Thank you for your response. But in the gro file there are no names for chains in mdrun.gro file. Moreover, if I am selecting only CA of residue 14 for chain A using the following command, I get 10 atoms, but I should get only 1 atom.
r 14 & a CA & chain A. It means that the tool is taking CA of residue 14 from all 10 chains.. Still the problem remains unsolved On Wed, Nov 5, 2014 at 2:27 PM, rajat desikan <rajatdesi...@gmail.com> wrote: > Hi, > As an example, assuming that I have four chains (A,B,C,D) and want to > select residue 14 in chains A,B and D > > > 1 & r 14 & chain A|1 & r 14 & chain B| 1 & r 14 & chain D > > 1 is usually the default group 'protein'. If that is not so in your case, > substitute it with the appropriate number. I think 3 is for CA atoms. > > I usually find that > > > 1 & r 14 > > Selects residue 14 in all chains in a multi chain protein. Hope that helps. > > Regards, > > On Wednesday, November 5, 2014, bharat gupta <bharat.85.m...@gmail.com> > wrote: > > > Hi, > > > > I want to make an index file for a certain residue, say residue 14 and > its > > atom CA. I can eaily do that if its a single chain protein, but my > protein > > contains 10 chains and I don't know how to select residue 14 from each > > chain. I tried splitting the protein into chains by using splitch option, > > but I don't know how proceed after that. > > > > > > Please help > > -- > > *Best Regards* > > Mn > > -- > > 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 <javascript:;>. > > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > 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.