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Stephanie Teich-McGoldrick (Sandai) is the current maintainer
of the msi2lmp tool. She can be contacted at steichm at sandia.gov
02 Aug 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Added rudimentary support for OPLS-AA based on
input provided by jeff greathouse.
18 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Added support for writing out image flags
Improved accuracy of atom masses
Added flag for shifting the entire system
Fixed some minor logic bugs and prepared
for supporting other force fields and morse style bonds.
12 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Fixed the bug that caused improper coefficients to be wrong
Cleaned up the handling of box parameters and center the box
by default around the system/molecule. Added a flag to make
this step optional and center the box around the origin instead.
Added a regression test script with examples.
1 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Cleanup and improved port to windows.
Removed some more static string limits.
Added print level 3 for additional output.
Make code stop at missing force field parameters
and added -i flag to override this.
Safer argument checking.
Provide short versions for all flags.
23 Sep 2011
added support for triclinic boxes
see msi2lmp/TriclinicModification.pdf doc for details
-----------------------------
msi2lmp V3.6 4/10/2005
This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
program to produce a LAMMPS data file.
1. Building msi2lmp3
Use the Makefile in the src directory. It is
currently set up for gcc. One will have to modify
it to use a different compiler.
2. Testing the program
There are three pairs (.car and .mdf) files in the
test directory: crambin, nylon and phen3_cff97. The
atom types in crambin and nylon are cvff (Class I) atom
types and those in phen3_cff97 are cff9x (Class II) atom types.
Two forcefield files, cvff.frc and cff91.frc, are needed
generate lammps data files for these three test files. To
run it you would:
% setenv BIOSYM_LIBRARY ../biosym_frc_files
% ../src/msi2lmp.exe nylon -class I -frc cvff > data.nylon
% ../src/msi2lmp.exe crambin -class I -frc cvff > data.crambin
% ../src/msi2lmp.exe phen3_cff97 -class II -frc cff91 > data.phen3_cff97
Three files should be generated: data.nylon, data.crambin
and data.phen3_cff97. These can be compared against
data.x in the directory correct. If there are differences,
first recompile the program with no optimization and try again.
If there are still differences, send email to jec@mayo.edu
Note: you will see many "Unable to find..." parameters messages
in the phen3_cff97 test case. Most of those parameters
exist in cff95.frc, but not in cff91.frc
3. To run the program
The program is started by supplying information at the command prompt
according to the usage described below.
USAGE: msi2lmp.exe ROOTNAME {-2001} {-print #} {-class #} {-frc FRC_FILE}
-- msi2lmp.exe is the name of the executable
-- ROOTNAME is the base name of the .car and .mdf files
-- -2001
Output lammps files for LAMMPS version 2001 (F90 version)
Default is to write output for the C++ version of LAMMPS
-- -print (or -p)
# is the print level 0 - silent except for error messages
1 - minimal (default)
2 - verbose (usual for developing and
checking new data files for consistency)
3 - even more verbose (additional debug info)
-- -ignore (or -i) ignore errors about missing force field parameters
and treat them as warnings instead.
-- -class (or -c)
# is the class of forcefield to use (I or 1 = Class I e.g., CVFF)
(II or 2 = Class II e.g., CFFx)
default is -class I
-- -frc (or -f) specifies name of the forcefield file (e.g., cff91)
If the file name includes a directory component (or drive letter on Windows),
then the name is used as is. Otherwise, the program looks for the forcefield
file in $BIOSYM_LIBRARY (or %BIOSYM_LIBRARY% on Windows).
If $BIOSYM_LIBRARY is not set, ../biosym_frc_files is used (for testing).
If the file name does not end in .frc, then .frc is appended to the name.
For example, -frc cvff (assumes cvff.frc is in $BIOSYM_LIBRARY
or ../biosym_frc_files)
-frc cff/cff91 (assumes cff91.frc is in cff)
-frc /usr/local/biosym/forcefields/cff95
(assumes cff95.frc is in /usr/local/biosym/forcefields/)
By default, the program uses $BIOSYM_LIBRARY/cvff.frc or ../biosym_frc_files/cvff.frc
-- the LAMMPS data file is written to ROOTNAME.lammps{01/05},
protocol and error information is written to the screen.
****************************************************************
*
* Msi2lmp3
*
* This is the third version of a program that generates a LAMMPS
* data file based on the information in MSI .car (atom
* coordinates), .mdf (molecular topology) and .frc (forcefield)
* files. The .car and .mdf files are specific to a molecular
* system while the .frc file is specific to a forcefield version.
* The only coherency needed between .frc and .car/.mdf files are
* the atom types.
*
* 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 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.
*
* The current maintainer is only reluctantly doing so because John Mayo no longer
* needs this code.
*
* V3.2 corresponds to adding code to MakeLists.c to gracefully deal with
* systems that may only be molecules of 1 to 3 atoms. In V3.1, the values
* for number_of_dihedrals, etc. could be unpredictable in these systems.
*
* V3.3 was generated in response to a strange error reading a MDF file generated by
* Accelys' Materials Studio GUI. Simply rewriting the input part of ReadMdfFile.c
* seems to have fixed the problem.
*
* V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car and .mdf files
* written by Accelys' Materials Studio GUI.
*
* V3.6 outputs to LAMMPS 2005 (C++ version).
*
* Contact: Kelly L. Anderson, kelly.anderson@cantab.net
*
* April 2005

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Copy cvff.frc and cff9*.frc or any other *.frc files (which you have
license to use) to this directory for use with msi2lmp.
Note that LAMMPS does not distribute Accelrys (or old BioSym)
force field files, since they are proprietary. All the
files in this directory that are part of the LAMMPS distribution
are are openly available files that are in the public domain.

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!CLAYFF forcefield
#atom_types cvff
!Ver Ref Type Mass Element Connections Comment
!---- --- ---- ---------- ------- -----------------------------------------
1.0 1 st 28.08550 Si 4
1.0 1 ao 26.98154 Al 6
1.0 1 at 26.98154 Al 4
1.0 1 mgo 24.30500 Mg 6
1.0 1 cao 40.08000 Ca 6
1.0 1 feo 55.84700 Fe 6
1.0 1 lio 6.941000 Li 6
1.0 1 ob 15.99940 O 2
1.0 1 obss 15.99940 O 3
1.0 1 obts 15.99940 O 2
1.0 1 obos 15.99940 O 2
1.0 1 ohs 15.99940 O 2
1.0 1 oh 15.99940 O 2
1.0 1 oh- 15.99940 O 1
1.0 1 o* 15.99940 O 2
1.0 1 ho 1.007970 H 1
1.0 1 h* 1.007970 H 1
1.0 1 Na 22.99000 Na 0
1.0 1 K 39.10 K 0
1.0 1 Cs 132.9100 Cs 0
1.0 1 Ca 40.07980 Ca 0
1.0 1 Ba 137.3300 Ba 0
1.0 1 Mg 24.3050 Mg 0
1.0 1 Sr 87.6200 Sr 0
1.0 1 Pb 207.2000 Pb 0
1.0 1 Cl 35.45300 Cl 0
#equivalence cvff
> Equivalence table for any variant of cvff
! Equivalences
! -----------------------------------------
!Ver Ref Type NonB Bond Angle Torsion OOP
!---- --- ---- ---- ---- ----- ------- ----
1.0 1 h h h h h h
#auto_equivalence cvff_auto
! Equivalences
! -----------------------------------------
!Ver Ref Type NonB Bond Bond Angle Angle Torsion Torsion OOP OOP
! Inct End atom Apex atom End Atoms Center Atoms End Atom Center Atom
!---- --- ---- ---- ------ ---- ---------- --------- --------- ----------- -------- -----------
2.0 18 h h h h_ h_ h_ h_ h_ h_ h_
#hbond_definition cvff
#morse_bond cvff
> E = D * (1 - exp(-ALPHA*(R - R0)))^2
!Ver Ref I J R0 D ALPHA
!---- --- ---- ---- ------- -------- -------
2.3 23 no o- 1.2178 140.2486 2.0000
#quadratic_bond cvff
> E = K2 * (R - R0)^2
!Ver Ref I J R0 K2
!---- --- ---- ---- ------- --------
2.1 28 oh ho 1.0000 553.9350
2.1 28 ohs ho 1.0000 553.9350
#quadratic_angle cvff
> E = K2 * (Theta - Theta0)^2
!Ver Ref I J K Theta0 K2
!---- --- ---- ---- ---- -------- -------
2.3 23 cp cp c' 120.0000 34.6799
#torsion_1 cvff_auto
> E = Kphi * [ 1 + cos(n*Phi - Phi0) ]
!Ver Ref I J K L Kphi n Phi0
!---- --- ---- ---- ---- ---- ------- ------ -------
2.0 18 * c_ n3n_ * 0.0500 3 0.
#out_of_plane cvff_auto
> E = Kchi * [ 1 + cos(n*Chi - Chi0) ]
!Ver Ref I J K L Kchi n Chi0
!---- --- ---- ---- ---- ---- ------- ------ -------
2.0 18 * c'_ * * 10.0000 2 180.0000
#nonbond(12-6) cvff
@type A-B
@combination geometric
> E = Aij/r^12 - Bij/r^6
> where Aij = sqrt( Ai * Aj )
> Bij = sqrt( Bi * Bj )
!Ver Ref I A B
!---- --- ---- ----------- -----------
1.0 1 st 12.3645 0.00954
1.0 1 ao 196.1446 0.03230
1.0 1 at 12.3645 0.00954
1.0 1 mgo 1636.3265 0.07688
1.0 1 cao 17814.73 0.5987
1.0 1 feo 702.54 0.0504
1.0 1 lio 112.01 0.0201
1.0 1 ob 629358.0000 625.50000
1.0 1 obss 629358.0000 625.50000
1.0 1 obts 629358.0000 625.50000
1.0 1 obos 629358.0000 625.50000
1.0 1 ohs 629358.0000 625.50000
1.0 1 oh 629358.0000 625.50000
1.0 1 oh- 629358.0000 625.50000
1.0 1 o* 629358.0000 625.50000
1.0 1 ho 0.00000001 0.00000
1.0 1 h* 0.00000001 0.00000
1.0 1 Na 14763.1719 87.65132
1.0 1 K 754506.86 549.37
1.0 1 Cs 3998193.96 1264.63
1.0 1 Ca 125966.6068 224.46969
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
1.0 1 Cl 21081006.97 2905.31
#bond_increments cvff
!Ver Ref I J DeltaIJ DeltaJI
!---- --- ---- ---- ------- -------
2.3 23 no o- 0.1684 -0.1684

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!BIOSYM forcefield 1
! This is a modified version of msi2lmp for use specifically wtih the
! OPLS force field. No out-of-plane or cross-terms are included.
! Atom types from SPC water and CLAYFF are also included.
#atom_types cvff
> Masses from CRC 1973/74 pages B-250.
!Ver Ref Type Mass Element Connections Comment
!---- --- ---- ---------- ------- -----------------------------------------
1.0 1 HC 1.007970 H 1 H, RH, alkanes
1.0 1 HO 1.007970 H 1 H(O), ROH
1.0 1 HS 1.007970 H 1 H(S), RSH
1.0 1 HM 1.007970 H 1 H(C), CH3OH
1.0 1 CT 12.011150 C 4 Aliphatic C
1.0 1 OH 15.999400 O 2 O, ROH
1.0 1 SH 32.064000 S 2 S, RSH
1.0 1 S 32.064000 S 2 S, RSR
1.0 1 CG 12.011150 C 1 Graphite C
1.0 1 CL 35.453000 Cl 1 Cl, RCl
X.X X CC 12.011150 C 3 Carbonate ion C, AMBER
X.X X OC 15.035060 O 1 Carbonate ion O, AMBER
#equivalence cvff
> Equivalence table for any variant of cvff
! Equivalences
! -----------------------------------------
!Ver Ref Type NonB Bond Angle Torsion OOP
!---- --- ---- ---- ---- ----- ------- ----
1.0 1 h h h h h h
#quadratic_bond cvff
> E = K2 * (R - R0)^2
!Ver Ref I J R0 K2
!---- --- ---- ---- ------- --------
2.3 23 CT CT 1.529 268.0
2.3 23 CT HC 1.09 340.0
2.3 23 CT OH 1.410 320.0
2.3 23 CT SH 1.810 222.0
1.0 1 HO OH 0.96 553.0
1.0 1 HS SH 1.336 274.0
1.0 1 CT S 1.810 222.0
1.0 1 CT CL 1.781 245.0
X.X X CC OC 1.21 648.0
#quadratic_angle cvff
> E = K2 * (Theta - Theta0)^2
!Ver Ref I J K Theta0 K2
!---- --- ---- ---- ---- -------- -------
2.3 23 CT CT CT 112.7 58.35
2.3 23 CT CT HC 110.7 37.50
2.3 23 CT CT OH 109.5 50.00
2.3 23 HC CT HC 107.8 33.00
2.3 23 CT OH HO 108.5 55.00
2.3 23 HC CT OH 109.5 35.00
1.0 1 CT CT SH 108.6 50.00
1.0 1 CT SH HS 96.0 44.00
1.0 1 HC CT SH 109.5 35.00
1.0 1 CT CT S 114.7 50.00
1.0 1 CT S CT 98.9 62.00
1.0 1 HC CT S 109.5 35.00
1.0 1 CT CT CL 109.8 69.0
1.0 1 HC CT CL 107.6 51.0
X.X X OC CC OC 127.0 79.1
#bond-bond cvff
> E = K(b,b') * (R - R0) * (R' - R0')
!Ver Ref I J K K(b,b')
!---- --- ---- ---- ---- -------
1.0 1 c o c' 0.0000
#bond-angle cvff
> E = K * (R - R0) * (Theta - Theta0)
!Ver Ref I J K K(b,theta) K(b',theta)
!---- --- ---- ---- ---- ---------- -----------
1.0 1 c o c' 57.0000 57.0000
#torsion_1 opls
> E = 0.5*K1*[1 + cos(Phi)] + 0.5*K2*[1 + cos(2*Phi)] + 0.5*K3*[1 + cos(3*Phi)] + 0.5*K4*[1 + cos(4*Phi)]
!Ver Ref I J K L K1 K2 K3 K4
!---- --- ---- ---- ---- ---- ------- ------ ------ -----
X.X XX HC CT CT HC 0.0 0.0 0.318 0.0
X.X XX HC CT CT CT 0.0 0.0 0.366 0.0
X.X XX HC CT OH HO 0.0 0.0 0.450 0.0
X.X XX CT CT OH HO -0.356 -0.174 0.492 0.0
X.X XX HC CT CT OH 0.0 0.0 0.468 0.0
X.X XX CT CT CT OH 1.711 -0.500 0.663 0.0
X.X XX HC CT SH HS 0.0 0.0 0.451 0.0
X.X XX CT CT SH HS -0.759 -0.282 0.603 0.0
X.X XX HC CT CT SH 0.0 0.0 0.452 0.0
X.X XX CT CT CT SH 1.876 0.0 0.0 0.0
X.X XX HC CT CT S 0.0 0.0 0.452 0.0
X.X XX CT CT S CT 0.925 -0.576 0.677 0.0
X.X XX HC CT S CT 0.0 0.0 0.647 0.0
X.X XX S CT CT CL 0.0 0.0 0.452 0.0
X.X XX CL CT CT CL 0.250 -0.250 0.0 0.0
X.X XX HC CT CT CL 0.0 0.0 0.400 0.0
#angle-angle-torsion_1 cvff
> E = K * (Theta - Theta0) * (Theta' - Theta0') * cos(Phi)
!Ver Ref I J K L K(Ang,Ang,Tor)
!---- --- ---- ---- ---- ---- --------------
1.0 1 * c c * -10.5000
#out_of_plane cvff
> E = Kchi * [ 1 + cos(n*Chi - Chi0) ]
!Ver Ref I J K L Kchi n Chi0
!---- --- ---- ---- ---- ---- ------- ------ -------
2.3 0 hn n c c' 10.0 2 180.0
X.X X OC CC OC OC 1.1 2 180.0
#out_of_plane-out_of_plane cvff
> E = Koo * Chi * Chi'
!Ver Ref I J K L Koo
!---- --- ---- ---- ---- ---- -------
1.0 1 c c' n o' 0.0100
#angle-angle cvff
> E = K * (Theta - Theta0) * (Theta' - Theta0')
! J' I' K'
!Ver Ref I J K K
!---- --- ---- ---- ---- ---- -------
1.0 1 c c c c -7.9000
#morse_bond cvff_auto
> E = D * (1 - exp(-ALPHA*(R - R0)))^2
!Ver Ref I J R0 D ALPHA
!---- --- ---- ---- ------- -------- -------
2.0 18 c3m_ c3m_ 1.5100 88.0000 1.9150
#quadratic_bond cvff_auto
> E = K2 * (R - R0)^2
!Ver Ref I J R0 K2
!---- --- ---- ---- ------- --------
2.0 18 c3m_ c3m_ 1.5100 322.7158
#quadratic_angle cvff_auto
> E = K2 * (Theta - Theta0)^2
!Ver Ref I J K Theta0 K2
!---- --- ---- ---- ---- -------- -------
2.0 18 c3m_ c3m_ c3m_ 60.0000 46.0000
#torsion_1 cvff_auto
> E = Kphi * [ 1 + cos(n*Phi - Phi0) ]
!Ver Ref I J K L Kphi n Phi0
!---- --- ---- ---- ---- ---- ------- ------ -------
2.0 18 * c_ n3n_ * 0.0500 3 0.
#out_of_plane cvff_auto
> E = Kchi * [ 1 + cos(n*Chi - Chi0) ]
!Ver Ref I J K L Kchi n Chi0
!---- --- ---- ---- ---- ---- ------- ------ -------
2.0 18 * c'_ * * 10.0000 2 180.0000
#nonbond(12-6) cvff
@type A-B
@combination geometric
> E = Aij/r^12 - Bij/r^6
> where Aij = sqrt( Ai * Aj )
> Bij = sqrt( Bi * Bj )
!Ver Ref I A B
!---- --- ---- ----------- -----------
1.0 1 HC 7152.557 29.297
1.0 1 HO 0.0 0.0
1.0 1 HS 0.0 0.0
1.8 14 HM 7152.557 29.297
1.0 1 CT 892114.214 485.302
1.0 1 OH 578580.831 627.244
2.3 25 SH 4006270.2 2001.567
2.3 25 S 4006270.2 2001.567
1.0 1 CG 531140.879 343.824
1.0 1 CL 2863704.82 1853.765299
X.X X CC 819971.66216 531.10286
XX X OC 379876.39852 564.88598
#bond_increments cvff
!Ver Ref I J DeltaIJ DeltaJI
!---- --- ---- ---- ------- -------
2.3 23 no o- 0.1684 -0.1684

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VERSION
elib

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#include "msi2lmp.h"
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);
}
}
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])) {
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);
}
}
}

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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 6
#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_morse, 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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/*
* 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 & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_bond.keyword,"#quadratic_bond");
ff_bond.number_of_parameters = 2;
}
if (forcefield & FF_TYPE_CLASS2) {
strcpy(ff_bond.keyword,"#quartic_bond");
ff_bond.number_of_parameters = 4;
}
/* MORSE */
if (forcefield & FF_TYPE_CLASS1) {
ff_morse.number_of_members = 2;
strcpy(ff_morse.keyword,"#morse_bond");
ff_morse.number_of_parameters = 3;
}
/* ANGLE */
ff_ang.number_of_members = 3;
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_ang.keyword,"#quadratic_angle");
ff_ang.number_of_parameters = 2;
}
if (forcefield & FF_TYPE_CLASS2) {
strcpy(ff_ang.keyword,"#quartic_angle");
ff_ang.number_of_parameters = 4;
}
/* TORSION */
ff_tor.number_of_members = 4;
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_tor.keyword,"#torsion_1");
ff_tor.number_of_parameters = 3;
}
if (forcefield & FF_TYPE_CLASS2) {
strcpy(ff_tor.keyword,"#torsion_3");
ff_tor.number_of_parameters = 6;
}
/* OOP */
ff_oop.number_of_members = 4;
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_oop.keyword,"#out_of_plane");
ff_oop.number_of_parameters = 3;
}
if (forcefield & FF_TYPE_CLASS2) {
strcpy(ff_oop.keyword,"#wilson_out_of_plane");
ff_oop.number_of_parameters = 2;
}
if (forcefield & FF_TYPE_CLASS2) {
/* 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;
}
}

774
tools/msi2lmp/src/MakeLists.c
View File

@ -1,774 +0,0 @@
#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 & FF_TYPE_CLASS2) && (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 & FF_TYPE_CLASS2) & (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 & FF_TYPE_CLASS2)
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]);
}
}
}
}

44
tools/msi2lmp/src/Makefile
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@ -1,44 +0,0 @@
TARGET = msi2lmp.exe
SRCS = msi2lmp.c \
ReadCarFile.c \
ReadMdfFile.c \
MakeLists.c \
ReadFrcFile.c \
InitializeItems.c \
SearchAndFill.c \
GetParameters.c \
CheckLists.c \
WriteDataFile.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
WriteDataFile.o: WriteDataFile.c msi2lmp.h Forcefield.h

329
tools/msi2lmp/src/ReadCarFile.c
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@ -1,329 +0,0 @@
/*
* 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>
/* ----------------------------------------------------------------------
set global box params
assumes boxlo/hi and triclinic tilts are already set
------------------------------------------------------------------------- */
void set_box(double box[3][3], double *h, double *h_inv)
{
h[0] = box[1][0] - box[0][0];
h[1] = box[1][1] - box[0][1];
h[2] = box[1][2] - box[0][2];
h_inv[0] = 1.0/h[0];
h_inv[1] = 1.0/h[1];
h_inv[2] = 1.0/h[2];
h[3] = box[2][0];
h[4] = box[2][1];
h[5] = box[2][2];
h_inv[3] = -h[3] / (h[1]*h[2]);
h_inv[4] = (h[3]*h[5] - h[1]*h[4]) / (h[0]*h[1]*h[2]);
h_inv[5] = -h[5] / (h[0]*h[1]);
}
/* ----------------------------------------------------------------------
convert triclinic 0-1 lamda coords to box coords for one atom
x = H lamda + x0;
lamda and x can point to same 3-vector
------------------------------------------------------------------------- */
void lamda2x(double *lamda, double *x, double *h, double *boxlo)
{
x[0] = h[0]*lamda[0] + h[5]*lamda[1] + h[4]*lamda[2] + boxlo[0];
x[1] = h[1]*lamda[1] + h[3]*lamda[2] + boxlo[1];
x[2] = h[2]*lamda[2] + boxlo[2];
}
/* ----------------------------------------------------------------------
convert box coords to triclinic 0-1 lamda coords for one atom
lamda = H^-1 (x - x0)
x and lamda can point to same 3-vector
------------------------------------------------------------------------- */
void x2lamda(double *x, double *lamda, double *h_inv, double *boxlo)
{
double delta[3];
delta[0] = x[0] - boxlo[0];
delta[1] = x[1] - boxlo[1];
delta[2] = x[2] - boxlo[2];
lamda[0] = h_inv[0]*delta[0] + h_inv[5]*delta[1] + h_inv[4]*delta[2];
lamda[1] = h_inv[1]*delta[1] + h_inv[3]*delta[2];
lamda[2] = h_inv[2]*delta[2];
}
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;
double center[3];
double hmat[6];
double hinv[6];
double lamda[3];
/* 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 */
center[0] = center[1] = center[2] = 0.0;
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 %lf",
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));
atoms[k].x[0] += shift[0];
atoms[k].x[1] += shift[1];
atoms[k].x[2] += shift[2];
if (centerflag) {
center[0] += atoms[k].x[0];
center[1] += atoms[k].x[1];
center[2] += atoms[k].x[2];
}
}
fgets(line,MAX_LINE_LENGTH,CarF);
fgets(line,MAX_LINE_LENGTH,CarF);
} /* End m (molecule) loop */
center[0] /= (double) total_no_atoms;
center[1] /= (double) total_no_atoms;
center[2] /= (double) total_no_atoms;
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",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) {
/* no need to re-center the box, if we use min/max values */
center[0] = center[1] = center[2] = 0.0;
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];
}
box[0][k] = lowest - 0.5;
box[1][k] = highest + 0.5;
box[2][k] = 0.0;
}
} else {
printf("This tool only works for periodic systems with triclinic boxes");
exit(32);
}
} else {
if (TriclinicFlag == 0) {
for (k=0; k < 3; k++) {
box[0][k] = -0.5*pbc[k] + center[k] + shift[k];
box[1][k] = 0.5*pbc[k] + center[k] + shift[k];
box[2][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 > 2) {
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];
box[0][0] = -0.5*A + center[0] + shift[0];
box[1][0] = 0.5*A + center[0] + shift[0];
box[0][1] = -0.5*B*sin_gamma + center[1] + shift[1];
box[1][1] = 0.5*B*sin_gamma + center[1] + shift[1];
box[0][2] = -0.5*sqrt(sq_c * sin_beta*sin_beta - C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma) + center[2] + shift[2];
box[1][2] = 0.5*sqrt(sq_c * sin_beta*sin_beta - C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma) + center[2] + shift[2];
box[2][0] = B * cos_gamma; /* This is xy SLTM */
box[2][1] = C * cos_beta; /* This is xz SLTM */
box[2][2] = C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma; /* This is yz SLTM */
}
}
/* compute image flags */
set_box(box,hmat,hinv);
n = 0;
for (m = 0; m < total_no_atoms; m++) {
double tmp;
int w=0;
x2lamda(atoms[m].x,lamda,hinv,box[0]);
for (k = 0; k < 3; ++k) {
tmp = floor(lamda[k]);
atoms[m].image[k] = tmp;
lamda[k] -= tmp;
if (tmp != 0.0) ++w;
}
lamda2x(lamda, atoms[m].x,hmat,box[0]);
if (w > 0) ++n;
}
/* warn if atoms are outside the box */
if (n > 0) {
if (periodic) {
if (pflag > 1)
printf(" %d of %d atoms with nonzero image flags\n\n",n,total_no_atoms);
} else {
if (iflag == 0 || (pflag > 1))
printf(" %d of %d atoms outside the box\n\n",n,total_no_atoms);
condexit(32);
}
}
/* Close .car file */
if (fclose(CarF) !=0) {
printf("Error closing %s.car\n", rootname);
exit(31);
}
}
/* End ReadCarFile() */

95
tools/msi2lmp/src/ReadFrcFile.c
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@ -1,95 +0,0 @@
/*
* 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_morse, 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);
if (forcefield & FF_TYPE_CLASS1) { /* Morse bond terms for class I */
SearchAndFill(&ff_morse);
}
SearchAndFill(&ff_ang);
SearchAndFill(&ff_tor);
SearchAndFill(&ff_oop);
if (forcefield & FF_TYPE_CLASS2) { /* Cross terms for class II */
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);
if (forcefield & FF_TYPE_CLASS1)
fprintf(stderr," Item %s has %d entries\n",
ff_morse.keyword,ff_morse.entries);
fprintf(stderr," Item %s has %d entries\n",
ff_ang.keyword,ff_ang.entries);
if (forcefield & FF_TYPE_CLASS2) {
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 & FF_TYPE_CLASS2) {
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 & FF_TYPE_CLASS2) {
fprintf(stderr," Item %s has %d entries\n",
ff_angang.keyword,ff_angang.entries);
}
fprintf(stderr,"\n");
}
fclose(FrcF);
}

415
tools/msi2lmp/src/ReadMdfFile.c
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@ -1,415 +0,0 @@
/******************************
*
* 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';
}
}

225
tools/msi2lmp/src/SearchAndFill.c
View File

@ -1,225 +0,0 @@
/****************************
*
* 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 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;
}
}
}

390
tools/msi2lmp/src/WriteDataFile.c
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@ -1,390 +0,0 @@
/*
* This function creates and writes the data file to be used with LAMMPS
*/
#include "msi2lmp.h"
#include "Forcefield.h"
#include <stdlib.h>
void WriteDataFile(char *nameroot)
{
int i,j,k,m;
char line[MAX_LINE_LENGTH];
FILE *DatF;
/* Open data file */
sprintf(line,"%s.data",rootname);
if (pflag > 0) {
printf(" Writing LAMMPS data file %s.data",rootname);
if (forcefield & FF_TYPE_CLASS1) puts(" for Class I force field");
if (forcefield & FF_TYPE_CLASS2) puts(" for Class II force field");
if (forcefield & FF_TYPE_OPLSAA) puts(" for OPLS-AA force field");
}
if ((DatF = fopen(line,"w")) == NULL ) {
printf("Cannot open %s\n",line);
exit(62);
}
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) total_no_angle_angles = 0;
fprintf(DatF, "LAMMPS data file from msi2lmp v3.8 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);
fputs("\n",DatF);
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 & FF_TYPE_CLASS1) {
if (no_oop_types > 0)
fprintf (DatF, " %3d improper types\n", no_oop_types);
}
if (forcefield & FF_TYPE_CLASS2) {
if ((no_oop_types + no_angleangle_types) > 0)
fprintf (DatF, " %3d improper types\n",
no_oop_types + no_angleangle_types);
}
/* Modified by SLTM to print out triclinic box types 10/05/10 - lines 56-68 */
if (TriclinicFlag == 0) {
fputs("\n",DatF);
fprintf(DatF, " %15.9f %15.9f xlo xhi\n", box[0][0], box[1][0]);
fprintf(DatF, " %15.9f %15.9f ylo yhi\n", box[0][1], box[1][1]);
fprintf(DatF, " %15.9f %15.9f zlo zhi\n", box[0][2], box[1][2]);
} else {
fputs("\n",DatF);
fprintf(DatF, " %15.9f %15.9f xlo xhi\n", box[0][0], box[1][0]);
fprintf(DatF, " %15.9f %15.9f ylo yhi\n", box[0][1], box[1][1]);
fprintf(DatF, " %15.9f %15.9f zlo zhi\n", box[0][2], box[1][2]);
fprintf(DatF, " %15.9f %15.9f %15.9f xy xz yz\n",box[2][0], box[2][1], box[2][2]);
}
/* 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);
fputs("\n",DatF);
/* 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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
if (no_bond_types > 0) {
m = 0;
if (forcefield & FF_TYPE_CLASS1) m = 2;
if (forcefield & FF_TYPE_OPLSAA) m = 2;
if (forcefield & FF_TYPE_CLASS2) 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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
}
if (no_angle_types > 0) {
m = 0;
if (forcefield & FF_TYPE_CLASS1) m = 2;
if (forcefield & FF_TYPE_OPLSAA) m = 2;
if (forcefield & FF_TYPE_CLASS2) 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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
}
if (no_dihedral_types > 0) {
if (forcefield & FF_TYPE_CLASS1) {
fprintf(DatF,"Dihedral Coeffs\n\n");
for (i=0; i < no_dihedral_types; i++)
fprintf(DatF, "%3i %10.4f %3i %3i\n", i+1,
dihedraltypes[i].params[0],
(int) dihedraltypes[i].params[1],
(int) dihedraltypes[i].params[2]);
} else if (forcefield & FF_TYPE_OPLSAA) {
fprintf(DatF,"Dihedral 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].params[j]);
fputs("\n",DatF);
}
} else if (forcefield & FF_TYPE_CLASS2) {
fprintf(DatF,"Dihedral Coeffs\n\n");
for (i=0; i < no_dihedral_types; i++) {
fprintf(DatF, "%3i",i+1);
for ( j = 0; j < 6; j++)
fprintf(DatF, " %10.4f",dihedraltypes[i].params[j]);
fputs("\n",DatF);
}
}
fputs("\n",DatF);
}
if (forcefield & FF_TYPE_CLASS1) {
if (no_oop_types > 0) {
/* cvff improper coeffs are: type K0 d n */
fprintf(DatF,"Improper Coeffs\n\n");
for (i=0; i < no_oop_types; i++) {
fprintf(DatF,"%5i %10.4f %3i %3i\n",i+1,
ooptypes[i].params[0], (int) ooptypes[i].params[1],
(int) ooptypes[i].params[2]);
}
fputs("\n",DatF);
}
} else if (forcefield & FF_TYPE_OPLSAA) {
if (no_oop_types > 0) {
/* opls improper coeffs are like cvff: type K0 d(=-1) n(=2) */
fprintf(DatF,"Improper Coeffs\n\n");
for (i=0; i < no_oop_types; i++) {
fprintf(DatF,"%5i %10.4f %3i %3i\n",i+1,
ooptypes[i].params[0], (int) ooptypes[i].params[1],
(int) ooptypes[i].params[2]);
}
fputs("\n",DatF);
}
} else if (forcefield & FF_TYPE_CLASS2) {
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]);
fputs("\n",DatF);
}
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);
fputs("\n",DatF);
}
fputs("\n",DatF);
}
}
if (forcefield & FF_TYPE_CLASS2) {
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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
}
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]);
fputs("\n",DatF);
}
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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
}
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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
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]);
fputs("\n",DatF);
}
fputs("\n",DatF);
}
}
/*--------------------------------------------------------------------*/
/* 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 %3i %3i %3i\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],
atoms[k].image[0],
atoms[k].image[1],
atoms[k].image[2]);
}
fputs("\n",DatF);
/***** 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);
fputs("\n",DatF);
}
/***** 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);
fputs("\n",DatF);
}
/***** 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);
fputs("\n",DatF);
}
/***** 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 & FF_TYPE_CLASS2) {
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);
}
fputs("\n",DatF);
}
/* Close data file */
if (fclose(DatF) !=0) {
printf("Error closing %s.lammps05\n", rootname);
exit(61);
}
}

380
tools/msi2lmp/src/msi2lmp.c
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@ -1,380 +0,0 @@
/*
*
* msi2lmp.exe V3.9
*
* v3.9 AK - Rudimentary support for OPLS-AA
*
* 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} {-ignore} {-nocenter}
*
* -- msi2lmp3 is the name of the executable
* -- ROOTNAME is the base name of the .car and .mdf files
* -- all opther flags are optional and can be abbreviated (e.g. -p instead of -print)
*
* -- -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 or 1 = Class I e.g., CVFF, clayff)
* (II or 2 = Class II e.g., CFFx, COMPASS)
* (O or 0 = OPLS-AA)
* default is -class I
*
* -- -ignore - tells msi2lmp to ignore warnings and errors and keep going
*
* -- -nocenter - tells msi2lmp to not center the box around the (geometrical)
* center of the atoms, but around the origin
*
* -- -shift - tells msi2lmp to shift the entire system (box and coordinates)
* by a vector (default: 0.0 0.0 0.0)
*
* -- -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
*
* -- output is written to a file called ROOTNAME.data
*
*
****************************************************************
*
* 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[6];
double box[3][3];
double shift[3];
int periodic = 1;
int TriclinicFlag = 0;
int forcefield = 0;
int centerflag = 1;
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;
void condexit(int val)
{
if (iflag == 0) exit(val);
}
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;
const char *frc_dir_name = NULL;
const char *frc_file_name = NULL;
pflag = 1;
iflag = 0;
forcefield = FF_TYPE_CLASS1 | FF_TYPE_COMMON;
shift[0] = shift[1] = shift[2] = 0.0;
frc_dir_name = getenv("BIOSYM_LIBRARY");
if (argc < 2) {
printf("usage: %s <rootname> [-class <I|1|II|2>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter]\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 = FF_TYPE_CLASS1 | FF_TYPE_COMMON;
} else if ((strcmp(argv[n],"II") == 0) || (strcmp(argv[n],"2") == 0)) {
forcefield = FF_TYPE_CLASS2 | FF_TYPE_COMMON;
} else if ((strcmp(argv[n],"O") == 0) || (strcmp(argv[n],"0") == 0)) {
forcefield = FF_TYPE_OPLSAA | FF_TYPE_COMMON;
} else {
printf("Unrecognized Forcefield class: %s\n",argv[n]);
return 3;
}
} 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],"-s",2) == 0) {
if (n+3 > argc) {
printf("Missing argument(s) to \"-shift\" flag\n");
return 1;
}
shift[0] = atof(argv[++n]);
shift[1] = atof(argv[++n]);
shift[2] = atof(argv[++n]);
} else if (strncmp(argv[n],"-i",2) == 0 ) {
iflag = 1;
} else if (strncmp(argv[n],"-n",2) == 0 ) {
centerflag = 0;
} 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) {
puts("\nRunning msi2lmp.....\n");
if (forcefield & FF_TYPE_CLASS1) puts(" Forcefield: Class I");
if (forcefield & FF_TYPE_CLASS2) puts(" Forcefield: Class II");
if (forcefield & FF_TYPE_OPLSAA) puts(" Forcefield: OPLS-AA");
printf(" Forcefield file name: %s\n",FrcFileName);
}
n = 0;
if (forcefield & FF_TYPE_CLASS1) {
if (strstr(FrcFileName,"cvff") != NULL) ++n;
if (strstr(FrcFileName,"clayff") != NULL) ++n;
} else if (forcefield & FF_TYPE_OPLSAA) {
if (strstr(FrcFileName,"oplsaa") != NULL) ++n;
} else if (forcefield & FF_TYPE_CLASS2) {
if (strstr(FrcFileName,"pcff") != NULL) ++n;
if (strstr(FrcFileName,"cff91") != NULL) ++n;
if (strstr(FrcFileName,"compass") != NULL) ++n;
}
if (n == 0) {
if (iflag > 0) fputs(" WARNING",stderr);
else fputs(" Error ",stderr);
fputs("- forcefield name and class appear to be inconsistent\n\n",stderr);
if (iflag == 0) return 7;
}
/* 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();
/* Do internal check of internal coordinate lists */
if (pflag > 0)
printf("\n Check parameters for internal consistency\n");
CheckLists();
/* Write out the final data */
WriteDataFile(rootname);
free(rootname);
if (pflag > 0)
printf("\nNormal program termination\n");
return 0;
}

221
tools/msi2lmp/src/msi2lmp.h
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@ -1,221 +0,0 @@
/********************************
*
* 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.
*
* The thrid version was revised in Fall 2011 by
* Stephanie Teich-McGoldrick to add support non-orthogonal cells.
*
* The next revision was done in Summer 2013 by
* Axel Kohlmeyer to improve portability to Windows compilers,
* clean up command line parsing and improve compatibility with
* the then current LAMMPS versions. This revision removes
* compatibility with the obsolete LAMMPS version written in Fortran 90.
*/
# 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
#define FF_TYPE_COMMON 1<<0
#define FF_TYPE_CLASS1 1<<1
#define FF_TYPE_CLASS2 1<<2
#define FF_TYPE_OPLSAA 1<<3
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];
double 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 */
int image[3]; /* image flag */
char potential[6]; /* atom potential type */
char element[4]; /* atom element */
double 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[6]; /* A, B, C, alpha, beta, gamma */
extern double box[3][3]; /* hi/lo for x/y/z and xy, xz, yz for triclinic */
extern double shift[3]; /* shift vector for all coordinates and box positions */
extern int periodic; /* 0= nonperiodic 1= 3-D periodic */
extern int TriclinicFlag; /* 0= Orthogonal 1= Triclinic */
extern int forcefield; /* BitMask: the value FF_TYPE_COMMON is set for common components of the options below,
* FF_TYPE_CLASS1 = ClassI, FF_TYPE_CLASS2 = ClassII, FF_TYPE_OPLSAA = OPLS-AA*/
extern int centerflag; /* 1= center box 0= keep box */
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();
extern void CheckLists();
extern void WriteDataFile(char *);
extern void set_box(double box[3][3], double *h, double *h_inv);
extern void lamda2x(double *lamda, double *x, double *h, double *boxlo);
extern void x2lamda(double *x, double *lamda, double *h_inv, double *boxlo);
extern void condexit(int);

1287
tools/msi2lmp/test/PyAC_bulk-clayff.car
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1308
tools/msi2lmp/test/PyAC_bulk-clayff.mdf
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19
tools/msi2lmp/test/benzene-class1.car
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@ -1,19 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:34:43 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
H1 2.500000000 5.000000000 -5.000000000 BENZ 1 h H 0.102
C2 3.594720000 5.000000000 -5.000000000 BENZ 1 cp C -0.102
C3 4.290270000 6.204730000 -5.000000000 BENZ 1 cp C -0.102
C4 5.681370000 6.204730000 -5.000000000 BENZ 1 cp C -0.102
C5 6.376920000 5.000000000 -5.000000000 BENZ 1 cp C -0.102
C6 5.681370000 3.795270000 -5.000000000 BENZ 1 cp C -0.102
C7 4.290270000 3.795270000 -5.000000000 BENZ 1 cp C -0.102
H8 7.471640000 5.000000000 -5.000000000 BENZ 1 h H 0.102
H9 3.742910000 7.152785000 -5.000000000 BENZ 1 h H 0.102
H10 6.228730000 7.152785000 -5.000000000 BENZ 1 h H 0.102
H11 6.228730000 2.847215000 -5.000000000 BENZ 1 h H 0.102
H12 3.742910000 2.847215000 -5.000000000 BENZ 1 h H 0.102
end
end

40
tools/msi2lmp/test/benzene-class1.mdf
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@ -1,40 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:34:43 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule benzene
XXXX_1:H1 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C2
XXXX_1:C2 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5
XXXX_1:C3 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H9
XXXX_1:C4 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H10
XXXX_1:C5 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C4/1.5 H8 C6/1.5
XXXX_1:C6 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 H11
XXXX_1:C7 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H12
XXXX_1:H8 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C5
XXXX_1:H9 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C3
XXXX_1:H10 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C4
XXXX_1:H11 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C6
XXXX_1:H12 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C7
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

19
tools/msi2lmp/test/benzene-class2a.car
View File

@ -1,19 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:34:43 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
H1 2.500000000 5.000000000 -5.000000000 XXXX 1 h1 H 0.102
C2 3.594720000 5.000000000 -5.000000000 XXXX 1 c3a C -0.102
C3 4.290270000 6.204730000 -5.000000000 XXXX 1 c3a C -0.102
C4 5.681370000 6.204730000 -5.000000000 XXXX 1 c3a C -0.102
C5 6.376920000 5.000000000 -5.000000000 XXXX 1 c3a C -0.102
C6 5.681370000 3.795270000 -5.000000000 XXXX 1 c3a C -0.102
C7 4.290270000 3.795270000 -5.000000000 XXXX 1 c3a C -0.102
H8 7.471640000 5.000000000 -5.000000000 XXXX 1 h1 H 0.102
H9 3.742910000 7.152785000 -5.000000000 XXXX 1 h1 H 0.102
H10 6.228730000 7.152785000 -5.000000000 XXXX 1 h1 H 0.102
H11 6.228730000 2.847215000 -5.000000000 XXXX 1 h1 H 0.102
H12 3.742910000 2.847215000 -5.000000000 XXXX 1 h1 H 0.102
end
end

40
tools/msi2lmp/test/benzene-class2a.mdf
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@ -1,40 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:34:43 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule benzene
XXXX_1:H1 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C2
XXXX_1:C2 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5
XXXX_1:C3 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H9
XXXX_1:C4 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H10
XXXX_1:C5 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 C4/1.5 H8 C6/1.5
XXXX_1:C6 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 H11
XXXX_1:C7 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H12
XXXX_1:H8 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C5
XXXX_1:H9 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C3
XXXX_1:H10 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C4
XXXX_1:H11 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C6
XXXX_1:H12 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C7
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

19
tools/msi2lmp/test/benzene-class2b.car
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@ -1,19 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:34:43 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
H1 2.500000000 5.000000000 -5.000000000 XXXX 1 h H 0.102
C2 3.594720000 5.000000000 -5.000000000 XXXX 1 cp C -0.102
C3 4.290270000 6.204730000 -5.000000000 XXXX 1 cp C -0.102
C4 5.681370000 6.204730000 -5.000000000 XXXX 1 cp C -0.102
C5 6.376920000 5.000000000 -5.000000000 XXXX 1 cp C -0.102
C6 5.681370000 3.795270000 -5.000000000 XXXX 1 cp C -0.102
C7 4.290270000 3.795270000 -5.000000000 XXXX 1 cp C -0.102
H8 7.471640000 5.000000000 -5.000000000 XXXX 1 h H 0.102
H9 3.742910000 7.152785000 -5.000000000 XXXX 1 h H 0.102
H10 6.228730000 7.152785000 -5.000000000 XXXX 1 h H 0.102
H11 6.228730000 2.847215000 -5.000000000 XXXX 1 h H 0.102
H12 3.742910000 2.847215000 -5.000000000 XXXX 1 h H 0.102
end
end

40
tools/msi2lmp/test/benzene-class2b.mdf
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@ -1,40 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:34:43 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule benzene
XXXX_1:H1 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C2
XXXX_1:C2 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5
XXXX_1:C3 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H9
XXXX_1:C4 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H10
XXXX_1:C5 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C4/1.5 H8 C6/1.5
XXXX_1:C6 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 H11
XXXX_1:C7 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H12
XXXX_1:H8 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C5
XXXX_1:H9 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C3
XXXX_1:H10 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C4
XXXX_1:H11 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C6
XXXX_1:H12 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C7
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

649
tools/msi2lmp/test/crambin-class1.car
View File

@ -1,649 +0,0 @@
!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

840
tools/msi2lmp/test/crambin-class1.mdf
View File

@ -1,840 +0,0 @@
!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

942
tools/msi2lmp/test/data-compare.pl
View File

@ -1,942 +0,0 @@
#!/usr/bin/perl -w
# Tool to validate and compare two LAMMPS data files
# with "inexact" floating point comparisons
# July 2013 by Axel Kohlmeyer <akohlmey@gmail.com>
use strict;
use warnings;
my $version = 'v0.2';
# delta for floating point comparisons.
my $small = 1.0e-4;
# two hashes for storing system information
my %data1;
my %data2;
# simple checks after reading a section header
sub section_check {
my ($fh,$data,$section) = @_;
$_ = <$fh>;
# skip empty and whitespace-only lines
die "Line following '$section' is not empty" unless (/^\s*$/);
die "Incomplete or incorrect header" unless ($data->{natoms} > 0);
die "Incomplete or incorrect header" unless ($data->{natomtypes} > 0);
}
sub get_next {
my ($fh) = @_;
while (<$fh>) {
chomp;
# trim off comments
$_ =~ s/#.*$//;
# skip empty and whitespace-only lines
next if (/^\s*$/);
last;
}
return $_;
}
# fill hash with default data.
sub data_defaults {
my ($data) = @_;
$data->{natoms} = 0;
$data->{nbonds} = 0;
$data->{nangles} = 0;
$data->{ndihedrals} = 0;
$data->{nimpropers} = 0;
$data->{natomtypes} = 0;
$data->{nbondtypes} = 0;
$data->{nangletypes} = 0;
$data->{ndihedraltypes} = 0;
$data->{nimpropertypes} = 0;
$data->{xlo} = 0.5;
$data->{xhi} = -0.5;
$data->{ylo} = 0.5;
$data->{yhi} = -0.5;
$data->{zlo} = 0.5;
$data->{zhi} = -0.5;
$data->{xy} = 0.0;
$data->{xz} = 0.0;
$data->{yz} = 0.0;
$data->{triclinic} = 0;
}
# read/parse lammps data file
sub read_data {
my ($fh,$data) = @_;
my $section;
# read header. first line is already chopped off
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+atoms\s*$/) { $data->{natoms} = $1; next; }
if (/^\s*([0-9]+)\s+bonds\s*$/) { $data->{nbonds} = $1; next; }
if (/^\s*([0-9]+)\s+angles\s*$/) { $data->{nangles} = $1; next; }
if (/^\s*([0-9]+)\s+dihedrals\s*$/) { $data->{ndihedrals} = $1; next; }
if (/^\s*([0-9]+)\s+impropers\s*$/) { $data->{nimpropers} = $1; next; }
if (/^\s*([0-9]+)\s+atom types\s*$/) { $data->{natomtypes} = $1; next; }
if (/^\s*([0-9]+)\s+bond types\s*$/) { $data->{nbondtypes} = $1; next; }
if (/^\s*([0-9]+)\s+angle types\s*$/) { $data->{nangletypes} = $1; next; }
if (/^\s*([0-9]+)\s+dihedral types\s*$/)
{ $data->{ndihedraltypes} = $1; next; }
if (/^\s*([0-9]+)\s+improper types\s*$/)
{ $data->{nimpropertypes} =$1 ; next; }
if (/^\s*([-+.eE0-9]+)\s+([-+.eE0-9]+)\s+xlo xhi\s*$/) {
$data->{xlo}=$1;
$data->{xhi}=$2;
next;
}
if (/^\s*([-+.eE0-9]+)\s+([-+.eE0-9]+)\s+ylo yhi\s*$/) {
$data->{ylo}=$1;
$data->{yhi}=$2;
next;
}
if (/^\s*([-+.eE0-9]+)\s+([-+.eE0-9]+)\s+zlo zhi\s*$/) {
$data->{zlo}=$1;
$data->{zhi}=$2;
next;
}
if (/^\s*([-+.eE0-9]+)\s+([-+.eE0-9]+)\s+([-+.eE0-9]+)\s+xy xz yz\s*$/) {
$data->{xy}=$1;
$data->{xz}=$2;
$data->{yz}=$3;
$data->{triclinic} = 1;
next;
}
# if we reach this point, the header has ended;
last;
}
$a = $data->{natoms};
$b = $data->{natomtypes};
die "Invalid number of atoms: $a" unless ($a > 0);
die "Invalid number of atom types: $b" unless ($b > 0);
my ($i,$j,$k);
while (1) {
if (/^\s*(\S+|\S+ Coeffs)\s*$/) {
if ($1 eq "Masses") {
$data->{mass} = [];
$i = 0;
section_check($fh,$data,"Masses");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9]+)\s*$/) {
$j = $1 - 1;
die "Atom type $1 is out of range"
if (($1 < 1) || ($1 > $data->{natomtypes}));
++$i;
$data->{mass}[$j] = $2;
next;
}
die "Too many entries in Masses section"
if ($i > $data->{natomtypes});
die "Too few entries in Masses section"
if ($i < $data->{natomtypes});
die "Multiple mass assignments to the same atom type"
if (scalar @{$data->{mass}} != $data->{natomtypes});
last;
}
} elsif ($1 eq "Pair Coeffs") {
$data->{paircoeff} = [];
$i = 0;
section_check($fh,$data,"Pair Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "Atom type $1 is out of range"
if (($1 < 1) || ($1 > $data->{natomtypes}));
++$i;
$data->{paircoeff}[$j] = $2;
next;
}
die "Too many entries in Pair Coeffs section"
if ($i > $data->{natomtypes});
die "Too few entries in Pair Coeffs section"
if ($i < $data->{natomtypes});
die "Multiple pair coefficient assignments to the same atom type"
if (scalar @{$data->{paircoeff}} != $data->{natomtypes});
last;
}
} elsif ($1 eq "Bond Coeffs") {
$data->{bondcoeff} = [];
$i = 0;
section_check($fh,$data,"Bond Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "Bond type $1 is out of range"
if (($1 < 1) || ($1 > $data->{nbondtypes}));
++$i;
$data->{bondcoeff}[$j] = $2;
next;
}
die "Too many entries in Bond Coeffs section"
if ($i > $data->{nbondtypes});
die "Too few entries in Bond Coeffs section"
if ($i < $data->{nbondtypes});
die "Multiple bond coefficient assignments to the same bond type"
if (scalar @{$data->{bondcoeff}} != $data->{nbondtypes});
last;
}
} elsif ($1 eq "Angle Coeffs") {
$data->{anglecoeff} = [];
$i = 0;
section_check($fh,$data,"Angle Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "Angle type $1 is out of range"
if (($1 < 1) || ($1 > $data->{nangletypes}));
++$i;
$data->{anglecoeff}[$j] = $2;
next;
}
die "Too many entries in Angle Coeffs section"
if ($i > $data->{nangletypes});
die "Too few entries in Angle Coeffs section"
if ($i < $data->{nangletypes});
die "Multiple angle coefficient assignments to the same angle type"
if (scalar @{$data->{anglecoeff}} != $data->{nangletypes});
last;
}
} elsif ($1 eq "BondBond Coeffs") {
$data->{bondbondcoeff} = [];
$i = 0;
section_check($fh,$data,"BondBond Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "Angle type $1 is out of range"
if (($1 < 1) || ($1 > $data->{nangletypes}));
++$i;
$data->{bondbondcoeff}[$j] = $2;
next;
}
die "Too many entries in BondBond Coeffs section"
if ($i > $data->{nangletypes});
die "Too few entries in BondBond Coeffs section"
if ($i < $data->{nangletypes});
die "Multiple angle coefficient assignments to the same angle type"
if (scalar @{$data->{bondbondcoeff}} != $data->{nangletypes});
last;
}
} elsif ($1 eq "BondAngle Coeffs") {
$data->{bondanglecoeff} = [];
$i = 0;
section_check($fh,$data,"BondAngle Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "Angle type $1 is out of range"
if (($1 < 1) || ($1 > $data->{nangletypes}));
++$i;
$data->{bondanglecoeff}[$j] = $2;
next;
}
die "Too many entries in BondAngle Coeffs section"
if ($i > $data->{nangletypes});
die "Too few entries in BondAngle Coeffs section"
if ($i < $data->{nangletypes});
die "Multiple bondangle coefficient assignments to the same angle type"
if (scalar @{$data->{bondanglecoeff}} != $data->{nangletypes});
last;
}
} elsif ($1 eq "Dihedral Coeffs") {
$data->{dihedralcoeff} = [];
$i = 0;
section_check($fh,$data,"Dihedral Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "Dihedral type $1 is out of range"
if (($1 < 1) || ($1 > $data->{ndihedraltypes}));
++$i;
$data->{dihedralcoeff}[$j] = $2;
next;
}
die "Too many entries in Dihedral Coeffs section"
if ($i > $data->{ndihedraltypes});
die "Too few entries in Dihedral Coeffs section"
if ($i < $data->{ndihedraltypes});
die "Multiple dihedral coefficient assignments to the same dihedral type"
if (scalar @{$data->{dihedralcoeff}} != $data->{ndihedraltypes});
last;
}
} elsif ($1 eq "AngleAngleTorsion Coeffs") {
$data->{angleangletorsioncoeff} = [];
$i = 0;
section_check($fh,$data,"AngleAngleTorsion Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "AngleAngleTorsion type $1 is out of range"
if (($1 < 1) || ($1 > $data->{ndihedraltypes}));
++$i;
$data->{angleangletorsioncoeff}[$j] = $2;
next;
}
die "Too many entries in AngleAngleTorsion Coeffs section"
if ($i > $data->{ndihedraltypes});
die "Too few entries in AngleAngleTorsion Coeffs section"
if ($i < $data->{ndihedraltypes});
die "Multiple dihedral coefficient assignments to the same dihedral type"
if (scalar @{$data->{angleangletorsioncoeff}} != $data->{ndihedraltypes});
last;
}
} elsif ($1 eq "EndBondTorsion Coeffs") {
$data->{endbondtorsioncoeff} = [];
$i = 0;
section_check($fh,$data,"EndBondTorsion Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "EndBondTorsion type $1 is out of range"
if (($1 < 1) || ($1 > $data->{ndihedraltypes}));
++$i;
$data->{endbondtorsioncoeff}[$j] = $2;
next;
}
die "Too many entries in EndBondTorsion Coeffs section"
if ($i > $data->{ndihedraltypes});
die "Too few entries in EndBondTorsion Coeffs section"
if ($i < $data->{ndihedraltypes});
die "Multiple dihedral coefficient assignments to the same dihedral type"
if (scalar @{$data->{endbondtorsioncoeff}} != $data->{ndihedraltypes});
last;
}
} elsif ($1 eq "MiddleBondTorsion Coeffs") {
$data->{middlebondtorsioncoeff} = [];
$i = 0;
section_check($fh,$data,"MiddleBondTorsion Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "MiddleBondTorsion type $1 is out of range"
if (($1 < 1) || ($1 > $data->{ndihedraltypes}));
++$i;
$data->{middlebondtorsioncoeff}[$j] = $2;
next;
}
die "Too many entries in MiddleBondTorsion Coeffs section"
if ($i > $data->{ndihedraltypes});
die "Too few entries in MiddleBondTorsion Coeffs section"
if ($i < $data->{ndihedraltypes});
die "Multiple dihedral coefficient assignments to the same dihedral type"
if (scalar @{$data->{middlebondtorsioncoeff}} != $data->{ndihedraltypes});
last;
}
} elsif ($1 eq "BondBond13 Coeffs") {
$data->{bondbond13coeff} = [];
$i = 0;
section_check($fh,$data,"BondBond13 Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "BondBond13 type $1 is out of range"
if (($1 < 1) || ($1 > $data->{ndihedraltypes}));
++$i;
$data->{bondbond13coeff}[$j] = $2;
next;
}
die "Too many entries in BondBond13 Coeffs section"
if ($i > $data->{ndihedraltypes});
die "Too few entries in BondBond13 Coeffs section"
if ($i < $data->{ndihedraltypes});
die "Multiple dihedral coefficient assignments to the same dihedral type"
if (scalar @{$data->{bondbond13coeff}} != $data->{ndihedraltypes});
last;
}
} elsif ($1 eq "AngleTorsion Coeffs") {
$data->{angletorsioncoeff} = [];
$i = 0;
section_check($fh,$data,"AngleTorsion Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "AngleTorsion type $1 is out of range"
if (($1 < 1) || ($1 > $data->{ndihedraltypes}));
++$i;
$data->{angletorsioncoeff}[$j] = $2;
next;
}
die "Too many entries in AngleTorsion Coeffs section"
if ($i > $data->{ndihedraltypes});
die "Too few entries in AngleTorsion Coeffs section"
if ($i < $data->{ndihedraltypes});
die "Multiple dihedral coefficient assignments to the same dihedral type"
if (scalar @{$data->{angletorsioncoeff}} != $data->{ndihedraltypes});
last;
}
} elsif ($1 eq "Improper Coeffs") {
$data->{impropercoeff} = [];
$i = 0;
section_check($fh,$data,"Improper Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "Improper type $1 is out of range"
if (($1 < 1) || ($1 > $data->{nimpropertypes}));
++$i;
$data->{impropercoeff}[$j] = $2;
next;
}
die "Too many entries in Improper Coeffs section"
if ($i > $data->{nimpropertypes});
die "Too few entries in Improper Coeffs section"
if ($i < $data->{nimpropertypes});
die "Multiple improper coefficient assignments to the same improper type"
if (scalar @{$data->{impropercoeff}} != $data->{nimpropertypes});
last;
}
} elsif ($1 eq "AngleAngle Coeffs") {
$data->{angleanglecoeff} = [];
$i = 0;
section_check($fh,$data,"AngleAngle Coeffs");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9 ]+)\s*$/) {
$j = $1 - 1;
die "AngleAngle type $1 is out of range"
if (($1 < 1) || ($1 > $data->{nimpropertypes}));
++$i;
$data->{angleanglecoeff}[$j] = $2;
next;
}
die "Too many entries in AngleAngle Coeffs section"
if ($i > $data->{nimpropertypes});
die "Too few entries in AngleAngle Coeffs section"
if ($i < $data->{nimpropertypes});
die "Multiple angleangle coefficient assignments to the same angle type"
if (scalar @{$data->{angleanglecoeff}} != $data->{nimpropertypes});
last;
}
} elsif ($1 eq "Atoms") {
$data->{tag} = [];
$data->{type} = [];
$data->{molid} = [];
$data->{charge} = [];
$data->{posx} = [];
$data->{posy} = [];
$data->{posz} = [];
$data->{imgx} = [];
$data->{imgy} = [];
$data->{imgz} = [];
$i = 0;
section_check($fh,$data,"Atoms");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([0-9]+)\s+([0-9]+)\s+([-+.eE0-9]+)\s+([-+.eE0-9]+)\s+([-+.eE0-9]+)\s+([-+.eE0-9]+)(|\s+(-?[0-9]+)\s+(-?[0-9]+)\s+(-?[0-9]+))\s*$/) {
$k = $1 - 1;
die "Atom id $1 is out of range"
if (($1 < 1) || ($1 > $data->{natoms}));
$j = $3 - 1;
die "Atom type $2 is out of range"
if (($3 < 1) || ($3 > $data->{natomtypes}));
++$i;
$data->{tag}[$k] = $1;
$data->{molid}[$k] = $2;
$data->{type}[$k] = $3;
$data->{charge}[$k] = $4;
$data->{posx}[$k] = $5;
$data->{posy}[$k] = $6;
$data->{posz}[$k] = $7;
$data->{imgx}[$k] = 0;
$data->{imgy}[$k] = 0;
$data->{imgz}[$k] = 0;
if (! $8 eq "") {
$data->{imgx}[$k] = $9;
$data->{imgy}[$k] = $10;
$data->{imgz}[$k] = $11;
}
next;
# } else {
# print "Atoms: $_\n";
}
die "Too many entries in Atoms section: $i vs. $data->{natoms}"
if ($i > $data->{natoms});
die "Too few entries in Atoms section: $i vs. $data->{natoms}"
if ($i < $data->{natoms});
die "Multiple atoms assigned to the same atom ID"
if (scalar @{$data->{tag}} != $data->{natoms});
last;
}
} elsif ($1 eq "Velocities") {
$data->{velx} = [];
$data->{vely} = [];
$data->{velz} = [];
$i = 0;
section_check($fh,$data,"Velocities");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+([-+.eE0-9]+)\s+([-+.eE0-9]+)\s+([-+.eE0-9]+)\s*$/) {
$k = $1 - 1;
die "Atom id $1 is out of range"
if (($1 < 1) || ($1 > $data->{natoms}));
++$i;
$data->{velx}[$k] = $2;
$data->{vely}[$k] = $3;
$data->{velz}[$k] = $4;
next;
}
die "Too many entries in Velocities section"
if ($i > $data->{natoms});
die "Too few entries in Velocities section"
if ($i < $data->{natoms});
die "Multiple velocities assigned to the same atom ID"
if (scalar @{$data->{velx}} != $data->{natoms});
last;
}
} elsif ($1 eq "Bonds") {
$data->{bondt} = [];
$data->{bond1} = [];
$data->{bond2} = [];
$i = 0;
section_check($fh,$data,"Bonds");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+(-?[0-9]+)\s+([0-9]+)\s+([0-9]+)\s*$/) {
$k = $1 - 1;
die "Bond id $1 is out of range"
if (($1 < 1) || ($1 > $data->{nbonds}));
die "Bond type $2 is out of range"
if (($2 == 0) || ($2 > $data->{nbondtypes}));
die "Bond atom 1 ID $3 is out of range"
if (($3 < 1) || ($3 > $data->{natoms}));
die "Bond atom 2 ID $4 is out of range"
if (($4 < 1) || ($4 > $data->{natoms}));
++$i;
$data->{bondt}[$k] = $2;
$data->{bond1}[$k] = $3;
$data->{bond2}[$k] = $4;
next;
}
die "Too many entries in Bonds section"
if ($i > $data->{nbonds});
die "Too few entries in Bonds section"
if ($i < $data->{nbonds});
die "Multiple bonds assigned to the same bond ID"
if (scalar @{$data->{bondt}} != $data->{nbonds});
last;
}
} elsif ($1 eq "Angles") {
$data->{anglet} = [];
$data->{angle1} = [];
$data->{angle2} = [];
$data->{angle3} = [];
$i = 0;
section_check($fh,$data,"Angles");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+(-?[0-9]+)\s+([0-9]+)\s+([0-9]+)\s+([0-9]+)\s*$/) {
$k = $1 - 1;
die "Angle id $1 is out of range"
if (($1 < 1) || ($1 > $data->{nangles}));
die "Angle type $2 is out of range"
if (($2 == 0) || ($2 > $data->{nangletypes}));
die "Angle atom 1 ID $3 is out of range"
if (($3 < 1) || ($3 > $data->{natoms}));
die "Angle atom 2 ID $4 is out of range"
if (($4 < 1) || ($4 > $data->{natoms}));
die "Angle atom 3 ID $5 is out of range"
if (($5 < 1) || ($5 > $data->{natoms}));
++$i;
$data->{anglet}[$k] = $2;
$data->{angle1}[$k] = $3;
$data->{angle2}[$k] = $4;
$data->{angle3}[$k] = $5;
next;
}
die "Too many entries in Angles section"
if ($i > $data->{nangles});
die "Too few entries in Angles section"
if ($i < $data->{nangles});
die "Multiple angles assigned to the same angle ID"
if (scalar @{$data->{anglet}} != $data->{nangles});
last;
}
} elsif ($1 eq "Dihedrals") {
$data->{dihedralt} = [];
$data->{dihedral1} = [];
$data->{dihedral2} = [];
$data->{dihedral3} = [];
$data->{dihedral4} = [];
$i = 0;
section_check($fh,$data,"Dihedrals");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+(-?[0-9]+)\s+([0-9]+)\s+([0-9]+)\s+([0-9]+)\s+([0-9]+)\s*$/) {
$k = $1 - 1;
die "Dihedral id $1 is out of range"
if (($1 < 1) || ($1 > $data->{ndihedrals}));
die "Dihedral type $2 is out of range"
if (($2 == 0) || ($2 > $data->{ndihedraltypes}));
die "Dihedral atom 1 ID $3 is out of range"
if (($3 < 1) || ($3 > $data->{natoms}));
die "Dihedral atom 2 ID $4 is out of range"
if (($4 < 1) || ($4 > $data->{natoms}));
die "Dihedral atom 3 ID $5 is out of range"
if (($5 < 1) || ($5 > $data->{natoms}));
die "Dihedral atom 4 ID $6 is out of range"
if (($6 < 1) || ($6 > $data->{natoms}));
++$i;
$data->{dihedralt}[$k] = $2;
$data->{dihedral1}[$k] = $3;
$data->{dihedral2}[$k] = $4;
$data->{dihedral3}[$k] = $5;
$data->{dihedral4}[$k] = $6;
next;
}
die "Too many entries in Dihedrals section"
if ($i > $data->{ndihedrals});
die "Too few entries in Dihedrals section"
if ($i < $data->{ndihedrals});
die "Multiple dihedrals assigned to the same dihedral ID"
if (scalar @{$data->{dihedralt}} != $data->{ndihedrals});
last;
}
} elsif ($1 eq "Impropers") {
$data->{impropert} = [];
$data->{improper1} = [];
$data->{improper2} = [];
$data->{improper3} = [];
$data->{improper4} = [];
$i = 0;
section_check($fh,$data,"Impropers");
while (get_next($fh)) {
if (/^\s*([0-9]+)\s+(-?[0-9]+)\s+([0-9]+)\s+([0-9]+)\s+([0-9]+)\s+([0-9]+)\s*$/) {
$k = $1 - 1;
die "Improper id $1 is out of range"
if (($1 < 1) || ($1 > $data->{nimpropers}));
die "Improper type $2 is out of range"
if (($2 == 0) || ($2 > $data->{nimpropertypes}));
die "Improper atom 1 ID $3 is out of range"
if (($3 < 1) || ($3 > $data->{natoms}));
die "Improper atom 2 ID $4 is out of range"
if (($4 < 1) || ($4 > $data->{natoms}));
die "Improper atom 3 ID $5 is out of range"
if (($5 < 1) || ($5 > $data->{natoms}));
die "Improper atom 4 ID $6 is out of range"
if (($6 < 1) || ($6 > $data->{natoms}));
++$i;
$data->{impropert}[$k] = $2;
$data->{improper1}[$k] = $3;
$data->{improper2}[$k] = $4;
$data->{improper3}[$k] = $5;
$data->{improper4}[$k] = $6;
next;
}
die "Too many entries in Impropers section"
if ($i > $data->{nimpropers});
die "Too few entries in Impropers section"
if ($i < $data->{nimpropers});
die "Multiple impropers assigned to the same improper ID"
if (scalar @{$data->{impropert}} != $data->{nimpropers});
last;
}
} else {
die "Bad data: $_";
}
last unless ($_);
} else {
die "Bad data: $_";
}
}
}
sub floatdiff {
my ($n1,$n2,$rel) = @_;
my $diff = abs($n1-$n2);
my $avg = (abs($n1)+abs($n2))*0.5;
return 0 if ($avg == 0.0);
if ($rel) {
# print "relative difference: ",$diff/$avg," vs. $small\n";
return 0 if ($diff/$avg < $small);
} else {
# print "absolute difference: ",$diff," vs. $small\n";
return 0 if ($diff < $small);
}
return 1;
}
sub coeffcompare {
my ($d1,$d2,$coeff,$type) = @_;
my (@c1,@c2,$a,$b);
my ($field,$count,$i,$j,$t) = ($coeff . 'coeff', 'n' . $type . 'types', 0,0,0);
if (exists $d1->{$field} && exists $d2->{$field}) {
for ($i=0; $i < $d1->{$count}; ++$i) {
$t = $i+1;
@c1 = split /\s+/, ${$$d1{$field}}[$i];
@c2 = split /\s+/, ${$$d2{$field}}[$i];
die "Inconsistent number of $coeff coefficients for $type type $t: $#c1 vs $#c2\n"
if ($#c1 != $#c2);
for ($j = 0; $j <= $#c1; ++$j) {
$a = $c1[$j]; $b = $c2[$j];
die "Inconsistent $coeff coefficient ", $j+1,
" for $type type $t: $a vs. $b" if (floatdiff($a,$b,1));
}
}
} else {
die "Field $field only exists in data file 1" if (exists $d1->{$field});
die "Field $field only exists in data file 2" if (exists $d2->{$field});
}
}
sub topocompare {
my ($d1,$d2,$type,$count) = @_;
my ($num,$a,$b,$field,$i,$j,$t);
$field = 'n' . $type . 's';
$num = $d1->{$field};
for ($i=0; $i < $num; ++$i) {
$t = $i+1;
$field = $type . 't';
$a = $d1->{$field}[$i]; $b = $d2->{$field}[$i];
die "Inconsistent $type types for $type $t: $a vs. $b" if ($a != $b);
for ($j=1; $j <= $count; ++$j) {
$field = $type . $j;
$a = $d1->{$field}[$i]; $b = $d2->{$field}[$i];
die "Inconsistent $type atom $j for $type $t: $a vs. $b" if ($a != $b);
}
}
}
sub syscompare {
my ($d1,$d2) = @_;
my ($i,$j,$t,$a,$b,@l);
# check atoms.
die "Number of atoms does not match"
if ($d1->{natoms} != $d2->{natoms});
die "Number of atom types does not match"
if ($d1->{natomtypes} != $d2->{natomtypes});
# check bonded interactions
@l = ('bond','angle','dihedral','improper');
foreach $i (@l) {
$t = 'n' . $i . 's';
$a = $d1->{$t};
$b = $d2->{$t};
die "Number of ",$i,"s does not match: $a vs $b" unless ($a == $b);
$t = 'n' . $i . 'types';
$a = $d1->{$t};
$b = $d2->{$t};
die "Number of ",$i," types does not match: $a vs $b" unless ($a == $b);
}
topocompare($d1,$d2,'bond',2);
topocompare($d1,$d2,'angle',3);
topocompare($d1,$d2,'dihedral',4);
topocompare($d1,$d2,'improper',4);
coeffcompare($d1,$d2,'pair','atom');
coeffcompare($d1,$d2,'bond','bond');
coeffcompare($d1,$d2,'angle','angle');
coeffcompare($d1,$d2,'bondbond','angle');
coeffcompare($d1,$d2,'bondangle','angle');
coeffcompare($d1,$d2,'dihedral','dihedral');
coeffcompare($d1,$d2,'angleangletorsion','dihedral');
coeffcompare($d1,$d2,'bondbond13','dihedral');
coeffcompare($d1,$d2,'endbondtorsion','dihedral');
coeffcompare($d1,$d2,'middlebondtorsion','dihedral');
coeffcompare($d1,$d2,'improper','improper');
coeffcompare($d1,$d2,'angleangle','improper');
for ($i=0; $i < $d1->{natomtypes}; ++$i) {
$j = $i+1;
if (exists $d1->{mass}[$i]) {
$a = $d1->{mass}[$i];
} else {
die "No mass for atom type $j in data file 1";
}
if (exists $d2->{mass}[$i]) {
$a = $d2->{mass}[$i];
} else {
die "No mass for atom type $j in data file 2";
}
}
# check box information
die "Inconsistent box shape" if ($d1->{triclinic} != $d2->{triclinic});
@l = ('xlo','xhi','ylo','yhi','zlo','zhi');
if ($d1->{triclinic}) { push @l, ('xy','xz','yz'); }
for $i (@l) {
$a = $d1->{$i};
$b = $d2->{$i};
die "Box data for $i does not match: $a $b" if (floatdiff($a,$b,0));
}
for ($i=0; $i < $d1->{natoms}; ++$i) {
$j = $i+1;
for $t ('tag','molid','type','imgx','imgy','imgz') {
if (exists $d1->{$t}[$i]) {
$a = $d1->{$t}[$i];
} else {
$a = 0;
}
if (exists $d2->{$t}[$i]) {
$b = $d2->{$t}[$i];
} else {
$b = 0;
}
die "Inconsistent data for $t, atom $j: $a vs. $b" if ($a != $b);
}
for $t ('charge','posx','posy','posz') {
if (exists $d1->{$t}[$i]) {
$a = $d1->{$t}[$i];
} else {
$a = 0;
}
if (exists $d2->{$t}[$i]) {
$b = $d2->{$t}[$i];
} else {
$b = 0;
}
die "Inconsistent data for $t, atom $j: $a vs. $b" if (floatdiff($a,$b,0));
}
}
}
########################################################################
# main program
my $fp;
if ($#ARGV < 1) {
die "usage $0 <file 1> <file 2>";
}
print "\nLAMMPS data file validation tool. $version\n\n";
data_defaults(\%data1);
data_defaults(\%data2);
# read in first data file
open($fp, '<', $ARGV[0]) or die $!;
print "opened data file 1: $ARGV[0]\n";
$_=<$fp>;
print;
read_data($fp,\%data1);
print "done reading data file 1\n\n";
close $fp;
# read in second data file
open($fp, '<', $ARGV[1]) or die $!;
print "opened data file 2: $ARGV[1]\n";
$_=<$fp>;
print;
read_data($fp,\%data2);
print "done reading data file 2\n\n";
close $fp;
# compare data sets
syscompare(\%data1,\%data2);
print "File $ARGV[0] and $ARGV[1] match\n\n";
exit 0;

15
tools/msi2lmp/test/ethane-class1.car
View File

@ -1,15 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:42:22 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
C1 4.462910000 5.148330000 -5.000410000 XXXX 1 c C -0.080
C2 5.965490000 5.079930000 -4.999750000 XXXX 1 c C -0.080
H3 4.099550000 6.054480000 -5.502500000 XXXX 1 h H 0.027
H4 4.020330000 4.288350000 -5.519840000 XXXX 1 h H 0.027
H5 4.057610000 5.156680000 -3.980190000 XXXX 1 h H 0.027
H6 6.409980000 5.944880000 -4.490510000 XXXX 1 h H 0.027
H7 6.329880000 4.179410000 -4.488110000 XXXX 1 h H 0.027
H8 6.370610000 5.061380000 -6.019850000 XXXX 1 h H 0.027
end
end

36
tools/msi2lmp/test/ethane-class1.mdf
View File

@ -1,36 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule ethane
XXXX_1:C1 C c 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C2 H3 H4 H5
XXXX_1:C2 C c 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C1 H6 H7 H8
XXXX_1:H3 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1
XXXX_1:H4 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1
XXXX_1:H5 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1
XXXX_1:H6 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2
XXXX_1:H7 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2
XXXX_1:H8 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

15
tools/msi2lmp/test/ethane-class2a.car
View File

@ -1,15 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:42:22 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
C1 4.462910000 5.148330000 -5.000410000 XXXX 1 c4 C -0.080
C2 5.965490000 5.079930000 -4.999750000 XXXX 1 c4 C -0.080
H3 4.099550000 6.054480000 -5.502500000 XXXX 1 h1 H 0.027
H4 4.020330000 4.288350000 -5.519840000 XXXX 1 h1 H 0.027
H5 4.057610000 5.156680000 -3.980190000 XXXX 1 h1 H 0.027
H6 6.409980000 5.944880000 -4.490510000 XXXX 1 h1 H 0.027
H7 6.329880000 4.179410000 -4.488110000 XXXX 1 h1 H 0.027
H8 6.370610000 5.061380000 -6.019850000 XXXX 1 h1 H 0.027
end
end

36
tools/msi2lmp/test/ethane-class2a.mdf
View File

@ -1,36 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule ethane
XXXX_1:C1 C c4 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C2 H3 H4 H5
XXXX_1:C2 C c4 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C1 H6 H7 H8
XXXX_1:H3 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1
XXXX_1:H4 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1
XXXX_1:H5 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1
XXXX_1:H6 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2
XXXX_1:H7 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2
XXXX_1:H8 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

15
tools/msi2lmp/test/ethane-class2b.car
View File

@ -1,15 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:42:22 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
C1 4.462910000 5.148330000 -5.000410000 XXXX 1 c C -0.080
C2 5.965490000 5.079930000 -4.999750000 XXXX 1 c C -0.080
H3 4.099550000 6.054480000 -5.502500000 XXXX 1 h H 0.027
H4 4.020330000 4.288350000 -5.519840000 XXXX 1 h H 0.027
H5 4.057610000 5.156680000 -3.980190000 XXXX 1 h H 0.027
H6 6.409980000 5.944880000 -4.490510000 XXXX 1 h H 0.027
H7 6.329880000 4.179410000 -4.488110000 XXXX 1 h H 0.027
H8 6.370610000 5.061380000 -6.019850000 XXXX 1 h H 0.027
end
end

36
tools/msi2lmp/test/ethane-class2b.mdf
View File

@ -1,36 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule ethane
XXXX_1:C1 C c 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C2 H3 H4 H5
XXXX_1:C2 C c 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C1 H6 H7 H8
XXXX_1:H3 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1
XXXX_1:H4 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1
XXXX_1:H5 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1
XXXX_1:H6 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2
XXXX_1:H7 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2
XXXX_1:H8 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

15
tools/msi2lmp/test/ethane-oplsaa.car
View File

@ -1,15 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:42:22 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
C1 4.462910000 5.148330000 -5.000410000 XXXX 1 CT C -0.180
C2 5.965490000 5.079930000 -4.999750000 XXXX 1 CT C -0.180
H3 4.099550000 6.054480000 -5.502500000 XXXX 1 HC H 0.060
H4 4.020330000 4.288350000 -5.519840000 XXXX 1 HC H 0.060
H5 4.057610000 5.156680000 -3.980190000 XXXX 1 HC H 0.060
H6 6.409980000 5.944880000 -4.490510000 XXXX 1 HC H 0.060
H7 6.329880000 4.179410000 -4.488110000 XXXX 1 HC H 0.060
H8 6.370610000 5.061380000 -6.019850000 XXXX 1 HC H 0.060
end
end

36
tools/msi2lmp/test/ethane-oplsaa.mdf
View File

@ -1,36 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule ethane
XXXX_1:C1 C CT 1 0 0 -0.1800 0 0 8 1.0000 0.0000 C2 H3 H4 H5
XXXX_1:C2 C CT 1 0 0 -0.1800 0 0 8 1.0000 0.0000 C1 H6 H7 H8
XXXX_1:H3 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C1
XXXX_1:H4 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C1
XXXX_1:H5 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C1
XXXX_1:H6 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C2
XXXX_1:H7 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C2
XXXX_1:H8 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C2
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

13
tools/msi2lmp/test/h2-h2o-class1.car
View File

@ -1,13 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:42:22 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
H1 4.600000000 5.000000000 2.500000000 HYDR 1 h H 0.000
H2 5.400000000 5.000000000 2.500000000 HYDR 1 h H 0.000
end
O1 5.000000000 5.000000000 7.500000000 TIP3 2 otip O -0.834
H2 4.000000000 5.000000000 7.500000000 TIP3 2 htip H 0.417
H3 5.000000000 4.000000000 7.500000000 TIP3 2 htip H 0.417
end
end

33
tools/msi2lmp/test/h2-h2o-class1.mdf
View File

@ -1,33 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule hydrogen
HYDR_1:H1 H h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H2
HYDR_1:H2 H h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H1
TIP3_1:O1 O otip 2 0 0 -0.8340 0 0 8 1.0000 0.0000 H2 H3
TIP3_1:H2 H htip 2 0 0 0.4170 0 0 8 1.0000 0.0000 O1
TIP3_1:H3 H htip 2 0 0 0.4170 0 0 8 1.0000 0.0000 O1
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

13
tools/msi2lmp/test/h2-h2o-class2b.car
View File

@ -1,13 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:42:22 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
O1 5.000000000 5.000000000 2.500000000 TIP3 2 o* O -0.834
H2 4.000000000 5.000000000 2.500000000 TIP3 2 h* H 0.417
H3 5.000000000 4.000000000 2.500000000 TIP3 2 h* H 0.417
end
H1 4.600000000 5.000000000 7.500000000 HYDR 1 h H 0.000
H2 5.400000000 5.000000000 7.500000000 HYDR 1 h H 0.000
end
end

33
tools/msi2lmp/test/h2-h2o-class2b.mdf
View File

@ -1,33 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule hydrogen
TIP3_1:O1 O o* 1 0 0 -0.8340 0 0 8 1.0000 0.0000 H2 H3
TIP3_1:H2 H h* 1 0 0 0.4170 0 0 8 1.0000 0.0000 O1
TIP3_1:H3 H h* 1 0 0 0.4170 0 0 8 1.0000 0.0000 O1
HYDR_1:H1 H h 2 0 0 0.0000 0 0 8 1.0000 0.0000 H2
HYDR_1:H2 H h 2 0 0 0.0000 0 0 8 1.0000 0.0000 H1
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

9
tools/msi2lmp/test/hydrogen-class1.car
View File

@ -1,9 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:42:22 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
H1 4.600000000 5.000000000 5.000000000 HYDR 1 h H 0.000
H2 5.400000000 5.000000000 5.000000000 HYDR 1 h H 0.000
end
end

30
tools/msi2lmp/test/hydrogen-class1.mdf
View File

@ -1,30 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule hydrogen
HYDR_1:H1 H h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H2
HYDR_1:H2 H h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H1
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

9
tools/msi2lmp/test/hydrogen-class2a.car
View File

@ -1,9 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:42:22 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
H1 4.600000000 5.000000000 5.000000000 HYDR 1 h1h H 0.000
H2 5.400000000 5.000000000 5.000000000 HYDR 1 h1h H 0.000
end
end

30
tools/msi2lmp/test/hydrogen-class2a.mdf
View File

@ -1,30 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule hydrogen
HYDR_1:H1 H h1h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H2
HYDR_1:H2 H h1h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H1
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

15
tools/msi2lmp/test/in.PyAC_bulk-clayff
View File

@ -1,15 +0,0 @@
log log.PyAC_bulk-clayff
units real
boundary p p p
atom_style full
pair_style lj/cut/coul/long 15.0
pair_modify mix geometric
bond_style harmonic
kspace_style pppm 1.0e-5
read_data PyAC_bulk-clayff.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data PyAC_bulk-clayff.data2

15
tools/msi2lmp/test/in.benzene-class1
View File

@ -1,15 +0,0 @@
log log.benzene-class1
units real
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
read_data benzene-class1.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data benzene-class1.data2

15
tools/msi2lmp/test/in.benzene-class2a
View File

@ -1,15 +0,0 @@
log log.benzene-class2a
units real
atom_style full
pair_style lj/class2/coul/cut 15.0
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
read_data benzene-class2a.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data benzene-class2a.data2

15
tools/msi2lmp/test/in.benzene-class2b
View File

@ -1,15 +0,0 @@
log log.benzene-class2b
units real
atom_style full
pair_style lj/class2/coul/cut 15.0
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
read_data benzene-class2b.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data benzene-class2b.data2

16
tools/msi2lmp/test/in.crambin-class1
View File

@ -1,16 +0,0 @@
log log.crambin-class1
units real
boundary m m m
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
read_data crambin-class1.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data crambin-class1.data2

14
tools/msi2lmp/test/in.ethane-class1
View File

@ -1,14 +0,0 @@
log log.ethane-class1
units real
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
read_data ethane-class1.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data ethane-class1.data2

15
tools/msi2lmp/test/in.ethane-class2a
View File

@ -1,15 +0,0 @@
log log.ethane-class2a
units real
atom_style full
pair_style lj/class2/coul/cut 15.0
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
read_data ethane-class2a.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data ethane-class2a.data2

15
tools/msi2lmp/test/in.ethane-class2b
View File

@ -1,15 +0,0 @@
log log.ethane-class2b
units real
atom_style full
pair_style lj/class2/coul/cut 15.0
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
read_data ethane-class2b.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data ethane-class2b.data2

14
tools/msi2lmp/test/in.ethane-oplsaa
View File

@ -1,14 +0,0 @@
log log.ethane-oplsaa
units real
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
angle_style harmonic
dihedral_style opls
read_data ethane-oplsaa.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data ethane-oplsaa.data2

13
tools/msi2lmp/test/in.h2-h2o-class1
View File

@ -1,13 +0,0 @@
log log.h2-h2o-class1
units real
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
angle_style harmonic
read_data h2-h2o-class1.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data h2-h2o-class1.data2

13
tools/msi2lmp/test/in.h2-h2o-class2b
View File

@ -1,13 +0,0 @@
log log.h2-h2o-class2b
units real
atom_style full
pair_style lj/class2/coul/cut 15.0
bond_style class2
angle_style class2
read_data h2-h2o-class2b.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data h2-h2o-class2b.data2

12
tools/msi2lmp/test/in.hydrogen-class1
View File

@ -1,12 +0,0 @@
log log.hydrogen-class1
units real
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
read_data hydrogen-class1.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data hydrogen-class1.data2

12
tools/msi2lmp/test/in.hydrogen-class2a
View File

@ -1,12 +0,0 @@
log log.hydrogen-class2a
units real
atom_style full
pair_style lj/class2/coul/cut 15.0
bond_style class2
read_data hydrogen-class2a.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data hydrogen-class2a.data2

15
tools/msi2lmp/test/in.naphthalene-class1
View File

@ -1,15 +0,0 @@
log log.naphthalene-class1
units real
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
read_data naphthalene-class1.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data naphthalene-class1.data2

15
tools/msi2lmp/test/in.naphthalene-class2a
View File

@ -1,15 +0,0 @@
log log.naphthalene-class2a
units real
atom_style full
pair_style lj/class2/coul/cut 15.0
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
read_data naphthalene-class2a.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data naphthalene-class2a.data2

15
tools/msi2lmp/test/in.naphthalene-class2b
View File

@ -1,15 +0,0 @@
log log.naphthalene-class2b
units real
atom_style full
pair_style lj/class2/coul/cut 15.0
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
read_data naphthalene-class2b.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data naphthalene-class2b.data2

16
tools/msi2lmp/test/in.nylon-class1
View File

@ -1,16 +0,0 @@
log log.nylon-class1
units real
boundary m m m
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
read_data nylon-class1.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data nylon-class1.data2

16
tools/msi2lmp/test/in.phen3_cff97-class1
View File

@ -1,16 +0,0 @@
log log.phen3_cff97-class1
boundary m m m
units real
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
read_data phen3_cff97-class1.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data phen3_cff97-class1.data2

13
tools/msi2lmp/test/in.water-class1
View File

@ -1,13 +0,0 @@
log log.water-class1
units real
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
angle_style harmonic
read_data water-class1.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data water-class1.data2

13
tools/msi2lmp/test/in.water-class2b
View File

@ -1,13 +0,0 @@
log log.water-class2b
units real
atom_style full
pair_style lj/class2/coul/cut 15.0
bond_style class2
angle_style class2
read_data water-class2b.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data water-class2b.data2

25
tools/msi2lmp/test/naphthalene-class1.car
View File

@ -1,25 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:43:30 2013
PBC 20.0000 20.0000 20.0000 90.0000 90.0000 90.0000 (P1)
H1 6.500000000 -9.500000000 -10.000000000 NAPH 1 h H 0.132
C2 7.599900000 -9.500000000 -10.000000000 NAPH 1 cp C -0.128
C3 8.288980000 -8.262840000 -10.000000000 NAPH 1 cp C -0.127
C4 9.661860000 -8.228710000 -10.001500000 NAPH 1 cp C -0.117
C5 10.406020000 -9.440000000 -10.006040000 NAPH 1 cp C -0.037
C6 9.719960000 -10.680950000 -10.004000000 NAPH 1 cp C -0.036
C7 8.297670000 -10.682850000 -10.001160000 NAPH 1 cp C -0.117
H8 7.705780000 -7.329930000 -9.996380000 NAPH 1 h H 0.131
H9 10.206130000 -7.272850000 -10.002830000 NAPH 1 h H 0.133
H10 7.770540000 -11.648530000 -10.000400000 NAPH 1 h H 0.132
C11 11.828680000 -9.441740000 -10.010130000 NAPH 1 cp C -0.119
C12 12.527620000 -10.622850000 -10.015250000 NAPH 1 cp C -0.127
C13 11.844840000 -11.863540000 -10.015940000 NAPH 1 cp C -0.127
C14 10.470950000 -11.888220000 -10.009030000 NAPH 1 cp C -0.118
H15 12.355170000 -8.475370000 -10.009670000 NAPH 1 h H 0.132
H16 13.627550000 -10.611020000 -10.018380000 NAPH 1 h H 0.131
H17 12.414260000 -12.804680000 -10.020060000 NAPH 1 h H 0.133
H18 9.938140000 -12.850570000 -10.009550000 NAPH 1 h H 0.131
end
end

46
tools/msi2lmp/test/naphthalene-class1.mdf
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@ -1,46 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:43:30 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule naphthalene
NAPH_1:H1 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C2
NAPH_1:C2 C cp 1 0 0 -0.1280 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5
NAPH_1:C3 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H8
NAPH_1:C4 C cp 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H9
NAPH_1:C5 C cp 1 0 0 -0.0370 0 0 8 1.0000 0.0000 C4/1.5 C6/1.5 C11/1.5
NAPH_1:C6 C cp 1 0 0 -0.0360 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 C14/1.5
NAPH_1:C7 C cp 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H10
NAPH_1:H8 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C3
NAPH_1:H9 H h 1 0 0 0.1330 0 0 8 1.0000 0.0000 C4
NAPH_1:H10 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C7
NAPH_1:C11 C cp 1 0 0 -0.1190 0 0 8 1.0000 0.0000 C5/1.5 C12/1.5 H15
NAPH_1:C12 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C11/1.5 C13/1.5 H16
NAPH_1:C13 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C12/1.5 C14/1.5 H17
NAPH_1:C14 C cp 1 0 0 -0.1180 0 0 8 1.0000 0.0000 C6/1.5 C13/1.5 H18
NAPH_1:H15 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C11
NAPH_1:H16 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C12
NAPH_1:H17 H h 1 0 0 0.1330 0 0 8 1.0000 0.0000 C13
NAPH_1:H18 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C14
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

25
tools/msi2lmp/test/naphthalene-class2a.car
View File

@ -1,25 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:43:30 2013
PBC 20.0000 20.0000 20.0000 90.0000 90.0000 90.0000 (P1)
H1 6.500000000 -9.500000000 -10.000000000 NAPH 1 h1 H 0.132
C2 7.599900000 -9.500000000 -10.000000000 NAPH 1 c3a C -0.128
C3 8.288980000 -8.262840000 -10.000000000 NAPH 1 c3a C -0.127
C4 9.661860000 -8.228710000 -10.001500000 NAPH 1 c3a C -0.117
C5 10.406020000 -9.440000000 -10.006040000 NAPH 1 c3a C -0.037
C6 9.719960000 -10.680950000 -10.004000000 NAPH 1 c3a C -0.036
C7 8.297670000 -10.682850000 -10.001160000 NAPH 1 c3a C -0.117
H8 7.705780000 -7.329930000 -9.996380000 NAPH 1 h1 H 0.131
H9 10.206130000 -7.272850000 -10.002830000 NAPH 1 h1 H 0.133
H10 7.770540000 -11.648530000 -10.000400000 NAPH 1 h1 H 0.132
C11 11.828680000 -9.441740000 -10.010130000 NAPH 1 c3a C -0.119
C12 12.527620000 -10.622850000 -10.015250000 NAPH 1 c3a C -0.127
C13 11.844840000 -11.863540000 -10.015940000 NAPH 1 c3a C -0.127
C14 10.470950000 -11.888220000 -10.009030000 NAPH 1 c3a C -0.118
H15 12.355170000 -8.475370000 -10.009670000 NAPH 1 h1 H 0.132
H16 13.627550000 -10.611020000 -10.018380000 NAPH 1 h1 H 0.131
H17 12.414260000 -12.804680000 -10.020060000 NAPH 1 h1 H 0.133
H18 9.938140000 -12.850570000 -10.009550000 NAPH 1 h1 H 0.131
end
end

46
tools/msi2lmp/test/naphthalene-class2a.mdf
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@ -1,46 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:43:30 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule naphthalene
NAPH_1:H1 H h1 1 0 0 0.1320 0 0 8 1.0000 0.0000 C2
NAPH_1:C2 C c3a 1 0 0 -0.1280 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5
NAPH_1:C3 C c3a 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H8
NAPH_1:C4 C c3a 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H9
NAPH_1:C5 C c3a 1 0 0 -0.0370 0 0 8 1.0000 0.0000 C4/1.5 C6/1.5 C11/1.5
NAPH_1:C6 C c3a 1 0 0 -0.0360 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 C14/1.5
NAPH_1:C7 C c3a 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H10
NAPH_1:H8 H h1 1 0 0 0.1310 0 0 8 1.0000 0.0000 C3
NAPH_1:H9 H h1 1 0 0 0.1330 0 0 8 1.0000 0.0000 C4
NAPH_1:H10 H h1 1 0 0 0.1320 0 0 8 1.0000 0.0000 C7
NAPH_1:C11 C c3a 1 0 0 -0.1190 0 0 8 1.0000 0.0000 C5/1.5 C12/1.5 H15
NAPH_1:C12 C c3a 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C11/1.5 C13/1.5 H16
NAPH_1:C13 C c3a 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C12/1.5 C14/1.5 H17
NAPH_1:C14 C c3a 1 0 0 -0.1180 0 0 8 1.0000 0.0000 C6/1.5 C13/1.5 H18
NAPH_1:H15 H h1 1 0 0 0.1320 0 0 8 1.0000 0.0000 C11
NAPH_1:H16 H h1 1 0 0 0.1310 0 0 8 1.0000 0.0000 C12
NAPH_1:H17 H h1 1 0 0 0.1330 0 0 8 1.0000 0.0000 C13
NAPH_1:H18 H h1 1 0 0 0.1310 0 0 8 1.0000 0.0000 C14
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

25
tools/msi2lmp/test/naphthalene-class2b.car
View File

@ -1,25 +0,0 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:43:30 2013
PBC 20.0000 20.0000 20.0000 90.0000 90.0000 90.0000 (P1)
H1 6.500000000 -9.500000000 -10.000000000 NAPH 1 h H 0.132
C2 7.599900000 -9.500000000 -10.000000000 NAPH 1 cp C -0.128
C3 8.288980000 -8.262840000 -10.000000000 NAPH 1 cp C -0.127
C4 9.661860000 -8.228710000 -10.001500000 NAPH 1 cp C -0.117
C5 10.406020000 -9.440000000 -10.006040000 NAPH 1 cp C -0.037
C6 9.719960000 -10.680950000 -10.004000000 NAPH 1 cp C -0.036
C7 8.297670000 -10.682850000 -10.001160000 NAPH 1 cp C -0.117
H8 7.705780000 -7.329930000 -9.996380000 NAPH 1 h H 0.131
H9 10.206130000 -7.272850000 -10.002830000 NAPH 1 h H 0.133
H10 7.770540000 -11.648530000 -10.000400000 NAPH 1 h H 0.132
C11 11.828680000 -9.441740000 -10.010130000 NAPH 1 cp C -0.119
C12 12.527620000 -10.622850000 -10.015250000 NAPH 1 cp C -0.127
C13 11.844840000 -11.863540000 -10.015940000 NAPH 1 cp C -0.127
C14 10.470950000 -11.888220000 -10.009030000 NAPH 1 cp C -0.118
H15 12.355170000 -8.475370000 -10.009670000 NAPH 1 h H 0.132
H16 13.627550000 -10.611020000 -10.018380000 NAPH 1 h H 0.131
H17 12.414260000 -12.804680000 -10.020060000 NAPH 1 h H 0.133
H18 9.938140000 -12.850570000 -10.009550000 NAPH 1 h H 0.131
end
end

46
tools/msi2lmp/test/naphthalene-class2b.mdf
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@ -1,46 +0,0 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:43:30 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule naphthalene
NAPH_1:H1 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C2
NAPH_1:C2 C cp 1 0 0 -0.1280 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5
NAPH_1:C3 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H8
NAPH_1:C4 C cp 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H9
NAPH_1:C5 C cp 1 0 0 -0.0370 0 0 8 1.0000 0.0000 C4/1.5 C6/1.5 C11/1.5
NAPH_1:C6 C cp 1 0 0 -0.0360 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 C14/1.5
NAPH_1:C7 C cp 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H10
NAPH_1:H8 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C3
NAPH_1:H9 H h 1 0 0 0.1330 0 0 8 1.0000 0.0000 C4
NAPH_1:H10 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C7
NAPH_1:C11 C cp 1 0 0 -0.1190 0 0 8 1.0000 0.0000 C5/1.5 C12/1.5 H15
NAPH_1:C12 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C11/1.5 C13/1.5 H16
NAPH_1:C13 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C12/1.5 C14/1.5 H17
NAPH_1:C14 C cp 1 0 0 -0.1180 0 0 8 1.0000 0.0000 C6/1.5 C13/1.5 H18
NAPH_1:H15 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C11
NAPH_1:H16 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C12
NAPH_1:H17 H h 1 0 0 0.1330 0 0 8 1.0000 0.0000 C13
NAPH_1:H18 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C14
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

124
tools/msi2lmp/test/nylon-class1.car
View File

@ -1,124 +0,0 @@
!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

142
tools/msi2lmp/test/nylon-class1.mdf
View File

@ -1,142 +0,0 @@
!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

29
tools/msi2lmp/test/phen3_cff97-class1.car
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@ -1,29 +0,0 @@
!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

57
tools/msi2lmp/test/phen3_cff97-class1.mdf
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@ -1,57 +0,0 @@
!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

1450
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data
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2728
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data2
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135
tools/msi2lmp/test/reference/benzene-class1.data
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@ -1,135 +0,0 @@
LAMMPS data file from msi2lmp v3.8 for benzene-class1
12 atoms
12 bonds
18 angles
24 dihedrals
6 impropers
2 atom types
2 bond types
2 angle types
3 dihedral types
1 improper types
-0.014180000 9.985820000 xlo xhi
-0.000000000 10.000000000 ylo yhi
-10.000000000 0.000000000 zlo zhi
Masses
1 1.007970
2 12.011150
Pair Coeffs
1 0.0380000011 2.4499714540
2 0.1479999981 3.6170487995
Bond Coeffs
1 363.4164 1.0800
2 480.0000 1.3400
Angle Coeffs
1 37.0000 120.0000
2 90.0000 120.0000
Dihedral Coeffs
1 3.0000 -1 2
2 3.0000 -1 2
3 3.0000 -1 2
Improper Coeffs
1 0.3700 -1 2
Atoms
1 1 1 0.102000 2.500000000 5.000000000 -5.000000000
2 1 2 -0.102000 3.594720000 5.000000000 -5.000000000
3 1 2 -0.102000 4.290270000 6.204730000 -5.000000000
4 1 2 -0.102000 5.681370000 6.204730000 -5.000000000
5 1 2 -0.102000 6.376920000 5.000000000 -5.000000000
6 1 2 -0.102000 5.681370000 3.795270000 -5.000000000
7 1 2 -0.102000 4.290270000 3.795270000 -5.000000000
8 1 1 0.102000 7.471640000 5.000000000 -5.000000000
9 1 1 0.102000 3.742910000 7.152785000 -5.000000000
10 1 1 0.102000 6.228730000 7.152785000 -5.000000000
11 1 1 0.102000 6.228730000 2.847215000 -5.000000000
12 1 1 0.102000 3.742910000 2.847215000 -5.000000000
Bonds
1 1 1 2
2 2 2 3
3 2 2 7
4 2 3 4
5 1 9 3
6 2 4 5
7 1 10 4
8 1 8 5
9 2 5 6
10 2 6 7
11 1 11 6
12 1 12 7
Angles
1 1 1 2 3
2 1 1 2 7
3 2 3 2 7
4 2 2 3 4
5 1 9 3 2
6 1 9 3 4
7 2 3 4 5
8 1 10 4 3
9 1 10 4 5
10 1 8 5 4
11 2 4 5 6
12 1 8 5 6
13 2 5 6 7
14 1 11 6 5
15 1 11 6 7
16 2 2 7 6
17 1 12 7 2
18 1 12 7 6
Dihedrals
1 1 1 2 3 4
2 2 1 2 3 9
3 3 7 2 3 4
4 1 9 3 2 7
5 1 1 2 7 6
6 2 1 2 7 12
7 3 3 2 7 6
8 1 12 7 2 3
9 3 2 3 4 5
10 1 10 4 3 2
11 1 9 3 4 5
12 2 9 3 4 10
13 1 8 5 4 3
14 3 3 4 5 6
15 2 10 4 5 8
16 1 10 4 5 6
17 3 4 5 6 7
18 1 11 6 5 4
19 1 8 5 6 7
20 2 8 5 6 11
21 3 5 6 7 2
22 1 12 7 6 5
23 1 11 6 7 2
24 2 11 6 7 12
Impropers
1 1 1 2 3 7
2 1 9 3 4 2
3 1 10 4 5 3
4 1 8 5 4 6
5 1 11 6 7 5
6 1 12 7 6 2

148
tools/msi2lmp/test/reference/benzene-class1.data2
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@ -1,148 +0,0 @@
LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 13
12 atoms
2 atom types
12 bonds
2 bond types
18 angles
2 angle types
24 dihedrals
3 dihedral types
6 impropers
1 improper types
-1.4180000000000000e-02 9.9858200000000004e+00 xlo xhi
-0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi
-1.0000000000000000e+01 0.0000000000000000e+00 zlo zhi
Masses
1 1.00797
2 12.0112
Pair Coeffs
1 0.038 2.44997
2 0.148 3.61705
Bond Coeffs
1 363.416 1.08
2 480 1.34
Angle Coeffs
1 37 120
2 90 120
Dihedral Coeffs
1 3 -1 2
2 3 -1 2
3 3 -1 2
Improper Coeffs
1 0.37 -1 2
Atoms
1 1 1 1.0199999999999999e-01 2.5322412470592841e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0
2 1 2 -1.0199999999999999e-01 3.6267757821623108e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0
3 1 2 -1.0199999999999999e-01 4.3062979260545999e+00 6.1769792165387623e+00 -5.0000000000000000e+00 0 0 0
4 1 2 -1.0199999999999999e-01 5.6653420739454008e+00 6.1769792165387623e+00 -5.0000000000000000e+00 0 0 0
5 1 2 -1.0199999999999999e-01 6.3448642178376886e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0
6 1 2 -1.0199999999999999e-01 5.6653420739454008e+00 3.8230207834612400e+00 -5.0000000000000000e+00 0 0 0
7 1 2 -1.0199999999999999e-01 4.3062979260545999e+00 3.8230207834612400e+00 -5.0000000000000000e+00 0 0 0
8 1 1 1.0199999999999999e-01 7.4393987529407148e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0
9 1 1 1.0199999999999999e-01 3.7590103673565944e+00 7.1249089055380379e+00 -5.0000000000000000e+00 0 0 0
10 1 1 1.0199999999999999e-01 6.2126296326434041e+00 7.1249089055380379e+00 -5.0000000000000000e+00 0 0 0
11 1 1 1.0199999999999999e-01 6.2126296326434041e+00 2.8750910944619621e+00 -5.0000000000000000e+00 0 0 0
12 1 1 1.0199999999999999e-01 3.7590103673565944e+00 2.8750910944619625e+00 -5.0000000000000000e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 2 2 3
3 2 2 7
4 2 3 4
5 2 4 5
6 2 5 6
7 2 6 7
8 1 8 5
9 1 9 3
10 1 10 4
11 1 11 6
12 1 12 7
Angles
1 1 1 2 3
2 1 1 2 7
3 2 3 2 7
4 2 2 3 4
5 1 9 3 2
6 1 9 3 4
7 2 3 4 5
8 1 10 4 3
9 1 10 4 5
10 1 8 5 4
11 2 4 5 6
12 1 8 5 6
13 2 5 6 7
14 1 11 6 5
15 1 11 6 7
16 2 2 7 6
17 1 12 7 2
18 1 12 7 6
Dihedrals
1 1 1 2 3 4
2 2 1 2 3 9
3 3 7 2 3 4
4 1 1 2 7 6
5 2 1 2 7 12
6 3 3 2 7 6
7 1 9 3 2 7
8 3 2 3 4 5
9 1 9 3 4 5
10 2 9 3 4 10
11 1 10 4 3 2
12 3 3 4 5 6
13 2 10 4 5 8
14 1 10 4 5 6
15 1 8 5 4 3
16 3 4 5 6 7
17 1 8 5 6 7
18 2 8 5 6 11
19 1 11 6 5 4
20 3 5 6 7 2
21 1 11 6 7 2
22 2 11 6 7 12
23 1 12 7 2 3
24 1 12 7 6 5
Impropers
1 1 1 2 3 7
2 1 9 3 4 2
3 1 10 4 5 3
4 1 8 5 4 6
5 1 11 6 7 5
6 1 12 7 6 2

135
tools/msi2lmp/test/reference/benzene-class1.data3
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@ -1,135 +0,0 @@
LAMMPS data file from msi2lmp v3.8 for benzene-class1
12 atoms
12 bonds
18 angles
24 dihedrals
6 impropers
2 atom types
2 bond types
2 angle types
3 dihedral types
1 improper types
-0.014180000 9.985820000 xlo xhi
-0.000000000 10.000000000 ylo yhi
-10.000000000 0.000000000 zlo zhi
Masses
1 1.007970
2 12.011150
Pair Coeffs
1 0.0380000011 2.4499714540
2 0.1479999981 3.6170487995
Bond Coeffs
1 363.4164 1.0800
2 480.0000 1.3400
Angle Coeffs
1 37.0000 120.0000
2 90.0000 120.0000
Dihedral Coeffs
1 3.0000 -1 2
2 3.0000 -1 2
3 3.0000 -1 2
Improper Coeffs
1 0.3700 -1 2
Atoms
1 1 1 0.102000 2.500000000 5.000000000 -5.000000000
2 1 2 -0.102000 3.594720000 5.000000000 -5.000000000
3 1 2 -0.102000 4.290270000 6.204730000 -5.000000000
4 1 2 -0.102000 5.681370000 6.204730000 -5.000000000
5 1 2 -0.102000 6.376920000 5.000000000 -5.000000000
6 1 2 -0.102000 5.681370000 3.795270000 -5.000000000
7 1 2 -0.102000 4.290270000 3.795270000 -5.000000000
8 1 1 0.102000 7.471640000 5.000000000 -5.000000000
9 1 1 0.102000 3.742910000 7.152785000 -5.000000000
10 1 1 0.102000 6.228730000 7.152785000 -5.000000000
11 1 1 0.102000 6.228730000 2.847215000 -5.000000000
12 1 1 0.102000 3.742910000 2.847215000 -5.000000000
Bonds
1 1 1 2
2 2 2 3
3 2 2 7
4 2 3 4
5 1 9 3
6 2 4 5
7 1 10 4
8 1 8 5
9 2 5 6
10 2 6 7
11 1 11 6
12 1 12 7
Angles
1 1 1 2 3
2 1 1 2 7
3 2 3 2 7
4 2 2 3 4
5 1 9 3 2
6 1 9 3 4
7 2 3 4 5
8 1 10 4 3
9 1 10 4 5
10 1 8 5 4
11 2 4 5 6
12 1 8 5 6
13 2 5 6 7
14 1 11 6 5
15 1 11 6 7
16 2 2 7 6
17 1 12 7 2
18 1 12 7 6
Dihedrals
1 1 1 2 3 4
2 2 1 2 3 9
3 3 7 2 3 4
4 1 9 3 2 7
5 1 1 2 7 6
6 2 1 2 7 12
7 3 3 2 7 6
8 1 12 7 2 3
9 3 2 3 4 5
10 1 10 4 3 2
11 1 9 3 4 5
12 2 9 3 4 10
13 1 8 5 4 3
14 3 3 4 5 6
15 2 10 4 5 8
16 1 10 4 5 6
17 3 4 5 6 7
18 1 11 6 5 4
19 1 8 5 6 7
20 2 8 5 6 11
21 3 5 6 7 2
22 1 12 7 6 5
23 1 11 6 7 2
24 2 11 6 7 12
Impropers
1 1 1 2 3 7
2 1 9 3 4 2
3 1 10 4 5 3
4 1 8 5 4 6
5 1 11 6 7 5
6 1 12 7 6 2

179
tools/msi2lmp/test/reference/benzene-class2a.data
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@ -1,179 +0,0 @@
LAMMPS data file from msi2lmp v3.8 for benzene-class2
12 atoms
12 bonds
18 angles
24 dihedrals
6 impropers
2 atom types
2 bond types
2 angle types
3 dihedral types
1 improper types
-0.014180000 9.985820000 xlo xhi
-0.000000000 10.000000000 ylo yhi
-10.000000000 0.000000000 zlo zhi
Masses
1 1.007970
2 12.011150
Pair Coeffs
1 0.0230000000 2.8780000000
2 0.0680000000 3.9150000000
Bond Coeffs
1 1.0982 372.8251 -803.4526 894.3173
2 1.4170 470.8361 -627.6179 1327.6345
Angle Coeffs
1 117.9400 35.1558 -12.4682 0.0000
2 118.9000 61.0226 -34.9931 0.0000
Dihedral Coeffs
1 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000
2 0.0000 0.0000 2.3500 0.0000 0.0000 0.0000
3 8.3667 0.0000 1.2000 0.0000 0.0000 0.0000
Improper Coeffs
1 4.8912 0.0000
BondBond Coeffs
1 1.0795 1.0982 1.4170
2 68.2856 1.4170 1.4170
BondAngle Coeffs
1 24.2183 20.0033 1.0982 1.4170
2 28.8708 28.8708 1.4170 1.4170
AngleAngle Coeffs
1 0.0000 0.0000 0.0000 117.9400 118.9000 117.9400
AngleAngleTorsion Coeffs
1 -4.8141 117.9400 118.9000
2 0.3598 117.9400 117.9400
3 0.0000 118.9000 118.9000
EndBondTorsion Coeffs
1 0.0000 -0.4669 0.0000 0.0000 -6.8958 0.0000 1.0982 1.4170
2 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982
3 -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170
MiddleBondTorsion Coeffs
1 0.0000 -1.1521 0.0000 1.4170
2 0.0000 4.8228 0.0000 1.4170
3 27.5989 -2.3120 0.0000 1.4170
BondBond13 Coeffs
1 0.0000 1.0982 1.4170
2 0.0000 1.0982 1.0982
3 0.0000 1.4170 1.4170
AngleTorsion Coeffs
1 0.0000 2.7147 0.0000 0.0000 2.5014 0.0000 117.9400 118.9000
2 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400
3 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000
Atoms
1 1 1 0.102000 2.500000000 5.000000000 -5.000000000
2 1 2 -0.102000 3.594720000 5.000000000 -5.000000000
3 1 2 -0.102000 4.290270000 6.204730000 -5.000000000
4 1 2 -0.102000 5.681370000 6.204730000 -5.000000000
5 1 2 -0.102000 6.376920000 5.000000000 -5.000000000
6 1 2 -0.102000 5.681370000 3.795270000 -5.000000000
7 1 2 -0.102000 4.290270000 3.795270000 -5.000000000
8 1 1 0.102000 7.471640000 5.000000000 -5.000000000
9 1 1 0.102000 3.742910000 7.152785000 -5.000000000
10 1 1 0.102000 6.228730000 7.152785000 -5.000000000
11 1 1 0.102000 6.228730000 2.847215000 -5.000000000
12 1 1 0.102000 3.742910000 2.847215000 -5.000000000
Bonds
1 1 1 2
2 2 2 3
3 2 2 7
4 2 3 4
5 1 9 3
6 2 4 5
7 1 10 4
8 1 8 5
9 2 5 6
10 2 6 7
11 1 11 6
12 1 12 7
Angles
1 1 1 2 3
2 1 1 2 7
3 2 3 2 7
4 2 2 3 4
5 1 9 3 2
6 1 9 3 4
7 2 3 4 5
8 1 10 4 3
9 1 10 4 5
10 1 8 5 4
11 2 4 5 6
12 1 8 5 6
13 2 5 6 7
14 1 11 6 5
15 1 11 6 7
16 2 2 7 6
17 1 12 7 2
18 1 12 7 6
Dihedrals
1 1 1 2 3 4
2 2 1 2 3 9
3 3 7 2 3 4
4 1 9 3 2 7
5 1 1 2 7 6
6 2 1 2 7 12
7 3 3 2 7 6
8 1 12 7 2 3
9 3 2 3 4 5
10 1 10 4 3 2
11 1 9 3 4 5
12 2 9 3 4 10
13 1 8 5 4 3
14 3 3 4 5 6
15 2 10 4 5 8
16 1 10 4 5 6
17 3 4 5 6 7
18 1 11 6 5 4
19 1 8 5 6 7
20 2 8 5 6 11
21 3 5 6 7 2
22 1 12 7 6 5
23 1 11 6 7 2
24 2 11 6 7 12
Impropers
1 1 1 2 3 7
2 1 9 3 4 2
3 1 10 4 5 3
4 1 8 5 4 6
5 1 11 6 7 5
6 1 12 7 6 2

192
tools/msi2lmp/test/reference/benzene-class2a.data2
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@ -1,192 +0,0 @@
LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 11
12 atoms
2 atom types
12 bonds
2 bond types
18 angles
2 angle types
24 dihedrals
3 dihedral types
6 impropers
1 improper types
-1.4180000000000000e-02 9.9858200000000004e+00 xlo xhi
-0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi
-1.0000000000000000e+01 0.0000000000000000e+00 zlo zhi
Masses
1 1.00797
2 12.0112
Pair Coeffs
1 0.023 2.878
2 0.068 3.915
Bond Coeffs
1 1.0982 372.825 -803.453 894.317
2 1.417 470.836 -627.618 1327.63
Angle Coeffs
1 117.94 35.1558 -12.4682 0
2 118.9 61.0226 -34.9931 0
BondBond Coeffs
1 1.0795 1.0982 1.417
2 68.2856 1.417 1.417
BondAngle Coeffs
1 24.2183 20.0033 1.0982 1.417
2 28.8708 28.8708 1.417 1.417
Dihedral Coeffs
1 0 0 3.9661 0 0 0
2 0 0 2.35 0 0 0
3 8.3667 0 1.2 0 0 0
AngleAngleTorsion Coeffs
1 -4.8141 117.94 118.9
2 0.3598 117.94 117.94
3 0 118.9 118.9
EndBondTorsion Coeffs
1 0 -0.4669 0 0 -6.8958 0 1.0982 1.417
2 0 -0.689 0 0 -0.689 0 1.0982 1.0982
3 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417
MiddleBondTorsion Coeffs
1 0 -1.1521 0 1.417
2 0 4.8228 0 1.417
3 27.5989 -2.312 0 1.417
BondBond13 Coeffs
1 0 1.0982 1.417
2 0 1.0982 1.0982
3 0 1.417 1.417
AngleTorsion Coeffs
1 0 2.7147 0 0 2.5014 0 117.94 118.9
2 0 2.4501 0 0 2.4501 0 117.94 117.94
3 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9
Improper Coeffs
1 4.8912 0
AngleAngle Coeffs
1 0 0 0 117.94 118.9 117.94
Atoms
1 1 1 1.0199999999999999e-01 2.4952054314002501e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0
2 1 2 -1.0199999999999999e-01 3.5945091269535197e+00 5.0000000000000009e+00 -5.0000000000000000e+00 0 0 0
3 1 2 -1.0199999999999999e-01 4.2901451050500334e+00 6.2049812477418866e+00 -5.0000000000000000e+00 0 0 0
4 1 2 -1.0199999999999999e-01 5.6814948949499664e+00 6.2049812477418858e+00 -5.0000000000000000e+00 0 0 0
5 1 2 -1.0199999999999999e-01 6.3771308730464789e+00 5.0000000000000018e+00 -5.0000000000000000e+00 0 0 0
6 1 2 -1.0199999999999999e-01 5.6814948949499628e+00 3.7950187522581120e+00 -5.0000000000000000e+00 0 0 0
7 1 2 -1.0199999999999999e-01 4.2901451050500370e+00 3.7950187522581116e+00 -5.0000000000000000e+00 0 0 0
8 1 1 1.0199999999999999e-01 7.4764345685997498e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0
9 1 1 1.0199999999999999e-01 3.7404633343978420e+00 7.1570474148571899e+00 -5.0000000000000000e+00 0 0 0
10 1 1 1.0199999999999999e-01 6.2311766656021588e+00 7.1570474148571908e+00 -5.0000000000000000e+00 0 0 0
11 1 1 1.0199999999999999e-01 6.2311766656021579e+00 2.8429525851428088e+00 -5.0000000000000000e+00 0 0 0
12 1 1 1.0199999999999999e-01 3.7404633343978411e+00 2.8429525851428092e+00 -5.0000000000000000e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 2 2 3
3 2 2 7
4 2 3 4
5 2 4 5
6 2 5 6
7 2 6 7
8 1 8 5
9 1 9 3
10 1 10 4
11 1 11 6
12 1 12 7
Angles
1 1 1 2 3
2 1 1 2 7
3 2 3 2 7
4 2 2 3 4
5 1 9 3 2
6 1 9 3 4
7 2 3 4 5
8 1 10 4 3
9 1 10 4 5
10 1 8 5 4
11 2 4 5 6
12 1 8 5 6
13 2 5 6 7
14 1 11 6 5
15 1 11 6 7
16 2 2 7 6
17 1 12 7 2
18 1 12 7 6
Dihedrals
1 1 1 2 3 4
2 2 1 2 3 9
3 3 7 2 3 4
4 1 1 2 7 6
5 2 1 2 7 12
6 3 3 2 7 6
7 1 9 3 2 7
8 3 2 3 4 5
9 1 9 3 4 5
10 2 9 3 4 10
11 1 10 4 3 2
12 3 3 4 5 6
13 2 10 4 5 8
14 1 10 4 5 6
15 1 8 5 4 3
16 3 4 5 6 7
17 1 8 5 6 7
18 2 8 5 6 11
19 1 11 6 5 4
20 3 5 6 7 2
21 1 11 6 7 2
22 2 11 6 7 12
23 1 12 7 2 3
24 1 12 7 6 5
Impropers
1 1 1 2 3 7
2 1 9 3 4 2
3 1 10 4 5 3
4 1 8 5 4 6
5 1 11 6 7 5
6 1 12 7 6 2

179
tools/msi2lmp/test/reference/benzene-class2b.data
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@ -1,179 +0,0 @@
LAMMPS data file from msi2lmp v3.8 for benzene-class2b
12 atoms
12 bonds
18 angles
24 dihedrals
6 impropers
2 atom types
2 bond types
2 angle types
3 dihedral types
1 improper types
-0.014180000 9.985820000 xlo xhi
-0.000000000 10.000000000 ylo yhi
-10.000000000 0.000000000 zlo zhi
Masses
1 1.007970
2 12.011150
Pair Coeffs
1 0.0200000000 2.9950000000
2 0.0640000000 4.0100000000
Bond Coeffs
1 1.0982 372.8251 -803.4526 894.3173
2 1.4170 470.8361 -627.6179 1327.6345
Angle Coeffs
1 117.9400 35.1558 -12.4682 0.0000
2 118.9000 61.0226 -34.9931 0.0000
Dihedral Coeffs
1 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000
2 0.0000 0.0000 1.8769 0.0000 0.0000 0.0000
3 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000
Improper Coeffs
1 4.8912 0.0000
BondBond Coeffs
1 1.0795 1.0982 1.4170
2 68.2856 1.4170 1.4170
BondAngle Coeffs
1 24.2183 20.0033 1.0982 1.4170
2 28.8708 28.8708 1.4170 1.4170
AngleAngle Coeffs
1 0.0000 0.0000 0.0000 117.9400 118.9000 117.9400
AngleAngleTorsion Coeffs
1 -4.8141 117.9400 118.9000
2 0.3598 117.9400 117.9400
3 0.0000 118.9000 118.9000
EndBondTorsion Coeffs
1 0.0000 -0.4669 0.0000 0.0000 -6.8958 0.0000 1.0982 1.4170
2 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982
3 -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170
MiddleBondTorsion Coeffs
1 0.0000 -1.1521 0.0000 1.4170
2 0.0000 4.8228 0.0000 1.4170
3 27.5989 -2.3120 0.0000 1.4170
BondBond13 Coeffs
1 -6.2741 1.0982 1.4170
2 -1.7077 1.0982 1.0982
3 53.0000 1.4170 1.4170
AngleTorsion Coeffs
1 0.0000 2.7147 0.0000 0.0000 2.5014 0.0000 117.9400 118.9000
2 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400
3 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000
Atoms
1 1 1 0.102000 2.500000000 5.000000000 -5.000000000
2 1 2 -0.102000 3.594720000 5.000000000 -5.000000000
3 1 2 -0.102000 4.290270000 6.204730000 -5.000000000
4 1 2 -0.102000 5.681370000 6.204730000 -5.000000000
5 1 2 -0.102000 6.376920000 5.000000000 -5.000000000
6 1 2 -0.102000 5.681370000 3.795270000 -5.000000000
7 1 2 -0.102000 4.290270000 3.795270000 -5.000000000
8 1 1 0.102000 7.471640000 5.000000000 -5.000000000
9 1 1 0.102000 3.742910000 7.152785000 -5.000000000
10 1 1 0.102000 6.228730000 7.152785000 -5.000000000
11 1 1 0.102000 6.228730000 2.847215000 -5.000000000
12 1 1 0.102000 3.742910000 2.847215000 -5.000000000
Bonds
1 1 1 2
2 2 2 3
3 2 2 7
4 2 3 4
5 1 9 3
6 2 4 5
7 1 10 4
8 1 8 5
9 2 5 6
10 2 6 7
11 1 11 6
12 1 12 7
Angles
1 1 1 2 3
2 1 1 2 7
3 2 3 2 7
4 2 2 3 4
5 1 9 3 2
6 1 9 3 4
7 2 3 4 5
8 1 10 4 3
9 1 10 4 5
10 1 8 5 4
11 2 4 5 6
12 1 8 5 6
13 2 5 6 7
14 1 11 6 5
15 1 11 6 7
16 2 2 7 6
17 1 12 7 2
18 1 12 7 6
Dihedrals
1 1 1 2 3 4
2 2 1 2 3 9
3 3 7 2 3 4
4 1 9 3 2 7
5 1 1 2 7 6
6 2 1 2 7 12
7 3 3 2 7 6
8 1 12 7 2 3
9 3 2 3 4 5
10 1 10 4 3 2
11 1 9 3 4 5
12 2 9 3 4 10
13 1 8 5 4 3
14 3 3 4 5 6
15 2 10 4 5 8
16 1 10 4 5 6
17 3 4 5 6 7
18 1 11 6 5 4
19 1 8 5 6 7
20 2 8 5 6 11
21 3 5 6 7 2
22 1 12 7 6 5
23 1 11 6 7 2
24 2 11 6 7 12
Impropers
1 1 1 2 3 7
2 1 9 3 4 2
3 1 10 4 5 3
4 1 8 5 4 6
5 1 11 6 7 5
6 1 12 7 6 2

192
tools/msi2lmp/test/reference/benzene-class2b.data2
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@ -1,192 +0,0 @@
LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 13
12 atoms
2 atom types
12 bonds
2 bond types
18 angles
2 angle types
24 dihedrals
3 dihedral types
6 impropers
1 improper types
-1.4180000000000000e-02 9.9858200000000004e+00 xlo xhi
-0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi
-1.0000000000000000e+01 0.0000000000000000e+00 zlo zhi
Masses
1 1.00797
2 12.0112
Pair Coeffs
1 0.02 2.995
2 0.064 4.01
Bond Coeffs
1 1.0982 372.825 -803.453 894.317
2 1.417 470.836 -627.618 1327.63
Angle Coeffs
1 117.94 35.1558 -12.4682 0
2 118.9 61.0226 -34.9931 0
BondBond Coeffs
1 1.0795 1.0982 1.417
2 68.2856 1.417 1.417
BondAngle Coeffs
1 24.2183 20.0033 1.0982 1.417
2 28.8708 28.8708 1.417 1.417
Dihedral Coeffs
1 0 0 3.9661 0 0 0
2 0 0 1.8769 0 0 0
3 8.3667 0 1.1932 0 0 0
AngleAngleTorsion Coeffs
1 -4.8141 117.94 118.9
2 0.3598 117.94 117.94
3 0 118.9 118.9
EndBondTorsion Coeffs
1 0 -0.4669 0 0 -6.8958 0 1.0982 1.417
2 0 -0.689 0 0 -0.689 0 1.0982 1.0982
3 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417
MiddleBondTorsion Coeffs
1 0 -1.1521 0 1.417
2 0 4.8228 0 1.417
3 27.5989 -2.312 0 1.417
BondBond13 Coeffs
1 -6.2741 1.0982 1.417
2 -1.7077 1.0982 1.0982
3 53 1.417 1.417
AngleTorsion Coeffs
1 0 2.7147 0 0 2.5014 0 117.94 118.9
2 0 2.4501 0 0 2.4501 0 117.94 117.94
3 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9
Improper Coeffs
1 4.8912 0
AngleAngle Coeffs
1 0 0 0 117.94 118.9 117.94
Atoms
1 1 1 1.0199999999999999e-01 2.4934740594722666e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0
2 1 2 -1.0199999999999999e-01 3.5923803339560756e+00 4.9999999999999982e+00 -5.0000000000000000e+00 0 0 0
3 1 2 -1.0199999999999999e-01 4.2890818316483230e+00 6.2068241003441083e+00 -5.0000000000000000e+00 0 0 0
4 1 2 -1.0199999999999999e-01 5.6825581683516759e+00 6.2068241003441074e+00 -5.0000000000000000e+00 0 0 0
5 1 2 -1.0199999999999999e-01 6.3792596660439251e+00 4.9999999999999982e+00 -5.0000000000000000e+00 0 0 0
6 1 2 -1.0199999999999999e-01 5.6825581683516804e+00 3.7931758996558931e+00 -5.0000000000000000e+00 0 0 0
7 1 2 -1.0199999999999999e-01 4.2890818316483195e+00 3.7931758996558931e+00 -5.0000000000000000e+00 0 0 0
8 1 1 1.0199999999999999e-01 7.4781659405277336e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0
9 1 1 1.0199999999999999e-01 3.7395991894266301e+00 7.1585464568095123e+00 -5.0000000000000000e+00 0 0 0
10 1 1 1.0199999999999999e-01 6.2320408105733698e+00 7.1585464568095132e+00 -5.0000000000000000e+00 0 0 0
11 1 1 1.0199999999999999e-01 6.2320408105733698e+00 2.8414535431904864e+00 -5.0000000000000000e+00 0 0 0
12 1 1 1.0199999999999999e-01 3.7395991894266305e+00 2.8414535431904868e+00 -5.0000000000000000e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 2 2 3
3 2 2 7
4 2 3 4
5 2 4 5
6 2 5 6
7 2 6 7
8 1 8 5
9 1 9 3
10 1 10 4
11 1 11 6
12 1 12 7
Angles
1 1 1 2 3
2 1 1 2 7
3 2 3 2 7
4 2 2 3 4
5 1 9 3 2
6 1 9 3 4
7 2 3 4 5
8 1 10 4 3
9 1 10 4 5
10 1 8 5 4
11 2 4 5 6
12 1 8 5 6
13 2 5 6 7
14 1 11 6 5
15 1 11 6 7
16 2 2 7 6
17 1 12 7 2
18 1 12 7 6
Dihedrals
1 1 1 2 3 4
2 2 1 2 3 9
3 3 7 2 3 4
4 1 1 2 7 6
5 2 1 2 7 12
6 3 3 2 7 6
7 1 9 3 2 7
8 3 2 3 4 5
9 1 9 3 4 5
10 2 9 3 4 10
11 1 10 4 3 2
12 3 3 4 5 6
13 2 10 4 5 8
14 1 10 4 5 6
15 1 8 5 4 3
16 3 4 5 6 7
17 1 8 5 6 7
18 2 8 5 6 11
19 1 11 6 5 4
20 3 5 6 7 2
21 1 11 6 7 2
22 2 11 6 7 12
23 1 12 7 2 3
24 1 12 7 6 5
Impropers
1 1 1 2 3 7
2 1 9 3 4 2
3 1 10 4 5 3
4 1 8 5 4 6
5 1 11 6 7 5
6 1 12 7 6 2

4727
tools/msi2lmp/test/reference/crambin-class1.data
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File diff suppressed because it is too large Load Diff

5370
tools/msi2lmp/test/reference/crambin-class1.data2
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File diff suppressed because it is too large Load Diff

89
tools/msi2lmp/test/reference/ethane-class1.data
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@ -1,89 +0,0 @@
LAMMPS data file from msi2lmp v3.8 for ethane-class1
8 atoms
7 bonds
12 angles
9 dihedrals
0 impropers
2 atom types
2 bond types
2 angle types
1 dihedral types
0.214545000 10.214545000 xlo xhi
0.114180000 10.114180000 ylo yhi
-10.000145000 -0.000145000 zlo zhi
Masses
1 12.011150
2 1.007970
Pair Coeffs
1 0.1599999990 3.4745050026
2 0.0380000011 2.4499714540
Bond Coeffs
1 322.7158 1.5260
2 340.6175 1.1050
Angle Coeffs
1 44.4000 110.0000
2 39.5000 106.4000
Dihedral Coeffs
1 0.1581 1 3
Atoms
1 1 1 -0.080000 4.462910000 5.148330000 -5.000410000
2 1 1 -0.080000 5.965490000 5.079930000 -4.999750000
3 1 2 0.027000 4.099550000 6.054480000 -5.502500000
4 1 2 0.027000 4.020330000 4.288350000 -5.519840000
5 1 2 0.027000 4.057610000 5.156680000 -3.980190000
6 1 2 0.027000 6.409980000 5.944880000 -4.490510000
7 1 2 0.027000 6.329880000 4.179410000 -4.488110000
8 1 2 0.027000 6.370610000 5.061380000 -6.019850000
Bonds
1 1 1 2
2 2 1 3
3 2 1 4
4 2 1 5
5 2 2 6
6 2 2 7
7 2 2 8
Angles
1 1 2 1 3
2 1 2 1 4
3 1 2 1 5
4 2 3 1 4
5 2 3 1 5
6 2 4 1 5
7 1 1 2 6
8 1 1 2 7
9 1 1 2 8
10 2 6 2 7
11 2 6 2 8
12 2 7 2 8
Dihedrals
1 1 3 1 2 6
2 1 3 1 2 7
3 1 3 1 2 8
4 1 4 1 2 6
5 1 4 1 2 7
6 1 4 1 2 8
7 1 5 1 2 6
8 1 5 1 2 7
9 1 5 1 2 8

97
tools/msi2lmp/test/reference/ethane-class1.data2
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@ -1,97 +0,0 @@
LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 25
8 atoms
2 atom types
7 bonds
2 bond types
12 angles
2 angle types
9 dihedrals
1 dihedral types
2.1454500000000001e-01 1.0214544999999999e+01 xlo xhi
1.1418000000000000e-01 1.0114179999999999e+01 ylo yhi
-1.0000145000000000e+01 -1.4500000000000000e-04 zlo zhi
Masses
1 12.0112
2 1.00797
Pair Coeffs
1 0.16 3.47451
2 0.038 2.44997
Bond Coeffs
1 322.716 1.526
2 340.618 1.105
Angle Coeffs
1 44.4 110
2 39.5 106.4
Dihedral Coeffs
1 0.1581 1 3
Atoms
1 1 1 -8.0000000000000002e-02 4.4522764990937773e+00 5.1487511046615282e+00 -5.0006449916203035e+00 0 0 0
2 1 1 -8.0000000000000002e-02 5.9768273805528676e+00 5.0795969349105308e+00 -4.9996784038318287e+00 0 0 0
3 1 2 2.7000000000000000e-02 4.0937152091648477e+00 6.0615200249591963e+00 -5.5098793516651270e+00 0 0 0
4 1 2 2.7000000000000000e-02 4.0127917543504497e+00 4.2791840939081052e+00 -5.5219544098688100e+00 0 0 0
5 1 2 2.7000000000000000e-02 4.0519012676248316e+00 5.1599472846238843e+00 -3.9708004333084199e+00 0 0 0
6 1 2 2.7000000000000000e-02 6.4162840127964751e+00 5.9516990352467829e+00 -4.4826061356609284e+00 0 0 0
7 1 2 2.7000000000000000e-02 6.3354866010086379e+00 4.1693216707285279e+00 -4.4860915956817538e+00 0 0 0
8 1 2 2.7000000000000000e-02 6.3770772754081166e+00 5.0634198509614441e+00 -6.0295046783628319e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 2 1 3
3 2 1 4
4 2 1 5
5 2 2 6
6 2 2 7
7 2 2 8
Angles
1 1 2 1 3
2 1 2 1 4
3 1 2 1 5
4 2 3 1 4
5 2 3 1 5
6 2 4 1 5
7 1 1 2 6
8 1 1 2 7
9 1 1 2 8
10 2 6 2 7
11 2 6 2 8
12 2 7 2 8
Dihedrals
1 1 3 1 2 6
2 1 3 1 2 7
3 1 3 1 2 8
4 1 4 1 2 6
5 1 4 1 2 7
6 1 4 1 2 8
7 1 5 1 2 6
8 1 5 1 2 7
9 1 5 1 2 8

141
tools/msi2lmp/test/reference/ethane-class2a.data
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@ -1,141 +0,0 @@
LAMMPS data file from msi2lmp v3.8 for ethane-class2a
8 atoms
7 bonds
12 angles
9 dihedrals
8 impropers
2 atom types
2 bond types
2 angle types
1 dihedral types
2 improper types
0.214545000 10.214545000 xlo xhi
0.114180000 10.114180000 ylo yhi
-10.000145000 -0.000145000 zlo zhi
Masses
1 12.011150
2 1.007970
Pair Coeffs
1 0.0620000000 3.8540000000
2 0.0230000000 2.8780000000
Bond Coeffs
1 1.5300 299.6700 -501.7700 679.8100
2 1.1010 345.0000 -691.8900 844.6000
Angle Coeffs
1 110.7700 41.4530 -10.6040 5.1290
2 107.6600 39.6410 -12.9210 -2.4318
Dihedral Coeffs
1 -0.1432 0.0000 0.0617 0.0000 -0.1530 0.0000
Improper Coeffs
1 0.0000 0.0000
2 0.0000 0.0000
BondBond Coeffs
1 3.3872 1.5300 1.1010
2 5.3316 1.1010 1.1010
BondAngle Coeffs
1 20.7540 11.4210 1.5300 1.1010
2 18.1030 18.1030 1.1010 1.1010
AngleAngle Coeffs
1 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700
2 -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600
AngleAngleTorsion Coeffs
1 -12.5640 110.7700 110.7700
EndBondTorsion Coeffs
1 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010
MiddleBondTorsion Coeffs
1 -14.2610 -0.5322 -0.4864 1.5300
BondBond13 Coeffs
1 0.0000 1.1010 1.1010
AngleTorsion Coeffs
1 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700
Atoms
1 1 1 -0.080000 4.462910000 5.148330000 -5.000410000
2 1 1 -0.080000 5.965490000 5.079930000 -4.999750000
3 1 2 0.027000 4.099550000 6.054480000 -5.502500000
4 1 2 0.027000 4.020330000 4.288350000 -5.519840000
5 1 2 0.027000 4.057610000 5.156680000 -3.980190000
6 1 2 0.027000 6.409980000 5.944880000 -4.490510000
7 1 2 0.027000 6.329880000 4.179410000 -4.488110000
8 1 2 0.027000 6.370610000 5.061380000 -6.019850000
Bonds
1 1 1 2
2 2 1 3
3 2 1 4
4 2 1 5
5 2 2 6
6 2 2 7
7 2 2 8
Angles
1 1 2 1 3
2 1 2 1 4
3 1 2 1 5
4 2 3 1 4
5 2 3 1 5
6 2 4 1 5
7 1 1 2 6
8 1 1 2 7
9 1 1 2 8
10 2 6 2 7
11 2 6 2 8
12 2 7 2 8
Dihedrals
1 1 3 1 2 6
2 1 3 1 2 7
3 1 3 1 2 8
4 1 4 1 2 6
5 1 4 1 2 7
6 1 4 1 2 8
7 1 5 1 2 6
8 1 5 1 2 7
9 1 5 1 2 8
Impropers
1 1 2 1 3 4
2 1 2 1 3 5
3 1 2 1 4 5
4 2 3 1 4 5
5 1 1 2 6 7
6 1 1 2 6 8
7 1 1 2 7 8
8 2 6 2 7 8

150
tools/msi2lmp/test/reference/ethane-class2a.data2
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@ -1,150 +0,0 @@
LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 16
8 atoms
2 atom types
7 bonds
2 bond types
12 angles
2 angle types
9 dihedrals
1 dihedral types
8 impropers
2 improper types
2.1454500000000001e-01 1.0214544999999999e+01 xlo xhi
1.1418000000000000e-01 1.0114179999999999e+01 ylo yhi
-1.0000145000000000e+01 -1.4500000000000000e-04 zlo zhi
Masses
1 12.0112
2 1.00797
Pair Coeffs
1 0.062 3.854
2 0.023 2.878
Bond Coeffs
1 1.53 299.67 -501.77 679.81
2 1.101 345 -691.89 844.6
Angle Coeffs
1 110.77 41.453 -10.604 5.129
2 107.66 39.641 -12.921 -2.4318
BondBond Coeffs
1 3.3872 1.53 1.101
2 5.3316 1.101 1.101
BondAngle Coeffs
1 20.754 11.421 1.53 1.101
2 18.103 18.103 1.101 1.101
Dihedral Coeffs
1 -0.1432 0 0.0617 0 -0.153 0
AngleAngleTorsion Coeffs
1 -12.564 110.77 110.77
EndBondTorsion Coeffs
1 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
MiddleBondTorsion Coeffs
1 -14.261 -0.5322 -0.4864 1.53
BondBond13 Coeffs
1 0 1.101 1.101
AngleTorsion Coeffs
1 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
Improper Coeffs
1 0 0
2 0 0
AngleAngle Coeffs
1 0.2738 -0.4825 0.2738 110.77 107.66 110.77
2 -0.3157 -0.3157 -0.3157 107.66 107.66 107.66
Atoms
1 1 1 -8.0000000000000002e-02 4.4538690479219207e+00 5.1486853324416773e+00 -5.0006672124371478e+00 0 0 0
2 1 1 -8.0000000000000002e-02 5.9752252585627916e+00 5.0798075655744439e+00 -4.9995377368292795e+00 0 0 0
3 1 2 2.7000000000000000e-02 4.1027087891522536e+00 6.0611385178808801e+00 -5.5071158857325999e+00 0 0 0
4 1 2 2.7000000000000000e-02 4.0225279676710901e+00 4.2809595114650092e+00 -5.5235413488099159e+00 0 0 0
5 1 2 2.7000000000000000e-02 4.0609984589629926e+00 5.1568927206205277e+00 -3.9720889303942837e+00 0 0 0
6 1 2 2.7000000000000000e-02 6.4073305379766117e+00 5.9523193083814361e+00 -4.4853357079578036e+00 0 0 0
7 1 2 2.7000000000000000e-02 6.3263399259076571e+00 4.1720844297716164e+00 -4.4846057827102177e+00 0 0 0
8 1 2 2.7000000000000000e-02 6.3673600138446842e+00 5.0615526138644080e+00 -6.0282673951287471e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 2 1 3
3 2 1 4
4 2 1 5
5 2 2 6
6 2 2 7
7 2 2 8
Angles
1 1 2 1 3
2 1 2 1 4
3 1 2 1 5
4 2 3 1 4
5 2 3 1 5
6 2 4 1 5
7 1 1 2 6
8 1 1 2 7
9 1 1 2 8
10 2 6 2 7
11 2 6 2 8
12 2 7 2 8
Dihedrals
1 1 3 1 2 6
2 1 3 1 2 7
3 1 3 1 2 8
4 1 4 1 2 6
5 1 4 1 2 7
6 1 4 1 2 8
7 1 5 1 2 6
8 1 5 1 2 7
9 1 5 1 2 8
Impropers
1 1 2 1 3 4
2 1 2 1 3 5
3 1 2 1 4 5
4 2 3 1 4 5
5 1 1 2 6 7
6 1 1 2 6 8
7 1 1 2 7 8
8 2 6 2 7 8

141
tools/msi2lmp/test/reference/ethane-class2b.data
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@ -1,141 +0,0 @@
LAMMPS data file from msi2lmp v3.8 for ethane-class2b
8 atoms
7 bonds
12 angles
9 dihedrals
8 impropers
2 atom types
2 bond types
2 angle types
1 dihedral types
2 improper types
0.214545000 10.214545000 xlo xhi
0.114180000 10.114180000 ylo yhi
-10.000145000 -0.000145000 zlo zhi
Masses
1 12.011150
2 1.007970
Pair Coeffs
1 0.0540000000 4.0100000000
2 0.0200000000 2.9950000000
Bond Coeffs
1 1.5300 299.6700 -501.7700 679.8100
2 1.1010 345.0000 -691.8900 844.6000
Angle Coeffs
1 110.7700 41.4530 -10.6040 5.1290
2 107.6600 39.6410 -12.9210 -2.4318
Dihedral Coeffs
1 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000
Improper Coeffs
1 0.0000 0.0000
2 0.0000 0.0000
BondBond Coeffs
1 3.3872 1.5300 1.1010
2 5.3316 1.1010 1.1010
BondAngle Coeffs
1 20.7540 11.4210 1.5300 1.1010
2 18.1030 18.1030 1.1010 1.1010
AngleAngle Coeffs
1 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700
2 -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600
AngleAngleTorsion Coeffs
1 -12.5640 110.7700 110.7700
EndBondTorsion Coeffs
1 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010
MiddleBondTorsion Coeffs
1 -14.2610 -0.5322 -0.4864 1.5300
BondBond13 Coeffs
1 0.0000 1.1010 1.1010
AngleTorsion Coeffs
1 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700
Atoms
1 1 1 -0.080000 4.462910000 5.148330000 -5.000410000
2 1 1 -0.080000 5.965490000 5.079930000 -4.999750000
3 1 2 0.027000 4.099550000 6.054480000 -5.502500000
4 1 2 0.027000 4.020330000 4.288350000 -5.519840000
5 1 2 0.027000 4.057610000 5.156680000 -3.980190000
6 1 2 0.027000 6.409980000 5.944880000 -4.490510000
7 1 2 0.027000 6.329880000 4.179410000 -4.488110000
8 1 2 0.027000 6.370610000 5.061380000 -6.019850000
Bonds
1 1 1 2
2 2 1 3
3 2 1 4
4 2 1 5
5 2 2 6
6 2 2 7
7 2 2 8
Angles
1 1 2 1 3
2 1 2 1 4
3 1 2 1 5
4 2 3 1 4
5 2 3 1 5
6 2 4 1 5
7 1 1 2 6
8 1 1 2 7
9 1 1 2 8
10 2 6 2 7
11 2 6 2 8
12 2 7 2 8
Dihedrals
1 1 3 1 2 6
2 1 3 1 2 7
3 1 3 1 2 8
4 1 4 1 2 6
5 1 4 1 2 7
6 1 4 1 2 8
7 1 5 1 2 6
8 1 5 1 2 7
9 1 5 1 2 8
Impropers
1 1 2 1 3 4
2 1 2 1 3 5
3 1 2 1 4 5
4 2 3 1 4 5
5 1 1 2 6 7
6 1 1 2 6 8
7 1 1 2 7 8
8 2 6 2 7 8

150
tools/msi2lmp/test/reference/ethane-class2b.data2
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@ -1,150 +0,0 @@
LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 16
8 atoms
2 atom types
7 bonds
2 bond types
12 angles
2 angle types
9 dihedrals
1 dihedral types
8 impropers
2 improper types
2.1454500000000001e-01 1.0214544999999999e+01 xlo xhi
1.1418000000000000e-01 1.0114179999999999e+01 ylo yhi
-1.0000145000000000e+01 -1.4500000000000000e-04 zlo zhi
Masses
1 12.0112
2 1.00797
Pair Coeffs
1 0.054 4.01
2 0.02 2.995
Bond Coeffs
1 1.53 299.67 -501.77 679.81
2 1.101 345 -691.89 844.6
Angle Coeffs
1 110.77 41.453 -10.604 5.129
2 107.66 39.641 -12.921 -2.4318
BondBond Coeffs
1 3.3872 1.53 1.101
2 5.3316 1.101 1.101
BondAngle Coeffs
1 20.754 11.421 1.53 1.101
2 18.103 18.103 1.101 1.101
Dihedral Coeffs
1 -0.1432 0 0.0617 0 -0.1083 0
AngleAngleTorsion Coeffs
1 -12.564 110.77 110.77
EndBondTorsion Coeffs
1 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
MiddleBondTorsion Coeffs
1 -14.261 -0.5322 -0.4864 1.53
BondBond13 Coeffs
1 0 1.101 1.101
AngleTorsion Coeffs
1 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
Improper Coeffs
1 0 0
2 0 0
AngleAngle Coeffs
1 0.2738 -0.4825 0.2738 110.77 107.66 110.77
2 -0.3157 -0.3157 -0.3157 107.66 107.66 107.66
Atoms
1 1 1 -8.0000000000000002e-02 4.4539067675324455e+00 5.1486986318902179e+00 -5.0006830135109768e+00 0 0 0
2 1 1 -8.0000000000000002e-02 5.9751600079721632e+00 5.0797955572187083e+00 -4.9995540141910881e+00 0 0 0
3 1 2 2.7000000000000000e-02 4.1033596012021949e+00 6.0613345155354175e+00 -5.5072937752799866e+00 0 0 0
4 1 2 2.7000000000000000e-02 4.0231659653053988e+00 4.2806983991406238e+00 -5.5236463558028897e+00 0 0 0
5 1 2 2.7000000000000000e-02 4.0617348419454453e+00 5.1569019898534618e+00 -3.9718024714525497e+00 0 0 0
6 1 2 2.7000000000000000e-02 6.4066557479964903e+00 5.9525258920315016e+00 -4.4851777744839287e+00 0 0 0
7 1 2 2.7000000000000000e-02 6.3256343483059201e+00 4.1718757701514066e+00 -4.4844774576947133e+00 0 0 0
8 1 2 2.7000000000000000e-02 6.3667427197399409e+00 5.0616092441786620e+00 -6.0285251375838698e+00 0 0 0
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 2 1 3
3 2 1 4
4 2 1 5
5 2 2 6
6 2 2 7
7 2 2 8
Angles
1 1 2 1 3
2 1 2 1 4
3 1 2 1 5
4 2 3 1 4
5 2 3 1 5
6 2 4 1 5
7 1 1 2 6
8 1 1 2 7
9 1 1 2 8
10 2 6 2 7
11 2 6 2 8
12 2 7 2 8
Dihedrals
1 1 3 1 2 6
2 1 3 1 2 7
3 1 3 1 2 8
4 1 4 1 2 6
5 1 4 1 2 7
6 1 4 1 2 8
7 1 5 1 2 6
8 1 5 1 2 7
9 1 5 1 2 8
Impropers
1 1 2 1 3 4
2 1 2 1 3 5
3 1 2 1 4 5
4 2 3 1 4 5
5 1 1 2 6 7
6 1 1 2 6 8
7 1 1 2 7 8
8 2 6 2 7 8

89
tools/msi2lmp/test/reference/ethane-oplsaa.data
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@ -1,89 +0,0 @@
LAMMPS data file from msi2lmp v3.8 for ethane-oplsaa
8 atoms
7 bonds
12 angles
9 dihedrals
0 impropers
2 atom types
2 bond types
2 angle types
1 dihedral types
-5.000000000 5.000000000 xlo xhi
-5.000000000 5.000000000 ylo yhi
-5.000000000 5.000000000 zlo zhi
Masses
1 12.011150
2 1.007970
Pair Coeffs
1 0.0659999660 3.5000001502
2 0.0300002576 2.4999982005
Bond Coeffs
1 268.0000 1.5290
2 340.0000 1.0900
Angle Coeffs
1 37.5000 110.7000
2 33.0000 107.8000
Dihedral Coeffs
1 0.0000 0.0000 0.3180 0.0000
Atoms
1 1 1 -0.180000 4.462910000 -4.851670000 4.999590000 0 1 -1
2 1 1 -0.180000 -4.034510000 -4.920070000 -4.999750000 1 1 0
3 1 2 0.060000 4.099550000 -3.945520000 4.497500000 0 1 -1
4 1 2 0.060000 4.020330000 4.288350000 4.480160000 0 0 -1
5 1 2 0.060000 4.057610000 -4.843320000 -3.980190000 0 1 0
6 1 2 0.060000 -3.590020000 -4.055120000 -4.490510000 1 1 0
7 1 2 0.060000 -3.670120000 4.179410000 -4.488110000 1 0 0
8 1 2 0.060000 -3.629390000 -4.938620000 3.980150000 1 1 -1
Bonds
1 1 1 2
2 2 1 3
3 2 1 4
4 2 1 5
5 2 2 6
6 2 2 7
7 2 2 8
Angles
1 1 2 1 3
2 1 2 1 4
3 1 2 1 5
4 2 3 1 4
5 2 3 1 5
6 2 4 1 5
7 1 1 2 6
8 1 1 2 7
9 1 1 2 8
10 2 6 2 7
11 2 6 2 8
12 2 7 2 8
Dihedrals
1 1 3 1 2 6
2 1 3 1 2 7
3 1 3 1 2 8
4 1 4 1 2 6
5 1 4 1 2 7
6 1 4 1 2 8
7 1 5 1 2 6
8 1 5 1 2 7
9 1 5 1 2 8

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