Hi Sainitin, You can extract only the protein and ligand, using a suitable index file, or you can limit the number of frames.
Cheers, Tsjerk On Thu, Jun 27, 2013 at 5:36 PM, Thales Kronenberger < kronenberg...@gmail.com> wrote: > Don't you wanna try to use the VMD > > use vmd xxx.gro yyy.trr and then you could highlight your ligand > > > > > 2013/6/27 Sainitin Donakonda <saigr...@gmail.com> > > > Hi, > > > > I simulated protein ligand complex for 20 ns now i want to visualize > this > > complex after simulation in pymol.To look ligand interactions with > protein > > binding site > > > > I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too > huge > > with solvent molecules so pymol couldnot visualize complex > > > > Can anybody tell me command how to visualize protein ligand complex > > trajectory in pymol > > > > Thanks, > > Sainitin > > -- > > 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 > -- Tsjerk A. Wassenaar, Ph.D. -- 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
