<br>Hi Justin and Tsjerk, <br>Thank you for your answers, but I found a command that worked for me:)<br><br>First, I concatenated the ensemble of my trajectory.<br>& then, I did the following:<br><br>trjconv -s a.tpr -f traj.xtc -o traj1.xtc -pbc nojump -n b.ndx<br>
<br>Cheers,<br>Carla<br><br><div class="gmail_quote">On Thu, Feb 18, 2010 at 12:47 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;">
<br>
Hi Tsjerk,<br>
sorry I didn't understand this part of your explanation:"Can you make an image of the last frame and send a link<br>
to it?"<br>
</blockquote>
<br></div>
Render an image of your system from the end of your trajectory and post it somewhere online (like photobucket); do not send it as an attachment to your email.<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;"><div class="im">
But anyhow, please can you send me the version of trjconv that does the trick?<br>
<br>
Thanks,<br>
Carla<br>
<br></div><div class="im">
On Thu, Feb 18, 2010 at 11:42 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a> <mailto:<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>>> wrote:<br>
<br>
Hi Carla,<br>
<br>
> I checked with genconf & now I'm certain that my ATP molecule is<br>
still with<br>
> the protein<br>
<br>
That's good to know :)<br>
<br>
>>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol<br>
>>> (centering on "Protein")<br>
<br>
So what did come out of this then? It should have given you a compact<br>
representation of your system with the protein in the center. But if<br>
the protein's in the center and everything is put as close to that<br>
center as possible, which is what "compact" does, then the ATP should<br>
be there too. Can you make an image of the last frame and send a link<br>
to it? Alternatively, I have a patched version of trjconv that you can<br>
use to do the trick. I can send it if you want.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
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<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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