Thanks Teemu, That was spot on. I simply took the -select argument and dropped it into a text file then used the -sf option instead. Works perfectly.
Thanks again Anthony On 14/09/2015 12:34, "Nash, Anthony" <a.n...@ucl.ac.uk> wrote: >Thanks Teemu, > >I’ll look into this further. > >Thanks >Anthony > > > >On 14/09/2015 12:32, "Teemu Murtola" <teemu.murt...@gmail.com> wrote: > >>The error message really looks like that your shell does not understand >>the >>quoting. You need to pass the whole selection as a single command-line >>parameter (which your quotes in principle would do), but the error >>message >>indicates that each word is getting parsed as a separate selection, so >>your >>shell is passing them as separate arguments. >> >>Best regards, >>Teemu >> >>On Mon, Sep 14, 2015, 11:28 Nash, Anthony <a.n...@ucl.ac.uk> wrote: >> >>Dear all, >> >>I understand that this is quite a basic question, but I think I need a >>fresh set of eyes to figure out what¹s going on with gmx distance -select >>syntax. >> >>In my index file, I have 23 groups, two of which are ³ZINC² and >>³CARBONYL² >> >>Based on numerous mail archive suggestions and the gromacs website change >>in tools page, I¹m using: >> >>$CHEM/rungromacs505 gmx distance -n index.ndx -f umb_1_all.trr -s >>umb_1_umb.tpr -oh umb_1_distance_hist.xvg -oall umb_1_distance.xvg >>-select >>'com of group "ZINC" plus com of group "CARBONYL"' >> >>Which kicks up the error: >> >>Invalid command-line options >> In command-line option -select >> In keyword 'com' >> required parameter 'of' not specified >> invalid selection 'com' >> In command-line option -select >> syntax error >> invalid selection 'group' >> In command-line option -select >> syntax error >> invalid selection 'plus' >> In command-line option -select >> In keyword 'com' >> required parameter 'of' not specified >> invalid selection 'com' >> In command-line option -select >> syntax error >> invalid selection 'group' >> >>I¹d appreciate any suggestions. I¹ve also tried to do *something* via the >>interactive command line (when -select is not supplied), but what it¹s >>asking for is a bit cryptic. >> >>Thanks >>Anthony >>-- >>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.