provided by W. L. Jorgensen, Yale University during June 2009. These +parameters are taken from those distributed with BOSS Version 4.8. + +Note that "atom type" numbers and not "atom class" numbers are used +to index van der Waals parameters, see the "vdwindex" keyword above + +The atom types with (UA) in the description are "united atom" values, +ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their +attached atoms. All other parameters are "all-atom", OPLS-AA, including +explicit hydrogen atoms. + + + ############################# + ## ## + ## Atom Type Definitions ## + ## ## + ############################# + + +atom 88 47 CM "Alkene H2-C=" 6 12.011 3 +atom 89 46 HC "Alkene H-C=" 1 1.008 1 +atom 90 48 CA "Aromatic C" 6 12.011 3 +atom 91 49 HA "Aromatic H-C" 1 1.008 1 + + + ################################ + ## ## + ## Van der Waals Parameters ## + ## ## + ################################ + + +vdw 1 2.9400 0.0610 +vdw 2 3.9050 0.1180 +vdw 3 3.7500 0.1050 +vdw 4 2.9600 0.2100 +vdw 5 3.0000 0.1700 +vdw 6 3.9100 0.1600 +vdw 7 0.0000 0.0000 +vdw 8 3.7300 0.2940 +vdw 9 3.7750 0.2070 +vdw 10 3.9050 0.1750 +vdw 11 3.9100 0.1600 +vdw 12 3.9600 0.1450 +vdw 13 3.9050 0.1180 +vdw 14 3.8500 0.1400 +vdw 15 3.8500 0.0800 +vdw 16 3.8000 0.1150 +vdw 17 3.7500 0.1100 +vdw 18 3.8000 0.0500 +vdw 19 3.7500 0.1050 +vdw 20 3.0700 0.1700 +vdw 21 0.0000 0.0000 +vdw 22 3.7750 0.2070 +vdw 23 3.9050 0.1180 +vdw 24 3.7000 0.2500 +vdw 25 3.5500 0.2500 +vdw 26 3.5500 0.2500 +vdw 27 3.5500 0.2500 +vdw 28 0.0000 0.0000 +vdw 29 0.0000 0.0000 +vdw 30 3.7750 0.2070 +vdw 31 3.9050 0.1180 +vdw 32 3.8000 0.1700 +vdw 33 3.8000 0.1180 +vdw 34 3.8000 0.1700 +vdw 35 3.8000 0.1180 +vdw 36 3.2000 0.1700 +vdw 37 3.6500 0.1500 +vdw 38 3.7750 0.2070 +vdw 39 3.8500 0.0800 +vdw 40 3.8000 0.0500 +vdw 41 3.0000 0.1700 +vdw 42 3.8000 0.1700 +vdw 43 3.8000 0.1180 +vdw 44 3.8000 0.1180 +vdw 45 3.4000 0.3000 +vdw 46 3.8000 0.0800 +vdw 47 3.4700 0.3000 +vdw 48 3.8000 0.0500 +vdw 49 3.4700 0.2660 +vdw 50 3.5600 0.3950 +vdw 51 2.9300 0.2800 +vdw 52 3.8100 0.1600 +vdw 53 2.9600 0.2100 +vdw 54 3.2500 0.1700 +vdw 55 3.8000 0.1150 +vdw 56 3.8000 0.1700 +vdw 57 0.0000 0.0000 +vdw 58 2.5560 0.0200 +vdw 59 2.7800 0.0690 +vdw 60 3.4010 0.2339 +vdw 61 3.6240 0.3170 +vdw 62 3.9350 0.4330 +vdw 63 3.15061 0.1521 +vdw 64 0.0000 0.0000 +vdw 65 3.15365 0.1550 +vdw 66 0.0000 0.0000 +vdw 67 0.0000 0.0000 +vdw 68 3.1760 0.1500 +vdw 69 0.0000 0.0000 +vdw 70 3.2700 0.1000 +vdw 71 0.0000 0.0000 +vdw 72 0.0000 0.0000 +vdw 73 3.1200 0.1600 +vdw 74 0.0000 0.0000 +vdw 75 0.0000 0.0000 +vdw 76 3.16557 0.1554 +vdw 77 0.0000 0.0000 +vdw 78 3.4200 0.1700 +vdw 79 0.0000 0.0000 +vdw 80 3.5000 0.0660 +vdw 81 3.5000 0.0660 +vdw 82 3.5000 0.0660 +vdw 83 3.5000 0.0660 +vdw 84 3.5000 0.0660 +vdw 85 2.5000 0.0300 +vdw 86 3.5500 0.0760 +vdw 87 3.5500 0.0760 +vdw 88 3.5500 0.0760 +vdw 89 2.4200 0.0300 +vdw 90 3.5500 0.0700 +vdw 91 2.4200 0.0300 +vdw 92 3.5500 0.0700 +vdw 93 3.5000 0.0660 +vdw 94 3.5000 0.0660 +vdw 95 3.5500 0.0760 +vdw 96 3.1200 0.1700 +vdw 97 0.0000 0.0000 +vdw 98 2.5000 0.0300 +vdw 99 3.5000 0.0660 +vdw 100 3.5000 0.0660 +vdw 101 3.5000 0.0660 +vdw 102 3.5000 0.0660 +vdw 103 3.2500 0.0620 +vdw 104 3.0700 0.1700 +vdw 105 0.0000 0.0000 +vdw 106 2.9400 0.0610 +vdw 107 2.5000 0.0300 +vdw 108 3.5500 0.0700 +vdw 109 3.0700 0.1700 +vdw 110 0.0000 0.0000 +vdw 111 3.0700 0.1700 +vdw 112 0.0000 0.0000 +vdw 113 3.0700 0.1700 +vdw 114 0.0000 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0.0660 +vdw 810 2.9400 0.0610 +vdw 811 3.4000 0.3000 +vdw 812 3.4700 0.4700 +vdw 813 3.5500 0.0700 +vdw 814 2.9000 0.1400 +vdw 815 3.5000 0.0660 +vdw 816 2.9000 0.0600 +vdw 817 3.2500 0.1700 +vdw 818 3.5500 0.0700 +vdw 819 3.5000 0.0660 +vdw 820 3.7500 0.1050 +vdw 821 3.7500 0.1050 +vdw 822 2.9600 0.2100 +vdw 823 3.2500 0.1700 +vdw 824 0.0000 0.0000 +vdw 825 3.1200 0.1700 +vdw 826 0.0000 0.0000 +vdw 827 3.5000 0.0660 +vdw 828 3.5000 0.0660 +vdw 829 3.5500 0.0700 +vdw 830 3.5500 0.0700 +vdw 831 3.5500 0.0700 +vdw 832 3.5500 0.0700 +vdw 833 3.5500 0.0700 +vdw 834 1.9600 0.0125 +vdw 835 3.5000 0.0660 +vdw 836 3.5000 0.0660 +vdw 837 3.5000 0.0660 +vdw 838 3.7500 0.6000 +vdw 839 2.5000 0.0300 +vdw 840 3.2500 0.1700 +vdw 841 3.5500 0.0700 +vdw 842 3.5500 0.0700 +vdw 843 3.2500 0.1700 +vdw 844 3.5500 0.0700 +vdw 845 3.7500 0.1050 +vdw 846 2.9600 0.2100 +vdw 847 3.2500 0.1700 +vdw 848 3.5000 0.0660 +vdw 849 3.5000 0.0660 +vdw 850 3.5000 0.0660 +vdw 851 3.5000 0.0660 +vdw 852 2.4200 0.0150 +vdw 853 3.7500 0.1050 +vdw 854 2.9600 0.2100 +vdw 855 2.4200 0.0150 +vdw 856 3.5000 0.0660 +vdw 857 3.5000 0.0660 +vdw 858 3.5000 0.0660 +vdw 859 3.5000 0.0660 +vdw 860 3.5000 0.0660 +vdw 861 3.5000 0.0660 +vdw 862 3.5000 0.0660 +vdw 863 3.5000 0.0660 +vdw 864 3.5000 0.0660 +vdw 865 3.5000 0.0660 +vdw 866 4.0000 0.1000 +vdw 867 4.0000 0.1000 +vdw 868 4.0000 0.1000 +vdw 869 4.0000 0.1000 +vdw 870 2.5000 0.0300 +vdw 871 3.5000 0.0660 +vdw 872 3.5000 0.0660 +vdw 873 3.5000 0.0660 +vdw 874 3.5000 0.0660 +vdw 875 3.0800 0.7200 +vdw 876 4.1800 0.11779 +vdw 877 4.5100 0.0900 +vdw 878 5.1500 0.0700 +vdw 879 2.7000 0.018279 +vdw 880 3.3500 0.002772 +vdw 881 4.0600 0.000328 +vdw 882 4.3200 0.000171 +vdw 883 4.8200 0.000081 +vdw 884 2.9100 0.875044 +vdw 885 3.4700 0.449657 +vdw 886 3.8200 0.118226 +vdw 887 4.1800 0.047096 +vdw 888 3.5000 0.0660 +vdw 889 3.5000 0.0660 +vdw 890 3.5000 0.0660 +vdw 891 3.5000 0.0660 +vdw 892 2.5000 0.0300 +vdw 893 3.2500 0.1700 +vdw 894 3.5500 0.0700 +vdw 895 3.2500 0.1700 +vdw 896 3.5500 0.0700 +vdw 897 3.5500 0.0760 +vdw 898 3.5500 0.0760 +vdw 899 2.4200 0.0300 +vdw 900 3.3000 0.0860 +vdw 901 3.3000 0.0860 +vdw 902 3.3000 0.0860 +vdw 903 3.3000 0.0860 +vdw 904 3.3000 0.0860 +vdw 905 2.9600 0.2100 +vdw 906 3.5000 0.0660 + + + ################################## + ## ## + ## Bond Stretching Parameters ## + ## ## + ################################## + + +bond 1 2 367.00 1.3800 +bond 1 3 420.00 1.3570 +bond 1 13 367.00 1.3600 +bond 1 19 450.00 1.2790 +bond 1 25 300.00 0.3000 +bond 1 47 420.00 1.3400 +bond 1 48 420.00 1.3540 +bond 1 82 420.00 1.3540 +bond 1 83 420.00 1.3540 +bond 1 84 420.00 1.3540 +bond 1 87 420.00 1.3540 +bond 1 88 420.00 1.3540 +bond 1 108 461.00 1.5700 +bond 2 2 260.00 1.5260 +bond 2 3 317.00 1.5220 +bond 2 5 386.00 1.4250 +bond 2 6 260.00 1.5260 +bond 2 10 260.00 1.5260 +bond 2 11 317.00 1.5000 +bond 2 12 317.00 1.5100 +bond 2 13 260.00 1.5260 +bond 2 14 317.00 1.5000 +bond 2 15 222.00 1.8100 +bond 2 16 222.00 1.8100 +bond 2 20 320.00 1.4250 +bond 2 24 337.00 1.4490 +bond 2 44 382.00 1.4480 +bond 2 48 317.00 1.5100 +bond 2 51 260.00 1.5260 +bond 2 53 367.00 1.4710 +bond 2 55 337.00 1.4630 +bond 2 80 317.00 1.4950 +bond 3 3 350.00 1.5100 +bond 3 4 570.00 1.2290 +bond 3 5 450.00 1.3640 +bond 3 6 317.00 1.5220 +bond 3 10 317.00 1.5220 +bond 3 12 469.00 1.4000 +bond 3 13 317.00 1.5220 +bond 3 19 400.00 1.4440 +bond 3 20 214.00 1.3270 +bond 3 21 300.00 1.7900 +bond 3 24 490.00 1.3350 +bond 3 44 317.00 1.5220 +bond 3 46 340.00 1.0900 +bond 3 47 410.00 1.4440 +bond 3 48 400.00 1.4900 +bond 3 50 385.00 1.4600 +bond 3 52 656.00 1.2500 +bond 3 56 457.00 1.3580 +bond 3 57 418.00 1.3880 +bond 3 60 447.00 1.4190 +bond 3 65 300.00 1.9800 +bond 3 84 400.00 1.4900 +bond 3 86 385.00 1.4600 +bond 3 105 424.00 1.3830 +bond 3 107 490.00 1.3350 +bond 4 25 553.00 0.3000 +bond 4 64 525.00 1.4800 +bond 4 89 570.00 1.2290 +bond 4 110 700.00 1.1710 +bond 5 6 386.00 1.4250 +bond 5 7 553.00 0.9450 +bond 5 10 386.00 1.4250 +bond 5 13 320.00 1.4100 +bond 5 20 250.00 1.4700 +bond 5 24 400.00 1.3800 +bond 5 25 340.00 0.3000 +bond 5 44 320.00 1.4500 +bond 5 47 450.00 1.3700 +bond 5 48 450.00 1.3640 +bond 5 51 320.00 1.3800 +bond 5 64 230.00 1.6100 +bond 5 79 450.00 1.6700 +bond 5 106 94.00 1.8000 +bond 5 108 374.00 1.6400 +bond 6 6 260.00 1.5260 +bond 6 10 260.00 1.5260 +bond 6 11 317.00 1.5000 +bond 6 13 260.00 1.5260 +bond 6 14 317.00 1.5000 +bond 6 15 222.00 1.8100 +bond 6 16 222.00 1.8100 +bond 6 20 320.00 1.4250 +bond 6 24 337.00 1.4490 +bond 6 44 382.00 1.4480 +bond 6 47 317.00 1.5100 +bond 6 51 260.00 1.5260 +bond 6 53 367.00 1.4710 +bond 6 55 337.00 1.4630 +bond 6 79 222.00 1.8100 +bond 6 105 337.00 1.4750 +bond 7 20 553.00 0.9450 +bond 7 25 340.00 0.1000 +bond 9 9 530.00 1.3400 +bond 9 11 530.00 1.3400 +bond 9 14 530.00 1.3400 +bond 10 10 260.00 1.5260 +bond 10 11 317.00 1.5000 +bond 10 14 317.00 1.5000 +bond 10 20 320.00 1.4250 +bond 10 24 337.00 1.4490 +bond 10 44 382.00 1.4480 +bond 10 105 337.00 1.4750 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317.00 1.4950 +bond 13 90 337.00 1.4490 +bond 13 91 280.00 1.5100 +bond 13 95 532.80 1.4600 +bond 13 101 382.00 1.4480 +bond 13 102 375.00 1.4900 +bond 13 104 212.00 1.8200 +bond 13 105 337.00 1.4750 +bond 13 107 337.00 1.4490 +bond 13 108 187.00 1.8600 +bond 13 109 317.00 1.5100 +bond 14 14 530.00 1.3400 +bond 15 17 274.00 1.3360 +bond 15 48 250.00 1.7400 +bond 16 16 166.00 2.0380 +bond 16 19 300.00 1.6850 +bond 16 24 250.00 1.7300 +bond 16 25 340.00 0.5000 +bond 16 47 250.00 1.7600 +bond 16 48 250.00 1.7600 +bond 16 61 250.00 1.7300 +bond 16 82 250.00 1.7600 +bond 16 84 250.00 1.7400 +bond 16 91 222.00 1.8100 +bond 16 108 144.00 2.1500 +bond 17 25 340.00 0.1000 +bond 18 18 550.00 1.1200 +bond 18 19 650.00 1.1570 +bond 18 48 400.00 1.4100 +bond 18 56 550.00 1.2400 +bond 19 19 1150.00 1.2100 +bond 19 21 330.00 1.6370 +bond 19 46 420.00 1.0800 +bond 19 47 400.00 1.4260 +bond 19 48 400.00 1.4510 +bond 19 50 400.00 1.4260 +bond 19 65 330.00 1.7840 +bond 19 88 400.00 1.4510 +bond 19 91 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0.3000 +bond 25 44 340.00 0.3000 +bond 25 45 340.00 0.1000 +bond 25 46 340.00 0.3000 +bond 25 47 340.00 0.3000 +bond 25 48 367.00 0.3000 +bond 25 49 340.00 0.3000 +bond 25 53 340.00 0.3000 +bond 25 56 367.00 0.3000 +bond 25 61 367.00 0.3000 +bond 25 65 300.00 0.3000 +bond 25 103 340.00 0.1000 +bond 31 32 600.00 0.9572 +bond 31 33 900.00 0.1500 +bond 31 106 40.00 2.0500 +bond 34 35 529.60 0.9572 +bond 36 37 600.00 0.9572 +bond 36 38 900.00 0.1750 +bond 39 40 600.00 0.9572 +bond 39 41 900.00 0.7000 +bond 42 43 600.00 1.0000 +bond 44 44 350.00 1.4450 +bond 44 45 434.00 1.0100 +bond 44 48 481.00 1.3400 +bond 44 79 340.00 1.7700 +bond 44 91 382.00 1.4480 +bond 44 108 266.00 1.7400 +bond 45 53 434.00 1.0100 +bond 45 55 434.00 1.0100 +bond 45 56 434.00 1.0100 +bond 45 57 434.00 1.0100 +bond 45 101 434.00 1.0100 +bond 45 105 434.00 1.0100 +bond 45 108 166.00 1.4800 +bond 46 47 340.00 1.0800 +bond 46 50 340.00 1.0800 +bond 46 51 340.00 1.0900 +bond 46 80 340.00 1.0800 +bond 46 91 340.00 1.0880 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49 83 367.00 1.0800 +bond 49 84 367.00 1.0800 +bond 49 85 367.00 1.0800 +bond 49 87 367.00 1.0800 +bond 49 88 367.00 1.0800 +bond 50 50 385.00 1.4600 +bond 50 56 457.00 1.2900 +bond 50 84 549.00 1.3650 +bond 50 109 385.00 1.4600 +bond 51 105 337.00 1.4750 +bond 52 64 525.00 1.4800 +bond 53 54 434.00 1.0100 +bond 54 55 434.00 1.0100 +bond 55 59 481.00 1.3400 +bond 55 82 481.00 1.3400 +bond 56 56 500.00 1.3200 +bond 56 59 502.00 1.3240 +bond 56 60 461.00 1.3540 +bond 56 82 461.00 1.3540 +bond 56 86 483.00 1.3390 +bond 56 103 550.00 1.2100 +bond 56 109 457.00 1.2900 +bond 57 60 436.00 1.3740 +bond 57 61 400.00 1.3490 +bond 57 62 440.00 1.3710 +bond 57 81 428.00 1.3800 +bond 57 82 477.00 1.3430 +bond 57 84 427.00 1.3810 +bond 57 85 427.00 1.3810 +bond 57 86 385.00 1.4400 +bond 58 83 367.00 1.0800 +bond 58 84 367.00 1.0800 +bond 59 63 367.00 1.0800 +bond 60 60 520.00 1.3700 +bond 60 61 414.00 1.3910 +bond 60 80 388.00 1.4590 +bond 60 81 447.00 1.4190 +bond 60 87 469.00 1.4240 +bond 60 105 436.00 1.3740 +bond 61 61 400.00 1.2800 +bond 61 62 529.00 1.3040 +bond 61 82 488.00 1.3350 +bond 61 83 410.00 1.3940 +bond 61 84 410.00 1.3940 +bond 61 88 410.00 1.3200 +bond 62 63 367.00 1.0800 +bond 62 105 440.00 1.3710 +bond 63 82 367.00 1.0800 +bond 64 108 108.00 2.2500 +bond 65 82 300.00 1.8700 +bond 65 83 300.00 1.8700 +bond 65 84 300.00 1.8700 +bond 65 87 300.00 1.8700 +bond 65 88 300.00 1.8700 +bond 65 108 151.00 2.1900 +bond 66 82 250.00 2.0800 +bond 66 83 250.00 2.0800 +bond 66 84 250.00 2.0800 +bond 66 87 250.00 2.0800 +bond 66 88 250.00 2.0800 +bond 66 108 108.00 2.4400 +bond 77 78 500.00 1.8000 +bond 80 84 546.00 1.3520 +bond 82 86 385.00 1.4600 +bond 82 87 520.00 1.3700 +bond 83 84 520.00 1.3700 +bond 83 86 385.00 1.4600 +bond 84 84 512.00 1.3750 +bond 84 86 385.00 1.4600 +bond 84 87 546.00 1.3670 +bond 84 88 520.00 1.3700 +bond 85 85 520.00 1.3700 +bond 86 86 385.00 1.4600 +bond 86 87 385.00 1.4600 +bond 86 88 385.00 1.4600 +bond 87 87 469.00 1.4240 +bond 87 88 469.00 1.4240 +bond 89 90 490.00 1.3350 +bond 89 91 317.00 1.5220 +bond 90 91 337.00 1.4490 +bond 91 91 260.00 1.5200 +bond 102 103 550.00 1.2250 +bond 108 108 94.00 2.3200 +bond 109 109 549.00 1.3450 + + + ################################ + ## ## + ## Angle Bending Parameters ## + ## ## + ################################ + + +angle 25 1 25 33.00 109.47 +angle 1 2 2 50.00 109.50 +angle 2 2 2 63.00 112.40 +angle 2 2 3 63.00 112.40 +angle 2 2 5 80.00 109.50 +angle 2 2 6 63.00 112.40 +angle 6 2 6 63.00 112.40 +angle 5 2 6 80.00 109.50 +angle 2 2 10 63.00 112.40 +angle 3 2 10 63.00 112.40 +angle 6 2 10 63.00 112.40 +angle 10 2 10 63.00 112.40 +angle 5 2 10 80.00 109.50 +angle 10 2 12 63.00 114.00 +angle 6 2 13 63.00 112.40 +angle 10 2 15 50.00 108.60 +angle 2 2 16 50.00 114.70 +angle 10 2 16 50.00 114.70 +angle 2 2 20 80.00 109.50 +angle 6 2 20 80.00 109.50 +angle 10 2 20 80.00 109.50 +angle 3 2 24 80.00 110.30 +angle 2 2 24 80.00 111.20 +angle 2 2 44 56.20 109.47 +angle 6 2 44 56.20 109.47 +angle 10 2 44 56.20 109.47 +angle 13 2 44 56.20 109.47 +angle 3 2 44 80.00 111.20 +angle 2 2 48 63.00 112.40 +angle 10 2 48 63.00 114.00 +angle 2 2 51 63.00 112.40 +angle 6 2 51 63.00 112.40 +angle 2 2 53 80.00 111.20 +angle 2 2 55 80.00 111.20 +angle 10 2 80 63.00 115.60 +angle 2 3 4 80.00 120.40 +angle 1 3 4 80.00 121.00 +angle 3 3 4 80.00 121.40 +angle 4 3 4 80.00 126.00 +angle 4 3 5 80.00 121.00 +angle 4 3 6 80.00 120.40 +angle 5 3 10 70.00 115.00 +angle 4 3 10 80.00 120.40 +angle 5 3 12 70.00 120.00 +angle 12 3 12 85.00 120.00 +angle 5 3 13 70.00 108.00 +angle 13 3 13 70.00 116.00 +angle 1 3 13 80.00 111.00 +angle 3 3 13 80.00 117.20 +angle 4 3 13 80.00 120.40 +angle 10 3 20 81.00 111.40 +angle 13 3 20 81.00 111.40 +angle 4 3 20 83.00 123.40 +angle 13 3 21 75.00 109.00 +angle 4 3 21 75.00 119.00 +angle 24 3 24 70.00 114.20 +angle 2 3 24 70.00 116.60 +angle 3 3 24 70.00 116.60 +angle 6 3 24 70.00 116.60 +angle 10 3 24 70.00 116.60 +angle 13 3 24 70.00 116.60 +angle 4 3 24 80.00 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5 100.00 108.23 +angle 4 64 13 45.00 109.50 +angle 5 64 20 45.00 102.60 +angle 20 64 20 45.00 102.60 +angle 13 64 20 45.00 109.50 +angle 4 64 20 100.00 108.23 +angle 4 64 48 45.00 109.50 +angle 5 64 48 45.00 109.50 +angle 20 64 48 45.00 109.50 +angle 5 64 52 45.00 108.23 +angle 13 64 52 45.00 109.50 +angle 20 64 52 100.00 108.23 +angle 52 64 52 140.00 119.90 +angle 25 65 25 33.00 109.47 +angle 25 66 25 33.00 109.47 +angle 78 77 78 150.00 180.00 +angle 6 79 11 62.00 98.90 +angle 13 79 13 62.00 102.00 +angle 5 79 13 75.00 96.40 +angle 5 79 23 74.00 108.70 +angle 13 79 23 74.00 108.90 +angle 23 79 23 104.00 119.00 +angle 13 79 24 100.00 103.00 +angle 23 79 24 120.00 107.00 +angle 13 79 44 62.00 102.00 +angle 23 79 44 74.00 108.90 +angle 13 79 48 62.00 102.00 +angle 23 79 48 74.00 107.20 +angle 5 79 48 75.00 96.40 +angle 24 79 48 100.00 103.00 +angle 13 79 82 62.00 102.00 +angle 46 80 60 35.00 126.80 +angle 2 80 60 70.00 128.60 +angle 13 80 60 70.00 128.60 +angle 46 80 84 35.00 126.80 +angle 2 80 84 70.00 125.00 +angle 13 80 84 70.00 125.00 +angle 60 80 84 85.00 106.40 +angle 12 81 57 70.00 132.80 +angle 48 81 57 70.00 132.80 +angle 57 81 60 70.00 104.40 +angle 12 81 60 85.00 122.70 +angle 48 81 60 85.00 122.70 +angle 13 82 16 70.00 125.00 +angle 16 82 24 70.00 125.00 +angle 16 82 44 70.00 120.20 +angle 20 82 49 35.00 117.00 +angle 16 82 49 35.00 125.00 +angle 49 82 57 35.00 120.00 +angle 57 82 57 70.00 120.00 +angle 13 82 57 70.00 125.00 +angle 48 82 57 70.00 125.00 +angle 56 82 57 70.00 126.20 +angle 49 82 61 35.00 120.00 +angle 16 82 61 70.00 113.60 +angle 16 82 61 70.00 115.00 +angle 20 82 61 70.00 115.00 +angle 57 82 61 70.00 120.00 +angle 13 82 61 70.00 125.00 +angle 44 82 61 70.00 126.10 +angle 24 82 61 70.00 126.20 +angle 57 82 79 70.00 120.00 +angle 61 82 79 70.00 120.00 +angle 20 82 86 70.00 122.00 +angle 61 82 86 70.00 130.00 +angle 57 82 87 70.00 106.20 +angle 56 82 87 70.00 127.70 +angle 49 83 61 35.00 120.00 +angle 48 83 61 70.00 111.00 +angle 13 83 61 70.00 124.50 +angle 49 83 84 35.00 128.20 +angle 61 83 84 70.00 111.00 +angle 13 83 84 70.00 130.70 +angle 13 84 16 70.00 125.00 +angle 13 84 20 70.00 121.60 +angle 16 84 24 70.00 125.00 +angle 20 84 49 35.00 113.40 +angle 16 84 49 35.00 125.00 +angle 48 84 49 35.00 130.70 +angle 49 84 50 35.00 130.70 +angle 20 84 50 70.00 110.00 +angle 49 84 57 35.00 121.60 +angle 13 84 57 70.00 121.60 +angle 48 84 57 70.00 121.60 +angle 3 84 57 85.00 120.00 +angle 57 84 58 35.00 120.00 +angle 13 84 61 70.00 118.90 +angle 49 84 80 35.00 120.00 +angle 57 84 80 70.00 108.70 +angle 49 84 83 35.00 130.70 +angle 57 84 83 70.00 106.30 +angle 20 84 83 70.00 108.00 +angle 16 84 83 70.00 111.00 +angle 13 84 83 70.00 130.70 +angle 13 84 84 70.00 120.00 +angle 57 84 84 70.00 120.00 +angle 61 84 84 70.00 120.00 +angle 20 84 86 70.00 121.60 +angle 57 84 86 70.00 121.60 +angle 49 84 87 35.00 132.10 +angle 57 84 87 70.00 107.70 +angle 20 84 87 70.00 110.60 +angle 16 84 87 70.00 111.00 +angle 61 84 87 70.00 111.90 +angle 13 84 87 70.00 132.10 +angle 48 84 87 70.00 132.10 +angle 86 84 87 70.00 132.10 +angle 3 84 87 85.00 120.00 +angle 49 85 57 35.00 120.00 +angle 13 85 57 70.00 121.60 +angle 49 85 85 35.00 130.70 +angle 57 85 85 70.00 106.30 +angle 13 85 85 70.00 130.70 +angle 48 86 48 63.00 120.00 +angle 48 86 56 70.00 124.00 +angle 48 86 82 63.00 120.00 +angle 48 86 83 63.00 120.00 +angle 48 86 84 63.00 120.00 +angle 48 86 86 63.00 120.00 +angle 56 86 86 70.00 124.00 +angle 48 86 87 63.00 120.00 +angle 48 86 88 63.00 120.00 +angle 49 87 60 35.00 120.00 +angle 46 87 60 35.00 126.80 +angle 13 87 60 70.00 128.60 +angle 49 87 84 35.00 125.70 +angle 46 87 84 35.00 126.80 +angle 84 87 84 70.00 103.80 +angle 82 87 84 70.00 110.40 +angle 2 87 84 70.00 125.00 +angle 13 87 84 70.00 125.00 +angle 3 87 84 70.00 130.00 +angle 60 87 84 85.00 106.40 +angle 84 87 86 70.00 125.70 +angle 49 87 87 35.00 127.50 +angle 60 87 87 70.00 107.30 +angle 84 87 87 70.00 107.30 +angle 86 87 87 70.00 127.50 +angle 84 87 88 70.00 103.80 +angle 48 88 49 35.00 128.60 +angle 49 88 61 35.00 118.90 +angle 13 88 61 70.00 118.90 +angle 19 88 61 70.00 118.90 +angle 61 88 87 70.00 111.90 +angle 4 89 90 80.00 134.00 +angle 90 89 91 70.00 91.00 +angle 4 89 91 80.00 134.00 +angle 13 90 89 55.00 127.00 +angle 89 90 91 50.00 94.00 +angle 13 90 91 50.00 126.00 +angle 24 91 46 35.00 108.00 +angle 13 91 46 35.00 114.30 +angle 44 91 46 35.00 114.30 +angle 46 91 46 35.00 114.30 +angle 16 91 46 37.50 108.00 +angle 46 91 47 35.00 109.50 +angle 46 91 89 37.50 110.00 +angle 24 91 89 70.00 117.00 +angle 46 91 90 35.00 111.00 +angle 16 91 90 55.00 109.00 +angle 91 91 91 30.00 79.20 +angle 13 91 91 37.50 117.20 +angle 44 91 91 37.50 117.20 +angle 46 91 91 37.50 117.20 +angle 24 91 91 37.50 126.00 +angle 16 91 91 55.00 128.00 +angle 89 91 91 63.00 85.00 +angle 47 91 91 63.00 114.00 +angle 90 91 91 80.00 89.00 +angle 13 95 13 172.80 120.00 +angle 13 95 46 144.00 120.00 +angle 13 101 45 35.00 109.50 +angle 45 101 45 43.60 106.40 +angle 45 101 48 50.00 112.50 +angle 13 101 48 50.00 120.50 +angle 13 102 103 80.00 117.50 +angle 48 102 103 80.00 117.50 +angle 103 102 103 80.00 125.00 +angle 25 103 25 10.00 109.50 +angle 25 103 102 10.00 109.50 +angle 13 104 13 45.00 109.50 +angle 3 105 10 70.00 117.60 +angle 3 105 13 70.00 117.60 +angle 3 105 45 35.00 119.20 +angle 45 105 47 35.00 119.20 +angle 13 105 47 70.00 121.20 +angle 3 105 47 70.00 121.60 +angle 3 105 51 70.00 117.60 +angle 47 105 51 70.00 121.20 +angle 45 105 60 30.00 125.80 +angle 6 105 60 70.00 125.80 +angle 10 105 60 70.00 125.80 +angle 13 105 60 70.00 125.80 +angle 51 105 60 70.00 125.80 +angle 45 105 62 30.00 128.80 +angle 60 105 62 70.00 105.40 +angle 6 105 62 70.00 128.80 +angle 10 105 62 70.00 128.80 +angle 13 105 62 70.00 128.80 +angle 51 105 62 70.00 128.80 +angle 4 106 24 20.00 109.50 +angle 24 106 24 20.00 109.50 +angle 13 107 13 50.00 118.00 +angle 3 107 13 50.00 121.90 +angle 1 108 13 35.00 110.50 +angle 13 108 13 60.00 110.00 +angle 13 108 20 60.00 100.00 +angle 20 108 20 60.00 110.00 +angle 13 108 21 35.00 110.50 +angle 45 108 45 35.00 109.50 +angle 13 108 45 35.00 110.50 +angle 46 108 46 35.00 109.50 +angle 13 108 46 35.00 110.50 +angle 13 108 65 35.00 110.50 +angle 13 108 66 35.00 110.50 +angle 13 108 108 50.00 112.00 +angle 46 109 48 35.00 123.30 +angle 46 109 50 35.00 120.00 +angle 13 109 50 70.00 124.00 +angle 46 109 109 35.00 120.00 +angle 13 109 109 70.00 124.00 +angle 50 109 109 70.00 124.00 +angle 48 109 109 85.00 117.00 +angle 4 110 47 160.00 180.00 +angle 47 110 47 160.00 180.00 + + + ################################ + ## ## + ## Urey-Bradley Parameters ## + ## ## + ################################ + + +ureybrad 35 34 35 38.25 1.5537 + + + ##################################### + ## ## + ## Improper Torsional Parameters ## + ## ## + ##################################### + + +imptors 0 0 3 4 21.000 180.0 2 +imptors 0 0 3 52 21.000 180.0 2 +imptors 0 0 24 0 5.000 180.0 2 +imptors 0 0 47 0 30.000 180.0 2 +imptors 0 0 48 0 5.000 180.0 2 + + + ############################ + ## ## + ## Torsional Parameters ## + ## ## + ############################ + + + ################################################################### + ## ## + ## Alternative Torsional Parameter Values for Use with OPLS-AA ## + ## ## + ## For some torsions, OPLS-AA has multiple possible parameter ## + ## values; the list below shows functional groups for which ## + ## these alternate (commented) values should be preferred; the ## + ## values are in the same order as in the full parameter list ## + ## ## + ## 4 3 3 36 generic (default) ## + ## 4 3 3 36 dicarbonyls ## + ## 36 3 3 36 hydrocarbon (default) ## + ## 36 3 3 36 dicarbonyls ## + ## 13 3 5 7 carboxylic acid (default) ## + ## 13 3 5 7 1,2-diacid monoanion ## + ## 4 3 13 13 peptide (default) ## + ## 4 3 13 13 propanamide ## + ## 4 3 13 13 carboxylic acid ## + ## 4 3 13 13 dicarboxylic acid ## + ## 4 3 13 13 aldyhyde, ketone, acyl halide ## + ## 4 3 13 13 1,2-diacid monoanion ## + ## 5 3 13 13 carboxylic acid (default) ## + ## 5 3 13 13 dicarboxylic acid ## + ## 35 3 13 13 peptide psi' (default) ## + ## 35 3 13 13 propanamide ## + ## 35 3 13 13 beta-3-peptide, last psi ## + ## 4 3 29 13 esters (default) ## + ## 4 3 29 13 benzoic esters ## + ## 7 5 13 13 alcohols (default) ## + ## 7 5 13 13 trifluoroethanol ## + ## 7 5 13 13 hexopyranoses ## + ## 7 5 13 36 alcohols (default) ## + ## 7 5 13 36 axial cyclohexanol ## + ## 7 5 13 36 trifluoroethanol ## + ## 0 13 13 13 alcohols, ethers (default) ## + ## 0 13 13 13 hexopyranoses ## + ## 3 13 13 3 dicarboxylic acid (default) ## + ## 3 13 13 3 1,2-diacid monoanion ## + ## 3 13 13 13 butanamide (default) ## + ## 3 13 13 13 carboxylate ion ## + ## 3 13 13 13 aldyhyde, ketone, acyl halide ## + ## 3 13 13 36 all carbonyls (default) ## + ## 3 13 13 36 dicarboxylic acid ## + ## 3 13 13 36 aldehyde, ketone, acyl halide ## + ## 5 13 13 5 diols only (default) ## + ## 5 13 13 5 triols only ## + ## 5 13 13 5 hexopyranoses ## + ## 13 13 13 13 hydrocarbon (default) ## + ## 13 13 13 13 perfluoroalkane ## + ## 13 13 13 35 peptide chi-1 (default) ## + ## 13 13 13 35 N-propylformamide ## + ## 36 13 13 69 generic (default) ## + ## 36 13 13 69 sulfone ## + ## 13 13 33 13 amine (default) ## + ## 13 13 33 13 exocyclic amine ## + ## 13 13 33 13 exocyclic 1,4-diamine ## + ## 13 13 33 34 amine (default) ## + ## 13 13 33 34 azetidine, 4-ring ## + ## 13 13 33 34 pyrrolidine, 5-ring ## + ## 13 13 33 34 cyclic amine ## + ## 13 13 33 34 cyclic 1,4-diamine ## + ## 13 13 35 3 peptide phi' (default) ## + ## 13 13 35 3 N-ethylformamide ## + ## 13 13 35 3 beta-3-peptide, first theta tors ## + ## 13 13 35 13 proline, CD-N-CA-CB (default) ## + ## 13 13 35 13 proline, CG-CD-N-CA ## + ## 36 13 35 3 peptide phi'' (default) ## + ## 36 13 35 3 N-methylformamide ## + ## 13 13 47 0 imidazole, indole, purine (default) ## + ## 13 13 47 0 nucleoside chi ## + ## 13 13 47 52 nucleoside (default) ## + ## 13 13 47 52 imidazole, indole, purine ## + ## 29 13 47 0 imidazole, indole, purine (default) ## + ## 29 13 47 0 nucleoside chi ## + ## 29 13 95 52 nucleoside (default) ## + ## 29 13 95 52 imidazole, indole, purine ## + ## 13 13 97 13 generic (default) ## + ## 13 13 97 13 generic ## + ## 17 15 38 0 aromatic thiol (default) ## + ## 17 15 38 0 aromatic thiol, N-C-S-H ## + ## 13 29 54 42 phosphonates (default) ## + ## 13 29 54 42 dimethyl phosphate ## + ## 34 35 72 16 diaryl amine (default) ## + ## 34 35 72 16 aniline-like ## + ## 34 35 72 29 diaryl amine (default) ## + ## 34 35 72 29 aniline-like ## + ## 13 40 40 37 diene (default) ## + ## 13 40 40 37 2-methyl-1,3-butadiene ## + ## 0 46 72 0 generic (default) ## + ## 0 46 72 0 generic ## + ## 0 47 72 0 generic (default) ## + ## 0 47 72 0 generic ## + ## 0 47 74 0 generic (default) ## + ## 0 47 74 0 generic ## + ## 0 47 74 0 generic ## + ## 0 51 72 0 generic (default) ## + ## 0 51 72 0 HA-CR-NB-?? or N?-CR-NB-?? ## + ## 0 72 77 0 generic (default) ## + ## 0 72 77 0 biphenyl-like, N-C-C-C ## + ## ## + ################################################################### + + +torsion 0 2 2 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 0 2 2 6 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 1 2 2 2 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 +torsion 1 2 2 6 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 +torsion 2 2 2 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 13 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 +torsion 6 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 6 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 +torsion 10 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 +torsion 6 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 +torsion 10 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 +torsion 0 2 10 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 10 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 13 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 6 2 20 2 -7.400 0.0 1 3.000 180.0 2 1.800 0.0 3 +torsion 6 2 20 6 -8.400 0.0 1 3.000 180.0 2 1.800 0.0 3 +torsion 4 3 3 4 1.600 0.0 1 3.200 180.0 2 0.000 0.0 3 +torsion 4 3 3 13 0.000 0.0 1 0.500 180.0 2 0.000 0.0 3 +torsion 4 3 3 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 3 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +#torsion 4 3 3 36 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 +torsion 13 3 3 13 0.700 0.0 1 -1.500 180.0 2 0.000 0.0 3 +torsion 13 3 3 24 -0.500 0.0 1 0.200 180.0 2 0.000 0.0 3 +torsion 13 3 3 46 0.800 0.0 1 -0.760 180.0 2 0.000 0.0 3 +torsion 24 3 3 46 -0.900 0.0 1 0.300 180.0 2 0.000 0.0 3 +torsion 46 3 3 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +#torsion 36 3 3 36 0.800 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 3 3 5 7 3.000 0.0 1 5.500 180.0 2 0.000 0.0 3 +torsion 4 3 5 7 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 13 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 +#torsion 13 3 5 7 3.200 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 24 3 5 7 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 46 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 +torsion 48 3 5 7 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 1 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 +torsion 3 3 13 46 0.000 0.0 1 0.000 180.0 2 0.085 0.0 3 +torsion 4 3 13 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +#torsion 4 3 13 13 0.000 0.0 1 1.166 180.0 2 0.000 0.0 3 +#torsion 4 3 13 13 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 +#torsion 4 3 13 13 -0.750 0.0 1 -0.550 180.0 2 -0.250 0.0 3 +#torsion 4 3 13 13 -0.277 0.0 1 1.228 180.0 2 -0.694 0.0 3 +#torsion 4 3 13 13 -1.000 0.0 1 -1.900 180.0 2 -0.900 0.0 3 +torsion 4 3 13 21 -0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 +torsion 4 3 13 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 48 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 +torsion 5 3 13 13 0.000 0.0 1 1.412 180.0 2 0.000 0.0 3 +#torsion 5 3 13 13 1.000 0.0 1 0.546 180.0 2 0.450 0.0 3 +torsion 5 3 13 44 5.260 0.0 1 0.820 180.0 2 0.000 0.0 3 +torsion 5 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 3 13 13 1.454 0.0 1 -0.144 180.0 2 -0.775 0.0 3 +torsion 13 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3 +torsion 20 3 13 13 0.000 0.0 1 0.000 180.0 2 -0.553 0.0 3 +torsion 20 3 13 46 0.000 0.0 1 0.000 180.0 2 0.132 0.0 3 +torsion 21 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 21 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 +torsion 24 3 13 13 1.173 0.0 1 0.189 180.0 2 -1.200 0.0 3 +#torsion 35 3 13 13 3.250 0.0 1 -0.402 180.0 2 -0.136 0.0 3 +#torsion 35 3 13 13 3.260 0.0 1 0.440 180.0 2 0.600 0.0 3 +torsion 24 3 13 21 0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 24 3 13 24 1.816 0.0 1 1.222 180.0 2 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180.0 2 0.000 0.0 3 +torsion 46 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 46 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 46 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 48 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 48 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 48 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 50 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 50 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 109 109 109 109 1.423 0.0 1 4.055 180.0 2 0.858 0.0 3 + + + ################################################################ + ## ## + ## Additional Torsional Parameter Values Used with OPLS-AA ## + ## ## + ## The torsions listed below were added to official OPLS-AA ## + ## to complete the set needed for proteins; the values were ## + ## obtained by analogy from the closest OPLS-AA torsions; ## + ## most of the added values are for HIP or N-terminal AAs; ## + ## ## + 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180.0 2 0.462 0.0 3 +torsion 53 13 13 85 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 3 13 53 13 1.438 0.0 1 -0.124 180.0 2 0.264 0.0 3 +torsion 3 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3 +torsion 13 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3 +torsion 46 13 55 54 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 13 85 57 1.700 0.0 1 -0.600 180.0 2 0.000 0.0 3 +torsion 46 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 55 48 55 54 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3 +torsion 0 48 81 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 +torsion 0 57 85 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 0 85 85 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 + + + ################################################################ + ## ## + ## Additional Torsional Parameter Values Used with OPLS-AA ## + ## ## + ## The torsions listed below were added to official OPLS-AA ## + ## to complete the values needed for selected organics ## + ## ## + ################################################################ + + +torsion 13 13 13 20 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 +torsion 13 13 13 47 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 + + + ######################################## + ## ## + ## Atomic Partial Charge Parameters ## + ## ## + ######################################## + + +charge 1 -0.2200 +charge 2 0.2200 +charge 3 0.5500 +charge 4 -0.5000 +charge 5 -0.5800 +charge 6 0.0800 +charge 7 0.4500 +charge 8 0.0000 +charge 9 0.0000 +charge 10 0.0000 +charge 11 0.0000 +charge 12 0.0000 +charge 13 0.0000 +charge 14 0.0000 +charge 15 0.0000 +charge 16 0.0000 +charge 17 0.0000 +charge 18 0.0000 +charge 19 0.0000 +charge 20 -0.7000 +charge 21 0.4350 +charge 22 0.2650 +charge 23 0.2650 +charge 24 -0.4700 +charge 25 -0.4500 +charge 26 -0.4700 +charge 27 -0.3000 +charge 28 0.2350 +charge 29 0.2700 +charge 30 0.1800 +charge 31 0.1800 +charge 32 0.2350 +charge 33 0.2350 +charge 34 0.3000 +charge 35 0.3000 +charge 36 -0.4300 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0.1000 +charge 814 -0.2500 +charge 815 0.6000 +charge 816 -0.1500 +charge 817 -0.0250 +charge 818 -0.0450 +charge 819 0.1450 +charge 820 0.8880 +charge 821 1.0030 +charge 822 -0.6580 +charge 823 -0.6340 +charge 824 0.4110 +charge 825 -0.4420 +charge 826 0.4350 +charge 827 0.2250 +charge 828 0.2550 +charge 829 -0.0340 +charge 830 0.0030 +charge 831 0.3000 +charge 832 -0.0400 +charge 833 -0.0575 +charge 834 2.0000 +charge 835 -0.0700 +charge 836 0.0300 +charge 837 0.1300 +charge 838 -0.1300 +charge 839 0.1000 +charge 840 -0.6850 +charge 841 0.1550 +charge 842 -0.1000 +charge 843 -0.4270 +charge 844 0.2180 +charge 845 0.6000 +charge 846 -0.6000 +charge 847 -0.3600 +charge 848 0.0000 +charge 849 0.0600 +charge 850 0.1200 +charge 851 0.1800 +charge 852 0.0600 +charge 853 0.5700 +charge 854 -0.5700 +charge 855 0.0000 +charge 856 0.0200 +charge 857 -0.0400 +charge 858 0.0000 +charge 859 0.0600 +charge 860 -0.0700 +charge 861 -0.1400 +charge 862 0.1700 +charge 863 0.1100 +charge 864 0.1500 +charge 865 0.1700 +charge 866 1.0000 +charge 867 0.8500 +charge 868 0.7000 +charge 869 0.5500 +charge 870 -0.1000 +charge 871 -0.4300 +charge 872 -0.3700 +charge 873 -0.3100 +charge 874 -0.2500 +charge 875 -1.0000 +charge 876 -1.0000 +charge 877 -1.0000 +charge 878 -1.0000 +charge 879 1.0000 +charge 880 1.0000 +charge 881 1.0000 +charge 882 1.0000 +charge 883 1.0000 +charge 884 2.0000 +charge 885 2.0000 +charge 886 2.0000 +charge 887 2.0000 +charge 888 -0.0500 +charge 889 0.0500 +charge 890 0.1500 +charge 891 0.2500 +charge 892 0.1000 +charge 893 0.1150 +charge 894 0.1350 +charge 895 0.0150 +charge 896 0.1550 +charge 897 0.0000 +charge 898 -0.1150 +charge 899 0.1500 +charge 900 -0.2500 +charge 901 -0.1000 +charge 902 0.0500 +charge 903 -0.1000 +charge 904 0.2000 +charge 905 -0.2500 +charge 906 0.0880 + + + ######################################## + ## ## + ## Biopolymer Atom Type Conversions ## + ## ## + ######################################## + + +biotype 1 N "Glycine" 180 +biotype 2 CA "Glycine" 165 +biotype 3 C "Glycine" 177 +biotype 4 HN "Glycine" 183 +biotype 5 O "Glycine" 178 +biotype 6 HA "Glycine" 85 +biotype 7 N "Alanine" 180 +biotype 8 CA "Alanine" 166 +biotype 9 C "Alanine" 177 +biotype 10 HN "Alanine" 183 +biotype 11 O "Alanine" 178 +biotype 12 HA "Alanine" 85 +biotype 13 CB "Alanine" 80 +biotype 14 HB "Alanine" 85 +biotype 15 N "Valine" 180 +biotype 16 CA "Valine" 166 +biotype 17 C "Valine" 177 +biotype 18 HN "Valine" 183 +biotype 19 O "Valine" 178 +biotype 20 HA "Valine" 85 +biotype 21 CB "Valine" 82 +biotype 22 HB "Valine" 85 +biotype 23 CG1 "Valine" 80 +biotype 24 HG1 "Valine" 85 +biotype 25 CG2 "Valine" 80 +biotype 26 HG2 "Valine" 85 +biotype 27 N "Leucine" 180 +biotype 28 CA "Leucine" 166 +biotype 29 C "Leucine" 177 +biotype 30 HN "Leucine" 183 +biotype 31 O "Leucine" 178 +biotype 32 HA "Leucine" 85 +biotype 33 CB "Leucine" 81 +biotype 34 HB "Leucine" 85 +biotype 35 CG "Leucine" 82 +biotype 36 HG "Leucine" 85 +biotype 37 CD1 "Leucine" 80 +biotype 38 HD1 "Leucine" 85 +biotype 39 CD2 "Leucine" 80 +biotype 40 HD2 "Leucine" 85 +biotype 41 N "Isoleucine" 180 +biotype 42 CA "Isoleucine" 166 +biotype 43 C "Isoleucine" 177 +biotype 44 HN "Isoleucine" 183 +biotype 45 O "Isoleucine" 178 +biotype 46 HA "Isoleucine" 85 +biotype 47 CB "Isoleucine" 82 +biotype 48 HB "Isoleucine" 85 +biotype 49 CG1 "Isoleucine" 80 +biotype 50 HG1 "Isoleucine" 85 +biotype 51 CG2 "Isoleucine" 81 +biotype 52 HG2 "Isoleucine" 85 +biotype 53 CD "Isoleucine" 80 +biotype 54 HD "Isoleucine" 85 +biotype 55 N "Serine" 180 +biotype 56 CA "Serine" 166 +biotype 57 C "Serine" 177 +biotype 58 HN "Serine" 183 +biotype 59 O "Serine" 178 +biotype 60 HA "Serine" 85 +biotype 61 CB "Serine" 99 +biotype 62 HB "Serine" 85 +biotype 63 OG "Serine" 96 +biotype 64 HG "Serine" 97 +biotype 65 N "Threonine" 180 +biotype 66 CA "Threonine" 166 +biotype 67 C "Threonine" 177 +biotype 68 HN "Threonine" 183 +biotype 69 O "Threonine" 178 +biotype 70 HA "Threonine" 85 +biotype 71 CB "Threonine" 100 +biotype 72 HB "Threonine" 85 +biotype 73 OG1 "Threonine" 96 +biotype 74 HG1 "Threonine" 97 +biotype 75 CG2 "Threonine" 80 +biotype 76 HG2 "Threonine" 85 +biotype 77 N "Cysteine (SH)" 180 +biotype 78 CA "Cysteine (SH)" 166 +biotype 79 C "Cysteine (SH)" 177 +biotype 80 HN "Cysteine (SH)" 183 +biotype 81 O "Cysteine (SH)" 178 +biotype 82 HA "Cysteine (SH)" 85 +biotype 83 CB "Cysteine (SH)" 148 +biotype 84 HB "Cysteine (SH)" 85 +biotype 85 SG "Cysteine (SH)" 142 +biotype 86 HG "Cysteine (SH)" 146 +biotype 87 N "Cystine (SS)" 180 +biotype 88 CA "Cystine (SS)" 166 +biotype 89 C "Cystine (SS)" 177 +biotype 90 HN "Cystine (SS)" 183 +biotype 91 O "Cystine (SS)" 178 +biotype 92 HA "Cystine (SS)" 85 +biotype 93 CB "Cystine (SS)" 156 +biotype 94 HB "Cystine (SS)" 85 +biotype 95 SG "Cystine (SS)" 145 +biotype 96 N "Cysteine (S-)" -1 +biotype 97 CA "Cysteine (S-)" -1 +biotype 98 C "Cysteine (S-)" -1 +biotype 99 HN "Cysteine (S-)" -1 +biotype 100 O "Cysteine (S-)" -1 +biotype 101 HA "Cysteine (S-)" -1 +biotype 102 CB "Cysteine (S-)" -1 +biotype 103 HB "Cysteine (S-)" -1 +biotype 104 SG "Cysteine (S-)" -1 +biotype 105 N "Proline" 181 +biotype 106 CA "Proline" 188 +biotype 107 C "Proline" 177 +biotype 108 O "Proline" 178 +biotype 109 HA "Proline" 85 +biotype 110 CB "Proline" 81 +biotype 111 HB "Proline" 85 +biotype 112 CG "Proline" 81 +biotype 113 HG "Proline" 85 +biotype 114 CD "Proline" 187 +biotype 115 HD "Proline" 85 +biotype 116 N "Phenylalanine" 180 +biotype 117 CA "Phenylalanine" 166 +biotype 118 C "Phenylalanine" 177 +biotype 119 HN "Phenylalanine" 183 +biotype 120 O "Phenylalanine" 178 +biotype 121 HA "Phenylalanine" 85 +biotype 122 CB "Phenylalanine" 94 +biotype 123 HB "Phenylalanine" 85 +biotype 124 CG "Phenylalanine" 90 +biotype 125 CD "Phenylalanine" 90 +biotype 126 HD "Phenylalanine" 91 +biotype 127 CE "Phenylalanine" 90 +biotype 128 HE "Phenylalanine" 91 +biotype 129 CZ "Phenylalanine" 90 +biotype 130 HZ "Phenylalanine" 91 +biotype 131 N "Tyrosine" 180 +biotype 132 CA "Tyrosine" 166 +biotype 133 C "Tyrosine" 177 +biotype 134 HN "Tyrosine" 183 +biotype 135 O "Tyrosine" 178 +biotype 136 HA "Tyrosine" 85 +biotype 137 CB "Tyrosine" 94 +biotype 138 HB "Tyrosine" 85 +biotype 139 CG "Tyrosine" 90 +biotype 140 CD "Tyrosine" 90 +biotype 141 HD "Tyrosine" 91 +biotype 142 CE "Tyrosine" 90 +biotype 143 HE "Tyrosine" 91 +biotype 144 CZ "Tyrosine" 108 +biotype 145 OH "Tyrosine" 109 +biotype 146 HH "Tyrosine" 110 +biotype 147 N "Tyrosine (O-)" -1 +biotype 148 CA "Tyrosine (O-)" -1 +biotype 149 C "Tyrosine (O-)" -1 +biotype 150 HN "Tyrosine (O-)" -1 +biotype 151 O "Tyrosine (O-)" -1 +biotype 152 HA "Tyrosine (O-)" -1 +biotype 153 CB "Tyrosine (O-)" -1 +biotype 154 HB "Tyrosine (O-)" -1 +biotype 155 CG "Tyrosine (O-)" -1 +biotype 156 CD "Tyrosine (O-)" -1 +biotype 157 HD "Tyrosine (O-)" -1 +biotype 158 CE "Tyrosine (O-)" -1 +biotype 159 HE "Tyrosine (O-)" -1 +biotype 160 CZ "Tyrosine (O-)" -1 +biotype 161 OH "Tyrosine (O-)" -1 +biotype 162 N "Tryptophan" 180 +biotype 163 CA "Tryptophan" 166 +biotype 164 C "Tryptophan" 177 +biotype 165 HN "Tryptophan" 183 +biotype 166 O "Tryptophan" 178 +biotype 167 HA "Tryptophan" 85 +biotype 168 CB "Tryptophan" 81 +biotype 169 HB "Tryptophan" 85 +biotype 170 CG "Tryptophan" 441 +biotype 171 CD1 "Tryptophan" 455 +biotype 172 HD1 "Tryptophan" 91 +biotype 173 CD2 "Tryptophan" 442 +biotype 174 NE1 "Tryptophan" 444 +biotype 175 HE1 "Tryptophan" 445 +biotype 176 CE2 "Tryptophan" 443 +biotype 177 CE3 "Tryptophan" 90 +biotype 178 HE3 "Tryptophan" 91 +biotype 179 CZ2 "Tryptophan" 90 +biotype 180 HZ2 "Tryptophan" 91 +biotype 181 CZ3 "Tryptophan" 90 +biotype 182 HZ3 "Tryptophan" 91 +biotype 183 CH2 "Tryptophan" 90 +biotype 184 HH2 "Tryptophan" 91 +biotype 185 N "Histidine (+)" 180 +biotype 186 CA "Histidine (+)" 166 +biotype 187 C "Histidine (+)" 177 +biotype 188 HN "Histidine (+)" 183 +biotype 189 O "Histidine (+)" 178 +biotype 190 HA "Histidine (+)" 85 +biotype 191 CB "Histidine (+)" 446 +biotype 192 HB "Histidine (+)" 85 +biotype 193 CG "Histidine (+)" 451 +biotype 194 ND1 "Histidine (+)" 453 +biotype 195 HD1 "Histidine (+)" 454 +biotype 196 CD2 "Histidine (+)" 451 +biotype 197 HD2 "Histidine (+)" 91 +biotype 198 CE1 "Histidine (+)" 450 +biotype 199 HE1 "Histidine (+)" 91 +biotype 200 NE2 "Histidine (+)" 453 +biotype 201 HE2 "Histidine (+)" 454 +biotype 202 N "Histidine (HD)" 180 +biotype 203 CA "Histidine (HD)" 166 +biotype 204 C "Histidine (HD)" 177 +biotype 205 HN "Histidine (HD)" 183 +biotype 206 O "Histidine (HD)" 178 +biotype 207 HA "Histidine (HD)" 85 +biotype 208 CB "Histidine (HD)" 446 +biotype 209 HB "Histidine (HD)" 85 +biotype 210 CG "Histidine (HD)" 449 +biotype 211 ND1 "Histidine (HD)" 444 +biotype 212 HD1 "Histidine (HD)" 445 +biotype 213 CD2 "Histidine (HD)" 448 +biotype 214 HD2 "Histidine (HD)" 91 +biotype 215 CE1 "Histidine (HD)" 447 +biotype 216 HE1 "Histidine (HD)" 91 +biotype 217 NE2 "Histidine (HD)" 452 +biotype 218 N "Histidine (HE)" 180 +biotype 219 CA "Histidine (HE)" 166 +biotype 220 C "Histidine (HE)" 177 +biotype 221 HN "Histidine (HE)" 183 +biotype 222 O "Histidine (HE)" 178 +biotype 223 HA "Histidine (HE)" 85 +biotype 224 CB "Histidine (HE)" 446 +biotype 225 HB "Histidine (HE)" 85 +biotype 226 CG "Histidine (HE)" 448 +biotype 227 ND1 "Histidine (HE)" 452 +biotype 228 CD2 "Histidine (HE)" 449 +biotype 229 HD2 "Histidine (HE)" 91 +biotype 230 CE1 "Histidine (HE)" 447 +biotype 231 HE1 "Histidine (HE)" 91 +biotype 232 NE2 "Histidine (HE)" 444 +biotype 233 HE2 "Histidine (HE)" 445 +biotype 234 N "Aspartic Acid" 180 +biotype 235 CA "Aspartic Acid" 166 +biotype 236 C "Aspartic Acid" 177 +biotype 237 HN "Aspartic Acid" 183 +biotype 238 O "Aspartic Acid" 178 +biotype 239 HA "Aspartic Acid" 85 +biotype 240 CB "Aspartic Acid" 216 +biotype 241 HB "Aspartic Acid" 85 +biotype 242 CG "Aspartic Acid" 213 +biotype 243 OD "Aspartic Acid" 214 +biotype 244 N "Aspartic Acid (COOH)" -1 +biotype 245 CA "Aspartic Acid (COOH)" -1 +biotype 246 C "Aspartic Acid (COOH)" -1 +biotype 247 HN "Aspartic Acid (COOH)" -1 +biotype 248 O "Aspartic Acid (COOH)" -1 +biotype 249 HA "Aspartic Acid (COOH)" -1 +biotype 250 CB "Aspartic Acid (COOH)" -1 +biotype 251 HB "Aspartic Acid (COOH)" -1 +biotype 252 CG "Aspartic Acid (COOH)" -1 +biotype 253 OD1 "Aspartic Acid (COOH)" -1 +biotype 254 OD2 "Aspartic Acid (COOH)" -1 +biotype 255 HD2 "Aspartic Acid (COOH)" -1 +biotype 256 N "Asparagine" 180 +biotype 257 CA "Asparagine" 166 +biotype 258 C "Asparagine" 177 +biotype 259 HN "Asparagine" 183 +biotype 260 O "Asparagine" 178 +biotype 261 HA "Asparagine" 85 +biotype 262 CB "Asparagine" 81 +biotype 263 HB "Asparagine" 85 +biotype 264 CG "Asparagine" 177 +biotype 265 OD1 "Asparagine" 178 +biotype 266 ND2 "Asparagine" 179 +biotype 267 HD2 "Asparagine" 182 +biotype 268 N "Glutamic Acid" 180 +biotype 269 CA "Glutamic Acid" 166 +biotype 270 C "Glutamic Acid" 177 +biotype 271 HN "Glutamic Acid" 183 +biotype 272 O "Glutamic Acid" 178 +biotype 273 HA "Glutamic Acid" 85 +biotype 274 CB "Glutamic Acid" 81 +biotype 275 HB "Glutamic Acid" 85 +biotype 276 CG "Glutamic Acid" 216 +biotype 277 HG "Glutamic Acid" 85 +biotype 278 CD "Glutamic Acid" 213 +biotype 279 OE "Glutamic Acid" 214 +biotype 280 N "Glutamic Acid (COOH)" -1 +biotype 281 CA "Glutamic Acid (COOH)" -1 +biotype 282 C "Glutamic Acid (COOH)" -1 +biotype 283 HN "Glutamic Acid (COOH)" -1 +biotype 284 O "Glutamic Acid (COOH)" -1 +biotype 285 HA "Glutamic Acid (COOH)" -1 +biotype 286 CB "Glutamic Acid (COOH)" -1 +biotype 287 HB "Glutamic Acid (COOH)" -1 +biotype 288 CG "Glutamic Acid (COOH)" -1 +biotype 289 HG "Glutamic Acid (COOH)" -1 +biotype 290 CD "Glutamic Acid (COOH)" -1 +biotype 291 OE1 "Glutamic Acid (COOH)" -1 +biotype 292 OE2 "Glutamic Acid (COOH)" -1 +biotype 293 HE2 "Glutamic Acid (COOH)" -1 +biotype 294 N "Glutamine" 180 +biotype 295 CA "Glutamine" 166 +biotype 296 C "Glutamine" 177 +biotype 297 HN "Glutamine" 183 +biotype 298 O "Glutamine" 178 +biotype 299 HA "Glutamine" 85 +biotype 300 CB "Glutamine" 81 +biotype 301 HB "Glutamine" 85 +biotype 302 CG "Glutamine" 81 +biotype 303 HG "Glutamine" 85 +biotype 304 CD "Glutamine" 177 +biotype 305 OE1 "Glutamine" 178 +biotype 306 NE2 "Glutamine" 179 +biotype 307 HE2 "Glutamine" 182 +biotype 308 N "Methionine" 180 +biotype 309 CA "Methionine" 166 +biotype 310 C "Methionine" 177 +biotype 311 HN "Methionine" 183 +biotype 312 O "Methionine" 178 +biotype 313 HA "Methionine" 85 +biotype 314 CB "Methionine" 81 +biotype 315 HB "Methionine" 85 +biotype 316 CG "Methionine" 152 +biotype 317 HG "Methionine" 85 +biotype 318 SD "Methionine" 144 +biotype 319 CE "Methionine" 151 +biotype 320 HE "Methionine" 85 +biotype 321 N "Lysine" 180 +biotype 322 CA "Lysine" 166 +biotype 323 C "Lysine" 177 +biotype 324 HN "Lysine" 183 +biotype 325 O "Lysine" 178 +biotype 326 HA "Lysine" 85 +biotype 327 CB "Lysine" 81 +biotype 328 HB "Lysine" 85 +biotype 329 CG "Lysine" 81 +biotype 330 HG "Lysine" 85 +biotype 331 CD "Lysine" 81 +biotype 332 HD "Lysine" 85 +biotype 333 CE "Lysine" 235 +biotype 334 HE "Lysine" 85 +biotype 335 NZ "Lysine" 230 +biotype 336 HZ "Lysine" 233 +biotype 337 N "Lysine (NH2)" -1 +biotype 338 CA "Lysine (NH2)" -1 +biotype 339 C "Lysine (NH2)" -1 +biotype 340 HN "Lysine (NH2)" -1 +biotype 341 O "Lysine (NH2)" -1 +biotype 342 HA "Lysine (NH2)" -1 +biotype 343 CB "Lysine (NH2)" -1 +biotype 344 HB "Lysine (NH2)" -1 +biotype 345 CG "Lysine (NH2)" -1 +biotype 346 HG "Lysine (NH2)" -1 +biotype 347 CD "Lysine (NH2)" -1 +biotype 348 HD "Lysine (NH2)" -1 +biotype 349 CE "Lysine (NH2)" -1 +biotype 350 HE "Lysine (NH2)" -1 +biotype 351 NZ "Lysine (NH2)" -1 +biotype 352 HZ "Lysine (NH2)" -1 +biotype 353 N "Arginine" 180 +biotype 354 CA "Arginine" 166 +biotype 355 C "Arginine" 177 +biotype 356 HN "Arginine" 183 +biotype 357 O "Arginine" 178 +biotype 358 HA "Arginine" 85 +biotype 359 CB "Arginine" 81 +biotype 360 HB "Arginine" 85 +biotype 361 CG "Arginine" 251 +biotype 362 HG "Arginine" 85 +biotype 363 CD "Arginine" 250 +biotype 364 HD "Arginine" 85 +biotype 365 NE "Arginine" 246 +biotype 366 HE "Arginine" 247 +biotype 367 CZ "Arginine" 245 +biotype 368 NH "Arginine" 243 +biotype 369 HH "Arginine" 244 +biotype 370 N "Ornithine" 180 +biotype 371 CA "Ornithine" 166 +biotype 372 C "Ornithine" 177 +biotype 373 HN "Ornithine" 183 +biotype 374 O "Ornithine" 178 +biotype 375 HA "Ornithine" 85 +biotype 376 CB "Ornithine" 81 +biotype 377 HB "Ornithine" 85 +biotype 378 CG "Ornithine" 81 +biotype 379 HG "Ornithine" 85 +biotype 380 CD "Ornithine" 235 +biotype 381 HD "Ornithine" 85 +biotype 382 NE "Ornithine" 230 +biotype 383 HE "Ornithine" 233 +biotype 384 N "MethylAlanine (AIB)" 180 +biotype 385 CA "MethylAlanine (AIB)" 167 +biotype 386 C "MethylAlanine (AIB)" 177 +biotype 387 HN "MethylAlanine (AIB)" 183 +biotype 388 O "MethylAlanine (AIB)" 178 +biotype 389 CB "MethylAlanine (AIB)" 80 +biotype 390 HB "MethylAlanine (AIB)" 85 +biotype 391 N "Pyroglutamic Acid" 180 +biotype 392 CA "Pyroglutamic Acid" 166 +biotype 393 C "Pyroglutamic Acid" 177 +biotype 394 HN "Pyroglutamic Acid" 183 +biotype 395 O "Pyroglutamic Acid" 178 +biotype 396 HA "Pyroglutamic Acid" 85 +biotype 397 CB "Pyroglutamic Acid" 81 +biotype 398 HB "Pyroglutamic Acid" 85 +biotype 399 CG "Pyroglutamic Acid" 216 +biotype 400 HG "Pyroglutamic Acid" 85 +biotype 401 CD "Pyroglutamic Acid" 177 +biotype 402 OE "Pyroglutamic Acid" 178 +biotype 403 N "N-Terminal GLY" 230 +biotype 404 CA "N-Terminal GLY" 235 +biotype 405 C "N-Terminal GLY" 177 +biotype 406 HN "N-Terminal GLY" 233 +biotype 407 O "N-Terminal GLY" 178 +biotype 408 HA "N-Terminal GLY" 85 +biotype 409 N "N-Terminal ALA" 230 +biotype 410 CA "N-Terminal ALA" 236 +biotype 411 C "N-Terminal ALA" 177 +biotype 412 HN "N-Terminal ALA" 233 +biotype 413 O "N-Terminal ALA" 178 +biotype 414 HA "N-Terminal ALA" 85 +biotype 415 N "N-Terminal VAL" 230 +biotype 416 CA "N-Terminal VAL" 236 +biotype 417 C "N-Terminal VAL" 177 +biotype 418 HN "N-Terminal VAL" 233 +biotype 419 O "N-Terminal VAL" 178 +biotype 420 HA "N-Terminal VAL" 85 +biotype 421 N "N-Terminal LEU" 230 +biotype 422 CA "N-Terminal LEU" 236 +biotype 423 C "N-Terminal LEU" 177 +biotype 424 HN "N-Terminal LEU" 233 +biotype 425 O "N-Terminal LEU" 178 +biotype 426 HA "N-Terminal LEU" 85 +biotype 427 N "N-Terminal ILE" 230 +biotype 428 CA "N-Terminal ILE" 236 +biotype 429 C "N-Terminal ILE" 177 +biotype 430 HN "N-Terminal ILE" 233 +biotype 431 O "N-Terminal ILE" 178 +biotype 432 HA "N-Terminal ILE" 85 +biotype 433 N "N-Terminal SER" 230 +biotype 434 CA "N-Terminal SER" 236 +biotype 435 C "N-Terminal SER" 177 +biotype 436 HN "N-Terminal SER" 233 +biotype 437 O "N-Terminal SER" 178 +biotype 438 HA "N-Terminal SER" 85 +biotype 439 N "N-Terminal THR" 230 +biotype 440 CA "N-Terminal THR" 236 +biotype 441 C "N-Terminal THR" 177 +biotype 442 HN "N-Terminal THR" 233 +biotype 443 O "N-Terminal THR" 178 +biotype 444 HA "N-Terminal THR" 85 +biotype 445 N "N-Terminal CYS (SH)" 230 +biotype 446 CA "N-Terminal CYS (SH)" 236 +biotype 447 C "N-Terminal CYS (SH)" 177 +biotype 448 HN "N-Terminal CYS (SH)" 233 +biotype 449 O "N-Terminal CYS (SH)" 178 +biotype 450 HA "N-Terminal CYS (SH)" 85 +biotype 451 N "N-Terminal CYX (SS)" 230 +biotype 452 CA "N-Terminal CYX (SS)" 236 +biotype 453 C "N-Terminal CYX (SS)" 177 +biotype 454 HN "N-Terminal CYX (SS)" 233 +biotype 455 O "N-Terminal CYX (SS)" 178 +biotype 456 HA "N-Terminal CYX (SS)" 85 +biotype 457 N "N-Terminal CYD (S-)" -1 +biotype 458 CA "N-Terminal CYD (S-)" -1 +biotype 459 C "N-Terminal CYD (S-)" -1 +biotype 460 HN "N-Terminal CYD (S-)" -1 +biotype 461 O "N-Terminal CYD (S-)" -1 +biotype 462 HA "N-Terminal CYD (S-)" -1 +biotype 463 N "N-Terminal PRO" 252 +biotype 464 CA "N-Terminal PRO" 238 +biotype 465 C "N-Terminal PRO" 177 +biotype 466 HN "N-Terminal PRO" 253 +biotype 467 O "N-Terminal PRO" 178 +biotype 468 HA "N-Terminal PRO" 85 +biotype 469 CD "N-Terminal PRO" 239 +biotype 470 HD "N-Terminal PRO" 85 +biotype 471 N "N-Terminal PHE" 230 +biotype 472 CA "N-Terminal PHE" 236 +biotype 473 C "N-Terminal PHE" 177 +biotype 474 HN "N-Terminal PHE" 233 +biotype 475 O "N-Terminal PHE" 178 +biotype 476 HA "N-Terminal PHE" 85 +biotype 477 N "N-Terminal TYR" 230 +biotype 478 CA "N-Terminal TYR" 236 +biotype 479 C "N-Terminal TYR" 177 +biotype 480 HN "N-Terminal TYR" 233 +biotype 481 O "N-Terminal TYR" 178 +biotype 482 HA "N-Terminal TYR" 85 +biotype 483 N "N-Terminal TYD (O-)" -1 +biotype 484 CA "N-Terminal TYD (O-)" -1 +biotype 485 C "N-Terminal TYD (O-)" -1 +biotype 486 HN "N-Terminal TYD (O-)" -1 +biotype 487 O "N-Terminal TYD (O-)" -1 +biotype 488 HA "N-Terminal TYD (O-)" -1 +biotype 489 N "N-Terminal TRP" 230 +biotype 490 CA "N-Terminal TRP" 236 +biotype 491 C "N-Terminal TRP" 177 +biotype 492 HN "N-Terminal TRP" 233 +biotype 493 O "N-Terminal TRP" 178 +biotype 494 HA "N-Terminal TRP" 85 +biotype 495 N "N-Terminal HIS (+)" 230 +biotype 496 CA "N-Terminal HIS (+)" 236 +biotype 497 C "N-Terminal HIS (+)" 177 +biotype 498 HN "N-Terminal HIS (+)" 233 +biotype 499 O "N-Terminal HIS (+)" 178 +biotype 500 HA "N-Terminal HIS (+)" 85 +biotype 501 N "N-Terminal HIS (HD)" 230 +biotype 502 CA "N-Terminal HIS (HD)" 236 +biotype 503 C "N-Terminal HIS (HD)" 177 +biotype 504 HN "N-Terminal HIS (HD)" 233 +biotype 505 O "N-Terminal HIS (HD)" 178 +biotype 506 HA "N-Terminal HIS (HD)" 85 +biotype 507 N "N-Terminal HIS (HE)" 230 +biotype 508 CA "N-Terminal HIS (HE)" 236 +biotype 509 C "N-Terminal HIS (HE)" 177 +biotype 510 HN "N-Terminal HIS (HE)" 233 +biotype 511 O "N-Terminal HIS (HE)" 178 +biotype 512 HA "N-Terminal HIS (HE)" 85 +biotype 513 N "N-Terminal ASP" 230 +biotype 514 CA "N-Terminal ASP" 236 +biotype 515 C "N-Terminal ASP" 177 +biotype 516 HN "N-Terminal ASP" 233 +biotype 517 O "N-Terminal ASP" 178 +biotype 518 HA "N-Terminal ASP" 85 +biotype 519 N "N-Terminal ASH (COOH)" -1 +biotype 520 CA "N-Terminal ASH (COOH)" -1 +biotype 521 C "N-Terminal ASH (COOH)" -1 +biotype 522 HN "N-Terminal ASH (COOH)" -1 +biotype 523 O "N-Terminal ASH (COOH)" -1 +biotype 524 HA "N-Terminal ASH (COOH)" -1 +biotype 525 N "N-Terminal ASN" 230 +biotype 526 CA "N-Terminal ASN" 236 +biotype 527 C "N-Terminal ASN" 177 +biotype 528 HN "N-Terminal ASN" 233 +biotype 529 O "N-Terminal ASN" 178 +biotype 530 HA "N-Terminal ASN" 85 +biotype 531 N "N-Terminal GLU" 230 +biotype 532 CA "N-Terminal GLU" 236 +biotype 533 C "N-Terminal GLU" 177 +biotype 534 HN "N-Terminal GLU" 233 +biotype 535 O "N-Terminal GLU" 178 +biotype 536 HA "N-Terminal GLU" 85 +biotype 537 N "N-Terminal GLH (COOH)" -1 +biotype 538 CA "N-Terminal GLH (COOH)" -1 +biotype 539 C "N-Terminal GLH (COOH)" -1 +biotype 540 HN "N-Terminal GLH (COOH)" -1 +biotype 541 O "N-Terminal GLH (COOH)" -1 +biotype 542 HA "N-Terminal GLH (COOH)" -1 +biotype 543 N "N-Terminal GLN" 230 +biotype 544 CA "N-Terminal GLN" 236 +biotype 545 C "N-Terminal GLN" 177 +biotype 546 HN "N-Terminal GLN" 233 +biotype 547 O "N-Terminal GLN" 178 +biotype 548 HA "N-Terminal GLN" 85 +biotype 549 N "N-Terminal MET" 230 +biotype 550 CA "N-Terminal MET" 236 +biotype 551 C "N-Terminal MET" 177 +biotype 552 HN "N-Terminal MET" 233 +biotype 553 O "N-Terminal MET" 178 +biotype 554 HA "N-Terminal MET" 85 +biotype 555 N "N-Terminal LYS" 230 +biotype 556 CA "N-Terminal LYS" 236 +biotype 557 C "N-Terminal LYS" 177 +biotype 558 HN "N-Terminal LYS" 233 +biotype 559 O "N-Terminal LYS" 178 +biotype 560 HA "N-Terminal LYS" 85 +biotype 561 N "N-Terminal LYD (NH2)" -1 +biotype 562 CA "N-Terminal LYD (NH2)" -1 +biotype 563 C "N-Terminal LYD (NH2)" -1 +biotype 564 HN "N-Terminal LYD (NH2)" -1 +biotype 565 O "N-Terminal LYD (NH2)" -1 +biotype 566 HA "N-Terminal LYD (NH2)" -1 +biotype 567 N "N-Terminal ARG" 230 +biotype 568 CA "N-Terminal ARG" 236 +biotype 569 C "N-Terminal ARG" 177 +biotype 570 HN "N-Terminal ARG" 233 +biotype 571 O "N-Terminal ARG" 178 +biotype 572 HA "N-Terminal ARG" 85 +biotype 573 N "N-Terminal ORN" 230 +biotype 574 CA "N-Terminal ORN" 236 +biotype 575 C "N-Terminal ORN" 177 +biotype 576 HN "N-Terminal ORN" 233 +biotype 577 O "N-Terminal ORN" 178 +biotype 578 HA "N-Terminal ORN" 85 +biotype 579 N "N-Terminal AIB" 230 +biotype 580 CA "N-Terminal AIB" 237 +biotype 581 C "N-Terminal AIB" 177 +biotype 582 HN "N-Terminal AIB" 233 +biotype 583 O "N-Terminal AIB" 178 +biotype 584 N "C-Terminal GLY" 180 +biotype 585 CA "C-Terminal GLY" 226 +biotype 586 C "C-Terminal GLY" 213 +biotype 587 HN "C-Terminal GLY" 183 +biotype 588 OXT "C-Terminal GLY" 214 +biotype 589 HA "C-Terminal GLY" 85 +biotype 590 N "C-Terminal ALA" 180 +biotype 591 CA "C-Terminal ALA" 225 +biotype 592 C "C-Terminal ALA" 213 +biotype 593 HN "C-Terminal ALA" 183 +biotype 594 OXT "C-Terminal ALA" 214 +biotype 595 HA "C-Terminal ALA" 85 +biotype 596 N "C-Terminal VAL" 180 +biotype 597 CA "C-Terminal VAL" 225 +biotype 598 C "C-Terminal VAL" 213 +biotype 599 HN "C-Terminal VAL" 183 +biotype 600 OXT "C-Terminal VAL" 214 +biotype 601 HA "C-Terminal VAL" 85 +biotype 602 N "C-Terminal LEU" 180 +biotype 603 CA "C-Terminal LEU" 225 +biotype 604 C "C-Terminal LEU" 213 +biotype 605 HN "C-Terminal LEU" 183 +biotype 606 OXT "C-Terminal LEU" 214 +biotype 607 HA "C-Terminal LEU" 85 +biotype 608 N "C-Terminal ILE" 180 +biotype 609 CA "C-Terminal ILE" 225 +biotype 610 C "C-Terminal ILE" 213 +biotype 611 HN "C-Terminal ILE" 183 +biotype 612 OXT "C-Terminal ILE" 214 +biotype 613 HA "C-Terminal ILE" 85 +biotype 614 N "C-Terminal SER" 180 +biotype 615 CA "C-Terminal SER" 225 +biotype 616 C "C-Terminal SER" 213 +biotype 617 HN "C-Terminal SER" 183 +biotype 618 OXT "C-Terminal SER" 214 +biotype 619 HA "C-Terminal SER" 85 +biotype 620 N "C-Terminal THR" 180 +biotype 621 CA "C-Terminal THR" 225 +biotype 622 C "C-Terminal THR" 213 +biotype 623 HN "C-Terminal THR" 183 +biotype 624 OXT "C-Terminal THR" 214 +biotype 625 HA "C-Terminal THR" 85 +biotype 626 N "C-Terminal CYS (SH)" 180 +biotype 627 CA "C-Terminal CYS (SH)" 225 +biotype 628 C "C-Terminal CYS (SH)" 213 +biotype 629 HN "C-Terminal CYS (SH)" 183 +biotype 630 OXT "C-Terminal CYS (SH)" 214 +biotype 631 HA "C-Terminal CYS (SH)" 85 +biotype 632 N "C-Terminal CYX (SS)" 180 +biotype 633 CA "C-Terminal CYX (SS)" 225 +biotype 634 C "C-Terminal CYX (SS)" 213 +biotype 635 HN "C-Terminal CYX (SS)" 183 +biotype 636 OXT "C-Terminal CYX (SS)" 214 +biotype 637 HA "C-Terminal CYX (SS)" 85 +biotype 638 N "C-Terminal CYD (S-)" -1 +biotype 639 CA "C-Terminal CYD (S-)" -1 +biotype 640 C "C-Terminal CYD (S-)" -1 +biotype 641 HN "C-Terminal CYD (S-)" -1 +biotype 642 OXT "C-Terminal CYD (S-)" -1 +biotype 643 HA "C-Terminal CYD (S-)" -1 +biotype 644 N "C-Terminal PRO" 181 +biotype 645 CA "C-Terminal PRO" 228 +biotype 646 C "C-Terminal PRO" 213 +biotype 647 OXT "C-Terminal PRO" 214 +biotype 648 HA "C-Terminal PRO" 85 +biotype 649 N "C-Terminal PHE" 180 +biotype 650 CA "C-Terminal PHE" 225 +biotype 651 C "C-Terminal PHE" 213 +biotype 652 HN "C-Terminal PHE" 183 +biotype 653 OXT "C-Terminal PHE" 214 +biotype 654 HA "C-Terminal PHE" 85 +biotype 655 N "C-Terminal TYR" 180 +biotype 656 CA "C-Terminal TYR" 225 +biotype 657 C "C-Terminal TYR" 213 +biotype 658 HN "C-Terminal TYR" 183 +biotype 659 OXT "C-Terminal TYR" 214 +biotype 660 HA "C-Terminal TYR" 85 +biotype 661 N "C-Terminal TYD (O-)" -1 +biotype 662 CA "C-Terminal TYD (O-)" -1 +biotype 663 C "C-Terminal TYD (O-)" -1 +biotype 664 HN "C-Terminal TYD (O-)" -1 +biotype 665 OXT "C-Terminal TYD (O-)" -1 +biotype 666 HA "C-Terminal TYD (O-)" -1 +biotype 667 N "C-Terminal TRP" 180 +biotype 668 CA "C-Terminal TRP" 225 +biotype 669 C "C-Terminal TRP" 213 +biotype 670 HN "C-Terminal TRP" 183 +biotype 671 OXT "C-Terminal TRP" 214 +biotype 672 HA "C-Terminal TRP" 85 +biotype 673 N "C-Terminal HIS (+)" 180 +biotype 674 CA "C-Terminal HIS (+)" 225 +biotype 675 C "C-Terminal HIS (+)" 213 +biotype 676 HN "C-Terminal HIS (+)" 183 +biotype 677 OXT "C-Terminal HIS (+)" 214 +biotype 678 HA "C-Terminal HIS (+)" 85 +biotype 679 N "C-Terminal HIS (HD)" 180 +biotype 680 CA "C-Terminal HIS (HD)" 225 +biotype 681 C "C-Terminal HIS (HD)" 213 +biotype 682 HN "C-Terminal HIS (HD)" 183 +biotype 683 OXT "C-Terminal HIS (HD)" 214 +biotype 684 HA "C-Terminal HIS (HD)" 85 +biotype 685 N "C-Terminal HIS (HE)" 180 +biotype 686 CA "C-Terminal HIS (HE)" 225 +biotype 687 C "C-Terminal HIS (HE)" 213 +biotype 688 HN "C-Terminal HIS (HE)" 183 +biotype 689 OXT "C-Terminal HIS (HE)" 214 +biotype 690 HA "C-Terminal HIS (HE)" 85 +biotype 691 N "C-Terminal ASP" 180 +biotype 692 CA "C-Terminal ASP" 225 +biotype 693 C "C-Terminal ASP" 213 +biotype 694 HN "C-Terminal ASP" 183 +biotype 695 OXT "C-Terminal ASP" 214 +biotype 696 HA "C-Terminal ASP" 85 +biotype 697 N "C-Terminal ASH (COOH)" -1 +biotype 698 CA "C-Terminal ASH (COOH)" -1 +biotype 699 C "C-Terminal ASH (COOH)" -1 +biotype 700 HN "C-Terminal ASH (COOH)" -1 +biotype 701 OXT "C-Terminal ASH (COOH)" -1 +biotype 702 HA "C-Terminal ASH (COOH)" -1 +biotype 703 N "C-Terminal ASN" 180 +biotype 704 CA "C-Terminal ASN" 225 +biotype 705 C "C-Terminal ASN" 213 +biotype 706 HN "C-Terminal ASN" 183 +biotype 707 OXT "C-Terminal ASN" 214 +biotype 708 HA "C-Terminal ASN" 85 +biotype 709 N "C-Terminal GLU" 180 +biotype 710 CA "C-Terminal GLU" 225 +biotype 711 C "C-Terminal GLU" 213 +biotype 712 HN "C-Terminal GLU" 183 +biotype 713 OXT "C-Terminal GLU" 214 +biotype 714 HA "C-Terminal GLU" 85 +biotype 715 N "C-Terminal GLH (COOH)" -1 +biotype 716 CA "C-Terminal GLH (COOH)" -1 +biotype 717 C "C-Terminal GLH (COOH)" -1 +biotype 718 HN "C-Terminal GLH (COOH)" -1 +biotype 719 OXT "C-Terminal GLH (COOH)" -1 +biotype 720 HA "C-Terminal GLH (COOH)" -1 +biotype 721 N "C-Terminal GLN" 180 +biotype 722 CA "C-Terminal GLN" 225 +biotype 723 C "C-Terminal GLN" 213 +biotype 724 HN "C-Terminal GLN" 183 +biotype 725 OXT "C-Terminal GLN" 214 +biotype 726 HA "C-Terminal GLN" 85 +biotype 727 N "C-Terminal MET" 180 +biotype 728 CA "C-Terminal MET" 225 +biotype 729 C "C-Terminal MET" 213 +biotype 730 HN "C-Terminal MET" 183 +biotype 731 OXT "C-Terminal MET" 214 +biotype 732 HA "C-Terminal MET" 85 +biotype 733 N "C-Terminal LYS" 180 +biotype 734 CA "C-Terminal LYS" 225 +biotype 735 C "C-Terminal LYS" 213 +biotype 736 HN "C-Terminal LYS" 183 +biotype 737 OXT "C-Terminal LYS" 214 +biotype 738 HA "C-Terminal LYS" 85 +biotype 739 N "C-Terminal LYD (NH2)" -1 +biotype 740 CA "C-Terminal LYD (NH2)" -1 +biotype 741 C "C-Terminal LYD (NH2)" -1 +biotype 742 HN "C-Terminal LYD (NH2)" -1 +biotype 743 OXT "C-Terminal LYD (NH2)" -1 +biotype 744 HA "C-Terminal LYD (NH2)" -1 +biotype 745 N "C-Terminal ARG" 180 +biotype 746 CA "C-Terminal ARG" 225 +biotype 747 C "C-Terminal ARG" 213 +biotype 748 HN "C-Terminal ARG" 183 +biotype 749 OXT "C-Terminal ARG" 214 +biotype 750 HA "C-Terminal ARG" 85 +biotype 751 N "C-Terminal ORN" 180 +biotype 752 CA "C-Terminal ORN" 225 +biotype 753 C "C-Terminal ORN" 213 +biotype 754 HN "C-Terminal ORN" 183 +biotype 755 OXT "C-Terminal ORN" 214 +biotype 756 HA "C-Terminal ORN" 85 +biotype 757 N "C-Terminal AIB" 180 +biotype 758 CA "C-Terminal AIB" 227 +biotype 759 C "C-Terminal AIB" 213 +biotype 760 HN "C-Terminal AIB" 183 +biotype 761 OXT "C-Terminal AIB" 214 +biotype 762 N "Deprotonated N-Terminus" -1 +biotype 763 H "Deprotonated N-Terminus" -1 +biotype 764 C "Formyl N-Terminus" 177 +biotype 765 H "Formyl N-Terminus" 221 +biotype 766 O "Formyl N-Terminus" 178 +biotype 767 CH3 "Acetyl N-Terminus" 80 +biotype 768 H "Acetyl N-Terminus" 85 +biotype 769 C "Acetyl N-Terminus" 177 +biotype 770 O "Acetyl N-Terminus" 178 +biotype 771 C "Protonated C-Terminus" -1 +biotype 772 O "Protonated C-Terminus" -1 +biotype 773 OH "Protonated C-Terminus" -1 +biotype 774 HO "Protonated C-Terminus" -1 +biotype 775 N "Amide C-Terminus" 179 +biotype 776 HN "Amide C-Terminus" 182 +biotype 777 N "N-MeAmide C-Terminus" 180 +biotype 778 HN "N-MeAmide C-Terminus" 183 +biotype 779 CH3 "N-MeAmide C-Terminus" 184 +biotype 780 H "N-MeAmide C-Terminus" 85 +biotype 2001 O "Water" 63 +biotype 2002 H "Water" 64 +biotype 2003 NA "Sodium Ion" -1 +biotype 2004 K "Potassium Ion" -1 +biotype 2005 MG "Magnesium Ion" -1 +biotype 2006 CA "Calcium Ion" -1 +biotype 2007 CL "Chloride Ion" -1 diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/system.lt new file mode 100644 index 0000000000..fae58d65c9 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/moltemplate_files/system.lt @@ -0,0 +1,21 @@ +import "ethylene.lt" # <- defines the "Ethylene" molecule type. +import "benzene.lt" # <- defines the "Benzene" molecule type. + + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 80.00 xlo xhi + 0.0 80.00 ylo yhi + 0.0 80.00 zlo zhi +} + + +# Create 1000 ethylenes and 500 benzenes +# List them in the same order they appear in the PACKMOL .inp file(s). + +ethylenes = new Ethylene[1000] +benzenes = new Benzene[500] + +# Note: We can omit the .move() and .rot() commands which normally appear +# after the "new" command because we will be using a separate program +# (PACKMOL) to generate the coordinates of these molecules. diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/README.TXT b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/README.TXT new file mode 100644 index 0000000000..f0e39ec90a --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/README.TXT @@ -0,0 +1,5 @@ +You can use packmol to create a file containing the atomic coordinates +for a system of ethylene mixed with benzene using this command: + +packmol < mix_ethylene+benzene.inp + diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz new file mode 100644 index 0000000000..1a727ff40c --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz @@ -0,0 +1,14 @@ +12 + Benzene +C1 5.274 1.999 -8.568 +C2 6.627 2.018 -8.209 +C3 7.366 0.829 -8.202 +C4 6.752 -0.379 -8.554 +C5 5.399 -0.398 -8.912 +C6 4.660 0.791 -8.919 +H11 4.704 2.916 -8.573 +H21 7.101 2.950 -7.938 +H31 8.410 0.844 -7.926 +H41 7.322 -1.296 -8.548 +H51 4.925 -1.330 -9.183 +H61 3.616 0.776 -9.196 diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz new file mode 100644 index 0000000000..35326fe81f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz @@ -0,0 +1,8 @@ +6 + Ethylene +C1 -0.6695 0.000000 0.000000 +C2 0.6695 0.000000 0.000000 +H11 -1.234217 -0.854458 0.000000 +H12 -1.234217 0.854458 0.000000 +H21 1.234217 -0.854458 0.000000 +H22 1.234217 0.854458 0.000000 diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp new file mode 100644 index 0000000000..26fbc22fcf --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp @@ -0,0 +1,31 @@ +# +# A mixture of ethylene and benzene +# + +# All the atoms from diferent molecules will be separated at least 2.0 +# Anstroms at the solution. + +tolerance 2.0 + +# The file type of input and output files is PDB + +filetype xyz + +# The name of the output file + +output system.xyz + +# 1000 water molecules and 500 urea molecules will be put in a box +# defined by the minimum coordinates x, y and z = 0. 0. 0. and maximum +# coordinates 80. 80. 80. That is, they will be put in a cube of side +# 80. (the keyword "inside cube 0. 0. 0. 80.") could be used as well. + +structure ethylene.xyz + number 1000 + inside box 0. 0. 0. 80. 80. 80. +end structure + +structure benzene.xyz + number 500 + inside box 0. 0. 0. 80. 80. 80. +end structure diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/run.in.npt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/run.in.npt new file mode 100644 index 0000000000..930d93ee92 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/run.in.npt @@ -0,0 +1,57 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" + +# ------------------------------- Atom Definition Section ------------------- + +read_data "system.data" + +# OPLSAA atom charges are stored in a separate file. +# Load that file now: + +include "system.in.charges" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +minimize 1.0e-4 1.0e-6 100000 400000 + +# -- simulation protocol -- + +timestep 1.0 + +print "---------------------------------------------------------------------------" +print "First, use Langevin dynamics to randomize the initial shape of the molecules" +print "(This is not really necessary, but it seems to speed up equilibration.)" +print "---------------------------------------------------------------------------" + +fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K +fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 barr +run 2000 +unfix fxlan +unfix fxnph + +print "---------------------------------------------------------------------------" +print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" +print "---------------------------------------------------------------------------" +dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz +# temperature: 300 K, pressure: 50 barr +fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1.0 +thermo 100 +#thermo_modify flush yes + +run 100000 + +write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/run.in.nvt new file mode 100644 index 0000000000..b704d1f9d4 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene+benzene_PACKMOL/run.in.nvt @@ -0,0 +1,50 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" + +# ------------------------------- Atom Definition Section ------------------- + +# Read the coordinates generated by an earlier NPT simulation + +read_data "system_after_npt.data" + +# OPLSAA atom charges are stored in a separate file. +# Load that file now: + +include "system.in.charges" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" + + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo 500 +#thermo_modify flush yes + +run 200000 + +write_restart system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README.TXT b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README.TXT new file mode 100644 index 0000000000..6e1afd2e17 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README.TXT @@ -0,0 +1,13 @@ + +This is an example of how to use the OPLSAA force-field in LAMMPS +(using moltemplate.sh and the oplsaa_moltemplate.py conversion tool). +As of 2014-3-31, it has not been tested for accuracy. +(See the WARNING.TXT file.) + +step 1) +To build the files which LAMMPS needs, follow the instructions in: +README_setup.sh + +step 2) +To run LAMMPS with these files, follow these instructions: +README_run.sh diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README_run.sh b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README_run.sh new file mode 100755 index 0000000000..8b01ab92d7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README_run.sh @@ -0,0 +1,39 @@ +# --- Running LAMMPS --- +# -------- REQUIREMENTS: --------- +# 1) This example requires building LAMMPS with the "USER-MISC" package. +# (because it makes use of "gaff.lt" which uses dihedral_style fourier) +# To do this, type "make yes-user-misc" before compiling LAMMPS. +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# -------- PREREQUISITES: -------- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README_setup.sh new file mode 100755 index 0000000000..d80df900ef --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README_setup.sh @@ -0,0 +1,36 @@ +# -------- REQUIREMENTS: --------- +# You must define your MOLTEMPLATE_PATH environment variable +# and set it to the "common" subdirectory of your moltemplate distribution. +# (See the "Installation" section in the moltemplate manual.) + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # Create the "oplsaa.lt" file which moltemplate will need + + cd oplsaa_lt_generator/ + ./oplsaa_moltemplate.py oplsaa_subset.prm + mv -f oplsaa.lt .. + cd .. + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + + # Optional: + # Delete the "oplsaa.lt" file: + rm -f oplsaa.lt + + + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/images/ethylene.jpg b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/images/ethylene.jpg new file mode 100644 index 0000000000..ab5bbbf49b Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/images/ethylene.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/images/ethylene_box_pressure=50barr.jpg b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/images/ethylene_box_pressure=50barr.jpg new file mode 100644 index 0000000000..aa0d54a649 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/images/ethylene_box_pressure=50barr.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/ethylene.lt new file mode 100644 index 0000000000..45adb1faef --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/ethylene.lt @@ -0,0 +1,40 @@ +import "oplsaa.lt" + +# The "oplsaa.lt" file contains force-field definitions and masses for the +# atoms in your system. See oplsaa_lt_generator/README.TXT for details. + +# Note: +# Atom type 88 corresponds to "Alkene H2-C=" +# Atom type 89 corresponds to "Alkene H-C=" + + + +Ethylene inherits OPLSAA { + + # atom-id mol-id atom-type charge X Y Z + + write('Data Atoms') { + $atom:C1 $mol @atom:88 0.000 -0.6695 0.000000 0.000000 + $atom:C2 $mol @atom:88 0.000 0.6695 0.000000 0.000000 + $atom:H11 $mol @atom:89 0.000 -1.234217 -0.854458 0.000000 + $atom:H12 $mol @atom:89 0.000 -1.234217 0.854458 0.000000 + $atom:H21 $mol @atom:89 0.000 1.234217 -0.854458 0.000000 + $atom:H22 $mol @atom:89 0.000 1.234217 0.854458 0.000000 + } + + write('Data Bond List') { + $bond:C12 $atom:C1 $atom:C2 + $bond:C1H1 $atom:C1 $atom:H11 + $bond:C1H2 $atom:C1 $atom:H12 + $bond:C2H1 $atom:C2 $atom:H21 + $bond:C2H2 $atom:C2 $atom:H22 + } + +} # Ethylene + + + +# Note: You don't need to supply the partial partial charges of the atoms. +# If you like, just fill the fourth column with zeros ("0.000"). +# Moltemplate and LAMMPS will automatically assign the charge later + diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT new file mode 100644 index 0000000000..d5e469af37 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/AUTHOR.TXT @@ -0,0 +1,3 @@ + +OPLSAA force-field conversion tools provided by Jason Lambert. + diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/README.TXT new file mode 100644 index 0000000000..4191a6176c --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/README.TXT @@ -0,0 +1,106 @@ +This directory contains instructions for creating a a moltemplate file +("oplsaa.lt") containing force-field definitions relevant to the +"ethylene" example. (However, these instructions should work +for other molecules too.) + +First, check and see if there is an "oplsaa_subset.prm" file present. +If not, then download this file: + +http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm + This file is also available here: +http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm + +and save this file as "oplsaa_subset.prm". Then you must EDIT THIS FILE +so that it only contains atom types you plan to have in your simulation +(see below for details). Then run the opls_moltemplate.py script this way: + + +python oplsaa_moltemplate.py oplsaa_subset.prm + + +This will create a file named "oplsaa.lt" +Look over the newly created "oplsaa.lt" file. +Then move this file to wherever you plan to run moltemplate. For example: + +mv -f oplsaa.lt .. + +----- DETAILS: Editing the "oplsaa_subset.prm" file ------- + +Again, before you run "oplsaa_moltemplate.py", you must edit the "oplsaa.prm" +file (or "oplsaa_subset.prm file) and eliminate atom types which do not +correspond to any of the atoms in your simulation. This means you must +look for lines near the beginning of this file which begin with the word "atom" +and refer to atom types which appear in the simulation you plan to run. All +other lines (beginning with the word "atom") must be deleted or commented out. +(Leave the rest of the file alone.) + +For example: +If you were working with ethylene, you would delete every line +beginning with the word "atom", except for these two lines: + + +atom 88 47 CM "Alkene H2-C=" 6 12.011 3 +atom 89 46 HC "Alkene H-C=" 1 1.008 1 + + +Then you are ready to run oplsaa_moltemplate.py on this file. + +(You can try to delete more irrelevant information, but be careful. + It is not necessary, and it is easy to make mistakes.) + + +----- Using the "oplsaa.lt" file ----- + +Once you have created the "oplsaa.lt" file, you can create files (like +ethylene.lt) which define molecules that refer to these atom types. +Here is an excerpt from "ethyelene.lt": + +Ethylene inherits OPLSAA { + write('Data Atoms') { + list of atoms goes here ... + } + write('Data Bond List') { + list of bonds goes here ... + } +} + +And then run moltemplate. + + +----------- CHARGE: ----------- + +By default, the OPLSAA force-field assigns atom charge according to atom type. +When you run moltemplate, it will create a file named "system.in.charges", +containing commands like: + +set type 2 charge -0.42 +set type 3 charge 0.21 + +(This assumes your main moltemplate file is named "system.lt". If it was +named something else, eg "polymer.lt", then the file created by moltemplate +will be named "polymer.in.charges".) + +Include these commands somewhere in your LAMMPS input script +(or use the LAMMPS "include" command to load the commands in system.in.charges) + +Note that the atom numbers (eg "2", "3") in this file will not match the +OPLS atom numbers. (Check the output_ttree/ttree_assignments.txt file, +created by moltemplate, to see a table of "@atom" type numbers translated +from OPLSAA into LAMMPS.) + +----------- CREDIT ----------- + +If you use these tools and you publish a paper using OPLSAA, please also cite +the TINKER program. (Because these examples use the "oplsaa.prm" file which +is distributed with TINKER.) I think these are the relevant citations: + +1) Ponder, J. W., & Richards, F. M. (1987). "An efficient newtonâ€like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024. + +2) Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/ + +------------------------------- + +Jason Lambert and Andrew Jewett +April, 2014 + +Please email bugs to jewett.aij@gmail.com and jlamber9@gmail.com diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT new file mode 100644 index 0000000000..2fc1ea29ea --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/README.TXT @@ -0,0 +1,16 @@ +MOST USERS SHOULD IGNORE THIS DIRECTORY. + +This directory contains versions of the oplsaa_subset.prm file +which nearly all of the OPLSAA force-field information removed. +However for the "ethylene+benzene" example, all of the essential +parameters are contained in these files. You can use oplsaa_moltemplate.py +with either of these files and the physics should be the same. + +However there is no reason to do this. +When you download the "oplsaa.prm" file from: +http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm +(also http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm) +...just remove the lines beginning with "atom" for atoms you don't need. +You don't have to delete all the other irrelevant interactions. +(In fact, it is hard to do that without making a mistake. + I recommend that you leave the rest of the oplsaa.prm file alone.) diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm new file mode 100644 index 0000000000..031343dab8 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_minimal.prm @@ -0,0 +1,22 @@ + ############################# + ## Atom Type Definitions ## + ############################# + +atom 88 47 CM "Alkene H2-C=" 6 12.011 3 +atom 89 46 HC "Alkene H-C=" 1 1.008 1 + +vdw 88 3.5500 0.0760 +vdw 89 2.4200 0.0300 + +bond 46 47 340.00 1.0800 +bond 47 47 549.00 1.3400 + +angle 46 47 46 35.00 117.00 +angle 46 47 47 35.00 120.00 + +torsion 46 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 + +imptors 0 0 47 0 30.000 180.0 2 + +charge 88 -0.2300 +charge 89 0.1150 diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm new file mode 100644 index 0000000000..8beeb84076 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/minimal_versions/oplsaa_subset_simplified.prm @@ -0,0 +1,25 @@ + ############################# + ## Atom Type Definitions ## + ############################# + +atom 88 47 CM "Alkene H2-C=" 6 12.011 3 +atom 89 46 HC "Alkene H-C=" 1 1.008 1 + +vdw 88 3.5500 0.0760 +vdw 89 2.4200 0.0300 + +bond 46 47 340.00 1.0800 +bond 47 47 549.00 1.3400 + +angle 46 47 46 35.00 117.00 +angle 46 47 47 35.00 120.00 + +torsion 47 46 47 46 0.000 0.0 1 -8.000 180.0 2 0.000 0.0 3 +torsion 0 47 47 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 46 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 + +imptors 0 0 47 0 30.000 180.0 2 + +charge 88 -0.2300 +charge 89 0.1150 + diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py new file mode 100755 index 0000000000..49cef1aff1 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py @@ -0,0 +1,386 @@ +#! /usr/bin/env python +#The purpose of this script is to create a moltemplate lt file for the opls-aa forcefield. +#This will assist researchers in building complex simulations using this OPLS-UA and the OPLS-AA forcefields. +__author__="Jason Lambert" +__version__="0.15" + +import sys +import os +from operator import itemgetter + +print(""" + +Warning: + Run this program on a SUBSET of the OPLS atoms which are relevant + to your problem. If not, this program (and moltemplate) may crash + your computer and/or generate enormous files that you do not need. +""") +# To do that, first make a copy of the \"oplsaa.prm\" file +# (which can be downloaded from the TINKER web site). +# The lines in this file beginning with the word \"atoms\" should +# define the atoms which you plan to put in your simulation. All other +# lines beginning with the word \"atoms\" should be deleted. +# (Leave the other sections of this file alone.) +#""") + + + +#input data from file containing opls aa force field parameters. +try: + f=open(sys.argv[1],"r") +except: + print("need to specify file name as an input argument:") + print("python oplsaa_moltemplate.py ") + print("or file name is specified incorrectly") + sys.exit() +#output lt file +g=open("oplsaa.lt","w") + + + +lines = f.readlines() + + + +# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. + +for i in range(0, len(lines)): + if (lines[i].find("## Atom Type Definitions ##") != -1): + break + else: + lines[i] = '# ' + lines[i] + + +# As of 2014-4-19, there appear to be 906 atom types, but we don't assume this. +# First try to infer out how many atom types there were in the original +# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. +# (Keep track of the maximum value of the first column in the "atom" section.) +max_atomType = 0 +for line in lines: + # skip over text after a # comment character + ic = line.find('#') + if ic != -1: + line = (line[:ic]).strip() + else: + line = line.strip() + # now look for lines beginning with the word "atom" + tokens = line.split() + if ((len(tokens)>2) and + (tokens[0] == "atom") and + (int(tokens[1]) > max_atomType)): + max_atomType = int(tokens[1]) + + +#temporary storage file +h=open("temp.txt","w+") +atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key +#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms +atom=[[-10000,-10000] for i in range(0,max_atomType+1)] +#charge_by_type={} # lookup charge by atom type +#vdw_by_type={} # lookup epsilon & sigma paramters by atom type +charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom +vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma + + + +#atom is declared this way so for sorting purposes. +#atom contains the following data upon allocation +#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) +#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) +#atom[][2]=atom_mass +#atom[][3]=partial charge +#atom[][4]=non_bonding sigma +#atom[][5]=non_bonding epsilon +#atom[][6]=atom comment +bond=[] +#bond contains the following data +#bond[0]=atom 1 ffid +#bond[1]=atom 2 ffid +#bond[2]=bond spring constant(OPLS-aa compatible) +#bond[3]=equilibrium bond distance(Angstrom) +angle=[] +#angle contains the following data +#angle[0]=atom 1 ffid +#angle[1]=atom 2 ffid +#angle[2]=atom 3 ffid +#angle[3]=spring constant +#angle[4]=equilibrium angle (degrees) +dihedral=[] +#dihedral contains the following data +#dihedral[0]=atom 1 ffid +#dihedral[1]=atom 2 ffid +#dihedral[2]=atom 3 ffid +#dihedral[3]=atom 4 ffid +#dihedral[4]=v1 +#dihedral[5]=v2 +#dihedral[6]=v3 +#dihedral[7]=v4 +improper=[] +#improper[0]=atom 1 ffid +#improper[1]=atom 2 ffid(central atom) +#improper[2]=atom 3 ffid +#improper[3]=atom 4 ffid +#improper[4]=spring coefficient +#improper[5]=equilibrium angle + + +#This section gets all the parameters from the force field file +for line in lines: + + # skip over text after a # comment character + ic = line.find('#') + if ic != -1: + line = (line[:ic]).strip() + else: + line = line.strip() + + if line.find("atom") == 0: + line=line.split() + atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), + 0.0,0.0,0.0," ".join(line[3:-2])] + elif line.find("vdw") == 0: + line=line.split() + #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) + if (int(line[1]) <= max_atomType): + vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) + elif line.find("bond") == 0: + line=line.split() + bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) + elif line.find("angle") == 0: + line=line.split() + angle.append([int(line[1]),int(line[2]),int(line[3]), + float(line[4]),float(line[5])]) + elif line.find("torsion") == 0: + line=line.split() + dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), + float(line[5]),float(line[8]), float(line[11]), 0.0]) + elif line.find("charge") == 0: + line=line.split() + #charge_temp.append([int(line[1]),float(line[2])]) + if (int(line[1]) <= max_atomType): + charge_by_type[int(line[1])] = float(line[2]) + elif line.find("imptors") == 0: + line=line.split() + improper.append([int(line[1]), int(line[2]), + int(line[3]), int(line[4]), float(line[5]), float(line[6])]) + +if len(atom) > 600: + sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" + " (You were supposed to edit out the atoms you don't need.\n" + " Not doing this may crash your computer.)\n" + "\n" + " Proceed? (Y/N): ") + reply = sys.stdin.readline() + if find(reply.strip().lower(), 'y') != 0: + exit(0) + +#adding the charge and Lennard Jones parameters to +#to each atom type. +#----------------------------------------------# +for i in range(0,len(atom)): + atom_type_num = atom[i][0] + #q = charge_by_type.get(atomTypeNum) + #if q: + # atom[i][3] = q + if atom_type_num != -10000: + q = charge_by_type[atom_type_num] + atom[i][3] = q + +for i in range(0,len(atom)): + atom_type_num = atom[i][0] + #vdw_params = vdw_by_type.get(atomTypeNum) + #if vdw_params: + # atom[i][4] = vdw_params[0] + # atom[i][5] = vdw_params[1] + if atom_type_num != -10000: + vdw_params = vdw_by_type[atom_type_num] + atom[i][4] = vdw_params[0] + atom[i][5] = vdw_params[1] + +del(charge_by_type) +del(vdw_by_type) + +#----------------------------------------------------------# +#begin writing content to lt file +g.write("OPLSAA {\n\n" ) + +#write out the atom masses +#----------------------------------------------------------# +g.write(" write_once(\"Data Masses\"){\n")#checked with gaff +for i,x in enumerate(atom): + if x[0] != -10000: + g.write(" @atom:{} {} #{} partial charge={}\n".format( + x[0],x[2],x[6],x[3])) +g.write(" } #(end of atom masses)\n\n") +#----------------------------------------------------------# + + +#write out the pair coefficients +#----------------------------------------------------------# +g.write(" write_once(\"In Settings\"){\n")#checked with gaff +for i,x in enumerate(atom): + if x[0] != -10000: + g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4])) +g.write(" } #(end of pair coeffs)\n\n") + +g.write(" write_once(\"In Charges\"){\n")#checked with gaff +for i,x in enumerate(atom): + if x[0] != -10000: + g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) +g.write(" } #(end of atom charges)\n\n") + +#-----------------------------------------------------------# + +# This part of the code creates a lookup dictionary +# that allows you to find every type of atom by its +# force field id. force field id is the id number +# relevant to bonds, angles, dihedrals, and impropers. +# This greatly increases the speed of angle, bond, dihedral +# and improper assignment. +#------------------------------------------------------------# +atom=sorted(atom,key=itemgetter(1)) +atom_ffid=0 +for x in atom: + if x[1]==atom_ffid: + atom_lookup[x[1]].append(x[0]) + elif x[1]>atom_ffid: + atom_lookup[x[1]]=[x[0]] + atom_ffid=x[1] +atom_lookup[0]=["*"] +#-------------------------------------------------------------# + + +#writing out the bond coefficients and bond parameters# +#-------------------------------------------------------------# +g.write(" write_once(\"In Settings\") {\n") +index1=0 +for x in bond: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) + h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) +g.write(" } #(end of bond_coeffs)\n\n") +h.seek(0,0) +g.write(" write_once(\"Data Bonds By Type\") {\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of bonds by type)\n\n") +del(bond) +h.close() +#-----------------------------------------------------------# +h=open("temp.txt","w+") + +#writing out angle coefficients and angles by type.---------# +#-----------------------------------------------------------# +g.write(" write_once(\"Data Angles By Type\"){\n") +for x in angle: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + #print(y,z,u,x) + h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u, + x[3]/2.0,x[4])) + g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format( + y,z,u)) + + +g.write(" } #(end of angles by type)\n\n") +h.seek(0,0) +g.write(" write_once(\"In Settings\" ){\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of angle_coeffs)\n\n") +del(angle) +h.close() +#----------------------------------------------------------# + +#writing dihedrals by type and dihedral coefficients-------# +h=h=open("temp.txt","w+") +g.write(" write_once(\"Data Dihedrals By Type\") {\n") +#print(atom_lookup) +for x in dihedral: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + for v in atom_lookup.get(x[3],[]): + if x[0]!=0 and x[3]!=0: + g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( + y,z,u,v)) + h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( + y,z,u,v,x[4],x[5],x[6],x[7])) + elif x[0]==0 and x[3]!=0: + g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( + y,z,u,v)) + h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( + z,u,v,x[4],x[5],x[6],x[7])) + elif x[0]==0 and x[3]==0: + g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( + y,z,u,v)) + #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( + h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( + z,u,x[4],x[5],x[6],x[7])) + +del(dihedral) +g.write(" } #(end of Dihedrals by type)\n\n") +h.seek(0,0) +g.write(" write_once(\"In Settings\") {\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of dihedral_coeffs)\n\n") +h.close() +#-----------------------------------------------------------------------# + +#----writing out improper coefficients and impropers by type------------# +h=open("temp.txt","w+") +g.write(" write_once(\"Data Impropers By Type\") {\n") +for x in improper: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + for v in atom_lookup.get(x[3],[]): + if x[0]==0 and x[1]==0 and x[3]==0: + g.write(" @improper:{2}-0-0-0 @atom:{2} @atom:{0} @atom:{1} @atom:{3}\n".format( + y,z,u,v)) + h.write(" improper_coeff @improper:{2}-0-0-0 harmonic {4} {5} \n".format( + y,z,u,v,x[4]/2,0)) + else: + g.write(" @improper:{2}-0-0-{3} @atom:{2} @atom:{0} @atom:{1} @atom:{3}\n".format( + y,z,u,v)) + h.write(" improper_coeff @improper:{2}-0-0-{3} harmonic {4} {5} \n".format( + y,z,u,v,x[4]/2,0)) + + +g.write(" } #(end of impropers by type)\n\n") +h.seek(0,0) +g.write(" write_once(\"In Settings\") {\n") +for line in h.readlines(): + g.write(line) +g.write(" } #(end of improp_coeffs)\n\n") +#-----------------------------------------------------------------------# + +#This section writes out the input parameters required for an opls-aa simulation +# lammps. +g.write(" write_once(\"In Init\") {\n") +g.write(" units real\n") +g.write(" atom_style full\n") +g.write(" bond_style hybrid harmonic\n") +g.write(" angle_style hybrid harmonic\n") +g.write(" dihedral_style hybrid opls\n") +g.write(" improper_style hybrid harmonic\n") +#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n") +g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n") +g.write(" pair_modify mix arithmetic\n") +g.write(" special_bonds lj 0.0 0.0 0.5\n") +g.write(" kspace_style pppm 0.0001\n") +g.write(" } #end of init parameters\n\n") +g.write("} # OPLSAA\n") +f.close() +g.close() +h.close() +os.remove("temp.txt") + + + + + + diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm new file mode 100644 index 0000000000..38ebf32a54 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm @@ -0,0 +1,5125 @@ +# This is a modified version of the file "oplsaa.prm" distributed with TINKER +# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm +# In this version, all of the lines beginning with "atom" have been deleted +# except for the atom types we will be using in this simulation +# +# If you use this file, please also cite the software this file comes from: +# +# Ponder, J. W., and Richards, F. M. J. Comput. Chem. (1987) 8(7), 1016-1024 +# "An efficient newtonâ€like method for molecular mechanics energy +# minimization of large molecules." +# +# Ponder, J. W, (2004) +# "TINKER: Software tools for molecular design" +# http://dasher.wustl.edu/tinker/ + + ############################## + ## ## + ## Force Field Definition ## + ## ## + ############################## + + +forcefield OPLS-AA + +vdwindex TYPE +vdwtype LENNARD-JONES +radiusrule GEOMETRIC +radiustype SIGMA +radiussize DIAMETER +epsilonrule GEOMETRIC +torsionunit 0.5 +imptorunit 0.5 +vdw-14-scale 2.0 +chg-14-scale 2.0 +electric 332.06 +dielectric 1.0 + + + ############################# + ## ## + ## Literature References ## + ## ## + ############################# + + +The parameters supplied with TINKER are from "OPLS All-Atom Parameters +for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as +provided by W. L. Jorgensen, Yale University during June 2009. These +parameters are taken from those distributed with BOSS Version 4.8. + +Note that "atom type" numbers and not "atom class" numbers are used +to index van der Waals parameters, see the "vdwindex" keyword above + +The atom types with (UA) in the description are "united atom" values, +ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their +attached atoms. All other parameters are "all-atom", OPLS-AA, including +explicit hydrogen atoms. + + + ############################# + ## ## + ## Atom Type Definitions ## + ## ## + ############################# + + +atom 88 47 CM "Alkene H2-C=" 6 12.011 3 +atom 89 46 HC "Alkene H-C=" 1 1.008 1 + + + ################################ + ## ## + ## Van der Waals Parameters ## + ## ## + ################################ + + +vdw 1 2.9400 0.0610 +vdw 2 3.9050 0.1180 +vdw 3 3.7500 0.1050 +vdw 4 2.9600 0.2100 +vdw 5 3.0000 0.1700 +vdw 6 3.9100 0.1600 +vdw 7 0.0000 0.0000 +vdw 8 3.7300 0.2940 +vdw 9 3.7750 0.2070 +vdw 10 3.9050 0.1750 +vdw 11 3.9100 0.1600 +vdw 12 3.9600 0.1450 +vdw 13 3.9050 0.1180 +vdw 14 3.8500 0.1400 +vdw 15 3.8500 0.0800 +vdw 16 3.8000 0.1150 +vdw 17 3.7500 0.1100 +vdw 18 3.8000 0.0500 +vdw 19 3.7500 0.1050 +vdw 20 3.0700 0.1700 +vdw 21 0.0000 0.0000 +vdw 22 3.7750 0.2070 +vdw 23 3.9050 0.1180 +vdw 24 3.7000 0.2500 +vdw 25 3.5500 0.2500 +vdw 26 3.5500 0.2500 +vdw 27 3.5500 0.2500 +vdw 28 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726 3.7400 0.2000 +vdw 727 3.1181 0.0610 +vdw 728 3.1500 0.1700 +vdw 729 2.8600 0.2100 +vdw 730 3.3000 0.1700 +vdw 731 3.3000 0.1700 +vdw 732 3.3000 0.1700 +vdw 733 3.5000 0.0660 +vdw 734 3.5000 0.0660 +vdw 735 3.5000 0.0660 +vdw 736 3.5000 0.0660 +vdw 737 3.5000 0.0660 +vdw 738 3.5000 0.0660 +vdw 739 0.0000 0.0000 +vdw 740 0.0000 0.0000 +vdw 741 2.5000 0.0150 +vdw 742 3.5000 0.0660 +vdw 743 3.5000 0.0660 +vdw 744 3.5000 0.0660 +vdw 745 3.5000 0.0660 +vdw 746 3.5500 0.0700 +vdw 747 3.5500 0.0700 +vdw 748 3.5500 0.0700 +vdw 749 3.5000 0.0660 +vdw 750 3.5000 0.0660 +vdw 751 3.5000 0.0660 +vdw 752 3.5000 0.0660 +vdw 753 3.5000 0.0660 +vdw 754 3.5000 0.0660 +vdw 755 3.3000 0.0860 +vdw 756 2.4200 0.0150 +vdw 757 3.3000 0.2100 +vdw 758 3.3000 0.1350 +vdw 759 3.3000 0.1000 +vdw 760 2.5000 0.0150 +vdw 761 3.5000 0.0660 +vdw 762 3.5000 0.0660 +vdw 763 3.5000 0.0660 +vdw 764 3.1200 0.1700 +vdw 765 0.0000 0.0000 +vdw 766 3.2500 0.1700 +vdw 767 3.2500 0.1700 +vdw 768 3.2500 0.1700 +vdw 769 3.3000 0.2100 +vdw 770 3.2500 0.1700 +vdw 771 0.0000 0.0000 +vdw 772 3.5000 0.0660 +vdw 773 3.5000 0.0660 +vdw 774 3.5000 0.0660 +vdw 775 3.5000 0.0660 +vdw 776 3.5500 0.0700 +vdw 777 3.5500 0.0760 +vdw 778 3.5500 0.0700 +vdw 779 3.5500 0.0700 +vdw 780 2.5000 0.0300 +vdw 781 3.5000 0.0660 +vdw 782 3.7500 0.1050 +vdw 783 3.2500 0.1700 +vdw 784 2.9600 0.2100 +vdw 785 0.0000 0.0000 +vdw 786 2.9400 0.0610 +vdw 787 3.5000 0.0660 +vdw 788 2.5000 0.0300 +vdw 789 3.5000 0.0660 +vdw 790 3.5000 0.0660 +vdw 791 3.5000 0.0660 +vdw 792 3.5000 0.0660 +vdw 793 3.5000 0.0660 +vdw 794 3.5000 0.0970 +vdw 795 2.9500 0.0530 +vdw 796 3.2500 0.0620 +vdw 797 2.5000 0.0300 +vdw 798 3.5000 0.0660 +vdw 799 3.5000 0.0660 +vdw 800 3.4000 0.3000 +vdw 801 3.5000 0.0660 +vdw 802 2.5000 0.0300 +vdw 803 3.5000 0.0660 +vdw 804 3.5000 0.0660 +vdw 805 3.4700 0.4700 +vdw 806 3.5000 0.0660 +vdw 807 2.5000 0.0300 +vdw 808 3.5000 0.0660 +vdw 809 3.5000 0.0660 +vdw 810 2.9400 0.0610 +vdw 811 3.4000 0.3000 +vdw 812 3.4700 0.4700 +vdw 813 3.5500 0.0700 +vdw 814 2.9000 0.1400 +vdw 815 3.5000 0.0660 +vdw 816 2.9000 0.0600 +vdw 817 3.2500 0.1700 +vdw 818 3.5500 0.0700 +vdw 819 3.5000 0.0660 +vdw 820 3.7500 0.1050 +vdw 821 3.7500 0.1050 +vdw 822 2.9600 0.2100 +vdw 823 3.2500 0.1700 +vdw 824 0.0000 0.0000 +vdw 825 3.1200 0.1700 +vdw 826 0.0000 0.0000 +vdw 827 3.5000 0.0660 +vdw 828 3.5000 0.0660 +vdw 829 3.5500 0.0700 +vdw 830 3.5500 0.0700 +vdw 831 3.5500 0.0700 +vdw 832 3.5500 0.0700 +vdw 833 3.5500 0.0700 +vdw 834 1.9600 0.0125 +vdw 835 3.5000 0.0660 +vdw 836 3.5000 0.0660 +vdw 837 3.5000 0.0660 +vdw 838 3.7500 0.6000 +vdw 839 2.5000 0.0300 +vdw 840 3.2500 0.1700 +vdw 841 3.5500 0.0700 +vdw 842 3.5500 0.0700 +vdw 843 3.2500 0.1700 +vdw 844 3.5500 0.0700 +vdw 845 3.7500 0.1050 +vdw 846 2.9600 0.2100 +vdw 847 3.2500 0.1700 +vdw 848 3.5000 0.0660 +vdw 849 3.5000 0.0660 +vdw 850 3.5000 0.0660 +vdw 851 3.5000 0.0660 +vdw 852 2.4200 0.0150 +vdw 853 3.7500 0.1050 +vdw 854 2.9600 0.2100 +vdw 855 2.4200 0.0150 +vdw 856 3.5000 0.0660 +vdw 857 3.5000 0.0660 +vdw 858 3.5000 0.0660 +vdw 859 3.5000 0.0660 +vdw 860 3.5000 0.0660 +vdw 861 3.5000 0.0660 +vdw 862 3.5000 0.0660 +vdw 863 3.5000 0.0660 +vdw 864 3.5000 0.0660 +vdw 865 3.5000 0.0660 +vdw 866 4.0000 0.1000 +vdw 867 4.0000 0.1000 +vdw 868 4.0000 0.1000 +vdw 869 4.0000 0.1000 +vdw 870 2.5000 0.0300 +vdw 871 3.5000 0.0660 +vdw 872 3.5000 0.0660 +vdw 873 3.5000 0.0660 +vdw 874 3.5000 0.0660 +vdw 875 3.0800 0.7200 +vdw 876 4.1800 0.11779 +vdw 877 4.5100 0.0900 +vdw 878 5.1500 0.0700 +vdw 879 2.7000 0.018279 +vdw 880 3.3500 0.002772 +vdw 881 4.0600 0.000328 +vdw 882 4.3200 0.000171 +vdw 883 4.8200 0.000081 +vdw 884 2.9100 0.875044 +vdw 885 3.4700 0.449657 +vdw 886 3.8200 0.118226 +vdw 887 4.1800 0.047096 +vdw 888 3.5000 0.0660 +vdw 889 3.5000 0.0660 +vdw 890 3.5000 0.0660 +vdw 891 3.5000 0.0660 +vdw 892 2.5000 0.0300 +vdw 893 3.2500 0.1700 +vdw 894 3.5500 0.0700 +vdw 895 3.2500 0.1700 +vdw 896 3.5500 0.0700 +vdw 897 3.5500 0.0760 +vdw 898 3.5500 0.0760 +vdw 899 2.4200 0.0300 +vdw 900 3.3000 0.0860 +vdw 901 3.3000 0.0860 +vdw 902 3.3000 0.0860 +vdw 903 3.3000 0.0860 +vdw 904 3.3000 0.0860 +vdw 905 2.9600 0.2100 +vdw 906 3.5000 0.0660 + + + ################################## + ## ## + ## Bond Stretching Parameters ## + ## ## + ################################## + + +bond 1 2 367.00 1.3800 +bond 1 3 420.00 1.3570 +bond 1 13 367.00 1.3600 +bond 1 19 450.00 1.2790 +bond 1 25 300.00 0.3000 +bond 1 47 420.00 1.3400 +bond 1 48 420.00 1.3540 +bond 1 82 420.00 1.3540 +bond 1 83 420.00 1.3540 +bond 1 84 420.00 1.3540 +bond 1 87 420.00 1.3540 +bond 1 88 420.00 1.3540 +bond 1 108 461.00 1.5700 +bond 2 2 260.00 1.5260 +bond 2 3 317.00 1.5220 +bond 2 5 386.00 1.4250 +bond 2 6 260.00 1.5260 +bond 2 10 260.00 1.5260 +bond 2 11 317.00 1.5000 +bond 2 12 317.00 1.5100 +bond 2 13 260.00 1.5260 +bond 2 14 317.00 1.5000 +bond 2 15 222.00 1.8100 +bond 2 16 222.00 1.8100 +bond 2 20 320.00 1.4250 +bond 2 24 337.00 1.4490 +bond 2 44 382.00 1.4480 +bond 2 48 317.00 1.5100 +bond 2 51 260.00 1.5260 +bond 2 53 367.00 1.4710 +bond 2 55 337.00 1.4630 +bond 2 80 317.00 1.4950 +bond 3 3 350.00 1.5100 +bond 3 4 570.00 1.2290 +bond 3 5 450.00 1.3640 +bond 3 6 317.00 1.5220 +bond 3 10 317.00 1.5220 +bond 3 12 469.00 1.4000 +bond 3 13 317.00 1.5220 +bond 3 19 400.00 1.4440 +bond 3 20 214.00 1.3270 +bond 3 21 300.00 1.7900 +bond 3 24 490.00 1.3350 +bond 3 44 317.00 1.5220 +bond 3 46 340.00 1.0900 +bond 3 47 410.00 1.4440 +bond 3 48 400.00 1.4900 +bond 3 50 385.00 1.4600 +bond 3 52 656.00 1.2500 +bond 3 56 457.00 1.3580 +bond 3 57 418.00 1.3880 +bond 3 60 447.00 1.4190 +bond 3 65 300.00 1.9800 +bond 3 84 400.00 1.4900 +bond 3 86 385.00 1.4600 +bond 3 105 424.00 1.3830 +bond 3 107 490.00 1.3350 +bond 4 25 553.00 0.3000 +bond 4 64 525.00 1.4800 +bond 4 89 570.00 1.2290 +bond 4 110 700.00 1.1710 +bond 5 6 386.00 1.4250 +bond 5 7 553.00 0.9450 +bond 5 10 386.00 1.4250 +bond 5 13 320.00 1.4100 +bond 5 20 250.00 1.4700 +bond 5 24 400.00 1.3800 +bond 5 25 340.00 0.3000 +bond 5 44 320.00 1.4500 +bond 5 47 450.00 1.3700 +bond 5 48 450.00 1.3640 +bond 5 51 320.00 1.3800 +bond 5 64 230.00 1.6100 +bond 5 79 450.00 1.6700 +bond 5 106 94.00 1.8000 +bond 5 108 374.00 1.6400 +bond 6 6 260.00 1.5260 +bond 6 10 260.00 1.5260 +bond 6 11 317.00 1.5000 +bond 6 13 260.00 1.5260 +bond 6 14 317.00 1.5000 +bond 6 15 222.00 1.8100 +bond 6 16 222.00 1.8100 +bond 6 20 320.00 1.4250 +bond 6 24 337.00 1.4490 +bond 6 44 382.00 1.4480 +bond 6 47 317.00 1.5100 +bond 6 51 260.00 1.5260 +bond 6 53 367.00 1.4710 +bond 6 55 337.00 1.4630 +bond 6 79 222.00 1.8100 +bond 6 105 337.00 1.4750 +bond 7 20 553.00 0.9450 +bond 7 25 340.00 0.1000 +bond 9 9 530.00 1.3400 +bond 9 11 530.00 1.3400 +bond 9 14 530.00 1.3400 +bond 10 10 260.00 1.5260 +bond 10 11 317.00 1.5000 +bond 10 14 317.00 1.5000 +bond 10 20 320.00 1.4250 +bond 10 24 337.00 1.4490 +bond 10 44 382.00 1.4480 +bond 10 105 337.00 1.4750 +bond 11 11 530.00 1.3400 +bond 11 13 317.00 1.5000 +bond 11 14 530.00 1.3400 +bond 11 79 222.00 1.7600 +bond 12 12 469.00 1.4000 +bond 12 48 469.00 1.4000 +bond 12 60 469.00 1.4000 +bond 12 81 469.00 1.4000 +bond 13 13 268.00 1.5290 +bond 13 14 317.00 1.5000 +bond 13 15 222.00 1.8100 +bond 13 16 222.00 1.8100 +bond 13 18 390.00 1.4300 +bond 13 19 390.00 1.4700 +bond 13 20 320.00 1.4100 +bond 13 21 245.00 1.7810 +bond 13 22 340.00 1.7900 +bond 13 24 337.00 1.4490 +bond 13 25 340.00 0.3000 +bond 13 44 382.00 1.4480 +bond 13 46 340.00 1.0900 +bond 13 47 317.00 1.5100 +bond 13 48 317.00 1.5100 +bond 13 50 317.00 1.5100 +bond 13 51 268.00 1.5290 +bond 13 53 367.00 1.4710 +bond 13 55 337.00 1.4630 +bond 13 56 337.00 1.4490 +bond 13 57 337.00 1.4750 +bond 13 60 317.00 1.5100 +bond 13 64 212.00 1.8430 +bond 13 65 245.00 1.9450 +bond 13 66 200.00 2.1900 +bond 13 79 340.00 1.7700 +bond 13 80 317.00 1.4950 +bond 13 83 317.00 1.5040 +bond 13 84 317.00 1.5040 +bond 13 85 317.00 1.5040 +bond 13 87 317.00 1.4950 +bond 13 90 337.00 1.4490 +bond 13 91 280.00 1.5100 +bond 13 95 532.80 1.4600 +bond 13 101 382.00 1.4480 +bond 13 102 375.00 1.4900 +bond 13 104 212.00 1.8200 +bond 13 105 337.00 1.4750 +bond 13 107 337.00 1.4490 +bond 13 108 187.00 1.8600 +bond 13 109 317.00 1.5100 +bond 14 14 530.00 1.3400 +bond 15 17 274.00 1.3360 +bond 15 48 250.00 1.7400 +bond 16 16 166.00 2.0380 +bond 16 19 300.00 1.6850 +bond 16 24 250.00 1.7300 +bond 16 25 340.00 0.5000 +bond 16 47 250.00 1.7600 +bond 16 48 250.00 1.7600 +bond 16 61 250.00 1.7300 +bond 16 82 250.00 1.7600 +bond 16 84 250.00 1.7400 +bond 16 91 222.00 1.8100 +bond 16 108 144.00 2.1500 +bond 17 25 340.00 0.1000 +bond 18 18 550.00 1.1200 +bond 18 19 650.00 1.1570 +bond 18 48 400.00 1.4100 +bond 18 56 550.00 1.2400 +bond 19 19 1150.00 1.2100 +bond 19 21 330.00 1.6370 +bond 19 46 420.00 1.0800 +bond 19 47 400.00 1.4260 +bond 19 48 400.00 1.4510 +bond 19 50 400.00 1.4260 +bond 19 65 330.00 1.7840 +bond 19 88 400.00 1.4510 +bond 19 91 400.00 1.4510 +bond 20 20 250.00 1.4700 +bond 20 21 200.00 1.6900 +bond 20 24 320.00 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47 47 549.00 1.3400 +bond 47 48 427.00 1.4330 +bond 47 50 549.00 1.3400 +bond 47 57 448.00 1.3650 +bond 47 58 367.00 1.0800 +bond 47 65 300.00 1.9000 +bond 47 66 250.00 2.0800 +bond 47 86 385.00 1.4600 +bond 47 91 317.00 1.5100 +bond 47 105 448.00 1.3650 +bond 47 110 700.00 1.3050 +bond 48 48 469.00 1.4000 +bond 48 49 367.00 1.0800 +bond 48 50 427.00 1.4330 +bond 48 53 400.00 1.4500 +bond 48 55 481.00 1.3400 +bond 48 56 483.00 1.3390 +bond 48 57 427.00 1.3810 +bond 48 60 469.00 1.4040 +bond 48 61 414.00 1.3910 +bond 48 64 220.00 1.7800 +bond 48 65 300.00 1.8700 +bond 48 66 250.00 2.0800 +bond 48 79 340.00 1.7700 +bond 48 81 469.00 1.4000 +bond 48 84 546.00 1.3670 +bond 48 86 469.00 1.4000 +bond 48 88 469.00 1.4210 +bond 48 91 317.00 1.4900 +bond 48 101 382.00 1.3850 +bond 48 102 400.00 1.4600 +bond 48 109 427.00 1.4330 +bond 49 59 367.00 1.0800 +bond 49 62 340.00 1.0800 +bond 49 82 367.00 1.0800 +bond 49 83 367.00 1.0800 +bond 49 84 367.00 1.0800 +bond 49 85 367.00 1.0800 +bond 49 87 367.00 1.0800 +bond 49 88 367.00 1.0800 +bond 50 50 385.00 1.4600 +bond 50 56 457.00 1.2900 +bond 50 84 549.00 1.3650 +bond 50 109 385.00 1.4600 +bond 51 105 337.00 1.4750 +bond 52 64 525.00 1.4800 +bond 53 54 434.00 1.0100 +bond 54 55 434.00 1.0100 +bond 55 59 481.00 1.3400 +bond 55 82 481.00 1.3400 +bond 56 56 500.00 1.3200 +bond 56 59 502.00 1.3240 +bond 56 60 461.00 1.3540 +bond 56 82 461.00 1.3540 +bond 56 86 483.00 1.3390 +bond 56 103 550.00 1.2100 +bond 56 109 457.00 1.2900 +bond 57 60 436.00 1.3740 +bond 57 61 400.00 1.3490 +bond 57 62 440.00 1.3710 +bond 57 81 428.00 1.3800 +bond 57 82 477.00 1.3430 +bond 57 84 427.00 1.3810 +bond 57 85 427.00 1.3810 +bond 57 86 385.00 1.4400 +bond 58 83 367.00 1.0800 +bond 58 84 367.00 1.0800 +bond 59 63 367.00 1.0800 +bond 60 60 520.00 1.3700 +bond 60 61 414.00 1.3910 +bond 60 80 388.00 1.4590 +bond 60 81 447.00 1.4190 +bond 60 87 469.00 1.4240 +bond 60 105 436.00 1.3740 +bond 61 61 400.00 1.2800 +bond 61 62 529.00 1.3040 +bond 61 82 488.00 1.3350 +bond 61 83 410.00 1.3940 +bond 61 84 410.00 1.3940 +bond 61 88 410.00 1.3200 +bond 62 63 367.00 1.0800 +bond 62 105 440.00 1.3710 +bond 63 82 367.00 1.0800 +bond 64 108 108.00 2.2500 +bond 65 82 300.00 1.8700 +bond 65 83 300.00 1.8700 +bond 65 84 300.00 1.8700 +bond 65 87 300.00 1.8700 +bond 65 88 300.00 1.8700 +bond 65 108 151.00 2.1900 +bond 66 82 250.00 2.0800 +bond 66 83 250.00 2.0800 +bond 66 84 250.00 2.0800 +bond 66 87 250.00 2.0800 +bond 66 88 250.00 2.0800 +bond 66 108 108.00 2.4400 +bond 77 78 500.00 1.8000 +bond 80 84 546.00 1.3520 +bond 82 86 385.00 1.4600 +bond 82 87 520.00 1.3700 +bond 83 84 520.00 1.3700 +bond 83 86 385.00 1.4600 +bond 84 84 512.00 1.3750 +bond 84 86 385.00 1.4600 +bond 84 87 546.00 1.3670 +bond 84 88 520.00 1.3700 +bond 85 85 520.00 1.3700 +bond 86 86 385.00 1.4600 +bond 86 87 385.00 1.4600 +bond 86 88 385.00 1.4600 +bond 87 87 469.00 1.4240 +bond 87 88 469.00 1.4240 +bond 89 90 490.00 1.3350 +bond 89 91 317.00 1.5220 +bond 90 91 337.00 1.4490 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60 57 82 70.00 109.80 +angle 45 57 84 35.00 120.00 +angle 61 57 84 56.00 113.10 +angle 60 57 84 70.00 109.80 +angle 82 57 84 70.00 109.80 +angle 84 57 84 70.00 109.80 +angle 81 57 84 70.00 111.60 +angle 45 57 85 35.00 120.00 +angle 82 57 85 70.00 109.80 +angle 24 59 55 70.00 116.00 +angle 49 59 56 35.00 115.45 +angle 13 59 56 70.00 115.50 +angle 55 59 56 70.00 119.30 +angle 24 59 56 70.00 123.30 +angle 56 59 56 70.00 129.10 +angle 56 59 63 35.00 115.45 +angle 13 60 48 70.00 120.00 +angle 48 60 48 85.00 134.90 +angle 56 60 57 70.00 126.20 +angle 57 60 60 70.00 106.20 +angle 20 60 60 70.00 110.60 +angle 16 60 60 70.00 111.00 +angle 13 60 60 70.00 120.00 +angle 24 60 60 70.00 127.70 +angle 56 60 60 70.00 127.70 +angle 48 60 60 85.00 117.30 +angle 3 60 60 85.00 119.20 +angle 60 60 61 70.00 111.00 +angle 24 60 61 70.00 126.20 +angle 3 60 61 70.00 130.00 +angle 48 60 61 70.00 132.40 +angle 12 60 80 85.00 134.90 +angle 48 60 80 85.00 134.90 +angle 80 60 81 85.00 108.80 +angle 12 60 81 85.00 116.20 +angle 48 60 81 85.00 116.20 +angle 3 60 84 70.00 130.00 +angle 60 60 87 70.00 107.30 +angle 57 60 87 70.00 107.70 +angle 81 60 87 85.00 108.80 +angle 12 60 87 85.00 134.90 +angle 48 60 87 85.00 134.90 +angle 60 60 105 70.00 106.20 +angle 56 60 105 70.00 126.20 +angle 48 61 48 70.00 125.20 +angle 25 61 57 10.00 125.00 +angle 25 61 61 10.00 125.00 +angle 60 61 62 70.00 103.80 +angle 25 61 82 10.00 125.00 +angle 61 61 82 70.00 109.00 +angle 60 61 82 70.00 110.00 +angle 82 61 83 70.00 110.00 +angle 57 61 84 70.00 104.10 +angle 82 61 84 70.00 110.00 +angle 57 61 88 70.00 104.10 +angle 20 61 88 70.00 105.30 +angle 49 62 57 35.00 120.00 +angle 49 62 61 35.00 120.00 +angle 57 62 61 70.00 113.90 +angle 57 62 63 35.00 123.05 +angle 61 62 63 35.00 123.05 +angle 49 62 105 35.00 120.00 +angle 63 62 105 35.00 123.05 +angle 61 62 105 70.00 113.90 +angle 5 64 5 45.00 102.60 +angle 4 64 5 100.00 108.23 +angle 4 64 13 45.00 109.50 +angle 5 64 20 45.00 102.60 +angle 20 64 20 45.00 102.60 +angle 13 64 20 45.00 109.50 +angle 4 64 20 100.00 108.23 +angle 4 64 48 45.00 109.50 +angle 5 64 48 45.00 109.50 +angle 20 64 48 45.00 109.50 +angle 5 64 52 45.00 108.23 +angle 13 64 52 45.00 109.50 +angle 20 64 52 100.00 108.23 +angle 52 64 52 140.00 119.90 +angle 25 65 25 33.00 109.47 +angle 25 66 25 33.00 109.47 +angle 78 77 78 150.00 180.00 +angle 6 79 11 62.00 98.90 +angle 13 79 13 62.00 102.00 +angle 5 79 13 75.00 96.40 +angle 5 79 23 74.00 108.70 +angle 13 79 23 74.00 108.90 +angle 23 79 23 104.00 119.00 +angle 13 79 24 100.00 103.00 +angle 23 79 24 120.00 107.00 +angle 13 79 44 62.00 102.00 +angle 23 79 44 74.00 108.90 +angle 13 79 48 62.00 102.00 +angle 23 79 48 74.00 107.20 +angle 5 79 48 75.00 96.40 +angle 24 79 48 100.00 103.00 +angle 13 79 82 62.00 102.00 +angle 46 80 60 35.00 126.80 +angle 2 80 60 70.00 128.60 +angle 13 80 60 70.00 128.60 +angle 46 80 84 35.00 126.80 +angle 2 80 84 70.00 125.00 +angle 13 80 84 70.00 125.00 +angle 60 80 84 85.00 106.40 +angle 12 81 57 70.00 132.80 +angle 48 81 57 70.00 132.80 +angle 57 81 60 70.00 104.40 +angle 12 81 60 85.00 122.70 +angle 48 81 60 85.00 122.70 +angle 13 82 16 70.00 125.00 +angle 16 82 24 70.00 125.00 +angle 16 82 44 70.00 120.20 +angle 20 82 49 35.00 117.00 +angle 16 82 49 35.00 125.00 +angle 49 82 57 35.00 120.00 +angle 57 82 57 70.00 120.00 +angle 13 82 57 70.00 125.00 +angle 48 82 57 70.00 125.00 +angle 56 82 57 70.00 126.20 +angle 49 82 61 35.00 120.00 +angle 16 82 61 70.00 113.60 +angle 16 82 61 70.00 115.00 +angle 20 82 61 70.00 115.00 +angle 57 82 61 70.00 120.00 +angle 13 82 61 70.00 125.00 +angle 44 82 61 70.00 126.10 +angle 24 82 61 70.00 126.20 +angle 57 82 79 70.00 120.00 +angle 61 82 79 70.00 120.00 +angle 20 82 86 70.00 122.00 +angle 61 82 86 70.00 130.00 +angle 57 82 87 70.00 106.20 +angle 56 82 87 70.00 127.70 +angle 49 83 61 35.00 120.00 +angle 48 83 61 70.00 111.00 +angle 13 83 61 70.00 124.50 +angle 49 83 84 35.00 128.20 +angle 61 83 84 70.00 111.00 +angle 13 83 84 70.00 130.70 +angle 13 84 16 70.00 125.00 +angle 13 84 20 70.00 121.60 +angle 16 84 24 70.00 125.00 +angle 20 84 49 35.00 113.40 +angle 16 84 49 35.00 125.00 +angle 48 84 49 35.00 130.70 +angle 49 84 50 35.00 130.70 +angle 20 84 50 70.00 110.00 +angle 49 84 57 35.00 121.60 +angle 13 84 57 70.00 121.60 +angle 48 84 57 70.00 121.60 +angle 3 84 57 85.00 120.00 +angle 57 84 58 35.00 120.00 +angle 13 84 61 70.00 118.90 +angle 49 84 80 35.00 120.00 +angle 57 84 80 70.00 108.70 +angle 49 84 83 35.00 130.70 +angle 57 84 83 70.00 106.30 +angle 20 84 83 70.00 108.00 +angle 16 84 83 70.00 111.00 +angle 13 84 83 70.00 130.70 +angle 13 84 84 70.00 120.00 +angle 57 84 84 70.00 120.00 +angle 61 84 84 70.00 120.00 +angle 20 84 86 70.00 121.60 +angle 57 84 86 70.00 121.60 +angle 49 84 87 35.00 132.10 +angle 57 84 87 70.00 107.70 +angle 20 84 87 70.00 110.60 +angle 16 84 87 70.00 111.00 +angle 61 84 87 70.00 111.90 +angle 13 84 87 70.00 132.10 +angle 48 84 87 70.00 132.10 +angle 86 84 87 70.00 132.10 +angle 3 84 87 85.00 120.00 +angle 49 85 57 35.00 120.00 +angle 13 85 57 70.00 121.60 +angle 49 85 85 35.00 130.70 +angle 57 85 85 70.00 106.30 +angle 13 85 85 70.00 130.70 +angle 48 86 48 63.00 120.00 +angle 48 86 56 70.00 124.00 +angle 48 86 82 63.00 120.00 +angle 48 86 83 63.00 120.00 +angle 48 86 84 63.00 120.00 +angle 48 86 86 63.00 120.00 +angle 56 86 86 70.00 124.00 +angle 48 86 87 63.00 120.00 +angle 48 86 88 63.00 120.00 +angle 49 87 60 35.00 120.00 +angle 46 87 60 35.00 126.80 +angle 13 87 60 70.00 128.60 +angle 49 87 84 35.00 125.70 +angle 46 87 84 35.00 126.80 +angle 84 87 84 70.00 103.80 +angle 82 87 84 70.00 110.40 +angle 2 87 84 70.00 125.00 +angle 13 87 84 70.00 125.00 +angle 3 87 84 70.00 130.00 +angle 60 87 84 85.00 106.40 +angle 84 87 86 70.00 125.70 +angle 49 87 87 35.00 127.50 +angle 60 87 87 70.00 107.30 +angle 84 87 87 70.00 107.30 +angle 86 87 87 70.00 127.50 +angle 84 87 88 70.00 103.80 +angle 48 88 49 35.00 128.60 +angle 49 88 61 35.00 118.90 +angle 13 88 61 70.00 118.90 +angle 19 88 61 70.00 118.90 +angle 61 88 87 70.00 111.90 +angle 4 89 90 80.00 134.00 +angle 90 89 91 70.00 91.00 +angle 4 89 91 80.00 134.00 +angle 13 90 89 55.00 127.00 +angle 89 90 91 50.00 94.00 +angle 13 90 91 50.00 126.00 +angle 24 91 46 35.00 108.00 +angle 13 91 46 35.00 114.30 +angle 44 91 46 35.00 114.30 +angle 46 91 46 35.00 114.30 +angle 16 91 46 37.50 108.00 +angle 46 91 47 35.00 109.50 +angle 46 91 89 37.50 110.00 +angle 24 91 89 70.00 117.00 +angle 46 91 90 35.00 111.00 +angle 16 91 90 55.00 109.00 +angle 91 91 91 30.00 79.20 +angle 13 91 91 37.50 117.20 +angle 44 91 91 37.50 117.20 +angle 46 91 91 37.50 117.20 +angle 24 91 91 37.50 126.00 +angle 16 91 91 55.00 128.00 +angle 89 91 91 63.00 85.00 +angle 47 91 91 63.00 114.00 +angle 90 91 91 80.00 89.00 +angle 13 95 13 172.80 120.00 +angle 13 95 46 144.00 120.00 +angle 13 101 45 35.00 109.50 +angle 45 101 45 43.60 106.40 +angle 45 101 48 50.00 112.50 +angle 13 101 48 50.00 120.50 +angle 13 102 103 80.00 117.50 +angle 48 102 103 80.00 117.50 +angle 103 102 103 80.00 125.00 +angle 25 103 25 10.00 109.50 +angle 25 103 102 10.00 109.50 +angle 13 104 13 45.00 109.50 +angle 3 105 10 70.00 117.60 +angle 3 105 13 70.00 117.60 +angle 3 105 45 35.00 119.20 +angle 45 105 47 35.00 119.20 +angle 13 105 47 70.00 121.20 +angle 3 105 47 70.00 121.60 +angle 3 105 51 70.00 117.60 +angle 47 105 51 70.00 121.20 +angle 45 105 60 30.00 125.80 +angle 6 105 60 70.00 125.80 +angle 10 105 60 70.00 125.80 +angle 13 105 60 70.00 125.80 +angle 51 105 60 70.00 125.80 +angle 45 105 62 30.00 128.80 +angle 60 105 62 70.00 105.40 +angle 6 105 62 70.00 128.80 +angle 10 105 62 70.00 128.80 +angle 13 105 62 70.00 128.80 +angle 51 105 62 70.00 128.80 +angle 4 106 24 20.00 109.50 +angle 24 106 24 20.00 109.50 +angle 13 107 13 50.00 118.00 +angle 3 107 13 50.00 121.90 +angle 1 108 13 35.00 110.50 +angle 13 108 13 60.00 110.00 +angle 13 108 20 60.00 100.00 +angle 20 108 20 60.00 110.00 +angle 13 108 21 35.00 110.50 +angle 45 108 45 35.00 109.50 +angle 13 108 45 35.00 110.50 +angle 46 108 46 35.00 109.50 +angle 13 108 46 35.00 110.50 +angle 13 108 65 35.00 110.50 +angle 13 108 66 35.00 110.50 +angle 13 108 108 50.00 112.00 +angle 46 109 48 35.00 123.30 +angle 46 109 50 35.00 120.00 +angle 13 109 50 70.00 124.00 +angle 46 109 109 35.00 120.00 +angle 13 109 109 70.00 124.00 +angle 50 109 109 70.00 124.00 +angle 48 109 109 85.00 117.00 +angle 4 110 47 160.00 180.00 +angle 47 110 47 160.00 180.00 + + + ################################ + ## ## + ## Urey-Bradley Parameters ## + ## ## + ################################ + + +ureybrad 35 34 35 38.25 1.5537 + + + ##################################### + ## ## + ## Improper Torsional Parameters ## + ## ## + ##################################### + + +imptors 0 0 3 4 21.000 180.0 2 +imptors 0 0 3 52 21.000 180.0 2 +imptors 0 0 24 0 5.000 180.0 2 +imptors 0 0 47 0 30.000 180.0 2 +imptors 0 0 48 0 5.000 180.0 2 + + + ############################ + ## ## + ## Torsional Parameters ## + ## ## + ############################ + + + ################################################################### + ## ## + ## Alternative Torsional Parameter Values for Use with OPLS-AA ## + ## ## + ## For some torsions, OPLS-AA has multiple possible parameter ## + ## values; the list below shows functional groups for which ## + ## these alternate (commented) values should be preferred; the ## + ## values are in the same order as in the full parameter list ## + ## ## + ## 4 3 3 36 generic (default) ## + ## 4 3 3 36 dicarbonyls ## + ## 36 3 3 36 hydrocarbon (default) ## + ## 36 3 3 36 dicarbonyls ## + ## 13 3 5 7 carboxylic acid (default) ## + ## 13 3 5 7 1,2-diacid monoanion ## + ## 4 3 13 13 peptide (default) ## + ## 4 3 13 13 propanamide ## + ## 4 3 13 13 carboxylic acid ## + ## 4 3 13 13 dicarboxylic acid ## + ## 4 3 13 13 aldyhyde, ketone, acyl halide ## + ## 4 3 13 13 1,2-diacid monoanion ## + ## 5 3 13 13 carboxylic acid (default) ## + ## 5 3 13 13 dicarboxylic acid ## + ## 35 3 13 13 peptide psi' (default) ## + ## 35 3 13 13 propanamide ## + ## 35 3 13 13 beta-3-peptide, last psi ## + ## 4 3 29 13 esters (default) ## + ## 4 3 29 13 benzoic esters ## + ## 7 5 13 13 alcohols (default) ## + ## 7 5 13 13 trifluoroethanol ## + ## 7 5 13 13 hexopyranoses ## + ## 7 5 13 36 alcohols (default) ## + ## 7 5 13 36 axial cyclohexanol ## + ## 7 5 13 36 trifluoroethanol ## + ## 0 13 13 13 alcohols, ethers (default) ## + ## 0 13 13 13 hexopyranoses ## + ## 3 13 13 3 dicarboxylic acid (default) ## + ## 3 13 13 3 1,2-diacid monoanion ## + ## 3 13 13 13 butanamide (default) ## + ## 3 13 13 13 carboxylate ion ## + ## 3 13 13 13 aldyhyde, ketone, acyl halide ## + ## 3 13 13 36 all carbonyls (default) ## + ## 3 13 13 36 dicarboxylic acid ## + ## 3 13 13 36 aldehyde, ketone, acyl halide ## + ## 5 13 13 5 diols only (default) ## + ## 5 13 13 5 triols only ## + ## 5 13 13 5 hexopyranoses ## + ## 13 13 13 13 hydrocarbon (default) ## + ## 13 13 13 13 perfluoroalkane ## + ## 13 13 13 35 peptide chi-1 (default) ## + ## 13 13 13 35 N-propylformamide ## + ## 36 13 13 69 generic (default) ## + ## 36 13 13 69 sulfone ## + ## 13 13 33 13 amine (default) ## + ## 13 13 33 13 exocyclic amine ## + ## 13 13 33 13 exocyclic 1,4-diamine ## + ## 13 13 33 34 amine (default) ## + ## 13 13 33 34 azetidine, 4-ring ## + ## 13 13 33 34 pyrrolidine, 5-ring ## + ## 13 13 33 34 cyclic amine ## + ## 13 13 33 34 cyclic 1,4-diamine ## + ## 13 13 35 3 peptide phi' (default) ## + ## 13 13 35 3 N-ethylformamide ## + ## 13 13 35 3 beta-3-peptide, first theta tors ## + ## 13 13 35 13 proline, CD-N-CA-CB (default) ## + ## 13 13 35 13 proline, CG-CD-N-CA ## + ## 36 13 35 3 peptide phi'' (default) ## + ## 36 13 35 3 N-methylformamide ## + ## 13 13 47 0 imidazole, indole, purine (default) ## + ## 13 13 47 0 nucleoside chi ## + ## 13 13 47 52 nucleoside (default) ## + ## 13 13 47 52 imidazole, indole, purine ## + ## 29 13 47 0 imidazole, indole, purine (default) ## + ## 29 13 47 0 nucleoside chi ## + ## 29 13 95 52 nucleoside (default) ## + ## 29 13 95 52 imidazole, indole, purine ## + ## 13 13 97 13 generic (default) ## + ## 13 13 97 13 generic ## + ## 17 15 38 0 aromatic thiol (default) ## + ## 17 15 38 0 aromatic thiol, N-C-S-H ## + ## 13 29 54 42 phosphonates (default) ## + ## 13 29 54 42 dimethyl phosphate ## + ## 34 35 72 16 diaryl amine (default) ## + ## 34 35 72 16 aniline-like ## + ## 34 35 72 29 diaryl amine (default) ## + ## 34 35 72 29 aniline-like ## + ## 13 40 40 37 diene (default) ## + ## 13 40 40 37 2-methyl-1,3-butadiene ## + ## 0 46 72 0 generic (default) ## + ## 0 46 72 0 generic ## + ## 0 47 72 0 generic (default) ## + ## 0 47 72 0 generic ## + ## 0 47 74 0 generic (default) ## + ## 0 47 74 0 generic ## + ## 0 47 74 0 generic ## + ## 0 51 72 0 generic (default) ## + ## 0 51 72 0 HA-CR-NB-?? or N?-CR-NB-?? ## + ## 0 72 77 0 generic (default) ## + ## 0 72 77 0 biphenyl-like, N-C-C-C ## + ## ## + ################################################################### + + +torsion 0 2 2 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 0 2 2 6 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 1 2 2 2 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 +torsion 1 2 2 6 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 +torsion 2 2 2 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 13 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 +torsion 6 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 6 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 +torsion 10 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 +torsion 6 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 +torsion 10 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 +torsion 0 2 10 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 10 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 2 2 13 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 +torsion 6 2 20 2 -7.400 0.0 1 3.000 180.0 2 1.800 0.0 3 +torsion 6 2 20 6 -8.400 0.0 1 3.000 180.0 2 1.800 0.0 3 +torsion 4 3 3 4 1.600 0.0 1 3.200 180.0 2 0.000 0.0 3 +torsion 4 3 3 13 0.000 0.0 1 0.500 180.0 2 0.000 0.0 3 +torsion 4 3 3 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 3 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +#torsion 4 3 3 36 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 +torsion 13 3 3 13 0.700 0.0 1 -1.500 180.0 2 0.000 0.0 3 +torsion 13 3 3 24 -0.500 0.0 1 0.200 180.0 2 0.000 0.0 3 +torsion 13 3 3 46 0.800 0.0 1 -0.760 180.0 2 0.000 0.0 3 +torsion 24 3 3 46 -0.900 0.0 1 0.300 180.0 2 0.000 0.0 3 +torsion 46 3 3 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +#torsion 36 3 3 36 0.800 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 3 3 5 7 3.000 0.0 1 5.500 180.0 2 0.000 0.0 3 +torsion 4 3 5 7 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 13 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 +#torsion 13 3 5 7 3.200 0.0 1 4.900 180.0 2 0.000 0.0 3 +torsion 24 3 5 7 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 46 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 +torsion 48 3 5 7 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 1 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 +torsion 3 3 13 46 0.000 0.0 1 0.000 180.0 2 0.085 0.0 3 +torsion 4 3 13 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +#torsion 4 3 13 13 0.000 0.0 1 1.166 180.0 2 0.000 0.0 3 +#torsion 4 3 13 13 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 +#torsion 4 3 13 13 -0.750 0.0 1 -0.550 180.0 2 -0.250 0.0 3 +#torsion 4 3 13 13 -0.277 0.0 1 1.228 180.0 2 -0.694 0.0 3 +#torsion 4 3 13 13 -1.000 0.0 1 -1.900 180.0 2 -0.900 0.0 3 +torsion 4 3 13 21 -0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 +torsion 4 3 13 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 4 3 13 48 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 +torsion 5 3 13 13 0.000 0.0 1 1.412 180.0 2 0.000 0.0 3 +#torsion 5 3 13 13 1.000 0.0 1 0.546 180.0 2 0.450 0.0 3 +torsion 5 3 13 44 5.260 0.0 1 0.820 180.0 2 0.000 0.0 3 +torsion 5 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 13 3 13 13 1.454 0.0 1 -0.144 180.0 2 -0.775 0.0 3 +torsion 13 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3 +torsion 20 3 13 13 0.000 0.0 1 0.000 180.0 2 -0.553 0.0 3 +torsion 20 3 13 46 0.000 0.0 1 0.000 180.0 2 0.132 0.0 3 +torsion 21 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 21 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 +torsion 24 3 13 13 1.173 0.0 1 0.189 180.0 2 -1.200 0.0 3 +#torsion 35 3 13 13 3.250 0.0 1 -0.402 180.0 2 -0.136 0.0 3 +#torsion 35 3 13 13 3.260 0.0 1 0.440 180.0 2 0.600 0.0 3 +torsion 24 3 13 21 0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 24 3 13 24 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3 +torsion 24 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 46 3 13 13 0.000 0.0 1 0.000 180.0 2 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0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 46 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 48 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 48 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 48 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 50 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 50 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 +torsion 109 109 109 109 1.423 0.0 1 4.055 180.0 2 0.858 0.0 3 + + + ################################################################ + ## ## + ## Additional Torsional Parameter Values Used with OPLS-AA ## + ## ## + ## The torsions listed below were added to official OPLS-AA ## + ## to complete the set needed for proteins; the values were ## + ## obtained by analogy from the closest OPLS-AA torsions; ## + ## most of the added values are for HIP or N-terminal AAs; ## + ## ## + ################################################################ + + +torsion 24 3 13 53 1.816 0.0 1 1.222 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0.5500 +charge 870 -0.1000 +charge 871 -0.4300 +charge 872 -0.3700 +charge 873 -0.3100 +charge 874 -0.2500 +charge 875 -1.0000 +charge 876 -1.0000 +charge 877 -1.0000 +charge 878 -1.0000 +charge 879 1.0000 +charge 880 1.0000 +charge 881 1.0000 +charge 882 1.0000 +charge 883 1.0000 +charge 884 2.0000 +charge 885 2.0000 +charge 886 2.0000 +charge 887 2.0000 +charge 888 -0.0500 +charge 889 0.0500 +charge 890 0.1500 +charge 891 0.2500 +charge 892 0.1000 +charge 893 0.1150 +charge 894 0.1350 +charge 895 0.0150 +charge 896 0.1550 +charge 897 0.0000 +charge 898 -0.1150 +charge 899 0.1500 +charge 900 -0.2500 +charge 901 -0.1000 +charge 902 0.0500 +charge 903 -0.1000 +charge 904 0.2000 +charge 905 -0.2500 +charge 906 0.0880 + + + ######################################## + ## ## + ## Biopolymer Atom Type Conversions ## + ## ## + ######################################## + + +biotype 1 N "Glycine" 180 +biotype 2 CA "Glycine" 165 +biotype 3 C "Glycine" 177 +biotype 4 HN "Glycine" 183 +biotype 5 O "Glycine" 178 +biotype 6 HA "Glycine" 85 +biotype 7 N "Alanine" 180 +biotype 8 CA "Alanine" 166 +biotype 9 C "Alanine" 177 +biotype 10 HN "Alanine" 183 +biotype 11 O "Alanine" 178 +biotype 12 HA "Alanine" 85 +biotype 13 CB "Alanine" 80 +biotype 14 HB "Alanine" 85 +biotype 15 N "Valine" 180 +biotype 16 CA "Valine" 166 +biotype 17 C "Valine" 177 +biotype 18 HN "Valine" 183 +biotype 19 O "Valine" 178 +biotype 20 HA "Valine" 85 +biotype 21 CB "Valine" 82 +biotype 22 HB "Valine" 85 +biotype 23 CG1 "Valine" 80 +biotype 24 HG1 "Valine" 85 +biotype 25 CG2 "Valine" 80 +biotype 26 HG2 "Valine" 85 +biotype 27 N "Leucine" 180 +biotype 28 CA "Leucine" 166 +biotype 29 C "Leucine" 177 +biotype 30 HN "Leucine" 183 +biotype 31 O "Leucine" 178 +biotype 32 HA "Leucine" 85 +biotype 33 CB "Leucine" 81 +biotype 34 HB "Leucine" 85 +biotype 35 CG "Leucine" 82 +biotype 36 HG "Leucine" 85 +biotype 37 CD1 "Leucine" 80 +biotype 38 HD1 "Leucine" 85 +biotype 39 CD2 "Leucine" 80 +biotype 40 HD2 "Leucine" 85 +biotype 41 N "Isoleucine" 180 +biotype 42 CA "Isoleucine" 166 +biotype 43 C "Isoleucine" 177 +biotype 44 HN "Isoleucine" 183 +biotype 45 O "Isoleucine" 178 +biotype 46 HA "Isoleucine" 85 +biotype 47 CB "Isoleucine" 82 +biotype 48 HB "Isoleucine" 85 +biotype 49 CG1 "Isoleucine" 80 +biotype 50 HG1 "Isoleucine" 85 +biotype 51 CG2 "Isoleucine" 81 +biotype 52 HG2 "Isoleucine" 85 +biotype 53 CD "Isoleucine" 80 +biotype 54 HD "Isoleucine" 85 +biotype 55 N "Serine" 180 +biotype 56 CA "Serine" 166 +biotype 57 C "Serine" 177 +biotype 58 HN "Serine" 183 +biotype 59 O "Serine" 178 +biotype 60 HA "Serine" 85 +biotype 61 CB "Serine" 99 +biotype 62 HB "Serine" 85 +biotype 63 OG "Serine" 96 +biotype 64 HG "Serine" 97 +biotype 65 N "Threonine" 180 +biotype 66 CA "Threonine" 166 +biotype 67 C "Threonine" 177 +biotype 68 HN "Threonine" 183 +biotype 69 O "Threonine" 178 +biotype 70 HA "Threonine" 85 +biotype 71 CB "Threonine" 100 +biotype 72 HB "Threonine" 85 +biotype 73 OG1 "Threonine" 96 +biotype 74 HG1 "Threonine" 97 +biotype 75 CG2 "Threonine" 80 +biotype 76 HG2 "Threonine" 85 +biotype 77 N "Cysteine (SH)" 180 +biotype 78 CA "Cysteine (SH)" 166 +biotype 79 C "Cysteine (SH)" 177 +biotype 80 HN "Cysteine (SH)" 183 +biotype 81 O "Cysteine (SH)" 178 +biotype 82 HA "Cysteine (SH)" 85 +biotype 83 CB "Cysteine (SH)" 148 +biotype 84 HB "Cysteine (SH)" 85 +biotype 85 SG "Cysteine (SH)" 142 +biotype 86 HG "Cysteine (SH)" 146 +biotype 87 N "Cystine (SS)" 180 +biotype 88 CA "Cystine (SS)" 166 +biotype 89 C "Cystine (SS)" 177 +biotype 90 HN "Cystine (SS)" 183 +biotype 91 O "Cystine (SS)" 178 +biotype 92 HA "Cystine (SS)" 85 +biotype 93 CB "Cystine (SS)" 156 +biotype 94 HB "Cystine (SS)" 85 +biotype 95 SG "Cystine (SS)" 145 +biotype 96 N "Cysteine (S-)" -1 +biotype 97 CA "Cysteine (S-)" -1 +biotype 98 C "Cysteine (S-)" -1 +biotype 99 HN "Cysteine (S-)" -1 +biotype 100 O "Cysteine (S-)" -1 +biotype 101 HA "Cysteine (S-)" -1 +biotype 102 CB "Cysteine (S-)" -1 +biotype 103 HB "Cysteine (S-)" -1 +biotype 104 SG "Cysteine (S-)" -1 +biotype 105 N "Proline" 181 +biotype 106 CA "Proline" 188 +biotype 107 C "Proline" 177 +biotype 108 O "Proline" 178 +biotype 109 HA "Proline" 85 +biotype 110 CB "Proline" 81 +biotype 111 HB "Proline" 85 +biotype 112 CG "Proline" 81 +biotype 113 HG "Proline" 85 +biotype 114 CD "Proline" 187 +biotype 115 HD "Proline" 85 +biotype 116 N "Phenylalanine" 180 +biotype 117 CA "Phenylalanine" 166 +biotype 118 C "Phenylalanine" 177 +biotype 119 HN "Phenylalanine" 183 +biotype 120 O "Phenylalanine" 178 +biotype 121 HA "Phenylalanine" 85 +biotype 122 CB "Phenylalanine" 94 +biotype 123 HB "Phenylalanine" 85 +biotype 124 CG "Phenylalanine" 90 +biotype 125 CD "Phenylalanine" 90 +biotype 126 HD "Phenylalanine" 91 +biotype 127 CE "Phenylalanine" 90 +biotype 128 HE "Phenylalanine" 91 +biotype 129 CZ "Phenylalanine" 90 +biotype 130 HZ "Phenylalanine" 91 +biotype 131 N "Tyrosine" 180 +biotype 132 CA "Tyrosine" 166 +biotype 133 C "Tyrosine" 177 +biotype 134 HN "Tyrosine" 183 +biotype 135 O "Tyrosine" 178 +biotype 136 HA "Tyrosine" 85 +biotype 137 CB "Tyrosine" 94 +biotype 138 HB "Tyrosine" 85 +biotype 139 CG "Tyrosine" 90 +biotype 140 CD "Tyrosine" 90 +biotype 141 HD "Tyrosine" 91 +biotype 142 CE "Tyrosine" 90 +biotype 143 HE "Tyrosine" 91 +biotype 144 CZ "Tyrosine" 108 +biotype 145 OH "Tyrosine" 109 +biotype 146 HH "Tyrosine" 110 +biotype 147 N "Tyrosine (O-)" -1 +biotype 148 CA "Tyrosine (O-)" -1 +biotype 149 C "Tyrosine (O-)" -1 +biotype 150 HN "Tyrosine (O-)" -1 +biotype 151 O "Tyrosine (O-)" -1 +biotype 152 HA "Tyrosine (O-)" -1 +biotype 153 CB "Tyrosine (O-)" -1 +biotype 154 HB "Tyrosine (O-)" -1 +biotype 155 CG "Tyrosine (O-)" -1 +biotype 156 CD "Tyrosine (O-)" -1 +biotype 157 HD "Tyrosine (O-)" -1 +biotype 158 CE "Tyrosine (O-)" -1 +biotype 159 HE "Tyrosine (O-)" -1 +biotype 160 CZ "Tyrosine (O-)" -1 +biotype 161 OH "Tyrosine (O-)" -1 +biotype 162 N "Tryptophan" 180 +biotype 163 CA "Tryptophan" 166 +biotype 164 C "Tryptophan" 177 +biotype 165 HN "Tryptophan" 183 +biotype 166 O "Tryptophan" 178 +biotype 167 HA "Tryptophan" 85 +biotype 168 CB "Tryptophan" 81 +biotype 169 HB "Tryptophan" 85 +biotype 170 CG "Tryptophan" 441 +biotype 171 CD1 "Tryptophan" 455 +biotype 172 HD1 "Tryptophan" 91 +biotype 173 CD2 "Tryptophan" 442 +biotype 174 NE1 "Tryptophan" 444 +biotype 175 HE1 "Tryptophan" 445 +biotype 176 CE2 "Tryptophan" 443 +biotype 177 CE3 "Tryptophan" 90 +biotype 178 HE3 "Tryptophan" 91 +biotype 179 CZ2 "Tryptophan" 90 +biotype 180 HZ2 "Tryptophan" 91 +biotype 181 CZ3 "Tryptophan" 90 +biotype 182 HZ3 "Tryptophan" 91 +biotype 183 CH2 "Tryptophan" 90 +biotype 184 HH2 "Tryptophan" 91 +biotype 185 N "Histidine (+)" 180 +biotype 186 CA "Histidine (+)" 166 +biotype 187 C "Histidine (+)" 177 +biotype 188 HN "Histidine (+)" 183 +biotype 189 O "Histidine (+)" 178 +biotype 190 HA "Histidine (+)" 85 +biotype 191 CB "Histidine (+)" 446 +biotype 192 HB "Histidine (+)" 85 +biotype 193 CG "Histidine (+)" 451 +biotype 194 ND1 "Histidine (+)" 453 +biotype 195 HD1 "Histidine (+)" 454 +biotype 196 CD2 "Histidine (+)" 451 +biotype 197 HD2 "Histidine (+)" 91 +biotype 198 CE1 "Histidine (+)" 450 +biotype 199 HE1 "Histidine (+)" 91 +biotype 200 NE2 "Histidine (+)" 453 +biotype 201 HE2 "Histidine (+)" 454 +biotype 202 N "Histidine (HD)" 180 +biotype 203 CA "Histidine (HD)" 166 +biotype 204 C "Histidine (HD)" 177 +biotype 205 HN "Histidine (HD)" 183 +biotype 206 O "Histidine (HD)" 178 +biotype 207 HA "Histidine (HD)" 85 +biotype 208 CB "Histidine (HD)" 446 +biotype 209 HB "Histidine (HD)" 85 +biotype 210 CG "Histidine (HD)" 449 +biotype 211 ND1 "Histidine (HD)" 444 +biotype 212 HD1 "Histidine (HD)" 445 +biotype 213 CD2 "Histidine (HD)" 448 +biotype 214 HD2 "Histidine (HD)" 91 +biotype 215 CE1 "Histidine (HD)" 447 +biotype 216 HE1 "Histidine (HD)" 91 +biotype 217 NE2 "Histidine (HD)" 452 +biotype 218 N "Histidine (HE)" 180 +biotype 219 CA "Histidine (HE)" 166 +biotype 220 C "Histidine (HE)" 177 +biotype 221 HN "Histidine (HE)" 183 +biotype 222 O "Histidine (HE)" 178 +biotype 223 HA "Histidine (HE)" 85 +biotype 224 CB "Histidine (HE)" 446 +biotype 225 HB "Histidine (HE)" 85 +biotype 226 CG "Histidine (HE)" 448 +biotype 227 ND1 "Histidine (HE)" 452 +biotype 228 CD2 "Histidine (HE)" 449 +biotype 229 HD2 "Histidine (HE)" 91 +biotype 230 CE1 "Histidine (HE)" 447 +biotype 231 HE1 "Histidine (HE)" 91 +biotype 232 NE2 "Histidine (HE)" 444 +biotype 233 HE2 "Histidine (HE)" 445 +biotype 234 N "Aspartic Acid" 180 +biotype 235 CA "Aspartic Acid" 166 +biotype 236 C "Aspartic Acid" 177 +biotype 237 HN "Aspartic Acid" 183 +biotype 238 O "Aspartic Acid" 178 +biotype 239 HA "Aspartic Acid" 85 +biotype 240 CB "Aspartic Acid" 216 +biotype 241 HB "Aspartic Acid" 85 +biotype 242 CG "Aspartic Acid" 213 +biotype 243 OD "Aspartic Acid" 214 +biotype 244 N "Aspartic Acid (COOH)" -1 +biotype 245 CA "Aspartic Acid (COOH)" -1 +biotype 246 C "Aspartic Acid (COOH)" -1 +biotype 247 HN "Aspartic Acid (COOH)" -1 +biotype 248 O "Aspartic Acid (COOH)" -1 +biotype 249 HA "Aspartic Acid (COOH)" -1 +biotype 250 CB "Aspartic Acid (COOH)" -1 +biotype 251 HB "Aspartic Acid (COOH)" -1 +biotype 252 CG "Aspartic Acid (COOH)" -1 +biotype 253 OD1 "Aspartic Acid (COOH)" -1 +biotype 254 OD2 "Aspartic Acid (COOH)" -1 +biotype 255 HD2 "Aspartic Acid (COOH)" -1 +biotype 256 N "Asparagine" 180 +biotype 257 CA "Asparagine" 166 +biotype 258 C "Asparagine" 177 +biotype 259 HN "Asparagine" 183 +biotype 260 O "Asparagine" 178 +biotype 261 HA "Asparagine" 85 +biotype 262 CB "Asparagine" 81 +biotype 263 HB "Asparagine" 85 +biotype 264 CG "Asparagine" 177 +biotype 265 OD1 "Asparagine" 178 +biotype 266 ND2 "Asparagine" 179 +biotype 267 HD2 "Asparagine" 182 +biotype 268 N "Glutamic Acid" 180 +biotype 269 CA "Glutamic Acid" 166 +biotype 270 C "Glutamic Acid" 177 +biotype 271 HN "Glutamic Acid" 183 +biotype 272 O "Glutamic Acid" 178 +biotype 273 HA "Glutamic Acid" 85 +biotype 274 CB "Glutamic Acid" 81 +biotype 275 HB "Glutamic Acid" 85 +biotype 276 CG "Glutamic Acid" 216 +biotype 277 HG "Glutamic Acid" 85 +biotype 278 CD "Glutamic Acid" 213 +biotype 279 OE "Glutamic Acid" 214 +biotype 280 N "Glutamic Acid (COOH)" -1 +biotype 281 CA "Glutamic Acid (COOH)" -1 +biotype 282 C "Glutamic Acid (COOH)" -1 +biotype 283 HN "Glutamic Acid (COOH)" -1 +biotype 284 O "Glutamic Acid (COOH)" -1 +biotype 285 HA "Glutamic Acid (COOH)" -1 +biotype 286 CB "Glutamic Acid (COOH)" -1 +biotype 287 HB "Glutamic Acid (COOH)" -1 +biotype 288 CG "Glutamic Acid (COOH)" -1 +biotype 289 HG "Glutamic Acid (COOH)" -1 +biotype 290 CD "Glutamic Acid (COOH)" -1 +biotype 291 OE1 "Glutamic Acid (COOH)" -1 +biotype 292 OE2 "Glutamic Acid (COOH)" -1 +biotype 293 HE2 "Glutamic Acid (COOH)" -1 +biotype 294 N "Glutamine" 180 +biotype 295 CA "Glutamine" 166 +biotype 296 C "Glutamine" 177 +biotype 297 HN "Glutamine" 183 +biotype 298 O "Glutamine" 178 +biotype 299 HA "Glutamine" 85 +biotype 300 CB "Glutamine" 81 +biotype 301 HB "Glutamine" 85 +biotype 302 CG "Glutamine" 81 +biotype 303 HG "Glutamine" 85 +biotype 304 CD "Glutamine" 177 +biotype 305 OE1 "Glutamine" 178 +biotype 306 NE2 "Glutamine" 179 +biotype 307 HE2 "Glutamine" 182 +biotype 308 N "Methionine" 180 +biotype 309 CA "Methionine" 166 +biotype 310 C "Methionine" 177 +biotype 311 HN "Methionine" 183 +biotype 312 O "Methionine" 178 +biotype 313 HA "Methionine" 85 +biotype 314 CB "Methionine" 81 +biotype 315 HB "Methionine" 85 +biotype 316 CG "Methionine" 152 +biotype 317 HG "Methionine" 85 +biotype 318 SD "Methionine" 144 +biotype 319 CE "Methionine" 151 +biotype 320 HE "Methionine" 85 +biotype 321 N "Lysine" 180 +biotype 322 CA "Lysine" 166 +biotype 323 C "Lysine" 177 +biotype 324 HN "Lysine" 183 +biotype 325 O "Lysine" 178 +biotype 326 HA "Lysine" 85 +biotype 327 CB "Lysine" 81 +biotype 328 HB "Lysine" 85 +biotype 329 CG "Lysine" 81 +biotype 330 HG "Lysine" 85 +biotype 331 CD "Lysine" 81 +biotype 332 HD "Lysine" 85 +biotype 333 CE "Lysine" 235 +biotype 334 HE "Lysine" 85 +biotype 335 NZ "Lysine" 230 +biotype 336 HZ "Lysine" 233 +biotype 337 N "Lysine (NH2)" -1 +biotype 338 CA "Lysine (NH2)" -1 +biotype 339 C "Lysine (NH2)" -1 +biotype 340 HN "Lysine (NH2)" -1 +biotype 341 O "Lysine (NH2)" -1 +biotype 342 HA "Lysine (NH2)" -1 +biotype 343 CB "Lysine (NH2)" -1 +biotype 344 HB "Lysine (NH2)" -1 +biotype 345 CG "Lysine (NH2)" -1 +biotype 346 HG "Lysine (NH2)" -1 +biotype 347 CD "Lysine (NH2)" -1 +biotype 348 HD "Lysine (NH2)" -1 +biotype 349 CE "Lysine (NH2)" -1 +biotype 350 HE "Lysine (NH2)" -1 +biotype 351 NZ "Lysine (NH2)" -1 +biotype 352 HZ "Lysine (NH2)" -1 +biotype 353 N "Arginine" 180 +biotype 354 CA "Arginine" 166 +biotype 355 C "Arginine" 177 +biotype 356 HN "Arginine" 183 +biotype 357 O "Arginine" 178 +biotype 358 HA "Arginine" 85 +biotype 359 CB "Arginine" 81 +biotype 360 HB "Arginine" 85 +biotype 361 CG "Arginine" 251 +biotype 362 HG "Arginine" 85 +biotype 363 CD "Arginine" 250 +biotype 364 HD "Arginine" 85 +biotype 365 NE "Arginine" 246 +biotype 366 HE "Arginine" 247 +biotype 367 CZ "Arginine" 245 +biotype 368 NH "Arginine" 243 +biotype 369 HH "Arginine" 244 +biotype 370 N "Ornithine" 180 +biotype 371 CA "Ornithine" 166 +biotype 372 C "Ornithine" 177 +biotype 373 HN "Ornithine" 183 +biotype 374 O "Ornithine" 178 +biotype 375 HA "Ornithine" 85 +biotype 376 CB "Ornithine" 81 +biotype 377 HB "Ornithine" 85 +biotype 378 CG "Ornithine" 81 +biotype 379 HG "Ornithine" 85 +biotype 380 CD "Ornithine" 235 +biotype 381 HD "Ornithine" 85 +biotype 382 NE "Ornithine" 230 +biotype 383 HE "Ornithine" 233 +biotype 384 N "MethylAlanine (AIB)" 180 +biotype 385 CA "MethylAlanine (AIB)" 167 +biotype 386 C "MethylAlanine (AIB)" 177 +biotype 387 HN "MethylAlanine (AIB)" 183 +biotype 388 O "MethylAlanine (AIB)" 178 +biotype 389 CB "MethylAlanine (AIB)" 80 +biotype 390 HB "MethylAlanine (AIB)" 85 +biotype 391 N "Pyroglutamic Acid" 180 +biotype 392 CA "Pyroglutamic Acid" 166 +biotype 393 C "Pyroglutamic Acid" 177 +biotype 394 HN "Pyroglutamic Acid" 183 +biotype 395 O "Pyroglutamic Acid" 178 +biotype 396 HA "Pyroglutamic Acid" 85 +biotype 397 CB "Pyroglutamic Acid" 81 +biotype 398 HB "Pyroglutamic Acid" 85 +biotype 399 CG "Pyroglutamic Acid" 216 +biotype 400 HG "Pyroglutamic Acid" 85 +biotype 401 CD "Pyroglutamic Acid" 177 +biotype 402 OE "Pyroglutamic Acid" 178 +biotype 403 N "N-Terminal GLY" 230 +biotype 404 CA "N-Terminal GLY" 235 +biotype 405 C "N-Terminal GLY" 177 +biotype 406 HN "N-Terminal GLY" 233 +biotype 407 O "N-Terminal GLY" 178 +biotype 408 HA "N-Terminal GLY" 85 +biotype 409 N "N-Terminal ALA" 230 +biotype 410 CA "N-Terminal ALA" 236 +biotype 411 C "N-Terminal ALA" 177 +biotype 412 HN "N-Terminal ALA" 233 +biotype 413 O "N-Terminal ALA" 178 +biotype 414 HA "N-Terminal ALA" 85 +biotype 415 N "N-Terminal VAL" 230 +biotype 416 CA "N-Terminal VAL" 236 +biotype 417 C "N-Terminal VAL" 177 +biotype 418 HN "N-Terminal VAL" 233 +biotype 419 O "N-Terminal VAL" 178 +biotype 420 HA "N-Terminal VAL" 85 +biotype 421 N "N-Terminal LEU" 230 +biotype 422 CA "N-Terminal LEU" 236 +biotype 423 C "N-Terminal LEU" 177 +biotype 424 HN "N-Terminal LEU" 233 +biotype 425 O "N-Terminal LEU" 178 +biotype 426 HA "N-Terminal LEU" 85 +biotype 427 N "N-Terminal ILE" 230 +biotype 428 CA "N-Terminal ILE" 236 +biotype 429 C "N-Terminal ILE" 177 +biotype 430 HN "N-Terminal ILE" 233 +biotype 431 O "N-Terminal ILE" 178 +biotype 432 HA "N-Terminal ILE" 85 +biotype 433 N "N-Terminal SER" 230 +biotype 434 CA "N-Terminal SER" 236 +biotype 435 C "N-Terminal SER" 177 +biotype 436 HN "N-Terminal SER" 233 +biotype 437 O "N-Terminal SER" 178 +biotype 438 HA "N-Terminal SER" 85 +biotype 439 N "N-Terminal THR" 230 +biotype 440 CA "N-Terminal THR" 236 +biotype 441 C "N-Terminal THR" 177 +biotype 442 HN "N-Terminal THR" 233 +biotype 443 O "N-Terminal THR" 178 +biotype 444 HA "N-Terminal THR" 85 +biotype 445 N "N-Terminal CYS (SH)" 230 +biotype 446 CA "N-Terminal CYS (SH)" 236 +biotype 447 C "N-Terminal CYS (SH)" 177 +biotype 448 HN "N-Terminal CYS (SH)" 233 +biotype 449 O "N-Terminal CYS (SH)" 178 +biotype 450 HA "N-Terminal CYS (SH)" 85 +biotype 451 N "N-Terminal CYX (SS)" 230 +biotype 452 CA "N-Terminal CYX (SS)" 236 +biotype 453 C "N-Terminal CYX (SS)" 177 +biotype 454 HN "N-Terminal CYX (SS)" 233 +biotype 455 O "N-Terminal CYX (SS)" 178 +biotype 456 HA "N-Terminal CYX (SS)" 85 +biotype 457 N "N-Terminal CYD (S-)" -1 +biotype 458 CA "N-Terminal CYD (S-)" -1 +biotype 459 C "N-Terminal CYD (S-)" -1 +biotype 460 HN "N-Terminal CYD (S-)" -1 +biotype 461 O "N-Terminal CYD (S-)" -1 +biotype 462 HA "N-Terminal CYD (S-)" -1 +biotype 463 N "N-Terminal PRO" 252 +biotype 464 CA "N-Terminal PRO" 238 +biotype 465 C "N-Terminal PRO" 177 +biotype 466 HN "N-Terminal PRO" 253 +biotype 467 O "N-Terminal PRO" 178 +biotype 468 HA "N-Terminal PRO" 85 +biotype 469 CD "N-Terminal PRO" 239 +biotype 470 HD "N-Terminal PRO" 85 +biotype 471 N "N-Terminal PHE" 230 +biotype 472 CA "N-Terminal PHE" 236 +biotype 473 C "N-Terminal PHE" 177 +biotype 474 HN "N-Terminal PHE" 233 +biotype 475 O "N-Terminal PHE" 178 +biotype 476 HA "N-Terminal PHE" 85 +biotype 477 N "N-Terminal TYR" 230 +biotype 478 CA "N-Terminal TYR" 236 +biotype 479 C "N-Terminal TYR" 177 +biotype 480 HN "N-Terminal TYR" 233 +biotype 481 O "N-Terminal TYR" 178 +biotype 482 HA "N-Terminal TYR" 85 +biotype 483 N "N-Terminal TYD (O-)" -1 +biotype 484 CA "N-Terminal TYD (O-)" -1 +biotype 485 C "N-Terminal TYD (O-)" -1 +biotype 486 HN "N-Terminal TYD (O-)" -1 +biotype 487 O "N-Terminal TYD (O-)" -1 +biotype 488 HA "N-Terminal TYD (O-)" -1 +biotype 489 N "N-Terminal TRP" 230 +biotype 490 CA "N-Terminal TRP" 236 +biotype 491 C "N-Terminal TRP" 177 +biotype 492 HN "N-Terminal TRP" 233 +biotype 493 O "N-Terminal TRP" 178 +biotype 494 HA "N-Terminal TRP" 85 +biotype 495 N "N-Terminal HIS (+)" 230 +biotype 496 CA "N-Terminal HIS (+)" 236 +biotype 497 C "N-Terminal HIS (+)" 177 +biotype 498 HN "N-Terminal HIS (+)" 233 +biotype 499 O "N-Terminal HIS (+)" 178 +biotype 500 HA "N-Terminal HIS (+)" 85 +biotype 501 N "N-Terminal HIS (HD)" 230 +biotype 502 CA "N-Terminal HIS (HD)" 236 +biotype 503 C "N-Terminal HIS (HD)" 177 +biotype 504 HN "N-Terminal HIS (HD)" 233 +biotype 505 O "N-Terminal HIS (HD)" 178 +biotype 506 HA "N-Terminal HIS (HD)" 85 +biotype 507 N "N-Terminal HIS (HE)" 230 +biotype 508 CA "N-Terminal HIS (HE)" 236 +biotype 509 C "N-Terminal HIS (HE)" 177 +biotype 510 HN "N-Terminal HIS (HE)" 233 +biotype 511 O "N-Terminal HIS (HE)" 178 +biotype 512 HA "N-Terminal HIS (HE)" 85 +biotype 513 N "N-Terminal ASP" 230 +biotype 514 CA "N-Terminal ASP" 236 +biotype 515 C "N-Terminal ASP" 177 +biotype 516 HN "N-Terminal ASP" 233 +biotype 517 O "N-Terminal ASP" 178 +biotype 518 HA "N-Terminal ASP" 85 +biotype 519 N "N-Terminal ASH (COOH)" -1 +biotype 520 CA "N-Terminal ASH (COOH)" -1 +biotype 521 C "N-Terminal ASH (COOH)" -1 +biotype 522 HN "N-Terminal ASH (COOH)" -1 +biotype 523 O "N-Terminal ASH (COOH)" -1 +biotype 524 HA "N-Terminal ASH (COOH)" -1 +biotype 525 N "N-Terminal ASN" 230 +biotype 526 CA "N-Terminal ASN" 236 +biotype 527 C "N-Terminal ASN" 177 +biotype 528 HN "N-Terminal ASN" 233 +biotype 529 O "N-Terminal ASN" 178 +biotype 530 HA "N-Terminal ASN" 85 +biotype 531 N "N-Terminal GLU" 230 +biotype 532 CA "N-Terminal GLU" 236 +biotype 533 C "N-Terminal GLU" 177 +biotype 534 HN "N-Terminal GLU" 233 +biotype 535 O "N-Terminal GLU" 178 +biotype 536 HA "N-Terminal GLU" 85 +biotype 537 N "N-Terminal GLH (COOH)" -1 +biotype 538 CA "N-Terminal GLH (COOH)" -1 +biotype 539 C "N-Terminal GLH (COOH)" -1 +biotype 540 HN "N-Terminal GLH (COOH)" -1 +biotype 541 O "N-Terminal GLH (COOH)" -1 +biotype 542 HA "N-Terminal GLH (COOH)" -1 +biotype 543 N "N-Terminal GLN" 230 +biotype 544 CA "N-Terminal GLN" 236 +biotype 545 C "N-Terminal GLN" 177 +biotype 546 HN "N-Terminal GLN" 233 +biotype 547 O "N-Terminal GLN" 178 +biotype 548 HA "N-Terminal GLN" 85 +biotype 549 N "N-Terminal MET" 230 +biotype 550 CA "N-Terminal MET" 236 +biotype 551 C "N-Terminal MET" 177 +biotype 552 HN "N-Terminal MET" 233 +biotype 553 O "N-Terminal MET" 178 +biotype 554 HA "N-Terminal MET" 85 +biotype 555 N "N-Terminal LYS" 230 +biotype 556 CA "N-Terminal LYS" 236 +biotype 557 C "N-Terminal LYS" 177 +biotype 558 HN "N-Terminal LYS" 233 +biotype 559 O "N-Terminal LYS" 178 +biotype 560 HA "N-Terminal LYS" 85 +biotype 561 N "N-Terminal LYD (NH2)" -1 +biotype 562 CA "N-Terminal LYD (NH2)" -1 +biotype 563 C "N-Terminal LYD (NH2)" -1 +biotype 564 HN "N-Terminal LYD (NH2)" -1 +biotype 565 O "N-Terminal LYD (NH2)" -1 +biotype 566 HA "N-Terminal LYD (NH2)" -1 +biotype 567 N "N-Terminal ARG" 230 +biotype 568 CA "N-Terminal ARG" 236 +biotype 569 C "N-Terminal ARG" 177 +biotype 570 HN "N-Terminal ARG" 233 +biotype 571 O "N-Terminal ARG" 178 +biotype 572 HA "N-Terminal ARG" 85 +biotype 573 N "N-Terminal ORN" 230 +biotype 574 CA "N-Terminal ORN" 236 +biotype 575 C "N-Terminal ORN" 177 +biotype 576 HN "N-Terminal ORN" 233 +biotype 577 O "N-Terminal ORN" 178 +biotype 578 HA "N-Terminal ORN" 85 +biotype 579 N "N-Terminal AIB" 230 +biotype 580 CA "N-Terminal AIB" 237 +biotype 581 C "N-Terminal AIB" 177 +biotype 582 HN "N-Terminal AIB" 233 +biotype 583 O "N-Terminal AIB" 178 +biotype 584 N "C-Terminal GLY" 180 +biotype 585 CA "C-Terminal GLY" 226 +biotype 586 C "C-Terminal GLY" 213 +biotype 587 HN "C-Terminal GLY" 183 +biotype 588 OXT "C-Terminal GLY" 214 +biotype 589 HA "C-Terminal GLY" 85 +biotype 590 N "C-Terminal ALA" 180 +biotype 591 CA "C-Terminal ALA" 225 +biotype 592 C "C-Terminal ALA" 213 +biotype 593 HN "C-Terminal ALA" 183 +biotype 594 OXT "C-Terminal ALA" 214 +biotype 595 HA "C-Terminal ALA" 85 +biotype 596 N "C-Terminal VAL" 180 +biotype 597 CA "C-Terminal VAL" 225 +biotype 598 C "C-Terminal VAL" 213 +biotype 599 HN "C-Terminal VAL" 183 +biotype 600 OXT "C-Terminal VAL" 214 +biotype 601 HA "C-Terminal VAL" 85 +biotype 602 N "C-Terminal LEU" 180 +biotype 603 CA "C-Terminal LEU" 225 +biotype 604 C "C-Terminal LEU" 213 +biotype 605 HN "C-Terminal LEU" 183 +biotype 606 OXT "C-Terminal LEU" 214 +biotype 607 HA "C-Terminal LEU" 85 +biotype 608 N "C-Terminal ILE" 180 +biotype 609 CA "C-Terminal ILE" 225 +biotype 610 C "C-Terminal ILE" 213 +biotype 611 HN "C-Terminal ILE" 183 +biotype 612 OXT "C-Terminal ILE" 214 +biotype 613 HA "C-Terminal ILE" 85 +biotype 614 N "C-Terminal SER" 180 +biotype 615 CA "C-Terminal SER" 225 +biotype 616 C "C-Terminal SER" 213 +biotype 617 HN "C-Terminal SER" 183 +biotype 618 OXT "C-Terminal SER" 214 +biotype 619 HA "C-Terminal SER" 85 +biotype 620 N "C-Terminal THR" 180 +biotype 621 CA "C-Terminal THR" 225 +biotype 622 C "C-Terminal THR" 213 +biotype 623 HN "C-Terminal THR" 183 +biotype 624 OXT "C-Terminal THR" 214 +biotype 625 HA "C-Terminal THR" 85 +biotype 626 N "C-Terminal CYS (SH)" 180 +biotype 627 CA "C-Terminal CYS (SH)" 225 +biotype 628 C "C-Terminal CYS (SH)" 213 +biotype 629 HN "C-Terminal CYS (SH)" 183 +biotype 630 OXT "C-Terminal CYS (SH)" 214 +biotype 631 HA "C-Terminal CYS (SH)" 85 +biotype 632 N "C-Terminal CYX (SS)" 180 +biotype 633 CA "C-Terminal CYX (SS)" 225 +biotype 634 C "C-Terminal CYX (SS)" 213 +biotype 635 HN "C-Terminal CYX (SS)" 183 +biotype 636 OXT "C-Terminal CYX (SS)" 214 +biotype 637 HA "C-Terminal CYX (SS)" 85 +biotype 638 N "C-Terminal CYD (S-)" -1 +biotype 639 CA "C-Terminal CYD (S-)" -1 +biotype 640 C "C-Terminal CYD (S-)" -1 +biotype 641 HN "C-Terminal CYD (S-)" -1 +biotype 642 OXT "C-Terminal CYD (S-)" -1 +biotype 643 HA "C-Terminal CYD (S-)" -1 +biotype 644 N "C-Terminal PRO" 181 +biotype 645 CA "C-Terminal PRO" 228 +biotype 646 C "C-Terminal PRO" 213 +biotype 647 OXT "C-Terminal PRO" 214 +biotype 648 HA "C-Terminal PRO" 85 +biotype 649 N "C-Terminal PHE" 180 +biotype 650 CA "C-Terminal PHE" 225 +biotype 651 C "C-Terminal PHE" 213 +biotype 652 HN "C-Terminal PHE" 183 +biotype 653 OXT "C-Terminal PHE" 214 +biotype 654 HA "C-Terminal PHE" 85 +biotype 655 N "C-Terminal TYR" 180 +biotype 656 CA "C-Terminal TYR" 225 +biotype 657 C "C-Terminal TYR" 213 +biotype 658 HN "C-Terminal TYR" 183 +biotype 659 OXT "C-Terminal TYR" 214 +biotype 660 HA "C-Terminal TYR" 85 +biotype 661 N "C-Terminal TYD (O-)" -1 +biotype 662 CA "C-Terminal TYD (O-)" -1 +biotype 663 C "C-Terminal TYD (O-)" -1 +biotype 664 HN "C-Terminal TYD (O-)" -1 +biotype 665 OXT "C-Terminal TYD (O-)" -1 +biotype 666 HA "C-Terminal TYD (O-)" -1 +biotype 667 N "C-Terminal TRP" 180 +biotype 668 CA "C-Terminal TRP" 225 +biotype 669 C "C-Terminal TRP" 213 +biotype 670 HN "C-Terminal TRP" 183 +biotype 671 OXT "C-Terminal TRP" 214 +biotype 672 HA "C-Terminal TRP" 85 +biotype 673 N "C-Terminal HIS (+)" 180 +biotype 674 CA "C-Terminal HIS (+)" 225 +biotype 675 C "C-Terminal HIS (+)" 213 +biotype 676 HN "C-Terminal HIS (+)" 183 +biotype 677 OXT "C-Terminal HIS (+)" 214 +biotype 678 HA "C-Terminal HIS (+)" 85 +biotype 679 N "C-Terminal HIS (HD)" 180 +biotype 680 CA "C-Terminal HIS (HD)" 225 +biotype 681 C "C-Terminal HIS (HD)" 213 +biotype 682 HN "C-Terminal HIS (HD)" 183 +biotype 683 OXT "C-Terminal HIS (HD)" 214 +biotype 684 HA "C-Terminal HIS (HD)" 85 +biotype 685 N "C-Terminal HIS (HE)" 180 +biotype 686 CA "C-Terminal HIS (HE)" 225 +biotype 687 C "C-Terminal HIS (HE)" 213 +biotype 688 HN "C-Terminal HIS (HE)" 183 +biotype 689 OXT "C-Terminal HIS (HE)" 214 +biotype 690 HA "C-Terminal HIS (HE)" 85 +biotype 691 N "C-Terminal ASP" 180 +biotype 692 CA "C-Terminal ASP" 225 +biotype 693 C "C-Terminal ASP" 213 +biotype 694 HN "C-Terminal ASP" 183 +biotype 695 OXT "C-Terminal ASP" 214 +biotype 696 HA "C-Terminal ASP" 85 +biotype 697 N "C-Terminal ASH (COOH)" -1 +biotype 698 CA "C-Terminal ASH (COOH)" -1 +biotype 699 C "C-Terminal ASH (COOH)" -1 +biotype 700 HN "C-Terminal ASH (COOH)" -1 +biotype 701 OXT "C-Terminal ASH (COOH)" -1 +biotype 702 HA "C-Terminal ASH (COOH)" -1 +biotype 703 N "C-Terminal ASN" 180 +biotype 704 CA "C-Terminal ASN" 225 +biotype 705 C "C-Terminal ASN" 213 +biotype 706 HN "C-Terminal ASN" 183 +biotype 707 OXT "C-Terminal ASN" 214 +biotype 708 HA "C-Terminal ASN" 85 +biotype 709 N "C-Terminal GLU" 180 +biotype 710 CA "C-Terminal GLU" 225 +biotype 711 C "C-Terminal GLU" 213 +biotype 712 HN "C-Terminal GLU" 183 +biotype 713 OXT "C-Terminal GLU" 214 +biotype 714 HA "C-Terminal GLU" 85 +biotype 715 N "C-Terminal GLH (COOH)" -1 +biotype 716 CA "C-Terminal GLH (COOH)" -1 +biotype 717 C "C-Terminal GLH (COOH)" -1 +biotype 718 HN "C-Terminal GLH (COOH)" -1 +biotype 719 OXT "C-Terminal GLH (COOH)" -1 +biotype 720 HA "C-Terminal GLH (COOH)" -1 +biotype 721 N "C-Terminal GLN" 180 +biotype 722 CA "C-Terminal GLN" 225 +biotype 723 C "C-Terminal GLN" 213 +biotype 724 HN "C-Terminal GLN" 183 +biotype 725 OXT "C-Terminal GLN" 214 +biotype 726 HA "C-Terminal GLN" 85 +biotype 727 N "C-Terminal MET" 180 +biotype 728 CA "C-Terminal MET" 225 +biotype 729 C "C-Terminal MET" 213 +biotype 730 HN "C-Terminal MET" 183 +biotype 731 OXT "C-Terminal MET" 214 +biotype 732 HA "C-Terminal MET" 85 +biotype 733 N "C-Terminal LYS" 180 +biotype 734 CA "C-Terminal LYS" 225 +biotype 735 C "C-Terminal LYS" 213 +biotype 736 HN "C-Terminal LYS" 183 +biotype 737 OXT "C-Terminal LYS" 214 +biotype 738 HA "C-Terminal LYS" 85 +biotype 739 N "C-Terminal LYD (NH2)" -1 +biotype 740 CA "C-Terminal LYD (NH2)" -1 +biotype 741 C "C-Terminal LYD (NH2)" -1 +biotype 742 HN "C-Terminal LYD (NH2)" -1 +biotype 743 OXT "C-Terminal LYD (NH2)" -1 +biotype 744 HA "C-Terminal LYD (NH2)" -1 +biotype 745 N "C-Terminal ARG" 180 +biotype 746 CA "C-Terminal ARG" 225 +biotype 747 C "C-Terminal ARG" 213 +biotype 748 HN "C-Terminal ARG" 183 +biotype 749 OXT "C-Terminal ARG" 214 +biotype 750 HA "C-Terminal ARG" 85 +biotype 751 N "C-Terminal ORN" 180 +biotype 752 CA "C-Terminal ORN" 225 +biotype 753 C "C-Terminal ORN" 213 +biotype 754 HN "C-Terminal ORN" 183 +biotype 755 OXT "C-Terminal ORN" 214 +biotype 756 HA "C-Terminal ORN" 85 +biotype 757 N "C-Terminal AIB" 180 +biotype 758 CA "C-Terminal AIB" 227 +biotype 759 C "C-Terminal AIB" 213 +biotype 760 HN "C-Terminal AIB" 183 +biotype 761 OXT "C-Terminal AIB" 214 +biotype 762 N "Deprotonated N-Terminus" -1 +biotype 763 H "Deprotonated N-Terminus" -1 +biotype 764 C "Formyl N-Terminus" 177 +biotype 765 H "Formyl N-Terminus" 221 +biotype 766 O "Formyl N-Terminus" 178 +biotype 767 CH3 "Acetyl N-Terminus" 80 +biotype 768 H "Acetyl N-Terminus" 85 +biotype 769 C "Acetyl N-Terminus" 177 +biotype 770 O "Acetyl N-Terminus" 178 +biotype 771 C "Protonated C-Terminus" -1 +biotype 772 O "Protonated C-Terminus" -1 +biotype 773 OH "Protonated C-Terminus" -1 +biotype 774 HO "Protonated C-Terminus" -1 +biotype 775 N "Amide C-Terminus" 179 +biotype 776 HN "Amide C-Terminus" 182 +biotype 777 N "N-MeAmide C-Terminus" 180 +biotype 778 HN "N-MeAmide C-Terminus" 183 +biotype 779 CH3 "N-MeAmide C-Terminus" 184 +biotype 780 H "N-MeAmide C-Terminus" 85 +biotype 2001 O "Water" 63 +biotype 2002 H "Water" 64 +biotype 2003 NA "Sodium Ion" -1 +biotype 2004 K "Potassium Ion" -1 +biotype 2005 MG "Magnesium Ion" -1 +biotype 2006 CA "Calcium Ion" -1 +biotype 2007 CL "Chloride Ion" -1 diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/system.lt new file mode 100644 index 0000000000..9f577532e2 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/system.lt @@ -0,0 +1,19 @@ +import "ethylene.lt" # <- defines the "Ethylene" molecule type. + + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 70.00 xlo xhi + 0.0 70.00 ylo yhi + 0.0 70.00 zlo zhi +} + + +# The next command generates a cubic lattice with 10.0 Angstroms spacing. +# This lattice spacing was not chosen carefully. +# The pressure must be equilibrated later. + +ethylenes = new Ethylene [7].move(0, 0, 10.0) + [7].move(0, 10.0, 0) + [7].move(10.0, 0, 0) + diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/run.in.npt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/run.in.npt new file mode 100644 index 0000000000..450d5b0d7b --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/run.in.npt @@ -0,0 +1,57 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" + +# ------------------------------- Atom Definition Section ------------------- + +read_data "system.data" + +# OPLSAA atom charges are stored in a separate file. +# Load that file now: + +include "system.in.charges" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +minimize 1.0e-4 1.0e-6 100000 400000 + +# -- simulation protocol -- + +timestep 1.0 + +print "---------------------------------------------------------------------------" +print "First, use Langevin dynamics to randomize the initial shape of the molecules" +print "(This is not really necessary, but it seems to speed up equilibration.)" +print "---------------------------------------------------------------------------" + +fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K +fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 barr +run 2000 +unfix fxlan +unfix fxnph + +print "---------------------------------------------------------------------------" +print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" +print "---------------------------------------------------------------------------" +dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz +# temperature: 300 K, pressure: 50 barr +fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1.0 +thermo 100 +#thermo_modify flush yes + +run 50000 + +write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/run.in.nvt new file mode 100644 index 0000000000..b704d1f9d4 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/run.in.nvt @@ -0,0 +1,50 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" + +# ------------------------------- Atom Definition Section ------------------- + +# Read the coordinates generated by an earlier NPT simulation + +read_data "system_after_npt.data" + +# OPLSAA atom charges are stored in a separate file. +# Load that file now: + +include "system.in.charges" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" + + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo 500 +#thermo_modify flush yes + +run 200000 + +write_restart system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT new file mode 100644 index 0000000000..355fe42831 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT @@ -0,0 +1,54 @@ +NOTE: This example requires the "Al99.eam.alloy" file. + (It was not included in this directory because if its large size.) + As of 2012-11, I was able to obtain it here: + http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + Copy it to the directory containing this README file. +------------------------------------------------------------------------ +This example shows an alternative way to setup the +aluminum crystal loading simulation described here: +http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression +by Mark Tschopp and Nathan R. Rhodes +For additional backgroumd information, please consult that web page. + +In this example, I use moltemplate to build a "DATA" file for this system. +(I can't think of a compelling reason to do this for simple simulations like +this. But this approach might be useful if you want to artificially create +unusual structures out of aluminum crystals, or mix them with other molecules. +I created this example in response to a user request.) + + + --- To build the system --- + +Carry out the instructions in README_setup.sh, +to generate the LAMMPS DATA file and input scripts you need: +system.data, system.in.init, system.in.settings. +(The run.in script contains references to these files.) + + + --- To run LAMMPS, try a command like: --- + +lmp_linux -i run.in + + or (if you have mpi installed) + +mpirun -np 4 lmp_linux -i run.in + +This will create an ordinary LAMMPS dump file you can visualize with VMD +traj.lammpstrj (See README_visualize.txt) + +It will also create a number of other files, such as: +dump.comp_0.cfg +dump.comp_500.cfg +dump.comp_20000.cfg +Al_comp_100.def1.txt + +The dump.comp_*.cfg files can be visualized using +AtomEye if you have AtomEye and ImageJ installed. +The procedure for doing this is explained in the original tutorial at: +http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression + +The "Al_comp_100.def1.txt" file is a four-column text file containing: +column 1: v_strain = (lx - v_L0)/v_L0 +column 2: -pxx/10000 (diagonal components of the stress tensor) +column 3: -pyy/10000 +column 4: -pzz/10000 diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh new file mode 100755 index 0000000000..22eb8c4357 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh @@ -0,0 +1,29 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # We will also need the "Al99.eam.alloy" file: + #cp -f Al99.eam.alloy ../ + # This file was (can be) downloaded from: + # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg new file mode 100644 index 0000000000..bf07914dac Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg new file mode 100644 index 0000000000..8650cf5cb0 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg new file mode 100644 index 0000000000..582cf5fe6d Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh new file mode 100755 index 0000000000..64f350f641 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh @@ -0,0 +1,22 @@ +# This example shows an alternative way to setup the +# aluminum crystal loading simulation described here: +# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression +# by Mark Tschopp and Nathan R. Rhodes +# For additional backgroumd information, please consult that web page. +# +# In this example, I use moltemplate to build a "DATA" file for this system. +# (I can't think of a compelling reason to do this for simple simulations like +# this. But this approach might be useful if you want to artificially create +# unusual structures out of aluminum crystals, or mix them with other molecules. +# I created this example in response to a user request.) +# +# Use these commands to generate the LAMMPS input script and data file: + +moltemplate.sh system.lt + +# This will generate system.data, system.in.init, system.in.settings. +# In addition to will need to download "Al99.eam.alloy" file. +# (It was not included in this directory because if its large size.) +# As of 2012-11, I was able to obtain it here: +# http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt new file mode 100644 index 0000000000..3054a45e01 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt @@ -0,0 +1,64 @@ +# "AlCell" defines the 4-atom FCC unit cell +# of Aluminum (with a 4.05 angstrom spacing) + +AlCell { + + # AtomID MolID(IGNORE!) AtomType Charge X Y Z + + write("Data Atoms") { + $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 + $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 + $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 + $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 + } + + write_once("In Init") { + units metal + atom_style full # <- Requires each atom has a MolID and Charge. + # This is not necessary. (Why use "full"? + # The "full" atom style is useful if you want to + # mix the aluminum with other molecules later. + # Otherwise, just use "atom_style atomic", and + # and remove the 2nd and 4th columns above.) + pair_style eam/alloy + } + + write_once("In Settings") { + pair_coeff * * Al99.eam.alloy Al + } + + write_once("Data Masses") { + @atom:Al 27.0 + } + +} # AlCell + + + + + +# Here is an alternate way to define AlCell +# using "scale(4.05)" to select the lattice spacing: +# +#FccCell { +# write("Data Atoms") { +# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 +# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 +# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 +# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 +# } +# write_once("Data Masses") { +# @atom:Al 27.0 +# } +# write_once("In Init") { +# units metal +# atom_style full +# pair_style eam/alloy +# } +# write_once("In Settings") { +# pair_coeff * * Al99.eam.alloy Al +# } +#} +# +#AlCell = FccCell.scale(4.05) +# diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt new file mode 100644 index 0000000000..f813c6f662 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt @@ -0,0 +1,35 @@ + +import "al_cell.lt" # <- this defines the unit cell for aluminum + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 40.50 xlo xhi + 0.0 40.50 ylo yhi + 0.0 40.50 zlo zhi +} + +# The next command generates an array of 10x10x10 AlCell unit cells with +# spacing 4.05 Angstroms. + +unitcells = new AlCell [10].move(0.00, 0.00, 4.05) + [10].move(0.00, 4.05, 0.00) + [10].move(4.05, 0.00, 0.00) + + + + + + + + + + + + +################################################################ +# The next command is not necessary: +# + create_var { $mol } # <-This forces all of the Al atoms in the crystal +# # to share the same molecule ID number. +# # Molecule ID numbers are not necessary. Ignore this. +# diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in new file mode 100644 index 0000000000..677cc60cab --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in @@ -0,0 +1,76 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- +# +# The run-settings below were stolen from: +# +# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression + + +compute csym all centro/atom fcc +compute peratom all pe/atom + +# EQUILIBRATION +reset_timestep 0 +timestep 0.001 +velocity all create 300 12345 mom yes rot no +fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 + +# Set thermo output +thermo 1000 +thermo_style custom step lx ly lz press pxx pyy pzz pe temp + +# Run for at least 10 picosecond (assuming 1 fs timestep) +run 20000 +unfix 1 + +# Store final cell length for strain calculations +variable tmp equal "lx" +variable L0 equal ${tmp} +print "Initial Length, L0: ${L0}" + +###################################### +# DEFORMATION +reset_timestep 0 + +fix 1 all npt temp 300 300 1 y 0 0 1 z 0 0 1 drag 1 +variable srate equal 1.0e10 +variable srate1 equal "-v_srate / 1.0e12" +fix 2 all deform 1 x erate ${srate1} units box remap x + +# Output strain and stress info to file +# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa] +# p2, p3, p4 are in GPa +variable strain equal "(lx - v_L0)/v_L0" +variable p1 equal "v_strain" +variable p2 equal "-pxx/10000" +variable p3 equal "-pyy/10000" +variable p4 equal "-pzz/10000" +fix def1 all print 100 "${p1} ${p2} ${p3} ${p4}" file Al_comp_100.def1.txt screen no + +# Use cfg for AtomEye +dump dAtomEye all cfg 250 dump.comp_*.cfg id type xs ys zs c_csym c_peratom fx fy fz +dump_modify dAtomEye element Al + +# For users without AtomEye (like me), I decided to create a regular dump file: +dump dCoords all custom 250 traj.lammpstrj id type x y z ix iy iz + +# Display thermo +thermo 1000 +thermo_style custom step v_strain temp v_p2 v_p3 v_p4 ke pe press + +run 20000 + +###################################### +# SIMULATION DONE +print "All done" diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT new file mode 100644 index 0000000000..d69f1d6ffa --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT @@ -0,0 +1,83 @@ +########################################################### +# Interaction of a carbon nanotube with a pair of "mystery +# molecules" (extracted from the cnat-cnt.data/in files). +########################################################### +# Author: Aysun Itai and Andrew Jewett + +This example uses "ltemplify.py" to create molecule templates out +of two different molecules in a pre-existing LAMMPS IN/DATA file. +Then I show how to use "moltemplate.sh" to make copies of these +molecules and to move and rotate them (creating new LAMMPS IN/DATA files). + + Disclaimer: +The molecules in this example are not physically realistic. +The purpose of this example is to demonstrate ltemplify usage. + + REQUIRED INPUT FILES + +cnad-cnt.data cnad-cnt.in system.lt + + cnad-cnt.data + This is a LAMMPS data file containing the coordinates and the topology + for a system combining the two molecules together. ltemplify will extract + molecules from this file, one at a time. + + cnad-cnt.in + This file contains force-field parameters and old run settings for the system. + (We ignore the run settings in this file.) The force-field parameters in + the "cnad-cnt.in" file are only necessary because we are going to build + a completely new set of simulation input files. (We are not only going to + rotate them and duplicate the molecules.) ltemplify.py will extract the + force field parameters from this file. This approach allows us to combine + these molecules with other types of molecules later on.) + + system.lt + The "system.lt" contains the instructions what we will do with these molecules + after ltemplify.py has converted them into .LT format. In this example + it contains instructions for rotating and copying the two molecules, + (It also defines the periodic boundary conditions.) + + OUTPUT FILES + +cnad.lt +cnt.lt + +These files are referenced in system.lt. +Running moltemplate.sh on system.lt (using "moltemplate.sh system.lt") +creates new LAMMPS data and input files: +system.data, system.in, system.in.init, system.in.settings +(These files are referenced in run.in.nvt.) + +You can run a simulation from the files created by moltemplate using + +lmp_linux -i run.in.nvt + +NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY + ALTERED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY WHEN SIMULATED. + (This was done to protect the original source of the files.) + The goal of this example is only to demonstrate how to use + "ltemplify.py" to convert lammps input and data files into + LT format and back again.) + + ----------- + +Instructions: +Run the commands (follow the instructions) in these files: + +step 1) +README_step1_run_ltemplify.sh + +and then + +step 2) +README_step2_run_moltemplate.sh + +step 3) OPTIONAL + +To run a short LAMMPS simulation, you can use the "in.nvt" file, for example: + +$LAMMPS_BINARY -i run.in.nvt + +where "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +(such as lmp_linux, lmp_g++, lmp_mac, lmp_ubuntu, lmp_cygwin, etc...). + ----------- diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh new file mode 100755 index 0000000000..4bb42d7ea6 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh @@ -0,0 +1,13 @@ +#!/bin/sh + +# Aysun Itai's LAMMPS files contain two molecules: + +# The CNAD molecule has molecule-id 1 + +ltemplify.py -name CNAD -molid "1" cnad-cnt.in cnad-cnt.data > cnad.lt + +# The CNT (carbon nanotube) corresponds to molecule-id 2 +ltemplify.py -name CNT -molid "2" cnad-cnt.in cnad-cnt.data > cnt.lt + +# This will extract both molecules and save them as separate .LT files. +# (We can include these files later when preparing new simulations.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh new file mode 100755 index 0000000000..c99d4b9729 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh @@ -0,0 +1,18 @@ +# --- Running Moltemplate --- +# -- Prerequisites: -- +# The "system.lt" moltemplate file links to other ".lt" files +# files you hopefully have created earlier when you ran "ltemplify.py: +# cnad.lt and cnt.lt +# If not, carry out the instructions in "README_run_ltemplify.sh". + +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data. +# These files are the input files directly read by LAMMPS. + +# Optional: +# The "./output_ttree/" directory is full of temporary files generated by +# moltemplate. They can be useful for debugging, but are usually thrown away. + +rm -rf output_ttree/ + diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh new file mode 100755 index 0000000000..813c406c0e --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh @@ -0,0 +1,16 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" LAMMPS input script links to the input +# scripts and data files you hopefully have created earlier +# with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_run_moltemplate.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps this way: + +lmp_linux -i run.in.nvt + +# NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY +# REMOVED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY. diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt new file mode 100644 index 0000000000..3b9be3e9c3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt @@ -0,0 +1,50 @@ + + ------- To view the trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + + +Later, to Load a trajectory in VMD: + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it + +----- Wrap the coordinates to the unit cell + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Enter: + + DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT. + LOOKUP "pbctools" FOR DETAILS. + + pbc wrap -compound res -all + pbc box + +3) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data new file mode 100644 index 0000000000..1f18ff4aef --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data @@ -0,0 +1,1157 @@ +Created by Aysun Itai and modified by Andrew Jewett +NOTE: This file has been extensively modified. +Only the bond connectivity and atomic positions are accurate. + + 101 atoms + 134 bonds + 252 angles + 457 dihedrals + 0 impropers + + 16 atom types + 24 bond types + 50 angle types + 78 dihedral types + 0 improper types + + 0 50 xlo xhi + 0 50 ylo yhi + 0 50 zlo zhi + +Masses + + 1 10.0 + 2 10.0 # atom type names often appear + 3 10.0 # in the comments follwing + 4 10.0 # each line in the Masses section + 5 10.0 + 6 10.0 + 7 10.0 + 8 10.0 + 9 10.0 + 10 10.0 + 11 10.0 + 12 10.0 + 13 10.0 + 14 10.0 + 15 10.0 + 16 10.0 + +Atoms + +1 2 1 0.000000 12.345 10.000 4.328 +2 2 1 0.000000 12.031 11.173 5.037 +3 2 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@@ -0,0 +1,49 @@ +#Created by Aysun Itai and modified by Andrew Jewett +# NOTE: This file has been extensively modified. +# Only the bond connectivity and atomic positions are accurate. + +units real + +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +pair_style lj/charmm/coul/charmm 8.0 10.0 +pair_modify mix arithmetic + +read_data cnad-cnt.data + +pair_coeff 1 1 0.02 4.0 +pair_coeff 2 2 0.02 1.0 # atoms will not interact sterically +pair_coeff 3 3 0.02 2.0 # in this version of the file. +pair_coeff 4 4 0.02 2.0 # (All pair forces and atom names removed) +pair_coeff 5 5 0.02 2.0 +pair_coeff 6 6 0.02 3.0 +pair_coeff 7 7 0.02 3.0 +pair_coeff 8 8 0.02 3.0 +pair_coeff 9 9 0.02 4.0 +pair_coeff 10 10 0.02 4.0 +pair_coeff 11 11 0.02 4.0 +pair_coeff 12 12 0.02 4.0 +pair_coeff 13 13 0.02 3.0 +pair_coeff 14 14 0.02 3.0 +pair_coeff 15 15 0.02 3.0 +pair_coeff 16 16 0.02 3.0 + +group cnt type 1 +group cnad type 2-16 + +displace_atoms cnad move 0 -7 0 units box +special_bonds charmm + +velocity all create 0.0 54321 dist uniform + +thermo 1 +thermo_style multi +timestep 0.005 + +dump 1 all atom 10 cnad-cnt.dump + +run 20000 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg new file mode 100644 index 0000000000..3b79b405ef Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg new file mode 100644 index 0000000000..1f46c1b7b2 Binary files /dev/null and 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0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt new file mode 100644 index 0000000000..5c1d2d4172 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt @@ -0,0 +1,46 @@ +########################################################### +# Interaction of a carbon nanotube with a pair of mystery +# molecules (extracted from the cnat-cnt.data/in files). +########################################################### +# +# define the system being simulated: + +# -- init section -- +include system.in.init + +# -- atom definition section -- + +read_data system.data + +# -- settings section -- + +include system.in.settings + +# -- run section -- + + +timestep 0.05 +dump 1 all custom 2000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# The Nose-Hoover thermostat used with "fix nvt" can produce very odd-looking +# dynamics in dilute systems with few atoms (such as this one). +# Commenting this next line out: + +# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + +# Alternately, I receive fewer questions if I use langevin/nve instead: +fix fxlan all langevin 300.0 300.0 1000.0 48279 scale 3 1.5 +fix fxnve all nve + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data +#thermo_modify flush yes + +#restart 1000000 restart_nvt + +run 500000 + +write_restart system_after_nvt.rst + + diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt new file mode 100644 index 0000000000..70fdb7548b --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt @@ -0,0 +1,29 @@ +#Define the CNT and CNAD molecules, by including the files which define them +import cnt.lt +import cnad.lt + +# The cnt's center was originally at position 10,10,10, +# so I moved it back to the origin +cnt = new CNT.move(-10,-10,-10) + +# Rotation around the center of mass does not work (yet), +# so instead you have to move the molecule to the origin, +# rotate it, and move it back to where you want it. +# That's why the next line contains move().rot().move() +# I'll add center-of-mass rotation as a later feature. + +cnad1 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(90,0,1,0).move(-7,0,0) +cnad2 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(-90,0,1,0).move(7,0,0) + + +# You can leave the periodic boundary conditions unspecified +# and change them later, OR you can declare them +# using the "write_once("Data Boundary") {}" command: + +write_once("Data Boundary") +{ + 0 50.0 xlo xhi + 0 50.0 ylo yhi + 0 50.0 zlo zhi +} + diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT b/tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT new file mode 100644 index 0000000000..325cc95bd4 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT @@ -0,0 +1,38 @@ +This example is a simple simulation of 288 hexadecane molecules in a box at +room temperature and atmospheric pressure. Please read the WARNING.TXT file. + +-------- REQUIREMENTS: --------- +This example requires building LAMMPS with the "USER-MISC" package. +(because it uses dihedral_style fourier) +To do this, type "make yes-user-misc" before compiling LAMMPS. + http://lammps.sandia.gov/doc/Section_start.html#start_3 + +More detailed instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files: + +step 1) to setup the LAMMPS input files, run this file: +README_setup.sh + +step 2) to run LAMMPS, follow the instructions in this file: +README_run.sh + +------------ NOTE: There are two versions of this example. ---------------- + +Both examples use the same force-field parameters. + +1) In this directory, all of the force-field parameters are listed explicitly +in the "alkanes.lt" file (located in the "moltemplate_files" directory). +This allows the user to manually control all of the force-field details. + +2) However, there is an alternate version of this example in the +"../AMBER_force_field_examples" directory. +In that version, the force-fields are loaded from a much larger file named +"gaff.lt" which contains all of the parameters in the AMBER GAFF force-field +database. The "gaff.lt" is similar to the "alkanes.lt" file except that +it is larger (because it contains information for nearly all small organic +molecules). It is located in a different directory (in the "common" directory). + +Relying on "gaff.lt" frees the user from the drudgery of manually specifying +all of these force-field details for every molecule. (However, the user must +be careful to choose @atom-type names which match AMBER GAFF conventions, +such as "c3" and "h1", in this example.) diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_run.sh new file mode 100755 index 0000000000..8b01ab92d7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_run.sh @@ -0,0 +1,39 @@ +# --- Running LAMMPS --- +# -------- REQUIREMENTS: --------- +# 1) This example requires building LAMMPS with the "USER-MISC" package. +# (because it makes use of "gaff.lt" which uses dihedral_style fourier) +# To do this, type "make yes-user-misc" before compiling LAMMPS. +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# -------- PREREQUISITES: -------- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh new file mode 100755 index 0000000000..f632ada119 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh @@ -0,0 +1,25 @@ +# -------- REQUIREMENTS: --------- +# You must define your MOLTEMPLATE_PATH environment variable +# and set it to the "common" subdirectory of your moltemplate distribution. +# (See the "Installation" section in the moltemplate manual.) + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT b/tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT new file mode 100644 index 0000000000..faf178fbc2 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT @@ -0,0 +1,16 @@ +# -------- WARNING: -------- + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that the simulation +will reproduce the behavior of real hexadecane molecules, +(or even of hexadecane molecules simulated using AMBER, which should + be using the same force-field). + +# -------- REQUEST FOR HELP: -------- + +However, if you notice a problem with this example, please report it. +I confess I do not have a lot of experience running all-atom simulations. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2014-4-19) diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg new file mode 100644 index 0000000000..b0d31f8845 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg new file mode 100644 index 0000000000..f7c13d0989 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_LR.jpg new file mode 100644 index 0000000000..3ad353dbb4 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt new file mode 100644 index 0000000000..ee8cbadb5c --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt @@ -0,0 +1,78 @@ + +Alkanes { + + # LAMMPS offers many different force-field styles and atom-styles. + # We must select which kind of atoms and force fields we want to use. + # (This will effect the syntax of the "_coeff" commands below.) + + write_once("In Init") { + # Default styles and settings for AMBER based force-fields: + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + #improper_style hybrid cvff + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + kspace_style pppm 0.0001 + pair_modify shift yes + pair_modify mix arithmetic + special_bonds amber + } + + # The "Alkanes" object contains the definition of atoms, bonds, bond-angles, + # and all of the force-field parameters for simple n-Alkanes. + # (These parameters were taken from the January 2013 version of the + # AMBER GAFF force-field. See "common/gaff.lt" for details.) + + # atom-type mass + + write_once("Data Masses") { + @atom:c3 12.01 + @atom:h1 1.008 + } + + # Pairwise (non-bonded) force-field parameters: + + write_once("In Settings") { + pair_coeff @atom:c3 @atom:c3 lj/charmm/coul/long 0.1094 1.9080 + pair_coeff @atom:h1 @atom:h1 lj/charmm/coul/long 0.0157 1.3870 + } + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:CCC @atom:c3 @atom:c3 @atom:c3 @bond:* @bond:* + @angle:CCH @atom:c3 @atom:c3 @atom:h1 @bond:* @bond:* + @angle:HCH @atom:h1 @atom:c3 @atom:h1 @bond:* @bond:* + } + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 + + write_once("Data Dihedrals By Type") { + @dihedral:XCCX @atom:* @atom:c3 @atom:c3 @atom:* @bond:* @bond:* @bond:* + @dihedral:CCCC @atom:c3 @atom:c3 @atom:c3 @atom:c3 @bond:* @bond:* @bond:* + } + + # Parameters for these new angular interactions must be defined. (I recommend + # putting all force-field parameters (coeffs) in the "In Settings" section.) + + write_once("In Settings") { + + # bond-type k r0 + bond_coeff @bond:CC harmonic 303.1 1.5350 + bond_coeff @bond:CH harmonic 335.9 1.0930 + + # angle-type k theta0 + angle_coeff @angle:CCC harmonic 63.210 110.630 + angle_coeff @angle:CCH harmonic 46.360 110.070 + angle_coeff @angle:HCH harmonic 39.180 109.550 + + # dihedral-type + dihedral_coeff @dihedral:XCCX fourier 1 0.155555555556 3 0.0 + dihedral_coeff @dihedral:CCCC fourier 3 0.18 3 0.0 0.25 2 180.0 0.2 1 180.0 + } + +} # Alkanes diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt new file mode 100644 index 0000000000..e8c5b3bd08 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt @@ -0,0 +1,46 @@ + +import "alkanes.lt" # <-- Defines the atoms and force-field used for Alkanes + + +CH2 inherits Alkanes { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c3 -0.120 0.000 0.000 0.000 + $atom:H1 $mol:... @atom:h1 0.060 0.000 0.63104384422426 0.892430762954 + $atom:H2 $mol:... @atom:h1 0.060 0.000 0.63104384422426 -0.892430762954 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own. + # The CH2 group is part of the Hexadecane molecule. + + # Now specify which pairs of atoms are bonded: + # bond-id bond-type atom-id1 atom-id2 + + write('Data Bonds') { + $bond:b1 @bond:CH $atom:C $atom:H1 + $bond:b2 @bond:CH $atom:C $atom:H2 + } + +} # CH2 + + + + +# Atom charges for this example were taken from the OPLSAA force field file: +# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm +# +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 + + diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt new file mode 100644 index 0000000000..f06e958dc7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt @@ -0,0 +1,46 @@ + +import "alkanes.lt" # <-- Defines the atoms and force-field used for Alkanes + + +CH3 inherits Alkanes { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c3 -0.180 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.060 0.000000 0.6310438442242609 0.8924307629540046 + $atom:H2 $mol:... @atom:h1 0.060 0.000000 0.6310438442242609 -0.8924307629540046 + $atom:H3 $mol:... @atom:h1 0.060 -0.8924307629540046 -0.6310438442242609 0.000000 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own. + # The CH3 group is part of the Hexadecane molecule. + + # Now specify which pairs of atoms are bonded: + # bond-id bond-type atom-id1 atom-id2 + + write('Data Bonds') { + $bond:b1 @bond:CH $atom:C $atom:H1 + $bond:b2 @bond:CH $atom:C $atom:H2 + $bond:b3 @bond:CH $atom:C $atom:H3 + } + +} # CH3 + + + +# Atom charges for this example were taken from the OPLSAA force field file: +# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 + diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt new file mode 100644 index 0000000000..93a59e36a9 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt @@ -0,0 +1,85 @@ +# This example looks complicated because I split the +# hexadecane molecule into individual CH2 and CH3 monomers. +# +# I defined it this way so that you can easily modify +# it to change the length of the alkane chain. + +import "alkanes.lt" # load the "Alkanes" force-field information +import "ch2group.lt" # load the definition of the "CH2" object +import "ch3group.lt" # load the definition of the "CH3" object + + +Hexadecane inherits Alkanes { + + + # Create an array of 16 "CH2" objects distributed along the X axis + + monomers = new CH2.move(0,0.4431163,0) [16].rot(180,1,0,0).move(1.2533223,0,0) + + # Each CH2 monomer is initial moved in the +Y direction by 0.43116 + # angstroms. Then it is rotated 180 degrees with respect to the + # previous monomer, and moved 1.2533223 Angstroms down the X axis. + + # ---- Now, modify the ends: --- + # Delete the CH2 groups at the beginning and end, and replace them with CH3. + # (Note: Alternately, instead of deleting the CH2 groups at each end, you + # could modify them by adding an extra hydrogen atom to those carbons.) + + delete monomers[0] + delete monomers[15] + endcap1 = new CH3 + endcap2 = new CH3 + + # Move the CH3 groups to the correct location at either end of the chain: + + endcap1.move(0,0.4431163,0) + endcap2.move(0,0.4431163,0).rot(180,0,0,1).move(18.7998345,0,0) + + # Note: 18.7998345 = (16-1) * 1.2533223 + + + # Now add a list of bonds connecting the carbon atoms together: + + write('Data Bonds') { + $bond:b1 @bond:CC $atom:endcap1/C $atom:monomers[1]/C + $bond:b2 @bond:CC $atom:monomers[1]/C $atom:monomers[2]/C + $bond:b3 @bond:CC $atom:monomers[2]/C $atom:monomers[3]/C + $bond:b4 @bond:CC $atom:monomers[3]/C $atom:monomers[4]/C + $bond:b5 @bond:CC $atom:monomers[4]/C $atom:monomers[5]/C + $bond:b6 @bond:CC $atom:monomers[5]/C $atom:monomers[6]/C + $bond:b7 @bond:CC $atom:monomers[6]/C $atom:monomers[7]/C + $bond:b8 @bond:CC $atom:monomers[7]/C $atom:monomers[8]/C + $bond:b9 @bond:CC $atom:monomers[8]/C $atom:monomers[9]/C + $bond:b10 @bond:CC $atom:monomers[9]/C $atom:monomers[10]/C + $bond:b11 @bond:CC $atom:monomers[10]/C $atom:monomers[11]/C + $bond:b12 @bond:CC $atom:monomers[11]/C $atom:monomers[12]/C + $bond:b13 @bond:CC $atom:monomers[12]/C $atom:monomers[13]/C + $bond:b14 @bond:CC $atom:monomers[13]/C $atom:monomers[14]/C + $bond:b15 @bond:CC $atom:monomers[14]/C $atom:endcap2/C + } + + # OPTIONAL: + create_var { $mol } # Create a molecule ID number. This number will + # be shared by all of the atoms in this polymer. + # In ch2group.lt, "$mol:..." refers to this number. + +} # Hexadecane + + + + + + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt new file mode 100644 index 0000000000..4e0cfaec69 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt @@ -0,0 +1,18 @@ +import "hexadecane.lt" # <- defines the "Hexadecane" molecule type. + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 62.4 xlo xhi + 0.0 62.4 ylo yhi + 0.0 62.4 zlo zhi +} + +molecules = new Hexadecane [12].move(0, 0, 5.2) + [12].move(0, 5.2, 0) + [2].move(31.2, 0, 0) + + +# NOTE: The spacing between molecules is large. There should be extra room to +# move during the initial stages of equilibration. However, you will have to +# run the simulation at NPT conditions later to compress the system to a +# more realistic density. diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt new file mode 100644 index 0000000000..9793764643 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt @@ -0,0 +1,85 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# To avvoid explosions, I have a 4-step equilibraion process (expand, minimize, +# reorient, compress). The system (as defined in the "system.data" file) +# is already expanded. That means there are 3 steps left: + +dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz +thermo 50 + +# -- Equilibration: part 1: initial minimization -- + +# Note: In general, it's always a good idea to minimize the system at first. + +minimize 1.0e-5 1.0e-7 100000 400000 +undump dumpeq1 + +write_data system_after_eq1_min.data + +# -- Equilibration part 2: reorienting the molecules (NVT) -- + +timestep 1.0 +dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz + +# Run the system at high temperature (at constant volume) to reorient the +# the molecules (which would otherwise be pointing in the same direction). + +# To speed it up, I randomize the atomic positions for a few thousand steps +# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). +# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) + + +fix fxlan all langevin 900.0 900.0 120 48279 +fix fxnve all nve + +run 2000 + +unfix fxlan +unfix fxnve +# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). +fix fxnvt all nvt temp 900.0 900.0 100.0 + +run 5000 +undump dumpeq2 + + +write_data system_after_eq2_reorient.data + +unfix fxnvt + +# -- equilibration part 3: Equilibrating the density (NPT) -- + +# Originally, the simulation box (in "system.data" and "system.lt") was +# unrealistically large. The spacing between the molecules was large also. +# I did this to enable the molecules to move freely and reorient themselves. +# After doing that, we should run the simulation under NPT conditions to +# allow the simulation box to contract to it's natural size. We do that here: +# We begin the simulation at 100 barr (a relatively low pressure), and +# slowly decrease it to 1 barr, maintianing the temperature at 300K. + +dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0 + +timestep 1.0 +run 60000 + +write_data system_after_eq3_npt.data + diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt new file mode 100644 index 0000000000..f8b2d31d09 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt @@ -0,0 +1,42 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_eq3_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1 +thermo 100 +#thermo_modify flush yes + +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh new file mode 100755 index 0000000000..cf51fa8705 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure + +# or + +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +# or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh new file mode 100755 index 0000000000..3a08212692 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt new file mode 100644 index 0000000000..73358e55dc --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 500 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg b/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg new file mode 100644 index 0000000000..2cdc08b312 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_unitcell.png b/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_unitcell.png new file mode 100644 index 0000000000..5bd6057e1e Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_unitcell.png differ diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt new file mode 100644 index 0000000000..2b550b6309 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fSHAKE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt new file mode 100644 index 0000000000..ccfd2f18c6 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt @@ -0,0 +1,57 @@ +# This ice (1h) unit cell is rectangular and contains 8 water molecules. +# (Coordinates and cell dimensions converted were from a PDB file.) +# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362 + + +import "spce.lt" # <-- define the "SPCE" molecule + +SpceIceRect8 { + + # Create a 3-dimensional array of 8 water molecules + + wat = new SPCE[2][2][2] + + # Array indices will be correlated with position [xindex][yindex][zindex] + + # You can overwrite coordinates of atoms after they were created this way: + # (Order is not important) + # atom-ID molecule-ID atomType charge newX newY newZ + + write("Data Atoms") { + $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 + $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710 + $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710 + $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 + $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970 + $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652 + $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 + $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289 + $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971 + $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 + $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391 + $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391 + $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 + $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710 + $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710 + $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 + $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970 + $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652 + $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 + $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289 + $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971 + $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 + $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391 + $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391 + } +} # IceRect8 + +# Credit goes to Martin Chaplin. +# These coordinates were orignally downloaded from Martin Chaplin's +# website: http://www.btinternet.com/~martin.chaplin/ice1h.html +# ... and then they were stretched independently in the xy and z +# directions in order to match the lattice parameters measured by +# Rottger et al., +# "Lattice constants and thermal expansion of H2O and D2O ice Ih" +# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 +# I am using the lattice constants measured at temperature 265K +# (and pressure=100Torr). diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt new file mode 100644 index 0000000000..b4f22f9dcf --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt @@ -0,0 +1,11 @@ +import "spce_ice_rect8.lt" + +cells = new SpceIceRect8 [3].move(4.521, 0.0, 0.0) + [2].move( 0.0, 7.832, 0.0) + [2].move( 0.0, 0.0, 7.362) + +write_once("Data Boundary") { + 0 13.563 xlo xhi + 0 15.664 ylo yhi + 0 14.724 zlo zhi +} diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt new file mode 100644 index 0000000000..2bf2e0c03f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt @@ -0,0 +1,38 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". +unfix fSHAKE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fSHAKE again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 2.0 +dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 400.0 400.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 + +thermo 100 +#thermo_modify flush yes + +run 20000 + +write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt new file mode 100644 index 0000000000..b23a288c47 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt @@ -0,0 +1,61 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Normally, I would minimize the system and equilibrate the system at constant +# pressure and temperature beforehand. If you run lammps with "run.in.npt", +# it will generate a restart file "system_after_npt.rst" with reasonable +# coordinates at that temperature and pressure. Then we could load it now: +# +#read_restart system_after_npt.rst +# +# Unfortunately the LAMMPS "read_restart" command has been undependable over +# the past year (2012), and I feel it is safer to remove it from the examples. +# Instead, for this example, I just read the raw coordinates generated by +# moltemplate (and the default volume). (I get fewer questions this way.) +# However you should never run any liquid simulations at constant volume without +# pressure equilibration first. Hopefully in the future "read_restart" will +# work. Until then, try "read_dump", "dump2data.py", or "restart2data". + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". +unfix fSHAKE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fSHAKE again: +include system.in.settings + +# -- simulation protocol -- + + + +timestep 2.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + + +thermo 500 +#thermo_modify flush yes + + +#restart 100000 restart_nvt + +run 50000 + +write_restart system_after_nvt.rst + + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT new file mode 100644 index 0000000000..83b4ad80bf --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT @@ -0,0 +1,51 @@ +This is a small version of a carbon-nanotube, water capillary system. +It was inspired by this paper: + + Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) + +-------- Requirements: ------- +To run this system at constant pressure, it might help to compile LAMMPS +with the optional RIGID package, and use "fix rigid" on the carbon. +(The use of fix rigid is controversial.) Running at NVT does not require this. +------------------------------ + +Note: To investigate the behavior from that paper, it might be a good + idea to increase the size of the water reservoir, the spacing between + the walls, and the size of the system in the X and Y directions. + +Note: Explicit carbon-carbon bonds: + In the graphene and nanotube structures, I did not try to connect the + carbon atoms together with bonds. Instead we will hold these structures + rigid by not integrating their equations of motion. + (If you want to simulate movement of the carbon atoms at high + temperatures or tension, LAMMPS has 3-body/many-body LAMMPS force-fields + available for simulating the behaviour of carbon in graphite. I know + that you don't need to specify bonds to use these force fields. I do + not know know if these force fields work for nanotubes or graphene.) + +Note: Other modeling tools: + If you need explicit bonds between carbon atoms, then you must add them + yourself or use a different tool. Currently (2012-10-20), moltemplate does + not generate bonds automatically. The "Nanotube Builder" and "topotools" + plugins for for VMD can generate a nanotube with bonds in LAMMPS data + format. You can then convert this data file to .LT format using the + ltemplify.py utility and then import it into another .LT file and play + with it later. (In the "cnad-cnt" example, the carbon nanotube was built + using "Nanotube Builder" and topotools, and processed with ltemplify.py) + + +# WARNING: THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION. +# A real junction would be curved and deformed near the boundary, +# (not 90 degrees) and it would not be built entirely from hexagons. +# (This is not a problem in this example because the carbon atoms +# are immobilized.) If you want to simulate the behavior of +# real graphene or nanotube junctions, you must be more careful. +# To solve this problem: +# Moltemplate allows you to move, customize or delete individual +# atoms near the boundary. You can move atoms by overwriting their +# coordinates using additional write("Data Atoms") statements (after +# the walls and tube are created). You can also change their charge. +# Alternately, you could start with the structure provided here, and +# relax/minimize the coordinates of the carbon atoms using LAMMPS +# before using it in other simulations. +# Or you could do both (customization & minimization). diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh new file mode 100755 index 0000000000..8a470b9551 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh @@ -0,0 +1,24 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_linux -i run.in.npt # minimization and simulation at constant pressure + # (WARNING: The "run.in.npt" example has not been + # rigorously tested and may fail.) + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh new file mode 100755 index 0000000000..acc5fbbaad --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt new file mode 100644 index 0000000000..206db99038 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt @@ -0,0 +1,77 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + To shift the box by a fraction in the x direction (for example) + do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 } + pbc box -shiftcenterrel {-0.50 -0.52 0.0 } + + # Alternately if you have a solute whose atoms are all of type 1, + # then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..bf019b4c31 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,3195 @@ +PSF + + 1 !NTITLE + REMARKS VMD-generated NAMD/X-Plor PSF structure file + + 2454 !NATOM + 1 1 1 1 0.000000 12.0000 0 + 2 1 1 1 0.000000 12.0000 0 + 3 2 1 1 0.000000 12.0000 0 + 4 2 1 1 0.000000 12.0000 0 + 5 3 1 1 0.000000 12.0000 0 + 6 3 1 1 0.000000 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b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/water_side_nopbc_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh new file mode 100644 index 0000000000..8b16c87e3f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh @@ -0,0 +1,27 @@ +# This is a small version of a carbon-nanotube, water capillary system. +# It was inspired by this paper: +# +# Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) +# +# Note: To investigate the behavior from that paper, you would have to increase +# the spacing between the two graphene sheets to prevent the water from +# making contact with the lower graphene wall. +# +# Requirements: 1) Set your $MOLTEMPLATE_PATH variable +# 2) The "RIGID" LAMMPS package may be needed later +# To run this system at constant pressure, it might help to compile LAMMPS with +# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) +# +# Also, if you have not yet done this set your MOLTEMPLATE_PATH environment +# variable to access it. (See installation instructions.) +# Most likely some of the files in this example (like graphene.lt, tip3p2004.lt) +# are not in this directory, but are in the "common" directory. +# Set MOLTEMPLATE_PATH to point to the "common" directory. +# +# ----------------------------------------------------------- +# +# To run moltemplate, use: + +moltemplate.sh system.lt + +# This will generate:system.data, system.in, system.in.init, system.in.settings diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt new file mode 100644 index 0000000000..949e16e6b5 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt @@ -0,0 +1,119 @@ +# This file contains a unit cell for building graphene and nanotubes +# +# +# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any +# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg") +# Surfaces constructed with this unit cell can be flat or curved into tubes. +# The distance between nearest-neighbor carbon atoms (ie the length of a +# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms. +# +# d = length of each hexagon's side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms +# w = width of hexagon rows = 1.5*d = 2.13 Angstroms +# +# Consequently, the Lattice-cell vectors for singe-layer graphene are: +# (2.4595121467478, 0, 0) (aligned with X axis) +# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d) +# So, to build a sheet of graphite, you could use: +# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) + + + + +Graphene { + + 2AtomCellAlignX + { + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 + $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 + } + } + + # Now define properties of the Carbon graphene atom + + write_once("In Init") { + # If all of the graphene carbon atoms have zero charge, try this: + pair_style hybrid lj/cut 10.0 + + # If some of the boundary atoms have non-zero (partial) charge, try these: + #pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 + #pair_style hybrid lj/charmm/coul/long 9.0 10.0 + } + + write_once("Data Masses") { + @atom:C 12.0 + } + + write_once("In Settings") { + # If all graphene carbon atoms have zero charge, try this: + pair_coeff @atom:C @atom:C lj/cut 0.068443 3.407 + + # i j epsilon sigma + # If some of the boundary atoms have non-zero (partial) charge, try these: + #pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407 + #pair_coeff @atom:C @atom:C lj/charmm/coul/long 0.068443 3.407 + + # These Lennard-Jones parameters come from + # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, + # Chem Phys Lett, 348:187 (2001) + # LAMMPS provides more realistic manybody force fields for graphene. + # But in this example, we immobilize the atoms so it does not matter.) + + # Define a group consisting of only carbon atoms in graphene molecules + group Cgraphene type @atom:C + } + + # Notice that the two atoms in the unit-cell above lie in the XY plane. + # (Their z-coordinate is zero). It's also useful to have a version of + # this object which lies in the XZ plan. So we define this below: + + 2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0) + +} # Graphene + + + + + + + + + + +# ------------ Graphite ----------- +# +# Note: For graphite: sheets stacked in the Z direction are separated by a +# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction +# by a distance of d (1.42 Angstroms). To add additional graphene layers +# you could use: +# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet2[*][*].move(0, 1.42, 3.35) +# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet3[*][*].move(0, -1.42, 6.70) +# etc... +# However, to build a thick sheet of graphite, it would +# be more efficient to use a 4-atom unit cell: +# +#Graphene { +# GraphiteCell { +# # atomID molID atomType charge x y z +# write("Data Atoms") { +# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 +# $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 +# $atom:C3 $mol:... @atom:../C 0.0 -0.61487803668695 1.065 3.35 +# $atom:C4 $mol:... @atom:../C 0.0 0.61487803668695 1.775 3.35 +# } +# } # GraphiteCell +#} +# +# Then you could create a thick sheet of graphite this way: +# +# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# [5].move(0,0,6.70) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt new file mode 100644 index 0000000000..53499334de --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt @@ -0,0 +1,54 @@ + +import "graphene.lt" + +# -------------- graphene sheet ----------------- + +# Notes: +# Hexagonal lattice with: +# d = length of each hexagonal side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478 Angstroms +# w = width of hexagon rows = 1.5*d = 2.13 Angstroms + +Wall { + unitcells = new Graphene/2AtomCellAlignX [14].move(1.2297560733739, 2.13, 0) + [13].move(2.4595121467478, 0, 0) + unitcells[*][*].move(-24.595121467478, -14.91, 0.000) + + # Now cut a hole in the graphene sheet roughly where the nanotube is located + delete unitcells[5][7-8] # delete 2 unit cells (2 atoms each, 4 atoms total) + delete unitcells[6][6-8] # delete 3 unit cells (2 atoms each, 6 atoms total) + delete unitcells[7][5-8] # delete 4 unit cells (2 atoms each, 8 atoms total) + delete unitcells[8][5-7] # delete 3 unit cells (2 atoms each, 6 atoms total) + delete unitcells[9][5-6] # delete 2 unit cells (2 atoms each, 4 atoms total) + # Optional fine tuning: delete a few additional atoms around the edges + delete unitcells[5][6]/C2 # delete a single atom + delete unitcells[6][5]/C2 # delete a single atom + delete unitcells[6][9]/C1 # delete a single atom + delete unitcells[8][4]/C2 # delete a single atom + delete unitcells[8][8]/C1 # delete a single atom + delete unitcells[9][7]/C1 # delete a single atom +} + +# Make two copies of the wall, and place them on either end of the nanotube + +wall1 = new Wall.move(0, 0, 32.0) +wall2 = new Wall.move(0, 0, 58.26) + + +# WARNING: A reader has emailed me to point out that: +# THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION. +# A real junction would be curved and deformed near the boundary, +# (not 90 degrees) and it would not be built entirely from hexagons. +# (This is not a problem in this example because the carbon atoms +# are immobilized.) If you want to simulate the behavior of +# real graphene or nanotube junctions, you must be more careful. +# To solve this problem: +# Moltemplate allows you to move, customize or delete individual +# atoms near the boundary. You can move atoms by overwriting their +# coordinates using additional write("Data Atoms") statements (after +# the walls and tube are created). You can also change their charge. +# Alternately, you could start with the structure provided here, and +# relax/minimize the coordinates of the carbon atoms using LAMMPS +# before using it in other simulations. +# Or you could do both (customization & minimization). diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt new file mode 100644 index 0000000000..ee6786d7c2 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt @@ -0,0 +1,96 @@ +import "graphene.lt" + +# ------------------ nanotube --------------- + +# Now use this to build a simple ("zigzag") nanotube where the long-axis of each +# hexagon is aligned with the tube axis (along the Z direction). If the +# cicumference of a "zigzag" nanotube contains N hexagons, then the radius of +# the tube, R=(W/4)/tan((2*pi)/(4*N)), where W=2*d*sqrt(3)/2, and d = the carbon +# bond length. If N=14 and d=1.42 Ansgroms then R=5.457193512764 Angstroms +# In the Joly 2011 paper, the tube radii varied between 5.14 and 18.7 Angstroms. + + + + +nanotube = new Graphene/2AtomCellAlignXZ.move(0, 5.457193512764, 0) # 5.45 = R + [14].rot(25.7142857,0,0,1) #25.7=360/14 + [12].rot(12.8571429,0,0,1).move(0, 0, 2.13) #12.9=180/14 + #2.13= d*1.5 + + + # Note: The length is 12 hexegons, the circumference is + # 14 hexegons (~=25.56 and 34.43 Angstroms, respectively). + + +# Move all of the unit-cells in the nanotube between the two graphene sheets. + +nanotube[*][*].move(0, 0, 33.42) + + + + + +# ---------- BUILDING CHIRAL NANOTUBES USING EXTERNAL SOFTWARE ------------- +# +# The approach shown here works well for "zig-zag" nanotubes. +# Nanotubes with other chiralities are more difficult to make this way +# (because the tube axis is no longer perpendicular to graphene basis vectors). +# For those nanotubes, I recommend using an external program to generate +# a LAMMPS data file for the nanotube. If you want to combine the tube +# with other molecules created by moltemplate, you can then import it into +# moltemplate as a molecule object using the "ltemplify.py" utility. Details: +# +# --- VMD plugins (by Axel Kohlmeyer and Robert R. Johnson) --- +# +# The nanotube-builder for VMD can generate nanotubes (with smooth tips) +# for any chirality. These tubes also have explicit bonds between carbons: +# http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/ +# +# The resulting nanotube can be converted to a data file using topotools: +# https://sites.google.com/site/akohlmey/software/topotools +# To do that, select the "Extensions"->"Tk Console" menu and enter +# +# topo writelammpsdata nanotube.data full +# +# --- ltemplify.py --- +# +# That data file can be converted to moltemplate format (an .LT file) +# using the "ltemplify.py" utility. +# +# The first step is to create a short input script containing the atom_style +# command (ltemplify.py will read this script. Presumably atom_style is "full"). +# +# echo "atom_style full" > nanotube.in +# +# Then run ltemplify to convert nanotube.data into a moltemplate file: +# ltemplify.py -name Nanotube nanotube.in nanotube.data > nanotube.lt +# +# You will need to edit the "nanotuble.lt" file to replace all of the +# "@atom:type1" atoms types file to match the carbon atom types in the other lt +# files (ie "@atom:../C"). If you don't plan on defining bonded interactions +# between carbon atoms, then be sure to remove the write("Data Bonds") section +# of the "nanotube.lt" file (if it is present). +# +# Finally make sure the "system.lt" contains these lines: +# +# import "nanotube.lt" +# nanotube = new Nanotube.move(?,?,?) +# +# (Replace ?,?,? with the location where you want the nanotube to go. +# You can also rotate it using .rot(angle,axisx,axisy,axiz).) +# +# ... and then run moltemplate the normal way +# +# Let me know if you run into trouble with this approach, +# and I will make note of that in this file. +# +# --- links --- +# Note: there are numerous programs for specifying the coordinates +# of the atoms in a nanotube, some of which are below. +# http://www.nanotube.msu.edu/tubeASP/ +# http://turin.nss.udel.edu/research/tubegenonline.html +# http://www.ugr.es/~gmdm/java/contub/contub.html +# (You can load coordinates into moltemplate using the "-xyz" or "-pdb" +# arguments. However currently (2013-12-01), the file must contain coordinates +# for all of the atoms in your sytem, not just the nanotube.) +# ------------------------------------------------------------------------- diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt new file mode 100644 index 0000000000..019911c19b --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeSPCE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt new file mode 100644 index 0000000000..e8a9b1bbc4 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt @@ -0,0 +1,46 @@ +# This is a small version of a carbon-nanotube, water capillary system. It was +# inspired by this paper: Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) + +import "graphene_walls.lt" + +import "nanotube.lt" + +import "water_box.lt" + + +# ------------ boundary conditions ------------ + +write_once("Data Boundary") { + -15.98682895386 15.98682895386 xlo xhi + -14.91 14.91 ylo yhi + 0.0 80.00 zlo zhi +} + +# --------------------------------------------- + + + +write_once("In Init") { + # -- override any earlier pair_style settings: -- + # If some of the junction carbon atoms have non-zero partial charge, try this + #pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 + + # If all graphened atoms have zero charge, you can use this: + pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 & + lj/cut 10.0 + + # I was too lazy to figure out what these partial charges would be, so I set + # them to zero, but a serious investigation into carbon-nanotube-graphene + # junctions would adjust the charge and geometry of the boundary atoms. +} + + +write_once("In Settings") { + # --- We must eventually specify the interactions between the atoms --- + # --- in different molecule types (graphene-water interactions). --- + # (See Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) for details + + pair_coeff @atom:Graphene/C @atom:SPCE/O lj/charmm/coul/long 0.114 3.28 + pair_coeff @atom:Graphene/C @atom:SPCE/H lj/charmm/coul/long 0.0 3.28 +} + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt new file mode 100644 index 0000000000..c825276f5a --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt @@ -0,0 +1,20 @@ +import "spce.lt" + +# --------------- water ------------------ + +# Create a rhombohedral box of water. (A rectangular box works also.) + +wat = new SPCE [9].move(3.5526287, 0, 0 ) + [9].move(1.77631435, 3.3133, 0 ) + [6].move( 0, 0, 3.45) + +# Optional: Center the water box at the origin. (Not really necessary.) + +wat[*][*][*].move(-23.9802437, -14.90985, 11.47) + +# --------------- Note: ----------------- +# The spacing between water molecules does not matter much as long as it is +# reasonable. (I adjusted the spacing try to insure that the waters are spread +# uniformly throughout the box. We do not want bubles to form if there are +# gaps near the XY periodic boundaries.) We will have to equilibrate it later. + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt new file mode 100644 index 0000000000..6bd4fd8a18 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt @@ -0,0 +1,102 @@ +# THIS EXAMPLE HAS NOT BEEN RIGOROUSLY TESTED. +# (This simulation may fail. +# However the "run.in.nvt" example in this directory should work.) +# +# Requirements: +# To run this system at constant pressure, it might help to compile LAMMPS with +# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) +# The use of fix rigid is controversial. This method is demonstrated below. + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# Only the Cgraphene atoms are immobile. +group mobile subtract all Cgraphene + + +# Unfortunately you can not use the LAMMPS "minimize" command on this system +# because there is no way to immobilize the carbon graphene & nanotube atoms +# during minimization. Instead, we can use langevin dynamics with a large +# damping parameter and a small timestep. + +print "--------- beginning minimization (using fix langevin) ---------" + +timestep 0.1 +fix fxlan mobile langevin 1.0 1.0 100.0 48279 +fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) +thermo 100 +run 2500 + +unfix fxlan +unfix fxnve + +# -- simulation protocol -- + +print "--------- beginning simulation (using fix nvt) ---------" + +timestep 0.25 +dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data + + + + + +# ------------------------- NPT --------------------------- + +# Set temp=300K, pressure=100bar, and equilibrate volume only in the z direction + +fix fxMoveStuff mobile npt temp 300 300 100 z 100 100 1000.0 dilate mobile + +# ------ QUESTIONABLE (see below): ------ + +fix Ffreezestuff Cgraphene rigid/npt single temp 300 300 100 z 100 100 1000.0 force * off off off torque * off off off dilate mobile + +# -- Alternate npt rigid method -- +# I'm not sure which way is more correct, however +# this also seems to behave in a reasonable-looking way: +#fix Ffreezestuff Cgraphene rigid single force * off off off torque * off off off +# +# The use of either "fix rigid" or "fix rigid/npt" to immobilize +# an object is somewhat controversial. Feel free to omit it. +#(Neither Trung or Steve Plimpton use rigid or rigid/npt for immobilizing +#molecules, but I noticed that at NPT, it does a better job of maintaining +# the correct volume. However "fix rigid" has changed since then (2011), +# so this may no longer be true. Please use this example with caution.) +# ---------------------------------------- + +# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the +# forces between immobilized atoms. +neigh_modify exclude group Cgraphene Cgraphene + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp +compute pressMobile all pressure tempMobile + +thermo_style custom step c_tempMobile c_pressMobile temp press vol + +fix_modify fxMoveStuff temp tempMobile + +run 100000 + +write_data system_after_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also.) + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt new file mode 100644 index 0000000000..59c847c07d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt @@ -0,0 +1,79 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# (You do not need to run LAMMPS to equilibrate the system before +# using this file.) + +# ----------------------------- Initialization Section -------------------- + +include system.in.init + + +# ----------------------------- Atom Definition Section ------------------- + +read_data system.data + + +# ----------------------------- Settings Section -------------------------- + +include system.in.settings + + +# ----------------------------- Run Section ------------------------------- + + + +# Optional: Improve efficiency by omitting the calcuation of interactions +# between immobile atoms. (Note: This is not optional under NPT conditions.) +neigh_modify exclude group Cgraphene Cgraphene + +# Only the Cgraphene atoms are immobile. +group mobile subtract all Cgraphene + + + +# -- minimization protocol -- + +# Unfortunately you can not use the LAMMPS "minimize" command on this system +# because there is no way to immobilize the carbon graphene & nanotube atoms +# during minimization. Instead, we can use langevin dynamics with a large +# damping parameter and a small timestep. + +print "--------- beginning minimization (using fix langevin) ---------" + +timestep 0.1 +fix fxlan mobile langevin 1.0 1.0 100.0 48279 +fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) +thermo 100 +run 2500 + +unfix fxlan +unfix fxnve + +# -- simulation protocol -- + +print "--------- beginning simulation (using fix nvt) ---------" + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair #ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + + +# Integrate the equations of motion: +fix fxMoveStuff mobile nvt temp 300.0 300.0 100.0 + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp +fix_modify fxMoveStuff temp tempMobile + +restart 5000000 restart_nvt +run 10000000 + +write_data system_after_nvt.data + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT new file mode 100644 index 0000000000..0e58ef44c7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT @@ -0,0 +1,10 @@ +This is a simple system of 260 water molecules. + +In this example, the coordinates of the atoms are read from a PDB file +instead of being specified manually (as well as the boundary information). + +The PDB file was generated by the useful "solvate" utility which comes with VMD. +(To generate this file yourself, run VMD, click on the "Extensions" menu, +and select Modeling-->Add Solvation Box. +In this example, I made a box whose x,y,z dimensions were 16,24,24.) + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh new file mode 100755 index 0000000000..022c53ce3b --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh @@ -0,0 +1,31 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh new file mode 100755 index 0000000000..5d2be21331 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh @@ -0,0 +1,32 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + +cd moltemplate_files/ # (The .lt input files are in this directory) + + moltemplate.sh -pdb solvate.pdb system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + +# +#This will prepare LAMMPS input files for a box of water +#(In this example, we are using the "SPC/E" water model.) +#The number of water molecules in the "wat = new SPCE [260]" command +#must equal the number of water molecules in the PDB file. +# +#Coordinates and boundary-box information is read from the .pdb file. +# +#You can also specify this information directly in the ttree file. +#See the comments section in "system.lt" for details. +# diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt new file mode 100644 index 0000000000..8063d535f8 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt @@ -0,0 +1,64 @@ + ------- Instructions to view a trajectory in VMD -------- + + ------- Disclaimer ------- + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + + (Note, at this point the image shown in the VMD graphics window may + not appear correct or incomplete. The coordinates of the atoms may + overlap if you asked moltemplate.sh to load your coordinates from + a PDB or XYZ file. + However, later after you have run a simulation, the trajectories + should appear reasonably correct when you load them in VMD using + the PSF file you just generated.) + + +Later, to Load a trajectory in VMD: + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it + +----- Wrap the coordinates to the unit cell + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Enter: + + DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT. + LOOKUP "pbctools" FOR DETAILS. + + pbc wrap -compound res -all + pbc box + + # If you have a solute of type 1, then use this: + #pbc wrap -sel type=1 -all -centersel type=2 -center com + +"1" corresponds to the "O" atom type +"2" corresponds to the "H" atom type + +3) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types: + +sed -e 's/ 1 1 / O O /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > system.psf + +(If you do this, I guess that you might have to use + "type=O" and "type=H" in step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0 b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0 new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh new file mode 100755 index 0000000000..4ebc7b17a3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh @@ -0,0 +1,11 @@ + +# Run moltemplate this way: + +moltemplate.sh -pdb solvate.pdb system.lt + + +# The PDB file was generated by the "solvate" utility which comes with VMD. +# (To generate this file yourself, run VMD, click on the "Extensions" menu, +# and select Modeling-->Add Solvation Box. +# In this example, I made a box whose x,y,z dimensions were 16,24,24.) + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb new file mode 100644 index 0000000000..0ed5103cbb --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb @@ -0,0 +1,782 @@ +CRYST1 16.000 24.000 24.000 90.00 90.00 90.00 P 1 1 +ATOM 1 OH2 TIP3W 5 3.668 10.082 15.904 1.00 0.00 WT1 O +ATOM 2 H1 TIP3W 5 3.224 10.451 15.101 1.00 0.00 WT1 H +ATOM 3 H2 TIP3W 5 3.092 10.379 16.627 1.00 0.00 WT1 H +ATOM 4 OH2 TIP3W 7 6.033 4.876 20.891 1.00 0.00 WT1 O +ATOM 5 H1 TIP3W 7 6.078 5.224 21.798 1.00 0.00 WT1 H +ATOM 6 H2 TIP3W 7 6.592 4.088 20.961 1.00 0.00 WT1 H +ATOM 7 OH2 TIP3W 21 5.186 16.696 12.072 1.00 0.00 WT1 O +ATOM 8 H1 TIP3W 21 6.083 16.979 11.816 1.00 0.00 WT1 H +ATOM 9 H2 TIP3W 21 5.337 15.832 12.490 1.00 0.00 WT1 H +ATOM 10 OH2 TIP3W 29 8.324 13.811 21.332 1.00 0.00 WT1 O +ATOM 11 H1 TIP3W 29 8.633 13.348 22.112 1.00 0.00 WT1 H +ATOM 12 H2 TIP3W 29 8.506 13.116 20.645 1.00 0.00 WT1 H +ATOM 13 OH2 TIP3W 44 3.786 16.318 1.310 1.00 0.00 WT1 O +ATOM 14 H1 TIP3W 44 3.781 15.388 1.196 1.00 0.00 WT1 H +ATOM 15 H2 TIP3W 44 4.528 16.580 0.781 1.00 0.00 WT1 H +ATOM 16 OH2 TIP3W 46 6.205 6.991 18.442 1.00 0.00 WT1 O +ATOM 17 H1 TIP3W 46 6.782 7.347 19.152 1.00 0.00 WT1 H +ATOM 18 H2 TIP3W 46 5.309 7.062 18.800 1.00 0.00 WT1 H +ATOM 19 OH2 TIP3W 48 2.750 8.844 9.629 1.00 0.00 WT1 O +ATOM 20 H1 TIP3W 48 2.110 8.290 9.998 1.00 0.00 WT1 H +ATOM 21 H2 TIP3W 48 2.164 9.245 8.962 1.00 0.00 WT1 H +ATOM 22 OH2 TIP3W 52 3.935 16.195 22.109 1.00 0.00 WT1 O +ATOM 23 H1 TIP3W 52 4.870 16.034 21.985 1.00 0.00 WT1 H +ATOM 24 H2 TIP3W 52 3.655 15.367 22.581 1.00 0.00 WT1 H +ATOM 25 OH2 TIP3W 64 10.674 8.909 4.986 1.00 0.00 WT1 O +ATOM 26 H1 TIP3W 64 10.998 8.871 5.932 1.00 0.00 WT1 H +ATOM 27 H2 TIP3W 64 9.748 9.270 5.075 1.00 0.00 WT1 H +ATOM 28 OH2 TIP3W 67 0.002 5.667 14.591 1.00 0.00 WT1 O +ATOM 29 H1 TIP3W 67 0.483 5.990 13.830 1.00 0.00 WT1 H +ATOM 30 H2 TIP3W 67 0.608 5.781 15.347 1.00 0.00 WT1 H +ATOM 31 OH2 TIP3W 68 9.882 9.156 14.916 1.00 0.00 WT1 O +ATOM 32 H1 TIP3W 68 9.574 9.753 15.597 1.00 0.00 WT1 H +ATOM 33 H2 TIP3W 68 10.021 8.264 15.289 1.00 0.00 WT1 H +ATOM 34 OH2 TIP3W 87 1.661 6.681 1.943 1.00 0.00 WT1 O +ATOM 35 H1 TIP3W 87 1.943 5.739 1.981 1.00 0.00 WT1 H +ATOM 36 H2 TIP3W 87 0.778 6.599 1.483 1.00 0.00 WT1 H +ATOM 37 OH2 TIP3W 88 4.821 20.603 11.239 1.00 0.00 WT1 O +ATOM 38 H1 TIP3W 88 5.466 20.782 11.963 1.00 0.00 WT1 H +ATOM 39 H2 TIP3W 88 5.384 20.914 10.456 1.00 0.00 WT1 H +ATOM 40 OH2 TIP3W 90 15.022 20.855 12.831 1.00 0.00 WT1 O +ATOM 41 H1 TIP3W 90 14.222 20.809 13.292 1.00 0.00 WT1 H +ATOM 42 H2 TIP3W 90 14.673 21.057 11.918 1.00 0.00 WT1 H +ATOM 43 OH2 TIP3W 94 1.339 3.782 22.814 1.00 0.00 WT1 O +ATOM 44 H1 TIP3W 94 0.839 3.425 22.087 1.00 0.00 WT1 H +ATOM 45 H2 TIP3W 94 1.775 3.077 23.138 1.00 0.00 WT1 H +ATOM 46 OH2 TIP3W 95 0.485 15.137 22.476 1.00 0.00 WT1 O +ATOM 47 H1 TIP3W 95 0.644 15.425 23.349 1.00 0.00 WT1 H +ATOM 48 H2 TIP3W 95 0.312 15.961 21.975 1.00 0.00 WT1 H +ATOM 49 OH2 TIP3W 111 10.426 7.604 2.404 1.00 0.00 WT1 O +ATOM 50 H1 TIP3W 111 10.761 8.401 1.994 1.00 0.00 WT1 H +ATOM 51 H2 TIP3W 111 10.248 7.889 3.308 1.00 0.00 WT1 H +ATOM 52 OH2 TIP3W 113 4.269 22.752 16.265 1.00 0.00 WT1 O +ATOM 53 H1 TIP3W 113 4.149 23.680 15.888 1.00 0.00 WT1 H +ATOM 54 H2 TIP3W 113 5.061 22.796 16.776 1.00 0.00 WT1 H +ATOM 55 OH2 TIP3W 130 10.926 5.365 1.018 1.00 0.00 WT1 O +ATOM 56 H1 TIP3W 130 11.138 4.769 1.754 1.00 0.00 WT1 H +ATOM 57 H2 TIP3W 130 10.657 6.212 1.493 1.00 0.00 WT1 H +ATOM 58 OH2 TIP3W 133 8.647 4.314 19.278 1.00 0.00 WT1 O +ATOM 59 H1 TIP3W 133 7.964 3.611 19.326 1.00 0.00 WT1 H +ATOM 60 H2 TIP3W 133 8.043 5.064 19.153 1.00 0.00 WT1 H +ATOM 61 OH2 TIP3W 134 8.381 17.319 23.275 1.00 0.00 WT1 O +ATOM 62 H1 TIP3W 134 7.516 17.340 23.695 1.00 0.00 WT1 H +ATOM 63 H2 TIP3W 134 8.431 18.263 23.009 1.00 0.00 WT1 H +ATOM 64 OH2 TIP3W 150 4.299 17.774 7.169 1.00 0.00 WT1 O +ATOM 65 H1 TIP3W 150 3.303 17.803 7.322 1.00 0.00 WT1 H +ATOM 66 H2 TIP3W 150 4.533 18.755 6.924 1.00 0.00 WT1 H +ATOM 67 OH2 TIP3W 152 8.892 12.977 5.321 1.00 0.00 WT1 O +ATOM 68 H1 TIP3W 152 8.119 12.478 5.443 1.00 0.00 WT1 H +ATOM 69 H2 TIP3W 152 9.342 12.557 4.536 1.00 0.00 WT1 H +ATOM 70 OH2 TIP3W 167 2.174 18.468 2.212 1.00 0.00 WT1 O +ATOM 71 H1 TIP3W 167 2.632 17.628 2.203 1.00 0.00 WT1 H +ATOM 72 H2 TIP3W 167 2.931 19.120 2.281 1.00 0.00 WT1 H +ATOM 73 OH2 TIP3W 239 13.612 17.680 18.622 1.00 0.00 WT1 O +ATOM 74 H1 TIP3W 239 13.744 17.414 19.508 1.00 0.00 WT1 H +ATOM 75 H2 TIP3W 239 14.526 17.831 18.347 1.00 0.00 WT1 H +ATOM 76 OH2 TIP3W 443 9.935 12.876 10.191 1.00 0.00 WT1 O +ATOM 77 H1 TIP3W 443 9.709 12.098 9.634 1.00 0.00 WT1 H +ATOM 78 H2 TIP3W 443 9.472 12.766 11.018 1.00 0.00 WT1 H +ATOM 79 OH2 TIP3W 450 7.060 2.074 19.830 1.00 0.00 WT1 O +ATOM 80 H1 TIP3W 450 7.650 1.619 20.528 1.00 0.00 WT1 H +ATOM 81 H2 TIP3W 450 6.148 1.796 20.035 1.00 0.00 WT1 H +ATOM 82 OH2 TIP3W 465 13.891 1.919 2.992 1.00 0.00 WT1 O +ATOM 83 H1 TIP3W 465 14.198 2.681 3.422 1.00 0.00 WT1 H +ATOM 84 H2 TIP3W 465 13.212 1.577 3.578 1.00 0.00 WT1 H +ATOM 85 OH2 TIP3W 466 8.823 10.581 8.827 1.00 0.00 WT1 O +ATOM 86 H1 TIP3W 466 8.183 10.753 8.148 1.00 0.00 WT1 H +ATOM 87 H2 TIP3W 466 8.389 10.061 9.534 1.00 0.00 WT1 H +ATOM 88 OH2 TIP3W 469 9.078 11.967 12.734 1.00 0.00 WT1 O +ATOM 89 H1 TIP3W 469 8.228 11.561 12.993 1.00 0.00 WT1 H +ATOM 90 H2 TIP3W 469 9.512 12.194 13.560 1.00 0.00 WT1 H +ATOM 91 OH2 TIP3W 484 10.282 0.640 2.053 1.00 0.00 WT1 O +ATOM 92 H1 TIP3W 484 10.367 0.959 3.016 1.00 0.00 WT1 H +ATOM 93 H2 TIP3W 484 9.743 1.323 1.667 1.00 0.00 WT1 H +ATOM 94 OH2 TIP3W 485 4.618 8.125 7.777 1.00 0.00 WT1 O +ATOM 95 H1 TIP3W 485 5.405 7.919 8.314 1.00 0.00 WT1 H +ATOM 96 H2 TIP3W 485 4.002 8.458 8.422 1.00 0.00 WT1 H +ATOM 97 OH2 TIP3W 486 3.403 4.687 9.815 1.00 0.00 WT1 O +ATOM 98 H1 TIP3W 486 3.109 5.272 9.097 1.00 0.00 WT1 H +ATOM 99 H2 TIP3W 486 3.817 3.973 9.327 1.00 0.00 WT1 H +ATOM 100 OH2 TIP3W 489 3.276 7.465 19.325 1.00 0.00 WT1 O +ATOM 101 H1 TIP3W 489 2.772 6.991 19.964 1.00 0.00 WT1 H +ATOM 102 H2 TIP3W 489 3.604 8.288 19.753 1.00 0.00 WT1 H +ATOM 103 OH2 TIP3W 503 3.119 10.325 13.158 1.00 0.00 WT1 O +ATOM 104 H1 TIP3W 503 3.598 10.900 12.512 1.00 0.00 WT1 H +ATOM 105 H2 TIP3W 503 3.440 9.430 12.962 1.00 0.00 WT1 H +ATOM 106 OH2 TIP3W 506 2.378 5.806 16.253 1.00 0.00 WT1 O +ATOM 107 H1 TIP3W 506 2.157 6.161 17.099 1.00 0.00 WT1 H +ATOM 108 H2 TIP3W 506 3.301 6.032 16.126 1.00 0.00 WT1 H +ATOM 109 OH2 TIP3W 507 6.382 22.271 2.319 1.00 0.00 WT1 O +ATOM 110 H1 TIP3W 507 5.550 22.035 1.847 1.00 0.00 WT1 H +ATOM 111 H2 TIP3W 507 6.859 21.472 2.192 1.00 0.00 WT1 H +ATOM 112 OH2 TIP3W 509 4.017 3.905 19.418 1.00 0.00 WT1 O +ATOM 113 H1 TIP3W 509 3.142 4.042 19.132 1.00 0.00 WT1 H +ATOM 114 H2 TIP3W 509 4.582 4.727 19.295 1.00 0.00 WT1 H +ATOM 115 OH2 TIP3W 511 2.344 20.472 21.631 1.00 0.00 WT1 O +ATOM 116 H1 TIP3W 511 2.932 20.821 20.945 1.00 0.00 WT1 H +ATOM 117 H2 TIP3W 511 1.467 20.548 21.138 1.00 0.00 WT1 H +ATOM 118 OH2 TIP3W 517 14.526 10.532 20.137 1.00 0.00 WT1 O +ATOM 119 H1 TIP3W 517 14.162 9.733 20.503 1.00 0.00 WT1 H +ATOM 120 H2 TIP3W 517 14.466 10.420 19.194 1.00 0.00 WT1 H +ATOM 121 OH2 TIP3W 533 5.573 14.804 19.090 1.00 0.00 WT1 O +ATOM 122 H1 TIP3W 533 5.959 15.339 19.808 1.00 0.00 WT1 H +ATOM 123 H2 TIP3W 533 5.869 15.413 18.331 1.00 0.00 WT1 H +ATOM 124 OH2 TIP3W 543 5.458 13.097 4.589 1.00 0.00 WT1 O +ATOM 125 H1 TIP3W 543 5.673 13.019 3.612 1.00 0.00 WT1 H +ATOM 126 H2 TIP3W 543 4.899 13.894 4.657 1.00 0.00 WT1 H +ATOM 127 OH2 TIP3W 550 4.552 1.370 20.330 1.00 0.00 WT1 O +ATOM 128 H1 TIP3W 550 4.274 2.194 19.953 1.00 0.00 WT1 H +ATOM 129 H2 TIP3W 550 4.235 0.801 19.571 1.00 0.00 WT1 H +ATOM 130 OH2 TIP3W 554 5.160 13.744 7.954 1.00 0.00 WT1 O +ATOM 131 H1 TIP3W 554 6.048 13.422 8.207 1.00 0.00 WT1 H +ATOM 132 H2 TIP3W 554 5.008 14.493 8.528 1.00 0.00 WT1 H +ATOM 133 OH2 TIP3W 558 10.390 6.386 18.828 1.00 0.00 WT1 O +ATOM 134 H1 TIP3W 558 10.688 6.484 19.731 1.00 0.00 WT1 H +ATOM 135 H2 TIP3W 558 9.844 5.589 18.921 1.00 0.00 WT1 H +ATOM 136 OH2 TIP3W 562 1.678 21.942 1.035 1.00 0.00 WT1 O +ATOM 137 H1 TIP3W 562 1.272 21.280 1.592 1.00 0.00 WT1 H +ATOM 138 H2 TIP3W 562 1.498 22.809 1.493 1.00 0.00 WT1 H +ATOM 139 OH2 TIP3W 568 9.630 21.547 3.000 1.00 0.00 WT1 O +ATOM 140 H1 TIP3W 568 9.601 22.471 2.643 1.00 0.00 WT1 H +ATOM 141 H2 TIP3W 568 9.287 20.954 2.312 1.00 0.00 WT1 H +ATOM 142 OH2 TIP3W 575 2.344 10.571 2.624 1.00 0.00 WT1 O +ATOM 143 H1 TIP3W 575 2.122 10.753 3.553 1.00 0.00 WT1 H +ATOM 144 H2 TIP3W 575 2.947 9.791 2.617 1.00 0.00 WT1 H +ATOM 145 OH2 TIP3W 584 0.823 23.668 2.888 1.00 0.00 WT1 O +ATOM 146 H1 TIP3W 584 1.636 23.316 3.340 1.00 0.00 WT1 H +ATOM 147 H2 TIP3W 584 0.253 23.978 3.640 1.00 0.00 WT1 H +ATOM 148 OH2 TIP3W 594 2.710 6.185 7.540 1.00 0.00 WT1 O +ATOM 149 H1 TIP3W 594 2.467 6.236 6.561 1.00 0.00 WT1 H +ATOM 150 H2 TIP3W 594 3.410 6.855 7.580 1.00 0.00 WT1 H +ATOM 151 OH2 TIP3W 595 6.911 19.458 17.335 1.00 0.00 WT1 O +ATOM 152 H1 TIP3W 595 7.517 20.118 16.957 1.00 0.00 WT1 H +ATOM 153 H2 TIP3W 595 6.315 19.136 16.588 1.00 0.00 WT1 H +ATOM 154 OH2 TIP3W 613 13.540 22.220 2.748 1.00 0.00 WT1 O +ATOM 155 H1 TIP3W 613 12.965 22.475 3.462 1.00 0.00 WT1 H +ATOM 156 H2 TIP3W 613 14.428 22.404 3.074 1.00 0.00 WT1 H +ATOM 157 OH2 TIP3W 634 10.929 14.750 5.718 1.00 0.00 WT1 O +ATOM 158 H1 TIP3W 634 10.050 14.541 5.408 1.00 0.00 WT1 H +ATOM 159 H2 TIP3W 634 11.401 13.879 5.717 1.00 0.00 WT1 H +ATOM 160 OH2 TIP3W 822 0.747 4.469 10.579 1.00 0.00 WT1 O +ATOM 161 H1 TIP3W 822 0.426 3.568 10.339 1.00 0.00 WT1 H +ATOM 162 H2 TIP3W 822 1.505 4.585 9.990 1.00 0.00 WT1 H +ATOM 163 OH2 TIP3W 849 5.356 5.388 16.046 1.00 0.00 WT1 O +ATOM 164 H1 TIP3W 849 5.884 6.064 16.461 1.00 0.00 WT1 H +ATOM 165 H2 TIP3W 849 5.592 4.622 16.537 1.00 0.00 WT1 H +ATOM 166 OH2 TIP3W 867 10.704 6.721 15.883 1.00 0.00 WT1 O +ATOM 167 H1 TIP3W 867 10.901 6.912 16.836 1.00 0.00 WT1 H +ATOM 168 H2 TIP3W 867 10.127 5.972 15.998 1.00 0.00 WT1 H +ATOM 169 OH2 TIP3W 891 11.763 19.614 9.958 1.00 0.00 WT1 O +ATOM 170 H1 TIP3W 891 12.279 20.405 9.866 1.00 0.00 WT1 H +ATOM 171 H2 TIP3W 891 12.435 18.905 9.901 1.00 0.00 WT1 H +ATOM 172 OH2 TIP3W 906 7.027 2.224 13.411 1.00 0.00 WT1 O +ATOM 173 H1 TIP3W 906 6.185 2.801 13.535 1.00 0.00 WT1 H +ATOM 174 H2 TIP3W 906 6.692 1.403 13.742 1.00 0.00 WT1 H +ATOM 175 OH2 TIP3W 908 4.028 7.699 12.776 1.00 0.00 WT1 O +ATOM 176 H1 TIP3W 908 4.577 7.193 12.138 1.00 0.00 WT1 H +ATOM 177 H2 TIP3W 908 3.171 7.320 12.544 1.00 0.00 WT1 H +ATOM 178 OH2 TIP3W 924 12.493 9.451 2.215 1.00 0.00 WT1 O +ATOM 179 H1 TIP3W 924 12.908 9.840 2.987 1.00 0.00 WT1 H +ATOM 180 H2 TIP3W 924 12.982 8.641 2.039 1.00 0.00 WT1 H +ATOM 181 OH2 TIP3W 927 11.177 9.610 7.928 1.00 0.00 WT1 O +ATOM 182 H1 TIP3W 927 10.443 10.172 8.053 1.00 0.00 WT1 H +ATOM 183 H2 TIP3W 927 10.866 8.788 8.298 1.00 0.00 WT1 H +ATOM 184 OH2 TIP3W 928 1.838 3.206 15.398 1.00 0.00 WT1 O +ATOM 185 H1 TIP3W 928 2.201 4.081 15.545 1.00 0.00 WT1 H +ATOM 186 H2 TIP3W 928 2.117 2.999 14.422 1.00 0.00 WT1 H +ATOM 187 OH2 TIP3W 930 1.899 11.624 17.893 1.00 0.00 WT1 O +ATOM 188 H1 TIP3W 930 1.139 11.678 17.305 1.00 0.00 WT1 H +ATOM 189 H2 TIP3W 930 2.258 12.535 17.855 1.00 0.00 WT1 H +ATOM 190 OH2 TIP3W 932 9.220 13.904 17.340 1.00 0.00 WT1 O +ATOM 191 H1 TIP3W 932 10.062 14.198 17.738 1.00 0.00 WT1 H +ATOM 192 H2 TIP3W 932 9.394 12.999 17.102 1.00 0.00 WT1 H +ATOM 193 OH2 TIP3W 933 3.458 9.868 22.419 1.00 0.00 WT1 O +ATOM 194 H1 TIP3W 933 4.398 10.016 22.654 1.00 0.00 WT1 H +ATOM 195 H2 TIP3W 933 3.448 10.189 21.495 1.00 0.00 WT1 H +ATOM 196 OH2 TIP3W 947 15.430 3.274 7.407 1.00 0.00 WT1 O +ATOM 197 H1 TIP3W 947 15.458 2.741 8.157 1.00 0.00 WT1 H +ATOM 198 H2 TIP3W 947 15.933 2.740 6.770 1.00 0.00 WT1 H +ATOM 199 OH2 TIP3W 948 13.134 4.535 6.559 1.00 0.00 WT1 O +ATOM 200 H1 TIP3W 948 12.434 3.932 6.938 1.00 0.00 WT1 H +ATOM 201 H2 TIP3W 948 13.959 4.162 6.965 1.00 0.00 WT1 H +ATOM 202 OH2 TIP3W 951 10.295 14.066 14.320 1.00 0.00 WT1 O +ATOM 203 H1 TIP3W 951 10.592 14.067 15.226 1.00 0.00 WT1 H +ATOM 204 H2 TIP3W 951 9.322 14.226 14.350 1.00 0.00 WT1 H +ATOM 205 OH2 TIP3W 964 7.830 19.751 1.995 1.00 0.00 WT1 O +ATOM 206 H1 TIP3W 964 7.257 19.870 1.247 1.00 0.00 WT1 H +ATOM 207 H2 TIP3W 964 8.329 18.923 1.885 1.00 0.00 WT1 H +ATOM 208 OH2 TIP3W 972 15.027 11.249 9.806 1.00 0.00 WT1 O +ATOM 209 H1 TIP3W 972 15.636 10.953 9.104 1.00 0.00 WT1 H +ATOM 210 H2 TIP3W 972 14.929 12.194 9.545 1.00 0.00 WT1 H +ATOM 211 OH2 TIP3W 974 10.274 11.448 20.959 1.00 0.00 WT1 O +ATOM 212 H1 TIP3W 974 10.893 11.073 21.654 1.00 0.00 WT1 H +ATOM 213 H2 TIP3W 974 10.344 10.891 20.238 1.00 0.00 WT1 H +ATOM 214 OH2 TIP3W 975 11.473 6.075 21.702 1.00 0.00 WT1 O +ATOM 215 H1 TIP3W 975 12.046 5.667 22.431 1.00 0.00 WT1 H +ATOM 216 H2 TIP3W 975 10.554 5.939 22.100 1.00 0.00 WT1 H +ATOM 217 OH2 TIP3W 995 6.800 16.659 17.184 1.00 0.00 WT1 O +ATOM 218 H1 TIP3W 995 7.143 16.649 16.327 1.00 0.00 WT1 H +ATOM 219 H2 TIP3W 995 7.109 17.502 17.568 1.00 0.00 WT1 H +ATOM 220 OH2 TIP3W1007 14.603 18.110 3.213 1.00 0.00 WT1 O +ATOM 221 H1 TIP3W1007 14.275 17.655 3.963 1.00 0.00 WT1 H +ATOM 222 H2 TIP3W1007 13.842 18.606 2.878 1.00 0.00 WT1 H +ATOM 223 OH2 TIP3W1011 4.753 20.139 5.475 1.00 0.00 WT1 O +ATOM 224 H1 TIP3W1011 4.769 21.053 5.846 1.00 0.00 WT1 H +ATOM 225 H2 TIP3W1011 5.663 20.031 5.201 1.00 0.00 WT1 H +ATOM 226 OH2 TIP3W1013 1.615 17.355 14.355 1.00 0.00 WT1 O +ATOM 227 H1 TIP3W1013 1.225 16.480 14.420 1.00 0.00 WT1 H +ATOM 228 H2 TIP3W1013 0.859 17.984 14.051 1.00 0.00 WT1 H +ATOM 229 OH2 TIP3W1014 11.087 15.787 20.150 1.00 0.00 WT1 O +ATOM 230 H1 TIP3W1014 11.221 14.877 19.698 1.00 0.00 WT1 H +ATOM 231 H2 TIP3W1014 11.936 15.940 20.591 1.00 0.00 WT1 H +ATOM 232 OH2 TIP3W1017 9.784 18.060 16.439 1.00 0.00 WT1 O +ATOM 233 H1 TIP3W1017 10.576 18.166 15.922 1.00 0.00 WT1 H +ATOM 234 H2 TIP3W1017 9.941 18.584 17.234 1.00 0.00 WT1 H +ATOM 235 OH2 TIP3W1018 2.369 19.620 10.838 1.00 0.00 WT1 O +ATOM 236 H1 TIP3W1018 2.051 19.425 11.701 1.00 0.00 WT1 H +ATOM 237 H2 TIP3W1018 3.347 19.717 10.923 1.00 0.00 WT1 H +ATOM 238 OH2 TIP3W1027 15.158 15.218 1.453 1.00 0.00 WT1 O +ATOM 239 H1 TIP3W1027 15.286 16.123 1.160 1.00 0.00 WT1 H +ATOM 240 H2 TIP3W1027 14.175 15.219 1.587 1.00 0.00 WT1 H +ATOM 241 OH2 TIP3W1032 7.929 9.601 4.322 1.00 0.00 WT1 O +ATOM 242 H1 TIP3W1032 7.364 10.340 3.912 1.00 0.00 WT1 H +ATOM 243 H2 TIP3W1032 7.318 9.011 4.820 1.00 0.00 WT1 H +ATOM 244 OH2 TIP3W1053 11.585 23.121 19.455 1.00 0.00 WT1 O +ATOM 245 H1 TIP3W1053 12.413 23.205 19.982 1.00 0.00 WT1 H +ATOM 246 H2 TIP3W1053 10.816 23.266 20.095 1.00 0.00 WT1 H +ATOM 247 OH2 TIP3W1301 3.320 1.439 3.693 1.00 0.00 WT1 O +ATOM 248 H1 TIP3W1301 3.018 1.263 2.795 1.00 0.00 WT1 H +ATOM 249 H2 TIP3W1301 4.218 1.737 3.533 1.00 0.00 WT1 H +ATOM 250 OH2 TIP3W1308 8.378 22.836 14.074 1.00 0.00 WT1 O +ATOM 251 H1 TIP3W1308 9.127 23.085 13.478 1.00 0.00 WT1 H +ATOM 252 H2 TIP3W1308 7.806 23.652 14.112 1.00 0.00 WT1 H +ATOM 253 OH2 TIP3W1328 4.539 2.605 8.295 1.00 0.00 WT1 O +ATOM 254 H1 TIP3W1328 5.460 2.702 8.123 1.00 0.00 WT1 H +ATOM 255 H2 TIP3W1328 4.434 1.616 8.363 1.00 0.00 WT1 H +ATOM 256 OH2 TIP3W1344 8.883 21.581 5.760 1.00 0.00 WT1 O +ATOM 257 H1 TIP3W1344 8.705 22.232 6.446 1.00 0.00 WT1 H +ATOM 258 H2 TIP3W1344 9.357 22.008 5.077 1.00 0.00 WT1 H +ATOM 259 OH2 TIP3W1349 12.793 13.364 12.168 1.00 0.00 WT1 O +ATOM 260 H1 TIP3W1349 12.787 13.548 11.223 1.00 0.00 WT1 H +ATOM 261 H2 TIP3W1349 11.995 13.794 12.399 1.00 0.00 WT1 H +ATOM 262 OH2 TIP3W1352 6.667 7.547 9.646 1.00 0.00 WT1 O +ATOM 263 H1 TIP3W1352 6.103 6.975 10.296 1.00 0.00 WT1 H +ATOM 264 H2 TIP3W1352 7.558 7.292 10.046 1.00 0.00 WT1 H +ATOM 265 OH2 TIP3W1354 0.182 23.403 21.361 1.00 0.00 WT1 O +ATOM 266 H1 TIP3W1354 0.301 23.585 22.346 1.00 0.00 WT1 H +ATOM 267 H2 TIP3W1354 1.001 22.867 21.220 1.00 0.00 WT1 H +ATOM 268 OH2 TIP3W1355 11.347 16.007 23.148 1.00 0.00 WT1 O +ATOM 269 H1 TIP3W1355 11.779 15.126 23.087 1.00 0.00 WT1 H +ATOM 270 H2 TIP3W1355 10.586 15.923 22.581 1.00 0.00 WT1 H +ATOM 271 OH2 TIP3W1367 10.129 17.485 6.550 1.00 0.00 WT1 O +ATOM 272 H1 TIP3W1367 9.231 17.467 6.920 1.00 0.00 WT1 H +ATOM 273 H2 TIP3W1367 10.108 16.702 5.985 1.00 0.00 WT1 H +ATOM 274 OH2 TIP3W1370 4.654 5.717 5.023 1.00 0.00 WT1 O +ATOM 275 H1 TIP3W1370 5.059 5.126 4.395 1.00 0.00 WT1 H +ATOM 276 H2 TIP3W1370 5.409 5.785 5.634 1.00 0.00 WT1 H +ATOM 277 OH2 TIP3W1371 12.336 14.905 9.350 1.00 0.00 WT1 O +ATOM 278 H1 TIP3W1371 11.849 15.588 8.883 1.00 0.00 WT1 H +ATOM 279 H2 TIP3W1371 11.568 14.375 9.770 1.00 0.00 WT1 H +ATOM 280 OH2 TIP3W1374 5.488 14.255 13.212 1.00 0.00 WT1 O +ATOM 281 H1 TIP3W1374 6.279 14.126 13.709 1.00 0.00 WT1 H +ATOM 282 H2 TIP3W1374 4.864 13.991 13.878 1.00 0.00 WT1 H +ATOM 283 OH2 TIP3W1387 3.686 8.353 3.401 1.00 0.00 WT1 O +ATOM 284 H1 TIP3W1387 4.494 7.930 3.084 1.00 0.00 WT1 H +ATOM 285 H2 TIP3W1387 3.041 7.727 3.197 1.00 0.00 WT1 H +ATOM 286 OH2 TIP3W1388 15.005 14.526 19.133 1.00 0.00 WT1 O +ATOM 287 H1 TIP3W1388 15.742 13.941 19.238 1.00 0.00 WT1 H +ATOM 288 H2 TIP3W1388 14.746 14.453 18.188 1.00 0.00 WT1 H +ATOM 289 OH2 TIP3W1389 15.427 13.899 13.418 1.00 0.00 WT1 O +ATOM 290 H1 TIP3W1389 15.598 14.703 13.915 1.00 0.00 WT1 H +ATOM 291 H2 TIP3W1389 14.569 14.032 12.994 1.00 0.00 WT1 H +ATOM 292 OH2 TIP3W1392 15.117 16.342 15.320 1.00 0.00 WT1 O +ATOM 293 H1 TIP3W1392 14.190 16.658 15.235 1.00 0.00 WT1 H +ATOM 294 H2 TIP3W1392 15.725 17.080 14.950 1.00 0.00 WT1 H +ATOM 295 OH2 TIP3W1407 13.263 23.513 7.326 1.00 0.00 WT1 O +ATOM 296 H1 TIP3W1407 14.083 23.900 7.689 1.00 0.00 WT1 H +ATOM 297 H2 TIP3W1407 13.669 22.803 6.739 1.00 0.00 WT1 H +ATOM 298 OH2 TIP3W1411 10.030 11.441 3.434 1.00 0.00 WT1 O +ATOM 299 H1 TIP3W1411 9.274 10.827 3.422 1.00 0.00 WT1 H +ATOM 300 H2 TIP3W1411 10.533 11.362 2.661 1.00 0.00 WT1 H +ATOM 301 OH2 TIP3W1412 10.550 9.544 11.315 1.00 0.00 WT1 O +ATOM 302 H1 TIP3W1412 10.055 10.343 11.396 1.00 0.00 WT1 H +ATOM 303 H2 TIP3W1412 11.460 9.846 11.337 1.00 0.00 WT1 H +ATOM 304 OH2 TIP3W1414 2.005 17.796 21.122 1.00 0.00 WT1 O +ATOM 305 H1 TIP3W1414 2.773 17.325 21.598 1.00 0.00 WT1 H +ATOM 306 H2 TIP3W1414 2.173 18.758 21.265 1.00 0.00 WT1 H +ATOM 307 OH2 TIP3W1415 13.553 15.240 21.435 1.00 0.00 WT1 O +ATOM 308 H1 TIP3W1415 14.103 14.959 20.726 1.00 0.00 WT1 H +ATOM 309 H2 TIP3W1415 13.422 14.470 21.979 1.00 0.00 WT1 H +ATOM 310 OH2 TIP3W1418 11.456 2.350 19.585 1.00 0.00 WT1 O +ATOM 311 H1 TIP3W1418 10.731 2.931 19.730 1.00 0.00 WT1 H +ATOM 312 H2 TIP3W1418 11.546 1.862 20.401 1.00 0.00 WT1 H +ATOM 313 OH2 TIP3W1428 13.068 2.914 10.149 1.00 0.00 WT1 O +ATOM 314 H1 TIP3W1428 12.803 2.473 9.295 1.00 0.00 WT1 H +ATOM 315 H2 TIP3W1428 14.010 2.849 10.112 1.00 0.00 WT1 H +ATOM 316 OH2 TIP3W1429 5.450 9.067 5.337 1.00 0.00 WT1 O +ATOM 317 H1 TIP3W1429 4.722 8.840 4.711 1.00 0.00 WT1 H +ATOM 318 H2 TIP3W1429 4.939 8.770 6.117 1.00 0.00 WT1 H +ATOM 319 OH2 TIP3W1433 3.297 18.771 17.303 1.00 0.00 WT1 O +ATOM 320 H1 TIP3W1433 3.913 19.272 17.825 1.00 0.00 WT1 H +ATOM 321 H2 TIP3W1433 3.616 18.935 16.408 1.00 0.00 WT1 H +ATOM 322 OH2 TIP3W1435 6.597 15.954 21.463 1.00 0.00 WT1 O +ATOM 323 H1 TIP3W1435 7.157 15.160 21.200 1.00 0.00 WT1 H +ATOM 324 H2 TIP3W1435 7.205 16.451 22.021 1.00 0.00 WT1 H +ATOM 325 OH2 TIP3W1440 1.443 3.980 18.627 1.00 0.00 WT1 O +ATOM 326 H1 TIP3W1440 1.536 3.050 18.247 1.00 0.00 WT1 H +ATOM 327 H2 TIP3W1440 0.589 4.282 18.256 1.00 0.00 WT1 H +ATOM 328 OH2 TIP3W1451 3.248 22.876 3.701 1.00 0.00 WT1 O +ATOM 329 H1 TIP3W1451 2.662 22.334 4.248 1.00 0.00 WT1 H +ATOM 330 H2 TIP3W1451 4.106 22.410 3.781 1.00 0.00 WT1 H +ATOM 331 OH2 TIP3W1454 8.943 19.607 9.393 1.00 0.00 WT1 O +ATOM 332 H1 TIP3W1454 9.890 19.666 9.174 1.00 0.00 WT1 H +ATOM 333 H2 TIP3W1454 8.551 19.202 8.586 1.00 0.00 WT1 H +ATOM 334 OH2 TIP3W1455 7.534 23.313 22.010 1.00 0.00 WT1 O +ATOM 335 H1 TIP3W1455 7.309 22.777 22.738 1.00 0.00 WT1 H +ATOM 336 H2 TIP3W1455 6.697 23.403 21.532 1.00 0.00 WT1 H +ATOM 337 OH2 TIP3W1457 13.340 13.560 16.477 1.00 0.00 WT1 O +ATOM 338 H1 TIP3W1457 13.400 13.568 15.542 1.00 0.00 WT1 H +ATOM 339 H2 TIP3W1457 12.852 14.406 16.633 1.00 0.00 WT1 H +ATOM 340 OH2 TIP3W1458 8.344 7.845 20.429 1.00 0.00 WT1 O +ATOM 341 H1 TIP3W1458 8.479 8.292 21.236 1.00 0.00 WT1 H +ATOM 342 H2 TIP3W1458 9.102 8.059 19.900 1.00 0.00 WT1 H +ATOM 343 OH2 TIP3W1474 6.901 21.557 9.326 1.00 0.00 WT1 O +ATOM 344 H1 TIP3W1474 7.410 20.744 9.384 1.00 0.00 WT1 H +ATOM 345 H2 TIP3W1474 7.474 22.077 8.759 1.00 0.00 WT1 H +ATOM 346 OH2 TIP3W1494 14.403 7.815 15.212 1.00 0.00 WT1 O +ATOM 347 H1 TIP3W1494 13.532 8.206 14.911 1.00 0.00 WT1 H +ATOM 348 H2 TIP3W1494 14.885 7.681 14.373 1.00 0.00 WT1 H +ATOM 349 OH2 TIP3W1497 6.857 11.138 6.829 1.00 0.00 WT1 O +ATOM 350 H1 TIP3W1497 6.107 11.750 6.800 1.00 0.00 WT1 H +ATOM 351 H2 TIP3W1497 6.480 10.387 6.353 1.00 0.00 WT1 H +ATOM 352 OH2 TIP3W1512 10.309 21.500 11.481 1.00 0.00 WT1 O +ATOM 353 H1 TIP3W1512 11.014 20.928 11.185 1.00 0.00 WT1 H +ATOM 354 H2 TIP3W1512 9.595 20.961 11.183 1.00 0.00 WT1 H +ATOM 355 OH2 TIP3W1532 13.235 22.943 15.633 1.00 0.00 WT1 O +ATOM 356 H1 TIP3W1532 12.613 22.525 16.194 1.00 0.00 WT1 H +ATOM 357 H2 TIP3W1532 14.027 22.981 16.180 1.00 0.00 WT1 H +ATOM 358 OH2 TIP3W1559 6.818 20.066 20.150 1.00 0.00 WT1 O +ATOM 359 H1 TIP3W1559 7.686 20.067 20.626 1.00 0.00 WT1 H +ATOM 360 H2 TIP3W1559 6.969 19.869 19.212 1.00 0.00 WT1 H +ATOM 361 OH2 TIP3W1611 7.975 20.030 22.745 1.00 0.00 WT1 O +ATOM 362 H1 TIP3W1611 8.632 20.654 22.435 1.00 0.00 WT1 H +ATOM 363 H2 TIP3W1611 7.441 20.490 23.501 1.00 0.00 WT1 H +ATOM 364 OH2 TIP3W1707 12.113 0.921 4.942 1.00 0.00 WT1 O +ATOM 365 H1 TIP3W1707 12.819 0.635 5.562 1.00 0.00 WT1 H +ATOM 366 H2 TIP3W1707 11.814 1.896 5.223 1.00 0.00 WT1 H +ATOM 367 OH2 TIP3W1723 9.197 4.375 15.964 1.00 0.00 WT1 O +ATOM 368 H1 TIP3W1723 9.163 3.590 15.387 1.00 0.00 WT1 H +ATOM 369 H2 TIP3W1723 8.516 4.167 16.604 1.00 0.00 WT1 H +ATOM 370 OH2 TIP3W1725 2.421 3.775 5.058 1.00 0.00 WT1 O +ATOM 371 H1 TIP3W1725 2.684 2.934 4.652 1.00 0.00 WT1 H +ATOM 372 H2 TIP3W1725 3.219 4.340 5.048 1.00 0.00 WT1 H +ATOM 373 OH2 TIP3W1729 6.794 6.875 22.997 1.00 0.00 WT1 O +ATOM 374 H1 TIP3W1729 7.166 7.815 23.093 1.00 0.00 WT1 H +ATOM 375 H2 TIP3W1729 5.834 7.029 23.036 1.00 0.00 WT1 H +ATOM 376 OH2 TIP3W1730 11.518 2.141 14.835 1.00 0.00 WT1 O +ATOM 377 H1 TIP3W1730 11.356 2.769 14.101 1.00 0.00 WT1 H +ATOM 378 H2 TIP3W1730 12.345 1.727 14.583 1.00 0.00 WT1 H +ATOM 379 OH2 TIP3W1733 3.174 1.584 16.976 1.00 0.00 WT1 O +ATOM 380 H1 TIP3W1733 2.370 2.077 16.810 1.00 0.00 WT1 H +ATOM 381 H2 TIP3W1733 3.270 0.961 16.252 1.00 0.00 WT1 H +ATOM 382 OH2 TIP3W1746 10.848 10.071 18.631 1.00 0.00 WT1 O +ATOM 383 H1 TIP3W1746 10.345 10.477 17.907 1.00 0.00 WT1 H +ATOM 384 H2 TIP3W1746 11.663 10.551 18.638 1.00 0.00 WT1 H +ATOM 385 OH2 TIP3W1752 12.069 8.766 23.082 1.00 0.00 WT1 O +ATOM 386 H1 TIP3W1752 12.023 9.290 23.888 1.00 0.00 WT1 H +ATOM 387 H2 TIP3W1752 11.590 7.956 23.400 1.00 0.00 WT1 H +ATOM 388 OH2 TIP3W1764 5.141 1.611 0.499 1.00 0.00 WT1 O +ATOM 389 H1 TIP3W1764 4.697 1.110 1.234 1.00 0.00 WT1 H +ATOM 390 H2 TIP3W1764 6.031 1.302 0.586 1.00 0.00 WT1 H +ATOM 391 OH2 TIP3W1771 2.509 3.505 12.910 1.00 0.00 WT1 O +ATOM 392 H1 TIP3W1771 2.114 4.138 12.315 1.00 0.00 WT1 H +ATOM 393 H2 TIP3W1771 2.715 2.712 12.383 1.00 0.00 WT1 H +ATOM 394 OH2 TIP3W1773 14.354 1.352 14.004 1.00 0.00 WT1 O +ATOM 395 H1 TIP3W1773 14.694 0.623 14.565 1.00 0.00 WT1 H +ATOM 396 H2 TIP3W1773 14.573 2.195 14.426 1.00 0.00 WT1 H +ATOM 397 OH2 TIP3W1788 14.578 23.489 17.850 1.00 0.00 WT1 O +ATOM 398 H1 TIP3W1788 15.476 23.267 17.861 1.00 0.00 WT1 H +ATOM 399 H2 TIP3W1788 14.359 23.484 18.771 1.00 0.00 WT1 H +ATOM 400 OH2 TIP3W1789 5.461 6.754 1.943 1.00 0.00 WT1 O +ATOM 401 H1 TIP3W1789 6.412 6.627 2.018 1.00 0.00 WT1 H +ATOM 402 H2 TIP3W1789 5.209 5.956 1.434 1.00 0.00 WT1 H +ATOM 403 OH2 TIP3W1795 14.101 1.902 22.316 1.00 0.00 WT1 O +ATOM 404 H1 TIP3W1795 14.886 2.398 22.002 1.00 0.00 WT1 H +ATOM 405 H2 TIP3W1795 14.108 1.041 21.813 1.00 0.00 WT1 H +ATOM 406 OH2 TIP3W1813 6.142 11.858 16.052 1.00 0.00 WT1 O +ATOM 407 H1 TIP3W1813 5.762 12.642 15.675 1.00 0.00 WT1 H +ATOM 408 H2 TIP3W1813 5.566 11.146 15.661 1.00 0.00 WT1 H +ATOM 409 OH2 TIP3W1814 11.187 19.104 18.681 1.00 0.00 WT1 O +ATOM 410 H1 TIP3W1814 12.029 18.566 18.863 1.00 0.00 WT1 H +ATOM 411 H2 TIP3W1814 10.574 18.773 19.364 1.00 0.00 WT1 H +ATOM 412 OH2 TIP3W1829 11.780 13.509 0.983 1.00 0.00 WT1 O +ATOM 413 H1 TIP3W1829 12.311 13.422 1.794 1.00 0.00 WT1 H +ATOM 414 H2 TIP3W1829 12.379 13.816 0.300 1.00 0.00 WT1 H +ATOM 415 OH2 TIP3W1830 13.410 13.796 3.206 1.00 0.00 WT1 O +ATOM 416 H1 TIP3W1830 12.860 13.342 3.952 1.00 0.00 WT1 H +ATOM 417 H2 TIP3W1830 14.378 13.624 3.486 1.00 0.00 WT1 H +ATOM 418 OH2 TIP3W1831 7.314 0.228 9.152 1.00 0.00 WT1 O +ATOM 419 H1 TIP3W1831 7.447 0.196 8.157 1.00 0.00 WT1 H +ATOM 420 H2 TIP3W1831 8.219 0.336 9.426 1.00 0.00 WT1 H +ATOM 421 OH2 TIP3W1853 0.289 10.538 13.468 1.00 0.00 WT1 O +ATOM 422 H1 TIP3W1853 0.286 10.937 12.602 1.00 0.00 WT1 H +ATOM 423 H2 TIP3W1853 1.262 10.357 13.669 1.00 0.00 WT1 H +ATOM 424 OH2 TIP3W1856 12.440 12.407 5.370 1.00 0.00 WT1 O +ATOM 425 H1 TIP3W1856 11.652 11.887 5.105 1.00 0.00 WT1 H +ATOM 426 H2 TIP3W1856 12.893 11.867 5.977 1.00 0.00 WT1 H +ATOM 427 OH2 TIP3W1871 6.968 11.629 2.353 1.00 0.00 WT1 O +ATOM 428 H1 TIP3W1871 6.575 10.896 1.807 1.00 0.00 WT1 H +ATOM 429 H2 TIP3W1871 7.083 12.290 1.590 1.00 0.00 WT1 H +ATOM 430 OH2 TIP3W1873 13.533 10.550 7.160 1.00 0.00 WT1 O +ATOM 431 H1 TIP3W1873 12.608 10.309 7.490 1.00 0.00 WT1 H +ATOM 432 H2 TIP3W1873 14.008 10.940 7.925 1.00 0.00 WT1 H +ATOM 433 OH2 TIP3W1874 13.043 18.831 22.933 1.00 0.00 WT1 O +ATOM 434 H1 TIP3W1874 13.439 17.936 22.986 1.00 0.00 WT1 H +ATOM 435 H2 TIP3W1874 12.139 18.764 23.145 1.00 0.00 WT1 H +ATOM 436 OH2 TIP3W1894 11.706 15.811 16.829 1.00 0.00 WT1 O +ATOM 437 H1 TIP3W1894 10.892 16.347 16.590 1.00 0.00 WT1 H +ATOM 438 H2 TIP3W1894 12.344 16.466 17.162 1.00 0.00 WT1 H +ATOM 439 OH2 TIP3W1911 11.642 19.030 4.866 1.00 0.00 WT1 O +ATOM 440 H1 TIP3W1911 10.752 18.786 5.209 1.00 0.00 WT1 H +ATOM 441 H2 TIP3W1911 11.534 19.147 3.897 1.00 0.00 WT1 H +ATOM 442 OH2 TIP3W1912 13.550 21.522 9.565 1.00 0.00 WT1 O +ATOM 443 H1 TIP3W1912 13.279 21.744 8.655 1.00 0.00 WT1 H +ATOM 444 H2 TIP3W1912 13.859 22.419 9.914 1.00 0.00 WT1 H +ATOM 445 OH2 TIP3W1914 12.001 20.877 14.108 1.00 0.00 WT1 O +ATOM 446 H1 TIP3W1914 12.060 21.566 14.774 1.00 0.00 WT1 H +ATOM 447 H2 TIP3W1914 11.186 21.104 13.629 1.00 0.00 WT1 H +ATOM 448 OH2 TIP3W1915 12.814 17.906 7.383 1.00 0.00 WT1 O +ATOM 449 H1 TIP3W1915 13.379 17.410 6.688 1.00 0.00 WT1 H +ATOM 450 H2 TIP3W1915 11.963 17.994 6.954 1.00 0.00 WT1 H +ATOM 451 OH2 TIP3W1952 15.989 19.751 4.862 1.00 0.00 WT1 O +ATOM 452 H1 TIP3W1952 15.952 20.632 4.460 1.00 0.00 WT1 H +ATOM 453 H2 TIP3W1952 15.557 19.210 4.188 1.00 0.00 WT1 H +ATOM 454 OH2 TIP3W2123 10.963 1.737 11.790 1.00 0.00 WT1 O +ATOM 455 H1 TIP3W2123 10.319 2.240 11.334 1.00 0.00 WT1 H +ATOM 456 H2 TIP3W2123 11.709 2.167 11.210 1.00 0.00 WT1 H +ATOM 457 OH2 TIP3W2163 5.526 8.369 14.858 1.00 0.00 WT1 O +ATOM 458 H1 TIP3W2163 4.950 8.218 14.072 1.00 0.00 WT1 H +ATOM 459 H2 TIP3W2163 4.945 8.919 15.363 1.00 0.00 WT1 H +ATOM 460 OH2 TIP3W2165 14.776 4.939 12.443 1.00 0.00 WT1 O +ATOM 461 H1 TIP3W2165 14.636 5.952 12.252 1.00 0.00 WT1 H +ATOM 462 H2 TIP3W2165 13.865 4.712 12.604 1.00 0.00 WT1 H +ATOM 463 OH2 TIP3W2167 7.529 4.508 1.396 1.00 0.00 WT1 O +ATOM 464 H1 TIP3W2167 8.313 4.582 0.857 1.00 0.00 WT1 H +ATOM 465 H2 TIP3W2167 6.783 4.511 0.768 1.00 0.00 WT1 H +ATOM 466 OH2 TIP3W2172 11.435 0.836 22.059 1.00 0.00 WT1 O +ATOM 467 H1 TIP3W2172 11.858 0.103 21.657 1.00 0.00 WT1 H +ATOM 468 H2 TIP3W2172 12.219 1.281 22.508 1.00 0.00 WT1 H +ATOM 469 OH2 TIP3W2227 11.200 4.151 3.471 1.00 0.00 WT1 O +ATOM 470 H1 TIP3W2227 12.053 4.360 3.928 1.00 0.00 WT1 H +ATOM 471 H2 TIP3W2227 10.572 4.426 4.138 1.00 0.00 WT1 H +ATOM 472 OH2 TIP3W2231 4.884 4.081 13.713 1.00 0.00 WT1 O +ATOM 473 H1 TIP3W2231 4.970 4.746 14.373 1.00 0.00 WT1 H +ATOM 474 H2 TIP3W2231 3.932 3.975 13.593 1.00 0.00 WT1 H +ATOM 475 OH2 TIP3W2244 13.867 4.624 3.954 1.00 0.00 WT1 O +ATOM 476 H1 TIP3W2244 14.067 4.641 4.904 1.00 0.00 WT1 H +ATOM 477 H2 TIP3W2244 14.122 5.494 3.648 1.00 0.00 WT1 H +ATOM 478 OH2 TIP3W2270 3.174 11.159 5.954 1.00 0.00 WT1 O +ATOM 479 H1 TIP3W2270 3.904 11.073 5.352 1.00 0.00 WT1 H +ATOM 480 H2 TIP3W2270 3.204 12.104 6.129 1.00 0.00 WT1 H +ATOM 481 OH2 TIP3W2272 12.922 2.911 17.412 1.00 0.00 WT1 O +ATOM 482 H1 TIP3W2272 12.421 2.431 18.089 1.00 0.00 WT1 H +ATOM 483 H2 TIP3W2272 12.240 2.996 16.701 1.00 0.00 WT1 H +ATOM 484 OH2 TIP3W2277 13.644 7.961 20.946 1.00 0.00 WT1 O +ATOM 485 H1 TIP3W2277 13.183 7.158 20.680 1.00 0.00 WT1 H +ATOM 486 H2 TIP3W2277 13.018 8.315 21.687 1.00 0.00 WT1 H +ATOM 487 OH2 TIP3W2280 6.612 3.396 17.042 1.00 0.00 WT1 O +ATOM 488 H1 TIP3W2280 6.138 2.987 17.830 1.00 0.00 WT1 H +ATOM 489 H2 TIP3W2280 6.248 2.883 16.306 1.00 0.00 WT1 H +ATOM 490 OH2 TIP3W2288 3.628 15.453 9.684 1.00 0.00 WT1 O +ATOM 491 H1 TIP3W2288 3.604 16.368 9.365 1.00 0.00 WT1 H +ATOM 492 H2 TIP3W2288 3.266 15.478 10.592 1.00 0.00 WT1 H +ATOM 493 OH2 TIP3W2293 1.641 18.264 8.136 1.00 0.00 WT1 O +ATOM 494 H1 TIP3W2293 0.755 18.490 8.008 1.00 0.00 WT1 H +ATOM 495 H2 TIP3W2293 1.981 19.003 8.665 1.00 0.00 WT1 H +ATOM 496 OH2 TIP3W2295 8.716 0.819 21.571 1.00 0.00 WT1 O +ATOM 497 H1 TIP3W2295 8.359 0.399 22.460 1.00 0.00 WT1 H +ATOM 498 H2 TIP3W2295 9.622 1.046 21.690 1.00 0.00 WT1 H +ATOM 499 OH2 TIP3W2309 14.269 10.001 4.369 1.00 0.00 WT1 O +ATOM 500 H1 TIP3W2309 14.973 10.528 4.752 1.00 0.00 WT1 H +ATOM 501 H2 TIP3W2309 13.690 9.859 5.092 1.00 0.00 WT1 H +ATOM 502 OH2 TIP3W2311 14.691 13.817 9.050 1.00 0.00 WT1 O +ATOM 503 H1 TIP3W2311 15.162 14.372 8.385 1.00 0.00 WT1 H +ATOM 504 H2 TIP3W2311 13.821 14.250 9.113 1.00 0.00 WT1 H +ATOM 505 OH2 TIP3W2316 12.273 5.424 10.404 1.00 0.00 WT1 O +ATOM 506 H1 TIP3W2316 12.384 4.472 10.210 1.00 0.00 WT1 H +ATOM 507 H2 TIP3W2316 13.153 5.714 10.501 1.00 0.00 WT1 H +ATOM 508 OH2 TIP3W2317 3.759 13.253 15.143 1.00 0.00 WT1 O +ATOM 509 H1 TIP3W2317 3.552 13.546 16.059 1.00 0.00 WT1 H +ATOM 510 H2 TIP3W2317 2.862 13.321 14.740 1.00 0.00 WT1 H +ATOM 511 OH2 TIP3W2335 7.319 14.432 15.015 1.00 0.00 WT1 O +ATOM 512 H1 TIP3W2335 7.633 15.319 14.742 1.00 0.00 WT1 H +ATOM 513 H2 TIP3W2335 7.702 14.303 15.933 1.00 0.00 WT1 H +ATOM 514 OH2 TIP3W2357 3.117 11.819 10.070 1.00 0.00 WT1 O +ATOM 515 H1 TIP3W2357 3.490 12.496 9.523 1.00 0.00 WT1 H +ATOM 516 H2 TIP3W2357 3.937 11.583 10.539 1.00 0.00 WT1 H +ATOM 517 OH2 TIP3W2358 0.549 16.393 10.366 1.00 0.00 WT1 O +ATOM 518 H1 TIP3W2358 1.292 16.322 11.016 1.00 0.00 WT1 H +ATOM 519 H2 TIP3W2358 0.665 17.283 9.972 1.00 0.00 WT1 H +ATOM 520 OH2 TIP3W2607 10.050 5.605 5.758 1.00 0.00 WT1 O +ATOM 521 H1 TIP3W2607 10.155 6.554 5.556 1.00 0.00 WT1 H +ATOM 522 H2 TIP3W2607 10.797 5.389 6.309 1.00 0.00 WT1 H +ATOM 523 OH2 TIP3W2608 7.881 3.518 5.700 1.00 0.00 WT1 O +ATOM 524 H1 TIP3W2608 8.550 4.225 5.812 1.00 0.00 WT1 H +ATOM 525 H2 TIP3W2608 7.070 3.834 6.169 1.00 0.00 WT1 H +ATOM 526 OH2 TIP3W2634 8.559 3.515 11.535 1.00 0.00 WT1 O +ATOM 527 H1 TIP3W2634 8.435 4.298 12.155 1.00 0.00 WT1 H +ATOM 528 H2 TIP3W2634 7.955 2.899 11.952 1.00 0.00 WT1 H +ATOM 529 OH2 TIP3W2669 13.039 10.511 11.777 1.00 0.00 WT1 O +ATOM 530 H1 TIP3W2669 13.825 10.589 11.282 1.00 0.00 WT1 H +ATOM 531 H2 TIP3W2669 12.883 11.473 11.916 1.00 0.00 WT1 H +ATOM 532 OH2 TIP3W2691 15.316 3.976 15.033 1.00 0.00 WT1 O +ATOM 533 H1 TIP3W2691 15.353 4.265 14.065 1.00 0.00 WT1 H +ATOM 534 H2 TIP3W2691 14.585 4.533 15.460 1.00 0.00 WT1 H +ATOM 535 OH2 TIP3W2694 8.400 5.552 13.557 1.00 0.00 WT1 O +ATOM 536 H1 TIP3W2694 9.070 5.240 14.185 1.00 0.00 WT1 H +ATOM 537 H2 TIP3W2694 7.739 5.945 14.163 1.00 0.00 WT1 H +ATOM 538 OH2 TIP3W2714 4.281 21.161 19.066 1.00 0.00 WT1 O +ATOM 539 H1 TIP3W2714 5.157 21.058 19.381 1.00 0.00 WT1 H +ATOM 540 H2 TIP3W2714 4.169 22.110 18.904 1.00 0.00 WT1 H +ATOM 541 OH2 TIP3W2732 13.870 7.474 12.187 1.00 0.00 WT1 O +ATOM 542 H1 TIP3W2732 13.209 8.073 12.633 1.00 0.00 WT1 H +ATOM 543 H2 TIP3W2732 14.457 8.029 11.659 1.00 0.00 WT1 H +ATOM 544 OH2 TIP3W2735 13.600 17.247 9.998 1.00 0.00 WT1 O +ATOM 545 H1 TIP3W2735 13.256 16.385 10.107 1.00 0.00 WT1 H +ATOM 546 H2 TIP3W2735 13.616 17.337 9.047 1.00 0.00 WT1 H +ATOM 547 OH2 TIP3W2758 10.099 18.083 21.099 1.00 0.00 WT1 O +ATOM 548 H1 TIP3W2758 10.453 17.258 20.699 1.00 0.00 WT1 H +ATOM 549 H2 TIP3W2758 9.398 17.746 21.690 1.00 0.00 WT1 H +ATOM 550 OH2 TIP3W2778 15.465 7.955 17.814 1.00 0.00 WT1 O +ATOM 551 H1 TIP3W2778 15.150 7.979 16.932 1.00 0.00 WT1 H +ATOM 552 H2 TIP3W2778 14.706 7.563 18.306 1.00 0.00 WT1 H +ATOM 553 OH2 TIP3W3010 9.016 4.086 8.814 1.00 0.00 WT1 O +ATOM 554 H1 TIP3W3010 9.377 5.001 8.813 1.00 0.00 WT1 H +ATOM 555 H2 TIP3W3010 8.726 3.741 9.661 1.00 0.00 WT1 H +ATOM 556 OH2 TIP3W3072 6.439 5.144 7.455 1.00 0.00 WT1 O +ATOM 557 H1 TIP3W3072 7.310 4.836 7.837 1.00 0.00 WT1 H +ATOM 558 H2 TIP3W3072 6.121 5.819 8.116 1.00 0.00 WT1 H +ATOM 559 OH2 TIP3W3096 13.331 4.563 23.416 1.00 0.00 WT1 O +ATOM 560 H1 TIP3W3096 14.315 4.772 23.360 1.00 0.00 WT1 H +ATOM 561 H2 TIP3W3096 13.215 3.678 23.134 1.00 0.00 WT1 H +ATOM 562 OH2 TIP3W3134 11.401 21.480 17.136 1.00 0.00 WT1 O +ATOM 563 H1 TIP3W3134 11.522 22.112 17.856 1.00 0.00 WT1 H +ATOM 564 H2 TIP3W3134 11.255 20.672 17.636 1.00 0.00 WT1 H +ATOM 565 OH2 TIP3W3173 12.076 4.645 13.566 1.00 0.00 WT1 O +ATOM 566 H1 TIP3W3173 12.000 5.522 13.148 1.00 0.00 WT1 H +ATOM 567 H2 TIP3W3173 11.827 4.835 14.443 1.00 0.00 WT1 H +ATOM 568 OH2 TIP3W3177 9.131 1.075 15.841 1.00 0.00 WT1 O +ATOM 569 H1 TIP3W3177 9.948 1.463 15.412 1.00 0.00 WT1 H +ATOM 570 H2 TIP3W3177 9.113 0.161 15.464 1.00 0.00 WT1 H +ATOM 571 OH2 TIP3W3196 7.694 8.338 16.687 1.00 0.00 WT1 O +ATOM 572 H1 TIP3W3196 7.323 8.081 17.508 1.00 0.00 WT1 H +ATOM 573 H2 TIP3W3196 6.991 8.476 16.072 1.00 0.00 WT1 H +ATOM 574 OH2 TIP3W3218 11.912 13.212 19.726 1.00 0.00 WT1 O +ATOM 575 H1 TIP3W3218 12.854 13.225 19.881 1.00 0.00 WT1 H +ATOM 576 H2 TIP3W3218 11.504 12.764 20.555 1.00 0.00 WT1 H +ATOM 577 OH2 TIP3W3223 5.115 19.820 22.632 1.00 0.00 WT1 O +ATOM 578 H1 TIP3W3223 4.270 19.752 22.092 1.00 0.00 WT1 H +ATOM 579 H2 TIP3W3223 5.800 19.585 21.996 1.00 0.00 WT1 H +ATOM 580 OH2 TIP3W3303 14.170 23.047 20.478 1.00 0.00 WT1 O +ATOM 581 H1 TIP3W3303 15.015 22.883 20.902 1.00 0.00 WT1 H +ATOM 582 H2 TIP3W3303 13.757 22.177 20.579 1.00 0.00 WT1 H +ATOM 583 OH2 TIP3W3304 13.163 20.489 20.636 1.00 0.00 WT1 O +ATOM 584 H1 TIP3W3304 12.450 20.171 20.104 1.00 0.00 WT1 H +ATOM 585 H2 TIP3W3304 13.220 19.875 21.393 1.00 0.00 WT1 H +ATOM 586 OH2 TIP3W3447 11.316 2.273 7.956 1.00 0.00 WT1 O +ATOM 587 H1 TIP3W3447 11.391 1.358 8.151 1.00 0.00 WT1 H +ATOM 588 H2 TIP3W3447 10.423 2.479 8.181 1.00 0.00 WT1 H +ATOM 589 OH2 TIP3W3545 10.407 6.649 8.888 1.00 0.00 WT1 O +ATOM 590 H1 TIP3W3545 9.810 7.215 9.386 1.00 0.00 WT1 H +ATOM 591 H2 TIP3W3545 11.077 6.417 9.547 1.00 0.00 WT1 H +ATOM 592 OH2 TIP3W3596 7.574 19.420 4.717 1.00 0.00 WT1 O +ATOM 593 H1 TIP3W3596 7.704 19.335 3.679 1.00 0.00 WT1 H +ATOM 594 H2 TIP3W3596 7.970 20.255 4.957 1.00 0.00 WT1 H +ATOM 595 OH2 TIP3W3650 12.254 19.676 2.229 1.00 0.00 WT1 O +ATOM 596 H1 TIP3W3650 12.678 20.538 2.358 1.00 0.00 WT1 H +ATOM 597 H2 TIP3W3650 12.115 19.535 1.250 1.00 0.00 WT1 H +ATOM 598 OH2 TIP3W3660 14.036 7.730 6.644 1.00 0.00 WT1 O +ATOM 599 H1 TIP3W3660 14.358 7.138 7.346 1.00 0.00 WT1 H +ATOM 600 H2 TIP3W3660 13.886 8.589 7.123 1.00 0.00 WT1 H +ATOM 601 OH2 TIP3W3977 8.900 7.310 11.290 1.00 0.00 WT1 O +ATOM 602 H1 TIP3W3977 8.739 6.706 12.078 1.00 0.00 WT1 H +ATOM 603 H2 TIP3W3977 9.555 8.003 11.531 1.00 0.00 WT1 H +ATOM 604 OH2 TIP3W4012 9.495 14.416 1.979 1.00 0.00 WT1 O +ATOM 605 H1 TIP3W4012 10.354 14.203 1.548 1.00 0.00 WT1 H +ATOM 606 H2 TIP3W4012 9.165 13.566 2.099 1.00 0.00 WT1 H +ATOM 607 OH2 TIP3W4036 13.605 5.353 19.280 1.00 0.00 WT1 O +ATOM 608 H1 TIP3W4036 13.658 4.527 18.812 1.00 0.00 WT1 H +ATOM 609 H2 TIP3W4036 12.688 5.367 19.516 1.00 0.00 WT1 H +ATOM 610 OH2 TIP3W4074 7.334 17.973 7.090 1.00 0.00 WT1 O +ATOM 611 H1 TIP3W4074 7.571 18.390 6.200 1.00 0.00 WT1 H +ATOM 612 H2 TIP3W4074 6.533 17.444 6.885 1.00 0.00 WT1 H +ATOM 613 OH2 TIP3W4077 13.912 11.040 17.383 1.00 0.00 WT1 O +ATOM 614 H1 TIP3W4077 13.913 10.932 16.423 1.00 0.00 WT1 H +ATOM 615 H2 TIP3W4077 13.612 11.935 17.518 1.00 0.00 WT1 H +ATOM 616 OH2 TIP3W4501 14.682 11.334 14.388 1.00 0.00 WT1 O +ATOM 617 H1 TIP3W4501 15.236 11.941 13.876 1.00 0.00 WT1 H +ATOM 618 H2 TIP3W4501 14.266 10.683 13.763 1.00 0.00 WT1 H +ATOM 619 OH2 TIP3W4515 12.414 9.004 13.909 1.00 0.00 WT1 O +ATOM 620 H1 TIP3W4515 11.523 8.931 14.184 1.00 0.00 WT1 H +ATOM 621 H2 TIP3W4515 12.375 9.766 13.286 1.00 0.00 WT1 H +ATOM 622 OH2 TIP3W4809 15.898 3.293 1.648 1.00 0.00 WT1 O +ATOM 623 H1 TIP3W4809 15.837 3.977 2.359 1.00 0.00 WT1 H +ATOM 624 H2 TIP3W4809 15.065 2.796 1.789 1.00 0.00 WT1 H +ATOM 625 OH2 TIP3W6240 3.080 0.949 11.788 1.00 0.00 WT1 O +ATOM 626 H1 TIP3W6240 3.690 0.500 11.172 1.00 0.00 WT1 H +ATOM 627 H2 TIP3W6240 2.196 0.556 11.641 1.00 0.00 WT1 H +ATOM 628 OH2 TIP3W6671 0.897 12.813 20.940 1.00 0.00 WT1 O +ATOM 629 H1 TIP3W6671 1.234 13.577 21.489 1.00 0.00 WT1 H +ATOM 630 H2 TIP3W6671 1.110 12.083 21.442 1.00 0.00 WT1 H +ATOM 631 OH2 TIP3W7222 6.255 9.802 0.364 1.00 0.00 WT1 O +ATOM 632 H1 TIP3W7222 6.954 9.121 0.671 1.00 0.00 WT1 H +ATOM 633 H2 TIP3W7222 5.459 9.264 0.196 1.00 0.00 WT1 H +ATOM 634 OH2 TIP3W7479 6.140 3.669 3.704 1.00 0.00 WT1 O +ATOM 635 H1 TIP3W7479 6.732 3.837 2.949 1.00 0.00 WT1 H +ATOM 636 H2 TIP3W7479 6.807 3.408 4.378 1.00 0.00 WT1 H +ATOM 637 OH2 TIP3W7510 5.150 11.685 11.994 1.00 0.00 WT1 O +ATOM 638 H1 TIP3W7510 5.312 12.641 12.020 1.00 0.00 WT1 H +ATOM 639 H2 TIP3W7510 5.614 11.405 12.778 1.00 0.00 WT1 H +ATOM 640 OH2 TIP3W7563 5.196 19.304 15.315 1.00 0.00 WT1 O +ATOM 641 H1 TIP3W7563 5.227 20.213 14.942 1.00 0.00 WT1 H +ATOM 642 H2 TIP3W7563 5.252 18.720 14.569 1.00 0.00 WT1 H +ATOM 643 OH2 TIP3W7630 2.179 13.464 7.177 1.00 0.00 WT1 O +ATOM 644 H1 TIP3W7630 2.719 14.061 7.737 1.00 0.00 WT1 H +ATOM 645 H2 TIP3W7630 1.640 13.021 7.843 1.00 0.00 WT1 H +ATOM 646 OH2 TIP3W7631 1.926 21.439 17.027 1.00 0.00 WT1 O +ATOM 647 H1 TIP3W7631 2.672 21.817 16.545 1.00 0.00 WT1 H +ATOM 648 H2 TIP3W7631 2.398 20.912 17.662 1.00 0.00 WT1 H +ATOM 649 OH2 TIP3W7707 0.688 2.781 7.114 1.00 0.00 WT1 O +ATOM 650 H1 TIP3W7707 1.488 3.190 6.703 1.00 0.00 WT1 H +ATOM 651 H2 TIP3W7707 0.053 3.429 6.930 1.00 0.00 WT1 H +ATOM 652 OH2 TIP3W7985 0.449 7.366 9.140 1.00 0.00 WT1 O +ATOM 653 H1 TIP3W7985 0.202 6.479 9.095 1.00 0.00 WT1 H +ATOM 654 H2 TIP3W7985 0.796 7.563 8.256 1.00 0.00 WT1 H +ATOM 655 OH2 TIP3W8023 0.913 12.320 0.937 1.00 0.00 WT1 O +ATOM 656 H1 TIP3W8023 0.623 11.700 0.268 1.00 0.00 WT1 H +ATOM 657 H2 TIP3W8023 1.290 11.784 1.628 1.00 0.00 WT1 H +ATOM 658 OH2 TIP3W8029 7.889 16.997 14.360 1.00 0.00 WT1 O +ATOM 659 H1 TIP3W8029 7.935 17.181 13.358 1.00 0.00 WT1 H +ATOM 660 H2 TIP3W8029 8.602 17.562 14.734 1.00 0.00 WT1 H +ATOM 661 OH2 TIP3W8046 3.230 22.882 11.736 1.00 0.00 WT1 O +ATOM 662 H1 TIP3W8046 3.601 21.950 11.670 1.00 0.00 WT1 H +ATOM 663 H2 TIP3W8046 2.861 22.992 10.853 1.00 0.00 WT1 H +ATOM 664 OH2 TIP3W8064 4.620 22.335 7.130 1.00 0.00 WT1 O +ATOM 665 H1 TIP3W8064 3.754 22.591 7.590 1.00 0.00 WT1 H +ATOM 666 H2 TIP3W8064 5.178 22.349 7.907 1.00 0.00 WT1 H +ATOM 667 OH2 TIP3W8068 1.124 22.962 13.514 1.00 0.00 WT1 O +ATOM 668 H1 TIP3W8068 1.837 22.901 12.860 1.00 0.00 WT1 H +ATOM 669 H2 TIP3W8068 0.685 23.799 13.310 1.00 0.00 WT1 H +ATOM 670 OH2 TIP3W8364 8.561 10.924 16.881 1.00 0.00 WT1 O +ATOM 671 H1 TIP3W8364 7.916 11.188 16.202 1.00 0.00 WT1 H +ATOM 672 H2 TIP3W8364 8.309 10.008 17.123 1.00 0.00 WT1 H +ATOM 673 OH2 TIP3W8403 4.751 19.009 2.814 1.00 0.00 WT1 O +ATOM 674 H1 TIP3W8403 4.754 18.978 3.760 1.00 0.00 WT1 H +ATOM 675 H2 TIP3W8403 5.300 18.306 2.612 1.00 0.00 WT1 H +ATOM 676 OH2 TIP3W8411 3.406 0.117 14.493 1.00 0.00 WT1 O +ATOM 677 H1 TIP3W8411 3.348 0.244 13.546 1.00 0.00 WT1 H +ATOM 678 H2 TIP3W8411 4.378 0.190 14.724 1.00 0.00 WT1 H +ATOM 679 OH2 TIP3W8425 2.278 3.922 1.200 1.00 0.00 WT1 O +ATOM 680 H1 TIP3W8425 2.701 3.392 0.560 1.00 0.00 WT1 H +ATOM 681 H2 TIP3W8425 1.556 3.406 1.415 1.00 0.00 WT1 H +ATOM 682 OH2 TIP3W8441 6.246 21.216 13.564 1.00 0.00 WT1 O +ATOM 683 H1 TIP3W8441 7.127 21.533 13.794 1.00 0.00 WT1 H +ATOM 684 H2 TIP3W8441 5.802 22.075 13.455 1.00 0.00 WT1 H +ATOM 685 OH2 TIP3W8466 5.348 15.459 5.988 1.00 0.00 WT1 O +ATOM 686 H1 TIP3W8466 4.942 16.211 6.465 1.00 0.00 WT1 H +ATOM 687 H2 TIP3W8466 4.964 14.679 6.422 1.00 0.00 WT1 H +ATOM 688 OH2 TIP3W8468 1.312 13.577 13.829 1.00 0.00 WT1 O +ATOM 689 H1 TIP3W8468 1.594 13.350 12.963 1.00 0.00 WT1 H +ATOM 690 H2 TIP3W8468 0.905 14.443 13.634 1.00 0.00 WT1 H +ATOM 691 OH2 TIP3W8491 10.395 21.375 22.397 1.00 0.00 WT1 O +ATOM 692 H1 TIP3W8491 10.900 20.680 22.794 1.00 0.00 WT1 H +ATOM 693 H2 TIP3W8491 10.682 22.154 22.828 1.00 0.00 WT1 H +ATOM 694 OH2 TIP3W8528 6.013 16.085 3.326 1.00 0.00 WT1 O +ATOM 695 H1 TIP3W8528 6.016 16.035 4.292 1.00 0.00 WT1 H +ATOM 696 H2 TIP3W8528 5.249 15.516 3.046 1.00 0.00 WT1 H +ATOM 697 OH2 TIP3W8534 2.184 22.110 9.500 1.00 0.00 WT1 O +ATOM 698 H1 TIP3W8534 1.913 21.297 9.998 1.00 0.00 WT1 H +ATOM 699 H2 TIP3W8534 1.389 22.233 8.964 1.00 0.00 WT1 H +ATOM 700 OH2 TIP3W8536 3.207 13.979 17.772 1.00 0.00 WT1 O +ATOM 701 H1 TIP3W8536 3.947 14.082 18.373 1.00 0.00 WT1 H +ATOM 702 H2 TIP3W8536 2.585 14.685 17.921 1.00 0.00 WT1 H +ATOM 703 OH2 TIP3W8548 13.639 16.098 5.269 1.00 0.00 WT1 O +ATOM 704 H1 TIP3W8548 14.099 15.394 4.872 1.00 0.00 WT1 H +ATOM 705 H2 TIP3W8548 12.755 15.724 5.343 1.00 0.00 WT1 H +ATOM 706 OH2 TIP3W8556 1.981 16.635 18.663 1.00 0.00 WT1 O +ATOM 707 H1 TIP3W8556 1.921 17.181 19.529 1.00 0.00 WT1 H +ATOM 708 H2 TIP3W8556 2.656 17.117 18.156 1.00 0.00 WT1 H +ATOM 709 OH2 TIP3W8760 13.457 20.491 6.545 1.00 0.00 WT1 O +ATOM 710 H1 TIP3W8760 13.544 19.713 6.959 1.00 0.00 WT1 H +ATOM 711 H2 TIP3W8760 13.199 20.170 5.601 1.00 0.00 WT1 H +ATOM 712 OH2 TIP3W8780 3.438 8.099 0.316 1.00 0.00 WT1 O +ATOM 713 H1 TIP3W8780 2.547 7.847 0.577 1.00 0.00 WT1 H +ATOM 714 H2 TIP3W8780 3.889 7.775 1.093 1.00 0.00 WT1 H +ATOM 715 OH2 TIP3W8801 9.016 15.690 9.485 1.00 0.00 WT1 O +ATOM 716 H1 TIP3W8801 9.158 14.769 9.701 1.00 0.00 WT1 H +ATOM 717 H2 TIP3W8801 8.537 15.554 8.652 1.00 0.00 WT1 H +ATOM 718 OH2 TIP3W8822 1.562 6.536 12.239 1.00 0.00 WT1 O +ATOM 719 H1 TIP3W8822 0.960 7.250 12.049 1.00 0.00 WT1 H +ATOM 720 H2 TIP3W8822 1.197 5.827 11.553 1.00 0.00 WT1 H +ATOM 721 OH2 TIP3W8829 1.314 9.385 7.173 1.00 0.00 WT1 O +ATOM 722 H1 TIP3W8829 1.333 8.706 6.444 1.00 0.00 WT1 H +ATOM 723 H2 TIP3W8829 2.056 9.953 6.980 1.00 0.00 WT1 H +ATOM 724 OH2 TIP3W8843 7.572 0.420 3.478 1.00 0.00 WT1 O +ATOM 725 H1 TIP3W8843 7.636 0.339 2.503 1.00 0.00 WT1 H +ATOM 726 H2 TIP3W8843 6.628 0.234 3.530 1.00 0.00 WT1 H +ATOM 727 OH2 TIP3W8845 1.133 7.080 5.078 1.00 0.00 WT1 O +ATOM 728 H1 TIP3W8845 1.201 7.102 4.137 1.00 0.00 WT1 H +ATOM 729 H2 TIP3W8845 0.358 6.549 5.302 1.00 0.00 WT1 H +ATOM 730 OH2 TIP3W8865 11.515 22.342 4.827 1.00 0.00 WT1 O +ATOM 731 H1 TIP3W8865 10.875 21.911 4.185 1.00 0.00 WT1 H +ATOM 732 H2 TIP3W8865 11.205 21.919 5.694 1.00 0.00 WT1 H +ATOM 733 OH2 TIP3W8869 5.279 5.755 11.457 1.00 0.00 WT1 O +ATOM 734 H1 TIP3W8869 4.504 5.333 10.967 1.00 0.00 WT1 H +ATOM 735 H2 TIP3W8869 5.564 4.986 12.019 1.00 0.00 WT1 H +ATOM 736 OH2 TIP3W8887 8.890 21.041 16.070 1.00 0.00 WT1 O +ATOM 737 H1 TIP3W8887 8.698 21.572 15.300 1.00 0.00 WT1 H +ATOM 738 H2 TIP3W8887 9.800 21.340 16.244 1.00 0.00 WT1 H +ATOM 739 OH2 TIP3W8895 6.000 11.283 22.324 1.00 0.00 WT1 O +ATOM 740 H1 TIP3W8895 5.866 12.057 22.939 1.00 0.00 WT1 H +ATOM 741 H2 TIP3W8895 5.863 11.634 21.452 1.00 0.00 WT1 H +ATOM 742 OH2 TIP3W8905 7.834 14.408 7.527 1.00 0.00 WT1 O +ATOM 743 H1 TIP3W8905 7.105 14.717 6.993 1.00 0.00 WT1 H +ATOM 744 H2 TIP3W8905 8.194 13.714 6.926 1.00 0.00 WT1 H +ATOM 745 OH2 TIP3W8931 5.667 11.812 19.542 1.00 0.00 WT1 O +ATOM 746 H1 TIP3W8931 5.647 12.743 19.497 1.00 0.00 WT1 H +ATOM 747 H2 TIP3W8931 5.889 11.629 18.618 1.00 0.00 WT1 H +ATOM 748 OH2 TIP3W8932 12.997 18.576 15.207 1.00 0.00 WT1 O +ATOM 749 H1 TIP3W8932 12.617 19.193 14.493 1.00 0.00 WT1 H +ATOM 750 H2 TIP3W8932 13.582 19.163 15.737 1.00 0.00 WT1 H +ATOM 751 OH2 TIP3W8935 0.675 11.574 10.952 1.00 0.00 WT1 O +ATOM 752 H1 TIP3W8935 1.597 11.546 10.574 1.00 0.00 WT1 H +ATOM 753 H2 TIP3W8935 0.265 12.150 10.339 1.00 0.00 WT1 H +ATOM 754 OH2 TIP3W8949 8.782 17.187 2.362 1.00 0.00 WT1 O +ATOM 755 H1 TIP3W8949 8.004 16.786 2.797 1.00 0.00 WT1 H +ATOM 756 H2 TIP3W8949 9.140 16.422 1.970 1.00 0.00 WT1 H +ATOM 757 OH2 TIP3W8956 2.113 6.516 21.893 1.00 0.00 WT1 O +ATOM 758 H1 TIP3W8956 2.170 5.576 22.160 1.00 0.00 WT1 H +ATOM 759 H2 TIP3W8956 2.446 6.949 22.707 1.00 0.00 WT1 H +ATOM 760 OH2 TIP3W8977 2.583 16.123 12.046 1.00 0.00 WT1 O +ATOM 761 H1 TIP3W8977 3.491 16.508 12.059 1.00 0.00 WT1 H +ATOM 762 H2 TIP3W8977 2.312 16.312 12.887 1.00 0.00 WT1 H +ATOM 763 OH2 TIP3W8988 2.246 20.883 4.995 1.00 0.00 WT1 O +ATOM 764 H1 TIP3W8988 1.611 20.097 4.885 1.00 0.00 WT1 H +ATOM 765 H2 TIP3W8988 3.079 20.473 5.195 1.00 0.00 WT1 H +ATOM 766 OH2 TIP3W9082 8.156 17.564 11.520 1.00 0.00 WT1 O +ATOM 767 H1 TIP3W9082 8.355 18.345 10.921 1.00 0.00 WT1 H +ATOM 768 H2 TIP3W9082 8.334 16.820 10.874 1.00 0.00 WT1 H +ATOM 769 OH2 TIP3W9096 2.915 14.197 3.393 1.00 0.00 WT1 O +ATOM 770 H1 TIP3W9096 2.155 14.414 3.916 1.00 0.00 WT1 H +ATOM 771 H2 TIP3W9096 2.719 13.333 3.011 1.00 0.00 WT1 H +ATOM 772 OH2 TIP3W9226 8.578 0.832 6.351 1.00 0.00 WT1 O +ATOM 773 H1 TIP3W9226 7.928 0.530 5.693 1.00 0.00 WT1 H +ATOM 774 H2 TIP3W9226 8.563 1.801 6.335 1.00 0.00 WT1 H +ATOM 775 OH2 TIP3W9241 7.287 10.172 13.815 1.00 0.00 WT1 O +ATOM 776 H1 TIP3W9241 6.631 9.473 14.077 1.00 0.00 WT1 H +ATOM 777 H2 TIP3W9241 8.119 9.669 13.852 1.00 0.00 WT1 H +ATOM 778 OH2 TIP3W9250 3.347 10.487 19.814 1.00 0.00 WT1 O +ATOM 779 H1 TIP3W9250 2.792 10.955 19.188 1.00 0.00 WT1 H +ATOM 780 H2 TIP3W9250 4.264 10.639 19.456 1.00 0.00 WT1 H +END diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt new file mode 100644 index 0000000000..019911c19b --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeSPCE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt new file mode 100644 index 0000000000..274d8aeb11 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt @@ -0,0 +1,16 @@ +import "spce.lt" + +wat = new SPCE [260] + + + + + + + +# Open up the PDB file to count the number of water molecules inside. (Or just +# divide the number of atoms by 3). Put that in between the brackets ("[260]") +# +# The command above does not set the positions of the atoms. +# So they will have to be loaded later from a PDB or an XYZ file. +# (For example, using "moltemplate.sh -pdb solvate.pdb system.lt") diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt new file mode 100644 index 0000000000..4d8af42b5d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt @@ -0,0 +1,48 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize". +unfix fShakeSPCE +minimize 1.0e-3 1.0e-5 100000 400000 +# Now read "system.in.settings" in order to redefine fShakeSPCE again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 +thermo 100 + +run 10000 + +# Now that the system's temperature has become more equilibrated, +# we can increase the timestep: + +timestep 2.0 +run 50000 + +write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt new file mode 100644 index 0000000000..22fb1f271e --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt @@ -0,0 +1,58 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_npt.data + + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- +# Note: If you are reading the restart file instead of the data file, +# then you should not need to minimize the system beforehand.. +# fShakeSPCE was defined in system.in.settings. +# (It is incompatible with "minimize".) +unfix fShakeSPCE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fShakeSPCE again: +include system.in.settings + +# -- simulation protocol -- + + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo 500 + +run 10000 + +# Now that the system's temperature has become more equilibrated, +# we can increase the timestep: + +timestep 2.0 +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh new file mode 100755 index 0000000000..cf51fa8705 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure + +# or + +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +# or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh new file mode 100755 index 0000000000..3a08212692 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg new file mode 100644 index 0000000000..5261bedc2c Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg new file mode 100644 index 0000000000..78c4056f8c Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..d255bf3683 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,4257 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 3016 !NATOM + 1 1 3 3 -0.847600 15.9994 0 + 2 1 4 4 0.423800 1.0080 0 + 3 1 4 4 0.423800 1.0080 0 + 4 2 3 3 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0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/wat.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/wat.jpg new file mode 100644 index 0000000000..60aaf90b95 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/wat.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg new file mode 100644 index 0000000000..2c34754c4c Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg new file mode 100644 index 0000000000..220a717271 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt new file mode 100644 index 0000000000..8d36341253 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt @@ -0,0 +1,67 @@ +# We define two molecule classes to represent Na+ and Cl- ions, respectively. +# This may seem like overkill since they both only consist of one atom each. + + +# Note: Monovalent ion parameters for Ewald and SPC/E water +# are from: Joung & Cheatham JPCB (2008) +# These Lennard Jones parameters match the parameters for ions +# in SPC/E water in the "frcmod.ionsjc_spce" file distributed +# with Amber (the 2010 version). + + +NaIon { + + # The epsilong & sigma parameters from that paper were 0.3526418 & 1.212. + # However sigma must be divided by 2^(1/6), because they use the alternate + # Lennard-Jones convention: U(r)=epsilon*((s/r)^12 - 2*(s/r)^6), and + # pair_style lj/charmm/coul/long uses U(r)=4*epsilon*((s/r)^12 - (s/r)^6) + # (Note: This change does not effect the epsilon parameter.) + + write_once("In Settings") { + pair_coeff @atom:Na @atom:Na lj/charmm/coul/long 0.3526418 1.079769246386 + } + + write_once("Data Masses") { + @atom:Na 22.9898 + } + + # assumes "full" atom style + write("Data Atoms") { + $atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000 + } +} # NaIon + + +ClIon { + write_once("In Settings") { + pair_coeff @atom:Cl @atom:Cl lj/charmm/coul/long 0.0127850 2.711 + } + + write_once("Data Masses") { + @atom:Cl 35.453 + } + + # assumes "full" atom style + write("Data Atoms") { + $atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000 + } +} # ClIon + + +write_once("In Init") { + # -- Default styles for ions -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + kspace_style pppm 0.0001 + pair_modify mix arithmetic +} + +# Optional: Define a group named "ions" consisting of either Na or Cl ions. +write_once("In Settings") { + group ionNa type @atom:NaIon/Na @atom:NaIon/Na + group ionCl type @atom:ClIon/Cl @atom:ClIon/Cl + group ions type @atom:NaIon/Na @atom:ClIon/Cl +} + diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt new file mode 100644 index 0000000000..019911c19b --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeSPCE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt new file mode 100644 index 0000000000..f43f4263e8 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt @@ -0,0 +1,52 @@ +import "spce.lt" # <- This defines the SPCE water molecule. This file is + # located in the "common" directory. You can either copy it + # here, or (preferably), you can define a MOLTEMPLATE_PATH + # environment variable and point it to "common". + # (as explained in the installation section of the manual). + +import "ions.lt" # <- This defines the ions "NaIon" and "ClIon". + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 34.50 xlo xhi + 0.0 34.50 ylo yhi + 0.0 34.50 zlo zhi +} + + +# The next command generates a (rather dense) cubic lattice with +# spacing 3.45 Angstroms. (The pressure must be equilibrated later.) + +wat = new SPCE [10].move(0.00, 0.00, 3.45) + [10].move(0.00, 3.45, 0.00) + [10].move(3.45, 0.00, 0.00) + +# We now create a 2x2x2 lattice of Na+ and Cl- ions: + +na = new NaIon [2].move(0,0,17.25) + [2].move(0,17.25,0) + [2].move(17.25,0,0) + + +cl = new ClIon [2].move(0,0,17.25) + [2].move(0,17.25,0) + [2].move(17.25,0,0) + +na[*][*][*].move(5.175,5.175,5.6) +cl[*][*][*].move(12.075,12.075,12.5) + +# (The (5.175,5.175,5.175) and (12.075,12.075,12.075) translational shifts +# prevent the Na and Cl ions from overlapping +# with the water molecules or each other.) + + +# Comment: Fortunately the ions and the water in this example share the +# same force-field styles (so their was no need to use "hybrid" styles). +# If this were not the case, you might need to add something like this. +# +# write_once("In Init") { +# # -- Styles for the combined system (overrides earlier settings) -- +# pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 NEWPAIRSTYLE +# bond_style hybrid harmonic NEWBONDSTYLE +# angle_style hybrid harmonic NEWANGLESTYLE +# } diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt new file mode 100644 index 0000000000..4d8af42b5d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt @@ -0,0 +1,48 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize". +unfix fShakeSPCE +minimize 1.0e-3 1.0e-5 100000 400000 +# Now read "system.in.settings" in order to redefine fShakeSPCE again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 +thermo 100 + +run 10000 + +# Now that the system's temperature has become more equilibrated, +# we can increase the timestep: + +timestep 2.0 +run 50000 + +write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt new file mode 100644 index 0000000000..22fb1f271e --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt @@ -0,0 +1,58 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_npt.data + + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- +# Note: If you are reading the restart file instead of the data file, +# then you should not need to minimize the system beforehand.. +# fShakeSPCE was defined in system.in.settings. +# (It is incompatible with "minimize".) +unfix fShakeSPCE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fShakeSPCE again: +include system.in.settings + +# -- simulation protocol -- + + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo 500 + +run 10000 + +# Now that the system's temperature has become more equilibrated, +# we can increase the timestep: + +timestep 2.0 +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT new file mode 100644 index 0000000000..76caac02cc --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT @@ -0,0 +1,22 @@ + Description: + +This is a simulation of pyramid-shaped objects resting on an immobile surface +(resembling graphene). Each pyramid is built from spherical particles stacked +like cannon-balls, or stacked fruit. Ordinarily, the stack does not move +because the particles at the ground layer are immobilized. However, +given an initial (small) perturbation the pyramids collapse in an avalanche. + +(In this example, the perturbation is due to shock because we (intentionally) + did not minimize the system before starting the simulation. This shock + causes an avalanche to occur approximately 5000 timesteps later.) + +The particles roll down the pyramid and bounce off the "ground". The bouncing +is due to a repulsive external force which is added artificially. +(See the "run.in" file.) The simulation looks weird without something +to bounce off of. So I added a graphene surface at the bottom as scenery. +(It does not exert any force on the atoms.) + +(Random comment: This could be a fun example to illustrate the Boltzmann + distribution. Because there is no damping, in a small region, the particle + heights should eventually approach the Boltzmann distribution for some + suitable temperature.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt new file mode 100644 index 0000000000..096674f7ff --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt @@ -0,0 +1,28 @@ + ------- A note on building the graphene sheet in VMD: ------ + +Probably you can ignore these instructions. +These instructions are not necessary for this example to run. + +This example contains several pyramid shaped objects resting on a surface +made of graphene. The instructions in this file explain how to build the +graphene (representing the "ground") using VMD instead of with moltemplate. + Why do this? +VMD can create graphene sheets with bonds connecting neighboring carbon atoms, +(which looks more pretty). However, as of 2013-4-29, moltemplate currently +can not generate these bonds. It does not matter physically in this case, +because the graphene sheet used here does not move. It is only used as +scenery, to graphically represent the ground surface. + +Select "Extensions"->"Modeling"->"Carbon Nanotube Builder" + Build a graphene sheet of size 39.8 x 39.8 (units: nm) + 400.3358398 399.876008 + (try to use a size compatible with the periodic boundaries) +Select "Extensions"->"Tk Console", and type + display backgroundgradient on + +Note: If you want to do this, before you run moltemplate, you may want to delete + the sections of the "system.lt" file (located in "moltemplate_files") + which define the graphene wall. Instead create the graphene data file + in VMD. You will have to manually merge the data file for graphene + with the data file for the pyramids created by moltemplate, + (taking care to avoid overlapping atom-id numbers). diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh new file mode 100755 index 0000000000..acc5fbbaad --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt new file mode 100644 index 0000000000..10198fc92f --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt @@ -0,0 +1,76 @@ + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + To shift the box by a fraction in the x direction (for example) + do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 } + pbc box -shiftcenterrel {-0.50 -0.52 0.0 } + + # Alternately if you have a solute whose atoms are all of type 1, + # then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg new file mode 100644 index 0000000000..dc010258f0 Binary files /dev/null and b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg new file mode 100644 index 0000000000..53dc98f3e8 Binary files /dev/null and b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg new file mode 100644 index 0000000000..ba07b25372 Binary files /dev/null and b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh new file mode 100644 index 0000000000..365ab9fb03 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh @@ -0,0 +1,15 @@ +# This directory contains moltemplate files for the "Pyramids of Giza" example. +# (Note: the ground lattice work that appears in some images was not generated +# by moltemplate. Moltemplate can not currently create bonded periodic +# structures as of 2013-4-04. Those were generated by topotools.) +# +# To run moltemplate, use: + +moltemplate.sh system.lt + +# This will generate:system.data, system.in, system.in.init, system.in.settings +# +# The output_ttree/ directory will contain files like "Data Atoms", "Data Bonds" +# which contain the corresponding structures of the system.data file. +# (This might make it slightly easier to combine them with atom data and +# bond data generated by other programs, such as topotools, for example.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt new file mode 100644 index 0000000000..3b3e21333f --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt @@ -0,0 +1,61 @@ +# This file contains a unit cell for building graphene and nanotubes +# +# +# The 4AtomRectCellXY "molecule" defined below is a reactangular unit cell +# for hexagonal tesselations in 2-dimensions. (See "graphene_unit_cell.jpg") +# Surfaces constructed with this unit cell can be flat or curved into tubes. +# The distance between nearest-neighbor carbon atoms (ie the length of a +# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms. +# +# d = length of each hexagon's side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms +# 2w = width of hexagon rows = 3*l = 4.26 Angstroms +# +# Consequently, the Lattice-cell vectors for singe-layer graphene are: +# (2.4595121467478, 0, 0) (aligned with X axis) +# (0, 4.26, 0) (aligned with Y axis) +# So, to build a sheet of graphite, you could use: +# sheet = new Graphene/4AtomRectCellXY [10].move(2.4595121467478, 0, 0) +# [10].move(0, 4.26, 0) + + + + +Graphene { + + 4AtomRectCellXY + { + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:C11 $mol:... @atom:../C 0.0 0.61487803668695 0.71 0.0 + $atom:C21 $mol:... @atom:../C 0.0 1.84463411006085 1.42 0.0 + $atom:C12 $mol:... @atom:../C 0.0 0.61487803668695 3.55 0.0 + $atom:C22 $mol:... @atom:../C 0.0 1.84463411006085 2.84 0.0 + } + } + + # Now define properties of the Carbon graphene atom + + write_once("In Init") { + pair_style hybrid lj/cut 9.0 + } + + write_once("Data Masses") { + @atom:C 12.0 + } + + write_once("In Settings") { + # i j epsilon sigma + pair_coeff @atom:C @atom:C lj/cut 0.068443 3.407 + + # These Lennard-Jones parameters come from + # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, + # Chem Phys Lett, 348:187 (2001) + + # Define a group consisting of only carbon atoms in graphene molecules + group gGraphene type @atom:C + } + +} # Graphene + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt new file mode 100644 index 0000000000..759f0f5d06 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt @@ -0,0 +1,21 @@ +import "graphene.lt" + +# -------------- graphene sheet ----------------- + +# Notes: +# Hexagonal lattice with: +# l = length of each hexagonal side = 1.42 Angstroms +# L = length of each hexagon = 2*l = 2.84 Angstroms +# W = width of each hexagon = 2*l*sqrt(3)/2 ~= 2.4595121467478 Angstroms +# 2w = width of hexagon rows = 3.0*l = 4.26 Angstroms + + +GrapheneWall { + + unitcells = new Graphene/4AtomRectCellXY [163].move(2.456, 0, 0) + [94].move(0, 4.254, 0) + + # (Note: I fudged the spacing slightly to make it line up better with the + # lattice spacing for graphene generated by VMD's graphene builder.) +} + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt new file mode 100644 index 0000000000..84c2b6f6d1 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt @@ -0,0 +1,283 @@ +# Brick is a very simple molecule containing one "atom". +# "ImmobileBrick" and "GoldBrick" are identical to "Brick" but are +# given different atom types. (This makes it easier to put them in +# different groups and apply different LAMMPS "fixes" to them.) + +Brick { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom $mol @atom 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom 1.0 + } + + write_once("In Settings") { + # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) + # + # i j eps sig + pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 + } + + write_once("In Settings") { + group gMobile type @atom + # (Atoms of this type belong to the "gMobile" group) + } + + write_once("In Init") { + atom_style full + units lj + pair_style lj/cut 1.0 + } +} + + + +#We want to stack "Brick"s the same way a green-grocer sometimes stack apples: +#Place the apples at the base an square lattice of apples at the base. +#The apples in the next layer up are placed in between the 4 apples beneath them. +#Each new layer is smaller and placed above the previous layer at a height +#of sigma / sqrt(2), where "sigma" is the diameter of each spherical "Brick". +#We will artificially hold the apples at the base in place +#(to keep the entire stack from collapsing). +# +# The lines below were generated from the following python loop: +# +#from math import * +#N=50 +#s=1.0 +#for i in range(0,N): +# print(" layer"+str(i)+" = new Brick.move("+str(-(N-(i+1))*s*0.5)+","+ +# str(-(N-(i+1))*s*0.5)+","+str(i*s/sqrt(2))+") ["+str(N-i)+"].move("+ +# str(s)+",0,0) ["+str(N-i)+"].move(0,"+str(s)+",0)") + + +PyramidKhufu { + layer0 = new ImmobileBrick.move(-24.5,-24.5,0.0) [50].move(1.0,0,0) [50].move(0,1.0,0) + layer1 = new Brick.move(-24.0,-24.0,0.707106781187) [49].move(1.0,0,0) [49].move(0,1.0,0) + layer2 = new Brick.move(-23.5,-23.5,1.41421356237) [48].move(1.0,0,0) [48].move(0,1.0,0) + layer3 = new Brick.move(-23.0,-23.0,2.12132034356) [47].move(1.0,0,0) [47].move(0,1.0,0) + layer4 = new Brick.move(-22.5,-22.5,2.82842712475) [46].move(1.0,0,0) [46].move(0,1.0,0) + layer5 = new Brick.move(-22.0,-22.0,3.53553390593) [45].move(1.0,0,0) [45].move(0,1.0,0) + layer6 = new Brick.move(-21.5,-21.5,4.24264068712) [44].move(1.0,0,0) [44].move(0,1.0,0) + layer7 = new Brick.move(-21.0,-21.0,4.94974746831) [43].move(1.0,0,0) [43].move(0,1.0,0) + layer8 = new Brick.move(-20.5,-20.5,5.65685424949) [42].move(1.0,0,0) [42].move(0,1.0,0) + layer9 = new Brick.move(-20.0,-20.0,6.36396103068) [41].move(1.0,0,0) [41].move(0,1.0,0) + layer10 = new Brick.move(-19.5,-19.5,7.07106781187) [40].move(1.0,0,0) [40].move(0,1.0,0) + layer11 = new Brick.move(-19.0,-19.0,7.77817459305) [39].move(1.0,0,0) [39].move(0,1.0,0) + layer12 = new Brick.move(-18.5,-18.5,8.48528137424) [38].move(1.0,0,0) [38].move(0,1.0,0) + layer13 = new Brick.move(-18.0,-18.0,9.19238815543) [37].move(1.0,0,0) [37].move(0,1.0,0) + layer14 = new Brick.move(-17.5,-17.5,9.89949493661) [36].move(1.0,0,0) [36].move(0,1.0,0) + layer15 = new Brick.move(-17.0,-17.0,10.6066017178) [35].move(1.0,0,0) [35].move(0,1.0,0) + layer16 = new Brick.move(-16.5,-16.5,11.313708499) [34].move(1.0,0,0) [34].move(0,1.0,0) + layer17 = new Brick.move(-16.0,-16.0,12.0208152802) [33].move(1.0,0,0) [33].move(0,1.0,0) + layer18 = new Brick.move(-15.5,-15.5,12.7279220614) [32].move(1.0,0,0) [32].move(0,1.0,0) + layer19 = new Brick.move(-15.0,-15.0,13.4350288425) [31].move(1.0,0,0) [31].move(0,1.0,0) + layer20 = new Brick.move(-14.5,-14.5,14.1421356237) [30].move(1.0,0,0) [30].move(0,1.0,0) + layer21 = new Brick.move(-14.0,-14.0,14.8492424049) [29].move(1.0,0,0) [29].move(0,1.0,0) + layer22 = new Brick.move(-13.5,-13.5,15.5563491861) [28].move(1.0,0,0) [28].move(0,1.0,0) + layer23 = new Brick.move(-13.0,-13.0,16.2634559673) [27].move(1.0,0,0) [27].move(0,1.0,0) + layer24 = new Brick.move(-12.5,-12.5,16.9705627485) [26].move(1.0,0,0) [26].move(0,1.0,0) + layer25 = new Brick.move(-12.0,-12.0,17.6776695297) [25].move(1.0,0,0) [25].move(0,1.0,0) + layer26 = new Brick.move(-11.5,-11.5,18.3847763109) [24].move(1.0,0,0) [24].move(0,1.0,0) + layer27 = new Brick.move(-11.0,-11.0,19.091883092) [23].move(1.0,0,0) [23].move(0,1.0,0) + layer28 = new Brick.move(-10.5,-10.5,19.7989898732) [22].move(1.0,0,0) [22].move(0,1.0,0) + layer29 = new Brick.move(-10.0,-10.0,20.5060966544) [21].move(1.0,0,0) [21].move(0,1.0,0) + layer30 = new Brick.move(-9.5,-9.5,21.2132034356) [20].move(1.0,0,0) [20].move(0,1.0,0) + layer31 = new Brick.move(-9.0,-9.0,21.9203102168) [19].move(1.0,0,0) [19].move(0,1.0,0) + layer32 = new Brick.move(-8.5,-8.5,22.627416998) [18].move(1.0,0,0) [18].move(0,1.0,0) + layer33 = new Brick.move(-8.0,-8.0,23.3345237792) [17].move(1.0,0,0) [17].move(0,1.0,0) + layer34 = new Brick.move(-7.5,-7.5,24.0416305603) [16].move(1.0,0,0) [16].move(0,1.0,0) + layer35 = new Brick.move(-7.0,-7.0,24.7487373415) [15].move(1.0,0,0) [15].move(0,1.0,0) + layer36 = new Brick.move(-6.5,-6.5,25.4558441227) [14].move(1.0,0,0) [14].move(0,1.0,0) + layer37 = new Brick.move(-6.0,-6.0,26.1629509039) [13].move(1.0,0,0) [13].move(0,1.0,0) + layer38 = new Brick.move(-5.5,-5.5,26.8700576851) [12].move(1.0,0,0) [12].move(0,1.0,0) + layer39 = new Brick.move(-5.0,-5.0,27.5771644663) [11].move(1.0,0,0) [11].move(0,1.0,0) + layer40 = new GoldBrick.move(-4.5,-4.5,28.2842712475) [10].move(1.0,0,0) [10].move(0,1.0,0) + layer41 = new GoldBrick.move(-4.0,-4.0,28.9913780286) [9].move(1.0,0,0) [9].move(0,1.0,0) + layer42 = new GoldBrick.move(-3.5,-3.5,29.6984848098) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer43 = new GoldBrick.move(-3.0,-3.0,30.405591591) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer44 = new GoldBrick.move(-2.5,-2.5,31.1126983722) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer45 = new GoldBrick.move(-2.0,-2.0,31.8198051534) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer46 = new GoldBrick.move(-1.5,-1.5,32.5269119346) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer47 = new GoldBrick.move(-1.0,-1.0,33.2340187158) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer48 = new GoldBrick.move(-0.5,-0.5,33.941125497) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer49 = new GoldBrick.move(0.0,0.0,34.6482322781) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + + +PyramidKhafre { + layer0 = new ImmobileBrick.move(-23.5,-23.5,0.0) [48].move(1.0,0,0) [48].move(0,1.0,0) + layer1 = new Brick.move(-23.0,-23.0,0.707106781187) [47].move(1.0,0,0) [47].move(0,1.0,0) + layer2 = new Brick.move(-22.5,-22.5,1.41421356237) [46].move(1.0,0,0) [46].move(0,1.0,0) + layer3 = new Brick.move(-22.0,-22.0,2.12132034356) [45].move(1.0,0,0) [45].move(0,1.0,0) + layer4 = new Brick.move(-21.5,-21.5,2.82842712475) [44].move(1.0,0,0) [44].move(0,1.0,0) + layer5 = new Brick.move(-21.0,-21.0,3.53553390593) [43].move(1.0,0,0) [43].move(0,1.0,0) + layer6 = new Brick.move(-20.5,-20.5,4.24264068712) [42].move(1.0,0,0) [42].move(0,1.0,0) + layer7 = new Brick.move(-20.0,-20.0,4.94974746831) [41].move(1.0,0,0) [41].move(0,1.0,0) + layer8 = new Brick.move(-19.5,-19.5,5.65685424949) [40].move(1.0,0,0) [40].move(0,1.0,0) + layer9 = new Brick.move(-19.0,-19.0,6.36396103068) [39].move(1.0,0,0) [39].move(0,1.0,0) + layer10 = new Brick.move(-18.5,-18.5,7.07106781187) [38].move(1.0,0,0) [38].move(0,1.0,0) + layer11 = new Brick.move(-18.0,-18.0,7.77817459305) [37].move(1.0,0,0) [37].move(0,1.0,0) + layer12 = new Brick.move(-17.5,-17.5,8.48528137424) [36].move(1.0,0,0) [36].move(0,1.0,0) + layer13 = new Brick.move(-17.0,-17.0,9.19238815543) [35].move(1.0,0,0) [35].move(0,1.0,0) + layer14 = new Brick.move(-16.5,-16.5,9.89949493661) [34].move(1.0,0,0) [34].move(0,1.0,0) + layer15 = new Brick.move(-16.0,-16.0,10.6066017178) [33].move(1.0,0,0) [33].move(0,1.0,0) + layer16 = new Brick.move(-15.5,-15.5,11.313708499) [32].move(1.0,0,0) [32].move(0,1.0,0) + layer17 = new Brick.move(-15.0,-15.0,12.0208152802) [31].move(1.0,0,0) [31].move(0,1.0,0) + layer18 = new Brick.move(-14.5,-14.5,12.7279220614) [30].move(1.0,0,0) [30].move(0,1.0,0) + layer19 = new Brick.move(-14.0,-14.0,13.4350288425) [29].move(1.0,0,0) [29].move(0,1.0,0) + layer20 = new Brick.move(-13.5,-13.5,14.1421356237) [28].move(1.0,0,0) [28].move(0,1.0,0) + layer21 = new Brick.move(-13.0,-13.0,14.8492424049) [27].move(1.0,0,0) [27].move(0,1.0,0) + layer22 = new Brick.move(-12.5,-12.5,15.5563491861) [26].move(1.0,0,0) [26].move(0,1.0,0) + layer23 = new Brick.move(-12.0,-12.0,16.2634559673) [25].move(1.0,0,0) [25].move(0,1.0,0) + layer24 = new Brick.move(-11.5,-11.5,16.9705627485) [24].move(1.0,0,0) [24].move(0,1.0,0) + layer25 = new Brick.move(-11.0,-11.0,17.6776695297) [23].move(1.0,0,0) [23].move(0,1.0,0) + layer26 = new Brick.move(-10.5,-10.5,18.3847763109) [22].move(1.0,0,0) [22].move(0,1.0,0) + layer27 = new Brick.move(-10.0,-10.0,19.091883092) [21].move(1.0,0,0) [21].move(0,1.0,0) + layer28 = new Brick.move(-9.5,-9.5,19.7989898732) [20].move(1.0,0,0) [20].move(0,1.0,0) + layer29 = new Brick.move(-9.0,-9.0,20.5060966544) [19].move(1.0,0,0) [19].move(0,1.0,0) + layer30 = new Brick.move(-8.5,-8.5,21.2132034356) [18].move(1.0,0,0) [18].move(0,1.0,0) + layer31 = new Brick.move(-8.0,-8.0,21.9203102168) [17].move(1.0,0,0) [17].move(0,1.0,0) + layer32 = new Brick.move(-7.5,-7.5,22.627416998) [16].move(1.0,0,0) [16].move(0,1.0,0) + layer33 = new Brick.move(-7.0,-7.0,23.3345237792) [15].move(1.0,0,0) [15].move(0,1.0,0) + layer34 = new Brick.move(-6.5,-6.5,24.0416305603) [14].move(1.0,0,0) [14].move(0,1.0,0) + layer35 = new GoldBrick.move(-6.0,-6.0,24.7487373415) [13].move(1.0,0,0) [13].move(0,1.0,0) + layer36 = new GoldBrick.move(-5.5,-5.5,25.4558441227) [12].move(1.0,0,0) [12].move(0,1.0,0) + layer37 = new GoldBrick.move(-5.0,-5.0,26.1629509039) [11].move(1.0,0,0) [11].move(0,1.0,0) + layer38 = new GoldBrick.move(-4.5,-4.5,26.8700576851) [10].move(1.0,0,0) [10].move(0,1.0,0) + layer39 = new GoldBrick.move(-4.0,-4.0,27.5771644663) [9].move(1.0,0,0) [9].move(0,1.0,0) + layer40 = new GoldBrick.move(-3.5,-3.5,28.2842712475) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer41 = new GoldBrick.move(-3.0,-3.0,28.9913780286) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer42 = new GoldBrick.move(-2.5,-2.5,29.6984848098) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer43 = new GoldBrick.move(-2.0,-2.0,30.405591591) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer44 = new GoldBrick.move(-1.5,-1.5,31.1126983722) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer45 = new GoldBrick.move(-1.0,-1.0,31.8198051534) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer46 = new GoldBrick.move(-0.5,-0.5,32.5269119346) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer47 = new GoldBrick.move(0.0,0.0,33.2340187158) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + + +PyramidMenkaure { + layer0 = new ImmobileBrick.move(-9.0,-9.0,0.0) [19].move(1.0,0,0) [19].move(0,1.0,0) + layer1 = new Brick.move(-8.5,-8.5,0.707106781187) [18].move(1.0,0,0) [18].move(0,1.0,0) + layer2 = new Brick.move(-8.0,-8.0,1.41421356237) [17].move(1.0,0,0) [17].move(0,1.0,0) + layer3 = new Brick.move(-7.5,-7.5,2.12132034356) [16].move(1.0,0,0) [16].move(0,1.0,0) + layer4 = new Brick.move(-7.0,-7.0,2.82842712475) [15].move(1.0,0,0) [15].move(0,1.0,0) + layer5 = new Brick.move(-6.5,-6.5,3.53553390593) [14].move(1.0,0,0) [14].move(0,1.0,0) + layer6 = new Brick.move(-6.0,-6.0,4.24264068712) [13].move(1.0,0,0) [13].move(0,1.0,0) + layer7 = new Brick.move(-5.5,-5.5,4.94974746831) [12].move(1.0,0,0) [12].move(0,1.0,0) + layer8 = new Brick.move(-5.0,-5.0,5.65685424949) [11].move(1.0,0,0) [11].move(0,1.0,0) + layer9 = new Brick.move(-4.5,-4.5,6.36396103068) [10].move(1.0,0,0) [10].move(0,1.0,0) + layer10 = new Brick.move(-4.0,-4.0,7.07106781187) [9].move(1.0,0,0) [9].move(0,1.0,0) + layer11 = new Brick.move(-3.5,-3.5,7.77817459305) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer12 = new Brick.move(-3.0,-3.0,8.48528137424) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer13 = new Brick.move(-2.5,-2.5,9.19238815543) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer14 = new Brick.move(-2.0,-2.0,9.89949493661) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer15 = new Brick.move(-1.5,-1.5,10.6066017178) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer16 = new Brick.move(-1.0,-1.0,11.313708499) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer17 = new Brick.move(-0.5,-0.5,12.0208152802) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer18 = new Brick.move(0.0,0.0,12.7279220614) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + +PyramidQueens1 { + layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + +PyramidQueens2 { + layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + +PyramidQueens3 { + layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer1 = new Brick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer2 = new Brick.move(-2.5,-2.5,1.41421356237) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer3 = new Brick.move(-2.0,-2.0,2.12132034356) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer4 = new Brick.move(-1.5,-1.5,2.82842712475) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer5 = new Brick.move(-1.0,-1.0,3.53553390593) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer6 = new Brick.move(-0.5,-0.5,4.24264068712) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer7 = new Brick.move(0.0,0.0,4.94974746831) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + + + + +# "ImmobileBrick"s are identical to "Brick"s, +# except that they have a different atom type. +# We can define groups based on atom type +# and apply fixes to them. + +ImmobileBrick { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom $mol @atom 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom 1.0 + } + + write_once("In Settings") { + # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) + # + # i j eps sig + pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 + } + + write_once("In Settings") { + group gImmobile type @atom + # (Atoms of this type belong to the "gImmobile" group) + } + + write_once("In Init") { + atom_style full + units lj + pair_style hybrid lj/cut 1.0 + } +} + + + +GoldBrick { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom $mol @atom 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom 1.0 + } + + write_once("In Settings") { + # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) + # + # i j eps sig + pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 + } + + write_once("In Settings") { + group gMobile type @atom + # (Atoms of this type belong to the "gMobile" group) + } + + write_once("In Init") { + atom_style full + units lj + pair_style lj/cut 1.0 + } +} + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt new file mode 100644 index 0000000000..0c9c50ae9b --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt @@ -0,0 +1,80 @@ +# Description. +# This is a simulation of pyramid-like objects made of particles stacked +# and arranged like cannon-balls, or fruit-stands. Ordinarilly, the stack +# does not collapse because the particles at the ground layer are immobilized. +# However given an initial perterbation the pyramids collapse in an avalanche. +# (This can happen, for example when you do not minimize the system beforehand.) +# The particles roll down the pyramid and bounce off the "ground". The bouncing +# is due to a repulsive external force which is added artificially. +# (See the "run.in" file.) The simulation looks weird without something +# to bounce off of. So I added a graphene surface at the bottom as scenery. +# The ground does not serve any purpose except to look pretty. +# +# (Because there is no damping, I suspect that the distribution of heights of +# the particles in a small area should approach the Boltzmann distribution, +# if you run the simulation long enough.) + + +# ----------------- Pyramids: ----------------- + +import "pyramids.lt" + +# Move the pyramids into their locations in Giza (approximate) + +pyramidKhufu = new PyramidKhufu.move(210, 215, 1) +pyramidKhafre = new PyramidKhafre.move(150, 150, 1) +pyramidMenkaure = new PyramidMenkaure.move(105, 082, 1) +PyramidQueens1 = new PyramidQueens1.move(089, 059, 1) +PyramidQueens2 = new PyramidQueens2.move(100, 059, 1) +PyramidQueens3 = new PyramidQueens3.move(111, 059, 1) + + +# --------------- Scenery: -------------------- + +import "graphene_wall.lt" + +graphene_wall = new GrapheneWall + +write_once("In Settings") { + # Turn off all interactions with the graphene atoms by setting epsilon to 0. + # (We will use a different repulsive barrier to represent the ground instead.) + # These atoms are just "for show". epsilon sigma + pair_coeff @atom:Graphene/C @atom:Graphene/C lj/cut 0.00000 3.407 + + # Optional: Add the graphene atoms to the "gImmobile" group. Later freeze them + group gImmobile type @atom:Graphene/C +} + +# Unfortunately, the ground still looks kind of ugly because moltemplate does +# not yet know how to automatically connect nearby carbon atoms with C-C bonds +# (based on distance). (As of 2013-4-29, moltemplate is not good at +# generating crystalline objects containing explicit bonds.) +# If you want bonds between atoms, use VMD's "carbon-nanotube-builder plugin" +# (which creates data files with bonds) and then merge the two data files +# manually later. (This is not done here.) + + +# -------- override earlier settings ---------- + +write_once("In Init") { + # Override any earlier style settings + atom_style full + units lj + pair_style hybrid lj/cut 1.0 + bond_style none + angle_style none + dihedral_style none + improper_style none + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 +} + +# ------------ boundary conditions ------------ + +write_once("Data Boundary") { + -1.842033 398.493813 xlo xhi + -0.708994 399.167013 ylo yhi + 0.0 400.0 zlo zhi +} +# --------------------------------------------- + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in b/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in new file mode 100644 index 0000000000..4feec9ff4e --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in @@ -0,0 +1,64 @@ +# -- Init Section -- + +include system.in.init +boundary p p f + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.0025 +dump 1 all custom 200 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal +thermo 100 # time interval for printing out "thermo" data + +# ---- Set up the physical environment ---- + +# Add gravity: +fix fxGrav gMobile gravity 0.05 vector 0 0 -1 + +# Create a "ground" surface. +# This is a repulsive "wall" which particles can bounce off of: + +fix fxWall gMobile wall/lj126 zlo EDGE 1.0 0.8908987181403393 1.0 + + +# ---- Evolve the system: ---- + +# Evolve the (mobile) atoms using ordinary Newton's laws (NVE) + +fix fxNVE gMobile nve + + +# IF YOU WANT TO ADD DAMPING, THEN UNCOMMENT THE NEXT LINE: +#fix fxLan gMobile langevin 0.001 0.001 10000.0 48279 +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve" +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) +# This was not tested. + +# For efficient simulation in parallel, try using "fix balance": +# (This will adjust the spatial decomposition as the distribution of +# particles changes over time.) + +fix fxBalance gMobile balance 1000 xy 20 1.3 + +# Optional: Improve efficiency by omitting the calcuation of interactions +# between immobile atoms: + +neigh_modify exclude group gImmobile gImmobile + + +restart 50000 restart_nvt + +run 200000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/silly/sierpinski/README.TXT b/tools/moltemplate/examples/silly/sierpinski/README.TXT new file mode 100644 index 0000000000..6bc152b186 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/README.TXT @@ -0,0 +1,45 @@ +NOTE: This example requires the "Al99.eam.alloy" file. + (It was not included in this directory because if its large size.) + As of 2012-11, I was able to obtain it here: + http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + Copy it to the directory containing this README file. +------------------------------------------------------------------------ +3D fractal test + +Moltemplate is useful for building larger molecular structures from +smaller pieces. Although this simulation is of no scientific value, thiss +example illustrates how to build large (many-level) heirarchical objects +(Serpinski cubes) using moltemplate. (This is also called a "Menger Sponge".) + +The files in this directory demonstrate a way to build a periodic lattice of +3-dimensional Serpinski-cubes (with 3 levels of recursive self-similarity). + +In this example, the basic indivisible units are 4-atoms of Aluminum +(arranged in a cubic FCC unit-cell for bulk Aluminum). +This was an arbitrary choice. The resulting construct is not stable. +(But it makes pretty movies while collapsing.) + +To understand what is going on with this example, look at this file: + +./moltemplate_files/elegant_inefficient_version/serpinski_cubes.lt + +(This approach uses too much memory to be practical for large simulaions. +The version I actually use is here: ./moltemplate_files/serpinski_cubes.lt) + + --- To build the system --- + +Carry out the instructions in README_setup.sh, +to generate the LAMMPS DATA file and input scripts you need: +system.data, system.in.init, system.in.settings. +(The run.in script contains references to these files.) + + --- To run LAMMPS, try a command like: --- + +lmp_linux -i run.in + + or (if you have mpi installed) + +mpirun -np 4 lmp_linux -i run.in + +This will create an ordinary LAMMPS dump file you can visualize with VMD +traj.lammpstrj (See README_visualize.txt) diff --git a/tools/moltemplate/examples/silly/sierpinski/README_setup.sh b/tools/moltemplate/examples/silly/sierpinski/README_setup.sh new file mode 100755 index 0000000000..2af3d7372c --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/README_setup.sh @@ -0,0 +1,29 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # We will also need the "Al99.eam.alloy" file: + #cp -f Al99.eam.alloy ../ + # This file was downloaded from: + # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt b/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg new file mode 100644 index 0000000000..bf07914dac Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg new file mode 100644 index 0000000000..11174969a3 Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg new file mode 100644 index 0000000000..744c9af633 Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg new file mode 100644 index 0000000000..a72a1ea8d0 Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg new file mode 100644 index 0000000000..9020a3be0e Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg new file mode 100644 index 0000000000..0036c903a2 Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt new file mode 100644 index 0000000000..3054a45e01 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt @@ -0,0 +1,64 @@ +# "AlCell" defines the 4-atom FCC unit cell +# of Aluminum (with a 4.05 angstrom spacing) + +AlCell { + + # AtomID MolID(IGNORE!) AtomType Charge X Y Z + + write("Data Atoms") { + $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 + $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 + $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 + $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 + } + + write_once("In Init") { + units metal + atom_style full # <- Requires each atom has a MolID and Charge. + # This is not necessary. (Why use "full"? + # The "full" atom style is useful if you want to + # mix the aluminum with other molecules later. + # Otherwise, just use "atom_style atomic", and + # and remove the 2nd and 4th columns above.) + pair_style eam/alloy + } + + write_once("In Settings") { + pair_coeff * * Al99.eam.alloy Al + } + + write_once("Data Masses") { + @atom:Al 27.0 + } + +} # AlCell + + + + + +# Here is an alternate way to define AlCell +# using "scale(4.05)" to select the lattice spacing: +# +#FccCell { +# write("Data Atoms") { +# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 +# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 +# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 +# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 +# } +# write_once("Data Masses") { +# @atom:Al 27.0 +# } +# write_once("In Init") { +# units metal +# atom_style full +# pair_style eam/alloy +# } +# write_once("In Settings") { +# pair_coeff * * Al99.eam.alloy Al +# } +#} +# +#AlCell = FccCell.scale(4.05) +# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt new file mode 100644 index 0000000000..3054a45e01 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt @@ -0,0 +1,64 @@ +# "AlCell" defines the 4-atom FCC unit cell +# of Aluminum (with a 4.05 angstrom spacing) + +AlCell { + + # AtomID MolID(IGNORE!) AtomType Charge X Y Z + + write("Data Atoms") { + $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 + $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 + $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 + $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 + } + + write_once("In Init") { + units metal + atom_style full # <- Requires each atom has a MolID and Charge. + # This is not necessary. (Why use "full"? + # The "full" atom style is useful if you want to + # mix the aluminum with other molecules later. + # Otherwise, just use "atom_style atomic", and + # and remove the 2nd and 4th columns above.) + pair_style eam/alloy + } + + write_once("In Settings") { + pair_coeff * * Al99.eam.alloy Al + } + + write_once("Data Masses") { + @atom:Al 27.0 + } + +} # AlCell + + + + + +# Here is an alternate way to define AlCell +# using "scale(4.05)" to select the lattice spacing: +# +#FccCell { +# write("Data Atoms") { +# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 +# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 +# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 +# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 +# } +# write_once("Data Masses") { +# @atom:Al 27.0 +# } +# write_once("In Init") { +# units metal +# atom_style full +# pair_style eam/alloy +# } +# write_once("In Settings") { +# pair_coeff * * Al99.eam.alloy Al +# } +#} +# +#AlCell = FccCell.scale(4.05) +# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt new file mode 100644 index 0000000000..28c2d5ea24 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt @@ -0,0 +1,34 @@ +import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell + +# This approach uses the "delete" command. +# It works and it is elegant, but because the majority of atoms will be +# deleted, (and because memory is allocated for all atoms, including +# deleted atoms) this approach is not very memory efficient. + +SierpinskiCubeLvl1 { + cells = new AlCell [3].move(0.00, 0.00, 4.05) + [3].move(0.00, 4.05, 0.00) + [3].move(4.05, 0.00, 0.00) + delete cells[*][1][1] + delete cells[1][*][1] + delete cells[1][1][*] +} + +SierpinskiCubeLvl2 { + cells = new SierpinskiCubeLvl1 [3].move(0.00, 0.00, 12.15) + [3].move(0.00, 12.15, 0.00) + [3].move(12.15, 0.00, 0.00) + delete cells[*][1][1] + delete cells[1][*][1] + delete cells[1][1][*] +} + +SierpinskiCubeLvl3 { + cells = new SierpinskiCubeLvl2 [3].move(0.00, 0.00, 36.45) + [3].move(0.00, 36.45, 0.00) + [3].move(36.45, 0.00, 0.00) + delete cells[*][1][1] + delete cells[1][*][1] + delete cells[1][1][*] +} + diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt new file mode 100644 index 0000000000..b14929e986 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt @@ -0,0 +1,34 @@ +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 72.9 xlo xhi + 0.0 72.9 ylo yhi + 0.0 72.9 zlo zhi +} + +import "sierpinski_cubes.lt" + +cells = new SierpinskiCubeLvl2 [2].move(0.00, 0.00, 36.45) + [2].move(0.00, 36.45, 0.00) + [2].move(36.45, 0.00, 0.00) +delete cells[*][1][1] +delete cells[1][*][1] +delete cells[1][1][*] + + + + + + + + + + + + +################################################################ +# The next command is not necessary: +# + create_var { $mol } # <-This forces all of the Al atoms in the crystal +# # to share the same molecule ID number. +# # Molecule ID numbers are not necessary. Ignore this. +# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt new file mode 100644 index 0000000000..d45a8331b1 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt @@ -0,0 +1,66 @@ +import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell + +# A Sierpinski cube resembles a 3x3x3 Rubik's-cube-like object with the smaller +# cube in each central face (and in the interior) removed. There are 3x3x3-7=20 +# remaining sub-cubes. Each of these 20 sub-cubes is a smaller SierpinskiCube. +# To build a SierpinskiCube, you can list all 20 sub-cubes, or you can fill a +# 3x3x3 cube with sub-cubes and delete the interior sub-cubes. (The later +# approach is used in file "elegant_inefficient_version/sierpinski_cubes.lt") + + + +SierpinskiCubeLvl1 { + # Again, a Sierpinski-cube is constructed of 20 smaller cube-shaped objects. + # Here, the small cube-shaped objects are "AlCells" (defined in "al_cell.lt"). + # I could list out the positions of all 20 AlCells, (and this would be clearer + # for the reader). However instead I built it from a combination of + # two-dimensional and three-dimensional arrays of AlCells (explained below). + + # The next command creates 4 AlCells at: (0, 4.05, 0.0), (8.1, 4.05, 0.0), + # (0, 4.05, 8.1), (8.1, 4.05, 8.1) + + cells_xz = new AlCell.move(0.00, 4.05, 0.00) [2].move(8.10, 0.0, 0.0 ) + [2].move(0.0, 0.0, 8.10) + + # The next command creates 4 AlCells at: (4.05, 0, 0.0), (4.05, 8.1, 0.0), + # (4.05, 0, 8.1), (4.05, 8.1, 8.1) + + cells_yz = new AlCell.move(4.05, 0.00, 0.00) [2].move(0.0, 8.10, 0.0 ) + [2].move(0.0, 0.0, 8.10) + + # The next command creates 12 AlCells (2x2x3) at: + # (0.0, 0.0, 0.0), (0.0, 0.0, 4.05), (0.0, 0.0, 8.1) + # (0.0, 8.1, 0.0), (0.0, 8.1, 4.05), (0.0, 8.1, 8.1) + # (8.1, 8.1, 0.0), (8.1, 8.1, 4.05), (8.1, 8.1, 8.1) + + cells_z = new AlCell [2].move(8.10, 0.00, 0.00) + [2].move(0.00, 8.10, 0.00) + [3].move(0.00, 0.00, 4.05) +} + + + +SierpinskiCubeLvl2 { + # Identical arrangement to SierpinskiCube1 (with 3x larger length scales) + cells_xz= new SierpinskiCubeLvl1.move(0.0,12.15,0.0) [2].move(24.3, 0.0, 0.0 ) + [2].move(0.0, 0.0, 24.3) + cells_yz= new SierpinskiCubeLvl1.move(12.15,0.0,0.0) [2].move(0.0, 24.3, 0.0 ) + [2].move(0.0, 0.0, 24.3) + cells_z = new SierpinskiCubeLvl1 [2].move(24.3, 0.00, 0.00) + [2].move(0.00, 24.3, 0.00) + [3].move(0.00, 0.00, 12.15) +} + + + +SierpinskiCubeLvl3 { + # Identical arrangement to SierpinskiCube2 (with 3x larger length scales) + cells_xz= new SierpinskiCubeLvl2.move(0.0,36.45,0.0) [2].move(72.9, 0.0, 0.0 ) + [2].move(0.0, 0.0, 72.9) + cells_yz= new SierpinskiCubeLvl2.move(36.45,0.0,0.0) [2].move(0.0, 72.9, 0.0 ) + [2].move(0.0, 0.0, 72.9) + cells_z = new SierpinskiCubeLvl2 [2].move(72.9, 0.00, 0.00) + [2].move(0.00, 72.9, 0.00) + [3].move(0.00, 0.00, 36.45) +} + diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt new file mode 100644 index 0000000000..b226b77eed --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt @@ -0,0 +1,36 @@ +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 218.7 xlo xhi + 0.0 218.7 ylo yhi + 0.0 218.7 zlo zhi +} + +import "sierpinski_cubes.lt" + +cells_xyz = new SierpinskiCubeLvl3.move(0.0000, 0.0000, 0.0000) +cells_Xyz = new SierpinskiCubeLvl3.move(109.35, 0.0000, 0.0000) +cells_xYz = new SierpinskiCubeLvl3.move(0.0000, 109.35, 0.0000) +cells_xyZ = new SierpinskiCubeLvl3.move(0.0000, 0.0000, 109.35) + + + + + + + + + + + + + + + + +################################################################ +# The next command is not necessary: +# + create_var { $mol } # <-This forces all of the Al atoms in the crystal +# # to share the same molecule ID number. +# # Molecule ID numbers are not necessary. Ignore this. +# diff --git a/tools/moltemplate/examples/silly/sierpinski/run.in b/tools/moltemplate/examples/silly/sierpinski/run.in new file mode 100644 index 0000000000..6b9ad17e6e --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/run.in @@ -0,0 +1,38 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- +# +# Some of the run-settings below were stolen from: +# +# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression + +# EQUILIBRATION +reset_timestep 0 +timestep 0.001 +velocity all create 300 12345 mom yes rot no +fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 + +# Output files +thermo 100 +thermo_style custom step ke pe press +dump dCoords all custom 100 traj.lammpstrj id type x y z ix iy iz + +run 20000 + +# Run for at least 10 picosecond (assuming 1 fs timestep) +run 10000 + + +###################################### +# SIMULATION DONE +print "All done" diff --git a/tools/moltemplate/moltemplate_manual.pdf b/tools/moltemplate/moltemplate_manual.pdf new file mode 100644 index 0000000000..e775f26ed7 Binary files /dev/null and b/tools/moltemplate/moltemplate_manual.pdf differ diff --git a/tools/moltemplate/src/bonds_by_type.py b/tools/moltemplate/src/bonds_by_type.py new file mode 100755 index 0000000000..1c85eddc4f --- /dev/null +++ b/tools/moltemplate/src/bonds_by_type.py @@ -0,0 +1,379 @@ +#!/usr/bin/env python + +# Author: Andrew Jewett (jewett.aij at g mail) +# http://www.chem.ucsb.edu/~sheagroup +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2011, Regents of the University of California +# All rights reserved. + +""" + bonds_by_type.py reads a LAMMPS data file (or an excerpt of a LAMMPS) + data file containing bonded many-body interactions by atom type + (and bond type), and generates a list of additional interactions + in LAMMPS format consistent with those type (to the standard out). + + Typical Usage: + + bonds_by_type.py -atoms atoms.data \\ + -bonds bonds.data \\ + -bondsbytype bonds_by_type.data \\ + > new_bonds.data + +""" + +# -bonds-ids-atom-pairs bonds_ids_atom_pairs.data \\ + +import sys +#from extract_lammps_data import * +#from nbody_by_type_lib import GenInteractions_str +import ttree_lex +#from ttree_lex import * +from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid + + + +def LookupBondTypes(bond_types, + bond_ids, + bond_pairs, + lines_atoms, + lines_bonds, + lines_bondsbytype, + atom_style, + section_name, + prefix='', + suffix='', + bond_ids_offset=0): + #report_progress = False): + """ + LookupBondTypes() looks up bond types. + + Output: + ...It looks up the corresponding type of each bond and store it in the + "bond_types" list. (If the bond_ids were not specified by the user, + generate them and store them in the bond_ids list.) + + + Input (continued): + This function requires: + ...a list of bonded pairs of atoms + stored in the lines_bonds variable (from the "Data Bond List" + or "Data Bonds AtomId AtomId" sections) + ...and a list of atom types + stored in the lines_atoms variable (from the "Data Atoms" section) + ...and a list of bond-types-as-a-function-of-atom-types + stored in the lines_bondsbytype (from the "Data Bonds By Type" section) + + Generated bond_ids (if applicable) are of the form + prefix + str(number) + suffix + (where "number" begins at bond_ids_offset+1) + + """ + + column_names = AtomStyle2ColNames(atom_style) + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + + atomids = [] + atomtypes = [] + atomids2types = {} + + for iv in range(0, len(lines_atoms)): + line = lines_atoms[iv].strip() + if '#' in line: + icomment = line.find('#') + line = (line[:icomment]).strip() + if len(line) > 0: + tokens = ttree_lex.SplitQuotedString(line) + if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)): + sys.stderr.write("\""+line+"\"\n") + raise(ttree_lex.InputError('Error not enough columns on line '+str(iv+1)+' of \"Atoms\" section.')) + tokens = ttree_lex.SplitQuotedString(line) + atomid = ttree_lex.EscCharStrToChar(tokens[i_atomid]) + atomids.append(atomid) + atomtype = ttree_lex.EscCharStrToChar(tokens[i_atomtype]) + atomtypes.append(atomtype) + atomids2types[atomid] = atomtype + + + assert(isinstance(bond_ids, list)) + assert(isinstance(bond_types, list)) + assert(isinstance(bond_pairs, list)) + del bond_ids[:] + del bond_types[:] + del bond_pairs[:] + + for ie in range(0, len(lines_bonds)): + + line = lines_bonds[ie].strip() + if '#' in line: + icomment = line.find('#') + line = (line[:icomment]).strip() + + if len(line) == 0: + continue + + tokens = ttree_lex.SplitQuotedString(line) + + if section_name == "Data Bonds AtomId AtomId": + if len(tokens) == 2: + bondid_n = bond_ids_offset + len(bond_ids) + 1 + bond_ids.append(prefix+str(bondid_n)+suffix) + bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[0]), + ttree_lex.EscCharStrToChar(tokens[1])) ) + else: + raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.')) + + elif section_name == "Data Bond List": + if len(tokens) == 3: + bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0])) + bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[1]), + ttree_lex.EscCharStrToChar(tokens[2])) ) + else: + raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.')) + + #elif section_name == "Data Bonds BondType AtomId AtomId": + # if len(tokens) == 3: + # bondid_n = bond_ids_offset + len(bond_ids) + 1 + # bond_ids.append(prefix+str(bondid_n)+suffix) + # bond_types.append(ttree_lex.EscCharStrToChar(tokens[0])) + # bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[1]), + # ttree_lex.EscCharStrToChar(tokens[2])) ) + # else: + # raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.')) + + else: + raise(ttree_lex.InputError('Internal Error ('+g_program_name+'): Unknown section name: \"'+section_name+'\"')) + + + assert(len(bond_types) == 0) + typepattern_to_coefftypes = [] + + for i in range(0, len(lines_bondsbytype)): + line = lines_bondsbytype[i].strip() + if '#' in line: + icomment = line.find('#') + line = (line[:icomment]).strip() + if len(line) > 0: + tokens = ttree_lex.SplitQuotedString(line) + + if (len(tokens) != 3): + raise(ttree_lex.InputError('Error: Wrong number of columns in the \"Bonds By Type\" section of data file.\n' + 'Offending line:\n'+ + '\"'+line+'\"\n' + 'Expected 3 columns\n')) + + coefftype = ttree_lex.EscCharStrToChar(tokens[0]) + typepattern = [] + + for typestr in tokens[1:]: + if ((len(typestr) >= 2) and + (typestr[0] == '/') and (typestr[-1] == '/')): + regex_str = typestr[1:-1] + typepattern.append( re.compile(regex_str) ) + else: + typepattern.append(ttree_lex.EscCharStrToChar(typestr)) + + typepattern_to_coefftypes.append([typepattern, coefftype]) + + + + assert(len(bond_ids) == len(bond_pairs)) + + for ie in range(0,len(bond_ids)): + bond_types.append(None) + + for ie in range(0, len(bond_ids)): + bondid = bond_ids[ie] + (atomid1, atomid2) = bond_pairs[ie] + + #for n in range(0, len(typepattern_to_coefftypes)): + for typepattern, coefftype in typepattern_to_coefftypes: + + if atomid1 not in atomids2types: + raise ttree_lex.InputError('Error: atom \"'+atomid1+'\" not defined in \"Data Atoms\".\n' + ' This usually happens when the user mistypes one of the names of the\n' + ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n' + ' To find out where the mistake occured, search the \n' + ' \"ttree_assignments.txt\" file for:\n' + ' \"'+atomid1+'\"\n') + + if atomid2 not in atomids2types: + raise ttree_lex.InputError('Error: atom \"'+atomid2+'\" not defined in \"Data Atoms\".\n' + ' This usually happens when the user mistypes one of the names of the\n' + ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n' + ' To find out where the mistake occured, search the \n' + ' \"ttree_assignments.txt\" file for:\n' + ' \"'+atomid2+'\"\n') + + atomtype1 = atomids2types[atomid1] + atomtype2 = atomids2types[atomid2] + + # use string comparisons to check if atom types match the pattern + if (ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern) or + ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern)): + # ("MatchesAll()" defined in "ttree_lex.py") + + bond_types[ie] = coefftype + + for ie in range(0, len(bond_ids)): + if not bond_types[ie]: + atomtype1 = atomids2types[atomid1] + atomtype2 = atomids2types[atomid2] + raise ttree_lex.InputError('Error: No bond types defined for the bond between\n' + ' atoms '+atomid1+'(type '+atomtype1+') and '+atomid2+'(type '+atomtype2+')\n') + + + + +if __name__ == "__main__": + + g_program_name = __file__.split('/')[-1] # = 'nbody_by_type.py' + g_date_str = '2013-8-06' + g_version_str = '0.1' + + ####### Main Code Below: ####### + sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ') + if sys.version < '3': + sys.stderr.write(' (python version < 3)\n') + else: + sys.stderr.write('\n') + + try: + fname_atoms = None + fname_bonds = None + fname_bondsbytype = None + section_name = 'Data Bond List' # (This will be replaced later.) + atom_style = 'full' + prefix='' + suffix='' + bond_lack_types = False + + argv = [arg for arg in sys.argv] + + + # Loop over the remaining arguments not processed yet. + # These arguments are specific to the lttree.py program + # and are not understood by ttree.py: + i = 1 + while i < len(argv): + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + if ((argv[i].lower() == '-?') or + (argv[i].lower() == '--?') or + (argv[i].lower() == '-help') or + (argv[i].lower() == '-help')): + if i+1 >= len(argv): + sys.stdout.write(man_page_text+'\n') + sys.exit(0) + + elif argv[i].lower() == '-atoms': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n' + ' text which might appear in the "Atoms" section of a LAMMPS data file.\n') + fname_atoms = argv[i+1] + del(argv[i:i+2]) + + elif argv[i].lower() == '-bonds': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n' + ' text which might appear in the "Bonds" section of a LAMMPS data file.\n') + fname_bonds = argv[i+1] + del(argv[i:i+2]) + + elif argv[i].lower() == '-bond-list': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name\n') + #raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n' + # ' text which might appear in the "Bonds No Types" section of a LAMMPS data file.\n') + fname_bonds = argv[i+1] + section_name = "Data Bond List" + del(argv[i:i+2]) + + elif argv[i].lower() == '-bondsbytype': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name\n') + + #raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing\n' + # ' text which might appear in the "'+section_name+' By Type" section\n' + # ' of a LAMMPS data file.\n') + fname_bondsbytype = argv[i+1] + del(argv[i:i+2]) + + elif ((argv[i].lower() == '-atom-style') or + (argv[i].lower() == '-atom_style')): + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n' + ' (Or single quoted string which includes a space-separated\n' + ' list of column names.)\n') + atom_style = argv[i+1] + del(argv[i:i+2]) + + elif argv[i].lower() == '-prefix': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a prefix string\n' + ' (a string you want to appear to the left of the integer\n' + ' which counts the bonded interactions you have generated.)\n') + prefix = argv[i+1] + del(argv[i:i+2]) + + elif argv[i].lower() == '-suffix': + if i+1 >= len(argv): + raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a suffix string\n' + ' (a string you want to appear to the right of the integer\n' + ' which counts the bonded interactions you have generated.)\n') + prefix = argv[i+1] + del(argv[i:i+2]) + + elif argv[i][0] == '-': + raise ttree_lex.InputError('Error('+g_program_name+'):\n' + 'Unrecogized command line argument \"'+argv[i]+'\"\n') + else: + i += 1 + + if len(argv) != 1: + # if there are more than 2 remaining arguments, + problem_args = ['\"'+arg+'\"' for arg in argv[1:]] + raise ttree_lex.InputError('Syntax Error('+g_program_name+'):\n\n' + ' Problem with argument list.\n' + ' The remaining arguments are:\n\n' + ' '+(' '.join(problem_args))+'\n\n' + ' (The actual problem may be earlier in the argument list.)\n') + + bond_types = [] + bond_ids = [] + bond_pairs = [] + + fatoms = open(fname_atoms, 'r') + fbonds = open(fname_bonds, 'r') + fbondsbytype = open(fname_bondsbytype, 'r') + lines_atoms = fatoms.readlines() + lines_bonds = fbonds.readlines() + lines_bondsbytype = fbondsbytype.readlines() + fatoms.close() + fbonds.close() + fbondsbytype.close() + + LookupBondTypes(bond_types, + bond_ids, + bond_pairs, + lines_atoms, + lines_bonds, + lines_bondsbytype, + atom_style, + section_name, + prefix='', + suffix='') + + assert(len(bond_types) == len(bond_ids) == len(bond_pairs)) + + ie=0 + N = len(bond_types) + for ie in range(0, N): + sys.stdout.write(bond_ids[ie] + ' ' + + bond_types[ie] + ' ' + + bond_pairs[ie][0] + ' ' + + bond_pairs[ie][1] + '\n') + + + except (ValueError, ttree_lex.InputError) as err: + sys.stderr.write('\n'+str(err)+'\n') + sys.exit(-1) + diff --git a/tools/moltemplate/src/docs_useful_scripts/docs_dump2data.txt b/tools/moltemplate/src/docs_useful_scripts/docs_dump2data.txt new file mode 100644 index 0000000000..0794fc76c8 --- /dev/null +++ b/tools/moltemplate/src/docs_useful_scripts/docs_dump2data.txt @@ -0,0 +1,109 @@ + (Rough-draft documentation for dump2data.py and raw2data.py) + + ---- Description ---- + +"dump2data.py" was originally designed to convert dump files into LAMMPS DATA format (for restarting a simulation from where it left off). However it also reads and writes .XYZ and .RAW (simple 3-column text format) files also. This script duplicates some of the tools in pizza.py, but you don't have to learn python to use it. If you are willing to learn a little python, pizza.py, can handle more general dump files which might cause dump2data.py to crash (eg "atom_style tri"). Furthermore, unlike "dump2data.py", pizza.py is maintained by the lammps team: +http://pizza.sandia.gov/doc/Manual.html + + ----- General Usage ----- + +General usage: + +dump2data.py [old_data_file -xyz -raw -last -t time -tstart ta -tstop tb -interval n -center -scale x -atomstyle style] < DUMP_FILE > OUTPUT_FILE + + ----- examples ----- + + If your LAMMPS dump file is named "traj.lammpstrj", you can +extract the coordinates this way: + +dump2data.py -xyz < traj.lammpstrj > traj.xyz + +This generates a 3-column text file containing the xyz coordinates on each line of each atom (sorted by atomid). If there are multiple frames in the trajectory file, it will concatenate them together this way: + +8192 +LAMMPS data from timestep 50000 +1 -122.28 -19.2293 -7.93705 +2 -121.89 -19.2417 -8.85591 +3 -121.6 -19.2954 -7.20586 +: : : : +8192 +LAMMPS data from timestep 100000 +1 -121.59 -20.3273 -2.0079 +2 -122.2 -19.8527 -2.64669 +3 -120.83 -19.7342 -2.2393 + +(When using the "-raw" argument to create simple 3-column .RAW files, blank lines are used to delimit different frames in the trajectory.) + +---- optional command line arguments --- + +If you want to select a particular frame from the trajectory, use: + +dump2data.py -xyz -t 10000 < traj.lammpstrj > coords.xyz + +To select the most recent (complete) frame, use: + +dump2data.py -xyz -last < traj.lammpstrj > coords.xyz + +(If the last frame is incomplete, this script will attempt to use the previous frame.) + +If you want to select multiple frames, but there are too many frames in your trajectory, you can run dump2data.py this way... + +dump2data.py -xyz -interval 10000 < traj.lammpstrj > traj.xyz + +...to indicate the desired interval between frames (it must be a multiple of +the save interval). You can also use "-tstart 500000 and "-tstop 1000000" arguments to limit the output to a particular range of time. (500000-1000000 in this example). + +--- creating DATA files --- + +"dump2data.py" can also create lammps DATA files. You must supply it with an existing DATA file containing the correct number of atoms and topology information. + +If your coordinates are stored in a DUMP file (eg "traj.lammpstrj"), you can create a new data file this way: + +dump2data.py -t 10000 data_file < traj.lammpstrj > new_file + +Again, in this example, "10000" is the timestep for the frame you have selected. You can use "-last" to select the last frame. (If you do not specify the frame you want, multiple data files will be created.) + +If you have a file containing only the coordinates of the atoms (in sorted order), you can use "raw2data.py" to create a data file with those atoms coordinates. + +raw2data.py data_file < coords.raw > new_data_file + +(Warning: "raw2data.py" is not a stand-alone script. Make sure raw2data.py is located in the same directory with dump2data.py.) + +--- scaling and centering coordinates --- + +-center + This will center the coordinates around the geometric center, so that the average position of the atoms in each frame is located at the origin. (This script attempts to pay attention to the periodic image flags. As such, I think this script works with triclinic cells, but I have not tested that feature carefully.) + +-scale 1.6 + This will multiply the coordinates by a constant (eg "1.6") (Please email me if this fails with periodic image flags.) + +---- limitations ---- + +Speed. +The program is somewhat slow, although it should be able to handle big trajectories. If speed is important to you, you probably should write your own custom script or use pizza.py which might be faster. + +triclinic cells + Support for triclinic cells has been added, but not tested. + +exotic atom_styles + + This script was designed to work with point-like atoms, and it extracts the x,y,z (and if present vx,vy,vz velocity) degrees of freedom and (by default) copies it to the new data being created by this script. + +By default, this script assumes you are using "atom_style full". +If you are using some other atom style (eg "hybrid bond dipole"), then you can try to run it this way: + +dump2data.py -t 10000 \ + -atomstyle "hybrid bond dipole" \ + old_data_file < traj.lammpstrj > new_data_file + + +I have not tested this, and have no idea what will happen. (I suspect that the script will not crash, but the dipole orientations will not be updated.) + +You can also customize the order columns you want to appear in that file using -atomstyle â€molid x y z atomid atomtype mux muy muzâ€, but again, I don't think the mux, muy, muz information in the new data file will be accurate. + +I also strongly suspect that "dump2data.py" does not currently work with the "tri", "ellipsoid", and new "body" styles. + +Again, try using pizza.py if you are simulating systems with exotic data types. +http://pizza.sandia.gov/doc/Manual.html + +I hope this is useful to someone. diff --git a/tools/moltemplate/src/dump2data.py b/tools/moltemplate/src/dump2data.py new file mode 100755 index 0000000000..aa143defa6 --- /dev/null +++ b/tools/moltemplate/src/dump2data.py @@ -0,0 +1,1262 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +""" +dump2data.py + +Extract dynamical degrees of freedom from a lammps DUMP file (from the stdin) +and construct a new DATA file (to the stdout). +A reference DATA file is needed (argument). + + basic usage +./dump2data.py orig_file.data < dump.lammpstrj > new_file.data + (This extract last frame, uses "full" atom_style.) + + options: +./dump2data.py [-t t -atomstyle style] orig.data < dump.lammpstrj > new.data + +""" + +# Authors: Andrew Jewett +# License: New BSD License +# Copyright (c) 2014 +# All rights reserved. + + +import sys +from collections import defaultdict +from operator import itemgetter, attrgetter + + +class InputError(Exception): + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + + +def ErrorLeader(infile, lineno): + return '\"'+infile+'\", line '+str(lineno)+': ' + + +class MiscSettings(object): + def __init__(self): + self.tstart = None + self.tstop = None + self.timestep_str = '' + self.last_frame = False + self.center_frame = False + self.output_format = 'data' + self.input_format = 'dump' + self.multi = True + self.skip_interval = 1 + self.scale = None + + +class AtomStyleSettings(object): + def __init__(self): + # The following new member data indicate which columns store + # LAMMPS-specific information. + # The next 6 members store keep track of the different columns + # of the "Atoms" section of a LAMMPS data file: + self.column_names = [] #<--A list of column names (optional) + self.i_coords=[] #<--A triplet of integers indicating which columns store coordinate data + #self.ii_coords= [] #<--A list of triplets of column indexes storing coordinate data + self.ii_vects=[] #<--A list of triplets of column indexes storing directional data + # (such as dipole or ellipsoid orientations) + self.i_atomid=None #<--An integer indicating which column has the atomid + self.i_atomtype=None #<--An integer indicating which column has the atomtype + self.i_molid=None #<--An integer indicating which column has the molid, if applicable + + + +class DataSettings(AtomStyleSettings): + def __init__(self): + AtomStyleSettings.__init__(self) + self.contents = '' + self.file_name = '' + + + +# Atom Styles in LAMMPS as of 2011-7-29 +g_style_map = {'angle': ['atom-ID','molecule-ID','atom-type','x','y','z'], + 'atomic': ['atom-ID','atom-type','x','y','z'], + 'bond': ['atom-ID','molecule-ID','atom-type','x','y','z'], + 'charge': ['atom-ID','atom-type','q','x','y','z'], + 'colloid': ['atom-ID','atom-type','x','y','z'], + 'dipole': ['atom-ID','atom-type','q','x','y','z','mux','muy','muz'], + 'electron': ['atom-ID','atom-type','q','spin','eradius','x','y','z'], + 'ellipsoid':['atom-ID','atom-type','x','y','z','quatw','quati','quatj','quatk'], + 'full': ['atom-ID','molecule-ID','atom-type','q','x','y','z'], + 'granular': ['atom-ID','atom-type','diameter','density','x','y','z'], + 'molecular':['atom-ID','molecule-ID','atom-type','x','y','z'], + 'peri': ['atom-ID','atom-type','volume','density','x','y','z'], + 'hybrid': ['atom-ID','atom-type','x','y','z']} + + + + +def AtomStyle2ColNames(atom_style_string): + + atom_style_string = atom_style_string.strip() + if len(atom_style_string) == 0: + raise InputError('Error(dump2data): Invalid atom_style\n' + ' (The atom_style command was followed by an empty string.)\n') + atom_style_args = atom_style_string.split() + atom_style = atom_style_args[0] + + hybrid_args = atom_style_args[1:] + if (atom_style not in g_style_map): + if (len(atom_style_args) >= 2): + # If the atom_style_string includes at least 2 words, then we + # interpret this as a list of the individual column names + return atom_style_args + else: + raise InputError('Error(dump2data): Unrecognized atom_style: \"'+atom_style+'\"\n') + + if (atom_style != 'hybrid'): + return g_style_map[atom_style] + else: + column_names = ['atom-ID','atom-type','x','y','z'] + if (len(hybrid_args)==0): + raise InputError('Error(dump2data): atom_style hybrid must be followed by a sub_style.\n') + for sub_style in hybrid_args: + if (sub_style not in g_style_map): + raise InputError('Error(dump2data): Unrecognized atom_style: \"'+sub_style+'\"\n') + for cname in g_style_map[sub_style]: + if cname not in column_names: + column_names.append(cname) + + return column_names + + +def ColNames2AidAtypeMolid(column_names): + # Because of the diversity of ways that these + # numbers are referred to in the LAMMPS documentation, + # we have to be flexible and allow the user to refer + # to these quantities in a variety of ways. + # Hopefully this covers everything: + + i_atomid = None + if 'atom-ID' in column_names: + i_atomid = column_names.index('atom-ID') + elif 'atom−ID' in column_names: # (− is the character used in the manual) + i_atomid = column_names.index('atom−ID') + elif 'atomID' in column_names: + i_atomid = column_names.index('atomID') + elif 'atomid' in column_names: + i_atomid = column_names.index('atomid') + elif 'id' in column_names: + i_atomid = column_names.index('id') + elif 'atom' in column_names: + i_atomid = column_names.index('atom') + elif '$atom' in column_names: + i_atomid = column_names.index('$atom') + else: + raise InputError('Error(dump2data): List of column names lacks an \"atom-ID\"\n') + + i_atomtype = None + if 'atom-type' in column_names: + i_atomtype = column_names.index('atom-type') + elif 'atom−type' in column_names: # (− hyphen character used in manual) + i_atomtype = column_names.index('atom−type') + elif 'atomtype' in column_names: + i_atomtype = column_names.index('atomtype') + elif 'type' in column_names: + i_atomtype = column_names.index('type') + elif '@atom' in column_names: + i_atomtype = column_names.index('@atom') + else: + raise InputError('Error(dump2data): List of column names lacks an \"atom-type\"\n') + + i_molid = None + if 'molecule-ID' in column_names: + i_molid = column_names.index('molecule-ID') + elif 'molecule−ID' in column_names: # (− hyphen character used in manual) + i_molid = column_names.index('molecule−ID') + elif 'moleculeID' in column_names: + i_molid = column_names.index('moleculeID') + elif 'moleculeid' in column_names: + i_molid = column_names.index('moleculeid') + elif 'molecule' in column_names: + i_molid = column_names.index('molecule') + elif 'molID' in column_names: + i_molid = column_names.index('molID') + elif 'molid' in column_names: + i_molid = column_names.index('molid') + elif 'mol' in column_names: + i_molid = column_names.index('mol') + elif '$mol' in column_names: + i_molid = column_names.index('$mol') + else: + pass # some atom_types do not have a valid molecule-ID + + return i_atomid, i_atomtype, i_molid + + + +def ColNames2Coords(column_names): + """ Which of the columns correspond to coordinates + which must be transformed using rigid-body + (affine: rotation + translation) transformations? + This function outputs a list of lists of triplets of integers. + + """ + i_x = None + i_y = None + i_z = None + if 'x' in column_names: + i_x = column_names.index('x') + if 'y' in column_names: + i_y = column_names.index('y') + if 'z' in column_names: + i_z = column_names.index('z') + if (((i_x != None) != (i_y != None)) or + ((i_y != None) != (i_z != None)) or + ((i_z != None) != (i_x != None))): + raise InputError('Error(dump2data): columns must include \"x\", \"y\", and \"z\".\n') + return [[i_x, i_y, i_z]] + + +def ColNames2Vects(column_names): + """ Which of the columns correspond to coordinates + which must be transformed using rotations? + Some coordinates like dipole moments and + ellipsoid orientations should only be rotated + (not translated). + This function outputs a list of lists of triplets of integers. + + """ + vects = [] + i_mux = None + i_muy = None + i_muz = None + if 'mux' in column_names: + i_mux = column_names.index('mux') + if 'muy' in column_names: + i_muy = column_names.index('muy') + if 'muz' in column_names: + i_muz = column_names.index('muz') + if (((i_mux != None) != (i_muy != None)) or + ((i_muy != None) != (i_muz != None)) or + ((i_muz != None) != (i_mux != None))): + raise InputError('Error(dump2data): custom atom_style list must define mux, muy, and muz or none.\n') + if i_mux != None: + vects.append([i_mux, i_muy, i_muz]) + i_quati = None + i_quatj = None + i_quatk = None + if 'quati' in column_names: + i_quati = column_names.index('quati') + if 'quatj' in column_names: + i_quatj = column_names.index('quatj') + if 'quatk' in column_names: + i_quatk = column_names.index('quatk') + if (((i_quati != None) != (i_quatj != None)) or + ((i_quatj != None) != (i_quatk != None)) or + ((i_quatk != None) != (i_quati != None))): + raise InputError('Error(dump2data): custom atom_style list must define quati, quatj, and quatk or none.\n') + if i_quati != None: + vects.append([i_quati, i_quatj, i_quatk]) + return vects + + + + + +def ParseArgs(argv, + misc_settings, + data_settings, + warning_strings=None): + + # Loop over the remaining arguments not processed yet. + # These arguments are specific to the lttree.py program + # and are not understood by this program. + i = 1 + while i < len(argv): + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + if ((argv[i].lower() == '-atomstyle') or + (argv[i].lower() == '-atom_style') or + (argv[i].lower() == '-atom-style')): + in_init = [] + if i+1 >= len(argv): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by a an atom_style name.\n' + ' (Or single quoted string which includes a space-separated\n' + ' list of column names.)\n') + data_settings.column_names = AtomStyle2ColNames(argv[i+1]) + sys.stderr.write(' \"Atoms\" column format:\n') + sys.stderr.write(' '+(' '.join(data_settings.column_names))+'\n') + + # ColNames2Coords() and ColNames2Vects() generate lists of + # triplets of integers, storing the column numbers containing + # x, y, and z coordinate values, and vx,vy,vz direction vectors. + data_settings.ii_vects = ColNames2Vects(data_settings.column_names) + ii_coords = ColNames2Coords(data_settings.column_names) + # This program assumes that there is only one coordinate triplet + # (x,y,z) for each atom. Hence we assume that len(ii_coords)==1 + assert(len(ii_coords) == 1) + data_settings.i_coords = ii_coords[0] + + # Now figure out which columns correspond to atomid, atomtype, molid + data_settings.i_atomid, data_settings.i_atomtype, data_settings.i_molid = ColNames2AidAtypeMolid(data_settings.column_names) + del(argv[i:i+2]) + + elif (argv[i].lower() == '-icoord'): + if i+1 >= len(argv): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers\n' + ' corresponding to column numbers for coordinates in\n' + ' the \"Atoms\" section of a LAMMPS data file.\n') + ilist = argv[i+1].split() + if (len(ilist) % 3) != 0: + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers.\n' + ' This is usually a list of 3 intebers, but it can contain more.\n' + ' The number of cooridnate columns must be divisible by 3,\n' + ' (even if the simulation is in 2 dimensions)\n') + + #ii_coords = [] + #for i in range(0, len(ilist)/3): + # cols = [ilist[3*i]+1, ilist[3*i+1]+1, ilist[3*i+2]+1] + # ii_coords.append(cols) + #if ((len(ii_coords) != 0) or (len(ii_coords[0]) != 3)): + # raise InputError('Error(dump2data): Argument \"'+argv[i]+'\" must be followed by exactly 3 integers.\n') + + data_settings.i_coords = ilist + if (len(i_coords) != 3): + raise InputError('Error(dump2data): Argument \"'+argv[i]+'\" must be followed by exactly 3 integers.\n') + + data_settings.i_coords = ii_coords[0] + + del(argv[i:i+2]) + + elif (argv[i].lower() == '-ivect'): + if i+1 >= len(argv): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers\n' + ' corresponding to column numbers for direction vectors in\n' + ' the \"Atoms\" section of a LAMMPS data file.\n') + ilist = argv[i+1].split() + if (len(ilist) % 3) != 0: + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers.\n' + ' This is usually a list of 3 intebers, but it can contain more.\n' + ' The number of cooridnate columns must be divisible by 3,\n' + ' (even if the simulation is in 2 dimensions)\n') + + data_settings.ii_vects = [] + for i in range(0, len(ilist)/3): + cols = [ilist[3*i]+1, ilist[3*i+1]+1, ilist[3*i+2]+1] + setting.ii_vects.append(cols) + # This should override any earlier settings as a result of the + # -atomstyle argument. So you can specify a custom list of column + # names using -atomstyle "list of column names", and then afterwards + # specify which of these columns correspond to direction vectors + # using the "-ivect" command line argument later on. + # This way, in theory you should be able to read columns from + # new custom atom-styles that have not been invented yet. + # (Although I haven't tested this.) + + del(argv[i:i+2]) + # i_atomid is not really needed for this program, but I load it anyway + elif ((argv[i].lower() == '-iatomid') or + (argv[i].lower() == '-iid') or + (argv[i].lower() == '-iatom-id')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"Atoms\" section of a\n' + ' LAMMPS data file contains the atom id number (typically 1).\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_atomid = int(argv[i+1])-1 + del(argv[i:i+2]) + # i_atomtype is not really needed for this program, but I load it anyway + elif ((argv[i].lower() == '-iatomtype') or + (argv[i].lower() == '-itype') or + (argv[i].lower() == '-iatom-type')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"Atoms\" section of a\n' + ' LAMMPS data file contains the atom type.\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_atomtype = int(argv[i+1])-1 + del(argv[i:i+2]) + # i_molid is not really needed for this program, but I load it anyway + elif ((argv[i].lower() == '-imolid') or + (argv[i].lower() == '-imol') or + (argv[i].lower() == '-imol-id') or + (argv[i].lower() == '-imoleculeid') or + (argv[i].lower() == '-imolecule-id')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"Atoms\" section of a\n' + ' LAMMPS data file contains the molecule id number.\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + del(argv[i:i+2]) + # Which frame do we want? + elif (argv[i].lower() == '-t'): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer indicating\n' + ' the frame you want to extract from the dump file (trajectory).\n' + ' This integer should match the timestep corresponding to the frame\n' + ' whose coordinates you wish to extract.\n') + misc_settings.timestep_str = argv[i+1] + del(argv[i:i+2]) + misc_settings.multi = False + misc_settings.last_frame = False + + elif (argv[i].lower() == '-tstart'): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer indicating\n' + ' the first frame you want to extract from the dump file (trajectory).\n' + ' This integer should match the timestep corresponding to the frame\n' + ' (after which) you wish to extract coordinates.\n') + misc_settings.tstart = float(argv[i+1]) + del(argv[i:i+2]) + misc_settings.multi = True + + elif (argv[i].lower() == '-tstop'): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an number indicating\n' + ' the first frame you want to extract from the dump file (trajectory).\n' + ' Frames after this timestep will be ignored.\n') + misc_settings.tstop = float(argv[i+1]) + del(argv[i:i+2]) + misc_settings.multi = True + + elif (argv[i].lower() == '-center'): + misc_settings.center_frame = True + del(argv[i:i+1]) + + elif ((argv[i].lower() == '-raw') or (argv[i].lower() == '-rawout')): + misc_settings.output_format = 'raw' + del(argv[i:i+1]) + + elif (argv[i].lower() == '-rawin'): + misc_settings.input_format = 'raw' + misc_settings.multi = False + del(argv[i:i+1]) + + elif ((argv[i].lower() == '-xyz') or (argv[i].lower() == '-xyzout')): + misc_settings.output_format = 'xyz' + del(argv[i:i+1]) + + elif (argv[i].lower() == '-xyzin'): + misc_settings.input_format = 'xyz' + misc_settings.multi = False + del(argv[i:i+1]) + + elif (argv[i].lower() == '-multi'): + misc_settings.multi = True + del(argv[i:i+1]) + + elif (argv[i].lower() == '-last'): + misc_settings.last_frame = True + misc_settings.multi = False + del(argv[i:i+1]) + + elif (argv[i].lower() == '-interval'): + misc_settings.skip_interval = int(argv[i+1]) + del(argv[i:i+2]) + + elif (argv[i].lower() == '-scale'): + misc_settings.scale = float(argv[i+1]) + del(argv[i:i+2]) + + elif ((argv[i][0] == '-') and (__name__ == "__main__")): + raise InputError('Error(dump2data): Unrecogized command line argument \"'+argv[i]+'\"\n') + else: + i += 1 + + usage_examples = \ +""" Typical usage: +dump2data.py orig_file.data < dump.lammpstrj > new_file.data + (This extracts last frame, uses "full" atom_style.) + Additional options: +dump2data.py -t t -atomstyle style orig.data < dump.lammpstrj > new.data +""" + + #if __name__ == "__main__": + + if (len(argv) > 2): + # if there are more than 2 remaining arguments, + # AND + # no other function will process the remaining argument list + # (ie. if __name__ == "__main__") + # THEN + raise InputError(' ----\n' + 'ERROR(dump2data): You have too many arguments (or unrecognized arguments):\n' + ' \"'+(' '.join(argv))+'\"\n' + ' ----\n' + +usage_examples) + elif (len(argv) < 2): + if misc_settings.output_format == 'data': + raise InputError(' ----\n' + 'ERROR(dump2data): Problem with argument list:\n' + ' Expected a LAMMPS .data file as an argument.\n' + ' ----\n' + +usage_examples) + else: + in_data_file = open(argv[1], 'r') + data_settings.file_name = argv[1]; + data_settings.contents = in_data_file.readlines() + in_data_file.close() + + #end of if-then statement for "if __name__ == "__main__"" + + if len(data_settings.i_coords) == 0: + if warning_strings != None: + warning_strings.append('WARNING(dump2data): atom_style unknown. (Use -atomstyle style. Assuming \"full\")') + warn_atom_style_unspecified = True + # The default atom_style is "full" + data_settings.column_names = AtomStyle2ColNames('full') + ii_coords = ColNames2Coords(data_settings.column_names) + # This program assumes that there is only one coordinate triplet + # (x,y,z) for each atom. Hence we assume that len(ii_coords)==1 + assert(len(ii_coords) == 1) + data_settings.i_coords = ii_coords[0] + data_settings.ii_vects = ColNames2Vects(data_settings.column_names) + data_settings.i_atomid, data_settings.i_atomtype, data_settings.i_molid = ColNames2AidAtypeMolid(data_settings.column_names) + + ### sys.stderr.write('########################################################\n' + ### '## WARNING: atom_style unspecified ##\n' + ### '## --> \"Atoms\" column data has an unknown format. ##\n' + ### '## Assuming atom_style = \"full\" ##\n' + ### '########################################################\n' + ### '## To specify the \"Atoms\" column format you can: ##\n' + ### '## 1) Use the -atom_style \"STYLE\" argument ##\n' + ### '## where \"STYLE\" is a string indicating a LAMMPS ##\n' + ### '## atom_style, including hybrid styles.(Standard ##\n' + ### '## atom styles defined in 2011 are supported.) ##\n' + ### '## 2) Use the -atom_style \"COL_LIST\" argument ##\n' + ### '## where \"COL_LIST" is a quoted list of strings ##\n' + ### '## indicating the name of each column. ##\n' + ### '## Names \"x\",\"y\",\"z\" are interpreted as ##\n' + ### '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n' + ### '## and \"quati\",\"quatj\",\"quatk\" are ##\n' + ### '## interpreted as direction vectors. ##\n' + ### '## 3) Use the -icoord \"cx cy cz...\" argument ##\n' + ### '## where \"cx cy cz\" is a list of integers ##\n' + ### '## indicating the column numbers for the x,y,z ##\n' + ### '## coordinates of each atom. ##\n' + ### '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n' + ### '## where \"cmux cmuy cmuz...\" is a list of ##\n' + ### '## integers indicating the column numbers for ##\n' + ### '## the vector that determines the direction of a ##\n' + ### '## dipole or ellipsoid (ie. a rotateable vector).##\n' + ### '## (More than one triplet can be specified. The ##\n' + ### '## number of entries must be divisible by 3.) ##\n' + ### '## 5) Include a ##\n' + ### '## write(\"in_init.txt\"){atom_style ...} ##\n' + ### '## statement in your .ttree file. ##\n' + ### '########################################################\n') + + + + +def GetIntAtomID(pair): + return int(pair[0]) + + + +def WriteFrameToData(out_file, + descr_str, + misc_settings, + data_settings, + natoms, + coords, + coords_ixiyiz, + vects, + velocities, + xlo_str, xhi_str, + ylo_str, yhi_str, + zlo_str, zhi_str, + xy_str, xz_str, yz_str): + + """ + Open a data file. Read the LAMMPS DATA file line by line. + When the line contains information which is also in the dump file, + replace that information with information from the dump file. + (Information from a dump file is stored in the arguments to this function.) + The resulting file also has LAMMPS DATA format. + + """ + + section = '' + firstline = True + for line in data_settings.contents: + line = line.strip() + ic = line.find('#') + if ic != -1: + line = line[:ic] + if firstline: # Construct a new descriptive header line: + if descr_str != None: + line = descr_str + firstline = False + + if (len(line) > 0): + # The initial section (section='') is assumed to be + # the "LAMMPS Description" section. This is where the + # box boundaries are specified. + if section == '': + tokens = line.split() + if ((len(tokens) >= 2) and + ((tokens[-2] == 'xlo') and (tokens[-1] == 'xhi')) and + ((xlo_str != None) and (xhi_str != None))): + tokens[0] = xlo_str + tokens[1] = xhi_str + line = ' '.join(tokens) + elif ((len(tokens) >= 2) and + ((tokens[-2] == 'ylo') and (tokens[-1] == 'yhi')) and + ((ylo_str != None) and (yhi_str != None))): + tokens[0] = ylo_str + tokens[1] = yhi_str + line = ' '.join(tokens) + elif ((len(tokens) >= 2) and + ((tokens[-2] == 'zlo') and (tokens[-1] == 'zhi')) and + ((zlo_str != None) and (zhi_str != None))): + tokens[0] = zlo_str + tokens[1] = zhi_str + line = ' '.join(tokens) + elif ((len(tokens) >= 3) and + ((tokens[-3] == 'xy') and + (tokens[-2] == 'xz') and + (tokens[-1] == 'yz')) and + ((xy_str != None) and + (xz_str != None) and + (yz_str != None))): + tokens[0] = xy_str + tokens[1] = xz_str + tokens[2] = yz_str + line = ' '.join(tokens) + if (line in set(['Masses', 'Velocities', 'Atoms', + 'Bond Coeffs', 'Angle Coeffs', + 'Dihedral Coeffs', 'Improper Coeffs', + 'Bonds', 'Angles', 'Dihedrals', 'Impropers'])): + section = line + else: + if (section == 'Atoms'): + tokens = line.split() + atomid = tokens[0] + if atomid in coords: + # Loop over all of the vector degrees of + # freedom of the particle, excluding coords + # (for example: mu_x, mu_y, mu_z, + # or quat_i, quat_j, quat_k) + # In principle, depending on the atom_style, + # there could be multiple vectors per atom. + for I in range(0,len(data_settings.ii_vects)): + vxvyvz = vects[atomid][I] + i_vx = data_settings.ii_vects[I][0] + i_vy = data_settings.ii_vects[I][1] + i_vz = data_settings.ii_vects[I][2] + if ((i_vx >= len(tokens)) or + (i_vy >= len(tokens)) or + (i_vz >= len(tokens))): + raise InputError('Error(dump2data): Atom style incompatible with data file.\n' + ' Specify the atom_style using -atomstyle style.\n') + if ((vxvyvz == None) or + (type(vxvyvz) is not tuple)): + assert(data_settings.column_names[i_vx] not in dump_column_names) + raise InputError('Error(dump2data): You have a vector coordinate in your DATA file named \"'+data_settings.column_names[i_vx]+'\"\n' + ' However there are no columns with this name in your DUMP file\n' + ' (or the column was not in the expected place).\n' + ' Hence, the atom styles in the dump and data files do not match.') + + # Replace the vector components with numbers + # from the dump file + tokens[i_vx] = vxvyvz[0] + tokens[i_vy] = vxvyvz[1] + tokens[i_vz] = vxvyvz[2] + + # Now loop over the coordinates of each atom. + #for I in range(0,len(data_settings.ii_coords)): + # xyz = coords[atomid][I] + # THIS LOOP IS SILLY. + # EACH ATOM ONLY HAS ONE SET OF X,Y,Z + # COORDINATES. COMMENTING OUT THIS LOOP: + # i_x = data_settings.ii_coords[I][0] + # i_y = data_settings.ii_coords[I][1] + # i_z = data_settings.ii_coords[I][2] + # USING THIS INSTEAD: + + xyz = coords[atomid] + i_x = data_settings.i_coords[0] + i_y = data_settings.i_coords[1] + i_z = data_settings.i_coords[2] + if ((i_x >= len(tokens)) or + (i_y >= len(tokens)) or + (i_z >= len(tokens))): + raise InputError('Error(dump2data): Atom style incompatible with data file.\n' + ' Specify the atom_style using -atomstyle style.\n') + # Replace the coordinates with coordinates from + # the dump file into tokens[i_x]... + tokens[i_x] = str(xyz[0]) + tokens[i_y] = str(xyz[1]) + tokens[i_z] = str(xyz[2]) + + # Are there there any integer coords + # (ix, iy, iz) in the dump file? + if coords_ixiyiz[atomid]: + assert(len(coords_ixiyiz[atomid]) == 3) + # Integer coords stored in the DATA file too? + if len(tokens)==(len(data_settings.column_names)+3): + # Then replace the last 3 columns of the + # line in the data file with: ix iy iz + tokens[-3] = coords_ixiyiz[atomid][0] + tokens[-2] = coords_ixiyiz[atomid][1] + tokens[-1] = coords_ixiyiz[atomid][2] + else: + if (not misc_settings.center_frame): + # Append them to the end of the line: + tokens.append(coords_ixiyiz[atomid][0]) + tokens.append(coords_ixiyiz[atomid][1]) + tokens.append(coords_ixiyiz[atomid][2]) + + # Now finally paste all the tokens together: + line = ' '.join(tokens) + + + elif (section == 'Velocities'): + tokens = line.split() + atomid = tokens[0] + if atomid in velocities: + + vxvyvz = velocities[atomid] + if len(tokens) < 4: + raise InputError('Error(dump2data): Not enough columns in the \"Velocities\" file.\n') + # Replace the coordinates with coordinates from + # the dump file into tokens[i_x]... + tokens[1] = str(vxvyvz[0]) + tokens[2] = str(vxvyvz[1]) + tokens[3] = str(vxvyvz[2]) + + # Now finally paste all the tokens together: + line = ' '.join(tokens) + + + out_file.write(line+'\n') + + + + + + + + + + + + + + + +if __name__ == "__main__": + + g_program_name = 'dump2data.py' + g_date_str = '2013-10-30' + g_version_str = 'v0.43' + + ####### Main Code Below: ####### + sys.stderr.write(g_program_name+' '+g_version_str+' '+g_date_str+' ') + #if sys.version < '3': + # sys.stderr.write(' (python version < 3)\n') + #else: + sys.stderr.write('\n') + + try: + data_settings = DataSettings() + misc_settings = MiscSettings() + warning_strings = [] + ParseArgs(sys.argv, + misc_settings, + data_settings, + warning_strings) + + # Open the lammps dump file (trajectory file) + # Skip to the line containing the correct frame/timestep. + # (this is the last frame by default). + # Read the "BOX BOUNDS" and the "ATOMS" sections. + # Store the x,y,z coordinates in the "coords" associative array + # (indexed by atom id, which could be non-numeric in general). + + section = '' + + #coords = defaultdict(list) + #coords_ixiyiz = defaultdict(list) + #vects = defaultdict(list) + #xlo_str = xhi_str = ylo_str = yhi_str = zlo_str = zhi_str = None + #xy_str = xz_str = yz_str = None + #natoms = -1 + #timestep_str = '' + + frame_coords = defaultdict(list) + frame_coords_ixiyiz = defaultdict(list) + frame_vects = defaultdict(list) + frame_velocities = defaultdict(list) + frame_xlo_str = frame_xhi_str = None + frame_ylo_str = frame_yhi_str = None + frame_zlo_str = frame_zhi_str = None + frame_xy_str = frame_xz_str = frame_yz_str = None + frame_natoms = -1 + frame_timestep_str = '' + i_atomid = i_atomtype = i_molid = -1 + i_x = i_y = i_z = i_xu = i_yu = i_zu = -1 + i_xs = i_ys = i_zs = i_xsu = i_ysu = i_zsu = -1 + + dump_column_names = [] + + #num_frames_in = -1 + num_frames_out = 0 + finished_reading_frame = False + read_last_frame = False + + #in_coord_file = open('traj_nvt.lammpstrj','r') + #in_coord_file = open('deleteme.lammpstrj','r') + in_coord_file = sys.stdin + + while True: + + line = in_coord_file.readline() + if line == '': # if EOF + if len(frame_coords) > 0: + finished_reading_frame = True + read_last_frame = True + + line = line.strip() + if (line.find('ITEM:') == 0): + section = line + if (section.find('ITEM: ATOMS ') == 0): + dump_column_names = line[12:].split() + i_atomid, i_atomtype, i_molid = \ + ColNames2AidAtypeMolid(dump_column_names) + #ii_coords = ColNames2Coords(dump_column_names) + + if 'x' in dump_column_names: + i_x = dump_column_names.index('x') + elif 'xu' in dump_column_names: + i_xu = dump_column_names.index('xu') + elif 'xs' in dump_column_names: + i_xs = dump_column_names.index('xs') + elif 'xsu' in dump_column_names: + i_xsu = dump_column_names.index('xsu') + else: + raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"x\" column.\n'+ + ' (excerpt below)\n' + line) + + if 'y' in dump_column_names: + i_y = dump_column_names.index('y') + elif 'yu' in dump_column_names: + i_yu = dump_column_names.index('yu') + elif 'ys' in dump_column_names: + i_ys = dump_column_names.index('ys') + elif 'ysu' in dump_column_names: + i_ysu = dump_column_names.index('ysu') + else: + raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"y\" column.\n'+ + ' (excerpt below)\n' + line) + + if 'z' in dump_column_names: + i_z = dump_column_names.index('z') + elif 'zu' in dump_column_names: + i_zu = dump_column_names.index('zu') + elif 'zs' in dump_column_names: + i_zs = dump_column_names.index('zs') + elif 'zsu' in dump_column_names: + i_zsu = dump_column_names.index('zsu') + else: + raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"z\" column.\n'+ + ' (excerpt below)\n' + line) + + + + + + ii_vects = ColNames2Vects(dump_column_names) + if (len(ii_vects) != len(data_settings.ii_vects)): + raise InputError('Error(dump2data): atom styles in data and dump files differ.\n' + ' Some needed columns from the atom_styles are missing in the dump file.') + + i_ix = i_iy = i_iz = -1 + if 'ix' in dump_column_names: + i_ix = dump_column_names.index('ix') + if 'iy' in dump_column_names: + i_iy = dump_column_names.index('iy') + if 'iz' in dump_column_names: + i_iz = dump_column_names.index('iz') + + + i_vx = i_vy = i_vz = -1 + if 'vx' in dump_column_names: + i_vx = dump_column_names.index('vx') + if 'vy' in dump_column_names: + i_vy = dump_column_names.index('vy') + if 'vz' in dump_column_names: + i_vz = dump_column_names.index('vz') + + + elif (section.find('ITEM: BOX BOUNDS') == 0): + avec=[1.0, 0.0, 0.0] + bvec=[0.0, 1.0, 0.0] + cvec=[0.0, 0.0, 1.0] + + elif (section.find('ITEM: TIMESTEP') == 0): + if len(frame_coords) > 0: + finished_reading_frame = True + + elif ((len(line) > 0) and (line[0] != '#')): + if (section.find('ITEM: TIMESTEP') == 0): + finished_reading_frame = False + frame_timestep_str = line + frame_coords = defaultdict(list) + frame_coords_ixiyiz = defaultdict(list) + frame_vects = defaultdict(list) + frame_velocities = defaultdict(list) + frame_xlo_str = frame_xhi_str = None + frame_ylo_str = frame_yhi_str = None + frame_zlo_str = frame_zhi_str = None + frame_xy_str = frame_xz_str = frame_yz_str = None + + elif (section == 'ITEM: NUMBER OF ATOMS'): + frame_natoms = int(line) + + elif (section.find('ITEM: BOX BOUNDS') == 0): + is_triclinic = (section.find('xy xz yz') == 0) + + tokens = line.split() + if not frame_xlo_str: + assert(not frame_xhi_str) + frame_xlo_str = tokens[0] + frame_xhi_str = tokens[1] + avec[0] = float(frame_xhi_str) - float(frame_xlo_str) + if (is_triclinic and (len(tokens) > 2)): + frame_xy_str = tokens[2] + bvec[0] = float(frame_xy_str) + #See http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + #sys.stderr.write('avec='+str(avec)+'\n') + + elif not frame_ylo_str: + assert(not frame_yhi_str) + frame_ylo_str = tokens[0] + frame_yhi_str = tokens[1] + bvec[1] = float(frame_yhi_str) - float(frame_ylo_str) + if (is_triclinic and (len(tokens) > 2)): + frame_xz_str = tokens[2] + cvec[0] = float(frame_xz_str) + #See http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + #sys.stderr.write('bvec='+str(bvec)+'\n') + + elif not frame_zlo_str: + assert(not frame_zhi_str) + frame_zlo_str = tokens[0] + frame_zhi_str = tokens[1] + cvec = [0.0, 0.0, float(frame_zhi_str) - float(frame_zlo_str)] + if (is_triclinic and (len(tokens) > 2)): + frame_yz_str = tokens[2] + cvec[1] = float(frame_yz_str) + #See http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + #sys.stderr.write('cvec='+str(cvec)+'\n') + + elif (section.find('ITEM: ATOMS') == 0): + tokens = line.split() + atomid = tokens[i_atomid] + + if ((i_x != -1) and (i_y != -1) and (i_z != -1)): + x = float(tokens[i_x]) #i_x determined above + y = float(tokens[i_y]) + z = float(tokens[i_z]) + + elif ((i_xu != -1) and (i_yu != -1) and (i_zu != -1)): + x = float(tokens[i_xu]) #i_x determined above + y = float(tokens[i_yu]) + z = float(tokens[i_zu]) + + elif ((i_xs != -1) and (i_ys != -1) and (i_zs != -1)): + xs = float(tokens[i_xs]) #i_xs determined above + ys = float(tokens[i_ys]) + zs = float(tokens[i_zs]) + + x = float(xlo_str) + xs*avec[0] + ys*bvec[0] + zs*cvec[0] + y = float(ylo_str) + xs*avec[1] + ys*bvec[1] + zs*cvec[1] + z = float(zlo_str) + xs*avec[2] + ys*bvec[2] + zs*cvec[2] + + # avec, bvec, cvec described here: + #http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + + elif ((i_xsu != -1) and (i_ysu != -1) and (i_zsu != -1)): + xsu = float(tokens[i_xsu]) #i_xs determined above + ysu = float(tokens[i_ysu]) + zsu = float(tokens[i_zsu]) + + x = float(xlo_str) + xsu*avec[0] + ysu*bvec[0] + zsu*cvec[0] + y = float(ylo_str) + xsu*avec[1] + ysu*bvec[1] + zsu*cvec[1] + z = float(zlo_str) + xsu*avec[2] + ysu*bvec[2] + zsu*cvec[2] + + # Now deal with ix, iy, iz + if i_ix != -1: + ix = int(tokens[i_ix]) + if (misc_settings.center_frame or + (misc_settings.output_format != 'data')): + #sys.stderr.write('ix = '+str(ix)+', avec='+str(avec)+'\n') + x += ix*avec[0] + y += ix*avec[1] + z += ix*avec[2] + else: + if atomid not in frame_coords_ixiyiz: + frame_coords_ixiyiz[atomid] = ["0", "0", "0"] + else: + frame_coords_ixiyiz[atomid][0] = str(ix) + + if i_iy != -1: + iy = int(tokens[i_iy]) + if (misc_settings.center_frame or + (misc_settings.output_format != 'data')): + #sys.stderr.write('iy = '+str(iy)+', bvec='+str(bvec)+'\n') + x += iy*bvec[0] + y += iy*bvec[1] + z += iy*bvec[2] + else: + if atomid not in frame_coords_ixiyiz: + frame_coords_ixiyiz[atomid] = ["0", "0", "0"] + else: + frame_coords_ixiyiz[atomid][1] = str(iy) + + if i_iz != -1: + iz = int(tokens[i_iz]) + if (misc_settings.center_frame or + (misc_settings.output_format != 'data')): + #sys.stderr.write('iz = '+str(iz)+', cvec='+str(cvec)+'\n') + x += iz*cvec[0] + y += iz*cvec[1] + z += iz*cvec[2] + else: + if atomid not in frame_coords_ixiyiz: + frame_coords_ixiyiz[atomid] = ["0", "0", "0"] + else: + frame_coords_ixiyiz[atomid][2] = str(iz) + + #frame_coords[atomid] = [str(x), str(y), str(z)] + frame_coords[atomid] = [x, y, z] + + vx = 0.0 + vy = 0.0 + vz = 0.0 + if i_vx != -1: + vx = float(tokens[i_vx]) + if i_vy != -1: + vy = float(tokens[i_vy]) + if i_vz != -1: + vz = float(tokens[i_vz]) + + frame_velocities[atomid] = [vx, vy, vz] + + # Ugly detail: + # There can be multiple "vects" associated with each atom + # (for example, dipole moments, ellipsoid directions, etc..) + + if atomid not in frame_vects: + frame_vects[atomid] = [None for I in range(0,len(ii_vects))] + + for I in range(0, len(ii_vects)): + i_vx = ii_vects[I][0] + i_vy = ii_vects[I][1] + i_vz = ii_vects[I][2] + vx_str = tokens[i_vx] + vy_str = tokens[i_vy] + vz_str = tokens[i_vz] + + # Now the annoying part: + # Which vect is it (mux,muy,muz) or (quati,quatj,quatk)? + # The columns could be listed in a different order + # in the data file and in the dump file. + # Figure out which vector it is in the data file (stored + # in the integer "I_data") so that column names match. + name_vx = dump_column_names[i_vx] + name_vy = dump_column_names[i_vy] + name_vz = dump_column_names[i_vz] + i_vx_data = 0 + I_data = -1 + # This code is ugly and inneficient. + # I never want to touch this code again. (Hope it works) + while i_vx_data < len(data_settings.column_names): + if name_vx == data_settings.column_names[i_vx_data]: + I_data = 0 + while I_data < len(data_settings.ii_vects): + if ii_vects[I] == data_settings.ii_vects[I_data]: + break + I_data += 1 + + if (0= + # float(misc_settings.timestep_str)): + # num_frames_in = 1 + # if not misc_settings.multi: + # read_last_frame = True + # else: + # num_frames_in = 1 + + + + # Should we write out the coordinates in this frame? + write_this_frame = False + + if misc_settings.multi: + + write_this_frame = True + if (misc_settings.tstart and + (int(frame_timestep_str) < misc_settings.tstart)): + write_this_frame = False + if (misc_settings.tstop and + (int(frame_timestep_str) > misc_settings.tstop)): + write_this_frame = False + read_last_frame = True + + if misc_settings.tstart: + tstart = misc_settings.tstart + else: + tstart = 0 + + if ((int(frame_timestep_str) - tstart) + % + misc_settings.skip_interval) != 0: + write_this_frame = False + + else: + if misc_settings.last_frame: + if read_last_frame: + write_this_frame = True + else: + assert(misc_settings.timestep_str) + if (int(frame_timestep_str) >= + int(misc_settings.timestep_str)): + write_this_frame = True + read_last_frame = True + + + if write_this_frame: + + num_frames_out += 1 + + sys.stderr.write(' (writing frame '+str(num_frames_out)+ + ' at timestep '+frame_timestep_str+')\n') + + + # Print the frame + # First check which format to output the data: + if misc_settings.output_format == 'raw': + # Print out the coordinates in simple 3-column text format + for atomid, xyz in iter(sorted(frame_coords.items(), key=GetIntAtomID)): + if misc_settings.scale == None: + sys.stdout.write(str(xyz[0])+' '+str(xyz[1])+' '+str(xyz[2])+'\n') + else: + # Only convert to float and back if misc_settings.scale != None + sys.stdout.write(str(misc_settings.scale*float(xyz[0]))+' '+ + str(misc_settings.scale*float(xyz[1]))+' '+ + str(misc_settings.scale*float(xyz[2]))+'\n') + sys.stdout.write('\n') + + elif misc_settings.output_format == 'xyz': + # Print out the coordinates in simple 3-column text format + sys.stdout.write(str(len(frame_coords))+'\n') + descr_str = 'LAMMPS data from timestep '+frame_timestep_str + sys.stdout.write(descr_str+'\n') + for atomid, xyz in iter(sorted(frame_coords.items(), key=GetIntAtomID)): + if misc_settings.scale == None: + sys.stdout.write(str(atomid)+' '+ + str(xyz[0])+' '+ + str(xyz[1])+' '+ + str(xyz[2])+'\n') + else: + # Only convert to float and back if misc_settings.scale != None + sys.stdout.write(str(atomid)+' '+ + str(misc_settings.scale*float(xyz[0]))+' '+ + str(misc_settings.scale*float(xyz[1]))+' '+ + str(misc_settings.scale*float(xyz[2]))+'\n') + + else: + # Parse the DATA file specified by the user + # and replace appropriate lines or fields with + # the corresponding text from the DUMP file. + descr_str = 'LAMMPS data from timestep '+frame_timestep_str + if misc_settings.multi and (misc_settings.output_format == 'data'): + out_file_name = data_settings.file_name + '.'\ + + str(num_frames_out) + sys.stderr.write(' (creating file \"'+out_file_name+'\")\n') + out_file = open(out_file_name, 'w') + else: + out_file = sys.stdout + + WriteFrameToData(out_file, + descr_str, + misc_settings, + data_settings, + frame_natoms, + frame_coords, + frame_coords_ixiyiz, + frame_vects, + frame_velocities, + frame_xlo_str, frame_xhi_str, + frame_ylo_str, frame_yhi_str, + frame_zlo_str, frame_zhi_str, + frame_xy_str, frame_xz_str, frame_yz_str) + + #if misc_settings.multi: + # out_file.close() + + + #if num_frames_in >= 0: + # num_frames_in += 1 + + + if read_last_frame: + exit(0) + + + for warning_str in warning_strings: + sys.stderr.write(warning_str+'\n') + + + + except (ValueError, InputError) as err: + sys.stderr.write('\n'+str(err)+'\n') + sys.exit(-1) + diff --git a/tools/moltemplate/src/extract_lammps_data.py b/tools/moltemplate/src/extract_lammps_data.py new file mode 100755 index 0000000000..4fe3ec743d --- /dev/null +++ b/tools/moltemplate/src/extract_lammps_data.py @@ -0,0 +1,119 @@ +#!/usr/bin/env python + +lammps_data_sections = set(['Atoms', + 'Masses', + 'Bonds', + 'Bond Coeffs', + 'Angles', + 'Angle Coeffs', + 'Dihedrals', + 'Dihedral Coeffs', + 'Impropers', + 'Improper Coeffs', + 'BondBond Coeffs', # class2 angles + 'BondAngle Coeffs', # class2 angles + 'MiddleBondTorsion Coeffs', # class2 dihedrals + 'EndBondTorsion Coeffs', # class2 dihedrals + 'AngleTorsion Coeffs', # class2 dihedrals + 'AngleAngleTorsion Coeffs', # class2 dihedrals + 'BondBond13 Coeffs', # class2 dihedrals + 'AngleAngle Coeffs', # class2 impropers + 'Angles By Type', # new. not standard LAMMPS + 'Dihedrals By Type',# new. not standard LAMMPS + 'Angles By Type']) # new. not standard LAMMPS + + +def DeleteComments(string, + escape='\\', + comment_char='#'): + escaped_state = False + for i in range(0,len(string)): + if string[i] in escape: + if escaped_state: + escaped_state = False + else: + escaped_state = True + elif string[i] == comment_char: + if not escaped_state: + return string[0:i] + return string + + + +def ExtractDataSection(f, + section_name, + comment_char = '#', + include_section_name = False, + return_line_nums = False): + + inside_section = False + if section_name in ('header','Header'): #"Header" section includes beginning + inside_section = True + + nonblank_encountered = False + nonheader_encountered = False + + i = 0 + for line_orig in f: + return_this_line = False + line = DeleteComments(line_orig).strip() + if line in lammps_data_sections: + nonheader_encountered = True + if section_name in ('header', 'Header'): + # The "header" section includes all lines at the beginning of the + # before any other section is encountered. + if nonheader_encountered: + return_this_line = False + else: + return_this_line = True + elif line == section_name: + inside_section = True + nonblank_encountered = False + if include_section_name: + return_this_line = True + # A block of blank lines (which dont immediately follow + # the section_name) signal the end of a section: + elif len(line) == 0: + if inside_section and include_section_name: + return_this_line = True + if nonblank_encountered: + inside_section = False + elif line[0] != comment_char: + if inside_section: + nonblank_encountered = True + return_this_line = True + + if return_this_line: + if return_line_nums: + yield i + else: + yield line_orig + + i += 1 + + + +if __name__ == "__main__": + + import sys + lines = sys.stdin.readlines() + exclude_sections = False + if sys.argv[1] == '-n': + exclude_sections = True + del sys.argv[1] + + if not exclude_sections: + for section_name in sys.argv[1:]: + for line in ExtractDataSection(lines, section_name): + sys.stdout.write(line) + else: + line_nums_exclude = set([]) + for section_name in sys.argv[1:]: + for line_num in ExtractDataSection(lines, + section_name, + include_section_name=True, + return_line_nums=True): + line_nums_exclude.add(line_num) + for i in range(0, len(lines)): + if i not in line_nums_exclude: + sys.stdout.write(lines[i]) diff --git a/tools/moltemplate/src/ltemplify.py b/tools/moltemplate/src/ltemplify.py new file mode 100755 index 0000000000..a71af2598d --- /dev/null +++ b/tools/moltemplate/src/ltemplify.py @@ -0,0 +1,2236 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +# Author: Andrew Jewett (jewett.aij at g mail) +# http://www.chem.ucsb.edu/~sheagroup +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2012, Regents of the University of California +# All rights reserved. + +""" +ltemplify.py + +The "ltemplify.py" script can be used to convert existing LAMMPS +input script and data files into a single .lt file +(which includes both topology and force-field information + for a single molecule in your system). + +Example: + + ltemplify.py -name Mol file.in file.data > mol.lt + +This creates a template for a new type of molecule (named "Mol"), +consisting of all the atoms in the lammps files you included, +and saves this data in a single ttree file ("mol.lt"). +This file can be used with moltemplate (ttree) to +define large systems containing this molecule. + +""" + +import sys +from ttree_lex import * +from lttree_styles import * + + + +def Intify(s): + if s.isdigit(): + return int(s) + elif s[0:2] == 'id': + return int(s[2:]) + elif s[0:4] == 'type': + return int(s[4:]) + else: + return s + +def StringToInterval(sel_str, slice_delim='*'): + i_slice = sel_str.find(slice_delim) + + if i_slice == -1: + if sel_str.isdigit(): + a = int(sel_str) + b = int(sel_str) + else: + a = sel_str + b = sel_str + + else: + a = sel_str[:i_slice] + b = sel_str[i_slice+len(slice_delim):] + + if (((len(a)>0) and (not a.isdigit())) or + ((len(b)>0) and (not b.isdigit()))): + raise InputError('Error: invalid selection string \"'+ + sel_str+'\"\n') + if (len(a) > 0): + a = int(a) + else: + a = None + + if (len(b) > 0): + b = int(b) + else: + b = None + + return a,b + + +# Selections are simply lists of 2-tuples (pairs) + +def LammpsSelectToIntervals(sel_str, slice_delim='*', or_delim=', '): + + """ + This function converts a string such as "1*4 6 9*12" into + a list of tuples, for example: [(1,4), (6,6), (9,12)] + In general, the of intervals has the form: + [(a1,b1), (a2,b2), (a3,b3), ... ] + + An atom is considered to belong to this selection + if it happens to lie within the closed interval [a,b] + for any pair of a,b values in the list of intervals. + If for a given pair a,b, either a or b is "None", then that a or b + value is not used to disqualify membership in the interval. + (Similar to -infinity or +infinity. In other words if a is set to None, + then to belong to the interval it is enough to be less than b.) + + """ + selection_list = [] + #tokens = sel_str.split(or_delim) <-- Not what we want when len(or_delim)>1 + tokens = LineLex.TextBlock2Lines(sel_str, or_delim, keep_delim=False) + for token in tokens: + token = token.strip() + (a,b) = StringToInterval(token, slice_delim) + selection_list.append((a, b)) + + return selection_list + + +def IntervalListToMinMax(interval_list): + min_a = None + max_b = None + for (a,b) in interval_list: + if ((not (type(a) is int)) or (not (type(b) is int))): + return None,None #only integer min/max makes sense. otherwise skip + + if (min_a == None) or (a < min_a): + min_a = a + if (max_b == None) or (b > max_b): + max_b = b + return min_a, max_b + + +def BelongsToSel(i, sel): + if (i == None) or (sel == None) or (len(sel) == 0): + # If the user has not specified a selection for this category, + # then by default all objects are accepted + return True + + elif (type(i) is str): + if i.isdigit(): + i = int(i) + else: + return True + + belongs = False + for interval in sel: + assert(len(interval) == 2) + if interval[0]: + if i >= interval[0]: + if (interval[1] == None) or (i <= interval[1]): + belongs = True + break + elif interval[1]: + if i <= interval[1]: + belongs = True + break + else: + # In that case, the user entered something like "*" + # which covers all possible numbers + belongs = True + break + + return belongs + + + +try: + + g_program_name = __file__.split('/')[-1] # = 'ltemplify.py' + g_version_str = '0.36' + g_date_str = '2013-8-22' + sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n') + + non_empty_output = False + no_warnings = True + indent = 2 + cindent = 0 + atomid_selection = [] + atomtype_selection = [] + molid_selection = [] + mol_name = '' + + min_sel_atomid = None + min_sel_atomtype = None + min_sel_bondid = None + min_sel_bondtype = None + min_sel_angleid = None + min_sel_angletype = None + min_sel_dihedralid = None + min_sel_dihedraltype = None + min_sel_improperid = None + min_sel_impropertype = None + + max_sel_atomid = None + max_sel_atomtype = None + max_sel_bondid = None + max_sel_bondtype = None + max_sel_angleid = None + max_sel_angletype = None + max_sel_dihedralid = None + max_sel_dihedraltype = None + max_sel_improperid = None + max_sel_impropertype = None + + needed_atomids = set([]) + needed_atomtypes = set([]) + needed_bondids = set([]) + needed_bondtypes = set([]) + needed_angleids = set([]) + needed_angletypes = set([]) + needed_dihedralids = set([]) + needed_dihedraltypes = set([]) + needed_improperids = set([]) + needed_impropertypes = set([]) + + min_needed_atomtype = None + max_needed_atomtype = None + min_needed_bondtype = None + max_needed_bondtype = None + min_needed_angletype = None + max_needed_angletype = None + min_needed_dihedraltype = None + max_needed_dihedraltype = None + min_needed_impropertype = None + max_needed_impropertype = None + + + # To process the selections, we need to know the atom style: + atom_style_undefined = True + + i_atomid = None + i_atomtype = None + i_molid = None + + l_in_init = [] + l_in_settings = [] + l_in_masses = [] + l_in_pair_coeffs = [] + l_in_bond_coeffs = [] + l_in_angle_coeffs = [] + l_in_dihedral_coeffs = [] + l_in_improper_coeffs = [] + l_data_masses = [] + l_data_bond_coeffs = [] + l_data_angle_coeffs = [] + l_data_dihedral_coeffs = [] + l_data_improper_coeffs = [] + l_data_pair_coeffs = [] + l_data_atoms = [] + l_data_velocities = [] + l_data_bonds = [] + l_data_angles = [] + l_data_dihedrals = [] + l_data_impropers = [] + + # class2 force fields + l_data_bondbond_coeffs = [] + l_data_bondangle_coeffs = [] + l_data_middlebondtorsion_coeffs = [] + l_data_endbondtorsion_coeffs = [] + l_data_angletorsion_coeffs = [] + l_data_angleangletorsion_coeffs = [] + l_data_bondbond13_coeffs = [] + l_data_angleangle_coeffs = [] + + # non-point-like particles: + l_data_ellipsoids = [] + l_data_lines = [] + l_data_triangles = [] + + # automatic generation of bonded interactions by type: + l_data_angles_by_type = [] + l_data_dihedrals_by_type = [] + l_data_impropers_by_type = [] + + atoms_already_read = False + some_pair_coeffs_read = False + complained_atom_style_mismatch = False + infer_types_from_comments = False + + + argv = sys.argv + + i = 1 + + while i < len(argv): + + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + + if argv[i] == '-columns': + if i+1 >= len(argv): + raise InputError('Error: the \"'+argv[i]+'\" argument should be followed by a quoted\n' + ' string which contains a space-delimited list of the names of\n' + ' of columns in the \"Atoms\" section of the LAMMPS data file.\n' + ' If the list contains the symbols:\n' + ' \"atom-ID\" or \"atomid\", they are interpreted\n' + ' as unique atom ID numbers, and columns named\n' + ' \"atom-type\" or \"atomtype\" are interpreted\n' + ' as atom types. Finally, columns named\n' + ' \"molecule-ID\", \"molecule\", or \"mol-ID\", or \"mol\"\n' + ' are interpreted as unique molecule id numbers.\n' + 'Example:\n' + ' '+argv[i]+' \'atom-ID atom-type q polarizability molecule-ID x y z\'\n' + ' defines a custom atom_style containing the properties\n' + ' atom-ID atom-type q polarizability molecule-ID x y z\n' + ' Make sure you enclose the entire list in quotes.\n'); + column_names = argv[i+1].strip('\"\'').strip().split() + del(argv[i:i+2]) + + elif (argv[i] == '-ignore-comments'): + infer_types_from_comments = False + del(argv[i:i+1]) + + elif (argv[i] == '-infer-comments'): + infer_types_from_comments = True + del(argv[i:i+1]) + + elif ((argv[i] == '-name') or + (argv[i] == '-molname') or + (argv[i] == '-molecule-name') or + (argv[i] == '-molecule_name')): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a a molecule type name.\n') + cindent = 2 + indent += cindent + mol_name = argv[i+1] + del(argv[i:i+2]) + + elif ((argv[i].lower() == '-atomstyle') or + (argv[i].lower() == '-atom_style') or + (argv[i].lower() == '-atom-style')): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n' + ' (or single quoted string which includes a space-separated\n' + ' list of column names).\n') + atom_style_undefined = False + column_names = AtomStyle2ColNames(argv[i+1]) + if (argv[i+1].strip().split()[0] in g_style_map): + l_in_init.append((' '*indent) + 'atom_style ' + argv[i+1] + '\n') + sys.stderr.write('\n \"Atoms\" column format:\n') + sys.stderr.write(' '+(' '.join(column_names))+'\n') + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + if i_molid: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n') + else: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n') + del(argv[i:i+2]) + + elif ((argv[i].lower() == '-id') or + #(argv[i].lower() == '-a') or + #(argv[i].lower() == '-atoms') or + (argv[i].lower() == '-atomid') or + #(argv[i].lower() == '-atomids') or + (argv[i].lower() == '-atom-id') + #(argv[i].lower() == '-atom-ids') or + #(argv[i].lower() == '-$atom') or + #(argv[i].lower() == '-$atoms') + ): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers\n' + ' (or strings). These identify the group of atoms you want to\n' + ' to include in the template you are creating.\n') + atomid_selection += LammpsSelectToIntervals(argv[i+1]) + min_sel_atomid, max_sel_atomid = IntervalListToMinMax(atomid_selection) + del(argv[i:i+2]) + elif ((argv[i].lower() == '-type') or + #(argv[i].lower() == '-t') or + (argv[i].lower() == '-atomtype') or + (argv[i].lower() == '-atom-type') + #(argv[i].lower() == '-atomtypes') or + #(argv[i].lower() == '-atom-types') or + #(argv[i].lower() == '-@atom') or + #(argv[i].lower() == '-@atoms') or + #(argv[i].lower() == '-@atomtype') or + #(argv[i].lower() == '-@atomtypes') + ): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers.\n' + ' (or strings). These identify the group of atom types you want to\n' + ' to include in the template you are creating.\n') + atomtype_selection += LammpsSelectToIntervals(argv[i+1]) + min_sel_atomtype, max_sel_atomtype = IntervalListToMinMax(atomtype_selection) + del(argv[i:i+2]) + elif ((argv[i].lower() == '-mol') or + #(argv[i].lower() == '-m') or + (argv[i].lower() == '-molid') or + #(argv[i].lower() == '-molids') or + (argv[i].lower() == '-mol-id') or + #(argv[i].lower() == '-mol-ids') or + #(argv[i].lower() == '-molecule') or + (argv[i].lower() == '-moleculeid') or + (argv[i].lower() == '-molecule-id') + #(argv[i].lower() == '-molecules') or + #(argv[i].lower() == '-molecule-ids') or + #(argv[i].lower() == '-$mol') or + #(argv[i].lower() == '-$molecule') + ): + if i+1 >= len(argv): + sys.stderr.write('Error: '+argv[i]+' flag should be followed by a list of integers.\n' + ' (or strings). These identify the group of molecules you want to\n' + ' include in the template you are creating.\n') + molid_selection += LammpsSelectToIntervals(argv[i+1]) + del(argv[i:i+2]) + else: + i += 1 + + + # atom type names + atomtypes_name2int = {} + atomtypes_int2name = {} + #atomids_name2int = {} not needed + atomids_int2name = {} + atomids_by_type = {} + + + if atom_style_undefined: + # The default atom_style is "full" + column_names = AtomStyle2ColNames('full') + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + + #--------------------------------------------------------- + #-- The remaining arguments are files that the user wants + #-- us to read and convert. It is typical to have + #-- multiple input files, because LAMMPS users often + #-- store their force field parameters in either the LAMMPS + #-- data files and input script files, or both. + #-- We want to search all of the LAMMPS input files in + #-- order to make sure we extracted all the force field + #-- parameters (coeff commands). + #--------------------------------------------------------- + + for i_arg in range(1,len(argv)): + fname = argv[i_arg] + try: + lammps_file = open(fname, 'r') + except IOError: + raise InputError('Error: unrecognized argument (\"'+fname+'\"),\n' + ' OR unable to open file:\n' + '\n' + ' \"'+fname+'\"\n' + ' for reading.\n' + '\n' + ' (If you were not trying to open a file with this name,\n' + ' then there is a problem in your argument list.)\n') + + sys.stderr.write('reading file \"'+fname+'\"\n') + + atomid2type = {} + atomid2mol = {} + data_file_header_names = set(['LAMMPS Description', + 'Atoms', 'Masses', 'Velocities', 'Bonds', + 'Angles', 'Dihedrals', 'Impropers', + 'Pair Coeffs', + 'Bond Coeffs', 'Angle Coeffs', + 'Dihedral Coeffs', 'Improper Coeffs', + #class2 force fields: + 'BondBond Coeffs', 'BondAngle Coeffs', + 'MiddleBondTorsion Coeffs', 'EndBondTorsion Coeffs', + 'AngleTorsion Coeffs', 'AngleAngleTorsion Coeffs', + 'BondBond13 Coeffs', + 'AngleAngle Coeffs', + # non-point-like particles: + 'Ellipsoids', 'Triangles', 'Lines', + #specifying bonded interactions by type: + 'Angles By Type', 'Dihedrals By Type', 'Impropers By Type' + ]) + + lex=LineLex(lammps_file, fname) + lex.source_triggers = set(['include','import']) + # set up lex to accept most characters in file names: + lex.wordterminators = '(){}' + lex.whitespace + # set up lex to understand the "include" statement: + lex.source = 'include' + lex.escape = '\\' + + while lex: + infile = lex.infile + lineno = lex.lineno + line = lex.ReadLine() + if (lex.infile != infile): + infile = lex.infile + lineno = lex.lineno + + #sys.stderr.write(' processing \"'+line.strip()+'\", (\"'+infile+'\":'+str(lineno)+')\n') + + if line == '': + break + + tokens = line.strip().split() + if (len(tokens) > 0): + if ((tokens[0] == 'atom_style') and + atom_style_undefined): + + sys.stderr.write(' Atom Style found. Processing: \"'+line.strip()+'\"\n') + if atoms_already_read: + raise InputError('Error: The file containing the \"atom_style\" command must\n' + ' come before the data file in the argument list.\n' + ' (The templify program needs to know the atom style before reading\n' + ' the data file. Either change the order of arguments so that the\n' + ' LAMMPS input script file is processed before the data file, or use\n' + ' the \"-atom_style\" command line argument to specify the atom_style.)\n') + + column_names = AtomStyle2ColNames(line.split()[1]) + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + + sys.stderr.write('\n \"Atoms\" column format:\n') + sys.stderr.write(' '+(' '.join(column_names))+'\n') + if i_molid: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n') + else: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n\n') + l_in_init.append((' '*indent)+line.lstrip()) + + elif (tokens[0] in set(['units', + 'angle_style', + 'bond_style', + 'dihedral_style', + 'impoper_style', + 'min_style', + 'pair_style', + 'pair_modify', + 'special_bonds', + 'kspace_style', + 'kspace_modify'])): + l_in_init.append((' '*indent)+line.lstrip()) + + #if (line.strip() == 'LAMMPS Description'): + # sys.stderr.write(' reading \"'+line.strip()+'\"\n') + # # skip over this section + # while lex: + # line = lex.ReadLine() + # if line.strip() in data_file_header_names: + # lex.push_raw_text(line) # <- Save line for later + # break + + elif (line.strip() == 'Atoms'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + atoms_already_read = True + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if ((len(tokens) <= i_atomid) or + (len(tokens) <= i_atomtype) or + ((i_molid != None) and + (len(tokens) <= i_molid))): + raise InputError('Error: The number of columns in the \"Atoms\" section does\n' + ' not match the atom_style (see column name list above).\n') + elif ((len(tokens) != len(column_names)) and + (not complained_atom_style_mismatch)): + complained_atom_style_mismatch = True + sys.stderr.write('Warning: The number of columns in the \"Atoms\" section does\n' + ' not match the atom_style (see column name list above).\n') + # this is not a very serious warning. + #no_warnings = False <--no need. commenting out + + + atomid = Intify(tokens[i_atomid]) + atomtype = Intify(tokens[i_atomtype]) + + molid = None + if i_molid: + molid = Intify(tokens[i_molid]) + + atomid2type[atomid] = atomtype + if i_molid: + atomid2mol[atomid] = molid + + + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + + tokens[i_atomid] = '$atom:id'+tokens[i_atomid] + #tokens[i_atomid] = '$atom:'+atomids_int2name[atomid] + # fill atomtype_int2str[] with a default name (change later): + #tokens[i_atomtype] = '@atom:type'+tokens[i_atomtype] + atomtype = int(tokens[i_atomtype]) + atomtype_name = 'type'+tokens[i_atomtype] + atomtypes_int2name[atomtype] = atomtype_name + tokens[i_atomtype] = '@atom:'+atomtype_name + + # I can't use atomids_int2names or atomtypes_int2names yet + # because they probably have not been defined yet. + # (Instead assign these names in a later pass.) + + if i_molid: + tokens[i_molid] = '$mol:id'+tokens[i_molid] + l_data_atoms.append((' '*indent)+(' '.join(tokens)+'\n')) + needed_atomids.add(atomid) + needed_atomtypes.add(int(atomtype)) + + for atomtype in needed_atomtypes: + if type(atomtype) is int: + if ((min_needed_atomtype == None) or + (min_needed_atomtype > atomtype)): + min_needed_atomtype = atomtype + if ((max_needed_atomtype == None) or + (max_needed_atomtype < atomtype)): + max_needed_atomtype = atomtype + + + elif (line.strip() == 'Masses'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + # Read the next line of text but don't skip comments + comment_char_backup = lex.commenters + lex.commenters = '' + line_orig = lex.ReadLine() + lex.commenters = comment_char_backup + + comment_text = '' + ic = line_orig.find('#') + line = line_orig[:ic] + if ic != -1: + comment_text = line_orig[ic+1:].strip() + + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + + tokens = line.strip().split() + if len(tokens) > 0: + atomtype = Intify(tokens[0]) + atomtype_name = str(atomtype) + + if comment_text != '': + comment_tokens = comment_text.split() + # Assume the first word after the # is the atom type name + atomtype_name = comment_tokens[0] + + if BelongsToSel(atomtype, atomtype_selection): + #tokens[0] = '@atom:type'+tokens[0] + l_data_masses.append((' '*indent)+(' '.join(tokens)+'\n')) + # infer atom type names from comment strings? + if infer_types_from_comments: + if atomtype_name in atomtypes_name2int: + raise InputError('Error: duplicate atom type names in mass section: \"'+atomtype_name+'\"\n' + ' (By default '+g_program_name+' attempts to infer atom type names from\n' + ' comments which appear in the \"Masses\" section of your data file.)\n' + ' You can avoid this error by adding the \"-ignore-comments\" argument.\n') + atomtypes_name2int[atomtype_name] = atomtype + atomtypes_int2name[atomtype] = atomtype_name + else: + atomtypes_int2name[atomtype] = 'type'+str(atomtype) + + + elif (line.strip() == 'Velocities'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + #tokens[0] = '$atom:id'+tokens[0] + tokens[0] = '$atom:'+atomids_int2name[atomid] + l_data_velocities.append((' '*indent)+(' '.join(tokens)+'\n')) + + # non-point-like-particles: + elif (line.strip() == 'Ellipsoids'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + #tokens[0] = '$atom:id'+tokens[0] + tokens[0] = '$atom:'+atomids_int2name[atomid] + l_data_ellipsoids.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (line.strip() == 'Lines'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + #tokens[0] = '$atom:id'+tokens[0] + tokens[0] = '$atom:'+atomids_int2name[atomid] + l_data_lines.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (line.strip() == 'Triangles'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + #tokens[0] = '$atom:id'+tokens[0] + tokens[0] = '$atom:'+atomids_int2name[atomid] + l_data_triangles.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Bonds'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 4): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Bonds section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$bond:id'+tokens[0] + #tokens[1] = '@bond:type'+tokens[1] + atomids = [None, None] + atomtypes = [None, None] + molids = [None, None] + in_selections = True + some_in_selection = False + for n in range(0,2): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_bonds.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS BONDS\n') + sys.stderr.write(' (between atom ids: ') + + for n in range(0,2): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected are bonded\n' + ' to other atoms you didn\'t select.\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + + elif (line.strip() == 'Angles'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line == '': + break + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 5): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Angles section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$angle:id'+tokens[0] + #tokens[1] = '@angle:type'+tokens[1] + atomids = [None, None, None] + atomtypes = [None, None, None] + molids = [None, None, None] + in_selections = True + some_in_selection = False + for n in range(0,3): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_angles.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS ANGLES\n') + sys.stderr.write(' (between atom ids: ') + for n in range(0,3): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected participate in 3-body \"Angle\"\n' + ' interactions with other atoms you didn\'t select.\n' + ' (They will be ignored.)\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + elif (line.strip() == 'Dihedrals'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 6): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Dihedrals section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$dihedral:id'+tokens[0] + #tokens[1] = '@dihedral:type'+tokens[1] + atomids = [None, None, None, None] + atomtypes = [None, None, None, None] + molids = [None, None, None, None] + in_selections = True + some_in_selection = False + for n in range(0,4): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_dihedrals.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS DIHEDRALS\n') + sys.stderr.write(' (between atom ids: ') + for n in range(0,4): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected participate in 4-body \"Dihedral\"\n' + ' interactions with other atoms you didn\'t select.\n' + ' (They will be ignored.)\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + elif (line.strip() == 'Impropers'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 6): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Impropers section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$improper:id'+tokens[0] + #tokens[1] = '@improper:type'+tokens[1] + atomids = [None, None, None, None] + atomtypes = [None, None, None, None] + molids = [None, None, None, None] + in_selections = True + some_in_selection = False + for n in range(0,4): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_impropers.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS IMPROPERS\n') + sys.stderr.write(' (between atom ids: ') + for n in range(0,4): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected participate in 4-body \"Improper\"\n' + ' interactions with other atoms you didn\'t select.\n' + ' (They will be ignored.)\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + elif (line.strip() == 'Bond Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@bond:type'+tokens[0] + l_data_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Angle Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@angle:type'+tokens[0] + l_data_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Dihedral Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@dihedral:type'+tokens[0] + l_data_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Improper Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@improper:type'+tokens[0] + l_data_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Pair Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + some_pair_coeffs_read = True + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Pair Coeffs section:\n' + ' \"'+line.strip()+'\"\n') + atomtype_i_str = tokens[0] + if '*' in atomtype_i_str: + raise InputError('PROBLEM near or before '+ErrorLeader(infile, lineno)+'\n' + ' As of 2012-7, moltemplate forbids use of the "\*\" wildcard\n' + ' character in the \"Pair Coeffs\" section.\n') + else: + i = int(atomtype_i_str) + if ((not i) or + BelongsToSel(i, atomtype_selection)): + i_str = '@atom:type'+str(i) + tokens[0] = i_str + l_data_pair_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'pair_coeff'): + some_pair_coeffs_read = True + if (len(tokens) < 3): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical pair_coeff command:\n' + ' \"'+line.strip()+'\"\n') + l_in_pair_coeffs.append(' '*indent+line.strip()) + + elif (tokens[0] == 'mass'): + some_pair_coeffs_read = True + if (len(tokens) < 3): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical \"mass\" command:\n' + ' \"'+line.strip()+'\"\n') + l_in_masses.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'bond_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical bond_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@bond:type'+tokens[1] + l_in_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'angle_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical angle_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@angle:type'+tokens[1] + l_in_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'dihedral_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical dihedral_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@dihedral:type'+tokens[1] + l_in_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (tokens[0] == 'improper_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical improper_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@improper:type'+tokens[1] + l_in_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + + # -- class2 force fields -- + elif (line.strip() == 'BondBond Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@angle:type'+tokens[0] + l_data_bondbond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'BondAngle Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@angle:type'+tokens[0] + l_data_bondangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'MiddleBondTorsion Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_middlebondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'EndBondTorsion Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_endbondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'AngleTorsion Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_angletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'AngleAngleTorsion Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_angleangletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'BondBond13 Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_bondbond13_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'AngleAngle Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@improper:type'+tokens[0] + l_data_angleangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Angles By Type'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@angle:type'+tokens[0] + l_data_angles_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Dihedrals By Type'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_dihedrals_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Impropers By Type'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@improper:type'+tokens[0] + l_data_impropers_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) + + else: + sys.stderr.write(' Ignoring line \"'+line.strip()+'\"\n') + + sys.stderr.write('\n\n') + + sys.stderr.write(' processing \"Atoms\" section (') + + # post-processing: + + if len(l_data_masses) == 0: + infer_types_from_comments = False + + # Pass 1 through l_data_atoms: + # Now do a second-pass throught the "l_data_atoms" section, and + # finish dealing with "infer_types_from_comments". + # During this pass, peplace the atomtype names and atomid names with + # atom type names which were inferred from comments read earlier. + + sys.stderr.write('pass1') + for i in range(0, len(l_data_atoms)): + tokens = l_data_atoms[i].split() + atomid = tokens[i_atomid] + if atomid.find('$atom:') == 0: + atomid = atomid[6:] + # convert to an integer + atomid = Intify(atomid) + + if infer_types_from_comments: + atomtype = tokens[i_atomtype] + # remove the "@atom:" prefix (we will put it back later) + if atomtype.find('@atom:') == 0: + atomtype = atomtype[6:] + # convert to an integer + atomtype = Intify(atomtype) + atomtype_name = atomtypes_int2name[atomtype] + if atomtype in atomids_by_type: + l_atomids = atomids_by_type[atomtype] + prev_count = len(l_atomids) + # lookup the most recently added atom of this type: + #prev_atomid_name = l_atomids[-1] + #ic = prev_atomid_name.rfind('_') + #prev_count = int(prev_atomid_name[ic+1:]) + atomid_name = atomtype_name+'_'+str(prev_count+1) + atomids_by_type[atomtype].append(atomid) + else: + atomids_by_type[atomtype] = [atomid] + atomid_name = atomtype_name+'_1' + atomids_int2name[atomid] = atomid_name + #atomids_name2str[atomid_name] = atomid + else: + atomids_int2name[atomid] = 'id'+str(atomid) + + sys.stderr.write(', pass2') + # Pass 2: If any atom types only appear once, simplify their atomid names. + for i in range(0, len(l_data_atoms)): + tokens = l_data_atoms[i].split() + + # remove the "@atom:" prefix (we will put it back later) + atomtype = tokens[i_atomtype] + if atomtype.find('@atom:') == 0: + atomtype = atomtype[6:] + atomtype = Intify(atomtype) + if infer_types_from_comments: + if len(atomids_by_type[atomtype]) == 1: + atomid = tokens[i_atomid] + if atomid.find('$atom:') == 0: + atomid = atomid[6:] + atomid = Intify(atomid) + atomtype_name = atomtypes_int2name[atomtype] + atomids_int2name[atomid] = atomtype_name + + sys.stderr.write(', pass3') + # Pass 3: substitute the atomid names and atom type names into l_data_atoms + for i in range(0, len(l_data_atoms)): + tokens = l_data_atoms[i].split() + atomid = tokens[i_atomid] + if atomid.find('$atom:') == 0: + atomid = atomid[6:] + # convert to an integer + atomid = Intify(atomid) + atomtype = tokens[i_atomtype] + if atomtype.find('@atom:') == 0: + atomtype = atomtype[6:] + atomtype = Intify(atomtype) + tokens = l_data_atoms[i].split() + tokens[i_atomid] = '$atom:'+atomids_int2name[atomid] + tokens[i_atomtype] = '@atom:'+atomtypes_int2name[atomtype] + l_data_atoms[i] = (' '*indent)+(' '.join(tokens)+'\n') + sys.stderr.write(')\n') + + + if len(l_data_atoms) == 0: + raise InputError('Error('+g_program_name+'): You have no atoms in you selection!\n' + '\n' + ' Either you have chosen a set of atoms, molecules, or atom types which\n' + ' does not exist, or there is a problem with (the format of) your\n' + ' arguments. Check the documentation and examples.\n') + + + # --- Now delete items that were not selected from the other lists --- + + # --- MASSES --- + + # delete masses for atom types we don't care about anymore: + i_line = 0 + while i_line < len(l_data_masses): + line = l_data_masses[i_line] + tokens = line.strip().split() + atomtype = Intify(tokens[0]) + if ((not (atomtype in needed_atomtypes)) and + (not ((len(atomtype_selection) > 0) and + BelongsToSel(atomtype, atomtype_selection)))): + del(l_data_masses[i_line]) + else: + atomtype_name = atomtypes_int2name[atomtype] + tokens[0] = '@atom:'+atomtype_name + l_data_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + + + # --- PAIR COEFFS --- + + # delete data_pair_coeffs for atom types we don't care about anymore: + i_line = 0 + while i_line < len(l_data_pair_coeffs): + line = l_data_pair_coeffs[i_line] + tokens = line.strip().split() + assert(len(tokens) > 0) + split_colon = tokens[0].split(':') + assert(len(split_colon) == 2) + atomtype = Intify(split_colon[1]) + if ((not (atomtype in needed_atomtypes)) and + (not ((len(atomtype_selection) > 0) and + BelongsToSel(atomtype, atomtype_selection)))): + del(l_data_pair_coeffs[i_line]) + else: + i_line += 1 + + # delete in_pair_coeffs for atom we don't care about anymore: + i_line = 0 + while i_line < len(l_in_pair_coeffs): + line = l_in_pair_coeffs[i_line] + tokens = line.strip().split() + atomtype_i_str = tokens[1] + atomtype_j_str = tokens[2] + #if (('*' in atomtype_i_str) or + # ('*' in atomtype_j_str)): + # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n' + # ' pair_coeff command contains a \"*\" character.\n' + # ' Keep in mind that using moltemplate.sh you can manually change the\n' + # ' numbers assigned to each atom type (when using -a or -b). Make sure\n' + # ' nor to accidentally change the order of atom types in one of these\n' + # ' pair_coeff commands. For example, commands like\n' + # ' pair_coeff 10*4 20*10 0.15 3.6\n' + # ' can be generated by moltemplate.sh, however\n' + # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n' + # ' pair_coeff 4*10 10*20 0.15 3.6)\n' + # ' Later on, you may want to check to make sure moltemplate.sh\n' + # ' is not doing this. (Fortunately you never have to worry unless\n' + # ' you are using the -a or -b arguments with moltemplate.sh)\n') + + if ('*' in atomtype_i_str): + atomtype_i_tokens = atomtype_i_str.split('*') + + if atomtype_i_tokens[0] == '': + if (min_sel_atomtype and + (min_sel_atomtype < min_needed_atomtype)): + i_a = min_sel_atomtype + else: + i_a = min_needed_atomtype + else: + i_a = Intify(atomtype_i_tokens[0]) + + if atomtype_i_tokens[1] == '': + if (max_sel_atomtype and + (max_sel_atomtype > max_needed_atomtype)): + i_b = max_sel_atomtype + else: + i_b = max_needed_atomtype + else: + i_b = Intify(atomtype_i_tokens[1]) + + else: + i_a = i_b = Intify(atomtype_i_str) + + i_a_final = None + i_b_final = None + for i in range(i_a, i_b+1): + if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): + i_a_final = i + break + for i in reversed(range(i_a, i_b+1)): + if ((i in needed_atomtypes) or (max_sel_atomtype >= i)): + i_b_final = i + break + + #if i_a_final and i_b_final: + # if i_a_final == i_b_final: + # i_str = '@atom:type'+str(i_a_final) + # tokens[1] = i_str + # else: + # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}' + + + + if ('*' in atomtype_j_str): + atomtype_j_tokens = atomtype_j_str.split('*') + + if atomtype_j_tokens[0] == '': + if (min_sel_atomtype and + (min_sel_atomtype < min_needed_atomtype)): + j_a = min_sel_atomtype + else: + j_a = min_needed_atomtype + else: + j_a = Intify(atomtype_j_tokens[0]) + + if atomtype_j_tokens[1] == '': + if (max_sel_atomtype and + (max_sel_atomtype > max_needed_atomtype)): + j_b = max_sel_atomtype + else: + j_b = max_needed_atomtype + else: + j_b = Intify(atomtype_j_tokens[1]) + + else: + j_a = j_b = Intify(atomtype_j_str) + + j_a_final = None + j_b_final = None + for j in range(j_a, j_b+1): + if ((j in needed_atomtypes) or (min_sel_atomtype <= j)): + j_a_final = j + break + for j in reversed(range(j_a, j_b+1)): + if ((j in needed_atomtypes) or (max_sel_atomtype >= j)): + j_b_final = j + break + + #if j_a_final and j_b_final: + # if j_a_final == j_b_final: + # j_str = '@atom:type'+str(j_a_final) + # tokens[1] = j_str + # else: + # j_str = '@{atom:type'+str(j_a_final)+'}*@{atom:type'+str(j_b_final)+'}' + + + + if not (i_a_final and i_b_final and j_a_final and j_b_final): + del(l_in_pair_coeffs[i_line]) + elif (('*' in atomtype_i_str) or ('*' in atomtype_j_str)): + del(l_in_pair_coeffs[i_line]) + for i in range(i_a_final, i_b_final+1): + for j in range(j_a_final, j_b_final+1): + if j >= i: + #tokens[1] = '@atom:type'+str(i) + #tokens[2] = '@atom:type'+str(j) + tokens[1] = '@atom:'+atomtypes_int2name[i] + tokens[2] = '@atom:'+atomtypes_int2name[j] + l_in_pair_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + #tokens[1] = '@atom:type'+tokens[1] + #tokens[2] = '@atom:type'+tokens[2] + tokens[1] = '@atom:'+atomtypes_int2name[int(tokens[1])] + tokens[2] = '@atom:'+atomtypes_int2name[int(tokens[2])] + l_in_pair_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + + + + # delete mass commands for atom types we don't care about anymore: + i_line = 0 + while i_line < len(l_in_masses): + line = l_in_masses[i_line] + tokens = line.strip().split() + atomtype_i_str = tokens[1] + #if (('*' in atomtype_i_str) or + # ('*' in atomtype_j_str)): + # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n' + # ' pair_coeff command contains a \"*\" character.\n' + # ' Keep in mind that using moltemplate.sh you can manually change the\n' + # ' numbers assigned to each atom type (when using -a or -b). Make sure\n' + # ' nor to accidentally change the order of atom types in one of these\n' + # ' pair_coeff commands. For example, commands like\n' + # ' pair_coeff 10*4 20*10 0.15 3.6\n' + # ' can be generated by moltemplate.sh, however\n' + # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n' + # ' pair_coeff 4*10 10*20 0.15 3.6)\n' + # ' Later on, you may want to check to make sure moltemplate.sh\n' + # ' is not doing this. (Fortunately you never have to worry unless\n' + # ' you are using the -a or -b arguments with moltemplate.sh)\n') + + if ('*' in atomtype_i_str): + atomtype_i_tokens = atomtype_i_str.split('*') + + if atomtype_i_tokens[0] == '': + if (min_sel_atomtype and + (min_sel_atomtype < min_needed_atomtype)): + i_a = min_sel_atomtype + else: + i_a = min_needed_atomtype + else: + i_a = Intify(atomtype_i_tokens[0]) + + if atomtype_i_tokens[1] == '': + if (max_sel_atomtype and + (max_sel_atomtype > max_needed_atomtype)): + i_b = max_sel_atomtype + else: + i_b = max_needed_atomtype + else: + i_b = Intify(atomtype_i_tokens[1]) + + else: + i_a = i_b = Intify(atomtype_i_str) + + i_a_final = None + i_b_final = None + for i in range(i_a, i_b+1): + if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): + i_a_final = i + break + for i in reversed(range(i_a, i_b+1)): + if ((i in needed_atomtypes) or (max_sel_atomtype >= i)): + i_b_final = i + break + #if i_a_final and i_b_final: + # if i_a_final == i_b_final: + # i_str = '@atom:type'+str(i_a_final) + # tokens[1] = i_str + # else: + # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}' + + if not (i_a_final and i_b_final and j_a_final and j_b_final): + del(l_in_masses[i_line]) + elif ('*' in atomtype_i_str): + del(l_in_masses[i_line]) + for i in range(i_a_final, i_b_final+1): + #tokens[1] = '@atom:type'+str(i) + tokens[1] = '@atom:'+atomtypes_int2name[i] + # CONTINUEHERE: CHECK THAT THIS IS WORKING + l_in_masses.insert(i_line, (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + assert(i_a == i_b) + #tokens[1] = '@atom:type'+str(i_a) + tokens[1] = '@atom:'+atomtypes_int2name[i_a] + # CONTINUEHERE: CHECK THAT THIS IS WORKING + l_in_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + + + + # --- BONDS AND BOND COEFFS --- + + # delete lines from data_bonds if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_bonds): + line = l_data_bonds[i_line] + tokens = line.strip().split() + assert(len(tokens) == 4) + + bondid = Intify(tokens[0]) + bondtype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$bond:id'+str(bondid) + tokens[1] = '@bond:type'+str(bondtype) + #tokens[2] = '$atom:id'+str(atomid1) + #tokens[3] = '$atom:id'+str(atomid2) + tokens[2] = '$atom:'+atomids_int2name[atomid1] + tokens[3] = '$atom:'+atomids_int2name[atomid2] + needed_bondids.add(bondid) + needed_bondtypes.add(bondtype) + l_data_bonds[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_bonds[i_line]) + + # delete data_bond_coeffs for bondtypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_bond_coeffs): + line = l_data_bond_coeffs[i_line] + tokens = line.strip().split() + bondtype = Intify(tokens[0]) + if (not (bondtype in needed_bondtypes)): + del(l_data_bond_coeffs[i_line]) + else: + tokens[0] = '@bond:type'+str(bondtype) + l_data_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_bond_coeffs for bondtypes we don't care about anymore: + for bondtype in needed_bondtypes: + if type(bondtype) is int: + if ((min_needed_bondtype == None) or + (min_needed_bondtype > bondtype)): + min_needed_bondtype = bondtype + if ((max_needed_bondtype == None) or + (max_needed_bondtype < bondtype)): + max_needed_bondtype = bondtype + i_line = 0 + while i_line < len(l_in_bond_coeffs): + line = l_in_bond_coeffs[i_line] + tokens = line.strip().split() + bondtype_str = tokens[1] + + if ('*' in bondtype_str): + bondtype_tokens = bondtype_str.split('*') + + if bondtype_tokens[0] == '': + i_a = min_needed_bondtype + else: + i_a = Intify(bondtype_tokens[0]) + + if bondtype_tokens[1] == '': + i_b = max_needed_bondtype + else: + i_b = Intify(bondtype_tokens[1]) + + else: + i_a = Intify(bondtype_str) + i_b = i_a + + if i_a < min_needed_bondtype: + i_a = min_needed_bondtype + if i_b > max_needed_bondtype: + i_b = max_needed_bondtype + + #if i_a == i_b: + # i_str = '@bond:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{bond:type'+str(j_a)+'}*@{bond:type'+str(j_b)+'}' + + if ('*' in bondtype_str): + del(l_in_bond_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_bondtypes): + tokens[1] = '@bond:type'+str(i) + l_in_bond_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + if i_a < i_b: + raise InputError('Error: number of bond types in data file is not consistent with the\n' + ' number of bond types you have define bond_coeffs for.\n') + if (i_a == i_b) and (i_a in needed_bondtypes): + tokens[1] = '@bond:type'+str(i_a) + l_in_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_bond_coeffs[i_line]) + + + + + + # --- ANGLES AND ANGLE COEFFS --- + + # delete lines from data_angles if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_angles): + line = l_data_angles[i_line] + tokens = line.strip().split() + assert(len(tokens) == 5) + + angleid = Intify(tokens[0]) + angletype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + atomid3 = Intify(tokens[4]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$angle:id'+str(angleid) + tokens[1] = '@angle:type'+str(angletype) + #tokens[2] = '$atom:id'+str(atomid1) + #tokens[3] = '$atom:id'+str(atomid2) + #tokens[4] = '$atom:id'+str(atomid3) + tokens[2] = '$atom:'+atomids_int2name[atomid1] + tokens[3] = '$atom:'+atomids_int2name[atomid2] + tokens[4] = '$atom:'+atomids_int2name[atomid3] + needed_angleids.add(angleid) + needed_angletypes.add(angletype) + l_data_angles[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_angles[i_line]) + + # delete data_angle_coeffs for angletypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_angle_coeffs): + line = l_data_angle_coeffs[i_line] + tokens = line.strip().split() + angletype = Intify(tokens[0]) + if (not (angletype in needed_angletypes)): + del(l_data_angle_coeffs[i_line]) + else: + tokens[0] = '@angle:type'+str(angletype) + l_data_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_angle_coeffs for angletypes we don't care about anymore: + for angletype in needed_angletypes: + if type(angletype) is int: + if ((min_needed_angletype == None) or + (min_needed_angletype > angletype)): + min_needed_angletype = angletype + if ((max_needed_angletype == None) or + (max_needed_angletype < angletype)): + max_needed_angletype = angletype + i_line = 0 + while i_line < len(l_in_angle_coeffs): + line = l_in_angle_coeffs[i_line] + tokens = line.strip().split() + angletype_str = tokens[1] + + if ('*' in angletype_str): + angletype_tokens = angletype_str.split('*') + + if angletype_tokens[0] == '': + i_a = min_needed_angletype + else: + i_a = Intify(angletype_tokens[0]) + + if angletype_tokens[1] == '': + i_b = max_needed_angletype + else: + i_b = Intify(angletype_tokens[1]) + + else: + i_a = i_b = Intify(angletype_str) + + if i_a < min_needed_angletype: + i_a = min_needed_angletype + if i_b > max_needed_angletype: + i_b = max_needed_angletype + + #if i_a == i_b: + # i_str = '@angle:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{angle:type'+str(j_a)+'}*@{angle:type'+str(j_b)+'}' + + if ('*' in angletype_str): + del(l_in_angle_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_angletypes): + tokens[1] = '@angle:type'+str(i) + l_in_angle_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + if i_a < i_b: + raise InputError('Error: number of angle types in data file is not consistent with the\n' + ' number of angle types you have define angle_coeffs for.\n') + if (i_a == i_b) and (i_a in needed_angletypes): + tokens[1] = '@angle:type'+str(i_a) + l_in_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_angle_coeffs[i_line]) + + + + # --- DIHEDRALS AND DIHEDRAL COEFFS --- + + # delete lines from data_dihedrals if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_dihedrals): + line = l_data_dihedrals[i_line] + tokens = line.strip().split() + assert(len(tokens) == 6) + + dihedralid = Intify(tokens[0]) + dihedraltype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + atomid3 = Intify(tokens[4]) + atomid4 = Intify(tokens[5]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$dihedral:id'+str(dihedralid) + tokens[1] = '@dihedral:type'+str(dihedraltype) + #tokens[2] = '$atom:id'+str(atomid1) + #tokens[3] = '$atom:id'+str(atomid2) + #tokens[4] = '$atom:id'+str(atomid3) + #tokens[5] = '$atom:id'+str(atomid4) + tokens[2] = '$atom:'+atomids_int2name[atomid1] + tokens[3] = '$atom:'+atomids_int2name[atomid2] + tokens[4] = '$atom:'+atomids_int2name[atomid3] + tokens[5] = '$atom:'+atomids_int2name[atomid4] + + needed_dihedralids.add(dihedralid) + needed_dihedraltypes.add(dihedraltype) + l_data_dihedrals[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_dihedrals[i_line]) + + # delete data_dihedral_coeffs for dihedraltypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_dihedral_coeffs): + line = l_data_dihedral_coeffs[i_line] + tokens = line.strip().split() + dihedraltype = Intify(tokens[0]) + if (not (dihedraltype in needed_dihedraltypes)): + del(l_data_dihedral_coeffs[i_line]) + else: + tokens[0] = '@dihedral:type'+str(dihedraltype) + l_data_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_dihedral_coeffs for dihedraltypes we don't care about anymore: + for dihedraltype in needed_dihedraltypes: + if type(dihedraltype) is int: + if ((min_needed_dihedraltype == None) or + (min_needed_dihedraltype > dihedraltype)): + min_needed_dihedraltype = dihedraltype + if ((max_needed_dihedraltype == None) or + (max_needed_dihedraltype < dihedraltype)): + max_needed_dihedraltype = dihedraltype + i_line = 0 + while i_line < len(l_in_dihedral_coeffs): + line = l_in_dihedral_coeffs[i_line] + tokens = line.strip().split() + dihedraltype_str = tokens[1] + + if ('*' in dihedraltype_str): + dihedraltype_tokens = dihedraltype_str.split('*') + + if dihedraltype_tokens[0] == '': + i_a = min_needed_dihedraltype + else: + i_a = Intify(dihedraltype_tokens[0]) + + if dihedraltype_tokens[1] == '': + i_b = max_needed_dihedraltype + else: + i_b = Intify(dihedraltype_tokens[1]) + + else: + i_a = i_b = Intify(dihedraltype_str) + + if i_a < min_needed_dihedraltype: + i_a = min_needed_dihedraltype + if i_b > max_needed_dihedraltype: + i_b = max_needed_dihedraltype + + #if i_a == i_b: + # i_str = '@dihedral:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{dihedral:type'+str(j_a)+'}*@{dihedral:type'+str(j_b)+'}' + + if ('*' in dihedraltype_str): + del(l_in_dihedral_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_dihedraltypes): + tokens[1] = '@dihedral:type'+str(i) + l_in_dihedral_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + if i_a < i_b: + raise InputError('Error: number of dihedral types in data file is not consistent with the\n' + ' number of dihedral types you have define bond_coeffs for.\n') + if (i_a == i_b) and (i_a in needed_dihedraltypes): + tokens[1] = '@dihedral:type'+str(i_a) + l_in_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_dihedral_coeffs[i_line]) + + + + # --- IMPROPERS AND IMPROPER COEFFS --- + + # delete lines from data_impropers if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_impropers): + line = l_data_impropers[i_line] + tokens = line.strip().split() + assert(len(tokens) == 6) + + improperid = Intify(tokens[0]) + impropertype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + atomid3 = Intify(tokens[4]) + atomid4 = Intify(tokens[5]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$improper:id'+str(improperid) + tokens[1] = '@improper:type'+str(impropertype) + #tokens[2] = '$atom:id'+str(atomid1) + #tokens[3] = '$atom:id'+str(atomid2) + #tokens[4] = '$atom:id'+str(atomid3) + #tokens[5] = '$atom:id'+str(atomid4) + tokens[2] = '$atom:'+atomids_int2name[atomid1] + tokens[3] = '$atom:'+atomids_int2name[atomid2] + tokens[4] = '$atom:'+atomids_int2name[atomid3] + tokens[5] = '$atom:'+atomids_int2name[atomid4] + + needed_improperids.add(improperid) + needed_impropertypes.add(impropertype) + l_data_impropers[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_impropers[i_line]) + + # delete data_improper_coeffs for impropertypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_improper_coeffs): + line = l_data_improper_coeffs[i_line] + tokens = line.strip().split() + impropertype = Intify(tokens[0]) + if (not (impropertype in needed_impropertypes)): + del(l_data_improper_coeffs[i_line]) + else: + tokens[0] = '@improper:type'+str(impropertype) + l_data_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_improper_coeffs for impropertypes we don't care about anymore: + for impropertype in needed_impropertypes: + if type(impropertype) is int: + if ((min_needed_impropertype == None) or + (min_needed_impropertype > impropertype)): + min_needed_impropertype = impropertype + if ((max_needed_impropertype == None) or + (max_needed_impropertype < impropertype)): + max_needed_impropertype = impropertype + i_line = 0 + while i_line < len(l_in_improper_coeffs): + line = l_in_improper_coeffs[i_line] + tokens = line.strip().split() + impropertype_str = tokens[1] + + if ('*' in impropertype_str): + impropertype_tokens = impropertype_str.split('*') + + if impropertype_tokens[0] == '': + i_a = min_needed_impropertype + else: + i_a = Intify(impropertype_tokens[0]) + + if impropertype_tokens[1] == '': + i_b = max_needed_impropertype + else: + i_b = Intify(impropertype_tokens[1]) + + else: + i_a = i_b = Intify(impropertype_str) + + if i_a < min_needed_impropertype: + i_a = min_needed_impropertype + if i_b > max_needed_impropertype: + i_b = max_needed_impropertype + + #if i_a == i_b: + # i_str = '@improper:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{improper:type'+str(j_a)+'}*@{improper:type'+str(j_b)+'}' + + if ('*' in impropertype_str): + del(l_in_improper_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_impropertypes): + tokens[1] = '@improper:type'+str(i) + l_in_improper_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + if i_a < i_b: + raise InputError('Error: number of improper types in data file is not consistent with the\n' + ' number of improper types you have define bond_coeffs for.\n') + if (i_a == i_b) and (i_a in needed_impropertypes): + tokens[1] = '@improper:type'+str(i_a) + l_in_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_improper_coeffs[i_line]) + + + + + + + + + if not some_pair_coeffs_read: + sys.stderr.write('Warning: No \"pair coeffs\" set.\n' + ' (No interactions between non-bonded atoms defined.)\n') + no_warnings = False + + #sys.stderr.write('Writing ttree data to standard out.\n' + # ' You can redirect this to a file using:\n'+ + # ' '+' '.join(sys.argv)+' > filename.ttree\n' + # ' ----------------------\n') + + if mol_name != '': + sys.stdout.write(mol_name + ' {\n') + + if len(l_in_init) > 0: + sys.stdout.write('\n### LAMMPS commands for initialization\n' + '### (These can be overridden later.)\n\n') + l_in_init.insert(0, (' '*cindent)+'write_once(\"'+in_init+'\") {\n') + l_in_init.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_init)) + if len(l_in_settings) > 0: + sys.stdout.write('\n### LAMMPS commands for settings\n' + '### (These can be overridden later.)\n\n') + l_in_settings.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_settings.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_settings)) + non_empty_output = True + if len(l_in_masses) > 0: + l_in_masses.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_masses.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_masses)) + non_empty_output = True + if len(l_in_pair_coeffs) > 0: + l_in_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_pair_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_pair_coeffs)) + non_empty_output = True + if len(l_in_bond_coeffs) > 0: + l_in_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_bond_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_bond_coeffs)) + non_empty_output = True + if len(l_in_angle_coeffs) > 0: + l_in_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_angle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_angle_coeffs)) + non_empty_output = True + if len(l_in_dihedral_coeffs) > 0: + l_in_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_dihedral_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_dihedral_coeffs)) + non_empty_output = True + if len(l_in_improper_coeffs) > 0: + l_in_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_improper_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_improper_coeffs)) + non_empty_output = True + + if non_empty_output: + sys.stdout.write('\n### DATA sections\n\n') + + if len(l_data_masses) > 0: + l_data_masses.insert(0, (' '*cindent)+'write_once(\"'+data_masses+'\") {\n') + l_data_masses.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_masses)) + non_empty_output = True + if len(l_data_bond_coeffs) > 0: + l_data_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bond_coeffs+'\") {\n') + l_data_bond_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bond_coeffs)) + non_empty_output = True + if len(l_data_angle_coeffs) > 0: + l_data_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angle_coeffs+'\") {\n') + l_data_angle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angle_coeffs)) + non_empty_output = True + if len(l_data_dihedral_coeffs) > 0: + l_data_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_dihedral_coeffs+'\") {\n') + l_data_dihedral_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_dihedral_coeffs)) + non_empty_output = True + if len(l_data_improper_coeffs) > 0: + l_data_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_improper_coeffs+'\") {\n') + l_data_improper_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_improper_coeffs)) + non_empty_output = True + if len(l_data_pair_coeffs) > 0: + l_data_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_pair_coeffs+'\") {\n') + l_data_pair_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_pair_coeffs)) + non_empty_output = True + + # class2 force fields: + if len(l_data_bondbond_coeffs) > 0: + l_data_bondbond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond_coeffs+'\") {\n') + l_data_bondbond_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bondbond_coeffs)) + non_empty_output = True + if len(l_data_bondangle_coeffs) > 0: + l_data_bondangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondangle_coeffs+'\") {\n') + l_data_bondangle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bondangle_coeffs)) + non_empty_output = True + if len(l_data_middlebondtorsion_coeffs) > 0: + l_data_middlebondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_middlebondtorsion_coeffs+'\") {\n') + l_data_middlebondtorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_middlebondtorsion_coeffs)) + non_empty_output = True + if len(l_data_endbondtorsion_coeffs) > 0: + l_data_endbondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_endbondtorsion_coeffs+'\") {\n') + l_data_endbondtorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_endbondtorsion_coeffs)) + non_empty_output = True + if len(l_data_angletorsion_coeffs) > 0: + l_data_angletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angletorsion_coeffs+'\") {\n') + l_data_angletorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angletorsion_coeffs)) + non_empty_output = True + if len(l_data_angleangletorsion_coeffs) > 0: + l_data_angleangletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangletorsion_coeffs+'\") {\n') + l_data_angleangletorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angleangletorsion_coeffs)) + non_empty_output = True + if len(l_data_bondbond13_coeffs) > 0: + l_data_bondbond13_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond13_coeffs+'\") {\n') + l_data_bondbond13_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bondbond13_coeffs)) + non_empty_output = True + if len(l_data_angleangle_coeffs) > 0: + l_data_angleangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangle_coeffs+'\") {\n') + l_data_angleangle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angleangle_coeffs)) + non_empty_output = True + + # automatic generation of bonded interactions by type: + if len(l_data_angles_by_type) > 0: + l_data_angles_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_angles_by_type+'\") {\n') + l_data_angles_by_type.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angles_by_type)) + non_empty_output = True + if len(l_data_dihedrals_by_type) > 0: + l_data_dihedrals_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_dihedrals_by_type+'\") {\n') + l_data_dihedrals_by_type.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_dihedrals_by_type)) + non_empty_output = True + if len(l_data_impropers_by_type) > 0: + l_data_impropers_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_impropers_by_type+'\") {\n') + l_data_impropers_by_type.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_impropers_by_type)) + non_empty_output = True + + if len(l_data_atoms) > 0: + l_data_atoms.insert(0, (' '*cindent)+'write(\"'+data_atoms+'\") {\n') + l_data_atoms.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_atoms)) + non_empty_output = True + else: + sys.stderr.write('Warning: missing \"Atoms\" section.\n' + ' (Did you include a LAMMPS data file in your argument list?)\n') + no_warnings = False + + # non-point-like particles + if len(l_data_ellipsoids) > 0: + l_data_ellipsoids.insert(0, (' '*cindent)+'write(\"'+data_ellipsoids+'\") {\n') + l_data_ellipsoids.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_ellipsoids)) + if len(l_data_lines) > 0: + l_data_lines.insert(0, (' '*cindent)+'write(\"'+data_lines+'\") {\n') + l_data_lines.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_lines)) + if len(l_data_triangles) > 0: + l_data_triangles.insert(0, (' '*cindent)+'write(\"'+data_triangles+'\") {\n') + l_data_triangles.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_triangles)) + + if len(l_data_velocities) > 0: + l_data_velocities.insert(0, (' '*cindent)+'write(\"'+data_velocities+'\") {\n') + l_data_velocities.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_velocities)) + if len(l_data_bonds) > 0: + l_data_bonds.insert(0, (' '*cindent)+'write(\"'+data_bonds+'\") {\n') + l_data_bonds.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bonds)) + non_empty_output = True + if len(l_data_angles) > 0: + l_data_angles.insert(0, (' '*cindent)+'write(\"'+data_angles+'\") {\n') + l_data_angles.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angles)) + non_empty_output = True + if len(l_data_dihedrals) > 0: + l_data_dihedrals.insert(0, (' '*cindent)+'write(\"'+data_dihedrals+'\") {\n') + l_data_dihedrals.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_dihedrals)) + non_empty_output = True + if len(l_data_impropers) > 0: + l_data_impropers.insert(0, (' '*cindent)+'write(\"'+data_impropers+'\") {\n') + l_data_impropers.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_impropers)) + non_empty_output = True + + if mol_name != '': + sys.stdout.write('\n} # end of \"'+mol_name+'\" type definition\n') + + #if non_empty_output and no_warnings: + if non_empty_output: + sys.stderr.write('\nWARNING: The '+g_program_name+' script has not been rigorously tested.\n' + ' Exotic (many-body) pair-styles and pair-styles with\n' + ' unusual syntax (such as hbond/dreiding) are not understood\n' + ' by '+g_program_name+' (...although they are supported by moltemplate).\n' + ' Please look over the resulting LT file and check for errors.\n' + ' Convert any remaining atom, bond, angle, dihedral, or improper id\n' + ' or type numbers to the corresponding $ or @-style counter variables.\n' + ' Feel free to report any bugs you find.\n' + ' (-Andrew Jewett 2013-8-14)\n') + +except (ValueError, InputError) as err: + sys.stderr.write('\n'+str(err)+'\n') + sys.exit(-1) diff --git a/tools/moltemplate/src/lttree.py b/tools/moltemplate/src/lttree.py new file mode 100755 index 0000000000..5d1b34b7b0 --- /dev/null +++ b/tools/moltemplate/src/lttree.py @@ -0,0 +1,745 @@ +#!/usr/bin/env python + +# Author: Andrew Jewett (jewett.aij at g mail) +# http://www.chem.ucsb.edu/~sheagroup +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2011, Regents of the University of California +# All rights reserved. + +""" +lttree.py + +lttree.py is an extension of the generic ttree.py program. +This version can understand and manipulate ttree-style templates which +are specialized for storing molecule-specific data for use in LAMMPS. + +The main difference between lttree.py and ttree.py is: +Unlike ttree.py, lttree.py understands rigid-body movement commands like +"rot()" and "move()" which allows it to reorient and move each copy +of a molecule to a new location. (ttree.py just ignores these commands. +Consequently LAMMPS input file (fragments) created with ttree.py have +invalid (overlapping) atomic coordinates and must be modified or aguemted +later (by loading atomic coordinates from a PDB file or an XYZ file). +lttree.py understands the "Data Atoms" section of a LAMMPS +data file (in addition to the various "atom_styles" which effect it). + +Additional LAMMPS-specific features may be added in the future. + +""" + +import sys +from ttree import * +from lttree_styles import * +from ttree_matrix_stack import * + +try: + unicode +except NameError: + # Python 3 + basestring = unicode = str + + + + +class LttreeSettings(BasicUISettings): + def __init__(self, + user_bindings_x=None, + user_bindings=None, + order_method='by_command'): + + BasicUISettings.__init__(self, + user_bindings_x, + user_bindings, + order_method) + + # The following new member data indicate which columns store + # LAMMPS-specific information. + # The next 6 members store keep track of the different columns + # of the "Data Atoms" section of a LAMMPS data file: + self.column_names = [] #<--A list of column names (optional) + self.ii_coords=[] #<--A list of triplets of column indexes storing coordinate data + self.ii_vects=[] #<--A list of triplets of column indexes storing directional data + # (such as dipole or ellipsoid orientations) + self.i_atomid=None #<--An integer indicating which column has the atomid + self.i_atomtype=None #<--An integer indicating which column has the atomtype + self.i_molid=None #<--An integer indicating which column has the molid, if applicable + self.infile=None # Name of the outermost file. This is the file + # which was read at the moment parsing begins. + + + + +def LttreeParseArgs(argv, settings): + + BasicUIParseArgs(argv, settings) + + # Loop over the remaining arguments not processed yet. + # These arguments are specific to the lttree.py program + # and are not understood by ttree.py: + i = 1 + while i < len(argv): + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + if ((argv[i].lower() == '-atomstyle') or + (argv[i].lower() == '-atom-style') or + (argv[i].lower() == '-atom_style')): + if i+1 >= len(argv): + raise InputError('Error('+g_program_name+'): The '+argv[i]+' flag should be followed by a LAMMPS\n' + ' atom_style name (or single quoted string containing a space-separated\n' + ' list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n') + settings.column_names = AtomStyle2ColNames(argv[i+1]) + sys.stderr.write('\n \"'+data_atoms+'\" column format:\n') + sys.stderr.write(' '+(' '.join(settings.column_names))+'\n\n') + settings.ii_coords = ColNames2Coords(settings.column_names) + settings.ii_vects = ColNames2Vects(settings.column_names) + settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names) + del(argv[i:i+2]) + elif (argv[i].lower() == '-icoord'): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n' + ' corresponding to column numbers for coordinates in\n' + ' the \"'+data_atoms+'\" section of a LAMMPS data file.\n') + ilist = argv[i+1].split() + if (len(ilist) % 3) != 0: + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n' + ' This is usually a list of 3 integers, but it can contain more.\n' + ' The number of cooridnate columns must be divisible by 3,\n' + ' (even if the simulation is in 2 dimensions)\n') + settings.iaffinevects = [] + for i in range(0, len(ilist)/3): + cols = [int(ilist[3*i])+1, + int(ilist[3*i+1])+1, + int(ilist[3*i+2])+1] + settings.iaffinevects.append(cols) + del(argv[i:i+2]) + elif (argv[i].lower() == '-ivect'): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n' + ' corresponding to column numbers for direction vectors in\n' + ' the \"'+data_atoms+'\" section of a LAMMPS data file.\n') + ilist = argv[i+1].split() + if (len(ilist) % 3) != 0: + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n' + ' This is usually a list of 3 integers, but it can contain more.\n' + ' The number of cooridnate columns must be divisible by 3,\n' + ' (even if the simulation is in 2 dimensions)\n') + settings.ivects = [] + for i in range(0, len(ilist)/3): + cols = [int(ilist[3*i])+1, + int(ilist[3*i+1])+1, + int(ilist[3*i+2])+1] + settings.ivects.append(cols) + del(argv[i:i+2]) + elif ((argv[i].lower() == '-iatomid') or + (argv[i].lower() == '-iid') or + (argv[i].lower() == '-iatom-id')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' + ' LAMMPS data file contains the atom id number (typically 1).\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_atomid = int(argv[i+1])-1 + del(argv[i:i+2]) + elif ((argv[i].lower() == '-iatomtype') or + (argv[i].lower() == '-itype') or + (argv[i].lower() == '-iatom-type')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' + ' LAMMPS data file contains the atom type.\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_atomtype = int(argv[i+1])-1 + del(argv[i:i+2]) + elif ((argv[i].lower() == '-imolid') or + (argv[i].lower() == '-imol') or + (argv[i].lower() == '-imol-id') or + (argv[i].lower() == '-imoleculeid') or + (argv[i].lower() == '-imolecule-id')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' + ' LAMMPS data file contains the molecule id number.\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_molid = int(argv[i+1])-1 + del(argv[i:i+2]) + + elif ((argv[i][0] == '-') and (__name__ == "__main__")): + #elif (__name__ == "__main__"): + raise InputError('Error('+g_program_name+'):\n' + 'Unrecogized command line argument \"'+argv[i]+'\"\n') + else: + i += 1 + + + if __name__ == "__main__": + + # Instantiate the lexer we will be using. + # (The lexer's __init__() function requires an openned file. + # Assuming __name__ == "__main__", then the name of that file should + # be the last remaining (unprocessed) argument in the argument list. + # Otherwise, then name of that file will be determined later by the + # python script which imports this module, so we let them handle it.) + + if len(argv) == 1: + raise InputError('Error: This program requires at least one argument\n' + ' the name of a file containing ttree template commands\n') + elif len(argv) == 2: + try: + settings.lex = TemplateLexer(open(argv[1], 'r'), argv[1]) # Parse text from file + except IOError: + sys.stderr.write('Error: unable to open file\n' + ' \"'+argv[1]+'\"\n' + ' for reading.\n') + sys.exit(1) + del(argv[1:2]) + + else: + # if there are more than 2 remaining arguments, + problem_args = ['\"'+arg+'\"' for arg in argv[1:]] + raise InputError('Syntax Error('+g_program_name+'):\n\n' + ' Problem with argument list.\n' + ' The remaining arguments are:\n\n' + ' '+(' '.join(problem_args))+'\n\n' + ' (The actual problem may be earlier in the argument list.\n' + ' If these arguments are source files, then keep in mind\n' + ' that this program can not parse multiple source files.)\n' + ' Check the syntax of the entire argument list.\n') + + + + if len(settings.ii_coords) == 0: + sys.stderr.write('########################################################\n' + '## WARNING: atom_style unspecified ##\n' + '## --> \"'+data_atoms+'\" column data has an unknown format ##\n' + '## Assuming atom_style = \"full\" ##\n' + # '########################################################\n' + # '## To specify the \"'+data_atoms+'\" column format you can: ##\n' + # '## 1) Use the -atomstyle \"STYLE\" argument ##\n' + # '## where \"STYLE\" is a string indicating a LAMMPS ##\n' + # '## atom_style, including hybrid styles.(Standard ##\n' + # '## atom styles defined in 2011 are supported.) ##\n' + # '## 2) Use the -atomstyle \"COL_LIST\" argument ##\n' + # '## where \"COL_LIST" is a quoted list of strings ##\n' + # '## indicating the name of each column. ##\n' + # '## Names \"x\",\"y\",\"z\" are interpreted as ##\n' + # '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n' + # '## are interpreted as direction vectors. ##\n' + # '## 3) Use the -icoord \"cx cy cz...\" argument ##\n' + # '## where \"cx cy cz\" is a list of integers ##\n' + # '## indicating the column numbers for the x,y,z ##\n' + # '## coordinates of each atom. ##\n' + # '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n' + # '## where \"cmux cmuy cmuz...\" is a list of ##\n' + # '## integers indicating the column numbers for ##\n' + # '## the vector that determines the direction of a ##\n' + # '## dipole or ellipsoid (ie. a rotateable vector).##\n' + # '## (More than one triplet can be specified. The ##\n' + # '## number of entries must be divisible by 3.) ##\n' + '########################################################\n') + + # The default atom_style is "full" + settings.column_names = AtomStyle2ColNames('full') + settings.ii_coords = ColNames2Coords(settings.column_names) + settings.ii_vects = ColNames2Vects(settings.column_names) + settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names) + + + + + + + + + +def TransformAtomText(text, matrix): + """ Apply transformations to the coordinates and other vector degrees + of freedom stored in the \"Data Atoms\" section of a LAMMPS data file. + This is the \"text\" argument. + The \"matrix\" stores the aggregate sum of combined transformations + to be applied. + + """ + + #sys.stderr.write('matrix_stack.M = \n'+ MatToStr(matrix) + '\n') + + lines = text.split('\n') + + for i in range(0, len(lines)): + line_orig = lines[i] + ic = line_orig.find('#') + if ic != -1: + line = line_orig[:ic] + comment = ' '+line_orig[ic:].rstrip('\n') + else: + line = line_orig.rstrip('\n') + comment = '' + + columns = line.split() + if len(columns) > 0: + if len(columns) == len(settings.column_names)+3: + raise InputError('Error: lttree.py does not yet support integer unit-cell counters \n' + ' within the \"'+data_atoms+'\" section of a LAMMPS data file.\n' + ' Instead please add the appropriate offsets (these offsets\n' + ' should be multiples of the cell size) to the atom coordinates\n' + ' in the data file, and eliminate the extra columns. Then try again.\n' + ' (If you get this message often, email me and I\'ll fix this limitation.)') + if len(columns) < len(settings.column_names): + raise InputError('Error: The number of columns in your data file does not\n' + ' match the LAMMPS atom_style you selected.\n' + ' Use the -atomstyle