[gmx-users] Structure deformation

[Justin A. Lemkul]

Carla Jamous wrote:
> 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?

Use make_ndx to merge the desired groups (i.e., 0 | 1 | 2) or simply !12 
(assuming group 12 is SOL).

-Justin

> 
> Carla
> 
> On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at 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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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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

========================================