Friday, March 27, 2015

TANI-C8(EB)

TANI-C8(EB)

Sunday, March 15, 2015

Wednesday, March 11, 2015

Toluene Prodgr

The PDB file (all hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  HAG DRG     1      -6.729   2.808   8.977  1.00 20.00           H  
HETATM    3  HAH DRG     1      -7.326   4.380   8.395  1.00 20.00           H  
HETATM    4  HAI DRG     1      -8.244   3.492   9.659  1.00 20.00           H  
HETATM    5  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    6  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    7  HAB DRG     1      -7.030   1.060   7.600  1.00 20.00           H  
HETATM    8  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    9  HAA DRG     1      -8.410  -0.070   5.850  1.00 20.00           H  
HETATM   10  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM   11  HAD DRG     1     -10.550   0.960   5.100  1.00 20.00           H  
HETATM   12  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM   13  HAE DRG     1     -11.340   3.130   6.070  1.00 20.00           H  
HETATM   14  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
HETATM   15  HAF DRG     1      -9.960   4.280   7.800  1.00 20.00           H  
CONECT    1    2    3    4    5
CONECT    2    1
CONECT    3    1
CONECT    4    1
CONECT    5    1    6   14
CONECT    6    5    7    8
CONECT    7    6
CONECT    8    6    9   10
CONECT    9    8
CONECT   10    8   11   12
CONECT   11   10
CONECT   12   10   13   14
CONECT   13   12
CONECT   14    5   12   15
CONECT   15   14
END

The PDB file (polar/aromatic hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    3  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    4  HAB DRG     1      -7.030   1.060   7.600  1.00 20.00           H  
HETATM    5  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    6  HAA DRG     1      -8.410  -0.070   5.850  1.00 20.00           H  
HETATM    7  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM    8  HAD DRG     1     -10.550   0.960   5.100  1.00 20.00           H  
HETATM    9  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM   10  HAE DRG     1     -11.340   3.130   6.070  1.00 20.00           H  
HETATM   11  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
HETATM   12  HAF DRG     1      -9.960   4.280   7.800  1.00 20.00           H  
CONECT    1    2
CONECT    2    1    3   11
CONECT    3    2    4    5
CONECT    4    3
CONECT    5    3    6    7
CONECT    6    5
CONECT    7    5    8    9
CONECT    8    7
CONECT    9    7   10   11
CONECT   10    9
CONECT   11    2    9   12
CONECT   12   11
END


The PDB file (polar hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    3  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    4  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    5  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM    6  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM    7  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
CONECT    1    2
CONECT    2    1    3    7
CONECT    3    2    4
CONECT    4    3    5
CONECT    5    4    6
CONECT    6    5    7
CONECT    7    2    6
END


The PDB file (no hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    3  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    4  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    5  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM    6  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM    7  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
CONECT    1    2
CONECT    2    1    3    7
CONECT    3    2    4
CONECT    4    3    5
CONECT    5    4    6
CONECT    6    5    7
CONECT    7    2    6
END

The GROMACS topology
;       
;       
;       This file was generated by PRODRG version AA100323.0717
;       PRODRG written/copyrighted by Daan van Aalten
;       and Alexander Schuettelkopf
;       
;       Questions/comments to dava@davapc1.bioch.dundee.ac.uk
;       
;       When using this software in a publication, cite:
;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;       PRODRG - a tool for high-throughput crystallography
;       of protein-ligand complexes.
;       Acta Crystallogr. D60, 1355--1363.
;       
;       

[ moleculetype ]
; Name nrexcl
DRG      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  DRG     CAG     1    0.040  15.0350   
     2         C     1  DRG     CAC     1   -0.020  12.0110   
     3       CR1     1  DRG     CAB     1   -0.012  12.0110   
     4        HC     1  DRG     HAB     1    0.008   1.0080   
     5       CR1     1  DRG     CAA     1   -0.012  12.0110   
     6        HC     1  DRG     HAA     1    0.008   1.0080   
     7       CR1     1  DRG     CAD     1   -0.012  12.0110   
     8        HC     1  DRG     HAD     1    0.008   1.0080   
     9       CR1     1  DRG     CAE     1   -0.012  12.0110   
    10        HC     1  DRG     HAE     1    0.008   1.0080   
    11       CR1     1  DRG     CAF     1   -0.012  12.0110   
    12        HC     1  DRG     HAF     1    0.008   1.0080   

[ bonds ]
; ai  aj  fu    c0, c1, ...
   2   1   2    0.139   8660000.0    0.139   8660000.0 ;   CAC  CAG   
   2   3   2    0.139  10800000.0    0.139  10800000.0 ;   CAC  CAB   
   2  11   2    0.139  10800000.0    0.139  10800000.0 ;   CAC  CAF   
   3   4   2    0.109  12300000.0    0.109  12300000.0 ;   CAB  HAB   
   3   5   2    0.139  10800000.0    0.139  10800000.0 ;   CAB  CAA   
   5   6   2    0.109  12300000.0    0.109  12300000.0 ;   CAA  HAA   
   5   7   2    0.139  10800000.0    0.139  10800000.0 ;   CAA  CAD   
   7   8   2    0.109  12300000.0    0.109  12300000.0 ;   CAD  HAD   
   7   9   2    0.139  10800000.0    0.139  10800000.0 ;   CAD  CAE   
   9  10   2    0.109  12300000.0    0.109  12300000.0 ;   CAE  HAE   
   9  11   2    0.139  10800000.0    0.139  10800000.0 ;   CAE  CAF   
  11  12   2    0.109  12300000.0    0.109  12300000.0 ;   CAF  HAF   

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   4   1                                           ;   CAG  HAB   
   1   5   1                                           ;   CAG  CAA   
   1   9   1                                           ;   CAG  CAE   
   1  12   1                                           ;   CAG  HAF   
   2   6   1                                           ;   CAC  HAA   
   2   7   1                                           ;   CAC  CAD   
   2  10   1                                           ;   CAC  HAE   
   3   8   1                                           ;   CAB  HAD   
   3   9   1                                           ;   CAB  CAE   
   3  12   1                                           ;   CAB  HAF   
   4   6   1                                           ;   HAB  HAA   
   4   7   1                                           ;   HAB  CAD   
   4  11   1                                           ;   HAB  CAF   
   5  10   1                                           ;   CAA  HAE   
   5  11   1                                           ;   CAA  CAF   
   6   8   1                                           ;   HAA  HAD   
   6   9   1                                           ;   HAA  CAE   
   7  12   1                                           ;   CAD  HAF   
   8  10   1                                           ;   HAD  HAE   
   8  11   1                                           ;   HAD  CAF   
  10  12   1                                           ;   HAE  HAF   

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    120.0       560.0    120.0       560.0 ;   CAG  CAC  CAB   
   1   2  11   2    120.0       560.0    120.0       560.0 ;   CAG  CAC  CAF   
   3   2  11   2    120.0       560.0    120.0       560.0 ;   CAB  CAC  CAF   
   2   3   4   2    120.0       505.0    120.0       505.0 ;   CAC  CAB  HAB   
   2   3   5   2    120.0       505.0    120.0       505.0 ;   CAC  CAB  CAA   
   4   3   5   2    120.0       505.0    120.0       505.0 ;   HAB  CAB  CAA   
   3   5   6   2    120.0       505.0    120.0       505.0 ;   CAB  CAA  HAA   
   3   5   7   2    120.0       505.0    120.0       505.0 ;   CAB  CAA  CAD   
   6   5   7   2    120.0       505.0    120.0       505.0 ;   HAA  CAA  CAD   
   5   7   8   2    120.0       505.0    120.0       505.0 ;   CAA  CAD  HAD   
   5   7   9   2    120.0       505.0    120.0       505.0 ;   CAA  CAD  CAE   
   8   7   9   2    120.0       505.0    120.0       505.0 ;   HAD  CAD  CAE   
   7   9  10   2    120.0       505.0    120.0       505.0 ;   CAD  CAE  HAE   
   7   9  11   2    120.0       505.0    120.0       505.0 ;   CAD  CAE  CAF   
  10   9  11   2    120.0       505.0    120.0       505.0 ;   HAE  CAE  CAF   
   2  11   9   2    120.0       505.0    120.0       505.0 ;   CAC  CAF  CAE   
   2  11  12   2    120.0       505.0    120.0       505.0 ;   CAC  CAF  HAF   
   9  11  12   2    120.0       505.0    120.0       505.0 ;   CAE  CAF  HAF   

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
   2   1  11   3   2      0.0  167.4        0.0  167.4   ; imp   CAC  CAG  CAF  CAB   
   3   2   5   4   2      0.0  167.4        0.0  167.4   ; imp   CAB  CAC  CAA  HAB   
   5   3   7   6   2      0.0  167.4        0.0  167.4   ; imp   CAA  CAB  CAD  HAA   
   7   5   9   8   2      0.0  167.4        0.0  167.4   ; imp   CAD  CAA  CAE  HAD   
   9   7  11  10   2      0.0  167.4        0.0  167.4   ; imp   CAE  CAD  CAF  HAE   
  11   2   9  12   2      0.0  167.4        0.0  167.4   ; imp   CAF  CAC  CAE  HAF   
   2   3   5   7   2      0.0  209.3        0.0  209.3   ; imp   CAC  CAB  CAA  CAD   
   3   5   7   9   2      0.0  209.3        0.0  209.3   ; imp   CAB  CAA  CAD  CAE   
   5   7   9  11   2      0.0  209.3        0.0  209.3   ; imp   CAA  CAD  CAE  CAF   
   7   9  11   2   2      0.0  209.3        0.0  209.3   ; imp   CAD  CAE  CAF  CAC   
   9  11   2   3   2      0.0  209.3        0.0  209.3   ; imp   CAE  CAF  CAC  CAB   
  11   2   3   5   2      0.0  209.3        0.0  209.3   ; imp   CAF  CAC  CAB  CAA   


Tetra(analine)

tetra(aniline)_5LDA_GROMOS96_allatom_optimised_geometry


Friday, March 06, 2015

Steps to Perform a Simulation

Below is presented a generalised procedure for performing a simulation. The exact steps and processes involved will vary depending on exactly what is being attempted. Use as a general guide only!

  1. Clearly identify the property / phenomena of interest to be studied by performing the simulation. Do not continue further until you are clear on this!
  2. Select the appropriate tools to be able to perform the simulation and observe the property / phenomena of interest. It is important to read and familiarise yourself with publications by other researchers on similar systems. Tools include:

    - software to perform the simulation with, consideration of force field may influence this decision.

    force field which describes how the atoms / particles within the system interact with each other. Select one that is appropriate for the system being studied and the property / phenomena of interest. Very important and non-trivial step! Consider now how you will analyze your simulation data to make your observations.
  3. Obtain / generate the initial coordinate file for each molecule to be placed within the system. The page linked there has some software suggestions.
  4. Generate the raw starting structure for the system by placing the molecules within the coordinate file as appropriate. Molecules may be specifically placed or arranged randomly.
  5. Obtain / generate the topology file for the system, using (for example)
    pdb2gmx
    SwissParam (for CHARMM forcefield), 
    PRODRG (for ffgmx/GROMOS96 43A1), 
    Automated Topology Builder (for GROMOS96 53A6), 
    MKTOP (for OPLS/AA) or
    - your favourite text editor in concert with chapter 5 of the
    GROMACS Manual.
    - For the 
    AMBER force fields, antechamber or acpype might be appropriate.
  6. Describe a simulation box (e.g. using editconf) whose size is appropriate for the eventual density you would like, fill it with solvent (e.g. using genbox), and add any counter-ions needed to neutralize the system (e.g. using grompp and genion). In these steps you may need to edit your topology file to stay current with your coordinate file.
  7. Run an energy minimization on the system (using grompp and mdrun). This is required to sort out any bad starting structures caused during generation of the system, which may cause the production simulation to crash. It may be necessary also to minimize your solute structure in vacuo before introducing solvent molecules (or your lipid bilayer or whatever else). You should consider using flexible water models and not using bond constraints or frozen groups. The use of position restraints and/or distance restraints should be evaluated carefully.
  8. Select the appropriate simulation parameters for the equilibration simulation (defined in .mdp file). You need to choose simulation parameters that are consistent with how force field was derived. You may need to simulate at NVT with position restraints on your solvent and/or solute to get the temperature almost right, then relax to NPT to fix the density (which should be done with Berendsen until after the density is stabilized, before a further switch to a barostat that produces the correct ensemble), then move further (if needed) to reach your production simulation ensemble (e.g. NVTNVE). If you have problems here with the system blowing up, consider using the suggestions on that page, e.g. position restraints on solutes, or not using bond constraints, or using smaller integration timesteps, or several gentler heating stage(s).
  9. Run the equilibration simulation for sufficient time so that the system relaxes sufficiently in the target ensemble to allow the production run to be commenced (using grompp and mdrun, then g_energy and trajectory visualization tools).
  10. Select the appropriate simulation parameters for the production simulation (defined in .mdp file). In particular, be careful not to re-generate the velocities. You still need to be consistent with how the force field was derived and how to measure the property / phenomena of interest.
  11. Run the production simulation for sufficient time so that property / phenomena of interest can be observed in required detail (using grompp / tpbconv and mdrun).
  12. Analyse / visualise the resulting trajectory and data files to obtain information on the property / phenomena of interest.

Thursday, March 05, 2015

Fatal error: Atomtype SDMSO not found

Fatal error:
Atomtype SDMSO not found

Error was deleted by changing SDMSO into SDmso in the itp file, obtained from the site of topology calculation PRODRG.

25     SDMSO     1  AMO     SAB     6    1.652  32.0600 

topol.top

;
; File 'topol.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Wed Mar 04 23:33:55 2015
;
; This is your topology file
; "Torture You.... Yeah, That's a Good Idea, I Like That." (Pulp Fiction)
;
; Include forcefield parameters
#include "ffG43a1.itp"
#include "AMO.ITP"

[ system ]
AMO 4

[ molecules ]
AMO 4

AMO.itp

;       
;       
;       This file was generated by PRODRG version AA100323.0717
;       PRODRG written/copyrighted by Daan van Aalten
;       and Alexander Schuettelkopf
;       
;       Questions/comments to dava@davapc1.bioch.dundee.ac.uk
;       
;       When using this software in a publication, cite:
;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;       PRODRG - a tool for high-throughput crystallography
;       of protein-ligand complexes.
;       Acta Crystallogr. D60, 1355--1363.
;       
;       

[ moleculetype ]
; Name nrexcl
AMO      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  AMO     CBE     1   -0.011  15.0350   
     2       CH2     1  AMO     CBD     1    0.011  14.0270   
     3       CH2     1  AMO     CBC     2    0.000  14.0270   
     4       CH2     1  AMO     CBB     2    0.000  14.0270   
     5       CH2     1  AMO     CBA     2    0.001  14.0270   
     6       CH2     1  AMO     CAZ     2   -0.001  14.0270   
     7       CH2     1  AMO     CAY     3    0.000  14.0270   
     8       CH2     1  AMO     CAX     3    0.002  14.0270   
     9       CH2     1  AMO     CAW     3    0.000  14.0270   
    10       CH2     1  AMO     CAV     3    0.000  14.0270   
    11       CH2     1  AMO     CAU     3    0.000  14.0270   
    12       CH2     1  AMO     CAT     3   -0.001  14.0270   
    13       CH2     1  AMO     CAS     3   -0.001  14.0270   
    14       CH2     1  AMO     CAR     4    0.037  14.0270   
    15       CH2     1  AMO     CAQ     4    0.038  14.0270   
    16       CH2     1  AMO     CAP     4    0.038  14.0270   
    17       CH2     1  AMO     CAO     4    0.036  14.0270   
    18       CH2     1  AMO     CAN     4    0.038  14.0270   
    19         C     1  AMO     CAL     4    0.219  12.0110   
    20         O     1  AMO     OAM     4   -0.406  15.9994   
    21         C     1  AMO     CAJ     5   -0.002  12.0110   
    22       CR1     1  AMO     CAK     5   -0.002  12.0110   
    23        HC     1  AMO     HAK     5    0.006   1.0080   
    24         C     1  AMO     CAE     5   -0.002  12.0110   
    25     SDMSO     1  AMO     SAB     6    1.652  32.0600   
    26        OM     1  AMO     OAC     6   -0.569  15.9994   
    27        OM     1  AMO     OAD     6   -0.569  15.9994   
    28        OM     1  AMO     OAA     6   -0.569  15.9994   
    29       CR1     1  AMO     CAI     6   -0.015  12.0110   
    30        HC     1  AMO     HAI     6    0.001   1.0080   
    31       CR1     1  AMO     CAG     6   -0.016  12.0110   
    32        HC     1  AMO     HAG     6    0.001   1.0080   
    33         C     1  AMO     CAF     6    0.084  12.0110   
    34         N     1  AMO     NAH     7    0.032  14.0067   
    35         H     1  AMO     HAH     7   -0.027   1.0080   
    36         C     1  AMO     CBF     7    0.032  12.0110   
    37       CR1     1  AMO     CBJ     7   -0.037  12.0110   
    38        HC     1  AMO     HBQ     7    0.000   1.0080   
    39       CR1     1  AMO     CBK     8   -0.021  12.0110   
    40        HC     1  AMO     HBR     8    0.001   1.0080   
    41       CR1     1  AMO     CBG     8   -0.020  12.0110   
    42        HC     1  AMO     HBO     8    0.000   1.0080   
    43       CR1     1  AMO     CBH     8   -0.021  12.0110   
    44        HC     1  AMO     HBP     8    0.001   1.0080   
    45         C     1  AMO     CBI     8    0.060  12.0110   
    46         N     1  AMO     NBL     9    0.044  14.0067   
    47         H     1  AMO     HBZ     9   -0.020   1.0080   
    48         C     1  AMO     CBM     9    0.044  12.0110   
    49       CR1     1  AMO     CBO     9   -0.028  12.0110   
    50        HC     1  AMO     HBT     9    0.000   1.0080   
    51         C     1  AMO     CBP     9   -0.040  12.0110   
    52     SDMSO     1  AMO     SCA    10    1.652  32.0600   
    53        OM     1  AMO     OCC    10   -0.569  15.9994   
    54        OM     1  AMO     OCD    10   -0.569  15.9994   
    55        OM     1  AMO     OCB    10   -0.569  15.9994   
    56       CR1     1  AMO     CBN    10   -0.015  12.0110   
    57        HC     1  AMO     HBS    10    0.001   1.0080   
    58       CR1     1  AMO     CBR    10   -0.016  12.0110   
    59        HC     1  AMO     HBU    10    0.001   1.0080   
    60         C     1  AMO     CBQ    10    0.084  12.0110   
    61         N     1  AMO     NBS    11    0.032  14.0067   
    62         H     1  AMO     HB0    11   -0.027   1.0080   
    63         C     1  AMO     CBT    11    0.032  12.0110   
    64       CR1     1  AMO     CBU    11   -0.037  12.0110   
    65        HC     1  AMO     HBV    11    0.000   1.0080   
    66       CR1     1  AMO     CBV    12   -0.019  12.0110   
    67        HC     1  AMO     HBW    12    0.001   1.0080   
    68         C     1  AMO     CBW    12    0.064  12.0110   
    69        NT     1  AMO     NBZ    12    0.019  14.0067   
    70         H     1  AMO     HB2    12   -0.014   1.0080   
    71         H     1  AMO     HB1    12   -0.014   1.0080   
    72       CR1     1  AMO     CBY    12   -0.020  12.0110   
    73        HC     1  AMO     HBY    12    0.001   1.0080   
    74       CR1     1  AMO     CBX    12   -0.019  12.0110   
    75        HC     1  AMO     HBX    12    0.001   1.0080   

[ bonds ]
; ai  aj  fu    c0, c1, ...
   2   1   2    0.153   7150000.0    0.153   7150000.0 ;   CBD  CBE   
   2   3   2    0.153   7150000.0    0.153   7150000.0 ;   CBD  CBC   
   3   4   2    0.153   7150000.0    0.153   7150000.0 ;   CBC  CBB   
   4   5   2    0.153   7150000.0    0.153   7150000.0 ;   CBB  CBA   
   5   6   2    0.153   7150000.0    0.153   7150000.0 ;   CBA  CAZ   
   6   7   2    0.153   7150000.0    0.153   7150000.0 ;   CAZ  CAY   
   7   8   2    0.153   7150000.0    0.153   7150000.0 ;   CAY  CAX   
   8   9   2    0.153   7150000.0    0.153   7150000.0 ;   CAX  CAW   
   9  10   2    0.153   7150000.0    0.153   7150000.0 ;   CAW  CAV   
  10  11   2    0.153   7150000.0    0.153   7150000.0 ;   CAV  CAU   
  11  12   2    0.153   7150000.0    0.153   7150000.0 ;   CAU  CAT   
  12  13   2    0.153   7150000.0    0.153   7150000.0 ;   CAT  CAS   
  13  14   2    0.153   7150000.0    0.153   7150000.0 ;   CAS  CAR   
  14  15   2    0.153   7150000.0    0.153   7150000.0 ;   CAR  CAQ   
  15  16   2    0.153   7150000.0    0.153   7150000.0 ;   CAQ  CAP   
  16  17   2    0.153   7150000.0    0.153   7150000.0 ;   CAP  CAO   
  17  18   2    0.153   7150000.0    0.153   7150000.0 ;   CAO  CAN   
  19  18   2    0.153   7150000.0    0.153   7150000.0 ;   CAL  CAN   
  19  20   2    0.123  16600000.0    0.123  16600000.0 ;   CAL  OAM   
  21  19   2    0.139  10800000.0    0.139  10800000.0 ;   CAJ  CAL   
  21  22   2    0.139  10800000.0    0.139  10800000.0 ;   CAJ  CAK   
  21  29   2    0.139  10800000.0    0.139  10800000.0 ;   CAJ  CAI   
  22  23   2    0.109  12300000.0    0.109  12300000.0 ;   CAK  HAK   
  24  22   2    0.139  10800000.0    0.139  10800000.0 ;   CAE  CAK   
  24  25   2    0.175   2619184.0    0.175   2619184.0 ;   CAE  SAB   
  24  33   2    0.139  10800000.0    0.139  10800000.0 ;   CAE  CAF   
  25  26   2    0.153   8040000.0    0.153   8040000.0 ;   SAB  OAC   
  25  27   2    0.153   8040000.0    0.153   8040000.0 ;   SAB  OAD   
  25  28   2    0.153   8040000.0    0.153   8040000.0 ;   SAB  OAA   
  29  30   2    0.109  12300000.0    0.109  12300000.0 ;   CAI  HAI   
  29  31   2    0.139  10800000.0    0.139  10800000.0 ;   CAI  CAG   
  31  32   2    0.109  12300000.0    0.109  12300000.0 ;   CAG  HAG   
  33  31   2    0.139  10800000.0    0.139  10800000.0 ;   CAF  CAG   
  33  34   2    0.133  10600000.0    0.133  10600000.0 ;   CAF  NAH   
  34  35   2    0.100  18700000.0    0.100  18700000.0 ;   NAH  HAH   
  36  34   2    0.133  10600000.0    0.133  10600000.0 ;   CBF  NAH   
  36  37   2    0.139  10800000.0    0.139  10800000.0 ;   CBF  CBJ   
  36  41   2    0.139  10800000.0    0.139  10800000.0 ;   CBF  CBG   
  37  38   2    0.109  12300000.0    0.109  12300000.0 ;   CBJ  HBQ   
  37  39   2    0.139  10800000.0    0.139  10800000.0 ;   CBJ  CBK   
  39  40   2    0.109  12300000.0    0.109  12300000.0 ;   CBK  HBR   
  45  39   2    0.139  10800000.0    0.139  10800000.0 ;   CBI  CBK   
  41  42   2    0.109  12300000.0    0.109  12300000.0 ;   CBG  HBO   
  41  43   2    0.139  10800000.0    0.139  10800000.0 ;   CBG  CBH   
  43  44   2    0.109  12300000.0    0.109  12300000.0 ;   CBH  HBP   
  45  43   2    0.139  10800000.0    0.139  10800000.0 ;   CBI  CBH   
  45  46   2    0.133  10600000.0    0.133  10600000.0 ;   CBI  NBL   
  46  47   2    0.100  18700000.0    0.100  18700000.0 ;   NBL  HBZ   
  48  46   2    0.133  10600000.0    0.133  10600000.0 ;   CBM  NBL   
  48  49   2    0.139  10800000.0    0.139  10800000.0 ;   CBM  CBO   
  48  56   2    0.139  10800000.0    0.139  10800000.0 ;   CBM  CBN   
  49  50   2    0.109  12300000.0    0.109  12300000.0 ;   CBO  HBT   
  51  49   2    0.139  10800000.0    0.139  10800000.0 ;   CBP  CBO   
  51  52   2    0.175   2619184.0    0.175   2619184.0 ;   CBP  SCA   
  51  60   2    0.139  10800000.0    0.139  10800000.0 ;   CBP  CBQ   
  52  53   2    0.153   8040000.0    0.153   8040000.0 ;   SCA  OCC   
  52  54   2    0.153   8040000.0    0.153   8040000.0 ;   SCA  OCD   
  52  55   2    0.153   8040000.0    0.153   8040000.0 ;   SCA  OCB   
  56  57   2    0.109  12300000.0    0.109  12300000.0 ;   CBN  HBS   
  56  58   2    0.139  10800000.0    0.139  10800000.0 ;   CBN  CBR   
  58  59   2    0.109  12300000.0    0.109  12300000.0 ;   CBR  HBU   
  60  58   2    0.139  10800000.0    0.139  10800000.0 ;   CBQ  CBR   
  60  61   2    0.133  10600000.0    0.133  10600000.0 ;   CBQ  NBS   
  61  62   2    0.100  18700000.0    0.100  18700000.0 ;   NBS  HB0   
  63  61   2    0.133  10600000.0    0.133  10600000.0 ;   CBT  NBS   
  63  64   2    0.139  10800000.0    0.139  10800000.0 ;   CBT  CBU   
  63  74   2    0.139  10800000.0    0.139  10800000.0 ;   CBT  CBX   
  64  65   2    0.109  12300000.0    0.109  12300000.0 ;   CBU  HBV   
  64  66   2    0.139  10800000.0    0.139  10800000.0 ;   CBU  CBV   
  66  67   2    0.109  12300000.0    0.109  12300000.0 ;   CBV  HBW   
  68  66   2    0.139  10800000.0    0.139  10800000.0 ;   CBW  CBV   
  68  69   2    0.133  10600000.0    0.133  10600000.0 ;   CBW  NBZ   
  68  72   2    0.139  10800000.0    0.139  10800000.0 ;   CBW  CBY   
  69  70   2    0.100  18700000.0    0.100  18700000.0 ;   NBZ  HB2   
  69  71   2    0.100  18700000.0    0.100  18700000.0 ;   NBZ  HB1   
  72  73   2    0.109  12300000.0    0.109  12300000.0 ;   CBY  HBY   
  72  74   2    0.139  10800000.0    0.139  10800000.0 ;   CBY  CBX   
  74  75   2    0.109  12300000.0    0.109  12300000.0 ;   CBX  HBX   

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   4   1                                           ;   CBE  CBB   
   2   5   1                                           ;   CBD  CBA   
   3   6   1                                           ;   CBC  CAZ   
   4   7   1                                           ;   CBB  CAY   
   5   8   1                                           ;   CBA  CAX   
   6   9   1                                           ;   CAZ  CAW   
   7  10   1                                           ;   CAY  CAV   
   8  11   1                                           ;   CAX  CAU   
   9  12   1                                           ;   CAW  CAT   
  10  13   1                                           ;   CAV  CAS   
  11  14   1                                           ;   CAU  CAR   
  12  15   1                                           ;   CAT  CAQ   
  13  16   1                                           ;   CAS  CAP   
  14  17   1                                           ;   CAR  CAO   
  15  18   1                                           ;   CAQ  CAN   
  16  19   1                                           ;   CAP  CAL   
  17  20   1                                           ;   CAO  OAM   
  17  21   1                                           ;   CAO  CAJ   
  18  22   1                                           ;   CAN  CAK   
  18  29   1                                           ;   CAN  CAI   
  19  23   1                                           ;   CAL  HAK   
  19  24   1                                           ;   CAL  CAE   
  19  30   1                                           ;   CAL  HAI   
  19  31   1                                           ;   CAL  CAG   
  20  22   1                                           ;   OAM  CAK   
  20  29   1                                           ;   OAM  CAI   
  21  25   1                                           ;   CAJ  SAB   
  21  32   1                                           ;   CAJ  HAG   
  21  33   1                                           ;   CAJ  CAF   
  22  26   1                                           ;   CAK  OAC   
  22  27   1                                           ;   CAK  OAD   
  22  28   1                                           ;   CAK  OAA   
  22  30   1                                           ;   CAK  HAI   
  22  31   1                                           ;   CAK  CAG   
  22  34   1                                           ;   CAK  NAH   
  23  25   1                                           ;   HAK  SAB   
  23  29   1                                           ;   HAK  CAI   
  23  33   1                                           ;   HAK  CAF   
  24  29   1                                           ;   CAE  CAI   
  24  32   1                                           ;   CAE  HAG   
  24  35   1                                           ;   CAE  HAH   
  24  36   1                                           ;   CAE  CBF   
  25  31   1                                           ;   SAB  CAG   
  25  34   1                                           ;   SAB  NAH   
  26  33   1                                           ;   OAC  CAF   
  27  33   1                                           ;   OAD  CAF   
  28  33   1                                           ;   OAA  CAF   
  29  34   1                                           ;   CAI  NAH   
  30  32   1                                           ;   HAI  HAG   
  30  33   1                                           ;   HAI  CAF   
  31  35   1                                           ;   CAG  HAH   
  31  36   1                                           ;   CAG  CBF   
  32  34   1                                           ;   HAG  NAH   
  33  37   1                                           ;   CAF  CBJ   
  33  41   1                                           ;   CAF  CBG   
  34  38   1                                           ;   NAH  HBQ   
  34  39   1                                           ;   NAH  CBK   
  34  42   1                                           ;   NAH  HBO   
  34  43   1                                           ;   NAH  CBH   
  35  37   1                                           ;   HAH  CBJ   
  35  41   1                                           ;   HAH  CBG   
  36  40   1                                           ;   CBF  HBR   
  36  44   1                                           ;   CBF  HBP   
  36  45   1                                           ;   CBF  CBI   
  37  42   1                                           ;   CBJ  HBO   
  37  43   1                                           ;   CBJ  CBH   
  37  46   1                                           ;   CBJ  NBL   
  38  40   1                                           ;   HBQ  HBR   
  38  41   1                                           ;   HBQ  CBG   
  38  45   1                                           ;   HBQ  CBI   
  39  41   1                                           ;   CBK  CBG   
  39  44   1                                           ;   CBK  HBP   
  39  47   1                                           ;   CBK  HBZ   
  39  48   1                                           ;   CBK  CBM   
  40  43   1                                           ;   HBR  CBH   
  40  46   1                                           ;   HBR  NBL   
  41  46   1                                           ;   CBG  NBL   
  42  44   1                                           ;   HBO  HBP   
  42  45   1                                           ;   HBO  CBI   
  43  47   1                                           ;   CBH  HBZ   
  43  48   1                                           ;   CBH  CBM   
  44  46   1                                           ;   HBP  NBL   
  45  49   1                                           ;   CBI  CBO   
  45  56   1                                           ;   CBI  CBN   
  46  50   1                                           ;   NBL  HBT   
  46  51   1                                           ;   NBL  CBP   
  46  57   1                                           ;   NBL  HBS   
  46  58   1                                           ;   NBL  CBR   
  47  49   1                                           ;   HBZ  CBO   
  47  56   1                                           ;   HBZ  CBN   
  48  52   1                                           ;   CBM  SCA   
  48  59   1                                           ;   CBM  HBU   
  48  60   1                                           ;   CBM  CBQ   
  49  53   1                                           ;   CBO  OCC   
  49  54   1                                           ;   CBO  OCD   
  49  55   1                                           ;   CBO  OCB   
  49  57   1                                           ;   CBO  HBS   
  49  58   1                                           ;   CBO  CBR   
  49  61   1                                           ;   CBO  NBS   
  50  52   1                                           ;   HBT  SCA   
  50  56   1                                           ;   HBT  CBN   
  50  60   1                                           ;   HBT  CBQ   
  51  56   1                                           ;   CBP  CBN   
  51  59   1                                           ;   CBP  HBU   
  51  62   1                                           ;   CBP  HB0   
  51  63   1                                           ;   CBP  CBT   
  52  58   1                                           ;   SCA  CBR   
  52  61   1                                           ;   SCA  NBS   
  53  60   1                                           ;   OCC  CBQ   
  54  60   1                                           ;   OCD  CBQ   
  55  60   1                                           ;   OCB  CBQ   
  56  61   1                                           ;   CBN  NBS   
  57  59   1                                           ;   HBS  HBU   
  57  60   1                                           ;   HBS  CBQ   
  58  62   1                                           ;   CBR  HB0   
  58  63   1                                           ;   CBR  CBT   
  59  61   1                                           ;   HBU  NBS   
  60  64   1                                           ;   CBQ  CBU   
  60  74   1                                           ;   CBQ  CBX   
  61  65   1                                           ;   NBS  HBV   
  61  66   1                                           ;   NBS  CBV   
  61  72   1                                           ;   NBS  CBY   
  61  75   1                                           ;   NBS  HBX   
  62  64   1                                           ;   HB0  CBU   
  62  74   1                                           ;   HB0  CBX   
  63  67   1                                           ;   CBT  HBW   
  63  68   1                                           ;   CBT  CBW   
  63  73   1                                           ;   CBT  HBY   
  64  69   1                                           ;   CBU  NBZ   
  64  72   1                                           ;   CBU  CBY   
  64  75   1                                           ;   CBU  HBX   
  65  67   1                                           ;   HBV  HBW   
  65  68   1                                           ;   HBV  CBW   
  65  74   1                                           ;   HBV  CBX   
  66  70   1                                           ;   CBV  HB2   
  66  71   1                                           ;   CBV  HB1   
  66  73   1                                           ;   CBV  HBY   
  66  74   1                                           ;   CBV  CBX   
  67  69   1                                           ;   HBW  NBZ   
  67  72   1                                           ;   HBW  CBY   
  68  75   1                                           ;   CBW  HBX   
  69  73   1                                           ;   NBZ  HBY   
  69  74   1                                           ;   NBZ  CBX   
  70  72   1                                           ;   HB2  CBY   
  71  72   1                                           ;   HB1  CBY   
  73  75   1                                           ;   HBY  HBX   

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    109.5       520.0    109.5       520.0 ;   CBE  CBD  CBC   
   2   3   4   2    109.5       520.0    109.5       520.0 ;   CBD  CBC  CBB   
   3   4   5   2    109.5       520.0    109.5       520.0 ;   CBC  CBB  CBA   
   4   5   6   2    109.5       520.0    109.5       520.0 ;   CBB  CBA  CAZ   
   5   6   7   2    109.5       520.0    109.5       520.0 ;   CBA  CAZ  CAY   
   6   7   8   2    109.5       520.0    109.5       520.0 ;   CAZ  CAY  CAX   
   7   8   9   2    109.5       520.0    109.5       520.0 ;   CAY  CAX  CAW   
   8   9  10   2    109.5       520.0    109.5       520.0 ;   CAX  CAW  CAV   
   9  10  11   2    109.5       520.0    109.5       520.0 ;   CAW  CAV  CAU   
  10  11  12   2    109.5       520.0    109.5       520.0 ;   CAV  CAU  CAT   
  11  12  13   2    109.5       520.0    109.5       520.0 ;   CAU  CAT  CAS   
  12  13  14   2    109.5       520.0    109.5       520.0 ;   CAT  CAS  CAR   
  13  14  15   2    109.5       520.0    109.5       520.0 ;   CAS  CAR  CAQ   
  14  15  16   2    109.5       520.0    109.5       520.0 ;   CAR  CAQ  CAP   
  15  16  17   2    109.5       520.0    109.5       520.0 ;   CAQ  CAP  CAO   
  16  17  18   2    109.5       520.0    109.5       520.0 ;   CAP  CAO  CAN   
  17  18  19   2    109.5       520.0    109.5       520.0 ;   CAO  CAN  CAL   
  18  19  20   2    121.0       685.0    121.0       685.0 ;   CAN  CAL  OAM   
  18  19  21   2    115.0       610.0    115.0       610.0 ;   CAN  CAL  CAJ   
  20  19  21   2    121.0       685.0    121.0       685.0 ;   OAM  CAL  CAJ   
  19  21  22   2    120.0       560.0    120.0       560.0 ;   CAL  CAJ  CAK   
  19  21  29   2    120.0       560.0    120.0       560.0 ;   CAL  CAJ  CAI   
  22  21  29   2    120.0       560.0    120.0       560.0 ;   CAK  CAJ  CAI   
  21  22  23   2    120.0       505.0    120.0       505.0 ;   CAJ  CAK  HAK   
  21  22  24   2    120.0       505.0    120.0       505.0 ;   CAJ  CAK  CAE   
  23  22  24   2    120.0       505.0    120.0       505.0 ;   HAK  CAK  CAE   
  22  24  25   2    120.0       560.0    120.0       560.0 ;   CAK  CAE  SAB   
  22  24  33   2    120.0       560.0    120.0       560.0 ;   CAK  CAE  CAF   
  25  24  33   2    120.0       560.0    120.0       560.0 ;   SAB  CAE  CAF   
  24  25  26   2    109.5       518.0    109.5       518.0 ;   CAE  SAB  OAC   
  24  25  27   2    109.5       518.0    109.5       518.0 ;   CAE  SAB  OAD   
  24  25  28   2    109.5       518.0    109.5       518.0 ;   CAE  SAB  OAA   
  26  25  27   2    109.5       518.0    109.5       518.0 ;   OAC  SAB  OAD   
  26  25  28   2    109.5       518.0    109.5       518.0 ;   OAC  SAB  OAA   
  27  25  28   2    109.5       518.0    109.5       518.0 ;   OAD  SAB  OAA   
  21  29  30   2    120.0       505.0    120.0       505.0 ;   CAJ  CAI  HAI   
  21  29  31   2    120.0       505.0    120.0       505.0 ;   CAJ  CAI  CAG   
  30  29  31   2    120.0       505.0    120.0       505.0 ;   HAI  CAI  CAG   
  29  31  32   2    120.0       505.0    120.0       505.0 ;   CAI  CAG  HAG   
  29  31  33   2    120.0       505.0    120.0       505.0 ;   CAI  CAG  CAF   
  32  31  33   2    120.0       505.0    120.0       505.0 ;   HAG  CAG  CAF   
  24  33  31   2    120.0       560.0    120.0       560.0 ;   CAE  CAF  CAG   
  24  33  34   2    115.0       610.0    115.0       610.0 ;   CAE  CAF  NAH   
  31  33  34   2    120.0       560.0    120.0       560.0 ;   CAG  CAF  NAH   
  33  34  35   2    123.0       415.0    123.0       415.0 ;   CAF  NAH  HAH   
  33  34  36   2    117.0       635.0    117.0       635.0 ;   CAF  NAH  CBF   
  35  34  36   2    123.0       415.0    123.0       415.0 ;   HAH  NAH  CBF   
  34  36  37   2    120.0       560.0    120.0       560.0 ;   NAH  CBF  CBJ   
  34  36  41   2    120.0       560.0    120.0       560.0 ;   NAH  CBF  CBG   
  37  36  41   2    120.0       560.0    120.0       560.0 ;   CBJ  CBF  CBG   
  36  37  38   2    120.0       505.0    120.0       505.0 ;   CBF  CBJ  HBQ   
  36  37  39   2    120.0       505.0    120.0       505.0 ;   CBF  CBJ  CBK   
  38  37  39   2    120.0       505.0    120.0       505.0 ;   HBQ  CBJ  CBK   
  37  39  40   2    120.0       505.0    120.0       505.0 ;   CBJ  CBK  HBR   
  37  39  45   2    120.0       505.0    120.0       505.0 ;   CBJ  CBK  CBI   
  40  39  45   2    120.0       505.0    120.0       505.0 ;   HBR  CBK  CBI   
  36  41  42   2    120.0       505.0    120.0       505.0 ;   CBF  CBG  HBO   
  36  41  43   2    120.0       505.0    120.0       505.0 ;   CBF  CBG  CBH   
  42  41  43   2    120.0       505.0    120.0       505.0 ;   HBO  CBG  CBH   
  41  43  44   2    120.0       505.0    120.0       505.0 ;   CBG  CBH  HBP   
  41  43  45   2    120.0       505.0    120.0       505.0 ;   CBG  CBH  CBI   
  44  43  45   2    120.0       505.0    120.0       505.0 ;   HBP  CBH  CBI   
  39  45  43   2    120.0       560.0    120.0       560.0 ;   CBK  CBI  CBH   
  39  45  46   2    120.0       560.0    120.0       560.0 ;   CBK  CBI  NBL   
  43  45  46   2    120.0       560.0    120.0       560.0 ;   CBH  CBI  NBL   
  45  46  47   2    123.0       415.0    123.0       415.0 ;   CBI  NBL  HBZ   
  45  46  48   2    117.0       635.0    117.0       635.0 ;   CBI  NBL  CBM   
  47  46  48   2    123.0       415.0    123.0       415.0 ;   HBZ  NBL  CBM   
  46  48  49   2    120.0       560.0    120.0       560.0 ;   NBL  CBM  CBO   
  46  48  56   2    120.0       560.0    120.0       560.0 ;   NBL  CBM  CBN   
  49  48  56   2    120.0       560.0    120.0       560.0 ;   CBO  CBM  CBN   
  48  49  50   2    120.0       505.0    120.0       505.0 ;   CBM  CBO  HBT   
  48  49  51   2    120.0       505.0    120.0       505.0 ;   CBM  CBO  CBP   
  50  49  51   2    120.0       505.0    120.0       505.0 ;   HBT  CBO  CBP   
  49  51  52   2    120.0       560.0    120.0       560.0 ;   CBO  CBP  SCA   
  49  51  60   2    120.0       560.0    120.0       560.0 ;   CBO  CBP  CBQ   
  52  51  60   2    120.0       560.0    120.0       560.0 ;   SCA  CBP  CBQ   
  51  52  53   2    109.5       518.0    109.5       518.0 ;   CBP  SCA  OCC   
  51  52  54   2    109.5       518.0    109.5       518.0 ;   CBP  SCA  OCD   
  51  52  55   2    109.5       518.0    109.5       518.0 ;   CBP  SCA  OCB   
  53  52  54   2    109.5       518.0    109.5       518.0 ;   OCC  SCA  OCD   
  53  52  55   2    109.5       518.0    109.5       518.0 ;   OCC  SCA  OCB   
  54  52  55   2    109.5       518.0    109.5       518.0 ;   OCD  SCA  OCB   
  48  56  57   2    120.0       505.0    120.0       505.0 ;   CBM  CBN  HBS   
  48  56  58   2    120.0       505.0    120.0       505.0 ;   CBM  CBN  CBR   
  57  56  58   2    120.0       505.0    120.0       505.0 ;   HBS  CBN  CBR   
  56  58  59   2    120.0       505.0    120.0       505.0 ;   CBN  CBR  HBU   
  56  58  60   2    120.0       505.0    120.0       505.0 ;   CBN  CBR  CBQ   
  59  58  60   2    120.0       505.0    120.0       505.0 ;   HBU  CBR  CBQ   
  51  60  58   2    120.0       560.0    120.0       560.0 ;   CBP  CBQ  CBR   
  51  60  61   2    115.0       610.0    115.0       610.0 ;   CBP  CBQ  NBS   
  58  60  61   2    120.0       560.0    120.0       560.0 ;   CBR  CBQ  NBS   
  60  61  62   2    123.0       415.0    123.0       415.0 ;   CBQ  NBS  HB0   
  60  61  63   2    117.0       635.0    117.0       635.0 ;   CBQ  NBS  CBT   
  62  61  63   2    123.0       415.0    123.0       415.0 ;   HB0  NBS  CBT   
  61  63  64   2    120.0       560.0    120.0       560.0 ;   NBS  CBT  CBU   
  61  63  74   2    120.0       560.0    120.0       560.0 ;   NBS  CBT  CBX   
  64  63  74   2    120.0       560.0    120.0       560.0 ;   CBU  CBT  CBX   
  63  64  65   2    120.0       505.0    120.0       505.0 ;   CBT  CBU  HBV   
  63  64  66   2    120.0       505.0    120.0       505.0 ;   CBT  CBU  CBV   
  65  64  66   2    120.0       505.0    120.0       505.0 ;   HBV  CBU  CBV   
  64  66  67   2    120.0       505.0    120.0       505.0 ;   CBU  CBV  HBW   
  64  66  68   2    120.0       505.0    120.0       505.0 ;   CBU  CBV  CBW   
  67  66  68   2    120.0       505.0    120.0       505.0 ;   HBW  CBV  CBW   
  66  68  69   2    120.0       560.0    120.0       560.0 ;   CBV  CBW  NBZ   
  66  68  72   2    120.0       560.0    120.0       560.0 ;   CBV  CBW  CBY   
  69  68  72   2    120.0       560.0    120.0       560.0 ;   NBZ  CBW  CBY   
  68  69  70   2    120.0       390.0    120.0       390.0 ;   CBW  NBZ  HB2   
  68  69  71   2    120.0       390.0    120.0       390.0 ;   CBW  NBZ  HB1   
  70  69  71   2    120.0       445.0    120.0       445.0 ;   HB2  NBZ  HB1   
  68  72  73   2    120.0       505.0    120.0       505.0 ;   CBW  CBY  HBY   
  68  72  74   2    120.0       505.0    120.0       505.0 ;   CBW  CBY  CBX   
  73  72  74   2    120.0       505.0    120.0       505.0 ;   HBY  CBY  CBX   
  63  74  72   2    120.0       505.0    120.0       505.0 ;   CBT  CBX  CBY   
  63  74  75   2    120.0       505.0    120.0       505.0 ;   CBT  CBX  HBX   
  72  74  75   2    120.0       505.0    120.0       505.0 ;   CBY  CBX  HBX   

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
  19  18  20  21   2      0.0  167.4        0.0  167.4   ; imp   CAL  CAN  OAM  CAJ   
  21  19  29  22   2      0.0  167.4        0.0  167.4   ; imp   CAJ  CAL  CAI  CAK   
  22  21  24  23   2      0.0  167.4        0.0  167.4   ; imp   CAK  CAJ  CAE  HAK   
  24  22  25  33   2      0.0  167.4        0.0  167.4   ; imp   CAE  CAK  SAB  CAF   
  25  24  27  26   2     35.3  334.8       35.3  334.8   ; imp   SAB  CAE  OAD  OAC   
  29  21  31  30   2      0.0  167.4        0.0  167.4   ; imp   CAI  CAJ  CAG  HAI   
  31  29  33  32   2      0.0  167.4        0.0  167.4   ; imp   CAG  CAI  CAF  HAG   
  33  34  31  24   2      0.0  167.4        0.0  167.4   ; imp   CAF  NAH  CAG  CAE   
  34  33  35  36   2      0.0  167.4        0.0  167.4   ; imp   NAH  CAF  HAH  CBF   
  36  34  41  37   2      0.0  167.4        0.0  167.4   ; imp   CBF  NAH  CBG  CBJ   
  37  36  39  38   2      0.0  167.4        0.0  167.4   ; imp   CBJ  CBF  CBK  HBQ   
  39  37  45  40   2      0.0  167.4        0.0  167.4   ; imp   CBK  CBJ  CBI  HBR   
  41  36  43  42   2      0.0  167.4        0.0  167.4   ; imp   CBG  CBF  CBH  HBO   
  43  41  45  44   2      0.0  167.4        0.0  167.4   ; imp   CBH  CBG  CBI  HBP   
  45  46  43  39   2      0.0  167.4        0.0  167.4   ; imp   CBI  NBL  CBH  CBK   
  46  45  47  48   2      0.0  167.4        0.0  167.4   ; imp   NBL  CBI  HBZ  CBM   
  48  46  56  49   2      0.0  167.4        0.0  167.4   ; imp   CBM  NBL  CBN  CBO   
  49  48  51  50   2      0.0  167.4        0.0  167.4   ; imp   CBO  CBM  CBP  HBT   
  51  49  52  60   2      0.0  167.4        0.0  167.4   ; imp   CBP  CBO  SCA  CBQ   
  52  51  54  53   2     35.3  334.8       35.3  334.8   ; imp   SCA  CBP  OCD  OCC   
  56  48  58  57   2      0.0  167.4        0.0  167.4   ; imp   CBN  CBM  CBR  HBS   
  58  56  60  59   2      0.0  167.4        0.0  167.4   ; imp   CBR  CBN  CBQ  HBU   
  60  61  58  51   2      0.0  167.4        0.0  167.4   ; imp   CBQ  NBS  CBR  CBP   
  61  60  62  63   2      0.0  167.4        0.0  167.4   ; imp   NBS  CBQ  HB0  CBT   
  63  61  74  64   2      0.0  167.4        0.0  167.4   ; imp   CBT  NBS  CBX  CBU   
  64  63  66  65   2      0.0  167.4        0.0  167.4   ; imp   CBU  CBT  CBV  HBV   
  66  64  68  67   2      0.0  167.4        0.0  167.4   ; imp   CBV  CBU  CBW  HBW   
  68  72  69  66   2      0.0  167.4        0.0  167.4   ; imp   CBW  CBY  NBZ  CBV   
  69  68  71  70   2      0.0  167.4        0.0  167.4   ; imp   NBZ  CBW  HB1  HB2   
  72  68  74  73   2      0.0  167.4        0.0  167.4   ; imp   CBY  CBW  CBX  HBY   
  74  63  72  75   2      0.0  167.4        0.0  167.4   ; imp   CBX  CBT  CBY  HBX   
  63  64  66  68   2      0.0  209.3        0.0  209.3   ; imp   CBT  CBU  CBV  CBW   
  64  66  68  72   2      0.0  209.3        0.0  209.3   ; imp   CBU  CBV  CBW  CBY   
  66  68  72  74   2      0.0  209.3        0.0  209.3   ; imp   CBV  CBW  CBY  CBX   
  68  72  74  63   2      0.0  209.3        0.0  209.3   ; imp   CBW  CBY  CBX  CBT   
  72  74  63  64   2      0.0  209.3        0.0  209.3   ; imp   CBY  CBX  CBT  CBU   
  74  63  64  66   2      0.0  209.3        0.0  209.3   ; imp   CBX  CBT  CBU  CBV   
  48  49  51  60   2      0.0  209.3        0.0  209.3   ; imp   CBM  CBO  CBP  CBQ   
  49  51  60  58   2      0.0  209.3        0.0  209.3   ; imp   CBO  CBP  CBQ  CBR   
  51  60  58  56   2      0.0  209.3        0.0  209.3   ; imp   CBP  CBQ  CBR  CBN   
  60  58  56  48   2      0.0  209.3        0.0  209.3   ; imp   CBQ  CBR  CBN  CBM   
  58  56  48  49   2      0.0  209.3        0.0  209.3   ; imp   CBR  CBN  CBM  CBO   
  56  48  49  51   2      0.0  209.3        0.0  209.3   ; imp   CBN  CBM  CBO  CBP   
  36  37  39  45   2      0.0  209.3        0.0  209.3   ; imp   CBF  CBJ  CBK  CBI   
  37  39  45  43   2      0.0  209.3        0.0  209.3   ; imp   CBJ  CBK  CBI  CBH   
  39  45  43  41   2      0.0  209.3        0.0  209.3   ; imp   CBK  CBI  CBH  CBG   
  45  43  41  36   2      0.0  209.3        0.0  209.3   ; imp   CBI  CBH  CBG  CBF   
  43  41  36  37   2      0.0  209.3        0.0  209.3   ; imp   CBH  CBG  CBF  CBJ   
  41  36  37  39   2      0.0  209.3        0.0  209.3   ; imp   CBG  CBF  CBJ  CBK   
  21  22  24  33   2      0.0  209.3        0.0  209.3   ; imp   CAJ  CAK  CAE  CAF   
  22  24  33  31   2      0.0  209.3        0.0  209.3   ; imp   CAK  CAE  CAF  CAG   
  24  33  31  29   2      0.0  209.3        0.0  209.3   ; imp   CAE  CAF  CAG  CAI   
  33  31  29  21   2      0.0  209.3        0.0  209.3   ; imp   CAF  CAG  CAI  CAJ   
  31  29  21  22   2      0.0  209.3        0.0  209.3   ; imp   CAG  CAI  CAJ  CAK   
  29  21  22  24   2      0.0  209.3        0.0  209.3   ; imp   CAI  CAJ  CAK  CAE   
   4   3   2   1   1      0.0    5.9 3      0.0    5.9 3 ; dih   CBB  CBC  CBD  CBE   
   5   4   3   2   1      0.0    5.9 3      0.0    5.9 3 ; dih   CBA  CBB  CBC  CBD   
   6   5   4   3   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAZ  CBA  CBB  CBC   
   7   6   5   4   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAY  CAZ  CBA  CBB   
   8   7   6   5   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAX  CAY  CAZ  CBA   
   9   8   7   6   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAW  CAX  CAY  CAZ   
  10   9   8   7   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAV  CAW  CAX  CAY   
  11  10   9   8   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAU  CAV  CAW  CAX   
  12  11  10   9   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAT  CAU  CAV  CAW   
  13  12  11  10   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAS  CAT  CAU  CAV   
  14  13  12  11   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAR  CAS  CAT  CAU   
  15  14  13  12   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAQ  CAR  CAS  CAT   
  16  15  14  13   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAP  CAQ  CAR  CAS   
  17  16  15  14   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAO  CAP  CAQ  CAR   
  18  17  16  15   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAN  CAO  CAP  CAQ   
  19  18  17  16   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAL  CAN  CAO  CAP   
  17  18  19  21   1      0.0    1.0 6      0.0    1.0 6 ; dih   CAO  CAN  CAL  CAJ   
  29  21  19  18   1    180.0    5.9 2    180.0    5.9 2 ; dih   CAI  CAJ  CAL  CAN   
  22  24  25  28   1      0.0    4.2 3      0.0    4.2 3 ; dih   CAK  CAE  SAB  OAA   
  24  33  34  36   1    180.0   33.5 2    180.0   33.5 2 ; dih   CAE  CAF  NAH  CBF   
  41  36  34  33   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBG  CBF  NAH  CAF   
  39  45  46  48   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBK  CBI  NBL  CBM   
  56  48  46  45   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBN  CBM  NBL  CBI   
  49  51  52  55   1      0.0    4.2 3      0.0    4.2 3 ; dih   CBO  CBP  SCA  OCB   
  51  60  61  63   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBP  CBQ  NBS  CBT   
  74  63  61  60   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBX  CBT  NBS  CBQ   
  66  68  69  71   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBV  CBW  NBZ  HB1   


AMOx4.mdp

; Define can be used to control processes
define = -DFLEXIBLE
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 250.0 ; Stop minimization when the maximum force < 1.0 kJ/mol
nsteps = 5000 ; Maximum number of (minimization) steps to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions (yes/no)

AMOx4conf.pdb

HEADER    Glycine aRginine prOline Methionine Alanine Cystine Serine
REMARK    THIS IS A SIMULATION BOX
CRYST1   95.137   95.137   95.137  90.00  90.00  90.00 P 1           1
MODEL
ATOM      1  CBE AMO S   1      40.976  55.387  19.931  1.00  0.00
ATOM      2  CBD AMO S   1      42.076  55.277  20.981  1.00  0.00
ATOM      3  CBC AMO S   1      41.466  54.917  22.331  1.00  0.00
ATOM      4  CBB AMO S   1      42.576  54.807  23.381  1.00  0.00
ATOM      5  CBA AMO S   1      41.976  54.437  24.731  1.00  0.00
ATOM      6  CAZ AMO S   1      43.106  54.287  25.751  1.00  0.00
ATOM      7  CAY AMO S   1      42.536  53.877  27.111  1.00  0.00
ATOM      8  CAX AMO S   1      43.696  53.677  28.091  1.00  0.00
ATOM      9  CAW AMO S   1      43.166  53.217  29.451  1.00  0.00
ATOM     10  CAV AMO S   1      44.366  52.947  30.361  1.00  0.00
ATOM     11  CAU AMO S   1      43.896  52.427  31.721  1.00  0.00
ATOM     12  CAT AMO S   1      45.136  52.077  32.541  1.00  0.00
ATOM     13  CAS AMO S   1      44.736  51.507  33.911  1.00  0.00
ATOM     14  CAR AMO S   1      46.006  51.097  34.641  1.00  0.00
ATOM     15  CAQ AMO S   1      45.666  50.507  36.011  1.00  0.00
ATOM     16  CAP AMO S   1      46.966  50.047  36.671  1.00  0.00
ATOM     17  CAO AMO S   1      46.686  49.457  38.051  1.00  0.00
ATOM     18  CAN AMO S   1      47.976  48.897  38.681  1.00  0.00
ATOM     19  CAL AMO S   1      48.406  47.577  38.041  1.00  0.00
ATOM     20  OAM AMO S   1      48.906  47.527  36.911  1.00  0.00
ATOM     21  CAJ AMO S   1      48.236  46.407  38.791  1.00  0.00
ATOM     22  CAK AMO S   1      49.346  45.827  39.431  1.00  0.00
ATOM     23  HAK AMO S   1      50.346  46.267  39.301  1.00  0.00
ATOM     24  CAE AMO S   1      49.166  44.697  40.241  1.00  0.00
ATOM     25  SAB AMO S   1      50.616  43.767  40.651  1.00  0.00
ATOM     26  OAC AMO S   1      50.256  42.377  41.181  1.00  0.00
ATOM     27  OAD AMO S   1      51.466  43.597  39.401  1.00  0.00
ATOM     28  OAA AMO S   1      51.406  44.547  41.701  1.00  0.00
ATOM     29  CAI AMO S   1      46.946  45.847  38.951  1.00  0.00
ATOM     30  HAI AMO S   1      46.096  46.267  38.421  1.00  0.00
ATOM     31  CAG AMO S   1      46.766  44.727  39.781  1.00  0.00
ATOM     32  HAG AMO S   1      45.766  44.307  39.891  1.00  0.00
ATOM     33  CAF AMO S   1      47.876  44.167  40.471  1.00  0.00
ATOM     34  NAH AMO S   1      47.686  43.787  41.751  1.00  0.00
ATOM     35  HAH AMO S   1      48.326  44.177  42.421  1.00  0.00
ATOM     36  CBF AMO S   1      46.766  42.927  42.231  1.00  0.00
ATOM     37  CBJ AMO S   1      46.456  43.107  43.591  1.00  0.00
ATOM     38  HBQ AMO S   1      47.056  43.767  44.221  1.00  0.00
ATOM     39  CBK AMO S   1      45.366  42.417  44.161  1.00  0.00
ATOM     40  HBR AMO S   1      45.146  42.547  45.221  1.00  0.00
ATOM     41  CBG AMO S   1      46.006  42.027  41.441  1.00  0.00
ATOM     42  HBO AMO S   1      46.276  41.837  40.401  1.00  0.00
ATOM     43  CBH AMO S   1      44.916  41.337  42.011  1.00  0.00
ATOM     44  HBP AMO S   1      44.326  40.657  41.391  1.00  0.00
ATOM     45  CBI AMO S   1      44.586  41.537  43.381  1.00  0.00
ATOM     46  NBL AMO S   1      43.336  41.337  43.831  1.00  0.00
ATOM     47  HBZ AMO S   1      42.986  41.997  44.501  1.00  0.00
ATOM     48  CBM AMO S   1      42.506  40.337  43.481  1.00  0.00
ATOM     49  CBO AMO S   1      42.946  39.007  43.301  1.00  0.00
ATOM     50  HBT AMO S   1      43.996  38.797  43.121  1.00  0.00
ATOM     51  CBP AMO S   1      42.026  37.937  43.411  1.00  0.00
ATOM     52  SCA AMO S   1      42.566  36.357  42.831  1.00  0.00
ATOM     53  OCC AMO S   1      43.466  35.727  43.891  1.00  0.00
ATOM     54  OCD AMO S   1      41.386  35.427  42.551  1.00  0.00
ATOM     55  OCB AMO S   1      43.336  36.547  41.531  1.00  0.00
ATOM     56  CBN AMO S   1      41.146  40.577  43.761  1.00  0.00
ATOM     57  HBS AMO S   1      40.786  41.597  43.861  1.00  0.00
ATOM     58  CBR AMO S   1      40.226  39.517  43.891  1.00  0.00
ATOM     59  HBU AMO S   1      39.186  39.737  44.121  1.00  0.00
ATOM     60  CBQ AMO S   1      40.676  38.187  43.751  1.00  0.00
ATOM     61  NBS AMO S   1      40.136  37.247  44.551  1.00  0.00
ATOM     62  HB0 AMO S   1      40.786  36.717  45.111  1.00  0.00
ATOM     63  CBT AMO S   1      38.826  36.927  44.691  1.00  0.00
ATOM     64  CBU AMO S   1      38.516  36.187  45.851  1.00  0.00
ATOM     65  HBV AMO S   1      39.296  35.857  46.531  1.00  0.00
ATOM     66  CBV AMO S   1      37.176  35.857  46.131  1.00  0.00
ATOM     67  HBW AMO S   1      36.926  35.287  47.021  1.00  0.00
ATOM     68  CBW AMO S   1      36.156  36.287  45.241  1.00  0.00
ATOM     69  NBZ AMO S   1      34.886  35.987  45.511  1.00  0.00
ATOM     70  HB2 AMO S   1      34.166  36.277  44.891  1.00  0.00
ATOM     71  HB1 AMO S   1      34.666  35.467  46.331  1.00  0.00
ATOM     72  CBY AMO S   1      36.456  37.027  44.081  1.00  0.00
ATOM     73  HBY AMO S   1      35.666  37.347  43.401  1.00  0.00
ATOM     74  CBX AMO S   1      37.796  37.347  43.801  1.00  0.00
ATOM     75  HBX AMO S   1      38.046  37.877  42.881  1.00  0.00
ATOM     76  CBE AMO S   2      55.680  60.867  46.291  1.00  0.00
ATOM     77  CBD AMO S   2      55.699  59.349  46.154  1.00  0.00
ATOM     78  CBC AMO S   2      55.189  58.709  47.441  1.00  0.00
ATOM     79  CBB AMO S   2      55.209  57.184  47.297  1.00  0.00
ATOM     80  CBA AMO S   2      54.690  56.537  48.574  1.00  0.00
ATOM     81  CAZ AMO S   2      54.676  55.019  48.390  1.00  0.00
ATOM     82  CAY AMO S   2      54.121  54.342  49.646  1.00  0.00
ATOM     83  CAX AMO S   2      54.064  52.830  49.405  1.00  0.00
ATOM     84  CAW AMO S   2      53.467  52.123  50.624  1.00  0.00
ATOM     85  CAV AMO S   2      53.350  50.633  50.298  1.00  0.00
ATOM     86  CAU AMO S   2      52.703  49.882  51.464  1.00  0.00
ATOM     87  CAT AMO S   2      52.518  48.428  51.037  1.00  0.00
ATOM     88  CAS AMO S   2      51.832  47.620  52.151  1.00  0.00
ATOM     89  CAR AMO S   2      51.596  46.209  51.634  1.00  0.00
ATOM     90  CAQ AMO S   2      50.900  45.361  52.700  1.00  0.00
ATOM     91  CAP AMO S   2      50.622  43.979  52.108  1.00  0.00
ATOM     92  CAO AMO S   2      49.936  43.084  53.136  1.00  0.00
ATOM     93  CAN AMO S   2      49.559  41.724  52.516  1.00  0.00
ATOM     94  CAL AMO S   2      48.353  41.828  51.583  1.00  0.00
ATOM     95  OAM AMO S   2      48.432  42.346  50.463  1.00  0.00
ATOM     96  CAJ AMO S   2      47.139  41.293  52.030  1.00  0.00
ATOM     97  CAK AMO S   2      46.714  40.042  51.547  1.00  0.00
ATOM     98  HAK AMO S   2      47.312  39.515  50.788  1.00  0.00
ATOM     99  CAE AMO S   2      45.535  39.471  52.046  1.00  0.00
ATOM    100  SAB AMO S   2      44.829  38.145  51.109  1.00  0.00
ATOM    101  OAC AMO S   2      43.377  37.884  51.519  1.00  0.00
ATOM    102  OAD AMO S   2      44.850  38.514  49.634  1.00  0.00
ATOM    103  OAA AMO S   2      45.677  36.894  51.333  1.00  0.00
ATOM    104  CAI AMO S   2      46.376  41.979  53.005  1.00  0.00
ATOM    105  HAI AMO S   2      46.679  42.965  53.345  1.00  0.00
ATOM    106  CAG AMO S   2      45.206  41.393  53.519  1.00  0.00
ATOM    107  HAG AMO S   2      44.629  41.937  54.267  1.00  0.00
ATOM    108  CAF AMO S   2      44.799  40.107  53.072  1.00  0.00
ATOM    109  NAH AMO S   2      44.337  39.243  53.999  1.00  0.00
ATOM    110  HAH AMO S   2      44.794  38.347  54.025  1.00  0.00
ATOM    111  CBF AMO S   2      43.323  39.424  54.867  1.00  0.00
ATOM    112  CBJ AMO S   2      43.392  38.619  56.018  1.00  0.00
ATOM    113  HBQ AMO S   2      44.110  37.799  56.087  1.00  0.00
ATOM    114  CBK AMO S   2      42.514  38.856  57.096  1.00  0.00
ATOM    115  HBR AMO S   2      42.561  38.214  57.976  1.00  0.00
ATOM    116  CBG AMO S   2      42.350  40.452  54.775  1.00  0.00
ATOM    117  HBO AMO S   2      42.251  41.042  53.863  1.00  0.00
ATOM    118  CBH AMO S   2      41.472  40.689  55.853  1.00  0.00
ATOM    119  HBP AMO S   2      40.735  41.494  55.780  1.00  0.00
ATOM    120  CBI AMO S   2      41.557  39.891  57.028  1.00  0.00
ATOM    121  NBL AMO S   2      41.142  40.359  58.218  1.00  0.00
ATOM    122  HBZ AMO S   2      41.709  40.132  59.014  1.00  0.00
ATOM    123  CBM AMO S   2      40.040  41.095  58.452  1.00  0.00
ATOM    124  CBO AMO S   2      38.806  40.846  57.813  1.00  0.00
ATOM    125  HBT AMO S   2      38.772  40.278  56.888  1.00  0.00
ATOM    126  CBP AMO S   2      37.600  41.291  58.406  1.00  0.00
ATOM    127  SCA AMO S   2      36.152  41.259  57.393  1.00  0.00
ATOM    128  OCC AMO S   2      35.626  39.827  57.334  1.00  0.00
ATOM    129  OCD AMO S   2      35.061  42.177  57.942  1.00  0.00
ATOM    130  OCB AMO S   2      36.518  41.744  55.997  1.00  0.00
ATOM    131  CBN AMO S   2      40.050  41.794  59.676  1.00  0.00
ATOM    132  HBS AMO S   2      40.995  42.028  60.157  1.00  0.00
ATOM    133  CBR AMO S   2      38.853  42.224  60.284  1.00  0.00
ATOM    134  HBU AMO S   2      38.896  42.750  61.235  1.00  0.00
ATOM    135  CBQ AMO S   2      37.619  41.939  59.663  1.00  0.00
ATOM    136  NBS AMO S   2      36.571  41.625  60.450  1.00  0.00
ATOM    137  HB0 AMO S   2      36.126  40.740  60.261  1.00  0.00
ATOM    138  CBT AMO S   2      36.042  42.357  61.462  1.00  0.00
ATOM    139  CBU AMO S   2      35.212  41.636  62.346  1.00  0.00
ATOM    140  HBV AMO S   2      34.980  40.589  62.169  1.00  0.00
ATOM    141  CBV AMO S   2      34.663  42.281  63.470  1.00  0.00
ATOM    142  HBW AMO S   2      34.022  41.736  64.157  1.00  0.00
ATOM    143  CBW AMO S   2      34.965  43.649  63.700  1.00  0.00
ATOM    144  NBZ AMO S   2      34.457  44.258  64.771  1.00  0.00
ATOM    145  HB2 AMO S   2      34.657  45.217  64.937  1.00  0.00
ATOM    146  HB1 AMO S   2      33.873  43.750  65.397  1.00  0.00
ATOM    147  CBY AMO S   2      35.794  44.377  62.824  1.00  0.00
ATOM    148  HBY AMO S   2      36.015  45.429  63.006  1.00  0.00
ATOM    149  CBX AMO S   2      36.333  43.731  61.698  1.00  0.00
ATOM    150  HBX AMO S   2      36.936  44.296  60.986  1.00  0.00
ATOM    151  CBE AMO S   3      53.853  69.094  73.884  1.00  0.00
ATOM    152  CBD AMO S   3      54.067  69.162  72.376  1.00  0.00
ATOM    153  CBC AMO S   3      53.581  67.871  71.728  1.00  0.00
ATOM    154  CBB AMO S   3      53.797  67.947  70.213  1.00  0.00
ATOM    155  CBA AMO S   3      53.304  66.665  69.555  1.00  0.00
ATOM    156  CAZ AMO S   3      53.487  66.782  68.041  1.00  0.00
ATOM    157  CAY AMO S   3      52.964  65.522  67.349  1.00  0.00
ATOM    158  CAX AMO S   3      53.106  65.697  65.834  1.00  0.00
ATOM    159  CAW AMO S   3      52.545  64.474  65.105  1.00  0.00
ATOM    160  CAV AMO S   3      52.630  64.739  63.600  1.00  0.00
ATOM    161  CAU AMO S   3      52.028  63.568  62.820  1.00  0.00
ATOM    162  CAT AMO S   3      52.044  63.938  61.338  1.00  0.00
ATOM    163  CAS AMO S   3      51.414  62.819  60.494  1.00  0.00
ATOM    164  CAR AMO S   3      51.379  63.282  59.045  1.00  0.00
ATOM    165  CAQ AMO S   3      50.745  62.209  58.158  1.00  0.00
ATOM    166  CAP AMO S   3      50.669  62.751  56.730  1.00  0.00
ATOM    167  CAO AMO S   3      50.052  61.714  55.796  1.00  0.00
ATOM    168  CAN AMO S   3      49.877  62.288  54.377  1.00  0.00
ATOM    169  CAL AMO S   3      48.711  63.273  54.292  1.00  0.00
ATOM    170  OAM AMO S   3      48.777  64.412  54.772  1.00  0.00
ATOM    171  CAJ AMO S   3      47.554  62.854  53.625  1.00  0.00
ATOM    172  CAK AMO S   3      47.310  63.298  52.314  1.00  0.00
ATOM    173  HAK AMO S   3      48.003  64.008  51.837  1.00  0.00
ATOM    174  CAE AMO S   3      46.190  62.823  51.618  1.00  0.00
ATOM    175  SAB AMO S   3      45.698  63.729  50.178  1.00  0.00
ATOM    176  OAC AMO S   3      44.273  63.368  49.752  1.00  0.00
ATOM    177  OAD AMO S   3      45.741  65.217  50.490  1.00  0.00
ATOM    178  OAA AMO S   3      46.683  63.416  49.053  1.00  0.00
ATOM    179  CAI AMO S   3      46.667  61.942  54.247  1.00  0.00
ATOM    180  HAI AMO S   3      46.830  61.634  55.276  1.00  0.00
ATOM    181  CAG AMO S   3      45.557  61.451  53.539  1.00  0.00
ATOM    182  HAG AMO S   3      44.883  60.752  54.034  1.00  0.00
ATOM    183  CAF AMO S   3      45.333  61.858  52.195  1.00  0.00
ATOM    184  NAH AMO S   3      44.941  60.913  51.316  1.00  0.00
ATOM    185  HAH AMO S   3      45.503  60.828  50.487  1.00  0.00
ATOM    186  CBF AMO S   3      43.872  60.096  51.401  1.00  0.00
ATOM    187  CBJ AMO S   3      43.988  58.909  50.656  1.00  0.00
ATOM    188  HBQ AMO S   3      44.798  58.774  49.937  1.00  0.00
ATOM    189  CBK AMO S   3      43.038  57.879  50.822  1.00  0.00
ATOM    190  HBR AMO S   3      43.124  56.971  50.225  1.00  0.00
ATOM    191  CBG AMO S   3      42.784  60.273  52.294  1.00  0.00
ATOM    192  HBO AMO S   3      42.655  61.214  52.832  1.00  0.00
ATOM    193  CBH AMO S   3      41.835  59.244  52.460  1.00  0.00
ATOM    194  HBP AMO S   3      41.008  59.382  53.162  1.00  0.00
ATOM    195  CBI AMO S   3      41.964  58.032  51.725  1.00  0.00
ATOM    196  NBL AMO S   3      41.440  56.882  52.182  1.00  0.00
ATOM    197  HBZ AMO S   3      41.993  56.054  52.060  1.00  0.00
ATOM    198  CBM AMO S   3      40.246  56.726  52.782  1.00  0.00
ATOM    199  CBO AMO S   3      39.082  57.404  52.355  1.00  0.00
ATOM    200  HBT AMO S   3      39.162  58.303  51.752  1.00  0.00
ATOM    201  CBP AMO S   3      37.805  56.880  52.667  1.00  0.00
ATOM    202  SCA AMO S   3      36.420  57.950  52.414  1.00  0.00
ATOM    203  OCC AMO S   3      36.080  57.967  50.926  1.00  0.00
ATOM    204  OCD AMO S   3      35.199  57.487  53.207  1.00  0.00
ATOM    205  OCB AMO S   3      36.787  59.350  52.887  1.00  0.00
ATOM    206  CBN AMO S   3      40.112  55.535  53.523  1.00  0.00
ATOM    207  HBS AMO S   3      40.997  55.026  53.893  1.00  0.00
ATOM    208  CBR AMO S   3      38.844  54.996  53.822  1.00  0.00
ATOM    209  HBU AMO S   3      38.777  54.068  54.385  1.00  0.00
ATOM    210  CBQ AMO S   3      37.684  55.654  53.360  1.00  0.00
ATOM    211  NBS AMO S   3      36.648  54.897  52.947  1.00  0.00
ATOM    212  HB0 AMO S   3      36.326  55.065  52.006  1.00  0.00
ATOM    213  CBT AMO S   3      35.987  53.941  53.645  1.00  0.00
ATOM    214  CBU AMO S   3      35.213  53.062  52.859  1.00  0.00
ATOM    215  HBV AMO S   3      35.121  53.201  51.786  1.00  0.00
ATOM    216  CBV AMO S   3      34.536  51.990  53.473  1.00  0.00
ATOM    217  HBW AMO S   3      33.937  51.307  52.878  1.00  0.00
ATOM    218  CBW AMO S   3      34.655  51.809  54.877  1.00  0.00
ATOM    219  NBZ AMO S   3      34.026  50.787  55.458  1.00  0.00
ATOM    220  HB2 AMO S   3      34.097  50.656  56.440  1.00  0.00
ATOM    221  HB1 AMO S   3      33.482  50.164  54.904  1.00  0.00
ATOM    222  CBY AMO S   3      35.426  52.681  55.669  1.00  0.00
ATOM    223  HBY AMO S   3      35.506  52.536  56.746  1.00  0.00
ATOM    224  CBX AMO S   3      36.093  53.755  55.053  1.00  0.00
ATOM    225  HBX AMO S   3      36.653  54.466  55.661  1.00  0.00
ATOM    226  CBE AMO S   4      55.617  66.293  39.703  1.00  0.00
ATOM    227  CBD AMO S   4      56.173  65.293  40.711  1.00  0.00
ATOM    228  CBC AMO S   4      55.593  63.910  40.439  1.00  0.00
ATOM    229  CBB AMO S   4      56.156  62.911  41.455  1.00  0.00
ATOM    230  CBA AMO S   4      55.590  61.523  41.183  1.00  0.00
ATOM    231  CAZ AMO S   4      56.201  60.535  42.178  1.00  0.00
ATOM    232  CAY AMO S   4      55.679  59.123  41.905  1.00  0.00
ATOM    233  CAX AMO S   4      56.355  58.151  42.877  1.00  0.00
ATOM    234  CAW AMO S   4      55.894  56.719  42.600  1.00  0.00
ATOM    235  CAV AMO S   4      56.663  55.783  43.535  1.00  0.00
ATOM    236  CAU AMO S   4      56.283  54.327  43.261  1.00  0.00
ATOM    237  CAT AMO S   4      57.158  53.441  44.146  1.00  0.00
ATOM    238  CAS AMO S   4      56.857  51.956  43.892  1.00  0.00
ATOM    239  CAR AMO S   4      57.818  51.129  44.733  1.00  0.00
ATOM    240  CAQ AMO S   4      57.572  49.636  44.508  1.00  0.00
ATOM    241  CAP AMO S   4      58.606  48.853  45.318  1.00  0.00
ATOM    242  CAO AMO S   4      58.400  47.351  45.139  1.00  0.00
ATOM    243  CAN AMO S   4      59.500  46.555  45.868  1.00  0.00
ATOM    244  CAL AMO S   4      60.838  46.609  45.131  1.00  0.00
ATOM    245  OAM AMO S   4      61.543  47.625  45.124  1.00  0.00
ATOM    246  CAJ AMO S   4      61.263  45.450  44.471  1.00  0.00
ATOM    247  CAK AMO S   4      62.245  44.636  45.064  1.00  0.00
ATOM    248  HAK AMO S   4      62.706  44.937  46.016  1.00  0.00
ATOM    249  CAE AMO S   4      62.619  43.437  44.440  1.00  0.00
ATOM    250  SAB AMO S   4      64.134  42.694  44.979  1.00  0.00
ATOM    251  OAC AMO S   4      64.628  41.646  43.979  1.00  0.00
ATOM    252  OAD AMO S   4      65.198  43.773  45.106  1.00  0.00
ATOM    253  OAA AMO S   4      63.894  42.052  46.345  1.00  0.00
ATOM    254  CAI AMO S   4      60.665  45.071  43.246  1.00  0.00
ATOM    255  HAI AMO S   4      59.940  45.721  42.765  1.00  0.00
ATOM    256  CAG AMO S   4      61.027  43.858  42.634  1.00  0.00
ATOM    257  HAG AMO S   4      60.559  43.583  41.689  1.00  0.00
ATOM    258  CAF AMO S   4      61.982  43.006  43.254  1.00  0.00
ATOM    259  NAH AMO S   4      61.733  41.681  43.245  1.00  0.00
ATOM    260  HAH AMO S   4      61.746  41.229  44.143  1.00  0.00
ATOM    261  CBF AMO S   4      61.501  40.890  42.179  1.00  0.00
ATOM    262  CBJ AMO S   4      60.782  39.717  42.471  1.00  0.00
ATOM    263  HBQ AMO S   4      60.604  39.410  43.503  1.00  0.00
ATOM    264  CBK AMO S   4      60.295  38.911  41.421  1.00  0.00
ATOM    265  HBR AMO S   4      59.757  37.993  41.657  1.00  0.00
ATOM    266  CBG AMO S   4      61.767  41.245  40.831  1.00  0.00
ATOM    267  HBO AMO S   4      62.374  42.121  40.597  1.00  0.00
ATOM    268  CBH AMO S   4      61.279  40.440  39.781  1.00  0.00
ATOM    269  HBP AMO S   4      61.475  40.729  38.746  1.00  0.00
ATOM    270  CBI AMO S   4      60.530  39.265  40.075  1.00  0.00
ATOM    271  NBL AMO S   4      59.646  38.767  39.195  1.00  0.00
ATOM    272  HBZ AMO S   4      58.783  38.418  39.569  1.00  0.00
ATOM    273  CBM AMO S   4      59.803  38.679  37.861  1.00  0.00
ATOM    274  CBO AMO S   4      61.025  38.309  37.258  1.00  0.00
ATOM    275  HBT AMO S   4      61.956  38.394  37.810  1.00  0.00
ATOM    276  CBP AMO S   4      61.033  37.771  35.949  1.00  0.00
ATOM    277  SCA AMO S   4      62.601  37.666  35.138  1.00  0.00
ATOM    278  OCC AMO S   4      63.348  36.447  35.672  1.00  0.00
ATOM    279  OCD AMO S   4      62.444  37.541  33.623  1.00  0.00
ATOM    280  OCB AMO S   4      63.390  38.936  35.428  1.00  0.00
ATOM    281  CBN AMO S   4      58.604  38.513  37.139  1.00  0.00
ATOM    282  HBS AMO S   4      57.661  38.831  37.574  1.00  0.00
ATOM    283  CBR AMO S   4      58.600  37.961  35.841  1.00  0.00
ATOM    284  HBU AMO S   4      57.656  37.834  35.317  1.00  0.00
ATOM    285  CBQ AMO S   4      59.819  37.554  35.257  1.00  0.00
ATOM    286  NBS AMO S   4      59.818  36.440  34.500  1.00  0.00
ATOM    287  HB0 AMO S   4      60.464  35.717  34.777  1.00  0.00
ATOM    288  CBT AMO S   4      59.056  36.176  33.410  1.00  0.00
ATOM    289  CBU AMO S   4      58.988  34.814  33.048  1.00  0.00
ATOM    290  HBV AMO S   4      59.564  34.063  33.581  1.00  0.00
ATOM    291  CBV AMO S   4      58.173  34.418  31.971  1.00  0.00
ATOM    292  HBW AMO S   4      58.113  33.373  31.683  1.00  0.00
ATOM    293  CBW AMO S   4      57.422  35.401  31.272  1.00  0.00
ATOM    294  NBZ AMO S   4      56.639  35.026  30.261  1.00  0.00
ATOM    295  HB2 AMO S   4      56.115  35.707  29.762  1.00  0.00
ATOM    296  HB1 AMO S   4      56.588  34.065  30.007  1.00  0.00
ATOM    297  CBY AMO S   4      57.483  36.762  31.627  1.00  0.00
ATOM    298  HBY AMO S   4      56.907  37.510  31.080  1.00  0.00
ATOM    299  CBX AMO S   4      58.305  37.155  32.698  1.00  0.00
ATOM    300  HBX AMO S   4      58.399  38.212  32.950  1.00  0.00
TER
ENDMDL

Sunday, March 01, 2015

Steps to Perform a Simulation

Below is presented a generalised procedure for performing a simulation. The exact steps and processes involved will vary depending on exactly what is being attempted. Use as a general guide only!

  1. Clearly identify the property / phenomena of interest to be studied by performing the simulation. Do not continue further until you are clear on this!
  2. Select the appropriate tools to be able to perform the simulation and observe the property / phenomena of interest. It is important to read and familiarise yourself with publications by other researchers on similar systems. Tools include:

    - software to perform the simulation with, consideration of force field may influence this decision.

    force field which describes how the atoms / particles within the system interact with each other. Select one that is appropriate for the system being studied and the property / phenomena of interest. Very important and non-trivial step! Consider now how you will analyze your simulation data to make your observations.
  3. Obtain / generate the initial coordinate file for each molecule to be placed within the system. The page linked there has some software suggestions.
  4. Generate the raw starting structure for the system by placing the molecules within the coordinate file as appropriate. Molecules may be specifically placed or arranged randomly.
  5. Obtain / generate the topology file for the system, using (for example)
    pdb2gmx
    SwissParam (for CHARMM forcefield), 
    PRODRG (for ffgmx/GROMOS96 43A1), 
    Automated Topology Builder (for GROMOS96 53A6), 
    MKTOP (for OPLS/AA) or
    - your favourite text editor in concert with chapter 5 of the
    GROMACS Manual.
    - For the 
    AMBER force fields, antechamber or acpype might be appropriate.
  6. Describe a simulation box (e.g. using editconf) whose size is appropriate for the eventual density you would like, fill it with solvent (e.g. using genbox), and add any counter-ions needed to neutralize the system (e.g. using grompp and genion). In these steps you may need to edit your topology file to stay current with your coordinate file.
  7. Run an energy minimization on the system (using grompp and mdrun). This is required to sort out any bad starting structures caused during generation of the system, which may cause the production simulation to crash. It may be necessary also to minimize your solute structure in vacuo before introducing solvent molecules (or your lipid bilayer or whatever else). You should consider using flexible water models and not using bond constraints or frozen groups. The use of position restraints and/or distance restraints should be evaluated carefully.
  8. Select the appropriate simulation parameters for the equilibration simulation (defined in .mdp file). You need to choose simulation parameters that are consistent with how force field was derived. You may need to simulate at NVT with position restraints on your solvent and/or solute to get the temperature almost right, then relax to NPT to fix the density (which should be done with Berendsen until after the density is stabilized, before a further switch to a barostat that produces the correct ensemble), then move further (if needed) to reach your production simulation ensemble (e.g. NVTNVE). If you have problems here with the system blowing up, consider using the suggestions on that page, e.g. position restraints on solutes, or not using bond constraints, or using smaller integration timesteps, or several gentler heating stage(s).
  9. Run the equilibration simulation for sufficient time so that the system relaxes sufficiently in the target ensemble to allow the production run to be commenced (using grompp and mdrun, then g_energy and trajectory visualization tools).
  10. Select the appropriate simulation parameters for the production simulation (defined in .mdp file). In particular, be careful not to re-generate the velocities. You still need to be consistent with how the force field was derived and how to measure the property / phenomena of interest.
  11. Run the production simulation for sufficient time so that property / phenomena of interest can be observed in required detail (using grompp / tpbconv and mdrun).
  12. Analyse / visualise the resulting trajectory and data files to obtain information on the property / phenomena of interest.


Notes

  • see REMD for additional information on steps for a replica-exchange simulation


Resources

  • Flow Chart - simple flow chart of a typical GROMACS MD run of a protein in a box of water.
  • GROMACS Flowsheet - flowsheet of the general procedure for performing a molecular dynamic simulation using GROMACS. Shows linkage between files required and generated in each step and general command lines used.