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
