[gmx-users] Re: Regarding mdrunfor small organic molecules
Ravi Kumar Venkatraman
ravikumarvenkatraman at gmail.com
Fri Aug 12 21:48:46 CEST 2011
Dear all,
Please can anybody send, step by step mdrun for small organic
molecules in gromacs.
> Dear All,
> When I try to grompp to generate .tpr file for mdrun from
> topology generated by prodrg I am getting the following error.
>
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'PRODRG'
>
> -------------------------------------------------------
> Program grompp_d, VERSION 4.5.4
> Source code file: toppush.c, line: 1987
>
> Fatal error:
> No such moleculetype SOL
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I am herewith attaching the chlor.top file please help me findout the
> problem.
>
>
> ;
> ; 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.
> ;
> ;
>
> #include "ffG43a1.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> PRODRG 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 O 1 PDB OAE 1 -0.6772 15.9994
> 2 C 1 PDB CAK 1 0.8450 12.0110
> 3 C 1 PDB CAG 1 0.0134 12.0110
> 4 CL 1 PDB CLAA 1 -0.0968 35.4530
> 5 C 1 PDB CAH 2 0.0134 12.0110
> 6 CL 1 PDB CLAB 2 -0.0968 35.4530
> 7 C 1 PDB CAL 2 0.8450 12.0110
> 8 O 1 PDB OAF 2 -0.6772 15.9994
> 9 C 1 PDB CAJ 2 0.0134 12.0110
> 10 CL 1 PDB CLAD 2 -0.0968 35.4530
> 11 C 1 PDB CAI 2 0.0134 12.0110
> 12 CL 1 PDB CLAC 3 -0.0968 35.4530
>
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 2 1 2 0.123 16600000.0 0.123 16600000.0 ; CAK OAE
> 2 3 2 0.139 10800000.0 0.139 10800000.0 ; CAK CAG
> 2 11 2 0.139 10800000.0 0.139 10800000.0 ; CAK CAI
> 3 4 2 0.173 2928800.0 0.173 2928800.0 ; CAG CLAA
> 3 5 2 0.139 10800000.0 0.139 10800000.0 ; CAG CAH
> 5 6 2 0.173 2928800.0 0.173 2928800.0 ; CAH CLAB
> 5 7 2 0.139 10800000.0 0.139 10800000.0 ; CAH CAL
> 7 8 2 0.123 16600000.0 0.123 16600000.0 ; CAL OAF
> 7 9 2 0.139 10800000.0 0.139 10800000.0 ; CAL CAJ
> 9 10 2 0.173 2928800.0 0.173 2928800.0 ; CAJ CLAD
> 9 11 2 0.139 10800000.0 0.139 10800000.0 ; CAJ CAI
> 11 12 2 0.173 2928800.0 0.173 2928800.0 ; CAI CLAC
>
> [ pairs ]
> ; ai aj fu c0, c1, ...
> 1 4 1 ; OAE CLAA
> 1 5 1 ; OAE CAH
> 1 9 1 ; OAE CAJ
> 1 12 1 ; OAE CLAC
> 2 6 1 ; CAK CLAB
> 2 7 1 ; CAK CAL
> 2 10 1 ; CAK CLAD
> 3 8 1 ; CAG OAF
> 3 9 1 ; CAG CAJ
> 3 12 1 ; CAG CLAC
> 4 6 1 ; CLAA CLAB
> 4 7 1 ; CLAA CAL
> 4 11 1 ; CLAA CAI
> 5 10 1 ; CAH CLAD
> 5 11 1 ; CAH CAI
> 6 8 1 ; CLAB OAF
> 6 9 1 ; CLAB CAJ
> 7 12 1 ; CAL CLAC
> 8 10 1 ; OAF CLAD
> 8 11 1 ; OAF CAI
> 10 12 1 ; CLAD CLAC
>
> [ angles ]
> ; ai aj ak fu c0, c1, ...
> 1 2 3 2 121.0 685.0 121.0 685.0 ; OAE CAK
> CAG
> 1 2 11 2 121.0 685.0 121.0 685.0 ; OAE CAK
> CAI
> 3 2 11 2 120.0 560.0 120.0 560.0 ; CAG CAK
> CAI
> 2 3 4 2 120.0 560.0 120.0 560.0 ; CAK CAG
> CLAA
> 2 3 5 2 120.0 560.0 120.0 560.0 ; CAK CAG
> CAH
> 4 3 5 2 120.0 560.0 120.0 560.0 ; CLAA CAG
> CAH
> 3 5 6 2 120.0 560.0 120.0 560.0 ; CAG CAH
> CLAB
> 3 5 7 2 120.0 560.0 120.0 560.0 ; CAG CAH
> CAL
> 6 5 7 2 120.0 560.0 120.0 560.0 ; CLAB CAH
> CAL
> 5 7 8 2 121.0 685.0 121.0 685.0 ; CAH CAL
> OAF
> 5 7 9 2 120.0 560.0 120.0 560.0 ; CAH CAL
> CAJ
> 8 7 9 2 121.0 685.0 121.0 685.0 ; OAF CAL
> CAJ
> 7 9 10 2 120.0 560.0 120.0 560.0 ; CAL CAJ
> CLAD
> 7 9 11 2 120.0 560.0 120.0 560.0 ; CAL CAJ
> CAI
> 10 9 11 2 120.0 560.0 120.0 560.0 ; CLAD CAJ
> CAI
> 2 11 9 2 120.0 560.0 120.0 560.0 ; CAK CAI
> CAJ
> 2 11 12 2 120.0 560.0 120.0 560.0 ; CAK CAI
> CLAC
> 9 11 12 2 120.0 560.0 120.0 560.0 ; CAJ CAI
> CLAC
>
> [ dihedrals ]
> ; ai aj ak al fu c0, c1, m, ...
> 2 1 11 3 2 0.0 167.4 0.0 167.4 ; imp CAK OAE
> CAI CAG
> 3 5 4 2 2 0.0 167.4 0.0 167.4 ; imp CAG CAH
> CLAA CAK
> 5 7 6 3 2 0.0 167.4 0.0 167.4 ; imp CAH CAL
> CLAB CAG
> 7 9 8 5 2 0.0 167.4 0.0 167.4 ; imp CAL CAJ
> OAF CAH
> 9 11 10 7 2 0.0 167.4 0.0 167.4 ; imp CAJ CAI
> CLAD CAL
> 11 12 9 2 2 0.0 167.4 0.0 167.4 ; imp CAI CLAC
> CAJ CAK
> 2 3 5 7 2 0.0 209.3 0.0 209.3 ; imp CAK CAG
> CAH CAL
> 3 5 7 9 2 0.0 209.3 0.0 209.3 ; imp CAG CAH
> CAL CAJ
> 5 7 9 11 2 0.0 209.3 0.0 209.3 ; imp CAH CAL
> CAJ CAI
> 7 9 11 2 2 0.0 209.3 0.0 209.3 ; imp CAL CAJ
> CAI CAK
> 9 11 2 3 2 0.0 209.3 0.0 209.3 ; imp CAJ CAI
> CAK CAG
> 11 2 3 5 2 0.0 209.3 0.0 209.3 ; imp CAI CAK
> CAG CAH
>
> [ system ]
> CHLORANIL BOX in water
>
> [ molecules ]
> PRODRG 1
> SOL 17122
>
> Thank you.
>
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