[gmx-users] Structure deformation

[Carla Jamous]

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 <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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