[gmx-users] Structure deformation
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 29 14:04:11 CET 2010
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).
> 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.
> Thank you
> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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