Thank you Justin, you were right I was looking at the wrong residue numbers.
I have another question that may also sound stupid, but I can't figure it out: I want to extract from my trajectory, the protein, the ligand and ions. However, when I try to do that with trjconv -f .trr -s .trr -n .ndx gromacs asks to choose a group from my index file. But if I choose group 0 1 2 it only takes the first group without the rest. So how can I extract many groups at once from my trajectory? Carla On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Carla Jamous wrote: > >> Hi everyone, >> I have a question about structure deformation >> Can pdb2gmx alter secondary structures of my protein, while adding >> hydrogens. Because I had a helix in my protein, that became a beta-sheet >> after pdb2gmx. >> > > Sorry to say, but this sounds completely unlikely. A bug of this magnitude > surely would've been noticed long ago. > > > What may be the problem? >> >> > Are you certain you're looking at the same residues? pdb2gmx renumbers > from 1, so if there are missing N-terminal residues, they will not have the > same numbers before and after pdb2gmx. > > -Justin > > Thank you >> Carla >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 >
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