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 > > > > > > I still have troubles of starting running md for creatine. For which I > > created topology using PRODRG programm. > > The only difference between creatine.top and creating.itp is that > creatine > > top has additional lines: > > #include "ffgmx.itp" > > #include "creatine.itp" > > > > Also please can you tell me where can I get "ffgmx.itp" file? > > > > By trying to run md I am getting an error: Fatal error: > > moleculetype UNK is redefined >
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