Hi Justin,<br>
Thank you for your answer but I'm still not getting my ligand to stay in the box.<br>
<br>
I tried the following(after taking a look at the mailing list archive):<br>
<br>
trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering on "Protein")<br>
trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans<br>
<br>
So please do you have another advise to give me?<br>
<br>
Thanks<br>
Carla<br><br><div class="gmail_quote">On Mon, Feb 15, 2010 at 4:32 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><div></div><div class="h5"><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'm using this command to extract my protein and my ligand from the trajectory.<br>
<br>
trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj<br>
<br>
Before, I had a problem with residues of my protein showing at the other end of the box, when I display my .xtc with VMD.<br>
the "-pbc whole" fixed it.<br>
<br>
However, now I have another issue: my ligand is at the other end of the box. So please can anyone tell me what can I do to fix that and get a reasonable RMSD value?<br>
<br>
</blockquote>
<br></div></div>
You may need several more iterations of trjconv (one rarely does the trick), employing -pbc nojump, -pbc cluster, and/or -center. For protein-ligand complexes, I have often found that the combination of:<br>
<br>
trjconv -pbc mol -ur compact -center<br>
<br>
(centering on "Protein")<br>
<br>
does the trick. And it makes molecules whole, as well :) I think there are also some breakdowns (documented somewhere in the list archive) when applying -fit and -pbc in the same step. I believe it is recommended to fix PBC first, then applying any sort of fitting in a separate, subsequent step.<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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