mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10210 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
da71a6b973
commit
7206633474
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Stephanie Teich-McGoldrick (Sandai) is the current maintainer
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of the msi2lmp tool. She can be contacted at steichm at sandia.gov
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1 Jul 2013
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Cleanup and improved port to windows.
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Removed some more static string limits.
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Added print level 3 for additional output.
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Make code stop at missing force field parameters
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and added -i flag to override this.
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Safer argument checking.
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Provide short versions for all flags.
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23 Sep 2011
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added support for triclinic boxes
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see msi2lmp/TriclinicModification.pdf doc for details
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-----------------------------
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msi2lmp V3.6 4/10/2005
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This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
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program to produce a LAMMPS data file.
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1. Building msi2lmp3
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Use the Makefile in the src directory. It is
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currently set up for gcc. One will have to modify
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it to use a different compiler.
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2. Testing the program
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There are three pairs (.car and .mdf) files in the
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test directory: crambin, nylon and phen3_cff97. The
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atom types in crambin and nylon are cvff (Class I) atom
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types and those in phen3_cff97 are cff9x (Class II) atom types.
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Two forcefield files, cvff.frc and cff91.frc, are needed
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generate lammps data files for these three test files. To
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run it you would:
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% setenv BIOSYM_LIBRARY ../biosym_frc_files
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% ../src/msi2lmp.exe nylon -class I -frc cvff > data.nylon
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% ../src/msi2lmp.exe crambin -class I -frc cvff > data.crambin
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% ../src/msi2lmp.exe phen3_cff97 -class II -frc cff91 > data.phen3_cff97
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Three files should be generated: data.nylon, data.crambin
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and data.phen3_cff97. These can be compared against
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data.x in the directory correct. If there are differences,
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first recompile the program with no optimization and try again.
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If there are still differences, send email to jec@mayo.edu
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Note: you will see many "Unable to find..." parameters messages
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in the phen3_cff97 test case. Most of those parameters
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exist in cff95.frc, but not in cff91.frc
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3. To run the program
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The program is started by supplying information at the command prompt
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according to the usage described below.
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USAGE: msi2lmp.exe ROOTNAME {-2001} {-print #} {-class #} {-frc FRC_FILE}
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-- msi2lmp.exe is the name of the executable
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-- ROOTNAME is the base name of the .car and .mdf files
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-- -2001
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Output lammps files for LAMMPS version 2001 (F90 version)
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Default is to write output for the C++ version of LAMMPS
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-- -print (or -p)
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# is the print level 0 - silent except for error messages
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1 - minimal (default)
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2 - verbose (usual for developing and
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checking new data files for consistency)
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3 - even more verbose (additional debug info)
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-- -ignore (or -i) ignore errors about missing force field parameters
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and treat them as warnings instead.
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-- -class (or -c)
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# is the class of forcefield to use (I or 1 = Class I e.g., CVFF)
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(II or 2 = Class II e.g., CFFx)
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default is -class I
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-- -frc (or -f) specifies name of the forcefield file (e.g., cff91)
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If the file name includes a directory component (or drive letter on Windows),
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then the name is used as is. Otherwise, the program looks for the forcefield
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file in $BIOSYM_LIBRARY (or %BIOSYM_LIBRARY% on Windows).
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If $BIOSYM_LIBRARY is not set, ../biosym_frc_files is used (for testing).
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If the file name does not end in .frc, then .frc is appended to the name.
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For example, -frc cvff (assumes cvff.frc is in $BIOSYM_LIBRARY
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or ../biosym_frc_files)
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-frc cff/cff91 (assumes cff91.frc is in cff)
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-frc /usr/local/biosym/forcefields/cff95
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(assumes cff95.frc is in /usr/local/biosym/forcefields/)
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By default, the program uses $BIOSYM_LIBRARY/cvff.frc or ../biosym_frc_files/cvff.frc
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-- the LAMMPS data file is written to ROOTNAME.lammps{01/05},
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protocol and error information is written to the screen.
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****************************************************************
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*
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* Msi2lmp3
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*
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* This is the third version of a program that generates a LAMMPS
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* data file based on the information in MSI .car (atom
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* coordinates), .mdf (molecular topology) and .frc (forcefield)
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* files. The .car and .mdf files are specific to a molecular
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* system while the .frc file is specific to a forcefield version.
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* The only coherency needed between .frc and .car/.mdf files are
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* the atom types.
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*
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* The first version was written by Steve Lustig at Dupont, but
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* required using Discover to derive internal coordinates and
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* forcefield parameters
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*
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* The second version was written by Michael Peachey while an
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* intern in the Cray Chemistry Applications Group managed
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* by John Carpenter. This version derived internal coordinates
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* from the mdf file and looked up parameters in the frc file
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* thus eliminating the need for Discover.
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*
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* The third version was written by John Carpenter to optimize
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* the performance of the program for large molecular systems
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* (the original code for deriving atom numbers was quadratic in time)
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* and to make the program fully dynamic. The second version used
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* fixed dimension arrays for the internal coordinates.
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*
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* The current maintainer is only reluctantly doing so because John Mayo no longer
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* needs this code.
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*
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* V3.2 corresponds to adding code to MakeLists.c to gracefully deal with
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* systems that may only be molecules of 1 to 3 atoms. In V3.1, the values
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* for number_of_dihedrals, etc. could be unpredictable in these systems.
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*
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* V3.3 was generated in response to a strange error reading a MDF file generated by
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* Accelys' Materials Studio GUI. Simply rewriting the input part of ReadMdfFile.c
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* seems to have fixed the problem.
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*
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* V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car and .mdf files
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* written by Accelys' Materials Studio GUI.
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*
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* V3.6 outputs to LAMMPS 2005 (C++ version).
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*
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* Contact: Kelly L. Anderson, kelly.anderson@cantab.net
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*
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* April 2005
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Binary file not shown.
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@ -0,0 +1,5 @@
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Copy cvff.frc and cff9*.frc or any other
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.frc files you have licensed to this
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directory for use with msi2lmp.
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,154 @@
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!CLAYFF forcefield
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#atom_types cvff
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!Ver Ref Type Mass Element Connections Comment
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!---- --- ---- ---------- ------- -----------------------------------------
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1.0 1 st 28.08550 Si 4
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1.0 1 ao 26.98154 Al 6
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1.0 1 at 26.98154 Al 4
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1.0 1 mgo 24.30500 Mg 6
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1.0 1 cao 40.08000 Ca 6
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1.0 1 feo 55.84700 Fe 6
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1.0 1 lio 6.941000 Li 6
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1.0 1 ob 15.99940 O 2
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1.0 1 obss 15.99940 O 3
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1.0 1 obts 15.99940 O 2
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1.0 1 obos 15.99940 O 2
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1.0 1 ohs 15.99940 O 2
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1.0 1 oh 15.99940 O 2
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1.0 1 oh- 15.99940 O 1
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1.0 1 o* 15.99940 O 2
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1.0 1 ho 1.007970 H 1
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1.0 1 h* 1.007970 H 1
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1.0 1 Na 22.99000 Na 0
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1.0 1 K 39.10 K 0
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1.0 1 Cs 132.9100 Cs 0
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1.0 1 Ca 40.07980 Ca 0
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1.0 1 Ba 137.3300 Ba 0
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1.0 1 Mg 24.3050 Mg 0
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1.0 1 Sr 87.6200 Sr 0
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1.0 1 Pb 207.2000 Pb 0
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1.0 1 Cl 35.45300 Cl 0
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#equivalence cvff
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> Equivalence table for any variant of cvff
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! Equivalences
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! -----------------------------------------
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!Ver Ref Type NonB Bond Angle Torsion OOP
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!---- --- ---- ---- ---- ----- ------- ----
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1.0 1 h h h h h h
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#auto_equivalence cvff_auto
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! Equivalences
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! -----------------------------------------
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!Ver Ref Type NonB Bond Bond Angle Angle Torsion Torsion OOP OOP
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! Inct End atom Apex atom End Atoms Center Atoms End Atom Center Atom
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!---- --- ---- ---- ------ ---- ---------- --------- --------- ----------- -------- -----------
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2.0 18 h h h h_ h_ h_ h_ h_ h_ h_
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#hbond_definition cvff
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#morse_bond cvff
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> E = D * (1 - exp(-ALPHA*(R - R0)))^2
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!Ver Ref I J R0 D ALPHA
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!---- --- ---- ---- ------- -------- -------
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2.3 23 no o- 1.2178 140.2486 2.0000
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#quadratic_bond cvff
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> E = K2 * (R - R0)^2
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!Ver Ref I J R0 K2
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!---- --- ---- ---- ------- --------
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2.1 28 oh ho 1.0000 553.9350
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2.1 28 ohs ho 1.0000 553.9350
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#quadratic_angle cvff
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> E = K2 * (Theta - Theta0)^2
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!Ver Ref I J K Theta0 K2
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!---- --- ---- ---- ---- -------- -------
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2.3 23 cp cp c' 120.0000 34.6799
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#torsion_1 cvff_auto
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> E = Kphi * [ 1 + cos(n*Phi - Phi0) ]
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!Ver Ref I J K L Kphi n Phi0
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!---- --- ---- ---- ---- ---- ------- ------ -------
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2.0 18 * c_ n3n_ * 0.0500 3 0.
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#out_of_plane cvff_auto
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> E = Kchi * [ 1 + cos(n*Chi - Chi0) ]
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!Ver Ref I J K L Kchi n Chi0
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!---- --- ---- ---- ---- ---- ------- ------ -------
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2.0 18 * c'_ * * 10.0000 2 180.0000
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#nonbond(12-6) cvff
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@type A-B
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@combination geometric
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> E = Aij/r^12 - Bij/r^6
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> where Aij = sqrt( Ai * Aj )
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> Bij = sqrt( Bi * Bj )
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|
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!Ver Ref I A B
|
||||
!---- --- ---- ----------- -----------
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||||
1.0 1 st 12.3645 0.00954
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1.0 1 ao 196.1446 0.03230
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1.0 1 at 12.3645 0.00954
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1.0 1 mgo 1636.3265 0.07688
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1.0 1 cao 17814.73 0.5987
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1.0 1 feo 702.54 0.0504
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1.0 1 lio 112.01 0.0201
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1.0 1 ob 629358.0000 625.50000
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||||
1.0 1 obss 629358.0000 625.50000
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||||
1.0 1 obts 629358.0000 625.50000
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1.0 1 obos 629358.0000 625.50000
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1.0 1 ohs 629358.0000 625.50000
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1.0 1 oh 629358.0000 625.50000
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||||
1.0 1 oh- 629358.0000 625.50000
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||||
1.0 1 o* 629358.0000 625.50000
|
||||
1.0 1 ho 0.00000001 0.00000
|
||||
1.0 1 h* 0.00000001 0.00000
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||||
1.0 1 Na 14763.1719 87.65132
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1.0 1 K 754506.86 549.37
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||||
1.0 1 Cs 3998193.96 1264.63
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1.0 1 Ca 125966.6068 224.46969
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1.0 1 Ba 1799606.56 582.25
|
||||
1.0 1 Mg 1369.00 69.22
|
||||
1.0 1 Sr 1185860.37 688.73
|
||||
1.0 1 Pb 861150.71 638.08
|
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1.0 1 Cl 21081006.97 2905.31
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||||
|
||||
|
||||
#bond_increments cvff
|
||||
|
||||
!Ver Ref I J DeltaIJ DeltaJI
|
||||
!---- --- ---- ---- ------- -------
|
||||
2.3 23 no o- 0.1684 -0.1684
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,2 @@
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VERSION
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elib
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,39 @@
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#include "msi2lmp.h"
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||||
|
||||
void CheckLists() {
|
||||
int i;
|
||||
|
||||
for (i=0; i < total_no_bonds; i++) {
|
||||
if ((atoms[bonds[i].members[0]].type != bondtypes[bonds[i].type].types[0])
|
||||
|| (atoms[bonds[i].members[1]].type != bondtypes[bonds[i].type].types[1])) {
|
||||
fprintf(stderr,"Warning atom types in bond %d are inconsistent with bond type %d\n",i,bonds[i].type);
|
||||
}
|
||||
}
|
||||
|
||||
for (i=0; i < total_no_angles;i++) {
|
||||
if ((atoms[angles[i].members[0]].type != angletypes[angles[i].type].types[0])
|
||||
|| (atoms[angles[i].members[1]].type != angletypes[angles[i].type].types[1])
|
||||
|| (atoms[angles[i].members[2]].type != angletypes[angles[i].type].types[2])) {
|
||||
fprintf(stderr,"Warning atom types in angle %d are inconsistent with angle type %d\n", i,angles[i].type);
|
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}
|
||||
}
|
||||
|
||||
for (i=0; i < total_no_dihedrals; i++) {
|
||||
if ((atoms[dihedrals[i].members[0]].type != dihedraltypes[dihedrals[i].type].types[0])
|
||||
|| (atoms[dihedrals[i].members[1]].type != dihedraltypes[dihedrals[i].type].types[1])
|
||||
|| (atoms[dihedrals[i].members[2]].type != dihedraltypes[dihedrals[i].type].types[2])
|
||||
|| (atoms[dihedrals[i].members[3]].type != dihedraltypes[dihedrals[i].type].types[3])) {
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||||
fprintf(stderr,"Warning atom types in dihedral %d are inconsistent with dihedral type %d\n",i,dihedrals[i].type);
|
||||
}
|
||||
}
|
||||
|
||||
for (i=0; i < total_no_oops; i++) {
|
||||
|
||||
if ((atoms[oops[i].members[0]].type != ooptypes[oops[i].type].types[0])
|
||||
|| (atoms[oops[i].members[1]].type != ooptypes[oops[i].type].types[1])
|
||||
|| (atoms[oops[i].members[2]].type != ooptypes[oops[i].type].types[2])
|
||||
|| (atoms[oops[i].members[3]].type != ooptypes[oops[i].type].types[3])) {
|
||||
fprintf(stderr,"Warning atom types in oop %d are inconsistent with oop type %d\n",i,oops[i].type);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,34 @@
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|||
/******************************
|
||||
*
|
||||
* This is the header file for the routine that reads the forcefield file
|
||||
* into memory in order to speed up searching.
|
||||
*
|
||||
* It defines the data structures used to store the force field in memory
|
||||
*/
|
||||
|
||||
#define MAX_NO_MEMS 5
|
||||
#define MAX_NO_PARAMS 8
|
||||
|
||||
struct FrcFieldData {
|
||||
float ver; /* Version number of forcefield entry */
|
||||
int ref; /* Reference within forcefield */
|
||||
char ff_types[MAX_NO_MEMS][5];
|
||||
double ff_param[MAX_NO_PARAMS];
|
||||
};
|
||||
|
||||
struct FrcFieldItem {
|
||||
char keyword[25];
|
||||
int number_of_members; /* number of members of item */
|
||||
int number_of_parameters; /* number of parameters of item */
|
||||
int entries; /* number of entries in item list */
|
||||
struct FrcFieldData *data; /* contains all eqiuv and param data */
|
||||
};
|
||||
|
||||
extern struct FrcFieldItem ff_atomtypes, equivalence, ff_vdw,ff_bond, ff_ang, ff_tor, ff_oop,
|
||||
ff_bonbon, ff_bonang, ff_angtor, ff_angangtor, ff_endbontor, ff_midbontor, ff_angang, ff_bonbon13;
|
||||
|
||||
/* prototypes */
|
||||
extern void InitializeItems(void);
|
||||
extern void SearchAndFill(struct FrcFieldItem *item);
|
||||
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||||
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File diff suppressed because it is too large
Load Diff
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|
@ -0,0 +1,122 @@
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|||
/*
|
||||
* This function fills in the keyword field, the number of members for each
|
||||
* item and the number of parameters for each item
|
||||
*
|
||||
*/
|
||||
|
||||
#include "msi2lmp.h"
|
||||
#include "Forcefield.h"
|
||||
|
||||
#include <string.h>
|
||||
|
||||
void InitializeItems(void)
|
||||
{
|
||||
/* ATOM TYPES */
|
||||
strcpy(ff_atomtypes.keyword,"#atom_types");
|
||||
ff_atomtypes.number_of_members = 1;
|
||||
ff_atomtypes.number_of_parameters = 1;
|
||||
|
||||
/* EQUIVALENCE */
|
||||
|
||||
strcpy(equivalence.keyword,"#equivalence");
|
||||
equivalence.number_of_members = 6;
|
||||
equivalence.number_of_parameters = 0;
|
||||
|
||||
/* NON-BOND */
|
||||
strcpy(ff_vdw.keyword,"#nonbond");
|
||||
ff_vdw.number_of_members = 1;
|
||||
ff_vdw.number_of_parameters = 2;
|
||||
|
||||
/* BOND */
|
||||
ff_bond.number_of_members = 2;
|
||||
if (forcefield == 1) {
|
||||
strcpy(ff_bond.keyword,"#quadratic_bond");
|
||||
ff_bond.number_of_parameters = 2;
|
||||
} else {
|
||||
strcpy(ff_bond.keyword,"#quartic_bond");
|
||||
ff_bond.number_of_parameters = 4;
|
||||
}
|
||||
|
||||
/* ANGLE */
|
||||
|
||||
ff_ang.number_of_members = 3;
|
||||
if (forcefield ==1) {
|
||||
strcpy(ff_ang.keyword,"#quadratic_angle");
|
||||
ff_ang.number_of_parameters = 2;
|
||||
} else {
|
||||
strcpy(ff_ang.keyword,"#quartic_angle");
|
||||
ff_ang.number_of_parameters = 4;
|
||||
}
|
||||
|
||||
/* TORSION */
|
||||
|
||||
ff_tor.number_of_members = 4;
|
||||
if (forcefield == 1) {
|
||||
strcpy(ff_tor.keyword,"#torsion_1");
|
||||
ff_tor.number_of_parameters = 3;
|
||||
} else {
|
||||
strcpy(ff_tor.keyword,"#torsion_3");
|
||||
ff_tor.number_of_parameters = 6;
|
||||
}
|
||||
|
||||
/* OOP */
|
||||
|
||||
ff_oop.number_of_members = 4;
|
||||
if (forcefield == 1) {
|
||||
strcpy(ff_oop.keyword,"#out_of_plane");
|
||||
ff_oop.number_of_parameters = 3;
|
||||
} else {
|
||||
strcpy(ff_oop.keyword,"#wilson_out_of_plane");
|
||||
ff_oop.number_of_parameters = 2;
|
||||
}
|
||||
|
||||
if (forcefield == 1) return; /* Do not try to read cross terms for Class I forcefield */
|
||||
|
||||
/* BOND-BOND */
|
||||
|
||||
strcpy(ff_bonbon.keyword,"#bond-bond");
|
||||
ff_bonbon.number_of_members = 3;
|
||||
ff_bonbon.number_of_parameters = 1;
|
||||
|
||||
/* BOND-ANGLE */
|
||||
|
||||
strcpy(ff_bonang.keyword,"#bond-angle");
|
||||
ff_bonang.number_of_members = 3;
|
||||
ff_bonang.number_of_parameters = 2;
|
||||
|
||||
/* ANGLE-TORSION */
|
||||
|
||||
strcpy(ff_angtor.keyword,"#angle-torsion_3");
|
||||
ff_angtor.number_of_members = 4;
|
||||
ff_angtor.number_of_parameters = 6;
|
||||
|
||||
/* ANGLE-ANGLE-TORSION */
|
||||
|
||||
strcpy(ff_angangtor.keyword,"#angle-angle-torsion_1");
|
||||
ff_angangtor.number_of_members = 4;
|
||||
ff_angangtor.number_of_parameters = 1;
|
||||
|
||||
/* END-BOND-TORSION */
|
||||
|
||||
strcpy(ff_endbontor.keyword,"#end_bond-torsion_3");
|
||||
ff_endbontor.number_of_members = 4;
|
||||
ff_endbontor.number_of_parameters = 6;
|
||||
|
||||
/* MID-BOND-TORSION */
|
||||
|
||||
strcpy(ff_midbontor.keyword,"#middle_bond-torsion_3");
|
||||
ff_midbontor.number_of_members = 4;
|
||||
ff_midbontor.number_of_parameters = 3;
|
||||
|
||||
/* ANGLE-ANGLE */
|
||||
|
||||
strcpy(ff_angang.keyword,"#angle-angle");
|
||||
ff_angang.number_of_members = 4;
|
||||
ff_angang.number_of_parameters = 1;
|
||||
|
||||
/* BOND-BOND-1-3 */
|
||||
|
||||
strcpy(ff_bonbon13.keyword,"#bond-bond_1_3");
|
||||
ff_bonbon13.number_of_members = 4;
|
||||
ff_bonbon13.number_of_parameters = 1;
|
||||
}
|
||||
|
|
@ -0,0 +1,785 @@
|
|||
|
||||
#include "msi2lmp.h"
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
static int count_bonds();
|
||||
static int count_angles();
|
||||
static int count_dihedrals();
|
||||
static int count_oops();
|
||||
static int count_angle_angles();
|
||||
|
||||
static void build_bonds_list();
|
||||
static void build_angles_list();
|
||||
static void build_dihedrals_list();
|
||||
static void build_oops_list();
|
||||
static void build_angleangles_list();
|
||||
|
||||
static void build_atomtypes_list();
|
||||
static void build_bondtypes_list();
|
||||
static void build_angletypes_list();
|
||||
static void build_dihedraltypes_list();
|
||||
static void build_ooptypes_list();
|
||||
static void build_angleangletypes_list();
|
||||
|
||||
static void swap_ints(int *,int *);
|
||||
static void bubble_sort(int, int *, int *);
|
||||
|
||||
void MakeLists()
|
||||
{
|
||||
|
||||
total_no_bonds = count_bonds();
|
||||
total_no_angles = count_angles();
|
||||
total_no_dihedrals = count_dihedrals();
|
||||
total_no_oops = count_oops();
|
||||
total_no_angle_angles = count_angle_angles();
|
||||
|
||||
|
||||
atomtypes = (struct AtomTypeList *)calloc(MAX_ATOM_TYPES,
|
||||
sizeof(struct AtomTypeList));
|
||||
if (atomtypes == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for atomtypes list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
build_atomtypes_list();
|
||||
|
||||
|
||||
if (total_no_bonds > 0) {
|
||||
bonds = (struct BondList *)calloc(total_no_bonds,sizeof(struct BondList));
|
||||
if (bonds == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for bonds list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
build_bonds_list();
|
||||
|
||||
bondtypes = (struct BondTypeList *)calloc(MAX_BOND_TYPES,
|
||||
sizeof(struct BondTypeList));
|
||||
if (bondtypes == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for bondtypes list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
build_bondtypes_list();
|
||||
}
|
||||
|
||||
if (total_no_angles > 0) {
|
||||
angles = (struct AngleList *)calloc(total_no_angles,
|
||||
sizeof(struct AngleList));
|
||||
if (angles == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for angles list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
build_angles_list();
|
||||
|
||||
angletypes = (struct AngleTypeList *)calloc(MAX_ANGLE_TYPES,
|
||||
sizeof(struct AngleTypeList));
|
||||
if (angletypes == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for angletypes list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
build_angletypes_list();
|
||||
}
|
||||
|
||||
if (total_no_dihedrals > 0) {
|
||||
|
||||
dihedrals = (struct DihedralList *)calloc(total_no_dihedrals,
|
||||
sizeof(struct DihedralList));
|
||||
if (dihedrals == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for dihedrals list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
build_dihedrals_list();
|
||||
|
||||
dihedraltypes = (struct DihedralTypeList *)calloc(MAX_DIHEDRAL_TYPES,
|
||||
sizeof(struct DihedralTypeList));
|
||||
if (dihedraltypes == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for dihedraltypes list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
build_dihedraltypes_list();
|
||||
}
|
||||
|
||||
if (total_no_oops > 0) {
|
||||
oops = (struct OOPList *)calloc(total_no_oops,sizeof(struct OOPList));
|
||||
if (oops == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for oops list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
build_oops_list();
|
||||
|
||||
ooptypes = (struct OOPTypeList *)calloc(MAX_OOP_TYPES,
|
||||
sizeof(struct OOPTypeList));
|
||||
if (ooptypes == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for ooptypes list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
build_ooptypes_list();
|
||||
}
|
||||
|
||||
if ((forcefield > 1) & (total_no_angle_angles > 0)) {
|
||||
|
||||
angleangles = (struct AngleAngleList *)calloc(total_no_angle_angles,
|
||||
sizeof(struct AngleAngleList));
|
||||
if (angleangles == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for angleangles list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
build_angleangles_list();
|
||||
|
||||
angleangletypes = (struct AngleAngleTypeList *)calloc(MAX_ANGLEANGLE_TYPES,
|
||||
sizeof(struct AngleAngleTypeList));
|
||||
if (angleangletypes == NULL) {
|
||||
fprintf(stderr,"Trouble allocating memory for angleangletypes list - Exiting\n");
|
||||
exit(1);
|
||||
}
|
||||
build_angleangletypes_list();
|
||||
}
|
||||
|
||||
|
||||
if (pflag > 2) {
|
||||
int i;
|
||||
fprintf(stderr,"Atom Types\n N Potential\n");
|
||||
for (i=0; i < no_atom_types; i++) {
|
||||
fprintf(stderr," %d %s\n",i,atomtypes[i].potential);
|
||||
}
|
||||
|
||||
fprintf(stderr,"Atoms\n");
|
||||
for (i=0; i < total_no_atoms; i++) {
|
||||
fprintf(stderr,"Atom %3d %2d %-5s %7.4f %9.6f %9.6f %9.6f\n",
|
||||
i,atoms[i].type,atoms[i].potential,atoms[i].q,
|
||||
atoms[i].x[0],atoms[i].x[1],atoms[i].x[2]);
|
||||
}
|
||||
|
||||
if (total_no_bonds > 0) {
|
||||
fprintf(stderr,"Bond Types\n");
|
||||
for (i=0; i < no_bond_types; i++) {
|
||||
fprintf(stderr," %d %d %d %-s %-s\n",i,bondtypes[i].types[0],
|
||||
bondtypes[i].types[1],
|
||||
atomtypes[bondtypes[i].types[0]].potential,
|
||||
atomtypes[bondtypes[i].types[1]].potential);
|
||||
}
|
||||
|
||||
fprintf(stderr,"Bonds\n N Type I J\n");
|
||||
for (i=0; i < total_no_bonds; i++) {
|
||||
fprintf(stderr," %d %d %d %d\n",i,bonds[i].type,
|
||||
bonds[i].members[0],
|
||||
bonds[i].members[1]);
|
||||
}
|
||||
}
|
||||
|
||||
if (total_no_angles > 0) {
|
||||
fprintf(stderr,"Angle Types\n");
|
||||
for (i=0; i < no_angle_types; i++) {
|
||||
fprintf(stderr," %d %d %d %d %-s %-s %-s\n",i,angletypes[i].types[0],
|
||||
angletypes[i].types[1],angletypes[i].types[2],
|
||||
atomtypes[angletypes[i].types[0]].potential,
|
||||
atomtypes[angletypes[i].types[1]].potential,
|
||||
atomtypes[angletypes[i].types[2]].potential);
|
||||
}
|
||||
|
||||
fprintf(stderr,"Angles\n N Type I J K\n");
|
||||
for (i=0; i < total_no_angles; i++) {
|
||||
fprintf(stderr," %d %d %d %d %d\n",i,angles[i].type,
|
||||
angles[i].members[0],
|
||||
angles[i].members[1],
|
||||
angles[i].members[2]);
|
||||
}
|
||||
}
|
||||
|
||||
if (total_no_dihedrals > 0) {
|
||||
fprintf(stderr,"Dihedral Types\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(stderr," %d %d %d %d %d %-s %-s %-s %-s\n",i,
|
||||
dihedraltypes[i].types[0],
|
||||
dihedraltypes[i].types[1],
|
||||
dihedraltypes[i].types[2],
|
||||
dihedraltypes[i].types[3],
|
||||
atomtypes[dihedraltypes[i].types[0]].potential,
|
||||
atomtypes[dihedraltypes[i].types[1]].potential,
|
||||
atomtypes[dihedraltypes[i].types[2]].potential,
|
||||
atomtypes[dihedraltypes[i].types[3]].potential);
|
||||
}
|
||||
|
||||
fprintf(stderr,"Dihedrals\n N Type I J K L\n");
|
||||
for (i=0; i < total_no_dihedrals; i++) {
|
||||
fprintf(stderr," %d %d %d %d %d %d\n",i,dihedrals[i].type,
|
||||
dihedrals[i].members[0],
|
||||
dihedrals[i].members[1],
|
||||
dihedrals[i].members[2],
|
||||
dihedrals[i].members[3]);
|
||||
}
|
||||
}
|
||||
|
||||
if (total_no_oops > 0) {
|
||||
fprintf(stderr,"Oop Types\n");
|
||||
for (i=0; i < no_oop_types; i++) {
|
||||
fprintf(stderr," %d %d %d %d %d %-s %-s %-s %-s\n",i,
|
||||
ooptypes[i].types[0],
|
||||
ooptypes[i].types[1],
|
||||
ooptypes[i].types[2],
|
||||
ooptypes[i].types[3],
|
||||
atomtypes[ooptypes[i].types[0]].potential,
|
||||
atomtypes[ooptypes[i].types[1]].potential,
|
||||
atomtypes[ooptypes[i].types[2]].potential,
|
||||
atomtypes[ooptypes[i].types[3]].potential);
|
||||
}
|
||||
|
||||
fprintf(stderr,"Oops\n N Type I J K L\n");
|
||||
for (i=0; i < total_no_oops; i++) {
|
||||
fprintf(stderr," %d %d %d %d %d %d\n",i,oops[i].type,
|
||||
oops[i].members[0],
|
||||
oops[i].members[1],
|
||||
oops[i].members[2],
|
||||
oops[i].members[3]);
|
||||
}
|
||||
}
|
||||
|
||||
if ((forcefield > 1) & (total_no_angle_angles > 0)) {
|
||||
|
||||
fprintf(stderr,"Angleangle Types\n");
|
||||
for (i=0; i < no_angleangle_types; i++) {
|
||||
fprintf(stderr," %d %d %d %d %d %-s %-s %-s %-s\n",i,
|
||||
angleangletypes[i].types[0],
|
||||
angleangletypes[i].types[1],
|
||||
angleangletypes[i].types[2],
|
||||
angleangletypes[i].types[3],
|
||||
atomtypes[angleangletypes[i].types[0]].potential,
|
||||
atomtypes[angleangletypes[i].types[1]].potential,
|
||||
atomtypes[angleangletypes[i].types[2]].potential,
|
||||
atomtypes[angleangletypes[i].types[3]].potential);
|
||||
}
|
||||
fprintf(stderr,"AngleAngles\n N Type I J K L\n");
|
||||
for (i=0; i < total_no_angle_angles; i++) {
|
||||
fprintf(stderr," %d %d %d %d %d %d\n",i,angleangles[i].type,
|
||||
angleangles[i].members[0],
|
||||
angleangles[i].members[1],
|
||||
angleangles[i].members[2],
|
||||
angleangles[i].members[3]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (pflag > 1) {
|
||||
fprintf(stderr,"\n");
|
||||
fprintf(stderr," Number of bonds, types = %7d %3d\n",
|
||||
total_no_bonds,no_bond_types);
|
||||
fprintf(stderr," Number of angles, types = %7d %3d\n",
|
||||
total_no_angles, no_angle_types);
|
||||
fprintf(stderr," Number of dihedrals, types = %7d %3d\n",
|
||||
total_no_dihedrals, no_dihedral_types);
|
||||
fprintf(stderr," Number of out-of-planes, types = %7d %3d\n",
|
||||
total_no_oops, no_oop_types);
|
||||
if (forcefield ==2)
|
||||
fprintf(stderr," Number of Angle Angle Terms, types = %7d %3d\n",
|
||||
total_no_angle_angles, no_angleangle_types);
|
||||
}
|
||||
}
|
||||
|
||||
int count_bonds()
|
||||
{
|
||||
int i,j,n;
|
||||
|
||||
for (n=0,i=0; i < total_no_atoms; i++) {
|
||||
for (j=0; j < atoms[i].no_connect; j++) {
|
||||
if (i < atoms[i].conn_no[j]) n++;
|
||||
}
|
||||
}
|
||||
return n;
|
||||
}
|
||||
|
||||
void build_bonds_list()
|
||||
{
|
||||
int i,j,n;
|
||||
|
||||
for (n=0,i=0; i < total_no_atoms; i++) {
|
||||
for (j=0; j < atoms[i].no_connect; j++) {
|
||||
if (i < atoms[i].conn_no[j]) {
|
||||
bonds[n ].type = 0;
|
||||
bonds[n ].members[0] = i;
|
||||
bonds[n++].members[1] = atoms[i].conn_no[j];
|
||||
}
|
||||
}
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
int count_angles()
|
||||
{
|
||||
int i,j,k,n;
|
||||
|
||||
for (n=0,j=0; j < total_no_atoms; j++) {
|
||||
if (atoms[j].no_connect > 1) {
|
||||
for (i=0; i < atoms[j].no_connect-1; i++) {
|
||||
for (k=i+1; k < atoms[j].no_connect; k++) {
|
||||
n++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
return n;
|
||||
}
|
||||
|
||||
void build_angles_list()
|
||||
{
|
||||
int i,j,k,n;
|
||||
|
||||
for (n=0,j=0; j < total_no_atoms; j++) {
|
||||
if (atoms[j].no_connect > 1) {
|
||||
for (i=0; i < atoms[j].no_connect-1; i++) {
|
||||
for (k=i+1; k < atoms[j].no_connect; k++) {
|
||||
angles[n ].type = 0;
|
||||
angles[n ].members[0] = atoms[j].conn_no[i];
|
||||
angles[n ].members[1] = j;
|
||||
angles[n++].members[2] = atoms[j].conn_no[k];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
int count_dihedrals()
|
||||
{
|
||||
int i,j,k,l,n;
|
||||
int ii,kk,ll;
|
||||
|
||||
for (n=0,j=0; j < total_no_atoms; j++) {
|
||||
if (atoms[j].no_connect > 1) {
|
||||
for (kk=0; kk < atoms[j].no_connect; kk++) {
|
||||
k = atoms[j].conn_no[kk];
|
||||
if (atoms[k].no_connect > 1) {
|
||||
if (j < k) {
|
||||
for (ii=0; ii < atoms[j].no_connect; ii++) {
|
||||
i = atoms[j].conn_no[ii];
|
||||
if (i != k) {
|
||||
for (ll=0; ll < atoms[k].no_connect; ll++) {
|
||||
l = atoms[k].conn_no[ll];
|
||||
if (l != j) n++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
return n;
|
||||
}
|
||||
|
||||
void build_dihedrals_list()
|
||||
{
|
||||
int i,j,k,l,n;
|
||||
int ii,kk,ll;
|
||||
|
||||
for (n=0,j=0; j < total_no_atoms; j++) {
|
||||
if (atoms[j].no_connect > 1) {
|
||||
for (kk=0; kk < atoms[j].no_connect; kk++) {
|
||||
k = atoms[j].conn_no[kk];
|
||||
if (atoms[k].no_connect > 1) {
|
||||
if (j < k) {
|
||||
for (ii=0; ii < atoms[j].no_connect; ii++) {
|
||||
i = atoms[j].conn_no[ii];
|
||||
if (i != k) {
|
||||
for (ll=0; ll < atoms[k].no_connect; ll++) {
|
||||
l = atoms[k].conn_no[ll];
|
||||
if (l != j) {
|
||||
dihedrals[n ].type = 0;
|
||||
dihedrals[n ].members[0] = i;
|
||||
dihedrals[n ].members[1] = j;
|
||||
dihedrals[n ].members[2] = k;
|
||||
dihedrals[n++].members[3] = l;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
int
|
||||
count_oops()
|
||||
{
|
||||
int j,n;
|
||||
|
||||
for (n=0,j=0; j < total_no_atoms; j++) {
|
||||
if (atoms[j].no_connect == 3) n++;
|
||||
}
|
||||
return n;
|
||||
}
|
||||
|
||||
void build_oops_list()
|
||||
{
|
||||
int j,n;
|
||||
|
||||
for (n=0,j=0; j < total_no_atoms; j++) {
|
||||
|
||||
if (atoms[j].no_connect == 3) {
|
||||
oops[n ].type = 0;
|
||||
oops[n ].members[0] = atoms[j].conn_no[0];
|
||||
oops[n ].members[1] = j;
|
||||
oops[n ].members[2] = atoms[j].conn_no[1];
|
||||
oops[n++].members[3] = atoms[j].conn_no[2];
|
||||
}
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
int count_angle_angles()
|
||||
{
|
||||
int num_triples[10] = {0,0,0,4,10,20,35,56,84,120};
|
||||
int j,n;
|
||||
|
||||
for (n=0,j=0; j < total_no_atoms; j++) {
|
||||
n += num_triples[atoms[j].no_connect-1];
|
||||
}
|
||||
return n;
|
||||
}
|
||||
|
||||
void build_angleangles_list()
|
||||
{
|
||||
int i,j,k,l,nc,n;
|
||||
|
||||
for (n=0,j=0; j < total_no_atoms; j++) {
|
||||
nc = atoms[j].no_connect;
|
||||
if (nc > 3) {
|
||||
for (i=0; i < nc-2; i++) {
|
||||
for (k=i+1; k < nc-1; k++) {
|
||||
for (l=k+1; l < nc; l++) {
|
||||
angleangles[n].type = 0;
|
||||
angleangles[n ].members[0] = atoms[j].conn_no[i];
|
||||
angleangles[n ].members[1] = j;
|
||||
angleangles[n ].members[2] = atoms[j].conn_no[k];
|
||||
angleangles[n++].members[3] = atoms[j].conn_no[l];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
|
||||
void build_atomtypes_list()
|
||||
{
|
||||
int j,k,n,match,atom_type=0;
|
||||
|
||||
strncpy(atomtypes[0].potential,atoms[0].potential,5);
|
||||
atoms[0].type = 0;
|
||||
|
||||
atomtypes[0].no_connect = atoms[0].no_connect;
|
||||
|
||||
for (n=1,j=1; j < total_no_atoms; j++) {
|
||||
match = 0;
|
||||
k = 0;
|
||||
while (!match && (k < n)) {
|
||||
if (strncmp(atomtypes[k].potential,atoms[j].potential,5) == 0) {
|
||||
match = 1;
|
||||
atom_type = k;
|
||||
if (atomtypes[k].no_connect != atoms[j].no_connect) {
|
||||
if (pflag > 0) fprintf(stderr," WARNING inconsistent # of connects on atom %d type %s\n",j,
|
||||
atomtypes[k].potential);
|
||||
}
|
||||
}
|
||||
else
|
||||
k++;
|
||||
}
|
||||
if (match == 0) {
|
||||
atom_type = n;
|
||||
atomtypes[n].no_connect = atoms[j].no_connect;
|
||||
strncpy(atomtypes[n++].potential,atoms[j].potential,5);
|
||||
}
|
||||
if (n >= MAX_ATOM_TYPES) {
|
||||
fprintf(stderr,"Too many atom types (> 100) - error\n");
|
||||
exit(1);
|
||||
}
|
||||
atoms[j].type = atom_type;
|
||||
}
|
||||
no_atom_types = n;
|
||||
return;
|
||||
}
|
||||
|
||||
void build_bondtypes_list() {
|
||||
int j,k,n,match,bond_type=0;
|
||||
int typei,typej;
|
||||
|
||||
for (n=0,j=0; j < total_no_bonds; j++) {
|
||||
typei = atoms[bonds[j].members[0]].type;
|
||||
typej = atoms[bonds[j].members[1]].type;
|
||||
if (typej < typei) {
|
||||
swap_ints(&typei,&typej);
|
||||
swap_ints(&bonds[j].members[0],&bonds[j].members[1]);
|
||||
}
|
||||
|
||||
match = 0;
|
||||
k = 0;
|
||||
while (!match && (k < n)) {
|
||||
if ((typei == bondtypes[k].types[0]) &&
|
||||
(typej == bondtypes[k].types[1])) {
|
||||
match = 1;
|
||||
bond_type = k;
|
||||
}
|
||||
else
|
||||
k++;
|
||||
}
|
||||
if (match == 0) {
|
||||
bond_type = n;
|
||||
bondtypes[n ].types[0] = typei;
|
||||
bondtypes[n++].types[1] = typej;
|
||||
}
|
||||
if (n >= MAX_BOND_TYPES) {
|
||||
fprintf(stderr,"Too many bond types (> 200) - error\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
bonds[j].type = bond_type;
|
||||
}
|
||||
no_bond_types = n;
|
||||
return;
|
||||
}
|
||||
|
||||
void build_angletypes_list()
|
||||
{
|
||||
int j,k,n,match,angle_type=0;
|
||||
int typei,typej,typek;
|
||||
|
||||
for (n=0,j=0; j < total_no_angles; j++) {
|
||||
typei = atoms[angles[j].members[0]].type;
|
||||
typej = atoms[angles[j].members[1]].type;
|
||||
typek = atoms[angles[j].members[2]].type;
|
||||
if (typek < typei) {
|
||||
swap_ints(&typei,&typek);
|
||||
swap_ints(&angles[j].members[0],&angles[j].members[2]);
|
||||
}
|
||||
|
||||
match = 0;
|
||||
k = 0;
|
||||
while (!match && (k < n)) {
|
||||
if ((typei == angletypes[k].types[0]) &&
|
||||
(typej == angletypes[k].types[1]) &&
|
||||
(typek == angletypes[k].types[2])) {
|
||||
match = 1;
|
||||
angle_type = k;
|
||||
}
|
||||
else
|
||||
k++;
|
||||
}
|
||||
if (match == 0) {
|
||||
angle_type = n;
|
||||
angletypes[n ].types[0] = typei;
|
||||
angletypes[n ].types[1] = typej;
|
||||
angletypes[n++].types[2] = typek;
|
||||
}
|
||||
if (n >= MAX_ANGLE_TYPES) {
|
||||
fprintf(stderr,"Too many angle types (> 300) - error\n");
|
||||
exit(1);
|
||||
}
|
||||
angles[j].type = angle_type;
|
||||
}
|
||||
no_angle_types = n;
|
||||
return;
|
||||
}
|
||||
|
||||
void build_dihedraltypes_list()
|
||||
{
|
||||
int j,k,n,match,dihedral_type=0;
|
||||
int typei,typej,typek,typel;
|
||||
|
||||
for (n=0,j=0; j < total_no_dihedrals; j++) {
|
||||
typei = atoms[dihedrals[j].members[0]].type;
|
||||
typej = atoms[dihedrals[j].members[1]].type;
|
||||
typek = atoms[dihedrals[j].members[2]].type;
|
||||
typel = atoms[dihedrals[j].members[3]].type;
|
||||
if ((typek < typej) || ((typej == typek) && (typel < typei))) {
|
||||
swap_ints(&typej,&typek);
|
||||
swap_ints(&dihedrals[j].members[1],&dihedrals[j].members[2]);
|
||||
swap_ints(&typei,&typel);
|
||||
swap_ints(&dihedrals[j].members[0],&dihedrals[j].members[3]);
|
||||
}
|
||||
|
||||
match = 0;
|
||||
k = 0;
|
||||
while (!match && (k < n)) {
|
||||
if ((typei == dihedraltypes[k].types[0]) &&
|
||||
(typej == dihedraltypes[k].types[1]) &&
|
||||
(typek == dihedraltypes[k].types[2]) &&
|
||||
(typel == dihedraltypes[k].types[3])) {
|
||||
match = 1;
|
||||
dihedral_type = k;
|
||||
}
|
||||
else
|
||||
k++;
|
||||
}
|
||||
if (match == 0) {
|
||||
dihedral_type = n;
|
||||
dihedraltypes[n ].types[0] = typei;
|
||||
dihedraltypes[n ].types[1] = typej;
|
||||
dihedraltypes[n ].types[2] = typek;
|
||||
dihedraltypes[n++].types[3] = typel;
|
||||
}
|
||||
if (n >= MAX_DIHEDRAL_TYPES) {
|
||||
fprintf(stderr,"Too many dihedral types (> 400) - error\n");
|
||||
exit(1);
|
||||
}
|
||||
dihedrals[j].type = dihedral_type;
|
||||
}
|
||||
no_dihedral_types = n;
|
||||
return;
|
||||
}
|
||||
|
||||
void build_ooptypes_list()
|
||||
{
|
||||
int j,k,n,match,oop_type=0;
|
||||
int temp_types[3],temp_pos[3];
|
||||
int typei,typej,typek,typel;
|
||||
|
||||
for (n=0,j=0; j < total_no_oops; j++) {
|
||||
typei = atoms[oops[j].members[0]].type;
|
||||
typej = atoms[oops[j].members[1]].type;
|
||||
typek = atoms[oops[j].members[2]].type;
|
||||
typel = atoms[oops[j].members[3]].type;
|
||||
temp_types[0] = typei;
|
||||
temp_types[1] = typek;
|
||||
temp_types[2] = typel;
|
||||
|
||||
bubble_sort(3,temp_types,temp_pos);
|
||||
|
||||
typei = temp_types[0];
|
||||
typek = temp_types[1];
|
||||
typel = temp_types[2];
|
||||
temp_types[0] = oops[j].members[0];
|
||||
temp_types[1] = oops[j].members[2];
|
||||
temp_types[2] = oops[j].members[3];
|
||||
oops[j].members[0] = temp_types[temp_pos[0]];
|
||||
oops[j].members[2] = temp_types[temp_pos[1]];
|
||||
oops[j].members[3] = temp_types[temp_pos[2]];
|
||||
|
||||
match = 0;
|
||||
k = 0;
|
||||
while (!match && (k < n)) {
|
||||
if ((typei == ooptypes[k].types[0]) &&
|
||||
(typej == ooptypes[k].types[1]) &&
|
||||
(typek == ooptypes[k].types[2]) &&
|
||||
(typel == ooptypes[k].types[3])) {
|
||||
match = 1;
|
||||
oop_type = k;
|
||||
}
|
||||
else
|
||||
k++;
|
||||
}
|
||||
if (match == 0) {
|
||||
|
||||
oop_type = n;
|
||||
ooptypes[n ].types[0] = typei;
|
||||
ooptypes[n ].types[1] = typej;
|
||||
ooptypes[n ].types[2] = typek;
|
||||
ooptypes[n++].types[3] = typel;
|
||||
}
|
||||
if (n >= MAX_OOP_TYPES) {
|
||||
fprintf(stderr,"Too many oop types (> 400) - error\n");
|
||||
exit(1);
|
||||
}
|
||||
oops[j].type = oop_type;
|
||||
}
|
||||
no_oop_types = n;
|
||||
return;
|
||||
}
|
||||
|
||||
void build_angleangletypes_list()
|
||||
{
|
||||
int j,k,n,match,angleangle_type=0;
|
||||
int temp_types[3],temp_pos[3];
|
||||
int typei,typej,typek,typel;
|
||||
|
||||
for (n=0,j=0; j < total_no_angle_angles; j++) {
|
||||
|
||||
typei = atoms[angleangles[j].members[0]].type;
|
||||
typej = atoms[angleangles[j].members[1]].type;
|
||||
typek = atoms[angleangles[j].members[2]].type;
|
||||
typel = atoms[angleangles[j].members[3]].type;
|
||||
|
||||
temp_types[0] = typei;
|
||||
temp_types[1] = typek;
|
||||
temp_types[2] = typel;
|
||||
|
||||
bubble_sort(3,temp_types,temp_pos);
|
||||
|
||||
typei = temp_types[0];
|
||||
typek = temp_types[1];
|
||||
typel = temp_types[2];
|
||||
|
||||
temp_types[0] = angleangles[j].members[0];
|
||||
temp_types[1] = angleangles[j].members[2];
|
||||
temp_types[2] = angleangles[j].members[3];
|
||||
|
||||
angleangles[j].members[0] = temp_types[temp_pos[0]];
|
||||
angleangles[j].members[2] = temp_types[temp_pos[1]];
|
||||
angleangles[j].members[3] = temp_types[temp_pos[2]];
|
||||
|
||||
match = 0;
|
||||
k = 0;
|
||||
while (!match && (k < n)) {
|
||||
if ((typei == angleangletypes[k].types[0]) &&
|
||||
(typej == angleangletypes[k].types[1]) &&
|
||||
(typek == angleangletypes[k].types[2]) &&
|
||||
(typel == angleangletypes[k].types[3])) {
|
||||
match = 1;
|
||||
angleangle_type = k;
|
||||
}
|
||||
else
|
||||
k++;
|
||||
}
|
||||
if (match == 0) {
|
||||
angleangle_type = n;
|
||||
angleangletypes[n ].types[0] = typei;
|
||||
angleangletypes[n ].types[1] = typej;
|
||||
angleangletypes[n ].types[2] = typek;
|
||||
angleangletypes[n++].types[3] = typel;
|
||||
}
|
||||
|
||||
if (n >= MAX_ANGLEANGLE_TYPES) {
|
||||
fprintf(stderr,"Too many angleangle types (> 400) - error\n");
|
||||
exit(1);
|
||||
}
|
||||
angleangles[j].type = angleangle_type;
|
||||
}
|
||||
no_angleangle_types = n;
|
||||
return;
|
||||
}
|
||||
|
||||
void swap_ints(int *i, int *j)
|
||||
{
|
||||
int temp;
|
||||
|
||||
temp = *i;
|
||||
*i = *j;
|
||||
*j = temp;
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
void bubble_sort(int n, int *val, int *pos)
|
||||
{
|
||||
int i,j;
|
||||
|
||||
for (i=0; i < n; i++) pos[i] = i;
|
||||
for (i=0; i < n-1; i++) {
|
||||
for (j=1; j < n; j++) {
|
||||
if (val[j] < val[i]) {
|
||||
swap_ints(&val[i],&val[j]);
|
||||
swap_ints(&pos[i],&pos[j]);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
|
||||
TARGET = msi2lmp.exe
|
||||
|
||||
SRCS = msi2lmp.c \
|
||||
ReadCarFile.c \
|
||||
ReadMdfFile.c \
|
||||
MakeLists.c \
|
||||
ReadFrcFile.c \
|
||||
InitializeItems.c \
|
||||
SearchAndFill.c \
|
||||
GetParameters.c \
|
||||
CheckLists.c \
|
||||
WriteDataFile05.c \
|
||||
WriteDataFile01.c
|
||||
|
||||
OBJS = $(SRCS:.c=.o)
|
||||
|
||||
HEADERS = msi2lmp.h Forcefield.h
|
||||
|
||||
CC = gcc
|
||||
CFLAGS = -O -Wall -W -g
|
||||
FRCFILE = cvff.frc
|
||||
FRCFILE2 = cff91.frc
|
||||
README = README
|
||||
MKFILE = Makefile
|
||||
|
||||
$(TARGET) : $(OBJS)
|
||||
$(CC) $(CFLAGS) -o $(TARGET) $(OBJS) -lm
|
||||
|
||||
.c.o:
|
||||
$(CC) $(CFLAGS) -c $<
|
||||
clean:
|
||||
rm -f $(OBJS) $(TARGET)
|
||||
|
||||
# dependencies
|
||||
CheckLists.o: CheckLists.c msi2lmp.h
|
||||
GetParameters.o: GetParameters.c msi2lmp.h Forcefield.h
|
||||
InitializeItems.o: InitializeItems.c msi2lmp.h Forcefield.h
|
||||
MakeLists.o: MakeLists.c msi2lmp.h
|
||||
msi2lmp.o: msi2lmp.c msi2lmp.h
|
||||
ReadCarFile.o: ReadCarFile.c msi2lmp.h
|
||||
ReadFrcFile.o: ReadFrcFile.c msi2lmp.h Forcefield.h
|
||||
ReadMdfFile.o: ReadMdfFile.c msi2lmp.h
|
||||
SearchAndFill.o: SearchAndFill.c msi2lmp.h Forcefield.h
|
||||
WriteDataFile01.o: WriteDataFile01.c msi2lmp.h Forcefield.h
|
||||
WriteDataFile05.o: WriteDataFile05.c msi2lmp.h Forcefield.h
|
||||
|
|
@ -0,0 +1,214 @@
|
|||
/*
|
||||
* This function opens the .car file and extracts coordinate information
|
||||
* into the atoms Atom structure
|
||||
*/
|
||||
|
||||
#include "msi2lmp.h"
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <math.h>
|
||||
|
||||
void ReadCarFile(void)
|
||||
{
|
||||
char line[MAX_LINE_LENGTH]; /* Stores lines as they are read in */
|
||||
int k,m,n; /* counters */
|
||||
int skip; /* lines to skip at beginning of file */
|
||||
double lowest, highest; /* temp coordinate finding variables */
|
||||
double total_q;
|
||||
double sq_c;
|
||||
double cos_alpha; // Added by SLTM Sept 13, 2010
|
||||
double cos_gamma;
|
||||
double sin_gamma;
|
||||
double cos_beta;
|
||||
double sin_beta;
|
||||
double A, B, C;
|
||||
|
||||
/* Open .car file for reading */
|
||||
|
||||
sprintf(line,"%s.car",rootname);
|
||||
if (pflag > 0) printf(" Reading car file: %s\n",line);
|
||||
if( (CarF = fopen(line,"r")) == NULL ) {
|
||||
printf("Cannot open %s\n",line);
|
||||
exit(33);
|
||||
}
|
||||
|
||||
/* Determine Number of molecules & atoms */
|
||||
|
||||
rewind(CarF);
|
||||
no_molecules = -1; /* Set to -1 because counter will be incremented an
|
||||
extra time at the end of the file */
|
||||
|
||||
fgets(line,MAX_LINE_LENGTH,CarF); /* Read header line */
|
||||
|
||||
/* Check for periodicity, if present, read cell constants */
|
||||
|
||||
if( strncmp(fgets(line,MAX_LINE_LENGTH,CarF),"PBC=ON",6) == 0) {
|
||||
periodic = 1;
|
||||
skip = 5; /* Data starts 5 lines from beginning of file */
|
||||
fgets(line,MAX_LINE_LENGTH,CarF); /* Comment line */
|
||||
fgets(line,MAX_LINE_LENGTH,CarF); /* Date stamp */
|
||||
fscanf(CarF,"%*s %lf %lf %lf %lf %lf %lf %*s",
|
||||
&pbc[0],&pbc[1],&pbc[2],&pbc[3],&pbc[4],&pbc[5]);
|
||||
|
||||
// Added triclinic flag for non-orthogonal boxes Oct 5, 2010 SLTM
|
||||
if(pbc[3] != 90.0 || pbc[4] != 90.0 || pbc[5] != 90.0) {
|
||||
TriclinicFlag = 1;
|
||||
} else TriclinicFlag = 0;
|
||||
} else {
|
||||
periodic = 0;
|
||||
skip = 4;
|
||||
if (pflag > 1) {
|
||||
printf(" %s is not a periodic system\n", rootname);
|
||||
printf(" Assigning cell parameters based on coordinates\n");
|
||||
}
|
||||
fgets(line,MAX_LINE_LENGTH, CarF); /* Comment line */
|
||||
fgets(line,MAX_LINE_LENGTH, CarF); /* Date Stamp */
|
||||
}
|
||||
|
||||
/* First pass through file -- Count molecules */
|
||||
|
||||
while(fgets(line,MAX_LINE_LENGTH,CarF) != NULL )
|
||||
if( strncmp(line,"end",3) == 0 )
|
||||
no_molecules++;
|
||||
|
||||
/* Allocate space to keep track of the number of atoms within a molecule */
|
||||
|
||||
no_atoms = (int *) calloc(no_molecules,sizeof(int));
|
||||
if ( no_atoms == NULL ) {
|
||||
printf("Could not allocate memory for no_atoms\n");
|
||||
exit(32);
|
||||
}
|
||||
|
||||
/* Second pass through file -- Count atoms */
|
||||
|
||||
rewind(CarF);
|
||||
for(n=0; n < skip; n++) /* Skip beginning lines */
|
||||
fgets(line,MAX_LINE_LENGTH,CarF);
|
||||
|
||||
for(n=0; n < no_molecules; n++)
|
||||
while( strncmp(fgets(line,MAX_LINE_LENGTH,CarF),"end",3) )
|
||||
no_atoms[n]++;
|
||||
|
||||
for( total_no_atoms=0, n=0; n < no_molecules; n++ )
|
||||
total_no_atoms += no_atoms[n];
|
||||
|
||||
molecule = (struct MoleculeList *) calloc(no_molecules,
|
||||
sizeof(struct MoleculeList));
|
||||
if (molecule == NULL) {
|
||||
printf("Unable to allocate memory for molecule structure\n");
|
||||
exit(32);
|
||||
}
|
||||
molecule[0].start = 0;
|
||||
molecule[0].end = no_atoms[0];
|
||||
for (n=1; n < no_molecules; n++) {
|
||||
molecule[n].start = molecule[n-1].end;
|
||||
molecule[n].end = molecule[n].start + no_atoms[n];
|
||||
}
|
||||
|
||||
/* Allocate space for atoms Atom structures */
|
||||
|
||||
atoms = (struct Atom *) calloc(total_no_atoms,sizeof(struct Atom));
|
||||
if( atoms == NULL ) {
|
||||
printf("Could not allocate memory for AtomList\n");
|
||||
exit(32);
|
||||
}
|
||||
|
||||
/* Third pass through file -- Read+Parse Car File */
|
||||
|
||||
rewind(CarF);
|
||||
for(n=0; n < skip; n++)
|
||||
fgets(line,MAX_LINE_LENGTH,CarF);
|
||||
|
||||
for(m=0; m < no_molecules; m++) {
|
||||
for(k=molecule[m].start; k <
|
||||
molecule[m].end; k++) {
|
||||
|
||||
atoms[k].molecule = m;
|
||||
atoms[k].no = k;
|
||||
|
||||
fscanf(CarF,"%s %lf %lf %lf %*s %d %s %s %f",
|
||||
atoms[k].name,
|
||||
&(atoms[k].x[0]),
|
||||
&(atoms[k].x[1]),
|
||||
&(atoms[k].x[2]),
|
||||
&(atoms[k].molecule),
|
||||
atoms[k].potential,
|
||||
atoms[k].element,
|
||||
&(atoms[k].q));
|
||||
}
|
||||
fgets(line,MAX_LINE_LENGTH,CarF);
|
||||
fgets(line,MAX_LINE_LENGTH,CarF);
|
||||
|
||||
} /* End m (molecule) loop */
|
||||
|
||||
for (total_q=0.0,k=0; k < total_no_atoms; k++)
|
||||
total_q += atoms[k].q;
|
||||
|
||||
if (pflag > 1) {
|
||||
printf(" There are %d atoms in %d molecules in this file\n",
|
||||
total_no_atoms,no_molecules);
|
||||
printf(" The total charge in the system is %7.3f.\n\n",total_q);
|
||||
}
|
||||
|
||||
/* Search coordinates to find lowest and highest for x, y, and z */
|
||||
|
||||
if (periodic == 0) {
|
||||
// Added if/else statment STLM Oct 5 2010
|
||||
if (TriclinicFlag == 0) {
|
||||
for ( k = 0; k < 3; k++) {
|
||||
lowest = atoms[0].x[k];
|
||||
highest = atoms[0].x[k];
|
||||
|
||||
for ( m = 1; m < total_no_atoms; m++) {
|
||||
if (atoms[m].x[k] < lowest) lowest = atoms[m].x[k];
|
||||
if (atoms[m].x[k] > highest) highest = atoms[m].x[k];
|
||||
}
|
||||
pbc[k] = lowest;
|
||||
pbc[k+3] = highest;
|
||||
}
|
||||
} else {
|
||||
printf("This tool only works for periodic systems with triclinic boxes");
|
||||
exit(32);
|
||||
}
|
||||
|
||||
} else {
|
||||
// Modified lines 176 - 201 Oct 5th 2010
|
||||
if (TriclinicFlag == 0) {
|
||||
for (k=0; k < 3; k++) {
|
||||
pbc[k+3] = pbc[k];
|
||||
pbc[k] = 0.0;
|
||||
}
|
||||
} else {
|
||||
sq_c = pbc[2]*pbc[2];
|
||||
cos_alpha = cos(pbc[3]*PI_180);
|
||||
cos_gamma = cos(pbc[5]*PI_180);
|
||||
sin_gamma = sin(pbc[5]*PI_180);
|
||||
cos_beta = cos(pbc[4]*PI_180);
|
||||
sin_beta = sin(pbc[4]*PI_180);
|
||||
if (pflag > 1) {
|
||||
printf("pbc[3] %f pbc[4] %f pbc[5] %f\n", pbc[3] ,pbc[4] ,pbc[5]);
|
||||
printf("cos_alpha %f cos_beta %f cos_gamma %f\n", cos_alpha ,cos_beta ,cos_gamma);
|
||||
}
|
||||
A = pbc[0];
|
||||
B = pbc[1];
|
||||
C = pbc[2];
|
||||
|
||||
|
||||
pbc[0] = A;
|
||||
pbc[1] = B*sin_gamma;
|
||||
pbc[2] = sqrt(sq_c * sin_beta*sin_beta - C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma);
|
||||
pbc[3] = B * cos_gamma; // This is xy SLTM
|
||||
pbc[4] = C * cos_beta; // This is xz SLTM
|
||||
pbc[5] = C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma; // This is yz SLTM
|
||||
}
|
||||
}
|
||||
|
||||
/* Close .car file */
|
||||
|
||||
if (fclose(CarF) !=0) {
|
||||
printf("Error closing %s.car\n", rootname);
|
||||
exit(31);
|
||||
}
|
||||
}
|
||||
/* End ReadCarFile() */
|
||||
|
|
@ -0,0 +1,89 @@
|
|||
/*
|
||||
* This routine reads the data from a .frc forcefield file and stores it in
|
||||
* dynamically allocated memory. This allows for fast searches of the
|
||||
* file.
|
||||
*
|
||||
*/
|
||||
|
||||
#include "msi2lmp.h"
|
||||
#include "Forcefield.h"
|
||||
|
||||
#include <stdlib.h>
|
||||
|
||||
struct FrcFieldItem ff_atomtypes, equivalence, ff_vdw,ff_bond, ff_ang, ff_tor, ff_oop,
|
||||
ff_bonbon, ff_bonang, ff_angtor, ff_angangtor, ff_endbontor, ff_midbontor, ff_angang, ff_bonbon13;
|
||||
|
||||
|
||||
void ReadFrcFile(void)
|
||||
{
|
||||
/* Open Forcefield File */
|
||||
if ( (FrcF = fopen(FrcFileName,"r")) == NULL ) {
|
||||
fprintf(stderr,"Cannot open %s\n", FrcFileName);
|
||||
exit(72);
|
||||
}
|
||||
InitializeItems(); /* sets keywords, number of members and number of
|
||||
parameters for each structure */
|
||||
/* allocate memory to and search and fill each structure */
|
||||
|
||||
|
||||
SearchAndFill(&ff_atomtypes);
|
||||
SearchAndFill(&equivalence);
|
||||
SearchAndFill(&ff_vdw);
|
||||
SearchAndFill(&ff_bond);
|
||||
SearchAndFill(&ff_ang);
|
||||
SearchAndFill(&ff_tor);
|
||||
SearchAndFill(&ff_oop);
|
||||
|
||||
if (forcefield != 1) { /* Skip cross terms for class I */
|
||||
SearchAndFill(&ff_bonbon);
|
||||
SearchAndFill(&ff_bonang);
|
||||
SearchAndFill(&ff_angtor);
|
||||
SearchAndFill(&ff_angangtor);
|
||||
SearchAndFill(&ff_endbontor);
|
||||
SearchAndFill(&ff_midbontor);
|
||||
SearchAndFill(&ff_bonbon13);
|
||||
SearchAndFill(&ff_angang);
|
||||
}
|
||||
if (pflag > 1) {
|
||||
|
||||
fprintf(stderr,"\n Item %s has %d entries\n",
|
||||
ff_atomtypes.keyword,ff_atomtypes.entries);
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
equivalence.keyword,equivalence.entries);
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_vdw.keyword,ff_vdw.entries);
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_bond.keyword,ff_bond.entries);
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_ang.keyword,ff_ang.entries);
|
||||
if (forcefield > 1) {
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_bonbon.keyword,ff_bonbon.entries);
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_bonang.keyword,ff_bonang.entries);
|
||||
}
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_tor.keyword,ff_tor.entries);
|
||||
if (forcefield > 1) {
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_angtor.keyword,ff_angtor.entries);
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_angangtor.keyword,ff_angangtor.entries);
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_endbontor.keyword,ff_endbontor.entries);
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_midbontor.keyword,ff_midbontor.entries);
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_bonbon13.keyword,ff_bonbon13.entries);
|
||||
}
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_oop.keyword,ff_oop.entries);
|
||||
if (forcefield > 1) {
|
||||
fprintf(stderr," Item %s has %d entries\n",
|
||||
ff_angang.keyword,ff_angang.entries);
|
||||
}
|
||||
fprintf(stderr,"\n");
|
||||
}
|
||||
fclose(FrcF);
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,421 @@
|
|||
/******************************
|
||||
*
|
||||
* This function opens the .mdf file and extracts connectivity information
|
||||
* into the atoms Atom structure. It also updates the charge from the .car
|
||||
* file because the charge in the .mdf file has more significant figures.
|
||||
*
|
||||
*/
|
||||
|
||||
#include "msi2lmp.h"
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <ctype.h>
|
||||
|
||||
|
||||
/* Prototype for function to process a single atom
|
||||
Returns int that flags end of data file */
|
||||
|
||||
static int get_molecule(char line[], int connect_col_no,
|
||||
int q_col_no, int *counter);
|
||||
|
||||
/* Prototype for function that takes connectivty record as stated in
|
||||
.mdf file and fills in any default values */
|
||||
static void MakeConnectFullForm(int *counter);
|
||||
|
||||
/* prototype for function to clean strange characters out of strings */
|
||||
|
||||
static void clean_string(char *);
|
||||
|
||||
static int blank_line(char *line)
|
||||
{
|
||||
while (*line != '\0') {
|
||||
if (isalnum((int) *line)) return 0;
|
||||
++line;
|
||||
}
|
||||
return 1;
|
||||
}
|
||||
|
||||
void ReadMdfFile(void)
|
||||
{
|
||||
char line[MAX_LINE_LENGTH]; /* Temporary storage for reading lines */
|
||||
char *col_no; /* Pointer to column number stored as char */
|
||||
char *col_name; /* Pointer to column name */
|
||||
int connect_col_no = 0; /* Column number where connection info begins */
|
||||
int q_col_no = 0; /* Column number containg charge information */
|
||||
int atom_counter=0; /* Keeps track of current atom number */
|
||||
|
||||
int i,j,k,kk,l,n,match,match2,status;
|
||||
char *temp_string;
|
||||
char *temp_residue;
|
||||
char *temp_atom_name;
|
||||
char *sptr;
|
||||
unsigned char at_end = 0;
|
||||
|
||||
/* Open .mdf file for reading */
|
||||
|
||||
|
||||
sprintf(line,"%s.mdf",rootname);
|
||||
if (pflag > 0) printf(" Reading mdf file: %s\n",line);
|
||||
if ((MdfF = fopen(line,"r")) == NULL ) {
|
||||
printf("Cannot open %s\n",line);
|
||||
exit(41);
|
||||
}
|
||||
|
||||
while (!at_end) {
|
||||
|
||||
sptr = fgets(line,MAX_LINE_LENGTH,MdfF);
|
||||
|
||||
if (sptr != NULL) {
|
||||
|
||||
clean_string(line);
|
||||
|
||||
if (strncmp(line,"#end",4) == 0) {
|
||||
at_end = 1;
|
||||
} else if (strncmp(line,"@column",7) == 0) {
|
||||
|
||||
temp_string = strtok(line," ");
|
||||
col_no = strtok(NULL," ");
|
||||
col_name = strtok(NULL," ");
|
||||
if (strncmp(col_name,"charge",6) == 0) {
|
||||
if (strlen(col_name) < 8) {
|
||||
q_col_no = atoi(col_no);
|
||||
}
|
||||
} else if (strncmp(col_name,"connect",7) == 0) {
|
||||
connect_col_no = atoi(col_no);
|
||||
}
|
||||
} else if (strncmp(line,"@molecule",9) == 0) {
|
||||
|
||||
if ((q_col_no == 0) | (connect_col_no == 0)) {
|
||||
printf("Unable to process molecule without knowing charge\n");
|
||||
printf("and connections columns\n");
|
||||
exit(42);
|
||||
}
|
||||
sptr = fgets(line,MAX_LINE_LENGTH,MdfF);
|
||||
status = get_molecule(line,connect_col_no,q_col_no,&atom_counter);
|
||||
if (status == 0) {
|
||||
printf("Trouble reading molecule - exiting\n");
|
||||
exit(43);
|
||||
}
|
||||
}
|
||||
} else {
|
||||
printf("End of File found or error reading line\n");
|
||||
at_end = 1;
|
||||
}
|
||||
}
|
||||
|
||||
/* Next build list of residues for each molecule This will
|
||||
facilitate assigning connections numbers as well as figuring
|
||||
out bonds, angles, etc. This first loop just figures out the
|
||||
number of residues in each molecule and allocates memory to
|
||||
store information for each residue. The second loop fills
|
||||
in starting and ending atom positions for each residue
|
||||
*/
|
||||
|
||||
temp_string = (char *)calloc(16,sizeof(char));
|
||||
|
||||
for (n=0; n < no_molecules; n++) {
|
||||
molecule[n].no_residues = 1;
|
||||
|
||||
strncpy(temp_string,atoms[molecule[n].start].residue_string,16);
|
||||
for (i=molecule[n].start+1; i < molecule[n].end; i++) {
|
||||
if (strncmp(temp_string,atoms[i].residue_string,16) != 0) {
|
||||
molecule[n].no_residues++;
|
||||
strncpy(temp_string,atoms[i].residue_string,16);
|
||||
}
|
||||
}
|
||||
|
||||
molecule[n].residue = (struct ResidueList *)
|
||||
calloc(molecule[n].no_residues, sizeof(struct ResidueList));
|
||||
|
||||
if (molecule[n].residue == NULL) {
|
||||
printf("Unable to allocate memory for residue list - molecule %d\n",n);
|
||||
exit(44);
|
||||
}
|
||||
}
|
||||
for (n=0; n < no_molecules; n++) {
|
||||
j = 0;
|
||||
strncpy(molecule[n].residue[j].name,
|
||||
atoms[molecule[n].start].residue_string,16);
|
||||
|
||||
molecule[n].residue[j].start = molecule[n].start;
|
||||
for (i=molecule[n].start+1; i < molecule[n].end; i++) {
|
||||
if (strncmp(molecule[n].residue[j].name,
|
||||
atoms[i].residue_string,16) != 0) {
|
||||
|
||||
molecule[n].residue[j].end = i;
|
||||
molecule[n].residue[++j].start = i;
|
||||
strncpy(molecule[n].residue[j].name,atoms[i].residue_string,16);
|
||||
}
|
||||
}
|
||||
molecule[n].residue[j].end = molecule[n].end;
|
||||
/*
|
||||
printf("Molecule %d has %d residues",n,molecule[n].no_residues);
|
||||
for (i=0; i < molecule[n].no_residues; i++) {
|
||||
printf(" %s",molecule[n].residue[i].name);
|
||||
}
|
||||
printf("\n");
|
||||
for (i=molecule[n].start; i < molecule[n].end; i++) {
|
||||
printf(" atom %d residue %s\n",i,atoms[i].residue_string);
|
||||
}
|
||||
printf(" residue %s start %d end %d\n",molecule[n].residue[i].name,
|
||||
molecule[n].residue[i].start,molecule[n].residue[i].end);
|
||||
}
|
||||
*/
|
||||
}
|
||||
|
||||
/* Assign atom names in connections[] to corresponding atom numbers */
|
||||
|
||||
for (n=0; n < no_molecules; n++) {
|
||||
for (j=0; j < molecule[n].no_residues; j++) {
|
||||
for (i=molecule[n].residue[j].start; i < molecule[n].residue[j].end;
|
||||
i++) {
|
||||
for (l=0; l < atoms[i].no_connect; l++) {
|
||||
strncpy(temp_string,atoms[i].connections[l],16);
|
||||
temp_residue = strtok(temp_string,":");
|
||||
temp_atom_name = strtok(NULL,"%");
|
||||
|
||||
if (strcmp(temp_residue,molecule[n].residue[j].name) == 0) {
|
||||
|
||||
/* atom and connection are part of same residue
|
||||
Search names on just that residue */
|
||||
|
||||
k = molecule[n].residue[j].start;
|
||||
match = 0;
|
||||
while (!match && (k < molecule[n].residue[j].end)) {
|
||||
if (strcmp(atoms[k].name,temp_atom_name) == 0) {
|
||||
atoms[i].conn_no[l] = k;
|
||||
match = 1;
|
||||
} else
|
||||
k++;
|
||||
}
|
||||
if (match == 0) {
|
||||
printf("Unable to resolve atom number of atom %d conn %d string %s:%s\n"
|
||||
" Something is wrong in the MDF file\n",
|
||||
i,l,temp_residue,temp_atom_name);
|
||||
exit(45);
|
||||
}
|
||||
} else {
|
||||
|
||||
/* atom and connection are on different residues
|
||||
First find the residue that the connection is
|
||||
on then loop over its atoms
|
||||
*/
|
||||
|
||||
k=0;
|
||||
match = 0;
|
||||
while (!match && (k < molecule[n].no_residues)) {
|
||||
if (strcmp(temp_residue,molecule[n].residue[k].name) == 0) {
|
||||
kk = molecule[n].residue[k].start;
|
||||
match2 = 0;
|
||||
while (!match2 && (kk < molecule[n].residue[k].end)) {
|
||||
if (strcmp(atoms[kk].name,temp_atom_name) == 0) {
|
||||
atoms[i].conn_no[l] = kk;
|
||||
match2 = 1;
|
||||
} else
|
||||
kk++;
|
||||
}
|
||||
if (match2 == 0) {
|
||||
printf("Unable to resolve atom number of atom %d conn %d string %s\n"
|
||||
" Something is wrong in the MDF file\n",
|
||||
i,l,atoms[i].connections[l]);
|
||||
exit(46);
|
||||
}
|
||||
match = 1;
|
||||
} else
|
||||
k++;
|
||||
}
|
||||
if (match == 0) {
|
||||
printf("Unable to find residue associated with conn %d %s on atom %d\n"
|
||||
" Something is wrong in the MDF file\n", l,atoms[i].connections[l],i);
|
||||
exit(47);
|
||||
}
|
||||
} /* end if */
|
||||
} /* l - loop over connections on atom i */
|
||||
} /* i - loop on atoms in residue j molecule n */
|
||||
} /* j - loop on residues in molecule n */
|
||||
} /* n - loop over molecules */
|
||||
|
||||
free(temp_string);
|
||||
/*
|
||||
for (n=0; n < no_molecules; n++) {
|
||||
|
||||
printf("Molecule %d has %d residues\n",n,molecule[n].no_residues);
|
||||
for (j=0; j < molecule[n].no_residues; j++) {
|
||||
printf(" Residue %d named %s\n",j,molecule[n].residue[j].name);
|
||||
for (i=molecule[n].residue[j].start; i < molecule[n].residue[j].end;
|
||||
i++) {
|
||||
printf(" Atom %d type %s connected to ",i,atoms[i].potential);
|
||||
for (l=0; l < atoms[i].no_connect; l++) printf(" %d ",
|
||||
atoms[i].conn_no[l]);
|
||||
printf("\n");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
*/
|
||||
|
||||
/* Close .mdf file */
|
||||
|
||||
if (fclose(MdfF) !=0) {
|
||||
printf("Error closing %s.car\n", rootname);
|
||||
exit(1);
|
||||
}
|
||||
|
||||
} /* End ReadMdfFile function */
|
||||
|
||||
/*--------------------- get_molecule Function-----------------------*/
|
||||
|
||||
int get_molecule(char *line, int connect_col_no, int q_col_no,
|
||||
int *counter)
|
||||
{
|
||||
char *cur_field; /* For storing current string token */
|
||||
int i; /* Used in loop counters */
|
||||
int connect_no; /* Connection number within atom */
|
||||
int r_val = 1; /* Return value. 1 = successful
|
||||
0 = EOF encountered */
|
||||
/* Loop over atoms */
|
||||
|
||||
/* blank line signals end of molecule*/
|
||||
while(!blank_line(fgets(line,MAX_LINE_LENGTH,MdfF))) {
|
||||
/* while(strlen(fgets(line,MAX_LINE_LENGTH,MdfF)) > 2) { */
|
||||
|
||||
clean_string(line);
|
||||
|
||||
/* Get atom name */
|
||||
cur_field = strtok(line,":");
|
||||
sscanf(cur_field, "%s", atoms[*counter].residue_string);
|
||||
cur_field = strtok(NULL," ");
|
||||
/* Compare atom name with that in .car file */
|
||||
if (strcmp(atoms[*counter].name, cur_field)) {
|
||||
printf("Names %s from .car file and %s from .mdf file do not match\n",
|
||||
atoms[*counter].name, cur_field);
|
||||
printf("counter = %d\n",*counter);
|
||||
printf("Program Terminating\n");
|
||||
exit(4);
|
||||
}
|
||||
|
||||
/* Skip unwanted fields until charge column, then update charge */
|
||||
|
||||
for (i=1; i < q_col_no; i++) strtok(NULL," ");
|
||||
cur_field = strtok(NULL, " ");
|
||||
atoms[*counter].q = atof(cur_field);
|
||||
|
||||
/* Continue skipping unwanted fields until connectivity records begin */
|
||||
|
||||
for ( i = (q_col_no + 1); i < connect_col_no; i++) strtok(NULL," ");
|
||||
|
||||
/* Process connections */
|
||||
|
||||
connect_no = 0; /* reset connections counter */
|
||||
while ((cur_field = strtok(NULL," ")) && (connect_no < MAX_CONNECTIONS)) {
|
||||
sscanf(cur_field, "%s", atoms[*counter].connections[connect_no++]);
|
||||
}
|
||||
atoms[*counter].no_connect = connect_no;
|
||||
MakeConnectFullForm(counter);
|
||||
(*counter)++;
|
||||
|
||||
} /* End atom processing loop */
|
||||
|
||||
return r_val;
|
||||
|
||||
} /* End get_molecule function */
|
||||
|
||||
|
||||
|
||||
/*------------------------MakeConnectFullForm Function--------------------*/
|
||||
|
||||
void MakeConnectFullForm(int *counter) {
|
||||
|
||||
/* This function processes the connection names after all connections
|
||||
for an atom have been read in.
|
||||
It replaces any short forms that use implied default values
|
||||
with the full form connectivity record */
|
||||
|
||||
int i; /* Counter for character array */
|
||||
int j; /* loop counter */
|
||||
char tempname[MAX_STRING]; /* name of connection */
|
||||
char tempcell[10]; /* Values from connectivity record */
|
||||
char tempsym[5]; /* " " */
|
||||
char tempbo[6]; /* " " */
|
||||
char *charptr;
|
||||
|
||||
for ( j = 0; j < atoms[*counter].no_connect; j++) {
|
||||
/* If not full name, make name full */
|
||||
if (strchr(atoms[*counter].connections[j],':') == NULL) {
|
||||
strcpy(tempname,atoms[*counter].residue_string);
|
||||
strcat(tempname,":");
|
||||
strcat(tempname,
|
||||
atoms[*counter].connections[j]);
|
||||
sscanf(tempname, "%s",
|
||||
atoms[*counter].connections[j]);
|
||||
}
|
||||
else
|
||||
sscanf(atoms[*counter].connections[j], "%s", tempname);
|
||||
/* Set cell variables */
|
||||
|
||||
i=0;
|
||||
charptr = (strchr(tempname,'%'));
|
||||
if (charptr != NULL) {
|
||||
while ( *charptr!='#' && *charptr!='/' && *charptr!='\000')
|
||||
tempcell[i++] = *(charptr++);
|
||||
tempcell[i] = '\000';
|
||||
}
|
||||
else
|
||||
strcpy(tempcell, "%000");
|
||||
|
||||
/* Set symmetry variables
|
||||
-- If not 1, cannot handle at this time */
|
||||
|
||||
i = 0;
|
||||
charptr = (strchr(tempname,'#'));
|
||||
if (charptr != NULL) {
|
||||
while (*charptr != '/' && *charptr !='\000') {
|
||||
tempsym[i++] = *(charptr++);
|
||||
if ((i==2) && (tempsym[1] != '1')) {
|
||||
printf("Msi2LMP is not equipped to handle symmetry operations\n");
|
||||
exit(5);
|
||||
}
|
||||
}
|
||||
tempsym[i] = '\000';
|
||||
}
|
||||
else
|
||||
strcpy(tempsym, "#1");
|
||||
|
||||
/* Set bond order and record in data structure */
|
||||
|
||||
i = 0;
|
||||
charptr = strchr(tempname,'/');
|
||||
if (charptr != NULL) {
|
||||
charptr++;
|
||||
while (*charptr != '\000')
|
||||
tempbo[i++] = *(charptr++);
|
||||
tempbo[i] = '\000';
|
||||
} else strcpy(tempbo, "1.0");
|
||||
|
||||
atoms[*counter].bond_order[j] = atof(tempbo);
|
||||
|
||||
/* Build connection name and store in atoms data structure */
|
||||
|
||||
strtok( tempname, "%#/");
|
||||
strcat( tempname, tempcell);
|
||||
strcat( tempname, tempsym);
|
||||
strcat( tempname, "/");
|
||||
strcat( tempname, tempbo);
|
||||
if (strlen(tempname) > 25) printf("tempname overrun %s\n",tempname);
|
||||
sscanf( tempname, "%s", atoms[*counter].connections[j]);
|
||||
}/*End for loop*/
|
||||
}/* End function MakeNameLong
|
||||
*/
|
||||
|
||||
void clean_string(char *string) {
|
||||
int i,n;
|
||||
short k;
|
||||
|
||||
n = strlen(string);
|
||||
for (i=0; i < n; i++) {
|
||||
k = (short)string[i];
|
||||
if ((k<32) | (k>127)) string[i] = '\0';
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,228 @@
|
|||
/****************************
|
||||
*
|
||||
* This function first allocates memory to the forcefield item
|
||||
* structures and then reads parameters from the forcefield file into the
|
||||
* allocated memory
|
||||
*
|
||||
*/
|
||||
|
||||
#include "msi2lmp.h"
|
||||
#include "Forcefield.h"
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <ctype.h>
|
||||
|
||||
static int blank_line(char *line)
|
||||
{
|
||||
while (*line != '\0') {
|
||||
if (isalnum((int) *line)) return 0;
|
||||
++line;
|
||||
}
|
||||
return 1;
|
||||
}
|
||||
|
||||
static unsigned char string_match(char *,char *);
|
||||
|
||||
void SearchAndFill(struct FrcFieldItem *item)
|
||||
{
|
||||
int i,j; /* counters */
|
||||
int got_it = 0;
|
||||
int ctr = 0;
|
||||
long file_pos;
|
||||
char line[MAX_LINE_LENGTH] = "empty";
|
||||
char *charptr,*status;
|
||||
|
||||
/***********************ALLOCATE MEMORY FOR STRUCTURE ********************/
|
||||
|
||||
/* Read and discard lines until keyword is found */
|
||||
|
||||
rewind(FrcF);
|
||||
while (got_it == 0) {
|
||||
status = fgets( line, MAX_LINE_LENGTH, FrcF );
|
||||
if (status == NULL) {
|
||||
fprintf(stderr," Unable to find forcefield keyword %s\n",item->keyword);
|
||||
fprintf(stderr," Check consistency of forcefield name and class \n");
|
||||
fprintf(stderr," Exiting....\n");
|
||||
exit(1);
|
||||
}
|
||||
if (line[0] == '#') {
|
||||
if (string_match(strtok(line," '\t'("),item->keyword)) got_it = 1;
|
||||
}
|
||||
/* if (strncmp(line, item->keyword,strlen(item->keyword))==0) got_it = 1; */
|
||||
}
|
||||
|
||||
file_pos = ftell(FrcF);
|
||||
|
||||
/* Count the number of lines until next item is found */
|
||||
|
||||
while( strncmp(fgets(line,MAX_LINE_LENGTH,FrcF), "#", 1) != 0 )
|
||||
ctr++;
|
||||
|
||||
/* Allocate the memory using calloc */
|
||||
|
||||
item->data = (struct FrcFieldData *)calloc(ctr, sizeof(struct FrcFieldData));
|
||||
|
||||
if (item->data == NULL) {
|
||||
fprintf(stderr,"Could not allocate memory to %s\n", item->keyword);
|
||||
exit(2);
|
||||
}
|
||||
|
||||
/********************FILL PARAMETERS AND EQUIVALENCES ********************/
|
||||
|
||||
/* Read lines until keyword is found */
|
||||
|
||||
fseek(FrcF,file_pos,SEEK_SET);
|
||||
strcpy(line,"empty");
|
||||
|
||||
/* Read lines until data starts (when !--- is found) */
|
||||
|
||||
ctr = 0;
|
||||
while ( strncmp(line,"!---", 4) != 0 ) {
|
||||
fgets(line, MAX_LINE_LENGTH, FrcF);
|
||||
}
|
||||
|
||||
/* Get first line of data that isn't commented out */
|
||||
|
||||
fgets(line, MAX_LINE_LENGTH, FrcF);
|
||||
while (strncmp(line,"!",1) == 0) {
|
||||
fgets( line, MAX_LINE_LENGTH, FrcF);
|
||||
}
|
||||
|
||||
/* Read data into structure */
|
||||
|
||||
while( strncmp( line, "#", 1 ) != 0 ) {
|
||||
|
||||
float version;
|
||||
int reference,replace;
|
||||
char atom_types[5][5];
|
||||
double parameters[8];
|
||||
|
||||
/* version number and reference number */
|
||||
|
||||
version = atof(strtok(line, " "));
|
||||
reference = atoi(strtok(NULL, " "));
|
||||
|
||||
/* equivalences */
|
||||
|
||||
for(i = 0; i < item->number_of_members; i++ ) {
|
||||
sscanf(strtok(NULL, " "), "%s", atom_types[i]);
|
||||
}
|
||||
|
||||
/* parameters -- Because of symmetrical terms, bonang, angtor, and
|
||||
endbontor have to be treated carefully */
|
||||
|
||||
for( i = 0; i < item->number_of_parameters; i++ ) {
|
||||
charptr = strtok(NULL, " ");
|
||||
if(charptr == NULL) {
|
||||
for ( j = i; j < item->number_of_parameters; j++ )
|
||||
parameters[j] = parameters[j-i];
|
||||
break;
|
||||
}
|
||||
else {
|
||||
parameters[i] = atof(charptr);
|
||||
}
|
||||
}
|
||||
/* Search for matching sets of atom types.
|
||||
If found and the version number is greater, substitute
|
||||
the current set of parameters in place of the found set.
|
||||
Otherwise, add the current set of parameters to the
|
||||
list.
|
||||
*/
|
||||
replace = ctr;
|
||||
for (j=0; j < ctr; j++) {
|
||||
|
||||
int k=0;
|
||||
int match = 1;
|
||||
while (match && (k < item->number_of_members)) {
|
||||
if (strncmp(item->data[j].ff_types[k],atom_types[k],5) == 0)
|
||||
k++;
|
||||
else
|
||||
match = 0;
|
||||
}
|
||||
if (match == 1) {
|
||||
replace = j;
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (replace != ctr) {
|
||||
if (version > item->data[replace].ver) {
|
||||
|
||||
if (pflag > 1) {
|
||||
fprintf(stderr," Using higher version of parameters for");
|
||||
fprintf(stderr," %s ",item->keyword);
|
||||
for (i=0; i < item->number_of_members; i++)
|
||||
fprintf(stderr,"%s ",atom_types[i]);
|
||||
fprintf(stderr," version %3.2f\n",version);
|
||||
}
|
||||
|
||||
item->data[replace].ver = version;
|
||||
item->data[replace].ref = reference;
|
||||
for (i=0; i < item->number_of_members; i++) {
|
||||
strncpy(item->data[replace].ff_types[i],atom_types[i],5);
|
||||
}
|
||||
for (i=0; i < item->number_of_parameters; i++) {
|
||||
item->data[replace].ff_param[i] = parameters[i];
|
||||
}
|
||||
} else {
|
||||
if (pflag > 1) {
|
||||
fprintf(stderr," Using higher version of parameters for");
|
||||
fprintf(stderr," %s ",item->keyword);
|
||||
for (i=0; i < item->number_of_members; i++)
|
||||
fprintf(stderr,"%s ",item->data[replace].ff_types[i]);
|
||||
fprintf(stderr," version %3.2f\n",item->data[replace].ver);
|
||||
}
|
||||
}
|
||||
} else {
|
||||
item->data[ctr].ver = version;
|
||||
item->data[ctr].ref = reference;
|
||||
for (i=0; i < item->number_of_members; i++) {
|
||||
strncpy(item->data[ctr].ff_types[i],atom_types[i],5);
|
||||
}
|
||||
for (i=0; i < item->number_of_parameters; i++) {
|
||||
item->data[ctr].ff_param[i] = parameters[i];
|
||||
}
|
||||
ctr++;
|
||||
}
|
||||
fgets( line, MAX_LINE_LENGTH, FrcF);
|
||||
/*if blank line encountered, get next */
|
||||
while((blank_line(line)) ||
|
||||
(strncmp(line,"!",1) == 0)) {
|
||||
status = fgets( line, MAX_LINE_LENGTH, FrcF);
|
||||
if (status == NULL) break;
|
||||
}
|
||||
}
|
||||
item->entries = ctr;
|
||||
|
||||
/*Debugging
|
||||
fprintf(stderr,"\n%s\n", item->keyword);
|
||||
for(i=0;i<ctr;i++) {
|
||||
for(j=0;j<item->number_of_members;j++)
|
||||
fprintf(stderr,"%3s ", item->data[i].ff_equiv[j]);
|
||||
fprintf(stderr," ");
|
||||
for(j=0;j<item->number_of_parameters;j++)
|
||||
fprintf(stderr,"%10.5f ",item->data[i].ff_param[j]);
|
||||
fprintf(stderr,"\n");
|
||||
}
|
||||
*/
|
||||
}
|
||||
|
||||
unsigned char string_match(char *string1,char *string2)
|
||||
{
|
||||
int len1,len2;
|
||||
|
||||
len1 = strlen(string1);
|
||||
len2 = strlen(string2);
|
||||
|
||||
if (len1 != len2) {
|
||||
return 0;
|
||||
}
|
||||
else {
|
||||
if (strncmp(string1,string2,len1) == 0) {
|
||||
return 1;
|
||||
}
|
||||
else {
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,331 @@
|
|||
/*
|
||||
* This function creates and writes the data file to be used with LAMMPS
|
||||
*/
|
||||
|
||||
#include "msi2lmp.h"
|
||||
#include "Forcefield.h"
|
||||
|
||||
#include <stdlib.h>
|
||||
|
||||
void WriteDataFile01(char *nameroot,int forcefield)
|
||||
{
|
||||
int i,j,k,m;
|
||||
char line[MAX_LINE_LENGTH];
|
||||
FILE *DatF;
|
||||
|
||||
/* Open data file */
|
||||
|
||||
sprintf(line,"%s.lammps01",rootname);
|
||||
if (pflag > 0) printf(" Writing LAMMPS 2001 data file: %s\n",line);
|
||||
if( (DatF = fopen(line,"w")) == NULL ) {
|
||||
printf("Cannot open %s\n",line);
|
||||
exit(52);
|
||||
}
|
||||
|
||||
if (forcefield == 1) total_no_angle_angles = 0;
|
||||
|
||||
fprintf(DatF, "LAMMPS data file for %s\n\n", nameroot);
|
||||
fprintf(DatF, " %6d atoms\n", total_no_atoms);
|
||||
fprintf(DatF, " %6d bonds\n", total_no_bonds);
|
||||
fprintf(DatF, " %6d angles\n",total_no_angles);
|
||||
fprintf(DatF, " %6d dihedrals\n", total_no_dihedrals);
|
||||
fprintf(DatF, " %6d impropers\n", total_no_oops+total_no_angle_angles);
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
|
||||
fprintf(DatF, " %3d atom types\n", no_atom_types);
|
||||
if (no_bond_types > 0)
|
||||
fprintf(DatF, " %3d bond types\n", no_bond_types);
|
||||
if (no_angle_types> 0)
|
||||
fprintf(DatF, " %3d angle types\n", no_angle_types);
|
||||
if (no_dihedral_types > 0) fprintf (DatF," %3d dihedral types\n",
|
||||
no_dihedral_types);
|
||||
if (forcefield > 1) {
|
||||
if ((no_oop_types + no_angleangle_types) > 0)
|
||||
fprintf (DatF, " %3d improper types\n",
|
||||
no_oop_types + no_angleangle_types);
|
||||
}
|
||||
else {
|
||||
if (no_oop_types > 0)
|
||||
fprintf (DatF, " %3d improper types\n", no_oop_types);
|
||||
}
|
||||
|
||||
fprintf(DatF, "\n");
|
||||
fprintf(DatF, " %15.9f %15.9f xlo xhi\n", pbc[0], pbc[3]);
|
||||
fprintf(DatF, " %15.9f %15.9f ylo yhi\n", pbc[1], pbc[4]);
|
||||
fprintf(DatF, " %15.9f %15.9f zlo zhi\n", pbc[2], pbc[5]);
|
||||
|
||||
/* MASSES */
|
||||
|
||||
|
||||
fprintf(DatF, "\nMasses\n\n");
|
||||
for(k=0; k < no_atom_types; k++)
|
||||
fprintf(DatF, " %3d %10.6f\n",k+1,atomtypes[k].mass);
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
|
||||
/* COEFFICIENTS */
|
||||
|
||||
fprintf(DatF,"Nonbond Coeffs\n\n");
|
||||
for (i=0; i < no_atom_types; i++) {
|
||||
fprintf(DatF, " %3i ", i+1);
|
||||
for ( j = 0; j < 2; j++)
|
||||
fprintf(DatF, "%14.10f ", atomtypes[i].params[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
if (no_bond_types > 0) {
|
||||
if (forcefield == 1) m = 2;
|
||||
if (forcefield == 2) m = 4;
|
||||
|
||||
fprintf(DatF,"Bond Coeffs\n\n");
|
||||
for (i=0; i < no_bond_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < m; j++)
|
||||
fprintf(DatF, "%10.4f ", bondtypes[i].params[j]);
|
||||
fprintf(DatF,"\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
if (no_angle_types > 0) {
|
||||
|
||||
m = 2; /* forcefield == 1 */
|
||||
if (forcefield == 2) m = 4;
|
||||
|
||||
fprintf(DatF,"Angle Coeffs\n\n");
|
||||
for (i=0; i < no_angle_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < m; j++)
|
||||
|
||||
fprintf(DatF, "%10.4f ", angletypes[i].params[j]);
|
||||
fprintf(DatF,"\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
if (no_dihedral_types > 0) {
|
||||
m = 3; /* forcefield == 1 */
|
||||
if (forcefield == 2) m = 6;
|
||||
|
||||
fprintf(DatF,"Dihedral Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < m; j++)
|
||||
fprintf(DatF, "%10.4f ", dihedraltypes[i].params[j]);
|
||||
fprintf(DatF,"\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
if (forcefield == 1) {
|
||||
if (no_oop_types > 0) {
|
||||
fprintf(DatF,"Improper Coeffs\n\n");
|
||||
for (i=0; i < no_oop_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 3; j++)
|
||||
fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
}
|
||||
else if (forcefield == 2) {
|
||||
if ((no_oop_types + no_angleangle_types) > 0) {
|
||||
fprintf(DatF,"Improper Coeffs\n\n");
|
||||
for (i=0; i < no_oop_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 2; j++)
|
||||
fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
for (i=0; i < no_angleangle_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+no_oop_types+1);
|
||||
for ( j = 0; j < 2; j++)
|
||||
fprintf(DatF, "%10.4f ", 0.0);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
}
|
||||
if (forcefield == 2) {
|
||||
|
||||
if (no_angle_types > 0) {
|
||||
fprintf(DatF,"BondBond Coeffs\n\n");
|
||||
for (i=0; i < no_angle_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 3; j++)
|
||||
fprintf(DatF, "%10.4f ", angletypes[i].bondbond_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
fprintf(DatF,"BondAngle Coeffs\n\n");
|
||||
|
||||
for (i=0; i < no_angle_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 4; j++)
|
||||
fprintf(DatF, "%10.4f ",angletypes[i].bondangle_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
if ((no_oop_types+no_angleangle_types) > 0) {
|
||||
fprintf(DatF,"AngleAngle Coeffs\n\n");
|
||||
for (i=0; i < no_oop_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 6; j++)
|
||||
fprintf(DatF, "%10.4f ", ooptypes[i].angleangle_params[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
for (i=0; i < no_angleangle_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+no_oop_types+1);
|
||||
for ( j = 0; j < 6; j++)
|
||||
fprintf(DatF, "%10.4f ", angleangletypes[i].params[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
if (no_dihedral_types > 0) {
|
||||
fprintf(DatF,"AngleAngleTorsion Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 3; j++)
|
||||
fprintf(DatF,"%10.4f ",
|
||||
dihedraltypes[i].angleangledihedral_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
fprintf(DatF,"EndBondTorsion Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%i ", i+1);
|
||||
for ( j = 0; j < 8; j++)
|
||||
fprintf(DatF, "%10.4f ",
|
||||
dihedraltypes[i].endbonddihedral_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
fprintf(DatF,"MiddleBondTorsion Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 4; j++)
|
||||
fprintf(DatF,"%10.4f ",
|
||||
dihedraltypes[i].midbonddihedral_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
|
||||
fprintf(DatF,"BondBond13 Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 3; j++)
|
||||
fprintf(DatF, "%10.4f ",
|
||||
dihedraltypes[i].bond13_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
fprintf(DatF,"AngleTorsion Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 8; j++)
|
||||
fprintf(DatF, "%10.4f ",
|
||||
dihedraltypes[i].angledihedral_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
}
|
||||
|
||||
/*--------------------------------------------------------------------*/
|
||||
|
||||
/* ATOMS */
|
||||
|
||||
fprintf(DatF, "Atoms\n\n");
|
||||
for(k=0; k < total_no_atoms; k++) {
|
||||
fprintf(DatF, " %6i %6i %3i %9.6f %15.9f %15.9f %15.9f\n",
|
||||
k+1,
|
||||
atoms[k].molecule,
|
||||
atoms[k].type+1,
|
||||
atoms[k].q,
|
||||
atoms[k].x[0],
|
||||
atoms[k].x[1],
|
||||
atoms[k].x[2]);
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
/***** BONDS *****/
|
||||
|
||||
if (total_no_bonds > 0) {
|
||||
fprintf(DatF, "Bonds\n\n");
|
||||
for(k=0; k < total_no_bonds; k++)
|
||||
fprintf(DatF, "%6i %3i %6i %6i\n",k+1,
|
||||
bonds[k].type+1,
|
||||
bonds[k].members[0]+1,
|
||||
bonds[k].members[1]+1);
|
||||
fprintf(DatF,"\n");
|
||||
}
|
||||
|
||||
/***** ANGLES *****/
|
||||
|
||||
if (total_no_angles > 0) {
|
||||
fprintf(DatF, "Angles\n\n");
|
||||
for(k=0; k < total_no_angles; k++)
|
||||
fprintf(DatF, "%6i %3i %6i %6i %6i\n",k+1,
|
||||
angles[k].type+1,
|
||||
angles[k].members[0]+1,
|
||||
angles[k].members[1]+1,
|
||||
angles[k].members[2]+1);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
|
||||
/***** TORSIONS *****/
|
||||
|
||||
if (total_no_dihedrals > 0) {
|
||||
fprintf(DatF,"Dihedrals\n\n");
|
||||
for(k=0; k < total_no_dihedrals; k++)
|
||||
fprintf(DatF, "%6i %3i %6i %6i %6i %6i\n",k+1,
|
||||
dihedrals[k].type+1,
|
||||
dihedrals[k].members[0]+1,
|
||||
dihedrals[k].members[1]+1,
|
||||
dihedrals[k].members[2]+1,
|
||||
dihedrals[k].members[3]+1);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
/***** OUT-OF-PLANES *****/
|
||||
|
||||
if (total_no_oops+total_no_angle_angles > 0) {
|
||||
fprintf(DatF,"Impropers\n\n");
|
||||
for (k=0; k < total_no_oops; k++)
|
||||
fprintf(DatF, "%6i %3i %6i %6i %6i %6i \n", k+1,
|
||||
oops[k].type+1,
|
||||
oops[k].members[0]+1,
|
||||
oops[k].members[1]+1,
|
||||
oops[k].members[2]+1,
|
||||
oops[k].members[3]+1);
|
||||
if (forcefield == 2) {
|
||||
for (k=0; k < total_no_angle_angles; k++)
|
||||
fprintf(DatF, "%6i %3i %6i %6i %6i %6i \n",k+total_no_oops+1,
|
||||
angleangles[k].type+no_oop_types+1,
|
||||
angleangles[k].members[0]+1,
|
||||
angleangles[k].members[1]+1,
|
||||
angleangles[k].members[2]+1,
|
||||
angleangles[k].members[3]+1);
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
/* Close data file */
|
||||
|
||||
if (fclose(DatF) !=0) {
|
||||
printf("Error closing %s.lammps01\n", rootname);
|
||||
exit(51);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,350 @@
|
|||
/*
|
||||
* This function creates and writes the data file to be used with LAMMPS
|
||||
*/
|
||||
|
||||
#include "msi2lmp.h"
|
||||
#include "Forcefield.h"
|
||||
|
||||
#include <stdlib.h>
|
||||
|
||||
void WriteDataFile05(char *nameroot,int forcefield)
|
||||
{
|
||||
int i,j,k,m;
|
||||
char line[MAX_LINE_LENGTH];
|
||||
FILE *DatF;
|
||||
|
||||
/* Open data file */
|
||||
|
||||
sprintf(line,"%s.lammps05",rootname);
|
||||
if (pflag > 0) printf(" Writing LAMMPS 2005 data file: %s\n",line);
|
||||
if( (DatF = fopen(line,"w")) == NULL ) {
|
||||
printf("Cannot open %s\n",line);
|
||||
exit(62);
|
||||
}
|
||||
|
||||
if (forcefield == 1) total_no_angle_angles = 0;
|
||||
|
||||
fprintf(DatF, "LAMMPS 2005 data file for %s\n\n", nameroot);
|
||||
fprintf(DatF, " %6d atoms\n", total_no_atoms);
|
||||
fprintf(DatF, " %6d bonds\n", total_no_bonds);
|
||||
fprintf(DatF, " %6d angles\n",total_no_angles);
|
||||
fprintf(DatF, " %6d dihedrals\n", total_no_dihedrals);
|
||||
fprintf(DatF, " %6d impropers\n", total_no_oops+total_no_angle_angles);
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
|
||||
fprintf(DatF, " %3d atom types\n", no_atom_types);
|
||||
if (no_bond_types > 0)
|
||||
fprintf(DatF, " %3d bond types\n", no_bond_types);
|
||||
if (no_angle_types> 0)
|
||||
fprintf(DatF, " %3d angle types\n", no_angle_types);
|
||||
if (no_dihedral_types > 0) fprintf (DatF," %3d dihedral types\n",
|
||||
no_dihedral_types);
|
||||
if (forcefield > 1) {
|
||||
if ((no_oop_types + no_angleangle_types) > 0)
|
||||
fprintf (DatF, " %3d improper types\n",
|
||||
no_oop_types + no_angleangle_types);
|
||||
}
|
||||
else {
|
||||
if (no_oop_types > 0)
|
||||
fprintf (DatF, " %3d improper types\n", no_oop_types);
|
||||
}
|
||||
|
||||
|
||||
// Modified by SLTM to print out triclinic box types 10/05/10 - lines 56-68
|
||||
|
||||
if (TriclinicFlag == 0) {
|
||||
fprintf(DatF, "\n");
|
||||
fprintf(DatF, " %15.9f %15.9f xlo xhi\n", pbc[0], pbc[3]);
|
||||
fprintf(DatF, " %15.9f %15.9f ylo yhi\n", pbc[1], pbc[4]);
|
||||
fprintf(DatF, " %15.9f %15.9f zlo zhi\n", pbc[2], pbc[5]);
|
||||
}
|
||||
else {
|
||||
fprintf(DatF, "\n");
|
||||
fprintf(DatF, " %15.9f %15.9f xlo xhi\n", 0.0, pbc[0]);
|
||||
fprintf(DatF, " %15.9f %15.9f ylo yhi\n", 0.0, pbc[1]);
|
||||
fprintf(DatF, " %15.9f %15.9f zlo zhi\n", 0.0, pbc[2]);
|
||||
fprintf(DatF, " %15.9f %15.9f %15.9f xy xz yz\n", pbc[3], pbc[4], pbc[5]);
|
||||
}
|
||||
|
||||
|
||||
/* MASSES */
|
||||
|
||||
|
||||
fprintf(DatF, "\nMasses\n\n");
|
||||
for(k=0; k < no_atom_types; k++)
|
||||
fprintf(DatF, " %3d %10.6f\n",k+1,atomtypes[k].mass);
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
|
||||
/* COEFFICIENTS */
|
||||
|
||||
fprintf(DatF,"Pair Coeffs\n\n");
|
||||
for (i=0; i < no_atom_types; i++) {
|
||||
fprintf(DatF, " %3i ", i+1);
|
||||
for ( j = 0; j < 2; j++)
|
||||
fprintf(DatF, "%14.10f ", atomtypes[i].params[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
if (no_bond_types > 0) {
|
||||
if (forcefield == 1) m = 2;
|
||||
if (forcefield == 2) m = 4;
|
||||
|
||||
fprintf(DatF,"Bond Coeffs\n\n");
|
||||
for (i=0; i < no_bond_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < m; j++)
|
||||
fprintf(DatF, "%10.4f ", bondtypes[i].params[j]);
|
||||
fprintf(DatF,"\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
if (no_angle_types > 0) {
|
||||
m = 2; /* forcefield == 1 */
|
||||
if (forcefield == 2) m = 4;
|
||||
|
||||
fprintf(DatF,"Angle Coeffs\n\n");
|
||||
for (i=0; i < no_angle_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < m; j++)
|
||||
|
||||
fprintf(DatF, "%10.4f ", angletypes[i].params[j]);
|
||||
fprintf(DatF,"\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
if (no_dihedral_types > 0) {
|
||||
m = 3; /* forcefield == 1 */
|
||||
if (forcefield == 2) m = 6;
|
||||
|
||||
fprintf(DatF,"Dihedral Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < m; j++)
|
||||
// Modified on 10/05/2010 by STLM to match with lammps reading in integers for the all but the first coefficients
|
||||
if (j == 0)
|
||||
fprintf(DatF, "%10.4f ", dihedraltypes[i].params[j]);
|
||||
else fprintf(DatF, "%10.0f ", dihedraltypes[i].params[j]);
|
||||
fprintf(DatF,"\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
if (forcefield == 1) {
|
||||
if (no_oop_types > 0) {
|
||||
fprintf(DatF,"Improper Coeffs\n\n");
|
||||
for (i=0; i < no_oop_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 3; j++)
|
||||
// Modified on 10/05/2010 by STLM to match with lammps reading in integers for the all but the first coefficients
|
||||
if (j == 0)
|
||||
fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
|
||||
else fprintf(DatF, "%10.0f ", ooptypes[i].params[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
}
|
||||
else if (forcefield == 2) {
|
||||
if ((no_oop_types + no_angleangle_types) > 0) {
|
||||
fprintf(DatF,"Improper Coeffs\n\n");
|
||||
for (i=0; i < no_oop_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 2; j++)
|
||||
fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
for (i=0; i < no_angleangle_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+no_oop_types+1);
|
||||
for ( j = 0; j < 2; j++)
|
||||
fprintf(DatF, "%10.4f ", 0.0);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
}
|
||||
if (forcefield == 2) {
|
||||
|
||||
if (no_angle_types > 0) {
|
||||
fprintf(DatF,"BondBond Coeffs\n\n");
|
||||
for (i=0; i < no_angle_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 3; j++)
|
||||
fprintf(DatF, "%10.4f ", angletypes[i].bondbond_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
fprintf(DatF,"BondAngle Coeffs\n\n");
|
||||
|
||||
for (i=0; i < no_angle_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 4; j++)
|
||||
fprintf(DatF, "%10.4f ",angletypes[i].bondangle_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
if ((no_oop_types+no_angleangle_types) > 0) {
|
||||
fprintf(DatF,"AngleAngle Coeffs\n\n");
|
||||
for (i=0; i < no_oop_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 6; j++)
|
||||
fprintf(DatF, "%10.4f ", ooptypes[i].angleangle_params[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
for (i=0; i < no_angleangle_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+no_oop_types+1);
|
||||
for ( j = 0; j < 6; j++)
|
||||
fprintf(DatF, "%10.4f ", angleangletypes[i].params[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
if (no_dihedral_types > 0) {
|
||||
fprintf(DatF,"AngleAngleTorsion Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 3; j++)
|
||||
fprintf(DatF,"%10.4f ",
|
||||
dihedraltypes[i].angleangledihedral_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
fprintf(DatF,"EndBondTorsion Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%i ", i+1);
|
||||
for ( j = 0; j < 8; j++)
|
||||
fprintf(DatF, "%10.4f ",
|
||||
dihedraltypes[i].endbonddihedral_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
fprintf(DatF,"MiddleBondTorsion Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 4; j++)
|
||||
fprintf(DatF,"%10.4f ",
|
||||
dihedraltypes[i].midbonddihedral_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
|
||||
fprintf(DatF,"BondBond13 Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 3; j++)
|
||||
fprintf(DatF, "%10.4f ",
|
||||
dihedraltypes[i].bond13_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
fprintf(DatF,"AngleTorsion Coeffs\n\n");
|
||||
for (i=0; i < no_dihedral_types; i++) {
|
||||
fprintf(DatF, "%3i ", i+1);
|
||||
for ( j = 0; j < 8; j++)
|
||||
fprintf(DatF, "%10.4f ",
|
||||
dihedraltypes[i].angledihedral_cross_term[j]);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
}
|
||||
|
||||
/*--------------------------------------------------------------------*/
|
||||
|
||||
/* ATOMS */
|
||||
|
||||
fprintf(DatF, "Atoms\n\n");
|
||||
for(k=0; k < total_no_atoms; k++) {
|
||||
fprintf(DatF, " %6i %6i %3i %9.6f %15.9f %15.9f %15.9f\n",
|
||||
k+1,
|
||||
atoms[k].molecule,
|
||||
atoms[k].type+1,
|
||||
atoms[k].q,
|
||||
atoms[k].x[0],
|
||||
atoms[k].x[1],
|
||||
atoms[k].x[2]);
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
|
||||
/***** BONDS *****/
|
||||
|
||||
if (total_no_bonds > 0) {
|
||||
fprintf(DatF, "Bonds\n\n");
|
||||
for(k=0; k < total_no_bonds; k++)
|
||||
fprintf(DatF, "%6i %3i %6i %6i\n",k+1,
|
||||
bonds[k].type+1,
|
||||
bonds[k].members[0]+1,
|
||||
bonds[k].members[1]+1);
|
||||
fprintf(DatF,"\n");
|
||||
}
|
||||
|
||||
/***** ANGLES *****/
|
||||
|
||||
if (total_no_angles > 0) {
|
||||
fprintf(DatF, "Angles\n\n");
|
||||
for(k=0; k < total_no_angles; k++)
|
||||
fprintf(DatF, "%6i %3i %6i %6i %6i\n",k+1,
|
||||
angles[k].type+1,
|
||||
angles[k].members[0]+1,
|
||||
angles[k].members[1]+1,
|
||||
angles[k].members[2]+1);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
|
||||
/***** TORSIONS *****/
|
||||
|
||||
if (total_no_dihedrals > 0) {
|
||||
fprintf(DatF,"Dihedrals\n\n");
|
||||
for(k=0; k < total_no_dihedrals; k++)
|
||||
fprintf(DatF, "%6i %3i %6i %6i %6i %6i\n",k+1,
|
||||
dihedrals[k].type+1,
|
||||
dihedrals[k].members[0]+1,
|
||||
dihedrals[k].members[1]+1,
|
||||
dihedrals[k].members[2]+1,
|
||||
dihedrals[k].members[3]+1);
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
/***** OUT-OF-PLANES *****/
|
||||
|
||||
if (total_no_oops+total_no_angle_angles > 0) {
|
||||
fprintf(DatF,"Impropers\n\n");
|
||||
for (k=0; k < total_no_oops; k++)
|
||||
fprintf(DatF, "%6i %3i %6i %6i %6i %6i \n", k+1,
|
||||
oops[k].type+1,
|
||||
oops[k].members[0]+1,
|
||||
oops[k].members[1]+1,
|
||||
oops[k].members[2]+1,
|
||||
oops[k].members[3]+1);
|
||||
if (forcefield == 2) {
|
||||
for (k=0; k < total_no_angle_angles; k++)
|
||||
fprintf(DatF, "%6i %3i %6i %6i %6i %6i \n",k+total_no_oops+1,
|
||||
angleangles[k].type+no_oop_types+1,
|
||||
angleangles[k].members[0]+1,
|
||||
angleangles[k].members[1]+1,
|
||||
angleangles[k].members[2]+1,
|
||||
angleangles[k].members[3]+1);
|
||||
}
|
||||
fprintf(DatF, "\n");
|
||||
}
|
||||
|
||||
/* Close data file */
|
||||
|
||||
if (fclose(DatF) !=0) {
|
||||
printf("Error closing %s.lammps05\n", rootname);
|
||||
exit(61);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,348 @@
|
|||
/*
|
||||
*
|
||||
* msi2lmp.exe V3.6
|
||||
*
|
||||
* v3.6 KLA - Changes to output to either lammps 2001 (F90 version) or to
|
||||
* lammps 2005 (C++ version)
|
||||
*
|
||||
* v3.4 JEC - a number of minor changes due to way newline and EOF are generated
|
||||
* on Materials Studio generated .car and .mdf files as well as odd
|
||||
* behavior out of newer Linux IO libraries. ReadMdfFile was restructured
|
||||
* in the process.
|
||||
*
|
||||
* v3.1 JEC - changed IO interface to standard in/out, forcefield file
|
||||
* location can be indicated by environmental variable; added
|
||||
* printing options, consistency checks and forcefield
|
||||
* parameter versions sensitivity (highest one used)
|
||||
*
|
||||
* v3.0 JEC - program substantially rewritten to reduce execution time
|
||||
* and be 98 % dynamic in memory use (still fixed limits on
|
||||
* number of parameter types for different internal coordinate
|
||||
* sets)
|
||||
*
|
||||
* v2.0 MDP - got internal coordinate information from mdf file and
|
||||
* forcefield parameters from frc file thus eliminating
|
||||
* need for Discover
|
||||
*
|
||||
* V1.0 SL - original version. Used .car file and internal coordinate
|
||||
* information from Discover to produce LAMMPS data file.
|
||||
*
|
||||
* This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
|
||||
* program to produce a LAMMPS data file.
|
||||
*
|
||||
* The program is started by supplying information at the command prompt
|
||||
* according to the usage described below.
|
||||
*
|
||||
* USAGE: msi2lmp3 ROOTNAME {-print #} {-class #} {-frc FRC_FILE} -2001
|
||||
*
|
||||
* -- msi2lmp3 is the name of the executable
|
||||
* -- ROOTNAME is the base name of the .car and .mdf files
|
||||
*
|
||||
* -- -print
|
||||
* # is the print level: 0 - silent except for errors
|
||||
* 1 - minimal (default)
|
||||
* 2 - more verbose
|
||||
* 3 - even more verbose
|
||||
* -- -class
|
||||
* # is the class of forcefield to use (I = Class I e.g., CVFF)
|
||||
* (II = Class II e.g., CFFx )
|
||||
* default is -class I
|
||||
*
|
||||
* -- -frc - specifies name of the forcefield file (e.g., cff91)
|
||||
*
|
||||
* If the name includes a hard wired directory (i.e., if the name
|
||||
* starts with . or /), then the name is used alone. Otherwise,
|
||||
* the program looks for the forcefield file in $BIOSYM_LIBRARY.
|
||||
* If $BIOSYM_LIBRARY is not set, then the current directory is
|
||||
* used.
|
||||
*
|
||||
* If the file name does not include a dot after the first
|
||||
* character, then .frc is appended to the name.
|
||||
*
|
||||
* For example, -frc cvff (assumes cvff.frc is in $BIOSYM_LIBRARY
|
||||
* or .)
|
||||
*
|
||||
* -frc cff/cff91 (assumes cff91.frc is in
|
||||
* $BIOSYM_LIBRARY/cff or ./cff)
|
||||
*
|
||||
* -frc /usr/local/biosym/forcefields/cff95 (absolute
|
||||
* location)
|
||||
*
|
||||
* By default, the program uses $BIOSYM_LIBRARY/cvff.frc
|
||||
*
|
||||
* -- -2001 will output a data file for the FORTRAN 90 version of LAMMPS (2001)
|
||||
* By default, the program will output for the C++ version of LAMMPS.
|
||||
*
|
||||
* -- output is written to a file called ROOTNAME.lammps{01/05}
|
||||
*
|
||||
*
|
||||
****************************************************************
|
||||
*
|
||||
* Msi2lmp3
|
||||
*
|
||||
* This is the third version of a program that generates a LAMMPS
|
||||
* data file based on the information in a MSI car file (atom
|
||||
* coordinates) and mdf file (molecular topology). A key part of
|
||||
* the program looks up forcefield parameters from an MSI frc file.
|
||||
*
|
||||
* The first version was written by Steve Lustig at Dupont, but
|
||||
* required using Discover to derive internal coordinates and
|
||||
* forcefield parameters
|
||||
*
|
||||
* The second version was written by Michael Peachey while an
|
||||
* in intern in the Cray Chemistry Applications Group managed
|
||||
* by John Carpenter. This version derived internal coordinates
|
||||
* from the mdf file and looked up parameters in the frc file
|
||||
* thus eliminating the need for Discover.
|
||||
*
|
||||
* The third version was written by John Carpenter to optimize
|
||||
* the performance of the program for large molecular systems
|
||||
* (the original code for deriving atom numbers was quadratic in time)
|
||||
* and to make the program fully dynamic. The second version used
|
||||
* fixed dimension arrays for the internal coordinates.
|
||||
*
|
||||
* John Carpenter can be contacted by sending email to
|
||||
* jec374@earthlink.net
|
||||
*
|
||||
* November 2000
|
||||
*/
|
||||
|
||||
#include "msi2lmp.h"
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <ctype.h>
|
||||
|
||||
/* global variables */
|
||||
|
||||
char *rootname;
|
||||
double pbc[9];
|
||||
int periodic = 1;
|
||||
int TriclinicFlag = 0;
|
||||
int forcefield = 0;
|
||||
|
||||
int pflag;
|
||||
int iflag;
|
||||
int *no_atoms;
|
||||
int no_molecules;
|
||||
int replicate[3];
|
||||
int total_no_atoms;
|
||||
int total_no_bonds;
|
||||
int total_no_angles;
|
||||
int total_no_dihedrals;
|
||||
int total_no_angle_angles;
|
||||
int total_no_oops;
|
||||
int no_atom_types;
|
||||
int no_bond_types;
|
||||
int no_angle_types;
|
||||
int no_dihedral_types;
|
||||
int no_oop_types;
|
||||
int no_angleangle_types;
|
||||
char *FrcFileName;
|
||||
FILE *CarF;
|
||||
FILE *FrcF;
|
||||
FILE *PrmF;
|
||||
FILE *MdfF;
|
||||
FILE *RptF;
|
||||
|
||||
struct Atom *atoms;
|
||||
struct MoleculeList *molecule;
|
||||
struct BondList *bonds;
|
||||
struct AngleList *angles;
|
||||
struct DihedralList *dihedrals;
|
||||
struct OOPList *oops;
|
||||
struct AngleAngleList *angleangles;
|
||||
struct AtomTypeList *atomtypes;
|
||||
struct BondTypeList *bondtypes;
|
||||
struct AngleTypeList *angletypes;
|
||||
struct DihedralTypeList *dihedraltypes;
|
||||
struct OOPTypeList *ooptypes;
|
||||
struct AngleAngleTypeList *angleangletypes;
|
||||
|
||||
|
||||
static int check_arg(char **arg, const char *flag, int num, int argc)
|
||||
{
|
||||
if (num >= argc) {
|
||||
printf("Missing argument to \"%s\" flag\n",flag);
|
||||
return 1;
|
||||
}
|
||||
if (arg[num][0] == '-') {
|
||||
printf("Incorrect argument to \"%s\" flag: %s\n",flag,arg[num]);
|
||||
return 1;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
int main (int argc, char *argv[])
|
||||
{
|
||||
int n,i,found_sep; /* Counter */
|
||||
int outv;
|
||||
const char *frc_dir_name = NULL;
|
||||
const char *frc_file_name = NULL;
|
||||
|
||||
outv = 2005;
|
||||
pflag = 1;
|
||||
iflag = 0;
|
||||
forcefield = 1;
|
||||
|
||||
frc_dir_name = getenv("BIOSYM_LIBRARY");
|
||||
|
||||
if (argc < 2) {
|
||||
printf("usage: %s <rootname> [-class <I|1|II|2>] [-frc <path to frc file>] [-p #] [-i]\n",argv[0]);
|
||||
return 1;
|
||||
} else { /* rootname was supplied as first argument, copy to rootname */
|
||||
int len = strlen(argv[1]) + 1;
|
||||
rootname = (char *)malloc(len);
|
||||
strcpy(rootname,argv[1]);
|
||||
}
|
||||
|
||||
n = 2;
|
||||
while (n < argc) {
|
||||
if (strncmp(argv[n],"-c",2) == 0) {
|
||||
n++;
|
||||
if (check_arg(argv,"-class",n,argc))
|
||||
return 2;
|
||||
if ((strcmp(argv[n],"I") == 0) || (strcmp(argv[n],"1") == 0)) {
|
||||
forcefield = 1;
|
||||
} else if ((strcmp(argv[n],"II") == 0) || (strcmp(argv[n],"2") == 0)) {
|
||||
forcefield = 2;
|
||||
} else {
|
||||
printf("Unrecognized Forcefield class: %s\n",argv[n]);
|
||||
return 3;
|
||||
}
|
||||
} else if (strcmp(argv[n],"-2001") == 0) {
|
||||
outv = 2001;
|
||||
} else if (strcmp(argv[n],"-2005") == 0) {
|
||||
outv = 2005;
|
||||
} else if (strncmp(argv[n],"-f",2) == 0) {
|
||||
n++;
|
||||
if (check_arg(argv,"-frc",n,argc))
|
||||
return 4;
|
||||
frc_file_name = argv[n];
|
||||
} else if (strncmp(argv[n],"-i",2) == 0 ) {
|
||||
iflag = 1;
|
||||
} else if (strncmp(argv[n],"-p",2) == 0) {
|
||||
n++;
|
||||
if (check_arg(argv,"-print",n,argc))
|
||||
return 5;
|
||||
pflag = atoi(argv[n]);
|
||||
} else {
|
||||
printf("Unrecognized option: %s\n",argv[n]);
|
||||
return 6;
|
||||
}
|
||||
n++;
|
||||
}
|
||||
|
||||
/* set defaults, if nothing else was given */
|
||||
if (frc_dir_name == NULL)
|
||||
#if (_WIN32)
|
||||
frc_dir_name = "..\\biosym_frc_files";
|
||||
#else
|
||||
frc_dir_name = "../biosym_frc_files";
|
||||
#endif
|
||||
if (frc_file_name == NULL)
|
||||
frc_file_name = "cvff.frc";
|
||||
|
||||
found_sep=0;
|
||||
#ifdef _WIN32
|
||||
if (isalpha(frc_file_name[0]) && (frc_file_name[1] == ':'))
|
||||
found_sep=1; /* windows drive letter => full path. */
|
||||
#endif
|
||||
|
||||
n = strlen(frc_file_name);
|
||||
for (i=0; i < n; ++i) {
|
||||
#ifdef _WIN32
|
||||
if ((frc_file_name[i] == '/') || (frc_file_name[i] == '\\'))
|
||||
found_sep=1+i;
|
||||
#else
|
||||
if (frc_file_name[i] == '/')
|
||||
found_sep=1+i;
|
||||
#endif
|
||||
}
|
||||
|
||||
/* full pathname given */
|
||||
if (found_sep) {
|
||||
i = 0;
|
||||
/* need to append extension? */
|
||||
if ((n < 5) || (strcmp(frc_file_name+n-4,".frc") !=0))
|
||||
i=1;
|
||||
|
||||
FrcFileName = (char *)malloc(n+1+i*4);
|
||||
strcpy(FrcFileName,frc_file_name);
|
||||
if (i) strcat(FrcFileName,".frc");
|
||||
} else {
|
||||
i = 0;
|
||||
/* need to append extension? */
|
||||
if ((n < 5) || (strcmp(frc_file_name+n-4,".frc") !=0))
|
||||
i=1;
|
||||
|
||||
FrcFileName = (char *)malloc(n+2+i*4+strlen(frc_dir_name));
|
||||
strcpy(FrcFileName,frc_dir_name);
|
||||
#ifdef _WIN32
|
||||
strcat(FrcFileName,"\\");
|
||||
#else
|
||||
strcat(FrcFileName,"/");
|
||||
#endif
|
||||
strcat(FrcFileName,frc_file_name);
|
||||
if (i) strcat(FrcFileName,".frc");
|
||||
}
|
||||
|
||||
|
||||
if (pflag > 0) {
|
||||
printf("\nRunning msi2lmp.....\n\n");
|
||||
printf(" Forcefield file name: %s\n",FrcFileName);
|
||||
printf(" Forcefield class: %d\n\n",forcefield);
|
||||
}
|
||||
|
||||
if (((forcefield == 1) && (strstr(FrcFileName,"cff") != NULL)) ||
|
||||
((forcefield == 2) &&
|
||||
! ((strstr(FrcFileName,"cvff") == NULL)
|
||||
|| (strstr(FrcFileName,"clayff") == NULL)
|
||||
|| (strstr(FrcFileName,"compass") == NULL)))) {
|
||||
fprintf(stderr," WARNING - forcefield name and class appear to\n");
|
||||
fprintf(stderr," be inconsistent - Errors may result\n\n");
|
||||
}
|
||||
|
||||
/* Read in .car file */
|
||||
ReadCarFile();
|
||||
|
||||
/*Read in .mdf file */
|
||||
|
||||
ReadMdfFile();
|
||||
|
||||
/* Define bonds, angles, etc...*/
|
||||
|
||||
if (pflag > 0)
|
||||
printf("\n Building internal coordinate lists \n");
|
||||
MakeLists();
|
||||
|
||||
/* Read .frc file into memory */
|
||||
|
||||
if (pflag > 0)
|
||||
printf("\n Reading forcefield file \n");
|
||||
ReadFrcFile();
|
||||
|
||||
/* Get forcefield parameters */
|
||||
|
||||
if (pflag > 0)
|
||||
printf("\n Get force field parameters for this system\n");
|
||||
GetParameters(forcefield);
|
||||
|
||||
/* Do internal check of internal coordinate lists */
|
||||
if (pflag > 0)
|
||||
printf("\n Check parameters for internal consistency\n");
|
||||
CheckLists();
|
||||
|
||||
if (outv == 2001) {
|
||||
WriteDataFile01(rootname,forcefield);
|
||||
|
||||
} else if (outv == 2005) {
|
||||
WriteDataFile05(rootname,forcefield);
|
||||
}
|
||||
|
||||
free(rootname);
|
||||
if (pflag > 0)
|
||||
printf("\nNormal program termination\n");
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,204 @@
|
|||
/********************************
|
||||
*
|
||||
* Header file for msi2lmp conversion program.
|
||||
*
|
||||
* This is the header file for the third version of a program
|
||||
* that generates a LAMMPS data file based on the information
|
||||
* in an MSI car file (atom coordinates) and mdf file (molecular
|
||||
* topology). A key part of the program looks up forcefield parameters
|
||||
* from an MSI frc file.
|
||||
*
|
||||
* The first version was written by Steve Lustig at Dupont, but
|
||||
* required using Discover to derive internal coordinates and
|
||||
* forcefield parameters
|
||||
*
|
||||
* The second version was written by Michael Peachey while an
|
||||
* intern in the Cray Chemistry Applications Group managed
|
||||
* by John Carpenter. This version derived internal coordinates
|
||||
* from the mdf file and looked up parameters in the frc file
|
||||
* thus eliminating the need for Discover.
|
||||
*
|
||||
* The third version was written by John Carpenter to optimize
|
||||
* the performance of the program for large molecular systems
|
||||
* (the original code for derving atom numbers was quadratic in time)
|
||||
* and to make the program fully dynamic. The second version used
|
||||
* fixed dimension arrays for the internal coordinates.
|
||||
*
|
||||
* John Carpenter can be contacted by sending email to
|
||||
* jec374@earthlink.net
|
||||
*
|
||||
* November 2000
|
||||
*
|
||||
*
|
||||
*/
|
||||
|
||||
# include <stdio.h>
|
||||
|
||||
#define PI_180 0.01745329251994329576
|
||||
|
||||
#define MAX_LINE_LENGTH 256
|
||||
#define MAX_CONNECTIONS 8
|
||||
#define MAX_STRING 64
|
||||
#define MAX_NAME 16
|
||||
|
||||
#define MAX_ATOM_TYPES 100
|
||||
#define MAX_BOND_TYPES 200
|
||||
#define MAX_ANGLE_TYPES 300
|
||||
#define MAX_DIHEDRAL_TYPES 400
|
||||
#define MAX_OOP_TYPES 400
|
||||
#define MAX_ANGLEANGLE_TYPES 400
|
||||
#define MAX_TYPES 12000
|
||||
|
||||
struct ResidueList {
|
||||
int start;
|
||||
int end;
|
||||
char name[MAX_NAME];
|
||||
};
|
||||
|
||||
struct MoleculeList {
|
||||
int start;
|
||||
int end;
|
||||
int no_residues;
|
||||
struct ResidueList *residue;
|
||||
};
|
||||
|
||||
/* Internal coodinate Lists */
|
||||
|
||||
struct BondList {
|
||||
int type;
|
||||
int members[2];
|
||||
};
|
||||
|
||||
struct AngleList {
|
||||
int type;
|
||||
int members[3];
|
||||
};
|
||||
|
||||
struct DihedralList {
|
||||
int type;
|
||||
int members[4];
|
||||
};
|
||||
|
||||
struct OOPList {
|
||||
int type;
|
||||
int members[4];
|
||||
};
|
||||
|
||||
struct AngleAngleList {
|
||||
int type;
|
||||
int members[4];
|
||||
};
|
||||
|
||||
/* Internal coodinate Types Lists */
|
||||
|
||||
|
||||
struct AtomTypeList
|
||||
{
|
||||
char potential[5];
|
||||
float mass;
|
||||
double params[2];
|
||||
int no_connect;
|
||||
};
|
||||
|
||||
struct BondTypeList {
|
||||
int types[2];
|
||||
double params[4];
|
||||
};
|
||||
|
||||
struct AngleTypeList {
|
||||
int types[3];
|
||||
double params[4];
|
||||
double bondangle_cross_term[4];
|
||||
double bondbond_cross_term[3];
|
||||
};
|
||||
|
||||
struct DihedralTypeList {
|
||||
int types[4];
|
||||
double params[6];
|
||||
double endbonddihedral_cross_term[8];
|
||||
double midbonddihedral_cross_term[4];
|
||||
double angledihedral_cross_term[8];
|
||||
double angleangledihedral_cross_term[3];
|
||||
double bond13_cross_term[3];
|
||||
};
|
||||
|
||||
struct OOPTypeList {
|
||||
int types[4];
|
||||
double params[3];
|
||||
double angleangle_params[6];
|
||||
};
|
||||
|
||||
struct AngleAngleTypeList {
|
||||
int types[4];
|
||||
double params[6];
|
||||
};
|
||||
|
||||
/* ---------------------------------------------- */
|
||||
|
||||
struct Atom {
|
||||
int molecule; /* molecule id */
|
||||
int no; /* atom id */
|
||||
char name[MAX_NAME]; /* atom name */
|
||||
double x[3]; /* position vector */
|
||||
char potential[6]; /* atom potential type */
|
||||
char element[4]; /* atom element */
|
||||
float q; /* charge */
|
||||
char residue_string[MAX_NAME]; /* residue string */
|
||||
int no_connect; /* number of connections to atom */
|
||||
char connections[MAX_CONNECTIONS][MAX_STRING]; /* long form, connection name*/
|
||||
double bond_order[MAX_CONNECTIONS];
|
||||
int conn_no[MAX_CONNECTIONS]; /* Atom number to which atom is connected */
|
||||
int type;
|
||||
};
|
||||
|
||||
extern char *rootname;
|
||||
extern char *FrcFileName;
|
||||
extern double pbc[9];
|
||||
extern int periodic; /* 0= nonperiodic 1= 3-D periodic */
|
||||
extern int TriclinicFlag; /* 0= Orthogonal 1= Triclinic */
|
||||
extern int forcefield; /* 1= ClassI 2= ClassII */
|
||||
extern int pflag; /* print level: 0, 1, 2, 3 */
|
||||
extern int iflag; /* 0 stop at errors 1 = ignore errors */
|
||||
extern int *no_atoms;
|
||||
extern int no_molecules;
|
||||
extern int replicate[3];
|
||||
extern int total_no_atoms;
|
||||
extern int total_no_bonds;
|
||||
extern int total_no_angles;
|
||||
extern int total_no_dihedrals;
|
||||
extern int total_no_angle_angles;
|
||||
extern int total_no_oops;
|
||||
extern int no_atom_types;
|
||||
extern int no_bond_types;
|
||||
extern int no_angle_types;
|
||||
extern int no_dihedral_types;
|
||||
extern int no_oop_types;
|
||||
extern int no_angleangle_types;
|
||||
extern FILE *CarF;
|
||||
extern FILE *FrcF;
|
||||
extern FILE *PrmF;
|
||||
extern FILE *MdfF;
|
||||
extern FILE *RptF;
|
||||
extern struct Atom *atoms;
|
||||
extern struct MoleculeList *molecule;
|
||||
extern struct BondList *bonds;
|
||||
extern struct AngleList *angles;
|
||||
extern struct DihedralList *dihedrals;
|
||||
extern struct OOPList *oops;
|
||||
extern struct AngleAngleList *angleangles;
|
||||
extern struct AtomTypeList *atomtypes;
|
||||
extern struct BondTypeList *bondtypes;
|
||||
extern struct AngleTypeList *angletypes;
|
||||
extern struct DihedralTypeList *dihedraltypes;
|
||||
extern struct OOPTypeList *ooptypes;
|
||||
extern struct AngleAngleTypeList *angleangletypes;
|
||||
|
||||
extern void FrcMenu();
|
||||
extern void ReadCarFile();
|
||||
extern void ReadMdfFile();
|
||||
extern void ReadFrcFile();
|
||||
extern void MakeLists();
|
||||
extern void GetParameters(int);
|
||||
extern void CheckLists();
|
||||
extern void WriteDataFile01(char *,int);
|
||||
extern void WriteDataFile05(char *,int);
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,898 @@
|
|||
LAMMPS data file for nylon
|
||||
|
||||
117 atoms
|
||||
116 bonds
|
||||
219 angles
|
||||
311 dihedrals
|
||||
11 impropers
|
||||
|
||||
8 atom types
|
||||
10 bond types
|
||||
19 angle types
|
||||
25 dihedral types
|
||||
3 improper types
|
||||
|
||||
-2.085999966 11.720000267 xlo xhi
|
||||
3.098999977 22.469999313 ylo yhi
|
||||
-1.845999956 35.515998840 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.011150
|
||||
2 14.006700
|
||||
3 12.011150
|
||||
4 15.999400
|
||||
5 1.007970
|
||||
6 1.007970
|
||||
7 15.999400
|
||||
8 14.006700
|
||||
|
||||
Nonbond Coeffs
|
||||
|
||||
1 0.0389999952 3.8754094636
|
||||
2 0.1669999743 3.5012320066
|
||||
3 0.1479999981 3.6170487995
|
||||
4 0.2280000124 2.8597848722
|
||||
5 0.0380000011 2.4499714540
|
||||
6 0.0000000000 0.0000000000
|
||||
7 0.2280000124 2.8597848722
|
||||
8 0.1669999743 3.5012320066
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 322.7158 1.5260
|
||||
2 340.6175 1.1050
|
||||
3 356.5988 1.4700
|
||||
4 377.5752 1.4600
|
||||
5 388.0000 1.3200
|
||||
6 483.4512 1.0260
|
||||
7 615.3220 1.2300
|
||||
8 283.0924 1.5200
|
||||
9 540.0000 1.2500
|
||||
10 457.4592 1.0260
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 44.4000 110.0000
|
||||
2 50.0000 109.5000
|
||||
3 39.5000 106.4000
|
||||
4 57.3000 109.5000
|
||||
5 46.6000 110.5000
|
||||
6 50.0000 109.5000
|
||||
7 51.5000 109.5000
|
||||
8 111.0000 118.0000
|
||||
9 35.0000 122.0000
|
||||
10 37.5000 115.0000
|
||||
11 68.0000 120.0000
|
||||
12 53.5000 114.1000
|
||||
13 68.0000 120.0000
|
||||
14 46.6000 110.5000
|
||||
15 45.0000 109.5000
|
||||
16 68.0000 120.0000
|
||||
17 145.0000 123.0000
|
||||
18 41.6000 110.0000
|
||||
19 36.0000 105.5000
|
||||
|
||||
Dihedral Coeffs
|
||||
|
||||
1 0.1581 1.0000 3.0000
|
||||
2 0.1581 1.0000 3.0000
|
||||
3 0.1581 1.0000 3.0000
|
||||
4 0.1581 1.0000 3.0000
|
||||
5 0.0889 1.0000 3.0000
|
||||
6 0.0889 1.0000 3.0000
|
||||
7 0.1581 1.0000 3.0000
|
||||
8 0.1581 1.0000 3.0000
|
||||
9 0.1581 1.0000 3.0000
|
||||
10 0.0000 1.0000 0.0000
|
||||
11 0.0000 1.0000 0.0000
|
||||
12 0.0000 1.0000 0.0000
|
||||
13 0.0000 1.0000 0.0000
|
||||
14 3.8000 -1.0000 2.0000
|
||||
15 3.2000 -1.0000 2.0000
|
||||
16 1.8000 -1.0000 2.0000
|
||||
17 1.2000 -1.0000 2.0000
|
||||
18 0.0000 1.0000 0.0000
|
||||
19 0.0000 1.0000 0.0000
|
||||
20 0.0000 1.0000 0.0000
|
||||
21 0.0000 1.0000 0.0000
|
||||
22 0.1581 1.0000 3.0000
|
||||
23 0.1581 1.0000 3.0000
|
||||
24 0.0000 1.0000 0.0000
|
||||
25 0.0000 1.0000 0.0000
|
||||
|
||||
Improper Coeffs
|
||||
|
||||
1 10.0000 -1.0000 2.0000
|
||||
2 10.0000 -1.0000 2.0000
|
||||
3 11.6000 -1.0000 2.0000
|
||||
|
||||
Atoms
|
||||
|
||||
1 0 1 0.220000 1.493000031 20.593999863 -0.449999988
|
||||
2 0 1 -0.200000 2.328000069 19.871000290 0.623000026
|
||||
3 0 1 -0.200000 2.887000084 20.902999878 1.621000051
|
||||
4 0 1 -0.200000 3.533999920 20.169000626 2.809999943
|
||||
5 0 1 -0.200000 4.085000038 21.201000214 3.812999964
|
||||
6 0 1 0.020000 4.731999874 20.466999054 5.001999855
|
||||
7 0 2 -0.500000 5.270999908 21.479000092 5.985000134
|
||||
8 0 3 0.380000 6.477000237 21.142000198 6.829999924
|
||||
9 0 4 -0.380000 7.435999870 22.232000351 7.244999886
|
||||
10 0 1 -0.200000 6.728000164 19.687000275 7.267000198
|
||||
11 0 1 -0.200000 7.763999939 19.665000916 8.406999588
|
||||
12 0 1 -0.200000 7.464000225 18.486000061 9.350999832
|
||||
13 0 1 -0.200000 8.416000366 18.541000366 10.560999870
|
||||
14 0 3 0.380000 8.112999916 17.364999771 11.506999969
|
||||
15 0 4 -0.380000 6.711999893 16.809000015 11.597000122
|
||||
16 0 5 0.100000 2.111000061 20.704999924 -1.401000023
|
||||
17 0 5 0.100000 1.195999980 21.625999451 -0.067000002
|
||||
18 0 5 0.100000 3.191999912 19.319000244 0.125000000
|
||||
19 0 5 0.100000 1.669999957 19.124000549 1.179000020
|
||||
20 0 5 0.100000 3.670000076 21.548999786 1.101999998
|
||||
21 0 5 0.100000 2.039000034 21.563999176 1.998999953
|
||||
22 0 5 0.100000 4.388000011 19.513999939 2.434000015
|
||||
23 0 5 0.100000 2.753999949 19.517999649 3.325999975
|
||||
24 0 5 0.100000 4.866000175 21.853000641 3.298000097
|
||||
25 0 5 0.100000 3.232000113 21.857000351 4.190000057
|
||||
26 0 5 0.100000 5.585000038 19.811000824 4.625999928
|
||||
27 0 5 0.100000 3.951999903 19.815999985 5.518000126
|
||||
28 0 6 0.280000 4.782000065 22.469999313 6.085999966
|
||||
29 0 5 0.100000 7.124000072 19.086999893 6.382999897
|
||||
30 0 5 0.100000 5.751999855 19.225000381 7.632999897
|
||||
31 0 5 0.100000 8.809000015 19.542999268 7.967999935
|
||||
32 0 5 0.100000 7.709000111 20.642000198 8.989999771
|
||||
33 0 5 0.100000 7.614999771 17.503000259 8.793999672
|
||||
34 0 5 0.100000 6.385000229 18.555000305 9.713999748
|
||||
35 0 5 0.100000 9.494999886 18.468999863 10.199000359
|
||||
36 0 5 0.100000 8.267000198 19.524000168 11.118000031
|
||||
37 0 2 -0.500000 9.217000008 16.766000748 12.345000267
|
||||
38 0 1 0.020000 8.902999878 16.179000854 13.701000214
|
||||
39 0 1 -0.200000 9.892000198 15.039999962 14.008999825
|
||||
40 0 1 -0.200000 9.138999939 13.871000290 14.671999931
|
||||
41 0 1 -0.200000 10.074000359 12.652999878 14.779999733
|
||||
42 0 1 -0.200000 9.317999840 11.480999947 15.434000015
|
||||
43 0 1 0.020000 10.253000259 10.262000084 15.543000221
|
||||
44 0 2 -0.500000 9.512000084 9.114000320 16.184000015
|
||||
45 0 3 0.380000 10.263999939 8.095999718 17.007999420
|
||||
46 0 4 -0.380000 11.720000267 8.319999695 17.337999344
|
||||
47 0 1 -0.200000 9.545000076 6.831999779 17.513000488
|
||||
48 0 1 -0.200000 10.385999680 6.170000076 18.621000290
|
||||
49 0 1 -0.200000 9.451999664 5.482999802 19.634000778
|
||||
50 0 1 -0.200000 10.281999588 4.934999943 20.809999466
|
||||
51 0 5 0.100000 10.808575630 5.755126953 21.298067093
|
||||
52 0 5 0.100000 11.006152153 4.209916592 20.438573837
|
||||
53 0 3 0.380000 9.347999573 4.250999928 21.825000763
|
||||
54 0 4 -0.380000 9.854000092 3.098999977 22.659999847
|
||||
55 0 6 0.280000 10.260000229 16.757999420 11.965000153
|
||||
56 0 5 0.100000 8.998000145 16.989000320 14.496999741
|
||||
57 0 5 0.100000 7.839000225 15.769000053 13.699999809
|
||||
58 0 5 0.100000 10.701999664 15.418999672 14.715999603
|
||||
59 0 5 0.100000 10.373000145 14.680000305 13.039999962
|
||||
60 0 5 0.100000 8.796999931 14.180999756 15.713999748
|
||||
61 0 5 0.100000 8.229999542 13.597000122 14.039999962
|
||||
62 0 5 0.100000 10.979000092 12.923000336 15.418000221
|
||||
63 0 5 0.100000 10.421999931 12.345999718 13.739000320
|
||||
64 0 5 0.100000 8.970999718 11.786999702 16.475999832
|
||||
65 0 5 0.100000 8.413000107 11.208999634 14.796999931
|
||||
66 0 5 0.100000 11.159000397 10.532999992 16.180000305
|
||||
67 0 5 0.100000 10.600999832 9.956000328 14.501000404
|
||||
68 0 6 0.280000 8.413999557 9.017000198 16.048999786
|
||||
69 0 5 0.100000 9.411000252 6.098999977 16.649999619
|
||||
70 0 5 0.100000 8.522999763 7.116000175 17.930999756
|
||||
71 0 5 0.100000 11.081000328 5.394000053 18.159000397
|
||||
72 0 5 0.100000 11.005000114 6.965000153 19.155000687
|
||||
73 0 5 0.100000 8.904000282 4.623000145 19.124000549
|
||||
74 0 5 0.100000 8.692000389 6.237999916 20.024999619
|
||||
75 0 2 -0.500000 7.925000191 4.731999874 21.985000610
|
||||
76 0 1 0.020000 7.053999901 4.160999775 23.077999115
|
||||
77 0 1 -0.200000 6.034999847 5.223000050 23.531999588
|
||||
78 0 1 -0.200000 5.895999908 5.179999828 25.065000534
|
||||
79 0 1 -0.200000 5.052000046 6.377999783 25.538000107
|
||||
80 0 1 -0.200000 4.921000004 6.340000153 27.072000504
|
||||
81 0 1 0.020000 4.077000141 7.538000107 27.545999527
|
||||
82 0 2 -0.500000 3.948999882 7.500999928 29.049999237
|
||||
83 0 3 0.380000 2.717999935 8.065999985 29.716999054
|
||||
84 0 4 -0.380000 1.600000024 8.638999939 28.878000259
|
||||
85 0 1 -0.200000 2.601000071 8.059000015 31.252000809
|
||||
86 0 1 -0.200000 1.139000058 8.319000244 31.658000946
|
||||
87 0 1 -0.200000 0.828000009 7.570000172 32.967998505
|
||||
88 0 1 -0.200000 -0.667999983 7.721000195 33.304000854
|
||||
89 0 3 0.450000 -0.978999972 6.969999790 34.611000061
|
||||
90 0 7 -0.500000 -2.085999966 7.455999851 35.515998840
|
||||
91 0 6 0.280000 7.519999981 5.506000042 21.299999237
|
||||
92 0 5 0.100000 6.498000145 3.246999979 22.683000565
|
||||
93 0 5 0.100000 7.703999996 3.855999947 23.962999344
|
||||
94 0 5 0.100000 5.022999763 5.008999825 23.052999496
|
||||
95 0 5 0.100000 6.395999908 6.256000042 23.211999893
|
||||
96 0 5 0.100000 5.383999825 4.209000111 25.372999191
|
||||
97 0 5 0.100000 6.929999828 5.231999874 25.541999817
|
||||
98 0 5 0.100000 4.014999866 6.322000027 25.068000793
|
||||
99 0 5 0.100000 5.559999943 7.348999977 25.224000931
|
||||
100 0 5 0.100000 4.413000107 5.369999886 27.386999130
|
||||
101 0 5 0.100000 5.958000183 6.395999908 27.544000626
|
||||
102 0 5 0.100000 3.039999962 7.482999802 27.075000763
|
||||
103 0 5 0.100000 4.585000038 8.508999825 27.232000351
|
||||
104 0 6 0.280000 4.760000229 7.059000015 29.665000916
|
||||
105 0 5 0.100000 3.266999960 8.875000000 31.687999725
|
||||
106 0 5 0.100000 2.931999922 7.044000149 31.653999329
|
||||
107 0 5 0.100000 0.980000019 9.437000275 31.813999176
|
||||
108 0 5 0.100000 0.442999989 7.947999954 30.834999084
|
||||
109 0 5 0.100000 1.452999949 8.008000374 33.813999176
|
||||
110 0 5 0.100000 1.078999996 6.465000153 32.842998505
|
||||
111 0 5 0.100000 -0.919000030 8.826000214 33.431999207
|
||||
112 0 5 0.100000 -1.294000030 7.285999775 32.457000732
|
||||
113 0 7 -0.500000 -0.179000005 5.745999813 34.987998962
|
||||
114 0 8 -0.500000 0.250000000 19.790000916 -0.746999979
|
||||
115 0 6 0.360000 0.118000001 19.704999924 -1.845999956
|
||||
116 0 6 0.360000 -0.634000003 20.298000336 -0.307000011
|
||||
117 0 6 0.360000 0.349999994 18.775999069 -0.307000011
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 2 1 16
|
||||
3 2 1 17
|
||||
4 3 1 114
|
||||
5 1 2 3
|
||||
6 2 2 18
|
||||
7 2 2 19
|
||||
8 1 3 4
|
||||
9 2 3 20
|
||||
10 2 3 21
|
||||
11 1 4 5
|
||||
12 2 4 22
|
||||
13 2 4 23
|
||||
14 1 5 6
|
||||
15 2 5 24
|
||||
16 2 5 25
|
||||
17 4 6 7
|
||||
18 2 6 26
|
||||
19 2 6 27
|
||||
20 5 7 8
|
||||
21 6 7 28
|
||||
22 7 8 9
|
||||
23 8 10 8
|
||||
24 1 10 11
|
||||
25 2 10 29
|
||||
26 2 10 30
|
||||
27 1 11 12
|
||||
28 2 11 31
|
||||
29 2 11 32
|
||||
30 1 12 13
|
||||
31 2 12 33
|
||||
32 2 12 34
|
||||
33 8 13 14
|
||||
34 2 13 35
|
||||
35 2 13 36
|
||||
36 7 14 15
|
||||
37 5 37 14
|
||||
38 4 38 37
|
||||
39 6 37 55
|
||||
40 1 38 39
|
||||
41 2 38 56
|
||||
42 2 38 57
|
||||
43 1 39 40
|
||||
44 2 39 58
|
||||
45 2 39 59
|
||||
46 1 40 41
|
||||
47 2 40 60
|
||||
48 2 40 61
|
||||
49 1 41 42
|
||||
50 2 41 62
|
||||
51 2 41 63
|
||||
52 1 42 43
|
||||
53 2 42 64
|
||||
54 2 42 65
|
||||
55 4 43 44
|
||||
56 2 43 66
|
||||
57 2 43 67
|
||||
58 5 44 45
|
||||
59 6 44 68
|
||||
60 7 45 46
|
||||
61 8 47 45
|
||||
62 1 47 48
|
||||
63 2 47 69
|
||||
64 2 47 70
|
||||
65 1 48 49
|
||||
66 2 48 71
|
||||
67 2 48 72
|
||||
68 1 49 50
|
||||
69 2 49 73
|
||||
70 2 49 74
|
||||
71 8 50 53
|
||||
72 2 50 51
|
||||
73 2 50 52
|
||||
74 7 53 54
|
||||
75 5 75 53
|
||||
76 4 76 75
|
||||
77 6 75 91
|
||||
78 1 76 77
|
||||
79 2 76 92
|
||||
80 2 76 93
|
||||
81 1 77 78
|
||||
82 2 77 94
|
||||
83 2 77 95
|
||||
84 1 78 79
|
||||
85 2 78 96
|
||||
86 2 78 97
|
||||
87 1 79 80
|
||||
88 2 79 98
|
||||
89 2 79 99
|
||||
90 1 80 81
|
||||
91 2 80 100
|
||||
92 2 80 101
|
||||
93 4 81 82
|
||||
94 2 81 102
|
||||
95 2 81 103
|
||||
96 5 82 83
|
||||
97 6 82 104
|
||||
98 7 83 84
|
||||
99 8 85 83
|
||||
100 1 85 86
|
||||
101 2 85 105
|
||||
102 2 85 106
|
||||
103 1 86 87
|
||||
104 2 86 107
|
||||
105 2 86 108
|
||||
106 1 87 88
|
||||
107 2 87 109
|
||||
108 2 87 110
|
||||
109 8 88 89
|
||||
110 2 88 111
|
||||
111 2 88 112
|
||||
112 9 89 90
|
||||
113 9 89 113
|
||||
114 10 115 114
|
||||
115 10 116 114
|
||||
116 10 117 114
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 16
|
||||
2 1 2 1 17
|
||||
3 2 2 1 114
|
||||
4 3 16 1 17
|
||||
5 4 16 1 114
|
||||
6 4 17 1 114
|
||||
7 5 1 2 3
|
||||
8 1 1 2 18
|
||||
9 1 1 2 19
|
||||
10 1 3 2 18
|
||||
11 1 3 2 19
|
||||
12 3 18 2 19
|
||||
13 5 2 3 4
|
||||
14 1 2 3 20
|
||||
15 1 2 3 21
|
||||
16 1 4 3 20
|
||||
17 1 4 3 21
|
||||
18 3 20 3 21
|
||||
19 5 3 4 5
|
||||
20 1 3 4 22
|
||||
21 1 3 4 23
|
||||
22 1 5 4 22
|
||||
23 1 5 4 23
|
||||
24 3 22 4 23
|
||||
25 5 4 5 6
|
||||
26 1 4 5 24
|
||||
27 1 4 5 25
|
||||
28 1 6 5 24
|
||||
29 1 6 5 25
|
||||
30 3 24 5 25
|
||||
31 6 5 6 7
|
||||
32 1 5 6 26
|
||||
33 1 5 6 27
|
||||
34 7 7 6 26
|
||||
35 7 7 6 27
|
||||
36 3 26 6 27
|
||||
37 8 6 7 8
|
||||
38 9 6 7 28
|
||||
39 10 8 7 28
|
||||
40 11 7 8 9
|
||||
41 12 10 8 7
|
||||
42 13 10 8 9
|
||||
43 14 11 10 8
|
||||
44 15 8 10 29
|
||||
45 15 8 10 30
|
||||
46 1 11 10 29
|
||||
47 1 11 10 30
|
||||
48 3 29 10 30
|
||||
49 5 10 11 12
|
||||
50 1 10 11 31
|
||||
51 1 10 11 32
|
||||
52 1 12 11 31
|
||||
53 1 12 11 32
|
||||
54 3 31 11 32
|
||||
55 5 11 12 13
|
||||
56 1 11 12 33
|
||||
57 1 11 12 34
|
||||
58 1 13 12 33
|
||||
59 1 13 12 34
|
||||
60 3 33 12 34
|
||||
61 14 12 13 14
|
||||
62 1 12 13 35
|
||||
63 1 12 13 36
|
||||
64 15 14 13 35
|
||||
65 15 14 13 36
|
||||
66 3 35 13 36
|
||||
67 13 13 14 15
|
||||
68 12 13 14 37
|
||||
69 11 37 14 15
|
||||
70 8 38 37 14
|
||||
71 10 14 37 55
|
||||
72 9 38 37 55
|
||||
73 6 39 38 37
|
||||
74 7 37 38 56
|
||||
75 7 37 38 57
|
||||
76 1 39 38 56
|
||||
77 1 39 38 57
|
||||
78 3 56 38 57
|
||||
79 5 38 39 40
|
||||
80 1 38 39 58
|
||||
81 1 38 39 59
|
||||
82 1 40 39 58
|
||||
83 1 40 39 59
|
||||
84 3 58 39 59
|
||||
85 5 39 40 41
|
||||
86 1 39 40 60
|
||||
87 1 39 40 61
|
||||
88 1 41 40 60
|
||||
89 1 41 40 61
|
||||
90 3 60 40 61
|
||||
91 5 40 41 42
|
||||
92 1 40 41 62
|
||||
93 1 40 41 63
|
||||
94 1 42 41 62
|
||||
95 1 42 41 63
|
||||
96 3 62 41 63
|
||||
97 5 41 42 43
|
||||
98 1 41 42 64
|
||||
99 1 41 42 65
|
||||
100 1 43 42 64
|
||||
101 1 43 42 65
|
||||
102 3 64 42 65
|
||||
103 6 42 43 44
|
||||
104 1 42 43 66
|
||||
105 1 42 43 67
|
||||
106 7 44 43 66
|
||||
107 7 44 43 67
|
||||
108 3 66 43 67
|
||||
109 8 43 44 45
|
||||
110 9 43 44 68
|
||||
111 10 45 44 68
|
||||
112 11 44 45 46
|
||||
113 12 47 45 44
|
||||
114 13 47 45 46
|
||||
115 14 48 47 45
|
||||
116 15 45 47 69
|
||||
117 15 45 47 70
|
||||
118 1 48 47 69
|
||||
119 1 48 47 70
|
||||
120 3 69 47 70
|
||||
121 5 47 48 49
|
||||
122 1 47 48 71
|
||||
123 1 47 48 72
|
||||
124 1 49 48 71
|
||||
125 1 49 48 72
|
||||
126 3 71 48 72
|
||||
127 5 48 49 50
|
||||
128 1 48 49 73
|
||||
129 1 48 49 74
|
||||
130 1 50 49 73
|
||||
131 1 50 49 74
|
||||
132 3 73 49 74
|
||||
133 14 49 50 53
|
||||
134 1 49 50 51
|
||||
135 1 49 50 52
|
||||
136 15 53 50 51
|
||||
137 15 53 50 52
|
||||
138 3 51 50 52
|
||||
139 13 50 53 54
|
||||
140 12 50 53 75
|
||||
141 11 75 53 54
|
||||
142 8 76 75 53
|
||||
143 10 53 75 91
|
||||
144 9 76 75 91
|
||||
145 6 77 76 75
|
||||
146 7 75 76 92
|
||||
147 7 75 76 93
|
||||
148 1 77 76 92
|
||||
149 1 77 76 93
|
||||
150 3 92 76 93
|
||||
151 5 76 77 78
|
||||
152 1 76 77 94
|
||||
153 1 76 77 95
|
||||
154 1 78 77 94
|
||||
155 1 78 77 95
|
||||
156 3 94 77 95
|
||||
157 5 77 78 79
|
||||
158 1 77 78 96
|
||||
159 1 77 78 97
|
||||
160 1 79 78 96
|
||||
161 1 79 78 97
|
||||
162 3 96 78 97
|
||||
163 5 78 79 80
|
||||
164 1 78 79 98
|
||||
165 1 78 79 99
|
||||
166 1 80 79 98
|
||||
167 1 80 79 99
|
||||
168 3 98 79 99
|
||||
169 5 79 80 81
|
||||
170 1 79 80 100
|
||||
171 1 79 80 101
|
||||
172 1 81 80 100
|
||||
173 1 81 80 101
|
||||
174 3 100 80 101
|
||||
175 6 80 81 82
|
||||
176 1 80 81 102
|
||||
177 1 80 81 103
|
||||
178 7 82 81 102
|
||||
179 7 82 81 103
|
||||
180 3 102 81 103
|
||||
181 8 81 82 83
|
||||
182 9 81 82 104
|
||||
183 10 83 82 104
|
||||
184 11 82 83 84
|
||||
185 12 85 83 82
|
||||
186 13 85 83 84
|
||||
187 14 86 85 83
|
||||
188 15 83 85 105
|
||||
189 15 83 85 106
|
||||
190 1 86 85 105
|
||||
191 1 86 85 106
|
||||
192 3 105 85 106
|
||||
193 5 85 86 87
|
||||
194 1 85 86 107
|
||||
195 1 85 86 108
|
||||
196 1 87 86 107
|
||||
197 1 87 86 108
|
||||
198 3 107 86 108
|
||||
199 5 86 87 88
|
||||
200 1 86 87 109
|
||||
201 1 86 87 110
|
||||
202 1 88 87 109
|
||||
203 1 88 87 110
|
||||
204 3 109 87 110
|
||||
205 14 87 88 89
|
||||
206 1 87 88 111
|
||||
207 1 87 88 112
|
||||
208 15 89 88 111
|
||||
209 15 89 88 112
|
||||
210 3 111 88 112
|
||||
211 16 88 89 90
|
||||
212 16 88 89 113
|
||||
213 17 90 89 113
|
||||
214 18 1 114 115
|
||||
215 18 1 114 116
|
||||
216 18 1 114 117
|
||||
217 19 115 114 116
|
||||
218 19 115 114 117
|
||||
219 19 116 114 117
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 1 3 2 1 16
|
||||
2 2 16 1 2 18
|
||||
3 2 16 1 2 19
|
||||
4 1 3 2 1 17
|
||||
5 2 17 1 2 18
|
||||
6 2 17 1 2 19
|
||||
7 3 3 2 1 114
|
||||
8 4 18 2 1 114
|
||||
9 4 19 2 1 114
|
||||
10 5 2 1 114 115
|
||||
11 5 2 1 114 116
|
||||
12 5 2 1 114 117
|
||||
13 6 16 1 114 115
|
||||
14 6 16 1 114 116
|
||||
15 6 16 1 114 117
|
||||
16 6 17 1 114 115
|
||||
17 6 17 1 114 116
|
||||
18 6 17 1 114 117
|
||||
19 7 1 2 3 4
|
||||
20 1 1 2 3 20
|
||||
21 1 1 2 3 21
|
||||
22 1 4 3 2 18
|
||||
23 2 18 2 3 20
|
||||
24 2 18 2 3 21
|
||||
25 1 4 3 2 19
|
||||
26 2 19 2 3 20
|
||||
27 2 19 2 3 21
|
||||
28 7 2 3 4 5
|
||||
29 1 2 3 4 22
|
||||
30 1 2 3 4 23
|
||||
31 1 5 4 3 20
|
||||
32 2 20 3 4 22
|
||||
33 2 20 3 4 23
|
||||
34 1 5 4 3 21
|
||||
35 2 21 3 4 22
|
||||
36 2 21 3 4 23
|
||||
37 7 3 4 5 6
|
||||
38 1 3 4 5 24
|
||||
39 1 3 4 5 25
|
||||
40 1 6 5 4 22
|
||||
41 2 22 4 5 24
|
||||
42 2 22 4 5 25
|
||||
43 1 6 5 4 23
|
||||
44 2 23 4 5 24
|
||||
45 2 23 4 5 25
|
||||
46 8 4 5 6 7
|
||||
47 1 4 5 6 26
|
||||
48 1 4 5 6 27
|
||||
49 9 7 6 5 24
|
||||
50 2 24 5 6 26
|
||||
51 2 24 5 6 27
|
||||
52 9 7 6 5 25
|
||||
53 2 25 5 6 26
|
||||
54 2 25 5 6 27
|
||||
55 10 5 6 7 8
|
||||
56 11 5 6 7 28
|
||||
57 12 26 6 7 8
|
||||
58 13 26 6 7 28
|
||||
59 12 27 6 7 8
|
||||
60 13 27 6 7 28
|
||||
61 14 6 7 8 9
|
||||
62 15 6 7 8 10
|
||||
63 16 28 7 8 9
|
||||
64 17 28 7 8 10
|
||||
65 18 11 10 8 7
|
||||
66 19 29 10 8 7
|
||||
67 19 30 10 8 7
|
||||
68 20 11 10 8 9
|
||||
69 21 29 10 8 9
|
||||
70 21 30 10 8 9
|
||||
71 22 12 11 10 8
|
||||
72 23 8 10 11 31
|
||||
73 23 8 10 11 32
|
||||
74 1 12 11 10 29
|
||||
75 2 29 10 11 31
|
||||
76 2 29 10 11 32
|
||||
77 1 12 11 10 30
|
||||
78 2 30 10 11 31
|
||||
79 2 30 10 11 32
|
||||
80 7 10 11 12 13
|
||||
81 1 10 11 12 33
|
||||
82 1 10 11 12 34
|
||||
83 1 13 12 11 31
|
||||
84 2 31 11 12 33
|
||||
85 2 31 11 12 34
|
||||
86 1 13 12 11 32
|
||||
87 2 32 11 12 33
|
||||
88 2 32 11 12 34
|
||||
89 22 11 12 13 14
|
||||
90 1 11 12 13 35
|
||||
91 1 11 12 13 36
|
||||
92 23 14 13 12 33
|
||||
93 2 33 12 13 35
|
||||
94 2 33 12 13 36
|
||||
95 23 14 13 12 34
|
||||
96 2 34 12 13 35
|
||||
97 2 34 12 13 36
|
||||
98 20 12 13 14 15
|
||||
99 18 12 13 14 37
|
||||
100 21 35 13 14 15
|
||||
101 19 35 13 14 37
|
||||
102 21 36 13 14 15
|
||||
103 19 36 13 14 37
|
||||
104 15 38 37 14 13
|
||||
105 17 55 37 14 13
|
||||
106 14 38 37 14 15
|
||||
107 16 55 37 14 15
|
||||
108 10 39 38 37 14
|
||||
109 12 56 38 37 14
|
||||
110 12 57 38 37 14
|
||||
111 11 39 38 37 55
|
||||
112 13 56 38 37 55
|
||||
113 13 57 38 37 55
|
||||
114 8 40 39 38 37
|
||||
115 9 37 38 39 58
|
||||
116 9 37 38 39 59
|
||||
117 1 40 39 38 56
|
||||
118 2 56 38 39 58
|
||||
119 2 56 38 39 59
|
||||
120 1 40 39 38 57
|
||||
121 2 57 38 39 58
|
||||
122 2 57 38 39 59
|
||||
123 7 38 39 40 41
|
||||
124 1 38 39 40 60
|
||||
125 1 38 39 40 61
|
||||
126 1 41 40 39 58
|
||||
127 2 58 39 40 60
|
||||
128 2 58 39 40 61
|
||||
129 1 41 40 39 59
|
||||
130 2 59 39 40 60
|
||||
131 2 59 39 40 61
|
||||
132 7 39 40 41 42
|
||||
133 1 39 40 41 62
|
||||
134 1 39 40 41 63
|
||||
135 1 42 41 40 60
|
||||
136 2 60 40 41 62
|
||||
137 2 60 40 41 63
|
||||
138 1 42 41 40 61
|
||||
139 2 61 40 41 62
|
||||
140 2 61 40 41 63
|
||||
141 7 40 41 42 43
|
||||
142 1 40 41 42 64
|
||||
143 1 40 41 42 65
|
||||
144 1 43 42 41 62
|
||||
145 2 62 41 42 64
|
||||
146 2 62 41 42 65
|
||||
147 1 43 42 41 63
|
||||
148 2 63 41 42 64
|
||||
149 2 63 41 42 65
|
||||
150 8 41 42 43 44
|
||||
151 1 41 42 43 66
|
||||
152 1 41 42 43 67
|
||||
153 9 44 43 42 64
|
||||
154 2 64 42 43 66
|
||||
155 2 64 42 43 67
|
||||
156 9 44 43 42 65
|
||||
157 2 65 42 43 66
|
||||
158 2 65 42 43 67
|
||||
159 10 42 43 44 45
|
||||
160 11 42 43 44 68
|
||||
161 12 66 43 44 45
|
||||
162 13 66 43 44 68
|
||||
163 12 67 43 44 45
|
||||
164 13 67 43 44 68
|
||||
165 14 43 44 45 46
|
||||
166 15 43 44 45 47
|
||||
167 16 68 44 45 46
|
||||
168 17 68 44 45 47
|
||||
169 18 48 47 45 44
|
||||
170 19 69 47 45 44
|
||||
171 19 70 47 45 44
|
||||
172 20 48 47 45 46
|
||||
173 21 69 47 45 46
|
||||
174 21 70 47 45 46
|
||||
175 22 49 48 47 45
|
||||
176 23 45 47 48 71
|
||||
177 23 45 47 48 72
|
||||
178 1 49 48 47 69
|
||||
179 2 69 47 48 71
|
||||
180 2 69 47 48 72
|
||||
181 1 49 48 47 70
|
||||
182 2 70 47 48 71
|
||||
183 2 70 47 48 72
|
||||
184 7 47 48 49 50
|
||||
185 1 47 48 49 73
|
||||
186 1 47 48 49 74
|
||||
187 1 50 49 48 71
|
||||
188 2 71 48 49 73
|
||||
189 2 71 48 49 74
|
||||
190 1 50 49 48 72
|
||||
191 2 72 48 49 73
|
||||
192 2 72 48 49 74
|
||||
193 22 48 49 50 53
|
||||
194 1 48 49 50 51
|
||||
195 1 48 49 50 52
|
||||
196 23 53 50 49 73
|
||||
197 2 73 49 50 51
|
||||
198 2 73 49 50 52
|
||||
199 23 53 50 49 74
|
||||
200 2 74 49 50 51
|
||||
201 2 74 49 50 52
|
||||
202 20 49 50 53 54
|
||||
203 18 49 50 53 75
|
||||
204 21 51 50 53 54
|
||||
205 19 51 50 53 75
|
||||
206 21 52 50 53 54
|
||||
207 19 52 50 53 75
|
||||
208 15 76 75 53 50
|
||||
209 17 91 75 53 50
|
||||
210 14 76 75 53 54
|
||||
211 16 91 75 53 54
|
||||
212 10 77 76 75 53
|
||||
213 12 92 76 75 53
|
||||
214 12 93 76 75 53
|
||||
215 11 77 76 75 91
|
||||
216 13 92 76 75 91
|
||||
217 13 93 76 75 91
|
||||
218 8 78 77 76 75
|
||||
219 9 75 76 77 94
|
||||
220 9 75 76 77 95
|
||||
221 1 78 77 76 92
|
||||
222 2 92 76 77 94
|
||||
223 2 92 76 77 95
|
||||
224 1 78 77 76 93
|
||||
225 2 93 76 77 94
|
||||
226 2 93 76 77 95
|
||||
227 7 76 77 78 79
|
||||
228 1 76 77 78 96
|
||||
229 1 76 77 78 97
|
||||
230 1 79 78 77 94
|
||||
231 2 94 77 78 96
|
||||
232 2 94 77 78 97
|
||||
233 1 79 78 77 95
|
||||
234 2 95 77 78 96
|
||||
235 2 95 77 78 97
|
||||
236 7 77 78 79 80
|
||||
237 1 77 78 79 98
|
||||
238 1 77 78 79 99
|
||||
239 1 80 79 78 96
|
||||
240 2 96 78 79 98
|
||||
241 2 96 78 79 99
|
||||
242 1 80 79 78 97
|
||||
243 2 97 78 79 98
|
||||
244 2 97 78 79 99
|
||||
245 7 78 79 80 81
|
||||
246 1 78 79 80 100
|
||||
247 1 78 79 80 101
|
||||
248 1 81 80 79 98
|
||||
249 2 98 79 80 100
|
||||
250 2 98 79 80 101
|
||||
251 1 81 80 79 99
|
||||
252 2 99 79 80 100
|
||||
253 2 99 79 80 101
|
||||
254 8 79 80 81 82
|
||||
255 1 79 80 81 102
|
||||
256 1 79 80 81 103
|
||||
257 9 82 81 80 100
|
||||
258 2 100 80 81 102
|
||||
259 2 100 80 81 103
|
||||
260 9 82 81 80 101
|
||||
261 2 101 80 81 102
|
||||
262 2 101 80 81 103
|
||||
263 10 80 81 82 83
|
||||
264 11 80 81 82 104
|
||||
265 12 102 81 82 83
|
||||
266 13 102 81 82 104
|
||||
267 12 103 81 82 83
|
||||
268 13 103 81 82 104
|
||||
269 14 81 82 83 84
|
||||
270 15 81 82 83 85
|
||||
271 16 104 82 83 84
|
||||
272 17 104 82 83 85
|
||||
273 18 86 85 83 82
|
||||
274 19 105 85 83 82
|
||||
275 19 106 85 83 82
|
||||
276 20 86 85 83 84
|
||||
277 21 105 85 83 84
|
||||
278 21 106 85 83 84
|
||||
279 22 87 86 85 83
|
||||
280 23 83 85 86 107
|
||||
281 23 83 85 86 108
|
||||
282 1 87 86 85 105
|
||||
283 2 105 85 86 107
|
||||
284 2 105 85 86 108
|
||||
285 1 87 86 85 106
|
||||
286 2 106 85 86 107
|
||||
287 2 106 85 86 108
|
||||
288 7 85 86 87 88
|
||||
289 1 85 86 87 109
|
||||
290 1 85 86 87 110
|
||||
291 1 88 87 86 107
|
||||
292 2 107 86 87 109
|
||||
293 2 107 86 87 110
|
||||
294 1 88 87 86 108
|
||||
295 2 108 86 87 109
|
||||
296 2 108 86 87 110
|
||||
297 22 86 87 88 89
|
||||
298 1 86 87 88 111
|
||||
299 1 86 87 88 112
|
||||
300 23 89 88 87 109
|
||||
301 2 109 87 88 111
|
||||
302 2 109 87 88 112
|
||||
303 23 89 88 87 110
|
||||
304 2 110 87 88 111
|
||||
305 2 110 87 88 112
|
||||
306 24 87 88 89 90
|
||||
307 24 87 88 89 113
|
||||
308 25 111 88 89 90
|
||||
309 25 111 88 89 113
|
||||
310 25 112 88 89 90
|
||||
311 25 112 88 89 113
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 28 7 6 8
|
||||
2 2 10 8 7 9
|
||||
3 2 13 14 37 15
|
||||
4 1 55 37 38 14
|
||||
5 1 68 44 43 45
|
||||
6 2 47 45 44 46
|
||||
7 2 50 53 75 54
|
||||
8 1 91 75 76 53
|
||||
9 1 104 82 81 83
|
||||
10 2 85 83 82 84
|
||||
11 3 88 89 90 113
|
||||
|
||||
|
|
@ -0,0 +1,442 @@
|
|||
LAMMPS data file for phen3_cff97
|
||||
|
||||
23 atoms
|
||||
23 bonds
|
||||
39 angles
|
||||
54 dihedrals
|
||||
19 impropers
|
||||
|
||||
7 atom types
|
||||
9 bond types
|
||||
16 angle types
|
||||
19 dihedral types
|
||||
12 improper types
|
||||
|
||||
-0.483345032 3.619415522 xlo xhi
|
||||
-5.980008125 2.346019268 ylo yhi
|
||||
-2.715474367 0.916701555 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 14.006700
|
||||
2 1.007970
|
||||
3 12.011150
|
||||
4 1.007970
|
||||
5 12.011150
|
||||
6 15.999400
|
||||
7 12.011150
|
||||
|
||||
Nonbond Coeffs
|
||||
|
||||
1 0.0650000000 3.2620000000
|
||||
2 0.0130000000 1.0980000000
|
||||
3 0.0540000000 4.0100000000
|
||||
4 0.0200000000 2.9950000000
|
||||
5 0.1200000000 3.9080000000
|
||||
6 0.1670000000 3.5960000000
|
||||
7 0.0640000000 4.0100000000
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 1.5185 293.1700 -603.7882 629.6900
|
||||
2 1.0119 448.6300 -963.1917 1248.4000
|
||||
3 1.1010 341.0000 -691.8900 844.6000
|
||||
4 1.5483 253.0800 -449.0300 457.3200
|
||||
5 1.5330 299.6700 -501.7700 679.8100
|
||||
6 1.2339 711.3500 -1543.9000 1858.6000
|
||||
7 1.5010 321.9021 -521.8208 572.1628
|
||||
8 1.4314 356.0904 -627.6179 1327.6345
|
||||
9 1.0862 377.7644 -803.4526 894.3173
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 110.5100 49.2170 -12.2153 -18.9667
|
||||
2 106.1100 45.3280 -14.0474 1.9350
|
||||
3 105.8500 72.2630 -28.1923 0.0000
|
||||
4 0.0000 0.0000 0.0000 0.0000
|
||||
5 112.1300 66.4520 4.8694 37.7860
|
||||
6 109.6700 37.9190 -7.3877 -8.0694
|
||||
7 110.7700 41.4530 -10.6040 5.1290
|
||||
8 104.4900 31.3750 -4.4023 -6.5271
|
||||
9 115.0600 59.0960 -15.1430 -12.9820
|
||||
10 130.0100 111.2900 -52.3390 -28.1070
|
||||
11 108.4000 43.9594 -8.3924 -9.3379
|
||||
12 107.6600 39.6410 -12.9210 -2.4318
|
||||
13 111.0000 44.3234 -9.4454 0.0000
|
||||
14 120.0500 44.7148 -22.7352 0.0000
|
||||
15 118.9000 61.0226 -34.9931 0.0000
|
||||
16 117.9400 35.1558 -12.4682 0.0000
|
||||
|
||||
Dihedral Coeffs
|
||||
|
||||
1 -0.2458 0.0000 -0.2789 0.0000 -0.0294 0.0000
|
||||
2 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
|
||||
3 -0.8792 0.0000 -0.5978 0.0000 -0.3242 0.0000
|
||||
4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
|
||||
5 -2.5999 0.0000 1.0488 0.0000 -0.2089 0.0000
|
||||
6 1.7311 0.0000 1.8510 0.0000 -0.1933 0.0000
|
||||
7 -0.2179 0.0000 -0.4127 0.0000 -0.1252 0.0000
|
||||
8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
|
||||
9 -0.2432 0.0000 0.0617 0.0000 -0.1383 0.0000
|
||||
10 -0.0228 0.0000 0.0280 0.0000 -0.1863 0.0000
|
||||
11 -1.2767 0.0000 0.5949 0.0000 0.2379 0.0000
|
||||
12 0.0972 0.0000 0.0722 0.0000 -0.2581 0.0000
|
||||
13 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000
|
||||
14 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000
|
||||
15 0.0000 0.0000 1.5590 0.0000 0.0000 0.0000
|
||||
16 0.0000 0.0000 4.4072 0.0000 0.0000 0.0000
|
||||
17 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000
|
||||
18 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000
|
||||
19 0.0000 0.0000 1.8769 0.0000 0.0000 0.0000
|
||||
|
||||
Improper Coeffs
|
||||
|
||||
1 44.1500 0.0000
|
||||
2 6.9644 0.0000
|
||||
3 7.6012 0.0000
|
||||
4 0.0000 0.0000
|
||||
5 0.0000 0.0000
|
||||
6 0.0000 0.0000
|
||||
7 0.0000 0.0000
|
||||
8 0.0000 0.0000
|
||||
9 0.0000 0.0000
|
||||
10 0.0000 0.0000
|
||||
11 0.0000 0.0000
|
||||
12 0.0000 0.0000
|
||||
|
||||
BondBond Coeffs
|
||||
|
||||
1 8.6951 1.0119 1.5185
|
||||
2 2.8266 1.0119 1.0119
|
||||
3 -1.4797 1.5185 1.1010
|
||||
4 0.0000 1.5185 1.5483
|
||||
5 16.4280 1.5185 1.5330
|
||||
6 -1.1701 1.1010 1.5483
|
||||
7 3.3872 1.5330 1.1010
|
||||
8 16.4650 1.5330 1.5483
|
||||
9 57.8750 1.5483 1.2339
|
||||
10 166.5900 1.2339 1.2339
|
||||
11 0.0000 1.5330 1.5010
|
||||
12 5.3316 1.1010 1.1010
|
||||
13 2.9168 1.1010 1.5010
|
||||
14 12.0676 1.5010 1.4314
|
||||
15 68.2856 1.4314 1.4314
|
||||
16 1.0795 1.0862 1.4314
|
||||
|
||||
BondAngle Coeffs
|
||||
|
||||
1 6.2182 27.8810 1.0119 1.5185
|
||||
2 10.1080 10.1080 1.0119 1.0119
|
||||
3 50.0180 15.8820 1.5185 1.1010
|
||||
4 0.0000 0.0000 1.5185 1.5483
|
||||
5 49.7730 14.0620 1.5185 1.5330
|
||||
6 14.9650 11.8650 1.1010 1.5483
|
||||
7 20.7540 11.4210 1.5330 1.1010
|
||||
8 23.0840 19.1590 1.5330 1.5483
|
||||
9 51.5840 62.0560 1.5483 1.2339
|
||||
10 73.3500 73.3500 1.2339 1.2339
|
||||
11 0.0000 0.0000 1.5330 1.5010
|
||||
12 18.1030 18.1030 1.1010 1.1010
|
||||
13 11.7717 26.4608 1.1010 1.5010
|
||||
14 47.0579 31.0771 1.5010 1.4314
|
||||
15 28.8708 28.8708 1.4314 1.4314
|
||||
16 24.2183 20.0033 1.0862 1.4314
|
||||
|
||||
AngleAngle Coeffs
|
||||
|
||||
1 0.0000 0.0000 0.0000 115.0600 130.0100 115.0600
|
||||
2 0.0000 0.0000 0.0000 120.0500 118.9000 120.0500
|
||||
3 0.0000 0.0000 0.0000 117.9400 118.9000 117.9400
|
||||
4 -2.0310 -2.0310 -3.6257 106.1100 110.5100 110.5100
|
||||
5 -1.9852 -1.9852 -1.9852 106.1100 106.1100 106.1100
|
||||
6 0.0000 0.0000 0.0000 105.8500 109.6700 0.0000
|
||||
7 6.0274 7.0292 4.2440 112.1300 110.7700 105.8500
|
||||
8 0.0000 0.0000 0.0000 112.1300 104.4900 0.0000
|
||||
9 2.4594 -1.0033 -0.0414 110.7700 109.6700 104.4900
|
||||
10 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700
|
||||
11 1.0827 -1.8202 2.0403 110.7700 111.0000 108.4000
|
||||
12 2.3794 2.3794 3.0118 107.6600 111.0000 111.0000
|
||||
|
||||
AngleAngleTorsion Coeffs
|
||||
|
||||
1 -9.0674 110.5100 105.8500
|
||||
2 0.0000 110.5100 0.0000
|
||||
3 -15.9511 110.5100 112.1300
|
||||
4 0.0000 0.0000 115.0600
|
||||
5 -19.4570 109.6700 115.0600
|
||||
6 -28.7420 104.4900 115.0600
|
||||
7 -18.9263 112.1300 110.7700
|
||||
8 0.0000 112.1300 108.4000
|
||||
9 -12.5640 110.7700 110.7700
|
||||
10 0.0000 110.7700 108.4000
|
||||
11 -15.6070 110.7700 104.4900
|
||||
12 0.0000 104.4900 108.4000
|
||||
13 0.0000 108.4000 120.0500
|
||||
14 -5.8888 111.0000 120.0500
|
||||
15 4.4444 120.0500 117.9400
|
||||
16 -14.4097 120.0500 118.9000
|
||||
17 -4.8141 117.9400 118.9000
|
||||
18 0.0000 118.9000 118.9000
|
||||
19 0.3598 117.9400 117.9400
|
||||
|
||||
EndBondTorsion Coeffs
|
||||
|
||||
1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0119 1.1010
|
||||
2 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0119 1.5483
|
||||
3 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0119 1.5330
|
||||
4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5185 1.2339
|
||||
5 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.1010 1.2339
|
||||
6 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5330 1.2339
|
||||
7 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5185 1.1010
|
||||
8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5185 1.5010
|
||||
9 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010
|
||||
10 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.1010 1.5010
|
||||
11 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.1010 1.5483
|
||||
12 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5483 1.5010
|
||||
13 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5330 1.4314
|
||||
14 1.3997 0.7756 0.0000 -0.5835 1.1220 0.3978 1.1010 1.4314
|
||||
15 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 1.5010 1.0862
|
||||
16 0.0000 0.2421 0.0000 0.0000 -0.6918 0.0000 1.5010 1.4314
|
||||
17 0.0000 -0.4669 0.0000 0.0000 -6.8958 0.0000 1.0862 1.4314
|
||||
18 -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4314 1.4314
|
||||
19 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0862 1.0862
|
||||
|
||||
MiddleBondTorsion Coeffs
|
||||
|
||||
1 -0.6980 0.8910 -0.1895 1.5185
|
||||
2 0.0000 0.0000 0.0000 1.5185
|
||||
3 -0.5922 -1.2262 0.4264 1.5185
|
||||
4 0.0000 0.0000 0.0000 1.5483
|
||||
5 -5.7009 0.7758 -0.4090 1.5483
|
||||
6 0.6798 0.9388 -1.8478 1.5483
|
||||
7 -9.8826 -3.7138 -0.1022 1.5330
|
||||
8 0.0000 0.0000 0.0000 1.5330
|
||||
9 -14.2610 -0.5322 -0.4864 1.5330
|
||||
10 0.0000 0.0000 0.0000 1.5330
|
||||
11 -13.6420 -0.8843 0.2118 1.5330
|
||||
12 0.0000 0.0000 0.0000 1.5330
|
||||
13 0.0000 0.0000 0.0000 1.5010
|
||||
14 -5.5679 1.4083 0.3010 1.5010
|
||||
15 0.0000 3.9421 0.0000 1.4314
|
||||
16 0.0000 9.1792 0.0000 1.4314
|
||||
17 0.0000 -1.1521 0.0000 1.4314
|
||||
18 27.5989 -2.3120 0.0000 1.4314
|
||||
19 0.0000 4.8228 0.0000 1.4314
|
||||
|
||||
BondBond13 Coeffs
|
||||
|
||||
1 0.0000 1.0119 1.1010
|
||||
2 0.0000 1.0119 1.5483
|
||||
3 0.0000 1.0119 1.5330
|
||||
4 0.0000 1.5185 1.2339
|
||||
5 0.0000 1.1010 1.2339
|
||||
6 0.0000 1.5330 1.2339
|
||||
7 0.0000 1.5185 1.1010
|
||||
8 0.0000 1.5185 1.5010
|
||||
9 0.0000 1.1010 1.1010
|
||||
10 0.0000 1.1010 1.5010
|
||||
11 0.0000 1.1010 1.5483
|
||||
12 0.0000 1.5483 1.5010
|
||||
13 0.0000 1.5330 1.4314
|
||||
14 -3.4826 1.1010 1.4314
|
||||
15 0.8743 1.5010 1.0862
|
||||
16 2.5085 1.5010 1.4314
|
||||
17 -6.2741 1.0862 1.4314
|
||||
18 -73.6169 1.4314 1.4314
|
||||
19 -1.7077 1.0862 1.0862
|
||||
|
||||
AngleTorsion Coeffs
|
||||
|
||||
1 -1.7705 -0.8407 -0.2881 -2.4112 -0.4658 -0.0738 110.5100 105.8500
|
||||
2 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 110.5100 0.0000
|
||||
3 -2.1025 -0.9363 0.4381 -3.5237 -0.3880 -0.4954 110.5100 112.1300
|
||||
4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 115.0600
|
||||
5 12.0720 0.2388 -0.0426 -4.2825 1.1254 -0.1481 109.6700 115.0600
|
||||
6 13.2220 1.3271 -0.3941 2.9333 2.2593 -0.5573 104.4900 115.0600
|
||||
7 -2.8694 1.6172 -1.4627 -3.4109 0.6476 -0.9584 112.1300 110.7700
|
||||
8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 112.1300 108.4000
|
||||
9 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700
|
||||
10 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 110.7700 108.4000
|
||||
11 3.9318 2.2235 0.3670 1.6575 -0.4577 0.3610 110.7700 104.4900
|
||||
12 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 104.4900 108.4000
|
||||
13 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 108.4000 120.0500
|
||||
14 4.6266 0.1632 0.0461 0.2251 0.6548 0.1237 111.0000 120.0500
|
||||
15 0.0000 -0.1242 0.0000 0.0000 3.4601 0.0000 120.0500 117.9400
|
||||
16 0.0000 -4.4683 0.0000 0.0000 3.8987 0.0000 120.0500 118.9000
|
||||
17 0.0000 2.7147 0.0000 0.0000 2.5014 0.0000 117.9400 118.9000
|
||||
18 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000
|
||||
19 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400
|
||||
|
||||
Atoms
|
||||
|
||||
1 0 1 -0.045000 0.109592088 -0.199880913 0.000000478
|
||||
2 0 2 0.280000 -0.124733858 -1.202872038 -0.000001981
|
||||
3 0 2 0.280000 -0.285811990 0.244572327 0.840843439
|
||||
4 0 2 0.280000 -0.285812497 0.244576558 -0.840839982
|
||||
5 0 3 -0.078000 1.560634732 -0.038402185 0.000000465
|
||||
6 0 4 0.053000 1.972637177 -0.500293911 0.916701555
|
||||
7 0 5 0.297400 1.942531705 1.422506809 0.000000450
|
||||
8 0 6 -0.533700 3.187694550 1.672445178 0.000000438
|
||||
9 0 6 -0.533700 1.070737839 2.346019268 0.000000449
|
||||
10 0 3 -0.106000 2.174581766 -0.718786478 -1.261021852
|
||||
11 0 4 0.053000 1.839982390 -0.182426706 -2.172762394
|
||||
12 0 4 0.053000 3.272250891 -0.569177628 -1.261509657
|
||||
13 0 7 0.000000 1.889680982 -2.218492746 -1.435816169
|
||||
14 0 7 -0.130530 0.737977445 -2.629161119 -2.116767168
|
||||
15 0 4 0.130530 0.061427273 -1.894254208 -2.533302307
|
||||
16 0 7 -0.130530 0.424228579 -3.980331659 -2.214080095
|
||||
17 0 4 0.130530 -0.483345032 -4.285143852 -2.715474367
|
||||
18 0 7 -0.130530 1.268485427 -4.931880474 -1.646431088
|
||||
19 0 4 0.130530 1.020345688 -5.980008125 -1.718327641
|
||||
20 0 7 -0.130530 2.423752546 -4.531005859 -0.977356374
|
||||
21 0 4 0.130530 3.074717045 -5.268786907 -0.531340718
|
||||
22 0 7 -0.130530 2.733307123 -3.177516222 -0.869901538
|
||||
23 0 4 0.130530 3.619415522 -2.873045444 -0.331384182
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 5
|
||||
2 2 1 2
|
||||
3 2 1 3
|
||||
4 2 1 4
|
||||
5 3 5 6
|
||||
6 4 5 7
|
||||
7 5 5 10
|
||||
8 6 7 9
|
||||
9 6 7 8
|
||||
10 3 10 11
|
||||
11 3 10 12
|
||||
12 7 10 13
|
||||
13 8 13 14
|
||||
14 8 13 22
|
||||
15 9 15 14
|
||||
16 8 14 16
|
||||
17 9 17 16
|
||||
18 8 16 18
|
||||
19 9 19 18
|
||||
20 8 18 20
|
||||
21 9 21 20
|
||||
22 8 20 22
|
||||
23 9 23 22
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 5
|
||||
2 1 3 1 5
|
||||
3 1 4 1 5
|
||||
4 2 2 1 3
|
||||
5 2 2 1 4
|
||||
6 2 3 1 4
|
||||
7 3 1 5 6
|
||||
8 4 1 5 7
|
||||
9 5 1 5 10
|
||||
10 6 6 5 7
|
||||
11 7 10 5 6
|
||||
12 8 10 5 7
|
||||
13 9 5 7 9
|
||||
14 9 5 7 8
|
||||
15 10 9 7 8
|
||||
16 7 5 10 11
|
||||
17 7 5 10 12
|
||||
18 11 5 10 13
|
||||
19 12 11 10 12
|
||||
20 13 11 10 13
|
||||
21 13 12 10 13
|
||||
22 14 10 13 14
|
||||
23 14 10 13 22
|
||||
24 15 14 13 22
|
||||
25 16 15 14 13
|
||||
26 15 13 14 16
|
||||
27 16 15 14 16
|
||||
28 16 17 16 14
|
||||
29 15 14 16 18
|
||||
30 16 17 16 18
|
||||
31 16 19 18 16
|
||||
32 15 16 18 20
|
||||
33 16 19 18 20
|
||||
34 16 21 20 18
|
||||
35 15 18 20 22
|
||||
36 16 21 20 22
|
||||
37 16 23 22 20
|
||||
38 15 20 22 13
|
||||
39 16 23 22 13
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 1 2 1 5 6
|
||||
2 2 2 1 5 7
|
||||
3 3 2 1 5 10
|
||||
4 1 3 1 5 6
|
||||
5 2 3 1 5 7
|
||||
6 3 3 1 5 10
|
||||
7 1 4 1 5 6
|
||||
8 2 4 1 5 7
|
||||
9 3 4 1 5 10
|
||||
10 4 1 5 7 9
|
||||
11 4 1 5 7 8
|
||||
12 5 6 5 7 9
|
||||
13 5 6 5 7 8
|
||||
14 6 10 5 7 9
|
||||
15 6 10 5 7 8
|
||||
16 7 1 5 10 11
|
||||
17 7 1 5 10 12
|
||||
18 8 1 5 10 13
|
||||
19 9 6 5 10 11
|
||||
20 9 6 5 10 12
|
||||
21 10 6 5 10 13
|
||||
22 11 11 10 5 7
|
||||
23 11 12 10 5 7
|
||||
24 12 7 5 10 13
|
||||
25 13 5 10 13 14
|
||||
26 13 5 10 13 22
|
||||
27 14 11 10 13 14
|
||||
28 14 11 10 13 22
|
||||
29 14 12 10 13 14
|
||||
30 14 12 10 13 22
|
||||
31 15 10 13 14 15
|
||||
32 16 10 13 14 16
|
||||
33 17 15 14 13 22
|
||||
34 18 22 13 14 16
|
||||
35 16 10 13 22 20
|
||||
36 15 10 13 22 23
|
||||
37 18 14 13 22 20
|
||||
38 17 23 22 13 14
|
||||
39 17 17 16 14 13
|
||||
40 18 13 14 16 18
|
||||
41 19 15 14 16 17
|
||||
42 17 15 14 16 18
|
||||
43 17 19 18 16 14
|
||||
44 18 14 16 18 20
|
||||
45 19 17 16 18 19
|
||||
46 17 17 16 18 20
|
||||
47 17 21 20 18 16
|
||||
48 18 16 18 20 22
|
||||
49 19 19 18 20 21
|
||||
50 17 19 18 20 22
|
||||
51 17 23 22 20 18
|
||||
52 18 18 20 22 13
|
||||
53 19 21 20 22 23
|
||||
54 17 21 20 22 13
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 5 7 9 8
|
||||
2 2 10 13 14 22
|
||||
3 3 15 14 13 16
|
||||
4 3 17 16 14 18
|
||||
5 3 19 18 16 20
|
||||
6 3 21 20 18 22
|
||||
7 3 23 22 20 13
|
||||
8 4 2 1 3 5
|
||||
9 4 2 1 4 5
|
||||
10 4 3 1 4 5
|
||||
11 5 2 1 3 4
|
||||
12 6 1 5 6 7
|
||||
13 7 1 5 10 6
|
||||
14 8 1 5 10 7
|
||||
15 9 10 5 6 7
|
||||
16 10 5 10 11 12
|
||||
17 11 5 10 11 13
|
||||
18 11 5 10 12 13
|
||||
19 12 11 10 12 13
|
||||
|
||||
|
|
@ -0,0 +1,649 @@
|
|||
!BIOSYM archive 3
|
||||
PBC=OFF
|
||||
input file for discover
|
||||
!DATE Mon Jul 14 13:41:23 1997
|
||||
N 17.047000885 14.098999977 3.625000000 THRN 1 n4 N -0.500
|
||||
HN3 16.238992691 14.681707382 3.886676073 THRN 1 hn H 0.360
|
||||
HN1 17.917675018 14.581335068 3.889913321 THRN 1 hn H 0.360
|
||||
HN2 17.039421082 13.939416885 2.607465982 THRN 1 hn H 0.360
|
||||
CA 16.966999054 12.784000397 4.337999821 THRN 1 ca C 0.320
|
||||
HA 16.972635269 11.928232193 3.662923098 THRN 1 h H 0.100
|
||||
C 15.685000420 12.755000114 5.132999897 THRN 1 c' C 0.380
|
||||
O 15.267999649 13.824999809 5.593999863 THRN 1 o' O -0.380
|
||||
CB 18.170000076 12.703000069 5.336999893 THRN 1 c1 C -0.070
|
||||
HB 18.120826721 13.621001244 5.922624588 THRN 1 h H 0.100
|
||||
OG1 19.333999634 12.829000473 4.462999821 THRN 1 oh O -0.380
|
||||
HG1 19.691650391 13.794054985 4.503693104 THRN 1 ho H 0.350
|
||||
CG2 18.149999619 11.545999527 6.303999901 THRN 1 c3 C -0.300
|
||||
HG21 19.007284164 11.616475105 6.973474979 THRN 1 h H 0.100
|
||||
HG22 17.230155945 11.575787544 6.888035774 THRN 1 h H 0.100
|
||||
HG23 18.198083878 10.608263016 5.750428200 THRN 1 h H 0.100
|
||||
N 15.114999771 11.555000305 5.264999866 THR 2 n N -0.500
|
||||
HN 15.528337479 10.717791557 4.830105782 THR 2 hn H 0.280
|
||||
CA 13.855999947 11.468999863 6.065999985 THR 2 ca C 0.120
|
||||
HA 13.508913994 12.491562843 6.214313030 THR 2 h H 0.100
|
||||
C 14.163999557 10.784999847 7.379000187 THR 2 c' C 0.380
|
||||
O 14.993000031 9.862000465 7.442999840 THR 2 o' O -0.380
|
||||
CB 12.732000351 10.711000443 5.261000156 THR 2 c1 C -0.070
|
||||
HB 11.753349304 10.621357918 5.732493877 THR 2 h H 0.100
|
||||
OG1 13.307999611 9.439000130 4.926000118 THR 2 oh O -0.380
|
||||
HG1 12.585855484 8.833214760 4.510751247 THR 2 ho H 0.350
|
||||
CG2 12.484000206 11.442000389 3.894999981 THR 2 c3 C -0.300
|
||||
HG21 11.803796768 10.849267006 3.283370495 THR 2 h H 0.100
|
||||
HG22 12.044157028 12.421771049 4.081242085 THR 2 h H 0.100
|
||||
HG23 13.431519508 11.563512802 3.370076180 THR 2 h H 0.100
|
||||
N 13.487999916 11.241000175 8.416999817 CYS 3 n N -0.500
|
||||
HN 12.810626030 12.002311707 8.267102242 CYS 3 hn H 0.280
|
||||
CA 13.659999847 10.706999779 9.786999702 CYS 3 ca C 0.120
|
||||
HA 14.238283157 9.783084869 9.778588295 CYS 3 h H 0.100
|
||||
C 12.269000053 10.430999756 10.322999954 CYS 3 c' C 0.380
|
||||
O 11.392999649 11.307999611 10.185000420 CYS 3 o' O -0.380
|
||||
CB 14.368000031 11.748000145 10.690999985 CYS 3 c2 C -0.300
|
||||
HB1 13.670405388 12.570071220 10.851186752 CYS 3 h H 0.100
|
||||
HB2 14.606354713 11.254445076 11.633172989 CYS 3 h H 0.100
|
||||
SG 15.885000229 12.425999641 10.015999794 CYS 3 s1 S 0.100
|
||||
N 12.019000053 9.272000313 10.928000450 CYS 4 n N -0.500
|
||||
HN 12.770128250 8.579818726 11.060630798 CYS 4 hn H 0.280
|
||||
CA 10.645999908 8.991000175 11.407999992 CYS 4 ca C 0.120
|
||||
HA 10.045209885 9.855814934 11.126492500 CYS 4 h H 0.100
|
||||
C 10.654000282 8.793000221 12.918999672 CYS 4 c' C 0.380
|
||||
O 11.659000397 8.295999527 13.491000175 CYS 4 o' O -0.380
|
||||
CB 10.057000160 7.751999855 10.682000160 CYS 4 c2 C -0.300
|
||||
HB1 10.731808662 6.925758839 10.905740738 CYS 4 h H 0.100
|
||||
HB2 9.122684479 7.521792412 11.194015503 CYS 4 h H 0.100
|
||||
SG 9.836999893 8.017999649 8.904000282 CYS 4 s1 S 0.100
|
||||
N 9.560999870 9.107999802 13.562999725 PRO 5 n N -0.420
|
||||
CA 9.447999954 9.034000397 15.012000084 PRO 5 ca C 0.060
|
||||
HA 10.341467857 9.534400940 15.385380745 PRO 5 h H 0.100
|
||||
CD 8.366000175 9.803999901 12.958000183 PRO 5 c2 C 0.060
|
||||
HD1 8.002507210 9.270477295 12.079748154 PRO 5 h H 0.100
|
||||
HD2 8.616027832 10.819077492 12.649448395 PRO 5 h H 0.100
|
||||
C 9.288000107 7.670000076 15.605999947 PRO 5 c' C 0.380
|
||||
O 9.489999771 7.519000053 16.819000244 PRO 5 o' O -0.380
|
||||
CB 8.229999542 9.956999779 15.345000267 PRO 5 c2 C -0.200
|
||||
HB1 7.714309216 9.644173622 16.252912521 PRO 5 h H 0.100
|
||||
HB2 8.527364731 10.997467041 15.475772858 PRO 5 h H 0.100
|
||||
CG 7.337999821 9.786000252 14.114000320 PRO 5 c2 C -0.200
|
||||
HG1 6.782078266 8.848659515 14.135046959 PRO 5 h H 0.100
|
||||
HG2 6.614880562 10.595389366 14.013560295 PRO 5 h H 0.100
|
||||
N 8.875000000 6.685999870 14.795999527 SER 6 n N -0.500
|
||||
HN 8.693690300 6.898229599 13.804543495 SER 6 hn H 0.280
|
||||
CA 8.673000336 5.314000130 15.279000282 SER 6 ca C 0.120
|
||||
HA 9.487320900 5.098019123 15.970617294 SER 6 h H 0.100
|
||||
C 8.753000259 4.375999928 14.083000183 SER 6 c' C 0.380
|
||||
O 8.725999832 4.857999802 12.923000336 SER 6 o' O -0.380
|
||||
CB 7.340000153 5.120999813 15.996000290 SER 6 c2 C -0.170
|
||||
HB1 7.303732872 4.135610104 16.460533142 SER 6 h H 0.100
|
||||
HB2 7.204785347 5.896010399 16.750438690 SER 6 h H 0.100
|
||||
OG 6.274000168 5.219999790 15.031000137 SER 6 oh O -0.380
|
||||
HG 6.086399078 6.211903572 14.826469421 SER 6 ho H 0.350
|
||||
N 8.880999565 3.075000048 14.357999802 ILE 7 n N -0.500
|
||||
HN 8.958233833 2.761164188 15.335978508 ILE 7 hn H 0.280
|
||||
CA 8.911999702 2.082999945 13.258000374 ILE 7 ca C 0.120
|
||||
HA 9.752125740 2.304961205 12.599957466 ILE 7 h H 0.100
|
||||
C 7.580999851 2.089999914 12.505999565 ILE 7 c' C 0.380
|
||||
O 7.670000076 2.030999899 11.244999886 ILE 7 o' O -0.380
|
||||
CB 9.206999779 0.676999986 13.923999786 ILE 7 c1 C -0.100
|
||||
HB 8.631069183 0.572530746 14.843504906 ILE 7 h H 0.100
|
||||
CG1 10.713999748 0.702000022 14.312000275 ILE 7 c2 C -0.200
|
||||
HG11 11.291265488 0.728613675 13.387794495 ILE 7 h H 0.100
|
||||
HG12 10.887344360 1.603095889 14.900283813 ILE 7 h H 0.100
|
||||
CG2 8.810999870 -0.476999998 12.968999863 ILE 7 c3 C -0.300
|
||||
HG21 9.032923698 -1.433422685 13.442394257 ILE 7 h H 0.100
|
||||
HG22 7.744652271 -0.418968171 12.750744820 ILE 7 h H 0.100
|
||||
HG23 9.376438141 -0.391609550 12.041049957 ILE 7 h H 0.100
|
||||
CD1 11.185000420 -0.515999973 15.142000198 ILE 7 c3 C -0.300
|
||||
HD11 11.020709038 -1.430322766 14.571805000 ILE 7 h H 0.100
|
||||
HD12 12.246717453 -0.414458960 15.366830826 ILE 7 h H 0.100
|
||||
HD13 10.619837761 -0.562440276 16.072879791 ILE 7 h H 0.100
|
||||
N 6.458000183 2.161999941 13.159000397 VAL 8 n N -0.500
|
||||
HN 6.476118088 2.187154531 14.188533783 VAL 8 hn H 0.280
|
||||
CA 5.144999981 2.209000111 12.453000069 VAL 8 ca C 0.120
|
||||
HA 5.026936531 1.265246391 11.920561790 VAL 8 h H 0.100
|
||||
C 5.114999771 3.378999949 11.461000443 VAL 8 c' C 0.380
|
||||
O 4.664000034 3.267999887 10.343000412 VAL 8 o' O -0.380
|
||||
CB 3.994999886 2.354000092 13.477999687 VAL 8 c1 C -0.100
|
||||
HB 4.418568611 3.051678419 14.200449944 VAL 8 h H 0.100
|
||||
CG1 2.716000080 2.891000032 12.869000435 VAL 8 c3 C -0.300
|
||||
HG11 1.981043458 3.059607983 13.656088829 VAL 8 h H 0.100
|
||||
HG12 2.923026085 3.831490993 12.358395576 VAL 8 h H 0.100
|
||||
HG13 2.322393417 2.168816090 12.153719902 VAL 8 h H 0.100
|
||||
CG2 3.757999897 1.031999946 14.208000183 VAL 8 c3 C -0.300
|
||||
HG21 3.374393702 0.292122275 13.505486488 VAL 8 h H 0.100
|
||||
HG22 4.697329521 0.676970363 14.631930351 VAL 8 h H 0.100
|
||||
HG23 3.033046246 1.182916164 15.007855415 VAL 8 h H 0.100
|
||||
N 5.605999947 4.546000004 11.940999985 ALA 9 n N -0.500
|
||||
HN 5.984637260 4.591287613 12.897809029 ALA 9 hn H 0.280
|
||||
CA 5.598000050 5.767000198 11.081999779 ALA 9 ca C 0.120
|
||||
HA 4.565777779 5.921326160 10.767674446 ALA 9 h H 0.100
|
||||
C 6.440999985 5.526999950 9.850000381 ALA 9 c' C 0.380
|
||||
O 6.052000046 5.933000088 8.744000435 ALA 9 o' O -0.380
|
||||
CB 6.021999836 6.977000237 11.890999794 ALA 9 c3 C -0.300
|
||||
HB1 5.950239658 7.871601582 11.272420883 ALA 9 h H 0.100
|
||||
HB2 5.369528770 7.081964016 12.757813454 ALA 9 h H 0.100
|
||||
HB3 7.051515102 6.848640919 12.225253105 ALA 9 h H 0.100
|
||||
N 7.646999836 4.908999920 10.005000114 ARG 10 n N -0.500
|
||||
HN 7.968383789 4.648912430 10.948380470 ARG 10 hn H 0.280
|
||||
CA 8.496000290 4.609000206 8.836999893 ARG 10 ca C 0.120
|
||||
HA 8.672454834 5.551135063 8.318015099 ARG 10 h H 0.100
|
||||
C 7.797999859 3.608999968 7.875999928 ARG 10 c' C 0.380
|
||||
O 7.877999783 3.778000116 6.651000023 ARG 10 o' O -0.380
|
||||
CB 9.847000122 4.019999981 9.305000305 ARG 10 c2 C -0.200
|
||||
HB1 10.292553902 4.780714035 9.946011543 ARG 10 h H 0.110
|
||||
HB2 9.592742920 3.191395044 9.965959549 ARG 10 h H 0.110
|
||||
CG 10.751999855 3.607000113 8.149000168 ARG 10 c2 C -0.200
|
||||
HG1 11.631093979 3.136696339 8.589575768 ARG 10 h H 0.130
|
||||
HG2 10.187005997 2.897431850 7.544521332 ARG 10 h H 0.130
|
||||
CD 11.225999832 4.698999882 7.243999958 ARG 10 c2 C -0.160
|
||||
HD1 11.795847893 4.300052166 6.404825211 ARG 10 h H 0.130
|
||||
HD2 10.397437096 5.319350719 6.902313709 ARG 10 h H 0.130
|
||||
NE 12.142999649 5.571000099 8.034999847 ARG 10 n N -0.560
|
||||
CZ 12.758000374 6.609000206 7.442999840 ARG 10 cr C 0.380
|
||||
NH1 12.538999557 6.932000160 6.157999992 ARG 10 n2 N -0.560
|
||||
HH11 11.887275696 6.371951103 5.590105534 ARG 10 hn H 0.280
|
||||
HH12 13.022671700 7.739827156 5.740416050 ARG 10 hn H 0.280
|
||||
NH2 13.600999832 7.322000027 8.201999664 ARG 10 n2 N -0.560
|
||||
HH21 13.756224632 7.059009075 9.185687065 ARG 10 hn H 0.280
|
||||
HH22 14.093895912 8.133021355 7.801752567 ARG 10 hn H 0.280
|
||||
N 7.185999870 2.582000017 8.444999695 SER 11 n N -0.500
|
||||
HN 7.181996822 2.472300768 9.469133377 SER 11 hn H 0.280
|
||||
CA 6.500000000 1.583999991 7.565000057 SER 11 ca C 0.120
|
||||
HA 7.232992172 1.158654571 6.879504681 SER 11 h H 0.100
|
||||
C 5.381999969 2.312999964 6.772999763 SER 11 c' C 0.380
|
||||
O 5.212999821 2.016000032 5.557000160 SER 11 o' O -0.380
|
||||
CB 5.907999992 0.462000012 8.399999619 SER 11 c2 C -0.170
|
||||
HB1 5.275885105 0.867496729 9.190001488 SER 11 h H 0.100
|
||||
HB2 5.339412212 -0.222457558 7.770455360 SER 11 h H 0.100
|
||||
OG 6.989999771 -0.272000015 9.012000084 SER 11 oh O -0.380
|
||||
HG 6.754035950 -0.477917194 9.993233681 SER 11 ho H 0.350
|
||||
N 4.647999763 3.181999922 7.446000099 ASN 12 n N -0.500
|
||||
HN 4.830713749 3.344167471 8.446608543 ASN 12 hn H 0.280
|
||||
CA 3.545000076 3.934999943 6.750999928 ASN 12 ca C 0.120
|
||||
HA 2.931945086 3.139469147 6.327450275 ASN 12 h H 0.100
|
||||
C 4.106999874 4.850999832 5.690999985 ASN 12 c' C 0.380
|
||||
O 3.536000013 5.000999928 4.617000103 ASN 12 o' O -0.380
|
||||
CB 2.663000107 4.677000046 7.748000145 ASN 12 c2 C -0.200
|
||||
HB1 3.340831280 5.294844151 8.336993217 ASN 12 h H 0.100
|
||||
HB2 2.070847750 5.373784065 7.154748440 ASN 12 h H 0.100
|
||||
CG 1.802000046 3.734999895 8.609999657 ASN 12 c' C 0.380
|
||||
OD1 1.567000031 2.612999916 8.164999962 ASN 12 o' O -0.380
|
||||
ND2 1.394000053 4.251999855 9.767000198 ASN 12 n2 N -0.560
|
||||
HD21 1.661958218 5.212530613 10.024837494 ASN 12 hn H 0.280
|
||||
HD22 0.810311615 3.691485643 10.404206276 ASN 12 hn H 0.280
|
||||
N 5.258999825 5.498000145 6.005000114 PHE 13 n N -0.500
|
||||
HN 5.665558815 5.373039246 6.943080425 PHE 13 hn H 0.280
|
||||
CA 5.928999901 6.357999802 5.054999828 PHE 13 ca C 0.120
|
||||
HA 5.242126465 7.176824093 4.840915680 PHE 13 h H 0.100
|
||||
C 6.303999901 5.578000069 3.799000025 PHE 13 c' C 0.380
|
||||
O 6.136000156 6.072000027 2.653000116 PHE 13 o' O -0.380
|
||||
CB 7.183000088 6.993999958 5.754000187 PHE 13 c2 C -0.200
|
||||
HB1 6.822110653 7.422051907 6.689217091 PHE 13 h H 0.100
|
||||
HB2 7.827757359 6.160566807 6.032885551 PHE 13 h H 0.100
|
||||
CG 7.883999825 8.005999565 4.882999897 PHE 13 cp C 0.000
|
||||
CD1 8.906000137 7.585999966 4.026999950 PHE 13 cp C -0.100
|
||||
HD1 9.200509071 6.536970615 3.996972561 PHE 13 h H 0.100
|
||||
CD2 7.532000065 9.373000145 4.982999802 PHE 13 cp C -0.100
|
||||
HD2 6.777885437 9.706417084 5.695912361 PHE 13 h H 0.100
|
||||
CE1 9.560000420 8.538999557 3.194000006 PHE 13 cp C -0.100
|
||||
HE1 10.356478691 8.246096611 2.509945869 PHE 13 h H 0.100
|
||||
CE2 8.175999641 10.281000137 4.144999981 PHE 13 cp C -0.100
|
||||
HE2 7.907211304 11.336964607 4.173122406 PHE 13 h H 0.100
|
||||
CZ 9.140999794 9.845000267 3.292000055 PHE 13 cp C -0.100
|
||||
HZ 9.614526749 10.580624580 2.641823530 PHE 13 h H 0.100
|
||||
N 6.900000095 4.389999866 3.989000082 ASN 14 n N -0.500
|
||||
HN 7.056817055 4.026083469 4.939722538 ASN 14 hn H 0.280
|
||||
CA 7.330999851 3.607000113 2.790999889 ASN 14 ca C 0.120
|
||||
HA 8.025202751 4.266238213 2.269859314 ASN 14 h H 0.100
|
||||
C 6.116000175 3.210000038 1.914999962 ASN 14 c' C 0.380
|
||||
O 6.239999771 3.144000053 0.684000015 ASN 14 o' O -0.380
|
||||
CB 8.145000458 2.404000044 3.240000010 ASN 14 c2 C -0.200
|
||||
HB1 7.607684612 1.901341796 4.044192791 ASN 14 h H 0.100
|
||||
HB2 8.238607407 1.714848042 2.400710344 ASN 14 h H 0.100
|
||||
CG 9.555000305 2.855999947 3.730000019 ASN 14 c' C 0.380
|
||||
OD1 10.012999535 3.894999981 3.322999954 ASN 14 o' O -0.380
|
||||
ND2 10.119999886 1.955999970 4.539000034 ASN 14 n2 N -0.560
|
||||
HD21 9.602790833 1.105753064 4.804471970 ASN 14 hn H 0.280
|
||||
HD22 11.072957993 2.112127066 4.897321224 ASN 14 hn H 0.280
|
||||
N 4.993000031 2.927000046 2.571000099 VAL 15 n N -0.500
|
||||
HN 4.955123901 2.932416916 3.600289106 VAL 15 hn H 0.280
|
||||
CA 3.782000065 2.598999977 1.741999984 VAL 15 ca C 0.120
|
||||
HA 4.121348858 1.813766837 1.066462040 VAL 15 h H 0.100
|
||||
C 3.296000004 3.871000051 1.003999949 VAL 15 c' C 0.380
|
||||
O 2.947000027 3.816999912 -0.188999996 VAL 15 o' O -0.380
|
||||
CB 2.697999954 1.952999949 2.608000040 VAL 15 c1 C -0.100
|
||||
HB 2.505213737 2.550559521 3.498986244 VAL 15 h H 0.100
|
||||
CG1 1.383999944 1.825999975 1.805999994 VAL 15 c3 C -0.300
|
||||
HG11 0.627347350 1.339950681 2.421900034 VAL 15 h H 0.100
|
||||
HG12 1.035640240 2.818121433 1.518877268 VAL 15 h H 0.100
|
||||
HG13 1.560454965 1.230180860 0.910475850 VAL 15 h H 0.100
|
||||
CG2 3.174000025 0.532999992 3.005000114 VAL 15 c3 C -0.300
|
||||
HG21 3.344338417 -0.058414809 2.105381727 VAL 15 h H 0.100
|
||||
HG22 4.101772785 0.605659664 3.572501659 VAL 15 h H 0.100
|
||||
HG23 2.411232710 0.051358268 3.616807222 VAL 15 h H 0.100
|
||||
N 3.321000099 4.986999989 1.720000029 CYS 16 n N -0.500
|
||||
HN 3.642014980 4.956790447 2.698231459 CYS 16 hn H 0.280
|
||||
CA 2.890000105 6.284999847 1.126000047 CYS 16 ca C 0.120
|
||||
HA 1.819724441 6.204565048 0.935894310 CYS 16 h H 0.100
|
||||
C 3.687000036 6.597000122 -0.111000001 CYS 16 c' C 0.380
|
||||
O 3.200000048 7.146999836 -1.103000045 CYS 16 o' O -0.380
|
||||
CB 3.039000034 7.368999958 2.240000010 CYS 16 c2 C -0.300
|
||||
HB1 2.427302361 7.046223164 3.082461596 CYS 16 h H 0.100
|
||||
HB2 4.076938152 7.344151497 2.571914196 CYS 16 h H 0.100
|
||||
SG 2.559000015 9.013999939 1.649000049 CYS 16 s1 S 0.100
|
||||
N 4.997000217 6.227000237 -0.100000001 ARG 17 n N -0.500
|
||||
HN 5.366806507 5.742030144 0.730028629 ARG 17 hn H 0.280
|
||||
CA 5.894999981 6.488999844 -1.213000059 ARG 17 ca C 0.120
|
||||
HA 5.606140137 7.505477905 -1.480268955 ARG 17 h H 0.100
|
||||
C 5.737999916 5.559999943 -2.408999920 ARG 17 c' C 0.380
|
||||
O 6.228000164 5.901000023 -3.506999969 ARG 17 o' O -0.380
|
||||
CB 7.369999886 6.506999969 -0.731000006 ARG 17 c2 C -0.200
|
||||
HB1 7.554117680 5.576966763 -0.193190947 ARG 17 h H 0.110
|
||||
HB2 8.006169319 6.572014809 -1.613701701 ARG 17 h H 0.110
|
||||
CG 7.717000008 7.686999798 0.206000000 ARG 17 c2 C -0.200
|
||||
HG1 6.892404079 7.845237732 0.901055515 ARG 17 h H 0.130
|
||||
HG2 8.617112160 7.442208767 0.769892812 ARG 17 h H 0.130
|
||||
CD 7.948999882 8.946999550 -0.615000010 ARG 17 c2 C -0.160
|
||||
HD1 7.120620728 9.063755989 -1.313753128 ARG 17 h H 0.130
|
||||
HD2 7.958537579 9.803778648 0.058749799 ARG 17 h H 0.130
|
||||
NE 9.211999893 8.855999947 -1.337000012 ARG 17 n N -0.560
|
||||
CZ 9.536999702 9.532999992 -2.430999994 ARG 17 cr C 0.380
|
||||
NH1 8.659000397 10.350000381 -3.032000065 ARG 17 n2 N -0.560
|
||||
HH11 7.687877178 10.401560783 -2.692646742 ARG 17 hn H 0.280
|
||||
HH12 8.956042290 10.925786018 -3.832710981 ARG 17 hn H 0.280
|
||||
NH2 10.793000221 9.491000175 -2.898999929 ARG 17 n2 N -0.560
|
||||
HH21 11.487204552 8.872345924 -2.456000090 ARG 17 hn H 0.280
|
||||
HH22 11.063426018 10.077307701 -3.701504469 ARG 17 hn H 0.280
|
||||
N 5.051000118 4.410999775 -2.203999996 LEU 18 n N -0.500
|
||||
HN 4.617259026 4.215945244 -1.290368676 LEU 18 hn H 0.280
|
||||
CA 4.933000088 3.430999994 -3.325999975 LEU 18 ca C 0.120
|
||||
HA 5.980045319 3.132587433 -3.378404140 LEU 18 h H 0.100
|
||||
C 4.396999836 4.013999939 -4.619999886 LEU 18 c' C 0.380
|
||||
O 4.987999916 3.755000114 -5.686999798 LEU 18 o' O -0.380
|
||||
CB 4.196000099 2.184000015 -2.862999916 LEU 18 c2 C -0.200
|
||||
HB1 3.339328766 2.530950308 -2.285211325 LEU 18 h H 0.100
|
||||
HB2 3.882649422 1.660040379 -3.765982628 LEU 18 h H 0.100
|
||||
CG 4.960000038 1.177999973 -1.991000056 LEU 18 c1 C -0.100
|
||||
HG 5.379372120 1.654240489 -1.104759574 LEU 18 h H 0.100
|
||||
CD1 3.907000065 0.097000003 -1.633999944 LEU 18 c3 C -0.300
|
||||
HD11 4.372385025 -0.676563323 -1.023166656 LEU 18 h H 0.100
|
||||
HD12 3.089181185 0.555318415 -1.077927470 LEU 18 h H 0.100
|
||||
HD13 3.518241882 -0.348654836 -2.549619913 LEU 18 h H 0.100
|
||||
CD2 6.129000187 0.606000006 -2.767999887 LEU 18 c3 C -0.300
|
||||
HD21 5.767732143 0.166402578 -3.697698832 LEU 18 h H 0.100
|
||||
HD22 6.839241505 1.401178122 -2.994605541 LEU 18 h H 0.100
|
||||
HD23 6.621874809 -0.161501810 -2.171245098 LEU 18 h H 0.100
|
||||
N 3.328999996 4.795000076 -4.543000221 PRO 19 n N -0.420
|
||||
CA 2.792000055 5.375999928 -5.796999931 PRO 19 ca C 0.060
|
||||
HA 2.750592709 4.562232971 -6.520994663 PRO 19 h H 0.100
|
||||
CD 2.421000004 4.940999985 -3.407999992 PRO 19 c2 C 0.060
|
||||
HD1 2.893075705 5.502179623 -2.601574659 PRO 19 h H 0.100
|
||||
HD2 2.129873276 3.967023134 -3.014662504 PRO 19 h H 0.100
|
||||
C 3.572999954 6.539999962 -6.322000027 PRO 19 c' C 0.380
|
||||
O 3.259999990 7.045000076 -7.421999931 PRO 19 o' O -0.380
|
||||
CB 1.358000040 5.765999794 -5.472000122 PRO 19 c2 C -0.200
|
||||
HB1 1.137144327 6.795158386 -5.755116940 PRO 19 h H 0.100
|
||||
HB2 0.636163235 5.061525822 -5.885241508 PRO 19 h H 0.100
|
||||
CG 1.223000050 5.693999767 -3.993000031 PRO 19 c2 C -0.200
|
||||
HG1 1.192069173 6.702612400 -3.580879211 PRO 19 h H 0.100
|
||||
HG2 0.303467065 5.167813301 -3.736705542 PRO 19 h H 0.100
|
||||
N 4.565000057 7.046999931 -5.559000015 GLY 20 n N -0.500
|
||||
HN 4.763685703 6.625352859 -4.640502453 GLY 20 hn H 0.280
|
||||
CA 5.366000175 8.190999985 -6.018000126 GLY 20 cg C 0.020
|
||||
HA1 6.411324024 7.914688587 -5.879978657 GLY 20 h H 0.100
|
||||
HA2 5.204787731 8.272821426 -7.092902660 GLY 20 h H 0.100
|
||||
C 5.006999969 9.480999947 -5.280000210 GLY 20 c' C 0.380
|
||||
O 5.534999847 10.510000229 -5.730000019 GLY 20 o' O -0.380
|
||||
N 4.181000233 9.437999725 -4.262000084 THR 21 n N -0.500
|
||||
HN 3.805485964 8.521671295 -3.978747845 THR 21 hn H 0.280
|
||||
CA 3.766999960 10.609000206 -3.513000011 THR 21 ca C 0.120
|
||||
HA 3.186850548 11.287978172 -4.137912750 THR 21 h H 0.100
|
||||
C 5.017000198 11.397000313 -3.042000055 THR 21 c' C 0.380
|
||||
O 5.947000027 10.756999969 -2.523000002 THR 21 o' O -0.380
|
||||
CB 2.992000103 10.187999725 -2.224999905 THR 21 c1 C -0.070
|
||||
HB 3.722551346 9.746408463 -1.547215223 THR 21 h H 0.100
|
||||
OG1 2.051000118 9.144000053 -2.622999907 THR 21 oh O -0.380
|
||||
HG1 1.135602355 9.567562103 -2.831667185 THR 21 ho H 0.350
|
||||
CG2 2.259999990 11.348999977 -1.550999999 THR 21 c3 C -0.300
|
||||
HG21 1.741620898 10.986124992 -0.663473487 THR 21 h H 0.100
|
||||
HG22 2.980043650 12.114913940 -1.262877345 THR 21 h H 0.100
|
||||
HG23 1.535783529 11.774766922 -2.245502472 THR 21 h H 0.100
|
||||
N 4.971000195 12.703000069 -3.176000118 PRO 22 n N -0.420
|
||||
CA 6.143000126 13.512999535 -2.696000099 PRO 22 ca C 0.060
|
||||
HA 7.038496494 13.344851494 -3.294257641 PRO 22 h H 0.100
|
||||
CD 3.963999987 13.567000389 -3.811000109 PRO 22 c2 C 0.060
|
||||
HD1 3.145355940 13.595741272 -3.091906309 PRO 22 h H 0.100
|
||||
HD2 3.722736835 13.055393219 -4.742746353 PRO 22 h H 0.100
|
||||
C 6.400000095 13.232999802 -1.225000024 PRO 22 c' C 0.380
|
||||
O 5.485000134 13.060999870 -0.381999999 PRO 22 o' O -0.380
|
||||
CB 5.703000069 14.968999863 -2.920000076 PRO 22 c2 C -0.200
|
||||
HB1 5.180837631 15.406009674 -2.068842649 PRO 22 h H 0.100
|
||||
HB2 6.486554623 15.606681824 -3.329272270 PRO 22 h H 0.100
|
||||
CG 4.676000118 14.892999649 -3.996000051 PRO 22 c2 C -0.200
|
||||
HG1 3.913127184 15.665482521 -3.899067879 PRO 22 h H 0.100
|
||||
HG2 5.117558002 14.866248131 -4.992198467 PRO 22 h H 0.100
|
||||
N 7.728000164 13.296999931 -0.921000004 GLU 23 n N -0.500
|
||||
HN 8.435604095 13.473001480 -1.648475647 GLU 23 hn H 0.280
|
||||
CA 8.114000320 13.102999687 0.500000000 GLU 23 ca C 0.120
|
||||
HA 7.816065788 12.094260216 0.785972416 GLU 23 h H 0.100
|
||||
C 7.427000046 14.072999954 1.409999967 GLU 23 c' C 0.380
|
||||
O 7.035999775 13.682000160 2.539999962 GLU 23 o' O -0.380
|
||||
CB 9.647999763 13.284999847 0.660000026 GLU 23 c2 C -0.200
|
||||
HB1 9.905550957 14.228507996 0.178793058 GLU 23 h H 0.100
|
||||
HB2 9.841214180 13.411215782 1.725287557 GLU 23 h H 0.100
|
||||
CG 10.439999580 12.093000412 0.063000001 GLU 23 c2 C -0.200
|
||||
HG1 9.979146957 11.185737610 0.453625947 GLU 23 h H 0.100
|
||||
HG2 10.252198219 12.100539207 -1.010673165 GLU 23 h H 0.100
|
||||
CD 11.940999985 12.170000076 0.391000003 GLU 23 c' C 0.380
|
||||
OE1 12.416000366 13.225000381 0.680999994 GLU 23 o' O -0.350
|
||||
OE2 12.538999557 11.069999695 0.291999996 GLU 23 oh O -0.380
|
||||
HE2 11.852339745 10.318097115 0.136945918 GLU 23 ho H 0.350
|
||||
N 7.211999893 15.333999634 0.966000021 ALA 24 n N -0.500
|
||||
HN 7.454528332 15.605654716 0.002525384 ALA 24 hn H 0.280
|
||||
CA 6.613999844 16.316999435 1.912999988 ALA 24 ca C 0.120
|
||||
HA 7.281579018 16.350204468 2.774008274 ALA 24 h H 0.100
|
||||
C 5.211999893 15.935999870 2.349999905 ALA 24 c' C 0.380
|
||||
O 4.782000065 16.166000366 3.494999886 ALA 24 o' O -0.380
|
||||
CB 6.605000019 17.694999695 1.246000051 ALA 24 c3 C -0.300
|
||||
HB1 6.237848759 18.439016342 1.952922821 ALA 24 h H 0.100
|
||||
HB2 7.617130280 17.956361771 0.937162876 ALA 24 h H 0.100
|
||||
HB3 5.953601360 17.672107697 0.372354269 ALA 24 h H 0.100
|
||||
N 4.445000172 15.317999840 1.404999971 ILE 25 n N -0.500
|
||||
HN 4.817237854 15.149471283 0.459517360 ILE 25 hn H 0.280
|
||||
CA 3.073999882 14.894000053 1.756000042 ILE 25 ca C 0.120
|
||||
HA 2.651019573 15.738821983 2.299565554 ILE 25 h H 0.100
|
||||
C 3.085000038 13.642999649 2.644999981 ILE 25 c' C 0.380
|
||||
O 2.315000057 13.522999763 3.578000069 ILE 25 o' O -0.380
|
||||
CB 2.203999996 14.637000084 0.462000012 ILE 25 c1 C -0.100
|
||||
HB 2.766484499 14.064008713 -0.275151134 ILE 25 h H 0.100
|
||||
CG1 1.815000057 16.048000336 -0.128999993 ILE 25 c2 C -0.200
|
||||
HG11 2.730222702 16.635150909 -0.204643890 ILE 25 h H 0.100
|
||||
HG12 1.443681121 15.888158798 -1.141261339 ILE 25 h H 0.100
|
||||
CG2 0.902999997 13.864000320 0.810999990 ILE 25 c3 C -0.300
|
||||
HG21 0.304098606 13.734000206 -0.090398379 ILE 25 h H 0.100
|
||||
HG22 1.159095764 12.886850357 1.220502138 ILE 25 h H 0.100
|
||||
HG23 0.331401974 14.427850723 1.548189402 ILE 25 h H 0.100
|
||||
CD1 0.755999982 16.760999680 0.757000029 ILE 25 c3 C -0.300
|
||||
HD11 1.158126354 16.905153275 1.759802103 ILE 25 h H 0.100
|
||||
HD12 0.510290921 17.729721069 0.321907312 ILE 25 h H 0.100
|
||||
HD13 -0.144283146 16.148948669 0.811632454 ILE 25 h H 0.100
|
||||
N 4.032000065 12.763999939 2.312999964 CYS 26 n N -0.500
|
||||
HN 4.636651039 12.911288261 1.492266655 CYS 26 hn H 0.280
|
||||
CA 4.179999828 11.548999786 3.187000036 CYS 26 ca C 0.120
|
||||
HA 3.168948889 11.146821976 3.251257181 CYS 26 h H 0.100
|
||||
C 4.631999969 11.944000244 4.596000195 CYS 26 c' C 0.380
|
||||
O 4.227000237 11.251999855 5.546999931 CYS 26 o' O -0.380
|
||||
CB 5.038000107 10.517999649 2.539000034 CYS 26 c2 C -0.300
|
||||
HB1 5.986673355 10.992624283 2.288298368 CYS 26 h H 0.100
|
||||
HB2 5.186637402 9.715300560 3.261275530 CYS 26 h H 0.100
|
||||
SG 4.348999977 9.793999672 1.021999955 CYS 26 s1 S 0.100
|
||||
N 5.407999992 13.012000084 4.693999767 ALA 27 n N -0.500
|
||||
HN 5.691634178 13.513016701 3.839930773 ALA 27 hn H 0.280
|
||||
CA 5.879000187 13.501999855 6.026000023 ALA 27 ca C 0.120
|
||||
HA 6.445541859 12.670074463 6.444367886 ALA 27 h H 0.100
|
||||
C 4.696000099 13.907999992 6.881999969 ALA 27 c' C 0.380
|
||||
O 4.527999878 13.421999931 8.024999619 ALA 27 o' O -0.380
|
||||
CB 6.880000114 14.614999771 5.829999924 ALA 27 c3 C -0.300
|
||||
HB1 7.267490864 14.930619240 6.798676968 ALA 27 h H 0.100
|
||||
HB2 7.702079296 14.259757042 5.208639622 ALA 27 h H 0.100
|
||||
HB3 6.394177914 15.459349632 5.340969563 ALA 27 h H 0.100
|
||||
N 3.826999903 14.802000046 6.357999802 THR 28 n N -0.500
|
||||
HN 3.955853701 15.176399231 5.407146454 THR 28 hn H 0.280
|
||||
CA 2.690999985 15.220999718 7.193999767 THR 28 ca C 0.120
|
||||
HA 3.191283464 15.484881401 8.125762939 THR 28 h H 0.100
|
||||
C 1.672000051 14.131999969 7.434000015 THR 28 c' C 0.380
|
||||
O 0.947000027 14.112000465 8.468000412 THR 28 o' O -0.380
|
||||
CB 1.985999942 16.520000458 6.613999844 THR 28 c1 C -0.070
|
||||
HB 1.055821180 16.708566666 7.150013447 THR 28 h H 0.100
|
||||
OG1 1.664000034 16.221000671 5.230000019 THR 28 oh O -0.380
|
||||
HG1 1.387834191 17.087430954 4.746335030 THR 28 ho H 0.350
|
||||
CG2 2.914000034 17.739000320 6.699999809 THR 28 c3 C -0.300
|
||||
HG21 2.420290470 18.604087830 6.257310867 THR 28 h H 0.100
|
||||
HG22 3.144372940 17.947925568 7.744690895 THR 28 h H 0.100
|
||||
HG23 3.837480545 17.532133102 6.159175873 THR 28 h H 0.100
|
||||
N 1.621000051 13.189999580 6.511000156 TYR 29 n N -0.500
|
||||
HN 2.223951578 13.259345055 5.678810120 TYR 29 hn H 0.280
|
||||
CA 0.714999974 12.045000076 6.657000065 TYR 29 ca C 0.120
|
||||
HA -0.294524491 12.413607597 6.838903904 TYR 29 h H 0.100
|
||||
C 1.125000000 11.125000000 7.815000057 TYR 29 c' C 0.380
|
||||
O 0.286000013 10.631999969 8.545000076 TYR 29 o' O -0.380
|
||||
CB 0.754999995 11.229000092 5.322000027 TYR 29 c2 C -0.200
|
||||
HB1 0.514248192 11.922528267 4.516296864 TYR 29 h H 0.100
|
||||
HB2 1.786919236 10.911371231 5.172484398 TYR 29 h H 0.100
|
||||
CG -0.202999994 10.043999672 5.354000092 TYR 29 cp C 0.000
|
||||
CD1 -1.547000051 10.336999893 5.644999981 TYR 29 cp C -0.100
|
||||
HD1 -1.844175816 11.365451813 5.850120068 TYR 29 h H 0.100
|
||||
CD2 0.193000004 8.750000000 5.099999905 TYR 29 cp C -0.100
|
||||
HD2 1.231727839 8.520407677 4.862445831 TYR 29 h H 0.100
|
||||
CE1 -2.496000051 9.329000473 5.672999859 TYR 29 cp C -0.100
|
||||
HE1 -3.542724609 9.551148415 5.880649567 TYR 29 h H 0.100
|
||||
CE2 -0.800999999 7.704999924 5.156000137 TYR 29 cp C -0.100
|
||||
HE2 -0.521442473 6.666428089 4.979036331 TYR 29 h H 0.100
|
||||
CZ -2.078999996 8.031000137 5.429999828 TYR 29 cp C 0.030
|
||||
OH -3.096999884 7.057000160 5.458000183 TYR 29 oh O -0.380
|
||||
HH -4.016462326 7.520978928 5.472573757 TYR 29 ho H 0.350
|
||||
N 2.470000029 10.984000206 7.994999886 THR 30 n N -0.500
|
||||
HN 3.124760151 11.572608948 7.460463524 THR 30 hn H 0.280
|
||||
CA 2.986000061 9.994000435 8.949999809 THR 30 ca C 0.120
|
||||
HA 2.109365702 9.410336494 9.230978012 THR 30 h H 0.100
|
||||
C 3.608999968 10.505000114 10.229999542 THR 30 c' C 0.380
|
||||
O 3.766000032 9.715000153 11.185999870 THR 30 o' O -0.380
|
||||
CB 4.076000214 9.102999687 8.225000381 THR 30 c1 C -0.070
|
||||
HB 4.516047001 8.447491646 8.976511002 THR 30 h H 0.100
|
||||
OG1 5.125000000 10.027000427 7.823999882 THR 30 oh O -0.380
|
||||
HG1 5.989885330 9.809993744 8.339540482 THR 30 ho H 0.350
|
||||
CG2 3.493000031 8.324000359 7.034999847 THR 30 c3 C -0.300
|
||||
HG21 4.283595562 7.746788025 6.555538177 THR 30 h H 0.100
|
||||
HG22 2.714145184 7.648486614 7.388787270 THR 30 h H 0.100
|
||||
HG23 3.067262888 9.023551941 6.315641403 THR 30 h H 0.100
|
||||
N 3.983999968 11.763999939 10.241000175 GLY 31 n N -0.500
|
||||
HN 3.725119591 12.370410919 9.449706078 GLY 31 hn H 0.280
|
||||
CA 4.769000053 12.336000443 11.359999657 GLY 31 cg C 0.020
|
||||
HA1 4.444449425 13.369131088 11.484130859 GLY 31 h H 0.100
|
||||
HA2 4.479221344 11.798232079 12.262736320 GLY 31 h H 0.100
|
||||
C 6.255000114 12.243000031 11.105999947 GLY 31 c' C 0.380
|
||||
O 7.037000179 12.750000000 11.954000473 GLY 31 o' O -0.380
|
||||
N 6.710000038 11.630999565 9.991999626 CYS 32 n N -0.500
|
||||
HN 6.054100990 11.116460800 9.387064934 CYS 32 hn H 0.280
|
||||
CA 8.140000343 11.694000244 9.635000229 CYS 32 ca C 0.120
|
||||
HA 8.678412437 11.410507202 10.539347649 CYS 32 h H 0.100
|
||||
C 8.500000000 13.140999794 9.206000328 CYS 32 c' C 0.380
|
||||
O 7.580999851 13.949000359 8.944000244 CYS 32 o' O -0.380
|
||||
CB 8.503999710 10.685999870 8.529999733 CYS 32 c2 C -0.300
|
||||
HB1 7.987734795 10.995699883 7.621343136 CYS 32 h H 0.100
|
||||
HB2 9.584586143 10.726516724 8.392916679 CYS 32 h H 0.100
|
||||
SG 8.048000336 8.987000465 8.880999565 CYS 32 s1 S 0.100
|
||||
N 9.793000221 13.409999847 9.173000336 ILE 33 n N -0.500
|
||||
HN 10.471553802 12.667460442 9.394585609 ILE 33 hn H 0.280
|
||||
CA 10.279999733 14.760000229 8.822999954 ILE 33 ca C 0.120
|
||||
HA 9.389740944 15.283022881 8.473735809 ILE 33 h H 0.100
|
||||
C 11.345999718 14.657999992 7.743000031 ILE 33 c' C 0.380
|
||||
O 11.970999718 13.583000183 7.552000046 ILE 33 o' O -0.380
|
||||
CB 10.789999962 15.534999847 10.085000038 ILE 33 c1 C -0.100
|
||||
HB 11.123229027 16.501873016 9.707884789 ILE 33 h H 0.100
|
||||
CG1 12.059000015 14.803000450 10.670999527 ILE 33 c2 C -0.200
|
||||
HG11 11.743847847 13.842393875 11.078448296 ILE 33 h H 0.100
|
||||
HG12 12.756343842 14.617484093 9.854057312 ILE 33 h H 0.100
|
||||
CG2 9.684000015 15.685999870 11.137999535 ILE 33 c3 C -0.300
|
||||
HG21 10.058896065 16.270494461 11.978191376 ILE 33 h H 0.100
|
||||
HG22 8.827452660 16.194667816 10.695638657 ILE 33 h H 0.100
|
||||
HG23 9.378940582 14.700247765 11.489184380 ILE 33 h H 0.100
|
||||
CD1 12.732999802 15.675999641 11.781000137 ILE 33 c3 C -0.300
|
||||
HD11 12.021772385 15.850844383 12.588270187 ILE 33 h H 0.100
|
||||
HD12 13.606328964 15.155009270 12.173381805 ILE 33 h H 0.100
|
||||
HD13 13.041068077 16.631135941 11.355658531 ILE 33 h H 0.100
|
||||
N 11.489999771 15.772999763 7.038000107 ILE 34 n N -0.500
|
||||
HN 10.853153229 16.566915512 7.196191311 ILE 34 hn H 0.280
|
||||
CA 12.552000046 15.876999855 6.035999775 ILE 34 ca C 0.120
|
||||
HA 13.043725967 14.912866592 5.906565666 ILE 34 h H 0.100
|
||||
C 13.590000153 16.916999817 6.559999943 ILE 34 c' C 0.380
|
||||
O 13.168000221 18.006000519 6.945000172 ILE 34 o' O -0.380
|
||||
CB 11.987000465 16.360000610 4.681000233 ILE 34 c1 C -0.100
|
||||
HB 11.502662659 17.321004868 4.854168892 ILE 34 h H 0.100
|
||||
CG1 10.913999557 15.338000298 4.163000107 ILE 34 c2 C -0.200
|
||||
HG11 11.380437851 14.426782608 3.788544178 ILE 34 h H 0.100
|
||||
HG12 10.170696259 15.118617058 4.929467201 ILE 34 h H 0.100
|
||||
CG2 13.130999565 16.517000198 3.628999949 ILE 34 c3 C -0.300
|
||||
HG21 12.714348793 16.881505966 2.690041304 ILE 34 h H 0.100
|
||||
HG22 13.869889259 17.228136063 3.998366594 ILE 34 h H 0.100
|
||||
HG23 13.608166695 15.551076889 3.463472128 ILE 34 h H 0.100
|
||||
CD1 10.151000023 16.024000168 2.937999964 ILE 34 c3 C -0.300
|
||||
HD11 10.865941048 16.258329391 2.149300337 ILE 34 h H 0.100
|
||||
HD12 9.395269394 15.340338707 2.551244020 ILE 34 h H 0.100
|
||||
HD13 9.670580864 16.941936493 3.276658058 ILE 34 h H 0.100
|
||||
N 14.855999947 16.493000031 6.535999775 ILE 35 n N -0.500
|
||||
HN 15.087069511 15.531770706 6.246958256 ILE 35 hn H 0.280
|
||||
CA 15.930000305 17.454000473 6.940999985 ILE 35 ca C 0.120
|
||||
HA 15.448633194 18.412040710 7.137327194 ILE 35 h H 0.100
|
||||
C 16.913000107 17.549999237 5.818999767 ILE 35 c' C 0.380
|
||||
O 17.097000122 16.659999847 4.969999790 ILE 35 o' O -0.380
|
||||
CB 16.621999741 16.995000839 8.284999847 ILE 35 c1 C -0.100
|
||||
HB 17.372821808 17.751832962 8.512095451 ILE 35 h H 0.100
|
||||
CG1 17.360000610 15.651000023 8.067000389 ILE 35 c2 C -0.200
|
||||
HG11 16.597890854 14.882443428 7.938127518 ILE 35 h H 0.100
|
||||
HG12 17.962522507 15.757192612 7.164896488 ILE 35 h H 0.100
|
||||
CG2 15.592000008 16.974000931 9.434000015 ILE 35 c3 C -0.300
|
||||
HG21 16.095645905 16.731447220 10.369737625 ILE 35 h H 0.100
|
||||
HG22 15.121275902 17.953468323 9.518616676 ILE 35 h H 0.100
|
||||
HG23 14.830537796 16.222230911 9.226348877 ILE 35 h H 0.100
|
||||
CD1 18.298000336 15.206000328 9.218999863 ILE 35 c3 C -0.300
|
||||
HD11 17.719526291 15.091951370 10.135765076 ILE 35 h H 0.100
|
||||
HD12 18.762899399 14.254055977 8.962544441 ILE 35 h H 0.100
|
||||
HD13 19.071800232 15.958778381 9.369535446 ILE 35 h H 0.100
|
||||
N 17.663999557 18.669000626 5.806000233 PRO 36 n N -0.420
|
||||
CA 18.635000229 18.861000061 4.737999916 PRO 36 ca C 0.060
|
||||
HA 18.191711426 18.625682831 3.770414352 PRO 36 h H 0.100
|
||||
CD 17.371000290 19.899999619 6.596000195 PRO 36 c2 C 0.060
|
||||
HD1 17.637220383 19.770334244 7.645006180 PRO 36 h H 0.100
|
||||
HD2 16.312007904 20.154773712 6.554459572 PRO 36 h H 0.100
|
||||
C 19.924999237 18.041999817 4.948999882 PRO 36 c' C 0.380
|
||||
O 20.593000412 17.742000580 3.944999933 PRO 36 o' O -0.380
|
||||
CB 18.944999695 20.364000320 4.782999992 PRO 36 c2 C -0.200
|
||||
HB1 20.011636734 20.533958435 4.929625034 PRO 36 h H 0.100
|
||||
HB2 18.596609116 20.857370377 3.875635624 PRO 36 h H 0.100
|
||||
CG 18.238000870 20.937000275 5.907999992 PRO 36 c2 C -0.200
|
||||
HG1 18.980670929 21.346309662 6.592840672 PRO 36 h H 0.100
|
||||
HG2 17.637973785 21.766929626 5.534794807 PRO 36 h H 0.100
|
||||
N 20.172000885 17.729999542 6.217000008 GLY 37 n N -0.500
|
||||
HN 19.520402908 17.994186401 6.969678879 GLY 37 hn H 0.280
|
||||
CA 21.451999664 16.968999863 6.513000011 GLY 37 cg C 0.020
|
||||
HA1 22.220170975 17.196077347 5.773777485 GLY 37 h H 0.100
|
||||
HA2 21.806970596 17.180898666 7.521560192 GLY 37 h H 0.100
|
||||
C 21.142999649 15.477999687 6.427000046 GLY 37 c' C 0.380
|
||||
O 20.138000488 15.022999763 5.877999783 GLY 37 o' O -0.380
|
||||
N 22.055000305 14.701000214 7.032000065 ALA 38 n N -0.500
|
||||
HN 22.826601028 15.162067413 7.534940720 ALA 38 hn H 0.280
|
||||
CA 22.018999100 13.241999626 7.019999981 ALA 38 ca C 0.120
|
||||
HA 21.118928909 12.994981766 6.457010269 ALA 38 h H 0.100
|
||||
C 21.944000244 12.628000259 8.395999908 ALA 38 c' C 0.380
|
||||
O 21.868999481 11.387000084 8.435000420 ALA 38 o' O -0.380
|
||||
CB 23.246000290 12.696999550 6.275000095 ALA 38 c3 C -0.300
|
||||
HB1 23.164216995 11.613998413 6.182674408 ALA 38 h H 0.100
|
||||
HB2 23.296331406 13.143034935 5.281710148 ALA 38 h H 0.100
|
||||
HB3 24.149721146 12.946521759 6.830985546 ALA 38 h H 0.100
|
||||
N 21.893999100 13.435000420 9.435999870 THR 39 n N -0.500
|
||||
HN 21.824220657 14.451409340 9.284524918 THR 39 hn H 0.280
|
||||
CA 21.936000824 12.911000252 10.809000015 THR 39 ca C 0.120
|
||||
HA 22.114582062 11.836632729 10.764920235 THR 39 h H 0.100
|
||||
C 20.614999771 13.190999985 11.520999908 THR 39 c' C 0.380
|
||||
O 20.357000351 14.317000389 11.947999954 THR 39 o' O -0.380
|
||||
CB 23.131000519 13.600999832 11.593000412 THR 39 c1 C -0.070
|
||||
HB 22.981323242 14.676721573 11.685302734 THR 39 h H 0.100
|
||||
OG1 24.284000397 13.401000023 10.708999634 THR 39 oh O -0.380
|
||||
HG1 24.421899796 14.240586281 10.128500938 THR 39 ho H 0.350
|
||||
CG2 23.340000153 12.935000420 12.961999893 THR 39 c3 C -0.300
|
||||
HG21 24.219049454 13.362584114 13.444229126 THR 39 h H 0.100
|
||||
HG22 22.463815689 13.106077194 13.587406158 THR 39 h H 0.100
|
||||
HG23 23.485591888 11.863260269 12.826802254 THR 39 h H 0.100
|
||||
N 19.826999664 12.109999657 11.642000198 CYS 40 n N -0.500
|
||||
HN 20.122940063 11.185415268 11.297814369 CYS 40 hn H 0.280
|
||||
CA 18.503999710 12.312000275 12.298000336 CYS 40 ca C 0.120
|
||||
HA 18.057098389 13.220839500 11.895023346 CYS 40 h H 0.100
|
||||
C 18.684000015 12.451000214 13.784000397 CYS 40 c' C 0.380
|
||||
O 19.533000946 11.718000412 14.362000465 CYS 40 o' O -0.380
|
||||
CB 17.582000732 11.116999626 11.996000290 CYS 40 c2 C -0.300
|
||||
HB1 18.086227417 10.251184464 12.425209045 CYS 40 h H 0.100
|
||||
HB2 16.700305939 11.271791458 12.617895126 CYS 40 h H 0.100
|
||||
SG 17.198999405 10.928999901 10.237000465 CYS 40 s1 S 0.100
|
||||
N 17.879999161 13.265999794 14.425999641 PRO 41 n N -0.420
|
||||
CA 17.923999786 13.420999527 15.876999855 PRO 41 ca C 0.060
|
||||
HA 18.941534042 13.662834167 16.183986664 PRO 41 h H 0.100
|
||||
CD 16.858999252 14.149999619 13.779000282 PRO 41 c2 C 0.060
|
||||
HD1 16.215919495 13.587250710 13.102345467 PRO 41 h H 0.100
|
||||
HD2 17.329374313 14.943244934 13.197958946 PRO 41 h H 0.100
|
||||
C 17.392000198 12.206000328 16.593999863 PRO 41 c' C 0.380
|
||||
O 16.652000427 11.368000031 16.033000946 PRO 41 o' O -0.380
|
||||
CB 17.076000214 14.657999992 16.145000458 PRO 41 c2 C -0.200
|
||||
HB1 16.444255829 14.584781647 17.030233383 PRO 41 h H 0.100
|
||||
HB2 17.617696762 15.599854469 16.057970047 PRO 41 h H 0.100
|
||||
CG 16.097999573 14.689000130 14.996999741 PRO 41 c2 C -0.200
|
||||
HG1 15.253420830 14.016077042 15.145191193 PRO 41 h H 0.100
|
||||
HG2 15.789084435 15.700772285 14.734343529 PRO 41 h H 0.100
|
||||
N 17.728000641 12.123999596 17.884000778 GLY 42 n N -0.500
|
||||
HN 18.268247604 12.885299683 18.319267273 GLY 42 hn H 0.280
|
||||
CA 17.333999634 10.956000328 18.690999985 GLY 42 cg C 0.020
|
||||
HA1 17.766984940 10.084270477 18.200376511 GLY 42 h H 0.100
|
||||
HA2 17.761390686 11.109748840 19.681858063 GLY 42 h H 0.100
|
||||
C 15.875000000 10.687999725 18.871000290 GLY 42 c' C 0.380
|
||||
O 15.434000015 9.550000191 19.166000366 GLY 42 o' O -0.380
|
||||
N 15.036000252 11.746999741 18.715000153 ASP 43 n N -0.500
|
||||
HN 15.424054146 12.679033279 18.510971069 ASP 43 hn H 0.280
|
||||
CA 13.564000130 11.572999954 18.836000443 ASP 43 ca C 0.120
|
||||
HA 13.474464417 10.696401596 19.477605820 ASP 43 h H 0.100
|
||||
C 12.935999870 11.227000237 17.469999313 ASP 43 c' C 0.380
|
||||
O 11.720000267 11.039999962 17.427999496 ASP 43 o' O -0.380
|
||||
CB 12.932999611 12.737000465 19.579999924 ASP 43 c2 C -0.200
|
||||
HB1 11.860553741 12.547567368 19.625556946 ASP 43 h H 0.100
|
||||
HB2 13.367670059 12.754883766 20.579420090 ASP 43 h H 0.100
|
||||
CG 13.140000343 14.093999863 18.958000183 ASP 43 c' C 0.380
|
||||
OD1 14.109000206 14.303000450 18.211999893 ASP 43 o' O -0.350
|
||||
OD2 12.267000198 14.963000298 19.264999390 ASP 43 oh O -0.380
|
||||
HD2 12.695192337 15.899699211 19.252908707 ASP 43 ho H 0.350
|
||||
N 13.725000381 11.173999786 16.424999237 TYR 44 n N -0.500
|
||||
HN 14.713005066 11.441411018 16.540052414 TYR 44 hn H 0.280
|
||||
CA 13.256999969 10.744999886 15.081000328 TYR 44 ca C 0.120
|
||||
HA 12.264418602 10.301728249 15.160951614 TYR 44 h H 0.100
|
||||
C 14.274999619 9.687000275 14.612000465 TYR 44 c' C 0.380
|
||||
O 14.930000305 9.862000465 13.567999840 TYR 44 o' O -0.380
|
||||
CB 13.199999809 11.913999557 14.071000099 TYR 44 c2 C -0.200
|
||||
HB1 14.121270180 12.493051529 14.134719849 TYR 44 h H 0.100
|
||||
HB2 13.091276169 11.516075134 13.062071800 TYR 44 h H 0.100
|
||||
CG 12.000000000 12.819000244 14.399000168 TYR 44 cp C 0.000
|
||||
CD1 12.119000435 13.852999687 15.331999779 TYR 44 cp C -0.100
|
||||
HD1 13.067806244 14.011770248 15.844503403 TYR 44 h H 0.100
|
||||
CD2 10.774999619 12.616999626 13.762000084 TYR 44 cp C -0.100
|
||||
HD2 10.673528671 11.813380241 13.032616615 TYR 44 h H 0.100
|
||||
CE1 11.045000076 14.675000191 15.609999657 TYR 44 cp C -0.100
|
||||
HE1 11.163392067 15.500525475 16.311847687 TYR 44 h H 0.100
|
||||
CE2 9.675999641 13.432999611 14.048000336 TYR 44 cp C -0.100
|
||||
HE2 8.726944923 13.273748398 13.536108017 TYR 44 h H 0.100
|
||||
CZ 9.802000046 14.456000328 14.996000290 TYR 44 cp C 0.030
|
||||
OH 8.739999771 15.265000343 15.269000053 TYR 44 oh O -0.380
|
||||
HH 9.048466682 16.247716904 15.272980690 TYR 44 ho H 0.350
|
||||
N 14.342000008 8.640000343 15.421999931 ALA 45 n N -0.500
|
||||
HN 13.638368607 8.505084991 16.162000656 ALA 45 hn H 0.280
|
||||
CA 15.444999695 7.666999817 15.246000290 ALA 45 ca C 0.120
|
||||
HA 16.332574844 8.216528893 14.932426453 ALA 45 h H 0.100
|
||||
C 15.170999527 6.532999992 14.279999733 ALA 45 c' C 0.380
|
||||
O 16.093000412 5.704999924 14.038999557 ALA 45 o' O -0.380
|
||||
CB 15.680000305 7.098999977 16.681999207 ALA 45 c3 C -0.300
|
||||
HB1 16.535034180 6.423069000 16.670495987 ALA 45 h H 0.100
|
||||
HB2 15.876356125 7.920741558 17.370683670 ALA 45 h H 0.100
|
||||
HB3 14.792826653 6.556271553 17.008296967 ALA 45 h H 0.100
|
||||
N 13.965999603 6.501999855 13.739000320 ASNC 46 n N -0.500
|
||||
HN 13.318986893 7.281283855 13.926057816 ASNC 46 hn H 0.280
|
||||
CA 13.512000084 5.394999981 12.878000259 ASNC 46 ca C 0.120
|
||||
HA 14.292015076 4.641647816 12.988171577 ASNC 46 h H 0.100
|
||||
C 13.310999870 5.853000164 11.454999924 ASNC 46 c- C 0.140
|
||||
O 13.732999802 6.928999901 11.026000023 ASNC 46 o- O -0.570
|
||||
OXT 12.703000069 4.973000050 10.746000290 ASNC 46 o- O -0.570
|
||||
CB 12.265999794 4.769000053 13.501000404 ASNC 46 c2 C -0.200
|
||||
HB1 11.471806526 5.515164375 13.476576805 ASNC 46 h H 0.100
|
||||
HB2 11.959742546 3.937092304 12.866779327 ASNC 46 h H 0.100
|
||||
CG 12.538000107 4.303999901 14.921999931 ASNC 46 c' C 0.380
|
||||
OD1 11.982000351 4.848999977 15.885999680 ASNC 46 o' O -0.380
|
||||
ND2 13.406999588 3.298000097 15.015000343 ASNC 46 n2 N -0.560
|
||||
HD21 13.826193810 2.899175167 14.162875175 ASNC 46 hn H 0.280
|
||||
HD22 13.659525871 2.919377804 15.938999176 ASNC 46 hn H 0.280
|
||||
end
|
||||
end
|
||||
|
||||
|
|
@ -0,0 +1,840 @@
|
|||
!BIOSYM molecular_data 4
|
||||
|
||||
!DATE: Mon Jul 14 13:41:24 1997 INSIGHT generated molecular data file
|
||||
|
||||
#topology
|
||||
|
||||
@column 1 element
|
||||
@column 2 atom_type cvff
|
||||
@column 3 charge_group cvff
|
||||
@column 4 isotope
|
||||
@column 5 formal_charge
|
||||
@column 6 charge cvff
|
||||
@column 7 switching_atom cvff
|
||||
@column 8 oop_flag cvff
|
||||
@column 9 chirality_flag
|
||||
@column 10 occupancy
|
||||
@column 11 xray_temp_factor
|
||||
@column 12 connections
|
||||
|
||||
@molecule CRAMBIN
|
||||
|
||||
THRN_1:N N n4 pep+ 0 0 -0.5000 1 0 8 1.0000 13.7900 CA HN1 HN2 HN3
|
||||
THRN_1:HN3 H hn pep+ 0 0 0.3600 0 0 8 1.0000 0.0000 N
|
||||
THRN_1:HN1 H hn pep+ 0 0 0.3600 0 0 8 1.0000 0.0000 N
|
||||
THRN_1:HN2 H hn pep+ 0 0 0.3600 0 0 8 1.0000 0.0000 N
|
||||
THRN_1:CA C ca pep+ 0 0 0.3200 0 0 8 1.0000 10.8000 C CB N HA
|
||||
THRN_1:HA H h pep+ 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
THRN_1:C C c' pepC 0 0 0.3800 1 1 8 1.0000 9.1900 O/2.0 CA THR_2:N/1.5
|
||||
THRN_1:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 9.8500 C/2.0
|
||||
THRN_1:CB C c1 cBoh 0 0 -0.0700 0 0 8 1.0000 13.0200 CG2 OG1 CA HB
|
||||
THRN_1:HB H h cBoh 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
THRN_1:OG1 O oh cBoh 0 0 -0.3800 1 0 8 1.0000 15.0600 CB HG1
|
||||
THRN_1:HG1 H ho cBoh 0 0 0.3500 0 0 8 1.0000 0.0000 OG1
|
||||
THRN_1:CG2 C c3 meG 0 0 -0.3000 1 0 8 1.0000 14.2300 CB HG21 HG22 HG23
|
||||
THRN_1:HG21 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THRN_1:HG22 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THRN_1:HG23 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_2:N N n pepN 0 0 -0.5000 1 1 8 1.0000 7.8100 CA THRN_1:C/1.5 HN
|
||||
THR_2:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
THR_2:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 8.3100 C CB N HA
|
||||
THR_2:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
THR_2:C C c' pepC 0 0 0.3800 1 1 8 1.0000 5.8000 O/2.0 CA CYS_3:N/1.5
|
||||
THR_2:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 6.9400 C/2.0
|
||||
THR_2:CB C c1 cBoh 0 0 -0.0700 0 0 8 1.0000 10.3200 CG2 OG1 CA HB
|
||||
THR_2:HB H h cBoh 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
THR_2:OG1 O oh cBoh 0 0 -0.3800 1 0 8 1.0000 12.8100 CB HG1
|
||||
THR_2:HG1 H ho cBoh 0 0 0.3500 0 0 8 1.0000 0.0000 OG1
|
||||
THR_2:CG2 C c3 meG 0 0 -0.3000 1 0 8 1.0000 11.9000 CB HG21 HG22 HG23
|
||||
THR_2:HG21 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_2:HG22 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_2:HG23 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
CYS_3:N N n pepN 0 0 -0.5000 1 1 8 1.0000 5.2400 CA THR_2:C/1.5 HN
|
||||
CYS_3:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
CYS_3:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 5.3900 C CB N HA
|
||||
CYS_3:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
CYS_3:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.4500 O/2.0 CA CYS_4:N/1.5
|
||||
CYS_3:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 6.5400 C/2.0
|
||||
CYS_3:CB C c2 cs 0 0 -0.3000 1 0 8 1.0000 5.9900 SG CA HB1 HB2
|
||||
CYS_3:HB1 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_3:HB2 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_3:SG S s1 cs 0 0 0.1000 0 0 8 1.0000 7.0100 CB CYS_40:SG
|
||||
CYS_4:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.9000 CA CYS_3:C/1.5 HN
|
||||
CYS_4:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
CYS_4:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 4.2400 C CB N HA
|
||||
CYS_4:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
CYS_4:C C c' pepC 0 0 0.3800 1 1 8 1.0000 3.7200 O/2.0 CA PRO_5:N/1.5
|
||||
CYS_4:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 5.3000 C/2.0
|
||||
CYS_4:CB C c2 cs 0 0 -0.3000 1 0 8 1.0000 4.4100 SG CA HB1 HB2
|
||||
CYS_4:HB1 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_4:HB2 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_4:SG S s1 cs 0 0 0.1000 0 0 8 1.0000 4.7200 CB CYS_32:SG
|
||||
PRO_5:N N n pepN 0 0 -0.4200 1 1 8 1.0000 3.9600 CA CD CYS_4:C/1.5
|
||||
PRO_5:CA C ca pepN 0 0 0.0600 0 0 8 1.0000 4.2500 C CB N HA
|
||||
PRO_5:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
PRO_5:CD C c2 pepN 0 0 0.0600 0 0 8 1.0000 5.2000 N CG HD1 HD2
|
||||
PRO_5:HD1 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CD
|
||||
PRO_5:HD2 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CD
|
||||
PRO_5:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.9600 O/2.0 CA SER_6:N/1.5
|
||||
PRO_5:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 7.4400 C/2.0
|
||||
PRO_5:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 5.1100 CG CA HB1 HB2
|
||||
PRO_5:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PRO_5:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PRO_5:CG C c2 meG 0 0 -0.2000 1 0 8 1.0000 5.2400 CD CB HG1 HG2
|
||||
PRO_5:HG1 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
PRO_5:HG2 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
SER_6:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.8300 CA PRO_5:C/1.5 HN
|
||||
SER_6:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
SER_6:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 4.4500 C CB N HA
|
||||
SER_6:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
SER_6:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.9900 O/2.0 CA ILE_7:N/1.5
|
||||
SER_6:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 4.6100 C/2.0
|
||||
SER_6:CB C c2 coh 0 0 -0.1700 0 0 8 1.0000 5.0500 OG CA HB1 HB2
|
||||
SER_6:HB1 H h coh 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
SER_6:HB2 H h coh 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
SER_6:OG O oh coh 0 0 -0.3800 1 0 8 1.0000 6.3900 CB HG
|
||||
SER_6:HG H ho coh 0 0 0.3500 0 0 8 1.0000 0.0000 OG
|
||||
ILE_7:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.9400 CA SER_6:C/1.5 HN
|
||||
ILE_7:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ILE_7:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 6.3300 C CB N HA
|
||||
ILE_7:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ILE_7:C C c' pepC 0 0 0.3800 1 1 8 1.0000 5.3200 O/2.0 CA VAL_8:N/1.5
|
||||
ILE_7:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 6.8500 C/2.0
|
||||
ILE_7:CB C c1 meB 0 0 -0.1000 1 0 8 1.0000 8.4300 CG2 CG1 CA HB
|
||||
ILE_7:HB H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ILE_7:CG1 C c2 meG1 0 0 -0.2000 1 0 8 1.0000 9.7800 CD1 CB HG11 HG12
|
||||
ILE_7:HG11 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
ILE_7:HG12 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
ILE_7:CG2 C c3 meG2 0 0 -0.3000 1 0 8 1.0000 11.7000 CB HG21 HG22 HG23
|
||||
ILE_7:HG21 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_7:HG22 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_7:HG23 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_7:CD1 C c3 meD1 0 0 -0.3000 1 0 8 1.0000 9.9200 CG1 HD11 HD12 HD13
|
||||
ILE_7:HD11 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_7:HD12 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_7:HD13 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
VAL_8:N N n pepN 0 0 -0.5000 1 1 8 1.0000 5.0200 CA ILE_7:C/1.5 HN
|
||||
VAL_8:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
VAL_8:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 6.9300 C CB N HA
|
||||
VAL_8:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
VAL_8:C C c' pepC 0 0 0.3800 1 1 8 1.0000 5.3900 O/2.0 CA ALA_9:N/1.5
|
||||
VAL_8:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 6.3000 C/2.0
|
||||
VAL_8:CB C c1 meB 0 0 -0.1000 1 0 8 1.0000 9.6400 CG1 CG2 CA HB
|
||||
VAL_8:HB H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
VAL_8:CG1 C c3 meG1 0 0 -0.3000 1 0 8 1.0000 13.8500 CB HG11 HG12 HG13
|
||||
VAL_8:HG11 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
VAL_8:HG12 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
VAL_8:HG13 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
VAL_8:CG2 C c3 meG2 0 0 -0.3000 1 0 8 1.0000 11.9700 CB HG21 HG22 HG23
|
||||
VAL_8:HG21 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
VAL_8:HG22 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
VAL_8:HG23 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ALA_9:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.7300 CA VAL_8:C/1.5 HN
|
||||
ALA_9:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ALA_9:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 3.5600 C CB N HA
|
||||
ALA_9:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ALA_9:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.1300 O/2.0 CA ARG_10:N/1.5
|
||||
ALA_9:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 4.3600 C/2.0
|
||||
ALA_9:CB C c3 meB 0 0 -0.3000 1 0 8 1.0000 4.8000 CA HB1 HB2 HB3
|
||||
ALA_9:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ALA_9:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ALA_9:HB3 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ARG_10:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.7300 CA ALA_9:C/1.5 HN
|
||||
ARG_10:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ARG_10:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 3.3800 C CB N HA
|
||||
ARG_10:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ARG_10:C C c' pepC 0 0 0.3800 1 1 8 1.0000 3.4700 O/2.0 CA SER_11:N/1.5
|
||||
ARG_10:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 4.6700 C/2.0
|
||||
ARG_10:CB C c2 c3nc 0 0 -0.2000 0 0 8 1.0000 3.9500 CG CA HB1 HB2
|
||||
ARG_10:HB1 H h c3nc 0 0 0.1100 0 0 8 1.0000 0.0000 CB
|
||||
ARG_10:HB2 H h c3nc 0 0 0.1100 0 0 8 1.0000 0.0000 CB
|
||||
ARG_10:CG C c2 c3nc 0 0 -0.2000 0 0 8 1.0000 4.5500 CD CB HG1 HG2
|
||||
ARG_10:HG1 H h c3nc 0 0 0.1300 0 0 8 1.0000 0.0000 CG
|
||||
ARG_10:HG2 H h c3nc 0 0 0.1300 0 0 8 1.0000 0.0000 CG
|
||||
ARG_10:CD C c2 c3nc 0 0 -0.1600 1 0 8 1.0000 5.8900 NE CG HD1 HD2
|
||||
ARG_10:HD1 H h c3nc 0 0 0.1300 0 0 8 1.0000 0.0000 CD
|
||||
ARG_10:HD2 H h c3nc 0 0 0.1300 0 0 8 1.0000 0.0000 CD
|
||||
ARG_10:NE N n c3nc 0 0 -0.5600 0 0 8 1.0000 6.2000 CZ/2.0 CD
|
||||
ARG_10:CZ C cr c3nc 0 0 0.3800 0 1 8 1.0000 7.5200 NH1 NH2 NE/2.0
|
||||
ARG_10:NH1 N n2 am1 0 0 -0.5600 1 1 8 1.0000 10.6800 CZ HH11 HH12
|
||||
ARG_10:HH11 H hn am1 0 0 0.2800 0 0 8 1.0000 0.0000 NH1
|
||||
ARG_10:HH12 H hn am1 0 0 0.2800 0 0 8 1.0000 0.0000 NH1
|
||||
ARG_10:NH2 N n2 am2 0 0 -0.5600 1 1 8 1.0000 9.4800 CZ HH21 HH22
|
||||
ARG_10:HH21 H hn am2 0 0 0.2800 0 0 8 1.0000 0.0000 NH2
|
||||
ARG_10:HH22 H hn am2 0 0 0.2800 0 0 8 1.0000 0.0000 NH2
|
||||
SER_11:N N n pepN 0 0 -0.5000 1 1 8 1.0000 5.1900 CA ARG_10:C/1.5 HN
|
||||
SER_11:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
SER_11:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 4.6000 C CB N HA
|
||||
SER_11:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
SER_11:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.8400 O/2.0 CA ASN_12:N/1.5
|
||||
SER_11:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 5.8400 C/2.0
|
||||
SER_11:CB C c2 coh 0 0 -0.1700 0 0 8 1.0000 5.9100 OG CA HB1 HB2
|
||||
SER_11:HB1 H h coh 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
SER_11:HB2 H h coh 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
SER_11:OG O oh coh 0 0 -0.3800 1 0 8 1.0000 8.3800 CB HG
|
||||
SER_11:HG H ho coh 0 0 0.3500 0 0 8 1.0000 0.0000 OG
|
||||
ASN_12:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.5400 CA SER_11:C/1.5 HN
|
||||
ASN_12:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ASN_12:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 4.5700 C CB N HA
|
||||
ASN_12:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ASN_12:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.1400 O/2.0 CA PHE_13:N/1.5
|
||||
ASN_12:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 5.5200 C/2.0
|
||||
ASN_12:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 6.4200 CG CA HB1 HB2
|
||||
ASN_12:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ASN_12:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ASN_12:CG C c' coG 0 0 0.3800 1 1 8 1.0000 8.2500 OD1/2.0 ND2/1.5 CB
|
||||
ASN_12:OD1 O o' coG 0 0 -0.3800 0 0 8 1.0000 12.7200 CG/2.0
|
||||
ASN_12:ND2 N n2 amD 0 0 -0.5600 1 1 8 1.0000 9.9200 CG/1.5 HD21 HD22
|
||||
ASN_12:HD21 H hn amD 0 0 0.2800 0 0 8 1.0000 0.0000 ND2
|
||||
ASN_12:HD22 H hn amD 0 0 0.2800 0 0 8 1.0000 0.0000 ND2
|
||||
PHE_13:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.4300 CA ASN_12:C/1.5 HN
|
||||
PHE_13:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
PHE_13:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 3.4900 C CB N HA
|
||||
PHE_13:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
PHE_13:C C c' pepC 0 0 0.3800 1 1 8 1.0000 3.4000 O/2.0 CA ASN_14:N/1.5
|
||||
PHE_13:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 4.0700 C/2.0
|
||||
PHE_13:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 5.4800 CG CA HB1 HB2
|
||||
PHE_13:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PHE_13:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PHE_13:CG C cp arG 0 0 0.0000 1 1 8 1.0000 5.5700 CD1/1.5 CD2/1.5 CB
|
||||
PHE_13:CD1 C cp arD1 0 0 -0.1000 1 1 8 1.0000 6.9900 CE1/1.5 CG/1.5 HD1
|
||||
PHE_13:HD1 H h arD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
PHE_13:CD2 C cp arD2 0 0 -0.1000 1 1 8 1.0000 6.5200 CG/1.5 CE2/1.5 HD2
|
||||
PHE_13:HD2 H h arD2 0 0 0.1000 0 0 8 1.0000 0.0000 CD2
|
||||
PHE_13:CE1 C cp arE1 0 0 -0.1000 1 1 8 1.0000 8.2000 CZ/1.5 CD1/1.5 HE1
|
||||
PHE_13:HE1 H h arE1 0 0 0.1000 0 0 8 1.0000 0.0000 CE1
|
||||
PHE_13:CE2 C cp arE2 0 0 -0.1000 1 1 8 1.0000 6.3400 CD2/1.5 CZ/1.5 HE2
|
||||
PHE_13:HE2 H h arE2 0 0 0.1000 0 0 8 1.0000 0.0000 CE2
|
||||
PHE_13:CZ C cp arZ 0 0 -0.1000 1 1 8 1.0000 6.8400 CE2/1.5 CE1/1.5 HZ
|
||||
PHE_13:HZ H h arZ 0 0 0.1000 0 0 8 1.0000 0.0000 CZ
|
||||
ASN_14:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.6400 CA PHE_13:C/1.5 HN
|
||||
ASN_14:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ASN_14:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 4.3100 C CB N HA
|
||||
ASN_14:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ASN_14:C C c' pepC 0 0 0.3800 1 1 8 1.0000 3.9800 O/2.0 CA VAL_15:N/1.5
|
||||
ASN_14:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 6.2200 C/2.0
|
||||
ASN_14:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 5.8100 CG CA HB1 HB2
|
||||
ASN_14:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ASN_14:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ASN_14:CG C c' coG 0 0 0.3800 1 1 8 1.0000 6.8200 OD1/2.0 ND2/1.5 CB
|
||||
ASN_14:OD1 O o' coG 0 0 -0.3800 0 0 8 1.0000 9.4300 CG/2.0
|
||||
ASN_14:ND2 N n2 amD 0 0 -0.5600 1 1 8 1.0000 8.2100 CG/1.5 HD21 HD22
|
||||
ASN_14:HD21 H hn amD 0 0 0.2800 0 0 8 1.0000 0.0000 ND2
|
||||
ASN_14:HD22 H hn amD 0 0 0.2800 0 0 8 1.0000 0.0000 ND2
|
||||
VAL_15:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.7600 CA ASN_14:C/1.5 HN
|
||||
VAL_15:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
VAL_15:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 3.9800 C CB N HA
|
||||
VAL_15:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
VAL_15:C C c' pepC 0 0 0.3800 1 1 8 1.0000 3.8000 O/2.0 CA CYS_16:N/1.5
|
||||
VAL_15:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 4.8500 C/2.0
|
||||
VAL_15:CB C c1 meB 0 0 -0.1000 1 0 8 1.0000 4.7100 CG1 CG2 CA HB
|
||||
VAL_15:HB H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
VAL_15:CG1 C c3 meG1 0 0 -0.3000 1 0 8 1.0000 6.6700 CB HG11 HG12 HG13
|
||||
VAL_15:HG11 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
VAL_15:HG12 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
VAL_15:HG13 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
VAL_15:CG2 C c3 meG2 0 0 -0.3000 1 0 8 1.0000 6.2600 CB HG21 HG22 HG23
|
||||
VAL_15:HG21 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
VAL_15:HG22 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
VAL_15:HG23 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
CYS_16:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.7900 CA VAL_15:C/1.5 HN
|
||||
CYS_16:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
CYS_16:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 3.5400 C CB N HA
|
||||
CYS_16:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
CYS_16:C C c' pepC 0 0 0.3800 1 1 8 1.0000 3.4800 O/2.0 CA ARG_17:N/1.5
|
||||
CYS_16:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 4.6300 C/2.0
|
||||
CYS_16:CB C c2 cs 0 0 -0.3000 1 0 8 1.0000 4.5800 SG CA HB1 HB2
|
||||
CYS_16:HB1 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_16:HB2 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_16:SG S s1 cs 0 0 0.1000 0 0 8 1.0000 5.6600 CB CYS_26:SG
|
||||
ARG_17:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.9900 CA CYS_16:C/1.5 HN
|
||||
ARG_17:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ARG_17:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 3.8300 C CB N HA
|
||||
ARG_17:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ARG_17:C C c' pepC 0 0 0.3800 1 1 8 1.0000 3.7900 O/2.0 CA LEU_18:N/1.5
|
||||
ARG_17:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 5.3900 C/2.0
|
||||
ARG_17:CB C c2 c3nc 0 0 -0.2000 0 0 8 1.0000 4.1100 CG CA HB1 HB2
|
||||
ARG_17:HB1 H h c3nc 0 0 0.1100 0 0 8 1.0000 0.0000 CB
|
||||
ARG_17:HB2 H h c3nc 0 0 0.1100 0 0 8 1.0000 0.0000 CB
|
||||
ARG_17:CG C c2 c3nc 0 0 -0.2000 0 0 8 1.0000 4.6900 CD CB HG1 HG2
|
||||
ARG_17:HG1 H h c3nc 0 0 0.1300 0 0 8 1.0000 0.0000 CG
|
||||
ARG_17:HG2 H h c3nc 0 0 0.1300 0 0 8 1.0000 0.0000 CG
|
||||
ARG_17:CD C c2 c3nc 0 0 -0.1600 1 0 8 1.0000 5.1000 NE CG HD1 HD2
|
||||
ARG_17:HD1 H h c3nc 0 0 0.1300 0 0 8 1.0000 0.0000 CD
|
||||
ARG_17:HD2 H h c3nc 0 0 0.1300 0 0 8 1.0000 0.0000 CD
|
||||
ARG_17:NE N n c3nc 0 0 -0.5600 0 0 8 1.0000 4.7100 CZ/2.0 CD
|
||||
ARG_17:CZ C cr c3nc 0 0 0.3800 0 1 8 1.0000 5.2800 NH1 NH2 NE/2.0
|
||||
ARG_17:NH1 N n2 am1 0 0 -0.5600 1 1 8 1.0000 6.6700 CZ HH11 HH12
|
||||
ARG_17:HH11 H hn am1 0 0 0.2800 0 0 8 1.0000 0.0000 NH1
|
||||
ARG_17:HH12 H hn am1 0 0 0.2800 0 0 8 1.0000 0.0000 NH1
|
||||
ARG_17:NH2 N n2 am2 0 0 -0.5600 1 1 8 1.0000 6.4100 CZ HH21 HH22
|
||||
ARG_17:HH21 H hn am2 0 0 0.2800 0 0 8 1.0000 0.0000 NH2
|
||||
ARG_17:HH22 H hn am2 0 0 0.2800 0 0 8 1.0000 0.0000 NH2
|
||||
LEU_18:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.7000 CA ARG_17:C/1.5 HN
|
||||
LEU_18:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
LEU_18:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 5.4600 C CB N HA
|
||||
LEU_18:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
LEU_18:C C c' pepC 0 0 0.3800 1 1 8 1.0000 5.1300 O/2.0 CA PRO_19:N/1.5
|
||||
LEU_18:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 5.5500 C/2.0
|
||||
LEU_18:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 6.4700 CG CA HB1 HB2
|
||||
LEU_18:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
LEU_18:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
LEU_18:CG C c1 meG 0 0 -0.1000 1 0 8 1.0000 7.4300 CD1 CD2 CB HG
|
||||
LEU_18:HG H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
LEU_18:CD1 C c3 meD1 0 0 -0.3000 1 0 8 1.0000 8.7000 CG HD11 HD12 HD13
|
||||
LEU_18:HD11 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
LEU_18:HD12 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
LEU_18:HD13 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
LEU_18:CD2 C c3 meD2 0 0 -0.3000 1 0 8 1.0000 9.3900 CG HD21 HD22 HD23
|
||||
LEU_18:HD21 H h meD2 0 0 0.1000 0 0 8 1.0000 0.0000 CD2
|
||||
LEU_18:HD22 H h meD2 0 0 0.1000 0 0 8 1.0000 0.0000 CD2
|
||||
LEU_18:HD23 H h meD2 0 0 0.1000 0 0 8 1.0000 0.0000 CD2
|
||||
PRO_19:N N n pepN 0 0 -0.4200 1 1 8 1.0000 4.2800 CA CD LEU_18:C/1.5
|
||||
PRO_19:CA C ca pepN 0 0 0.0600 0 0 8 1.0000 5.3800 C CB N HA
|
||||
PRO_19:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
PRO_19:CD C c2 pepN 0 0 0.0600 0 0 8 1.0000 6.4500 N CG HD1 HD2
|
||||
PRO_19:HD1 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CD
|
||||
PRO_19:HD2 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CD
|
||||
PRO_19:C C c' pepC 0 0 0.3800 1 1 8 1.0000 6.3000 O/2.0 CA GLY_20:N/1.5
|
||||
PRO_19:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 9.6200 C/2.0
|
||||
PRO_19:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 5.8700 CG CA HB1 HB2
|
||||
PRO_19:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PRO_19:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PRO_19:CG C c2 meG 0 0 -0.2000 1 0 8 1.0000 6.4700 CD CB HG1 HG2
|
||||
PRO_19:HG1 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
PRO_19:HG2 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
GLY_20:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.9400 CA PRO_19:C/1.5 HN
|
||||
GLY_20:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
GLY_20:CA C cg pepN 0 0 0.0200 0 0 8 1.0000 5.3900 C N HA1 HA2
|
||||
GLY_20:HA1 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
GLY_20:HA2 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
GLY_20:C C c' pepC 0 0 0.3800 1 1 8 1.0000 5.0300 O/2.0 CA THR_21:N/1.5
|
||||
GLY_20:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 7.3400 C/2.0
|
||||
THR_21:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.1000 CA GLY_20:C/1.5 HN
|
||||
THR_21:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
THR_21:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 3.9400 C CB N HA
|
||||
THR_21:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
THR_21:C C c' pepC 0 0 0.3800 1 1 8 1.0000 3.9600 O/2.0 CA PRO_22:N/1.5
|
||||
THR_21:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 5.8200 C/2.0
|
||||
THR_21:CB C c1 cBoh 0 0 -0.0700 0 0 8 1.0000 4.1300 CG2 OG1 CA HB
|
||||
THR_21:HB H h cBoh 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
THR_21:OG1 O oh cBoh 0 0 -0.3800 1 0 8 1.0000 5.4500 CB HG1
|
||||
THR_21:HG1 H ho cBoh 0 0 0.3500 0 0 8 1.0000 0.0000 OG1
|
||||
THR_21:CG2 C c3 meG 0 0 -0.3000 1 0 8 1.0000 5.4100 CB HG21 HG22 HG23
|
||||
THR_21:HG21 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_21:HG22 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_21:HG23 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
PRO_22:N N n pepN 0 0 -0.4200 1 1 8 1.0000 5.0400 CA CD THR_21:C/1.5
|
||||
PRO_22:CA C ca pepN 0 0 0.0600 0 0 8 1.0000 4.6900 C CB N HA
|
||||
PRO_22:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
PRO_22:CD C c2 pepN 0 0 0.0600 0 0 8 1.0000 4.9000 N CG HD1 HD2
|
||||
PRO_22:HD1 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CD
|
||||
PRO_22:HD2 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CD
|
||||
PRO_22:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.1900 O/2.0 CA GLU_23:N/1.5
|
||||
PRO_22:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 4.4700 C/2.0
|
||||
PRO_22:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 7.1200 CG CA HB1 HB2
|
||||
PRO_22:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PRO_22:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PRO_22:CG C c2 meG 0 0 -0.2000 1 0 8 1.0000 7.0300 CD CB HG1 HG2
|
||||
PRO_22:HG1 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
PRO_22:HG2 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
GLU_23:N N n pepN 0 0 -0.5000 1 1 8 1.0000 5.1600 CA PRO_22:C/1.5 HN
|
||||
GLU_23:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
GLU_23:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 5.3100 C CB N HA
|
||||
GLU_23:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
GLU_23:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.1100 O/2.0 CA ALA_24:N/1.5
|
||||
GLU_23:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 5.1100 C/2.0
|
||||
GLU_23:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 6.1600 CG CA HB1 HB2
|
||||
GLU_23:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
GLU_23:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
GLU_23:CG C c2 meG 0 0 -0.2000 1 0 8 1.0000 7.4800 CD CB HG1 HG2
|
||||
GLU_23:HG1 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
GLU_23:HG2 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
GLU_23:CD C c' cooh 0 0 0.3800 1 1 8 1.0000 9.4000 OE1/2.0 OE2 CG
|
||||
GLU_23:OE1 O o' cooh 0 0 -0.3500 0 0 8 1.0000 10.4000 CD/2.0
|
||||
GLU_23:OE2 O oh cooh 0 0 -0.3800 0 0 8 1.0000 13.3200 CD HE2
|
||||
GLU_23:HE2 H ho cooh 0 0 0.3500 0 0 8 1.0000 0.0000 OE2
|
||||
ALA_24:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.5600 CA GLU_23:C/1.5 HN
|
||||
ALA_24:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ALA_24:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 4.4900 C CB N HA
|
||||
ALA_24:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ALA_24:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.1000 O/2.0 CA ILE_25:N/1.5
|
||||
ALA_24:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 5.6400 C/2.0
|
||||
ALA_24:CB C c3 meB 0 0 -0.3000 1 0 8 1.0000 5.8000 CA HB1 HB2 HB3
|
||||
ALA_24:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ALA_24:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ALA_24:HB3 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ILE_25:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.3700 CA ALA_24:C/1.5 HN
|
||||
ILE_25:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ILE_25:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 5.4400 C CB N HA
|
||||
ILE_25:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ILE_25:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.3200 O/2.0 CA CYS_26:N/1.5
|
||||
ILE_25:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 4.7200 C/2.0
|
||||
ILE_25:CB C c1 meB 0 0 -0.1000 1 0 8 1.0000 6.4200 CG2 CG1 CA HB
|
||||
ILE_25:HB H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ILE_25:CG1 C c2 meG1 0 0 -0.2000 1 0 8 1.0000 7.5000 CD1 CB HG11 HG12
|
||||
ILE_25:HG11 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
ILE_25:HG12 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
ILE_25:CG2 C c3 meG2 0 0 -0.3000 1 0 8 1.0000 7.6500 CB HG21 HG22 HG23
|
||||
ILE_25:HG21 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_25:HG22 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_25:HG23 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_25:CD1 C c3 meD1 0 0 -0.3000 1 0 8 1.0000 7.8000 CG1 HD11 HD12 HD13
|
||||
ILE_25:HD11 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_25:HD12 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_25:HD13 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
CYS_26:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.9200 CA ILE_25:C/1.5 HN
|
||||
CYS_26:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
CYS_26:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 4.3700 C CB N HA
|
||||
CYS_26:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
CYS_26:C C c' pepC 0 0 0.3800 1 1 8 1.0000 3.9500 O/2.0 CA ALA_27:N/1.5
|
||||
CYS_26:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 4.7400 C/2.0
|
||||
CYS_26:CB C c2 cs 0 0 -0.3000 1 0 8 1.0000 4.6300 SG CA HB1 HB2
|
||||
CYS_26:HB1 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_26:HB2 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_26:SG S s1 cs 0 0 0.1000 0 0 8 1.0000 5.6100 CB CYS_16:SG
|
||||
ALA_27:N N n pepN 0 0 -0.5000 1 1 8 1.0000 3.8900 CA CYS_26:C/1.5 HN
|
||||
ALA_27:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ALA_27:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 4.4300 C CB N HA
|
||||
ALA_27:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ALA_27:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.2600 O/2.0 CA THR_28:N/1.5
|
||||
ALA_27:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 5.4400 C/2.0
|
||||
ALA_27:CB C c3 meB 0 0 -0.3000 1 0 8 1.0000 5.3600 CA HB1 HB2 HB3
|
||||
ALA_27:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ALA_27:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ALA_27:HB3 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
THR_28:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.5300 CA ALA_27:C/1.5 HN
|
||||
THR_28:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
THR_28:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 5.0800 C CB N HA
|
||||
THR_28:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
THR_28:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.6200 O/2.0 CA TYR_29:N/1.5
|
||||
THR_28:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 7.8000 C/2.0
|
||||
THR_28:CB C c1 cBoh 0 0 -0.0700 0 0 8 1.0000 6.0300 CG2 OG1 CA HB
|
||||
THR_28:HB H h cBoh 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
THR_28:OG1 O oh cBoh 0 0 -0.3800 1 0 8 1.0000 7.1900 CB HG1
|
||||
THR_28:HG1 H ho cBoh 0 0 0.3500 0 0 8 1.0000 0.0000 OG1
|
||||
THR_28:CG2 C c3 meG 0 0 -0.3000 1 0 8 1.0000 7.3400 CB HG21 HG22 HG23
|
||||
THR_28:HG21 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_28:HG22 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_28:HG23 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
TYR_29:N N n pepN 0 0 -0.5000 1 1 8 1.0000 5.0100 CA THR_28:C/1.5 HN
|
||||
TYR_29:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
TYR_29:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 6.6000 C CB N HA
|
||||
TYR_29:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
TYR_29:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.9200 O/2.0 CA THR_30:N/1.5
|
||||
TYR_29:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 7.1300 C/2.0
|
||||
TYR_29:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 9.6600 CG CA HB1 HB2
|
||||
TYR_29:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
TYR_29:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
TYR_29:CG C cp arG 0 0 0.0000 1 1 8 1.0000 11.5600 CD1/1.5 CD2/1.5 CB
|
||||
TYR_29:CD1 C cp arD1 0 0 -0.1000 1 1 8 1.0000 12.8500 CE1/1.5 CG/1.5 HD1
|
||||
TYR_29:HD1 H h arD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
TYR_29:CD2 C cp arD2 0 0 -0.1000 1 1 8 1.0000 14.4400 CG/1.5 CE2/1.5 HD2
|
||||
TYR_29:HD2 H h arD2 0 0 0.1000 0 0 8 1.0000 0.0000 CD2
|
||||
TYR_29:CE1 C cp arE1 0 0 -0.1000 1 1 8 1.0000 16.6100 CZ/1.5 CD1/1.5 HE1
|
||||
TYR_29:HE1 H h arE1 0 0 0.1000 0 0 8 1.0000 0.0000 CE1
|
||||
TYR_29:CE2 C cp arE2 0 0 -0.1000 1 1 8 1.0000 17.1100 CD2/1.5 CZ/1.5 HE2
|
||||
TYR_29:HE2 H h arE2 0 0 0.1000 0 0 8 1.0000 0.0000 CE2
|
||||
TYR_29:CZ C cp phol 0 0 0.0300 0 1 8 1.0000 19.9900 OH CE2/1.5 CE1/1.5
|
||||
TYR_29:OH O oh phol 0 0 -0.3800 1 0 8 1.0000 28.9800 CZ HH
|
||||
TYR_29:HH H ho phol 0 0 0.3500 0 0 8 1.0000 0.0000 OH
|
||||
THR_30:N N n pepN 0 0 -0.5000 1 1 8 1.0000 5.3100 CA TYR_29:C/1.5 HN
|
||||
THR_30:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
THR_30:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 5.7000 C CB N HA
|
||||
THR_30:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
THR_30:C C c' pepC 0 0 0.3800 1 1 8 1.0000 6.2800 O/2.0 CA GLY_31:N/1.5
|
||||
THR_30:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 8.7700 C/2.0
|
||||
THR_30:CB C c1 cBoh 0 0 -0.0700 0 0 8 1.0000 6.5500 CG2 OG1 CA HB
|
||||
THR_30:HB H h cBoh 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
THR_30:OG1 O oh cBoh 0 0 -0.3800 1 0 8 1.0000 6.5700 CB HG1
|
||||
THR_30:HG1 H ho cBoh 0 0 0.3500 0 0 8 1.0000 0.0000 OG1
|
||||
THR_30:CG2 C c3 meG 0 0 -0.3000 1 0 8 1.0000 7.2900 CB HG21 HG22 HG23
|
||||
THR_30:HG21 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_30:HG22 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_30:HG23 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
GLY_31:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.9900 CA THR_30:C/1.5 HN
|
||||
GLY_31:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
GLY_31:CA C cg pepN 0 0 0.0200 0 0 8 1.0000 5.5000 C N HA1 HA2
|
||||
GLY_31:HA1 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
GLY_31:HA2 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
GLY_31:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.1900 O/2.0 CA CYS_32:N/1.5
|
||||
GLY_31:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 6.1200 C/2.0
|
||||
CYS_32:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.3000 CA GLY_31:C/1.5 HN
|
||||
CYS_32:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
CYS_32:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 4.8900 C CB N HA
|
||||
CYS_32:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
CYS_32:C C c' pepC 0 0 0.3800 1 1 8 1.0000 5.5000 O/2.0 CA ILE_33:N/1.5
|
||||
CYS_32:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 5.8200 C/2.0
|
||||
CYS_32:CB C c2 cs 0 0 -0.3000 1 0 8 1.0000 4.6600 SG CA HB1 HB2
|
||||
CYS_32:HB1 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_32:HB2 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_32:SG S s1 cs 0 0 0.1000 0 0 8 1.0000 5.3300 CB CYS_4:SG
|
||||
ILE_33:N N n pepN 0 0 -0.5000 1 1 8 1.0000 6.0200 CA CYS_32:C/1.5 HN
|
||||
ILE_33:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ILE_33:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 5.2400 C CB N HA
|
||||
ILE_33:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ILE_33:C C c' pepC 0 0 0.3800 1 1 8 1.0000 5.1600 O/2.0 CA ILE_34:N/1.5
|
||||
ILE_33:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 7.1900 C/2.0
|
||||
ILE_33:CB C c1 meB 0 0 -0.1000 1 0 8 1.0000 5.4900 CG2 CG1 CA HB
|
||||
ILE_33:HB H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ILE_33:CG1 C c2 meG1 0 0 -0.2000 1 0 8 1.0000 6.8500 CD1 CB HG11 HG12
|
||||
ILE_33:HG11 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
ILE_33:HG12 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
ILE_33:CG2 C c3 meG2 0 0 -0.3000 1 0 8 1.0000 6.4500 CB HG21 HG22 HG23
|
||||
ILE_33:HG21 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_33:HG22 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_33:HG23 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_33:CD1 C c3 meD1 0 0 -0.3000 1 0 8 1.0000 8.9400 CG1 HD11 HD12 HD13
|
||||
ILE_33:HD11 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_33:HD12 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_33:HD13 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_34:N N n pepN 0 0 -0.5000 1 1 8 1.0000 5.5200 CA ILE_33:C/1.5 HN
|
||||
ILE_34:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ILE_34:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 6.8200 C CB N HA
|
||||
ILE_34:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ILE_34:C C c' pepC 0 0 0.3800 1 1 8 1.0000 6.9200 O/2.0 CA ILE_35:N/1.5
|
||||
ILE_34:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 9.2200 C/2.0
|
||||
ILE_34:CB C c1 meB 0 0 -0.1000 1 0 8 1.0000 8.1100 CG2 CG1 CA HB
|
||||
ILE_34:HB H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ILE_34:CG1 C c2 meG1 0 0 -0.2000 1 0 8 1.0000 9.5900 CD1 CB HG11 HG12
|
||||
ILE_34:HG11 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
ILE_34:HG12 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
ILE_34:CG2 C c3 meG2 0 0 -0.3000 1 0 8 1.0000 9.7300 CB HG21 HG22 HG23
|
||||
ILE_34:HG21 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_34:HG22 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_34:HG23 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_34:CD1 C c3 meD1 0 0 -0.3000 1 0 8 1.0000 13.4100 CG1 HD11 HD12 HD13
|
||||
ILE_34:HD11 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_34:HD12 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_34:HD13 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_35:N N n pepN 0 0 -0.5000 1 1 8 1.0000 7.0600 CA ILE_34:C/1.5 HN
|
||||
ILE_35:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ILE_35:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 7.5200 C CB N HA
|
||||
ILE_35:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ILE_35:C C c' pepC 0 0 0.3800 1 1 8 1.0000 6.6300 O/2.0 CA PRO_36:N/1.5
|
||||
ILE_35:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 7.9000 C/2.0
|
||||
ILE_35:CB C c1 meB 0 0 -0.1000 1 0 8 1.0000 8.0700 CG2 CG1 CA HB
|
||||
ILE_35:HB H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ILE_35:CG1 C c2 meG1 0 0 -0.2000 1 0 8 1.0000 9.4100 CD1 CB HG11 HG12
|
||||
ILE_35:HG11 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
ILE_35:HG12 H h meG1 0 0 0.1000 0 0 8 1.0000 0.0000 CG1
|
||||
ILE_35:CG2 C c3 meG2 0 0 -0.3000 1 0 8 1.0000 9.4600 CB HG21 HG22 HG23
|
||||
ILE_35:HG21 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_35:HG22 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_35:HG23 H h meG2 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
ILE_35:CD1 C c3 meD1 0 0 -0.3000 1 0 8 1.0000 9.8500 CG1 HD11 HD12 HD13
|
||||
ILE_35:HD11 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_35:HD12 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
ILE_35:HD13 H h meD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
PRO_36:N N n pepN 0 0 -0.4200 1 1 8 1.0000 8.0700 CA CD ILE_35:C/1.5
|
||||
PRO_36:CA C ca pepN 0 0 0.0600 0 0 8 1.0000 8.7800 C CB N HA
|
||||
PRO_36:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
PRO_36:CD C c2 pepN 0 0 0.0600 0 0 8 1.0000 9.5300 N CG HD1 HD2
|
||||
PRO_36:HD1 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CD
|
||||
PRO_36:HD2 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CD
|
||||
PRO_36:C C c' pepC 0 0 0.3800 1 1 8 1.0000 8.3100 O/2.0 CA GLY_37:N/1.5
|
||||
PRO_36:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 9.0900 C/2.0
|
||||
PRO_36:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 9.6700 CG CA HB1 HB2
|
||||
PRO_36:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PRO_36:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PRO_36:CG C c2 meG 0 0 -0.2000 1 0 8 1.0000 10.1500 CD CB HG1 HG2
|
||||
PRO_36:HG1 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
PRO_36:HG2 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
GLY_37:N N n pepN 0 0 -0.5000 1 1 8 1.0000 8.4800 CA PRO_36:C/1.5 HN
|
||||
GLY_37:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
GLY_37:CA C cg pepN 0 0 0.0200 0 0 8 1.0000 9.2000 C N HA1 HA2
|
||||
GLY_37:HA1 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
GLY_37:HA2 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
GLY_37:C C c' pepC 0 0 0.3800 1 1 8 1.0000 10.4100 O/2.0 CA ALA_38:N/1.5
|
||||
GLY_37:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 12.0600 C/2.0
|
||||
ALA_38:N N n pepN 0 0 -0.5000 1 1 8 1.0000 9.2400 CA GLY_37:C/1.5 HN
|
||||
ALA_38:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ALA_38:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 9.2400 C CB N HA
|
||||
ALA_38:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ALA_38:C C c' pepC 0 0 0.3800 1 1 8 1.0000 9.6000 O/2.0 CA THR_39:N/1.5
|
||||
ALA_38:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 13.6500 C/2.0
|
||||
ALA_38:CB C c3 meB 0 0 -0.3000 1 0 8 1.0000 10.4300 CA HB1 HB2 HB3
|
||||
ALA_38:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ALA_38:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ALA_38:HB3 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
THR_39:N N n pepN 0 0 -0.5000 1 1 8 1.0000 8.7000 CA ALA_38:C/1.5 HN
|
||||
THR_39:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
THR_39:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 9.4600 C CB N HA
|
||||
THR_39:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
THR_39:C C c' pepC 0 0 0.3800 1 1 8 1.0000 8.3200 O/2.0 CA CYS_40:N/1.5
|
||||
THR_39:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 9.8900 C/2.0
|
||||
THR_39:CB C c1 cBoh 0 0 -0.0700 0 0 8 1.0000 10.7200 CG2 OG1 CA HB
|
||||
THR_39:HB H h cBoh 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
THR_39:OG1 O oh cBoh 0 0 -0.3800 1 0 8 1.0000 11.6600 CB HG1
|
||||
THR_39:HG1 H ho cBoh 0 0 0.3500 0 0 8 1.0000 0.0000 OG1
|
||||
THR_39:CG2 C c3 meG 0 0 -0.3000 1 0 8 1.0000 11.8100 CB HG21 HG22 HG23
|
||||
THR_39:HG21 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_39:HG22 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
THR_39:HG23 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG2
|
||||
CYS_40:N N n pepN 0 0 -0.5000 1 1 8 1.0000 7.6400 CA THR_39:C/1.5 HN
|
||||
CYS_40:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
CYS_40:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 8.0500 C CB N HA
|
||||
CYS_40:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
CYS_40:C C c' pepC 0 0 0.3800 1 1 8 1.0000 7.6300 O/2.0 CA PRO_41:N/1.5
|
||||
CYS_40:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 9.6400 C/2.0
|
||||
CYS_40:CB C c2 cs 0 0 -0.3000 1 0 8 1.0000 7.8000 SG CA HB1 HB2
|
||||
CYS_40:HB1 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_40:HB2 H h cs 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
CYS_40:SG S s1 cs 0 0 0.1000 0 0 8 1.0000 7.3000 CB CYS_3:SG
|
||||
PRO_41:N N n pepN 0 0 -0.4200 1 1 8 1.0000 8.0000 CA CD CYS_40:C/1.5
|
||||
PRO_41:CA C ca pepN 0 0 0.0600 0 0 8 1.0000 8.9600 C CB N HA
|
||||
PRO_41:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
PRO_41:CD C c2 pepN 0 0 0.0600 0 0 8 1.0000 10.4900 N CG HD1 HD2
|
||||
PRO_41:HD1 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CD
|
||||
PRO_41:HD2 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CD
|
||||
PRO_41:C C c' pepC 0 0 0.3800 1 1 8 1.0000 9.0600 O/2.0 CA GLY_42:N/1.5
|
||||
PRO_41:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 8.8200 C/2.0
|
||||
PRO_41:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 10.3900 CG CA HB1 HB2
|
||||
PRO_41:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PRO_41:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
PRO_41:CG C c2 meG 0 0 -0.2000 1 0 8 1.0000 10.9900 CD CB HG1 HG2
|
||||
PRO_41:HG1 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
PRO_41:HG2 H h meG 0 0 0.1000 0 0 8 1.0000 0.0000 CG
|
||||
GLY_42:N N n pepN 0 0 -0.5000 1 1 8 1.0000 7.5500 CA PRO_41:C/1.5 HN
|
||||
GLY_42:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
GLY_42:CA C cg pepN 0 0 0.0200 0 0 8 1.0000 8.0000 C N HA1 HA2
|
||||
GLY_42:HA1 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
GLY_42:HA2 H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
GLY_42:C C c' pepC 0 0 0.3800 1 1 8 1.0000 7.2200 O/2.0 CA ASP_43:N/1.5
|
||||
GLY_42:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 8.4100 C/2.0
|
||||
ASP_43:N N n pepN 0 0 -0.5000 1 1 8 1.0000 5.5400 CA GLY_42:C/1.5 HN
|
||||
ASP_43:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ASP_43:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 5.8500 C CB N HA
|
||||
ASP_43:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ASP_43:C C c' pepC 0 0 0.3800 1 1 8 1.0000 5.8700 O/2.0 CA TYR_44:N/1.5
|
||||
ASP_43:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 7.2900 C/2.0
|
||||
ASP_43:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 6.7200 CG CA HB1 HB2
|
||||
ASP_43:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ASP_43:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ASP_43:CG C c' cooh 0 0 0.3800 1 1 8 1.0000 8.5900 OD1/2.0 OD2 CB
|
||||
ASP_43:OD1 O o' cooh 0 0 -0.3500 0 0 8 1.0000 9.5900 CG/2.0
|
||||
ASP_43:OD2 O oh cooh 0 0 -0.3800 0 0 8 1.0000 11.4500 CG HD2
|
||||
ASP_43:HD2 H ho cooh 0 0 0.3500 0 0 8 1.0000 0.0000 OD2
|
||||
TYR_44:N N n pepN 0 0 -0.5000 1 1 8 1.0000 5.2200 CA ASP_43:C/1.5 HN
|
||||
TYR_44:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
TYR_44:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 5.5600 C CB N HA
|
||||
TYR_44:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
TYR_44:C C c' pepC 0 0 0.3800 1 1 8 1.0000 4.6100 O/2.0 CA ALA_45:N/1.5
|
||||
TYR_44:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 6.0400 C/2.0
|
||||
TYR_44:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 5.4100 CG CA HB1 HB2
|
||||
TYR_44:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
TYR_44:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
TYR_44:CG C cp arG 0 0 0.0000 1 1 8 1.0000 5.3400 CD1/1.5 CD2/1.5 CB
|
||||
TYR_44:CD1 C cp arD1 0 0 -0.1000 1 1 8 1.0000 6.5900 CE1/1.5 CG/1.5 HD1
|
||||
TYR_44:HD1 H h arD1 0 0 0.1000 0 0 8 1.0000 0.0000 CD1
|
||||
TYR_44:CD2 C cp arD2 0 0 -0.1000 1 1 8 1.0000 5.9400 CG/1.5 CE2/1.5 HD2
|
||||
TYR_44:HD2 H h arD2 0 0 0.1000 0 0 8 1.0000 0.0000 CD2
|
||||
TYR_44:CE1 C cp arE1 0 0 -0.1000 1 1 8 1.0000 5.9700 CZ/1.5 CD1/1.5 HE1
|
||||
TYR_44:HE1 H h arE1 0 0 0.1000 0 0 8 1.0000 0.0000 CE1
|
||||
TYR_44:CE2 C cp arE2 0 0 -0.1000 1 1 8 1.0000 5.1700 CD2/1.5 CZ/1.5 HE2
|
||||
TYR_44:HE2 H h arE2 0 0 0.1000 0 0 8 1.0000 0.0000 CE2
|
||||
TYR_44:CZ C cp phol 0 0 0.0300 0 1 8 1.0000 5.9600 OH CE2/1.5 CE1/1.5
|
||||
TYR_44:OH O oh phol 0 0 -0.3800 1 0 8 1.0000 8.6000 CZ HH
|
||||
TYR_44:HH H ho phol 0 0 0.3500 0 0 8 1.0000 0.0000 OH
|
||||
ALA_45:N N n pepN 0 0 -0.5000 1 1 8 1.0000 4.7600 CA TYR_44:C/1.5 HN
|
||||
ALA_45:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ALA_45:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 5.8900 C CB N HA
|
||||
ALA_45:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ALA_45:C C c' pepC 0 0 0.3800 1 1 8 1.0000 6.6700 O/2.0 CA ASNC_46:N/1.5
|
||||
ALA_45:O O o' pepC 0 0 -0.3800 0 0 8 1.0000 7.5600 C/2.0
|
||||
ALA_45:CB C c3 meB 0 0 -0.3000 1 0 8 1.0000 6.8200 CA HB1 HB2 HB3
|
||||
ALA_45:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ALA_45:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ALA_45:HB3 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ASNC_46:N N n pepN 0 0 -0.5000 1 1 8 1.0000 5.8000 CA ALA_45:C/1.5 HN
|
||||
ASNC_46:HN H hn pepN 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
ASNC_46:CA C ca pepN 0 0 0.1200 0 0 8 1.0000 6.1500 C CB N HA
|
||||
ASNC_46:HA H h pepN 0 0 0.1000 0 0 8 1.0000 0.0000 CA
|
||||
ASNC_46:C C c- pep- 0 0 0.1400 1 1 8 1.0000 6.6100 O/1.5 OXT/1.5 CA
|
||||
ASNC_46:O O o- pep- 0 0 -0.5700 0 0 8 1.0000 7.1800 C/1.5
|
||||
ASNC_46:OXT O o- pep- 0 0 -0.5700 0 0 8 1.0000 7.8600 C/1.5
|
||||
ASNC_46:CB C c2 meB 0 0 -0.2000 1 0 8 1.0000 7.2700 CG CA HB1 HB2
|
||||
ASNC_46:HB1 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ASNC_46:HB2 H h meB 0 0 0.1000 0 0 8 1.0000 0.0000 CB
|
||||
ASNC_46:CG C c' coG 0 0 0.3800 1 1 8 1.0000 7.9800 OD1/2.0 ND2/1.5 CB
|
||||
ASNC_46:OD1 O o' coG 0 0 -0.3800 0 0 8 1.0000 11.0000 CG/2.0
|
||||
ASNC_46:ND2 N n2 amD 0 0 -0.5600 1 1 8 1.0000 10.3200 CG/1.5 HD21 HD22
|
||||
ASNC_46:HD21 H hn amD 0 0 0.2800 0 0 8 1.0000 0.0000 ND2
|
||||
ASNC_46:HD22 H hn amD 0 0 0.2800 0 0 8 1.0000 0.0000 ND2
|
||||
|
||||
|
||||
#atomset
|
||||
|
||||
|
||||
@quartet torsion *:*_*:chi1
|
||||
N CA CB OG1
|
||||
|
||||
@quartet torsion *:*_*:chi2
|
||||
CA CB OG1 HG1
|
||||
|
||||
@quartet torsion *:*_*:ch2'
|
||||
CA CB CG2 HG21
|
||||
|
||||
@quartet torsion *:*_*:psi
|
||||
N CA C *:N
|
||||
|
||||
@quartet torsion *:*_*:omeg
|
||||
CA C *:N *:CA
|
||||
|
||||
@quartet torsion *:*_*:phi
|
||||
*:C N CA C
|
||||
|
||||
@quartet torsion *:CYS_*:chi1
|
||||
N CA CB SG
|
||||
|
||||
@quartet torsion *:*_*:chi1
|
||||
N CA CB CG
|
||||
|
||||
@quartet torsion *:SER_*:chi1
|
||||
N CA CB OG
|
||||
|
||||
@quartet torsion *:SER_*:chi2
|
||||
CA CB OG HG
|
||||
|
||||
@quartet torsion *:*_*:chi1
|
||||
N CA CB CG1
|
||||
|
||||
@quartet torsion *:ILE_*:chi2
|
||||
CA CB CG1 CD1
|
||||
|
||||
@quartet torsion *:ILE_*:chi3
|
||||
CB CG1 CD1 HD11
|
||||
|
||||
@quartet torsion *:VAL_*:chi2
|
||||
CA CB CG1 HG11
|
||||
|
||||
@quartet torsion *:ALA_*:chi1
|
||||
N CA CB HB1
|
||||
|
||||
@quartet torsion *:*_*:chi2
|
||||
CA CB CG CD
|
||||
|
||||
@quartet torsion *:ARG_*:chi3
|
||||
CB CG CD NE
|
||||
|
||||
@quartet torsion *:ARG_*:chi4
|
||||
CG CD NE CZ
|
||||
|
||||
@quartet torsion *:ARG_*:chi5
|
||||
CD NE CZ NH1
|
||||
|
||||
@quartet torsion *:*_*:chi2
|
||||
CA CB CG ND2
|
||||
|
||||
@quartet torsion *:*_*:chi3
|
||||
CB CG ND2 HD21
|
||||
|
||||
@quartet torsion *:*_*:chi2
|
||||
CA CB CG CD1
|
||||
|
||||
@quartet torsion *:LEU_18:chi3
|
||||
CB CG CD1 HD11
|
||||
|
||||
@quartet torsion *:LEU_18:ch2'
|
||||
CA CB CG CD2
|
||||
|
||||
@quartet torsion *:LEU_18:ch3'
|
||||
CB CG CD2 HD21
|
||||
|
||||
@quartet torsion *:GLU_23:chi3
|
||||
CB CG CD OE2
|
||||
|
||||
@quartet torsion *:GLU_23:chi4
|
||||
CG CD OE2 HE2
|
||||
|
||||
@quartet torsion *:TYR_*:chi3
|
||||
CE1 CZ OH HH
|
||||
|
||||
@quartet torsion *:ASP_43:chi2
|
||||
CA CB CG OD2
|
||||
|
||||
@quartet torsion *:ASP_43:chi3
|
||||
CB CG OD2 HD2
|
||||
|
||||
|
||||
@list subset CRN$TURNT1
|
||||
CRAMBIN:PRO_41:N CA HA CD HD1 HD2 C O CB HB1 HB2 CG HG1 HG2
|
||||
GLY_42:N HN CA HA1 HA2 C O
|
||||
ASP_43:N HN CA HA C O CB HB1 HB2 CG OD1 OD2 HD2
|
||||
TYR_44:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ OH HH
|
||||
|
||||
@list subset CRN$TURN
|
||||
CRAMBIN:PRO_41:N CA HA CD HD1 HD2 C O CB HB1 HB2 CG HG1 HG2
|
||||
GLY_42:N HN CA HA1 HA2 C O
|
||||
ASP_43:N HN CA HA C O CB HB1 HB2 CG OD1 OD2 HD2
|
||||
TYR_44:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ OH HH
|
||||
|
||||
@list subset CRN$SHEETS1
|
||||
CRAMBIN:THRN_1:N HN3 HN1 HN2 CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23
|
||||
THR_2:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23
|
||||
CYS_3:N HN CA HA C O CB HB1 HB2 SG
|
||||
CYS_4:N HN CA HA C O CB HB1 HB2 SG
|
||||
CYS_32:N HN CA HA C O CB HB1 HB2 SG
|
||||
ILE_33:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
|
||||
ILE_34:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
|
||||
ILE_35:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
|
||||
|
||||
@list subset CRN$SHEET
|
||||
CRAMBIN:THRN_1:N HN3 HN1 HN2 CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23
|
||||
THR_2:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23
|
||||
CYS_3:N HN CA HA C O CB HB1 HB2 SG
|
||||
CYS_4:N HN CA HA C O CB HB1 HB2 SG
|
||||
CYS_32:N HN CA HA C O CB HB1 HB2 SG
|
||||
ILE_33:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
|
||||
ILE_34:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
|
||||
ILE_35:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
|
||||
|
||||
@list subset CRN$HELIXH2
|
||||
CRAMBIN:GLU_23:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD OE1 OE2 HE2
|
||||
ALA_24:N HN CA HA C O CB HB1 HB2 HB3
|
||||
ILE_25:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
|
||||
CYS_26:N HN CA HA C O CB HB1 HB2 SG
|
||||
ALA_27:N HN CA HA C O CB HB1 HB2 HB3
|
||||
THR_28:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23
|
||||
TYR_29:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ OH HH
|
||||
THR_30:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23
|
||||
|
||||
@list subset CRN$HELIXH1
|
||||
CRAMBIN:ILE_7:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
|
||||
VAL_8:N HN CA HA C O CB HB CG1 HG11 HG12 HG13 CG2 HG21 HG22 HG23
|
||||
ALA_9:N HN CA HA C O CB HB1 HB2 HB3
|
||||
ARG_10:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD HD1 HD2 NE CZ NH1 HH11 HH12 NH2 HH21 HH22
|
||||
SER_11:N HN CA HA C O CB HB1 HB2 OG HG
|
||||
ASN_12:N HN CA HA C O CB HB1 HB2 CG OD1 ND2 HD21 HD22
|
||||
PHE_13:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ HZ
|
||||
ASN_14:N HN CA HA C O CB HB1 HB2 CG OD1 ND2 HD21 HD22
|
||||
VAL_15:N HN CA HA C O CB HB CG1 HG11 HG12 HG13 CG2 HG21 HG22 HG23
|
||||
CYS_16:N HN CA HA C O CB HB1 HB2 SG
|
||||
ARG_17:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD HD1 HD2 NE CZ NH1 HH11 HH12 NH2 HH21 HH22
|
||||
LEU_18:N HN CA HA C O CB HB1 HB2 CG HG CD1 HD11 HD12 HD13 CD2 HD21 HD22 HD23
|
||||
PRO_19:N CA HA CD HD1 HD2 C O CB HB1 HB2 CG HG1 HG2
|
||||
|
||||
@list subset CRN$HELIX
|
||||
CRAMBIN:ILE_7:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
|
||||
VAL_8:N HN CA HA C O CB HB CG1 HG11 HG12 HG13 CG2 HG21 HG22 HG23
|
||||
ALA_9:N HN CA HA C O CB HB1 HB2 HB3
|
||||
ARG_10:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD HD1 HD2 NE CZ NH1 HH11 HH12 NH2 HH21 HH22
|
||||
SER_11:N HN CA HA C O CB HB1 HB2 OG HG
|
||||
ASN_12:N HN CA HA C O CB HB1 HB2 CG OD1 ND2 HD21 HD22
|
||||
PHE_13:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ HZ
|
||||
ASN_14:N HN CA HA C O CB HB1 HB2 CG OD1 ND2 HD21 HD22
|
||||
VAL_15:N HN CA HA C O CB HB CG1 HG11 HG12 HG13 CG2 HG21 HG22 HG23
|
||||
CYS_16:N HN CA HA C O CB HB1 HB2 SG
|
||||
ARG_17:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD HD1 HD2 NE CZ NH1 HH11 HH12 NH2 HH21 HH22
|
||||
LEU_18:N HN CA HA C O CB HB1 HB2 CG HG CD1 HD11 HD12 HD13 CD2 HD21 HD22 HD23
|
||||
PRO_19:N CA HA CD HD1 HD2 C O CB HB1 HB2 CG HG1 HG2
|
||||
GLU_23:N HN CA HA C O CB HB1 HB2 CG HG1 HG2 CD OE1 OE2 HE2
|
||||
ALA_24:N HN CA HA C O CB HB1 HB2 HB3
|
||||
ILE_25:N HN CA HA C O CB HB CG1 HG11 HG12 CG2 HG21 HG22 HG23 CD1 HD11 HD12 HD13
|
||||
CYS_26:N HN CA HA C O CB HB1 HB2 SG
|
||||
ALA_27:N HN CA HA C O CB HB1 HB2 HB3
|
||||
THR_28:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23
|
||||
TYR_29:N HN CA HA C O CB HB1 HB2 CG CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CZ OH HH
|
||||
THR_30:N HN CA HA C O CB HB OG1 HG1 CG2 HG21 HG22 HG23
|
||||
#end
|
||||
|
||||
|
|
@ -0,0 +1,124 @@
|
|||
!BIOSYM archive 3
|
||||
PBC=OFF
|
||||
input file for discover
|
||||
!DATE Mon Jul 14 17:01:24 1997
|
||||
C 1.493000031 20.593999863 -0.449999988 MOL 1 c2 C 0.220
|
||||
C1 2.328000069 19.871000290 0.623000026 MOL 1 c2 C -0.200
|
||||
C2 2.887000084 20.902999878 1.621000051 MOL 1 c2 C -0.200
|
||||
C3 3.533999920 20.169000626 2.809999943 MOL 1 c2 C -0.200
|
||||
C4 4.085000038 21.201000214 3.812999964 MOL 1 c2 C -0.200
|
||||
C5 4.731999874 20.466999054 5.001999855 MOL 1 c2 C 0.020
|
||||
N 5.270999908 21.479000092 5.985000134 MOL 1 n N -0.500
|
||||
C6 6.477000237 21.142000198 6.829999924 MOL 1 c' C 0.380
|
||||
O 7.435999870 22.232000351 7.244999886 MOL 1 o' O -0.380
|
||||
C7 6.728000164 19.687000275 7.267000198 MOL 1 c2 C -0.200
|
||||
C8 7.763999939 19.665000916 8.406999588 MOL 1 c2 C -0.200
|
||||
C9 7.464000225 18.486000061 9.350999832 MOL 1 c2 C -0.200
|
||||
C10 8.416000366 18.541000366 10.560999870 MOL 1 c2 C -0.200
|
||||
C11 8.112999916 17.364999771 11.506999969 MOL 1 c' C 0.380
|
||||
O1 6.711999893 16.809000015 11.597000122 MOL 1 o' O -0.380
|
||||
HC1 2.111000061 20.704999924 -1.401000023 MOL 1 h H 0.100
|
||||
HC2 1.195999980 21.625999451 -0.067000002 MOL 1 h H 0.100
|
||||
H11 3.191999912 19.319000244 0.125000000 MOL 1 h H 0.100
|
||||
H12 1.669999957 19.124000549 1.179000020 MOL 1 h H 0.100
|
||||
H21 3.670000076 21.548999786 1.101999998 MOL 1 h H 0.100
|
||||
H22 2.039000034 21.563999176 1.998999953 MOL 1 h H 0.100
|
||||
H31 4.388000011 19.513999939 2.434000015 MOL 1 h H 0.100
|
||||
H32 2.753999949 19.517999649 3.325999975 MOL 1 h H 0.100
|
||||
H41 4.866000175 21.853000641 3.298000097 MOL 1 h H 0.100
|
||||
H42 3.232000113 21.857000351 4.190000057 MOL 1 h H 0.100
|
||||
H51 5.585000038 19.811000824 4.625999928 MOL 1 h H 0.100
|
||||
H52 3.951999903 19.815999985 5.518000126 MOL 1 h H 0.100
|
||||
HN 4.782000065 22.469999313 6.085999966 MOL 1 hn H 0.280
|
||||
H71 7.124000072 19.086999893 6.382999897 MOL 1 h H 0.100
|
||||
H72 5.751999855 19.225000381 7.632999897 MOL 1 h H 0.100
|
||||
H81 8.809000015 19.542999268 7.967999935 MOL 1 h H 0.100
|
||||
H82 7.709000111 20.642000198 8.989999771 MOL 1 h H 0.100
|
||||
H91 7.614999771 17.503000259 8.793999672 MOL 1 h H 0.100
|
||||
H92 6.385000229 18.555000305 9.713999748 MOL 1 h H 0.100
|
||||
H101 9.494999886 18.468999863 10.199000359 MOL 1 h H 0.100
|
||||
H102 8.267000198 19.524000168 11.118000031 MOL 1 h H 0.100
|
||||
N1 9.217000008 16.766000748 12.345000267 MOL 1 n N -0.500
|
||||
C12 8.902999878 16.179000854 13.701000214 MOL 1 c2 C 0.020
|
||||
C13 9.892000198 15.039999962 14.008999825 MOL 1 c2 C -0.200
|
||||
C14 9.138999939 13.871000290 14.671999931 MOL 1 c2 C -0.200
|
||||
C15 10.074000359 12.652999878 14.779999733 MOL 1 c2 C -0.200
|
||||
C16 9.317999840 11.480999947 15.434000015 MOL 1 c2 C -0.200
|
||||
C17 10.253000259 10.262000084 15.543000221 MOL 1 c2 C 0.020
|
||||
N2 9.512000084 9.114000320 16.184000015 MOL 1 n N -0.500
|
||||
C18 10.263999939 8.095999718 17.007999420 MOL 1 c' C 0.380
|
||||
O2 11.720000267 8.319999695 17.337999344 MOL 1 o' O -0.380
|
||||
C19 9.545000076 6.831999779 17.513000488 MOL 1 c2 C -0.200
|
||||
C20 10.385999680 6.170000076 18.621000290 MOL 1 c2 C -0.200
|
||||
C21 9.451999664 5.482999802 19.634000778 MOL 1 c2 C -0.200
|
||||
C22 10.281999588 4.934999943 20.809999466 MOL 1 c2 C -0.200
|
||||
H221 10.808575630 5.755126953 21.298067093 MOL 1 h H 0.100
|
||||
H222 11.006152153 4.209916592 20.438573837 MOL 1 h H 0.100
|
||||
C23 9.347999573 4.250999928 21.825000763 MOL 1 c' C 0.380
|
||||
O3 9.854000092 3.098999977 22.659999847 MOL 1 o' O -0.380
|
||||
H1 10.260000229 16.757999420 11.965000153 MOL 1 hn H 0.280
|
||||
H121 8.998000145 16.989000320 14.496999741 MOL 1 h H 0.100
|
||||
H122 7.839000225 15.769000053 13.699999809 MOL 1 h H 0.100
|
||||
H131 10.701999664 15.418999672 14.715999603 MOL 1 h H 0.100
|
||||
H132 10.373000145 14.680000305 13.039999962 MOL 1 h H 0.100
|
||||
H141 8.796999931 14.180999756 15.713999748 MOL 1 h H 0.100
|
||||
H142 8.229999542 13.597000122 14.039999962 MOL 1 h H 0.100
|
||||
H151 10.979000092 12.923000336 15.418000221 MOL 1 h H 0.100
|
||||
H152 10.421999931 12.345999718 13.739000320 MOL 1 h H 0.100
|
||||
H161 8.970999718 11.786999702 16.475999832 MOL 1 h H 0.100
|
||||
H162 8.413000107 11.208999634 14.796999931 MOL 1 h H 0.100
|
||||
H171 11.159000397 10.532999992 16.180000305 MOL 1 h H 0.100
|
||||
H172 10.600999832 9.956000328 14.501000404 MOL 1 h H 0.100
|
||||
H2 8.413999557 9.017000198 16.048999786 MOL 1 hn H 0.280
|
||||
H191 9.411000252 6.098999977 16.649999619 MOL 1 h H 0.100
|
||||
H192 8.522999763 7.116000175 17.930999756 MOL 1 h H 0.100
|
||||
H201 11.081000328 5.394000053 18.159000397 MOL 1 h H 0.100
|
||||
H202 11.005000114 6.965000153 19.155000687 MOL 1 h H 0.100
|
||||
H211 8.904000282 4.623000145 19.124000549 MOL 1 h H 0.100
|
||||
H212 8.692000389 6.237999916 20.024999619 MOL 1 h H 0.100
|
||||
N3 7.925000191 4.731999874 21.985000610 MOL 1 n N -0.500
|
||||
C24 7.053999901 4.160999775 23.077999115 MOL 1 c2 C 0.020
|
||||
C25 6.034999847 5.223000050 23.531999588 MOL 1 c2 C -0.200
|
||||
C26 5.895999908 5.179999828 25.065000534 MOL 1 c2 C -0.200
|
||||
C27 5.052000046 6.377999783 25.538000107 MOL 1 c2 C -0.200
|
||||
C28 4.921000004 6.340000153 27.072000504 MOL 1 c2 C -0.200
|
||||
C29 4.077000141 7.538000107 27.545999527 MOL 1 c2 C 0.020
|
||||
N4 3.948999882 7.500999928 29.049999237 MOL 1 n N -0.500
|
||||
C30 2.717999935 8.065999985 29.716999054 MOL 1 c' C 0.380
|
||||
O4 1.600000024 8.638999939 28.878000259 MOL 1 o' O -0.380
|
||||
C31 2.601000071 8.059000015 31.252000809 MOL 1 c2 C -0.200
|
||||
C32 1.139000058 8.319000244 31.658000946 MOL 1 c2 C -0.200
|
||||
C33 0.828000009 7.570000172 32.967998505 MOL 1 c2 C -0.200
|
||||
C34 -0.667999983 7.721000195 33.304000854 MOL 1 c2 C -0.200
|
||||
C35 -0.978999972 6.969999790 34.611000061 MOL 1 c' C 0.450
|
||||
O5 -2.085999966 7.455999851 35.515998840 MOL 1 o- O -0.500
|
||||
H3 7.519999981 5.506000042 21.299999237 MOL 1 hn H 0.280
|
||||
H241 6.498000145 3.246999979 22.683000565 MOL 1 h H 0.100
|
||||
H242 7.703999996 3.855999947 23.962999344 MOL 1 h H 0.100
|
||||
H251 5.022999763 5.008999825 23.052999496 MOL 1 h H 0.100
|
||||
H252 6.395999908 6.256000042 23.211999893 MOL 1 h H 0.100
|
||||
H261 5.383999825 4.209000111 25.372999191 MOL 1 h H 0.100
|
||||
H262 6.929999828 5.231999874 25.541999817 MOL 1 h H 0.100
|
||||
H271 4.014999866 6.322000027 25.068000793 MOL 1 h H 0.100
|
||||
H272 5.559999943 7.348999977 25.224000931 MOL 1 h H 0.100
|
||||
H281 4.413000107 5.369999886 27.386999130 MOL 1 h H 0.100
|
||||
H282 5.958000183 6.395999908 27.544000626 MOL 1 h H 0.100
|
||||
H291 3.039999962 7.482999802 27.075000763 MOL 1 h H 0.100
|
||||
H292 4.585000038 8.508999825 27.232000351 MOL 1 h H 0.100
|
||||
H4 4.760000229 7.059000015 29.665000916 MOL 1 hn H 0.280
|
||||
H311 3.266999960 8.875000000 31.687999725 MOL 1 h H 0.100
|
||||
H312 2.931999922 7.044000149 31.653999329 MOL 1 h H 0.100
|
||||
H321 0.980000019 9.437000275 31.813999176 MOL 1 h H 0.100
|
||||
H322 0.442999989 7.947999954 30.834999084 MOL 1 h H 0.100
|
||||
H331 1.452999949 8.008000374 33.813999176 MOL 1 h H 0.100
|
||||
H332 1.078999996 6.465000153 32.842998505 MOL 1 h H 0.100
|
||||
H341 -0.919000030 8.826000214 33.431999207 MOL 1 h H 0.100
|
||||
H342 -1.294000030 7.285999775 32.457000732 MOL 1 h H 0.100
|
||||
O6 -0.179000005 5.745999813 34.987998962 MOL 1 o- O -0.500
|
||||
N5 0.250000000 19.790000916 -0.746999979 MOL 1 n4 N -0.500
|
||||
HN51 0.118000001 19.704999924 -1.845999956 MOL 1 hn H 0.360
|
||||
HN52 -0.634000003 20.298000336 -0.307000011 MOL 1 hn H 0.360
|
||||
H53 0.349999994 18.775999069 -0.307000011 MOL 1 hn H 0.360
|
||||
end
|
||||
end
|
||||
|
||||
|
|
@ -0,0 +1,142 @@
|
|||
!BIOSYM molecular_data 4
|
||||
|
||||
!DATE: Mon Jul 14 17:01:24 1997 INSIGHT generated molecular data file
|
||||
|
||||
#topology
|
||||
|
||||
@column 1 element
|
||||
@column 2 atom_type cvff
|
||||
@column 3 charge_group cvff
|
||||
@column 4 isotope
|
||||
@column 5 formal_charge
|
||||
@column 6 charge cvff
|
||||
@column 7 switching_atom cvff
|
||||
@column 8 oop_flag cvff
|
||||
@column 9 chirality_flag
|
||||
@column 10 occupancy
|
||||
@column 11 xray_temp_factor
|
||||
@column 12 connections
|
||||
|
||||
@molecule NYLON2
|
||||
|
||||
MOL_1:C C c2 MOL 0 0 0.2200 0 0 8 1.0000 0.0000 C1 HC1 HC2 N5
|
||||
MOL_1:C1 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C C2 H11 H12
|
||||
MOL_1:C2 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C1 C3 H21 H22
|
||||
MOL_1:C3 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C2 C4 H31 H32
|
||||
MOL_1:C4 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C3 C5 H41 H42
|
||||
MOL_1:C5 C c2 MOL 0 0 0.0200 0 0 8 1.0000 0.0000 C4 N H51 H52
|
||||
MOL_1:N N n MOL 0 0 -0.5000 0 1 8 1.0000 0.0000 C5 C6 HN
|
||||
MOL_1:C6 C c' MOL 0 0 0.3800 0 1 8 1.0000 0.0000 N O/2.0 C7
|
||||
MOL_1:O O o' MOL 0 0 -0.3800 0 0 8 1.0000 0.0000 C6/2.0
|
||||
MOL_1:C7 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C6 C8 H71 H72
|
||||
MOL_1:C8 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C7 C9 H81 H82
|
||||
MOL_1:C9 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C8 C10 H91 H92
|
||||
MOL_1:C10 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C9 C11 H101 H102
|
||||
MOL_1:C11 C c' MOL 0 0 0.3800 0 1 8 1.0000 0.0000 C10 O1/2.0 N1/1.5
|
||||
MOL_1:O1 O o' MOL 0 0 -0.3800 0 0 8 1.0000 0.0000 C11/2.0
|
||||
MOL_1:HC1 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C
|
||||
MOL_1:HC2 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C
|
||||
MOL_1:H11 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C1
|
||||
MOL_1:H12 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C1
|
||||
MOL_1:H21 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C2
|
||||
MOL_1:H22 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C2
|
||||
MOL_1:H31 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C3
|
||||
MOL_1:H32 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C3
|
||||
MOL_1:H41 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C4
|
||||
MOL_1:H42 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C4
|
||||
MOL_1:H51 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C5
|
||||
MOL_1:H52 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C5
|
||||
MOL_1:HN H hn MOL 0 0 0.2800 0 0 8 1.0000 0.0000 N
|
||||
MOL_1:H71 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C7
|
||||
MOL_1:H72 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C7
|
||||
MOL_1:H81 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C8
|
||||
MOL_1:H82 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C8
|
||||
MOL_1:H91 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C9
|
||||
MOL_1:H92 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C9
|
||||
MOL_1:H101 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C10
|
||||
MOL_1:H102 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C10
|
||||
MOL_1:N1 N n MOL 0 0 -0.5000 0 1 8 1.0000 0.0000 C11/1.5 C12 H1
|
||||
MOL_1:C12 C c2 MOL 0 0 0.0200 0 0 8 1.0000 0.0000 N1 C13 H121 H122
|
||||
MOL_1:C13 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C12 C14 H131 H132
|
||||
MOL_1:C14 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C13 C15 H141 H142
|
||||
MOL_1:C15 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C14 C16 H151 H152
|
||||
MOL_1:C16 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C15 C17 H161 H162
|
||||
MOL_1:C17 C c2 MOL 0 0 0.0200 0 0 8 1.0000 0.0000 C16 N2 H171 H172
|
||||
MOL_1:N2 N n MOL 0 0 -0.5000 0 1 8 1.0000 0.0000 C17 C18 H2
|
||||
MOL_1:C18 C c' MOL 0 0 0.3800 0 1 8 1.0000 0.0000 N2 O2/2.0 C19
|
||||
MOL_1:O2 O o' MOL 0 0 -0.3800 0 0 8 1.0000 0.0000 C18/2.0
|
||||
MOL_1:C19 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C18 C20 H191 H192
|
||||
MOL_1:C20 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C19 C21 H201 H202
|
||||
MOL_1:C21 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C20 C22 H211 H212
|
||||
MOL_1:C22 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C21 C23 H221 H222
|
||||
MOL_1:H221 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C22
|
||||
MOL_1:H222 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C22
|
||||
MOL_1:C23 C c' MOL 0 0 0.3800 0 1 8 1.0000 0.0000 C22 O3/2.0 N3/1.5
|
||||
MOL_1:O3 O o' MOL 0 0 -0.3800 0 0 8 1.0000 0.0000 C23/2.0
|
||||
MOL_1:H1 H hn MOL 0 0 0.2800 0 0 8 1.0000 0.0000 N1
|
||||
MOL_1:H121 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C12
|
||||
MOL_1:H122 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C12
|
||||
MOL_1:H131 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C13
|
||||
MOL_1:H132 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C13
|
||||
MOL_1:H141 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C14
|
||||
MOL_1:H142 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C14
|
||||
MOL_1:H151 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C15
|
||||
MOL_1:H152 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C15
|
||||
MOL_1:H161 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C16
|
||||
MOL_1:H162 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C16
|
||||
MOL_1:H171 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C17
|
||||
MOL_1:H172 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C17
|
||||
MOL_1:H2 H hn MOL 0 0 0.2800 0 0 8 1.0000 0.0000 N2
|
||||
MOL_1:H191 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C19
|
||||
MOL_1:H192 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C19
|
||||
MOL_1:H201 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C20
|
||||
MOL_1:H202 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C20
|
||||
MOL_1:H211 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C21
|
||||
MOL_1:H212 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C21
|
||||
MOL_1:N3 N n MOL 0 0 -0.5000 0 1 8 1.0000 0.0000 C23/1.5 C24 H3
|
||||
MOL_1:C24 C c2 MOL 0 0 0.0200 0 0 8 1.0000 0.0000 N3 C25 H241 H242
|
||||
MOL_1:C25 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C24 C26 H251 H252
|
||||
MOL_1:C26 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C25 C27 H261 H262
|
||||
MOL_1:C27 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C26 C28 H271 H272
|
||||
MOL_1:C28 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C27 C29 H281 H282
|
||||
MOL_1:C29 C c2 MOL 0 0 0.0200 0 0 8 1.0000 0.0000 C28 N4 H291 H292
|
||||
MOL_1:N4 N n MOL 0 0 -0.5000 0 1 8 1.0000 0.0000 C29 C30 H4
|
||||
MOL_1:C30 C c' MOL 0 0 0.3800 0 1 8 1.0000 0.0000 N4 O4/2.0 C31
|
||||
MOL_1:O4 O o' MOL 0 0 -0.3800 0 0 8 1.0000 0.0000 C30/2.0
|
||||
MOL_1:C31 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C30 C32 H311 H312
|
||||
MOL_1:C32 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C31 C33 H321 H322
|
||||
MOL_1:C33 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C32 C34 H331 H332
|
||||
MOL_1:C34 C c2 MOL 0 0 -0.2000 0 0 8 1.0000 0.0000 C33 C35 H341 H342
|
||||
MOL_1:C35 C c' MOL 0 0 0.4500 0 1 8 1.0000 0.0000 C34 O5 O6/2.0
|
||||
MOL_1:O5 O o- MOL 0 1- -0.5000 0 0 8 1.0000 0.0000 C35
|
||||
MOL_1:H3 H hn MOL 0 0 0.2800 0 0 8 1.0000 0.0000 N3
|
||||
MOL_1:H241 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C24
|
||||
MOL_1:H242 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C24
|
||||
MOL_1:H251 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C25
|
||||
MOL_1:H252 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C25
|
||||
MOL_1:H261 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C26
|
||||
MOL_1:H262 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C26
|
||||
MOL_1:H271 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C27
|
||||
MOL_1:H272 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C27
|
||||
MOL_1:H281 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C28
|
||||
MOL_1:H282 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C28
|
||||
MOL_1:H291 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C29
|
||||
MOL_1:H292 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C29
|
||||
MOL_1:H4 H hn MOL 0 0 0.2800 0 0 8 1.0000 0.0000 N4
|
||||
MOL_1:H311 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C31
|
||||
MOL_1:H312 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C31
|
||||
MOL_1:H321 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C32
|
||||
MOL_1:H322 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C32
|
||||
MOL_1:H331 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C33
|
||||
MOL_1:H332 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C33
|
||||
MOL_1:H341 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C34
|
||||
MOL_1:H342 H h MOL 0 0 0.1000 0 0 8 1.0000 0.0000 C34
|
||||
MOL_1:O6 O o- MOL 0 0 -0.5000 0 0 8 1.0000 0.0000 C35/2.0
|
||||
MOL_1:N5 N n4 MOL 0 1+ -0.5000 0 0 8 1.0000 0.0000 C HN51 HN52 H53
|
||||
MOL_1:HN51 H hn MOL 0 0 0.3600 0 0 8 1.0000 0.0000 N5
|
||||
MOL_1:HN52 H hn MOL 0 0 0.3600 0 0 8 1.0000 0.0000 N5
|
||||
MOL_1:H53 H hn MOL 0 0 0.3600 0 0 8 1.0000 0.0000 N5
|
||||
|
||||
|
||||
#end
|
||||
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
!BIOSYM archive 3
|
||||
PBC=OFF
|
||||
input file for discover
|
||||
!DATE Tue Jul 15 15:14:54 1997
|
||||
N 0.109592088 -0.199880913 0.000000478 PHEN 1 n+ N -0.0450
|
||||
HN1 -0.124733858 -1.202872038 -0.000001981 PHEN 1 h+ H 0.2800
|
||||
HN2 -0.285811990 0.244572327 0.840843439 PHEN 1 h+ H 0.2800
|
||||
HN3 -0.285812497 0.244576558 -0.840839982 PHEN 1 h+ H 0.2800
|
||||
CA 1.560634732 -0.038402185 0.000000465 PHEN 1 c C -0.0780
|
||||
HA 1.972637177 -0.500293911 0.916701555 PHEN 1 h H 0.0530
|
||||
C 1.942531705 1.422506809 0.000000450 PHEN 1 c- C 0.2974
|
||||
OXT 3.187694550 1.672445178 0.000000438 PHEN 1 o- O -0.5337
|
||||
O 1.070737839 2.346019268 0.000000449 PHEN 1 o- O -0.5337
|
||||
CB 2.174581766 -0.718786478 -1.261021852 PHEN 1 c C -0.1060
|
||||
HB1 1.839982390 -0.182426706 -2.172762394 PHEN 1 h H 0.0530
|
||||
HB2 3.272250891 -0.569177628 -1.261509657 PHEN 1 h H 0.0530
|
||||
CG 1.889680982 -2.218492746 -1.435816169 PHEN 1 cp C 0.0000
|
||||
CD1 0.737977445 -2.629161119 -2.116767168 PHEN 1 cp C -0.1305
|
||||
HD1 0.061427273 -1.894254208 -2.533302307 PHEN 1 h H 0.1305
|
||||
CE1 0.424228579 -3.980331659 -2.214080095 PHEN 1 cp C -0.1305
|
||||
HE1 -0.483345032 -4.285143852 -2.715474367 PHEN 1 h H 0.1305
|
||||
CZ 1.268485427 -4.931880474 -1.646431088 PHEN 1 cp C -0.1305
|
||||
HZ 1.020345688 -5.980008125 -1.718327641 PHEN 1 h H 0.1305
|
||||
CE2 2.423752546 -4.531005859 -0.977356374 PHEN 1 cp C -0.1305
|
||||
HE2 3.074717045 -5.268786907 -0.531340718 PHEN 1 h H 0.1305
|
||||
CD2 2.733307123 -3.177516222 -0.869901538 PHEN 1 cp C -0.1305
|
||||
HD2 3.619415522 -2.873045444 -0.331384182 PHEN 1 h H 0.1305
|
||||
end
|
||||
end
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
!BIOSYM molecular_data 4
|
||||
|
||||
!DATE: Tue Jul 15 15:14:54 1997 INSIGHT generated molecular data file
|
||||
|
||||
#topology
|
||||
|
||||
@column 1 element
|
||||
@column 2 atom_type cvff
|
||||
@column 3 charge_group cvff
|
||||
@column 4 isotope
|
||||
@column 5 formal_charge
|
||||
@column 6 charge cvff
|
||||
@column 7 switching_atom cvff
|
||||
@column 8 oop_flag cvff
|
||||
@column 9 chirality_flag
|
||||
@column 10 occupancy
|
||||
@column 11 xray_temp_factor
|
||||
@column 12 connections
|
||||
|
||||
@molecule PHE_CVFF
|
||||
|
||||
PHEN_1:N N n+ pepN 0 0 -0.04500 1 0 8 1.0000 0.0000 CA HN1 HN2 HN3
|
||||
PHEN_1:HN1 H h+ pepN 0 0 0.28000 0 0 8 1.0000 0.0000 N
|
||||
PHEN_1:HN2 H h+ pepN 0 0 0.28000 0 0 8 1.0000 0.0000 N
|
||||
PHEN_1:HN3 H h+ pepN 0 0 0.28000 0 0 8 1.0000 0.0000 N
|
||||
PHEN_1:CA C c pepN 0 0 -0.07800 0 0 8 1.0000 0.0000 N HA C CB
|
||||
PHEN_1:HA H h pepN 0 0 0.05300 0 0 8 1.0000 0.0000 CA
|
||||
PHEN_1:C C c- pepC 0 0 0.29740 1 1 8 1.0000 0.0000 CA O/1.5 OXT/1.5
|
||||
PHEN_1:OXT O o- pepC 0 0 -0.53370 0 0 8 1.0000 0.0000 C/1.5
|
||||
PHEN_1:O O o- pepC 0 0 -0.53370 0 0 8 1.0000 0.0000 C/1.5
|
||||
PHEN_1:CB C c meB 0 0 -0.10600 1 0 8 1.0000 0.0000 CA HB1 HB2 CG
|
||||
PHEN_1:HB1 H h meB 0 0 0.05300 0 0 8 1.0000 0.0000 CB
|
||||
PHEN_1:HB2 H h meB 0 0 0.05300 0 0 8 1.0000 0.0000 CB
|
||||
PHEN_1:CG C cp arG 0 0 0.00000 1 1 8 1.0000 0.0000 CB CD1/1.5 CD2/1.5
|
||||
PHEN_1:CD1 C cp arD1 0 0 -0.13053 1 1 8 1.0000 0.0000 CG/1.5 HD1 CE1/1.5
|
||||
PHEN_1:HD1 H h arD1 0 0 0.13053 0 0 8 1.0000 0.0000 CD1
|
||||
PHEN_1:CE1 C cp arE1 0 0 -0.13053 1 1 8 1.0000 0.0000 CD1/1.5 HE1 CZ/1.5
|
||||
PHEN_1:HE1 H h arE1 0 0 0.13053 0 0 8 1.0000 0.0000 CE1
|
||||
PHEN_1:CZ C cp arZ 0 0 -0.13053 1 1 8 1.0000 0.0000 CE1/1.5 HZ CE2/1.5
|
||||
PHEN_1:HZ H h arZ 0 0 0.13053 0 0 8 1.0000 0.0000 CZ
|
||||
PHEN_1:CE2 C cp arE2 0 0 -0.13053 1 1 8 1.0000 0.0000 CZ/1.5 HE2 CD2/1.5
|
||||
PHEN_1:HE2 H h arE2 0 0 0.13053 0 0 8 1.0000 0.0000 CE2
|
||||
PHEN_1:CD2 C cp arD2 0 0 -0.13053 1 1 8 1.0000 0.0000 CE2/1.5 HD2 CG/1.5
|
||||
PHEN_1:HD2 H h arD2 0 0 0.13053 0 0 8 1.0000 0.0000 CD2
|
||||
|
||||
|
||||
#atomset
|
||||
|
||||
|
||||
@quartet torsion *:PHEN_1:chi1
|
||||
N CA CB CG
|
||||
|
||||
@quartet torsion *:PHEN_1:chi2
|
||||
CA CB CG CD1
|
||||
|
||||
#end
|
||||
|
||||
|
|
@ -0,0 +1,27 @@
|
|||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/cut/coul/cut 10.0 8.0
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
improper_style harmonic
|
||||
|
||||
read_data crambin.lammps05
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
fix 1 all nvt 275.0 275.0 100.0
|
||||
|
||||
# fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
# group peptide type <= 12
|
||||
# dump 1 peptide atom 10 dump.peptide
|
||||
|
||||
run 10000
|
||||
|
||||
Loading…
Reference in New Issue