Hi, Is the pre-requisite for this command a separate index file for the glycine molecules I have?
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.