Hi, if there is a protein in your system you should have protein as standard group. Maybe you use a template mdp file in which the temperature coupling group is protein. if you have no protein in your simulation check the mdp files for tc-grps and adjust accordingly.
Max > On Jun 3, 2015, at 3:07 PM, Victor Rosas Garcia <rosas.vic...@gmail.com> > wrote: > > Hello, > > In your command line you do not specify an index file. Maybe you need to > generate one. Check out usage of make_ndx. > > Hope this helps > > Victor > > 2015-06-03 13:41 GMT-05:00 marzieh dehghan <dehghanmarz...@gmail.com>: > >> Hi every body >> >> I create a covalent bond and now I want to held MD by gromacs, >> >> after holding the following command : grompp -f nvt.mdp -c em.gro -p >> topol.top -o nvt.tpr >> >> I confornted to an 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. >> >> >> please let me know how can I solve this problem. >> >> I am looking forward to getting your answer >> >> thanks a lot >> >> >> -- >> >> >> >> >> *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and >> Biophysics (IBB)University of Tehran, Tehran- Iran.* >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
