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 <jalem...@vt.edu
<mailto:jalem...@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
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