Thank you Justin,<br>you were right I was looking at the wrong residue numbers.<br><br>I have another question that may also sound stupid, but I can't figure it out:<br>I want to extract from my trajectory, the protein, the ligand and ions.<br>
However, when I try to do that with trjconv -f .trr -s .trr -n .ndx<br>gromacs asks to choose a group from my index file.<br>But if I choose group 0 1 2<br>it only takes the first group without the rest.<br>So how can I extract many groups at once from my trajectory?<br>
<br>Carla<br><br><div class="gmail_quote">On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi everyone,<br>
I have a question about structure deformation<br>
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.<br>
</blockquote>
<br></div>
Sorry to say, but this sounds completely unlikely. A bug of this magnitude surely would've been noticed long ago.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
What may be the problem?<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thank you<br>
Carla<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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