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
