Hi, You need make_ndx: http://manual.gromacs.org/online/make_ndx.html
This command gives you an interactive dialogue, in which you can select the atoms/residues/molecules you want to include in the index file. The selection is a bit tricky, but using the help function and looking at examples should get you there in the end. Best wishes Andreas ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Lara Bunte [lara.bu...@yahoo.de] Sent: 19 March 2012 16:11 To: Discussion list for GROMACS users Subject: Re: [gmx-users] grompp - Group protein not found Hi I want to solve my problem by creating an index file but I did not understand what I have to write in this file. I read the content in this link: http://manual.gromacs.org/online/ndx.html but I can't apply this to my problem. Could you please help? Thanks Greetings Lara ----- Ursprüngliche Message ----- Von: Mark Abraham <mark.abra...@anu.edu.au> An: Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 21:41 Mittwoch, 7.März 2012 Betreff: Re: [gmx-users] grompp - Group protein not found On 8/03/2012 4:31 AM, Peter C. Lai wrote: > Check the molecules section at the bottom of your top file. Each molecule > entry there should match the corresponding name given to it in the molecule's > own topology (the name under [moleculetype]). Those names can match and this error arise because this error is probably because the .mdp file refers to "protein" and there is no such group generated for the default index groups (used when no -n file is supplied). Either * make an index file with such a group and name it "protein," * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Mark > > > On 2012-03-07 05:13:11PM +0000, Lara Bunte wrote: >> Hi >> >> I create a file pr.mdp for equilibrating the water around my molecule and >> used after that the command >> >> grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr >> >> And I got tthe error: >> >> Fatal error: >> Group protein not found in index file. >> Group names must match either [moleculetype] names >> or custom index group names,in which case you >> must supply an index file to the '-n' option of grompp. >> >> Could you explain that error to me please? How to fix it? >> >> Greetings >> Lara >> -- gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
