Hi, Can you please copy, paste and post your actual commands. I don't think your use of quote marks would have led to a valid shell command. The whole selection text will need to be inside some quotes.
Mark On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > I have used the same name in my coordinate file. For Glycine it is spelt > as Glyci, so the word has been cut off. I know this is correct because I > use the same name in VMD. > > -----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: 12 July 2017 22:42 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx select > > Hi, > > What are the residue names in your coordinate file? Glyci probably doesn't > fit > > Mark > > On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash <akash.pandya...@ucl.ac.uk> > wrote: > > > Hi all, > > > > > > I am trying to select all the glycine molecules with 0.5nm of my protein. > > I tried both of these commands I got from the gromacs website: > > > > gmx select -f output.gro -select "Close to protein" resname Glyci and > > within 0.5 of group "Protein"' -ofpdb > > > > gmx select -f output.xtc -s output.tpr (my converted input file) > > -select "Close to protein" resname Glyci and within 0.5 of group > > "Protein"' -ofpdb > > > > > > Nothing comes up when I enter them. Please could someone help me with > this? > > > > > > 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.