[gmx-users] Group protein not found in indexfile
Hello I am having trouble running a dimmer invacuo simulation. I can do energy minimization on it, but when I attempt to generate md.tpr file I get this weird message about “Group Protein not found in index”. I don’t see why I would need an index file. I have no trouble generating a md.tpr file for md (afer energy minimization) IF I solvate the system. It is only in a vacuum that I cannot generate a .tpr file using grompp. Has anyone else had this symptom with Gromacs? I have worked on this a couple of days and would appreciate any help… Thanks -- gmx-users mailing listgmx-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] Group protein not found in indexfile
Hello I am just trying to do a simple MD on a dimmer system (in which the dimmers are NOT identical). I can use pdb2gmx to create a topology file and four .itp files pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and system.Protein.chainX.itp. When I use grompp however, I get a fatal error “Group protein not found in index file. Maybe you have non-default groups in your .mdp file, while not using ‘-n’ option in grompp” I’ve looked up this error on-line but I don’t see people getting this error when using multiple chains. I only have protein present and nothing else. I am obviously doing something incorrect. I would greatly appreciate any comments that would help me.. Thanks. -- gmx-users mailing listgmx-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] Group protein not found in indexfile
Hi Justin Thanks for your response. Here are the files you asked for. They are all text files. I am still attempting to fix this, but am still getting the error I described no matter what I have done so far. Thanks again, Stevegrompp -f pr.mdp -n pr.ndx -c prbox.pdb -p system.top -o pr.tpr -- gmx-users mailing listgmx-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
