OK. I have a protein "ab" and ligand "lig", and I want to select the bound water between them. So I used
g_select -f trajout.xtc -s mdrun.tpr -n index.ndx -select '"boundwaters" resname SOL and within 0.4 of group "ab" and within 0.4 of group "lig"' -on boundwaters.ndx Then I can use the ndx file to do other things. The hard part is what after -select On Mon, Apr 2, 2012 at 5:11 PM, Dallas Warren <dallas.war...@monash.edu>wrote: > For future reference of others that may struggle with g_select, it would > be a very good idea for you to put on the emailing list how you achieved it. > **** > > ** ** > > Catch ya, > > Dr. Dallas Warren**** > > Medicinal Chemistry and Drug Action**** > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@monash.edu**** > > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. **** > > ** ** > > *From:* gmx-users-boun...@gromacs.org [mailto: > gmx-users-boun...@gromacs.org] *On Behalf Of *Yun Shi > *Sent:* Tuesday, 3 April 2012 9:58 AM > *To:* Discussion list for GROMACS users > *Subject:* [gmx-users] Re: how to g_select bound water molecules**** > > ** ** > > Never mind. I got it.**** > > On Mon, Apr 2, 2012 at 4:20 PM, Yun Shi <yunsh...@gmail.com> wrote:**** > > Hello all, > > Can anyone tell me how to get in "help examples" in g_select by typing > some commands? > > Anyway, I want to select bound waters between my ligand and protein using > -select 'resname SOL & within 0.5 ...'. Any idea? > > Thanks for any suggestion. > > Yun**** > > ** ** > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
