I am trying to create an index file just as I did for the protein but am lost when it comes to the following options
Keep 13 (this is ok as it is the ligand group number) a -> Not sure since after trying CA or C i ended up getting the number of atoms in the protein name 13 Calpha (Not sure) q What options should I use for a and name 13 prompts? Thank you On Tue, Apr 15, 2014 at 12:12 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > The same way you'd do it for a protein, but with a suitable group. > > Mark > On Apr 15, 2014 11:55 AM, "MUSYOKA THOMMAS" <mutemibiochemis...@gmail.com> > wrote: > > > Dear Users, > > How can one determine a ligand's rmsd, its radius of gyration, and its > SASA > > during a protein-ligand simulation? > > > > Thank you > > -- > > 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.