Olga - What is gromos43a1.ff? I do not remember the files with ff-extension in gromacs. I am sure you should include the topology files in the inverse order as compared to what is below: 1) general FF with atoms, bonds, angles, etc (~ include "gromos43a1.ff"); 2) molecule definition, its own atoms, bonds, etc (~ include "creatine.itp")
After that, you'll probably get another error, and it will be more informative. Good luck! Vitaly On Mon, Nov 15, 2010 at 12:09 PM, Olga Ivchenko <olga.ivche...@gmail.com> wrote: > > Hey Vitaly, > > Thank you for your reply. Here is the files: > > itp: > ; > ; > ; This file was generated by PRODRG version AA081006.0504 > ; PRODRG written/copyrighted by Daan van Aalten > ; and Alexander Schuettelkopf > ; > ; Questions/comments to d...@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 OM 1 DRG OXT 1 -0.701 15.9994 > 2 C 1 DRG C 1 0.402 12.0110 > 3 OM 1 DRG O 1 -0.701 15.9994 > 4 CH2 1 DRG CA 2 0.185 14.0270 > 5 N 1 DRG N 2 0.468 14.0067 > 6 CH3 1 DRG CAG 2 0.201 15.0350 > 7 C 1 DRG CAH 2 0.377 12.0110 > 8 NZ 1 DRG NAE 2 -0.163 14.0067 > 9 H 1 DRG HA6 2 0.023 1.0080 > 10 H 1 DRG HAE 2 0.024 1.0080 > 11 NZ 1 DRG NAD 2 -0.163 14.0067 > 12 H 1 DRG HA5 2 0.024 1.0080 > 13 H 1 DRG HAD 2 0.024 1.0080 > > [ bonds ] > ; ai aj fu c0, c1, ... > 2 1 2 0.125 13400000.0 0.125 13400000.0 ; C OXT > 2 3 2 0.125 13400000.0 0.125 13400000.0 ; C O > 2 4 2 0.153 7150000.0 0.153 7150000.0 ; C CA > 5 4 2 0.147 8710000.0 0.147 8710000.0 ; N CA > 5 6 2 0.147 8710000.0 0.147 8710000.0 ; N CAG > 5 7 2 0.134 10500000.0 0.134 10500000.0 ; N CAH > 7 8 2 0.134 10500000.0 0.134 10500000.0 ; CAH NAE > 7 11 2 0.134 10500000.0 0.134 10500000.0 ; CAH NAD > 8 9 2 0.100 18700000.0 0.100 18700000.0 ; NAE HA6 > 8 10 2 0.100 18700000.0 0.100 18700000.0 ; NAE HAE > 11 12 2 0.100 18700000.0 0.100 18700000.0 ; NAD HA5 > 11 13 2 0.100 18700000.0 0.100 18700000.0 ; NAD HAD > > [ pairs ] > ; ai aj fu c0, c1, ... > 1 5 1 ; OXT N > 2 6 1 ; C CAG > 2 7 1 ; C CAH > 3 5 1 ; O N > 4 8 1 ; CA NAE > 4 11 1 ; CA NAD > 5 9 1 ; N HA6 > 5 10 1 ; N HAE > 5 12 1 ; N HA5 > 5 13 1 ; N HAD > 6 8 1 ; CAG NAE > 6 11 1 ; CAG NAD > 8 12 1 ; NAE HA5 > 8 13 1 ; NAE HAD > 9 11 1 ; HA6 NAD > 10 11 1 ; HAE NAD > > [ angles ] > ; ai aj ak fu c0, c1, ... > 1 2 3 2 126.0 770.0 126.0 770.0 ; OXT C > O > 1 2 4 2 117.0 635.0 117.0 635.0 ; OXT C > CA > 3 2 4 2 117.0 635.0 117.0 635.0 ; O C > CA > 2 4 5 2 109.5 520.0 109.5 520.0 ; C CA > N > 4 5 6 2 121.0 685.0 121.0 685.0 ; CA N > CAG > 4 5 7 2 122.0 700.0 122.0 700.0 ; CA N > CAH > 6 5 7 2 117.0 635.0 117.0 635.0 ; CAG N > CAH > 5 7 8 2 120.0 670.0 120.0 670.0 ; N CAH > NAE > 5 7 11 2 120.0 670.0 120.0 670.0 ; N CAH > NAD > 8 7 11 2 120.0 670.0 120.0 670.0 ; NAE CAH > NAD > 7 8 9 2 120.0 390.0 120.0 390.0 ; CAH NAE > HA6 > 7 8 10 2 120.0 390.0 120.0 390.0 ; CAH NAE > HAE > 9 8 10 2 120.0 445.0 120.0 445.0 ; HA6 NAE > HAE > 7 11 12 2 120.0 390.0 120.0 390.0 ; CAH NAD > HA5 > 7 11 13 2 120.0 390.0 120.0 390.0 ; CAH NAD > HAD > 12 11 13 2 120.0 445.0 120.0 445.0 ; HA5 NAD > HAD > > [ dihedrals ] > ; ai aj ak al fu c0, c1, m, ... > 2 1 3 4 2 0.0 167.4 0.0 167.4 ; imp C OXT > O CA > 5 4 6 7 2 0.0 167.4 0.0 167.4 ; imp N CA > CAG CAH > 7 5 8 11 2 0.0 167.4 0.0 167.4 ; imp CAH N > NAE NAD > 8 7 10 9 2 0.0 167.4 0.0 167.4 ; imp NAE CAH > HAE HA6 > 11 7 13 12 2 0.0 167.4 0.0 167.4 ; imp NAD CAH > HAD HA5 > 5 4 2 1 1 0.0 1.0 6 0.0 1.0 6 ; dih N CA > C OXT > 2 4 5 7 1 180.0 1.0 6 180.0 1.0 6 ; dih C CA > N CAH > 11 7 5 4 1 180.0 33.5 2 180.0 33.5 2 ; dih NAD CAH > N CA > 5 7 8 10 1 180.0 33.5 2 180.0 33.5 2 ; dih N CAH > NAE HAE > 5 7 11 13 1 180.0 33.5 2 180.0 33.5 2 ; dih N CAH > NAD HAD > > > > > > > > > And top. I am prettu sure this file is wrong. And I do not know yet how to > modify it correctly: > > > > ; > ; File 'creatine.top' was generated > ; By user: onbekend (0) > ; On host: onbekend > ; At date: Mon Nov 15 13:24:44 2010 > ; > ; This is your topology file > ; it was generated using program: > ; pdb2gmx - version 4.5-beta2 > ; with command line: > ; pdb2gmx -f creatine_all_hyd_PRODRGBeta.pdb -o creatine.gro -p > creatine.top > ; > > #include "creatine.itp" > #include "gromos43a1.ff" > > > ; Include forcefield parameters > ;#include "gromos43a1.ff/forcefield.itp" > > ;"gromos43a1.ff/creatine.itp" > > > ;[ system ] > > ;[ molecules ] > ;DRG 3 > > > > > 2010/11/15 Vitaly Chaban <vvcha...@gmail.com> >> >> Hey, Olga - >> >> > Also please can you tell me where can I get "ffgmx.itp" file? >> >> /$gromacs_folder/share/gromacs/top/ffgmx.itp as well as all other >> standard topology files are there. >> >> By trying to run md I am getting an error: Fatal error: >> > moleculetype UNK is redefined >> >> Please post you top and itp files here. Looks like you have 2 creatine >> molecules in your topology right now. >> >> Good luck! >> >> Vitaly >> >>
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