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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