On Mon, 19 Jun 2006, Guillem Plasencia wrote:
> Then i was curious and did trjconv my system (before running mdrun energy > minimization) into a pdb, and had a look at it, and i saw my protein was > splitted in three different molecules, one was inside the water box (but far > away from box center, lying in touch of one of the boxes' sides) and the > other two parts were completely outside the box. Worst of all, they were no > more one single peptidic chain, but separated one. I was having somewhat similar problem recently when I had multiple peptides in my system (I used genconf to generate them) but in the final structure they all had the same chain identifier, so pdb2gmx thought that I have only one long peptide in the system (with some 1 nm long bonds). If this is the reason, one way to check how many chains there are is to interactively choose termini groups with pdb2gmx, you should be prompted for each peptide unit. By the way, if it is somehow possible to tell genconf to generate repeated units with different chain identifiers, I would be interested to know. regards, Olli _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
