[gmx-users] Structure deformation

[Justin A. Lemkul]

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
> 

-- 
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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

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