Thank you, Mark, for your tip, the indexing solution is perfect! Regards, Vis
--- On Tue, 12/22/09, Mark Abraham <mark.abra...@anu.edu.au> wrote: > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] trjconv -pbc: how to keep all parts of the system > "clustered" together in PDB? > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Tuesday, December 22, 2009, 7:29 PM > Visvaldas K. wrote: > > Dear GROMACS users and gurus, > > > > I am sorry if it's a stupid question...I'm fairly new > GROMACS, and something is been driving me crazy. I > have a protein, two metal ions, and inhibitor in my system. > Somehow in some of the frames I can't keep all those pieces > "clustered" compactly for some postprocessing, using > trjconv for conversion of trr/xtc into PDB format: > > > > "-pbc mol" option of trjconv: metal ions are far from > the rest of the protein. > > -pbc nojump or -pbc whole: inhibitor far from the > protein, metals are fine. > > -pbc atom or -pbc res: couple of residues are > disattached from the protein; metals and inhibitor are > fine. > > -pbc cluster: doesn't work (irrelevant?) > > -pbc cluster should work with a suitable index group of > protein+metal+inhibitor - that's what it is for. > > Once that's done, you may want to re-run trjconv to apply > other effects. Two-pass processing is often necessary. > > > Also -center and -boxcenter don't seem to help... > > Can anybody suggest some tricks? I used octahedral box > for my runs. > > "don't seem to help" also doesn't help. We can't guess what > it was about your inputs and outputs that was contrary to > your hopes :-) > > Mark > -- 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/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/mailing_lists/users.php > -- 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/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/mailing_lists/users.php
