Hi, You aren't getting output because you aren't actually making a selection - see "gmx help select" and its suggestions for where to look for the rest of the documentation and explained examples.
Mark On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > I'm not sure if the command I entered (shown below) is correct. No output > was given. I'm unclear as to how this command will enable me to isolate the > glycine molecules within 4A of the protein molecule? > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos whole_mol_com > -seltype dyn_mol_com -pdbatoms all > > Akash > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 16 June 2017 17:22 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > Hi, > > Gmx select will produce a selection eg of all molecules with an atom > within a cutoff of any atom in another molecule. > > Mark > > On Fri, 16 Jun 2017 18:15 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > > > Hi all, > > > > I have ran a simulation with a protein and multiple ligand molecules > > inserted randomly inside a box. I want to isolate those ligand > > molecules that are closest to the protein by a cut-off of four > > angstroms or so. Is there a command I could use to do this for me or > > would I have to use a molecular visualizer software for this? > > > > Thanks, > > > > Akash > > -- > > 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. > -- 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.