[gmx-users] grompp problem
Yang Ye
leafyoung81-group at yahoo.com
Fri Mar 16 14:21:05 CET 2007
Check the manual for file format.
Following steps are for your reference
How to Create Topology from PRODRG
1. Save the topology from PRODRG (what you pasted below) into an itp
file, e.g. ptr.itp. Save the PDB section into ptr.pdb.
2. Use your text editor, enter
#include "ffGxxxx"
#include "ptr.itp"
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 0 0 1000
#endif
[ system ]
A in Water. Anything
[ molecules ] # put what's in your moleculetype
PTR 1
SOL xxxx
Selection of force field is first specified in PRODGR and then pick
anyone fit to your needs. Use 43b1 for vacuum calculation and 53a5 or
53a6 for system including solvent.
ffG43a1 GROMOS96 43a1 force field
ffG43b1 GROMOS96 43b1 vacuum force field
ffG43a2 GROMOS96 43a2 force field (improved alkane dihedrals)
ffG45a3 GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
ffG53a5 GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
ffG53a6 GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
Save this file as B.top and use for grompp.
Regards,
Yang Ye
On 3/16/2007 4:47 AM, Tom Lenaerts wrote:
>> Not only in atp, but also in bon and nb. nb is a bit easy, only LJ
>> parameters. But for bon, you need to specify any bonded, angle, dihedral
>> interaction that CB and CR61 have in your molecule.
>>
>
> The structure of these files is completely unclear to me. I also didn't find any explanation of the gromacs website. Is there a online explanation of the format and how new entries can be added?
>
> I retrieved all information on PTR from the PRODRG server. Isn't there some way to directly copy and paste this information in the confuguration files?
>
> Below the PTR info obtained from PRODRG
>
> Tom
>
> ;
> ;
> ; This file was generated by PRODRG version 061128.0522
> ; PRODRG written/copyrighted by Daan van Aalten
> ; and Alexander Schuettelkopf
> ;
> ; Questions/comments to dava at 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
> PTR 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OA 1 PTR O2P 1 -1.099 15.9994
> 2 P 1 PTR P 1 1.162 30.9738
> 3 OA 1 PTR O3P 1 -1.099 15.9994
> 4 OM 1 PTR O1P 1 -0.786 15.9994
> 5 OA 1 PTR OH 1 -0.178 15.9994
> 6 CB 1 PTR CZ 2 0.077 12.0110
> 7 CR61 1 PTR CE2 2 -0.038 13.0190
> 8 CR61 1 PTR CD2 2 -0.039 13.0190
> 9 CR61 1 PTR CE1 3 -0.029 13.0190
> 10 CR61 1 PTR CD1 3 -0.029 13.0190
> 11 CB 1 PTR CG 3 0.002 12.0110
> 12 CH2 1 PTR CB 3 0.056 14.0270
> 13 CH1 1 PTR CA 4 0.184 13.0190
> 14 C 1 PTR C 4 0.436 12.0110
> 15 O 1 PTR O 4 -0.546 15.9994
> 16 NL 1 PTR N 4 0.835 14.0067
> 17 H 1 PTR HAB 4 0.031 1.0080
> 18 H 1 PTR HAC 4 0.030 1.0080
> 19 H 1 PTR HAA 4 0.030 1.0080
>
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 1 2 1 0.161 251040.0 0.161 251040.0 ; O2P P
> 2 3 1 0.161 251040.0 0.161 251040.0 ; P O3P
> 2 4 1 0.148 376560.0 0.148 376560.0 ; P O1P
> 2 5 1 0.161 251040.0 0.161 251040.0 ; P OH
> 5 6 1 0.136 376560.0 0.136 376560.0 ; OH CZ
> 6 7 1 0.139 418400.0 0.139 418400.0 ; CZ CE2
> 6 9 1 0.139 418400.0 0.139 418400.0 ; CZ CE1
> 7 8 1 0.139 418400.0 0.139 418400.0 ; CE2 CD2
> 8 11 1 0.139 418400.0 0.139 418400.0 ; CD2 CG
> 9 10 1 0.139 418400.0 0.139 418400.0 ; CE1 CD1
> 10 11 1 0.139 418400.0 0.139 418400.0 ; CD1 CG
> 11 12 1 0.153 334720.0 0.153 334720.0 ; CG CB
> 12 13 1 0.153 334720.0 0.153 334720.0 ; CB CA
> 13 14 1 0.153 334720.0 0.153 334720.0 ; CA C
> 13 16 1 0.147 376560.0 0.147 376560.0 ; CA N
> 14 15 1 0.123 502080.0 0.123 502080.0 ; C O
> 16 17 1 0.100 374468.0 0.100 374468.0 ; N HAB
> 16 18 1 0.100 374468.0 0.100 374468.0 ; N HAC
> 16 19 1 0.100 374468.0 0.100 374468.0 ; N HAA
>
> [ pairs ]
> ; ai aj fu c0, c1, ...
> 1 6 1 ; O2P CZ
> 2 7 1 ; P CE2
> 2 9 1 ; P CE1
> 3 6 1 ; O3P CZ
> 4 6 1 ; O1P CZ
> 5 8 1 ; OH CD2
> 5 10 1 ; OH CD1
> 6 11 1 ; CZ CG
> 7 10 1 ; CE2 CD1
> 7 12 1 ; CE2 CB
> 8 9 1 ; CD2 CE1
> 8 13 1 ; CD2 CA
> 9 12 1 ; CE1 CB
> 10 13 1 ; CD1 CA
> 11 14 1 ; CG C
> 11 16 1 ; CG N
> 12 15 1 ; CB O
> 12 17 1 ; CB HAB
> 12 18 1 ; CB HAC
> 12 19 1 ; CB HAA
> 14 17 1 ; C HAB
> 14 18 1 ; C HAC
> 14 19 1 ; C HAA
> 15 16 1 ; O N
>
> [ angles ]
> ; ai aj ak fu c0, c1, ...
> 1 2 3 1 103.0 397.5 103.0 397.5 ; O2P P O3P
> 1 2 4 1 109.6 397.5 109.6 397.5 ; O2P P O1P
> 1 2 5 1 103.0 397.5 103.0 397.5 ; O2P P OH
> 3 2 4 1 109.6 397.5 109.6 397.5 ; O3P P O1P
> 3 2 5 1 103.0 397.5 103.0 397.5 ; O3P P OH
> 4 2 5 1 109.6 397.5 109.6 397.5 ; O1P P OH
> 2 5 6 1 109.5 397.5 109.5 397.5 ; P OH CZ
> 5 6 7 1 120.0 418.4 120.0 418.4 ; OH CZ CE2
> 5 6 9 1 120.0 418.4 120.0 418.4 ; OH CZ CE1
> 7 6 9 1 120.0 418.4 120.0 418.4 ; CE2 CZ CE1
> 6 7 8 1 120.0 418.4 120.0 418.4 ; CZ CE2 CD2
> 7 8 11 1 120.0 418.4 120.0 418.4 ; CE2 CD2 CG
> 6 9 10 1 120.0 418.4 120.0 418.4 ; CZ CE1 CD1
> 9 10 11 1 120.0 418.4 120.0 418.4 ; CE1 CD1 CG
> 8 11 10 1 120.0 418.4 120.0 418.4 ; CD2 CG CD1
> 8 11 12 1 120.0 418.4 120.0 418.4 ; CD2 CG CB
> 10 11 12 1 120.0 418.4 120.0 418.4 ; CD1 CG CB
> 11 12 13 1 111.0 460.2 111.0 460.2 ; CG CB CA
> 12 13 14 1 109.5 460.2 109.5 460.2 ; CB CA C
> 12 13 16 1 109.5 460.2 109.5 460.2 ; CB CA N
> 14 13 16 1 109.5 460.2 109.5 460.2 ; C CA N
> 13 14 15 1 121.0 502.1 121.0 502.1 ; CA C O
> 13 16 17 1 109.5 376.6 109.5 376.6 ; CA N HAB
> 13 16 18 1 109.5 376.6 109.5 376.6 ; CA N HAC
> 13 16 19 1 109.5 376.6 109.5 376.6 ; CA N HAA
> 17 16 18 1 109.5 334.7 109.5 334.7 ; HAB N HAC
> 17 16 19 1 109.5 334.7 109.5 334.7 ; HAB N HAA
> 18 16 19 1 109.5 334.7 109.5 334.7 ; HAC N HAA
>
> [ dihedrals ]
> ; ai aj ak al fu c0, c1, m, ...
> 6 9 7 5 2 0.0 1673.6 0.0 1673.6 ; imp CZ CE1 CE2 OH
> 11 8 10 12 2 0.0 1673.6 0.0 1673.6 ; imp CG CD2 CD1 CB
> 2 1 4 3 2 35.3 836.8 35.3 836.8 ; imp P O2P O1P O3P
> 13 12 16 14 2 35.3 836.8 35.3 836.8 ; imp CA CB N C
> 16 13 18 17 2 35.3 836.8 35.3 836.8 ; imp N CA HAC HAB
> 6 7 8 11 2 0.0 1673.6 0.0 1673.6 ; imp CZ CE2 CD2 CG
> 7 8 11 10 2 0.0 1673.6 0.0 1673.6 ; imp CE2 CD2 CG CD1
> 8 11 10 9 2 0.0 1673.6 0.0 1673.6 ; imp CD2 CG CD1 CE1
> 11 10 9 6 2 0.0 1673.6 0.0 1673.6 ; imp CG CD1 CE1 CZ
> 10 9 6 7 2 0.0 1673.6 0.0 1673.6 ; imp CD1 CE1 CZ CE2
> 9 6 7 8 2 0.0 1673.6 0.0 1673.6 ; imp CE1 CZ CE2 CD2
> 1 2 5 6 1 0.0 1.0 3 0.0 1.0 3 ; dih O2P P OH CZ
> 1 2 5 6 1 0.0 3.1 2 0.0 3.1 2 ; dih O2P P OH CZ
> 9 6 5 2 1 180.0 7.1 2 180.0 7.1 2 ; dih CE1 CZ OH P
> 8 11 12 13 1 0.0 0.4 6 0.0 0.4 6 ; dih CD2 CG CB CA
> 11 12 13 16 1 0.0 5.9 3 0.0 5.9 3 ; dih CG CB CA N
> 12 13 14 15 1 0.0 0.4 6 0.0 0.4 6 ; dih CB CA C O
> 12 13 16 19 1 0.0 3.8 3 0.0 3.8 3 ; dih CB CA N HAA
>
>
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