Hi Servaas, > trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s top140.tpr
I think there's quite a bit of reason to start calling you names here :) Assumedly, fit.trr means that it results from fitting the trajectory to a reference? So what does this do with your PBC? > I also tried the -nojump option and after this the whole option but in > visualistion (with VMD) I got strange bonds... Right, so strange bonds should be quite an indication that there's something weird with your shifts. > An often reported problem was that the the structure in the tpr file is not > close enough to the starting structure in the trajectory, I tried it by > making a tpr file with a the strating structure of the trajectory (in this > structure the ligand is in the active site if I look at the structure). But > this did not help. Another often, or at least several times, mentioned problem relates to the fact that fitting a structure reorients the molecule, but leaves the PBC as it is, causing a mismatch between the system and the PBC. Therefore one can not execute any PBC related operations (nojump, cluster, whole), after the trajectory has been fitted. No hard feelings ;) Cheers, Tsjerk -- 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
