Hi Hadi, It appears to me that you've not included (eg. #include "drg.itp) the molecule specific topology in the *top file.
Also, (prob more for future reference) please note that the order you have your molecules in your coordinate (*pdb or *gro) file should be the order they are presented in your *top file. cheers Kia > Message: 4 > Date: Mon, 4 Dec 2006 09:52:01 -0800 (PST) > From: hadi behzadi <[EMAIL PROTECTED]> > Subject: [gmx-users] request > To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all users > I constructed topology and gro (1.gro and 1.top) file for propane ( CH3CH2CH3) molecule from PRODRG server as follow: > > 1.go > > PRODRG COORDS > 3 > 1DRG CAB 1 -0.128 0.172 0.000 > 1DRG CAA 2 -0.128 0.019 0.000 > 1DRG CAC 3 0.017 -0.033 0.000 > 0.35530 0.35530 0.35530 > > 1.top > ; > ; > ; This file was generated by PRODRG version 061128.0522 > ; PRODRG written/copyrighted by Daan van Aalten > ; and Alexander Schuettelkopf > ; > ; Questions/comments to [EMAIL PROTECTED] > ; > ; 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 CH3 1 DRG CAB 1 -0.012 15.0350 > 2 CH2 1 DRG CAA 1 0.024 14.0270 > 3 CH3 1 DRG CAC 1 -0.012 15.0350 > > [ bonds ] > ; ai aj fu c0, c1, ... > 1 2 1 0.153 334720.0 0.153 334720.0 ; CAB CAA > 2 3 1 0.153 334720.0 0.153 334720.0 ; CAA CAC > > [ pairs ] > ; ai aj fu c0, c1, ... > > [ angles ] > ; ai aj ak fu c0, c1, ... > 1 2 3 1 111.0 460.2 111.0 460.2 ; CAB CAA > CAC > > [ dihedrals ] > ; ai aj ak al fu c0, c1, m, ... > > Then, I construct 88 molecule of propane with editconf and genbox : > editconf f 1.gro -0 1.pdb d 0.3 > genbox -cs 1.pdb -p 1.top -o 3.pdb -box 3 3 3 > then I chaned the topology file by adding the following phrase in the end of 1.top: > > [ system ] > ; Name DRG > [ molecules ] > ; Compound #mols > DRG 88 > > When I want to performer the following commend : > grompp -v -f grompp.mdp -c b4em.pdb -p 1.top o > I encounter to this error : > > Program grompp, VERSION 3.3 > Source code file: topio.c, line: 385 > Fatal error: > Invalid order for directive moleculetype, file ""1.top"", line 17 > The line 17 is [ moleculetype ]. > > > I request you all to give suggestion for this. > > > > I will be very thankful to you. > > > > > > > > --------------------------------- > Any questions? Get answers on any topic at Yahoo! Answers. Try it now. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20061204/7d522ba9/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > > > End of gmx-users Digest, Vol 32, Issue 8 > **************************************** > -- Kia Balali-Mood PhD, CBiol, MIBiol Postdoctoral Research Associate, Department of Biochemistry, Oxford University, OX1 3QU, UK sansom.biop.ox.ac.uk/kia/ , tel. +44 (0)1865 275 (380 or 275) _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
