Hi Justin,<br>I'm still trying to figure out what happened with my ligand.<br>Meanwhile, I have another question: I can't figure out how to calculate an average structure in gromacs.<br>And does g_rmsf calculate the average structure automatically?<br>
<br>Thanks again<br>Carla<br><br><div class="gmail_quote">On Tue, Feb 16, 2010 at 5:44 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 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>
</blockquote>
<br></div>
If that's not working, then I wonder if your ligand is still actually bound to your protein :) The above sequence always works for me, as long as there actually is a complex. You can also try -pbc cluster, but I know that algorithm can hang.<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;">
Thanks<br>
Carla<div><div></div><div class="h5"><br>
<br>
On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Carla Jamous wrote:<br>
<br>
Hi everyone,<br>
I'm using this command to extract my protein and my ligand from<br>
the trajectory.<br>
<br>
trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc<br>
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<br>
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<br>
of the box. So please can anyone tell me what can I do to fix<br>
that and get a reasonable RMSD value?<br>
<br>
<br>
You may need several more iterations of trjconv (one rarely does the<br>
trick), employing -pbc nojump, -pbc cluster, and/or -center. For<br>
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<br>
there are also some breakdowns (documented somewhere in the list<br>
archive) when applying -fit and -pbc in the same step. I believe it<br>
is recommended to fix PBC first, then applying any sort of fitting<br>
in a separate, subsequent step.<br>
<br>
-Justin<br>
<br>
Thank you<br>
Carla<br>
<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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>
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</div></blockquote><div><div></div><div class="h5">
<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>
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