Hi David, If you use a structure file (.gro/.pdb) which corresponds to the starting structure and has the protein and ligand in the right place, you can do it with trjconv -pbc nojump.
Cheers, Tsjerk On Sun, Feb 24, 2008 at 4:47 AM, David Osguthorpe <[EMAIL PROTECTED]> wrote: > On Sun, Feb 24, 2008 at 01:35:51PM +1100, Mark Abraham wrote: > > > > > >Ive been using trjconv but it seems to be failing for a case where the > > >protein switches > > >image in the trajectory but the ligand does not. > > > > Check out trjconv -h, and if none of the options works, please describe > > why they're failing :-) > > > > Ive been using -pbc cluster with an index file of protein and ligand which > has worked for other systems > (which is the closest Ive got to the algorithm I described previously > although none of trjconvs options > or any other gromacs utility seem to implement the algorithm I described - > if you could suggest which > utility/option is the closest to the above algorithm Id be very grateful) > but for a particular system it went into an infinite loop printing out > COM: 0.911 1.167 5.420 iter = 1 > etc. (with iter going up forever) forever and a day. > Dumping coordinates before and after the step where this occurred and > inspection by molecular graphics > showed that the ligand coordinates were similar but the protein coordinates > were very different > - which I assume means the protein shifted to a different periodic image - > hence the comment. > > David > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
