[gmx-users] Structure deformation

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 29 12:48:12 CET 2010

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.


> Thank you
> Carla


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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