<div dir="ltr">When I try to work the command on a small portion of the backbone it seems to work just fine. But when I try the entire backbone (which is composed of several <u>separate</u> chains) I am getting segmentation fault.<br>
Any workaround for that, so I can use the entire backbone?<br>Thanks again,<br>-Shay<br><br><div class="gmail_quote">On Mon, Sep 12, 2011 at 5:29 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="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Shay Teaching wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi all,<br>
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt trajectory and one mutant trajectory using the following command:<br>
<br>
g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n wt_backbone.ndx<br>
<br>
The file wt_backbone.ndx contains the backbone of the protein (Backbone indices are identical between wt and mutant).<br>
<br>
The result is that I am getting a well deserved error saying that wt.xtc and mutant.xtc has different number of atoms (the tpr itself):<br>
Fatal error:<br>
Second trajectory (76128 atoms) does not match the first one (76129 atoms)<br>
<br>
So the question becomes: Is there a (convenient) way to produce rms-matrix between wt and mutant?<br>
Or perhaps circumvent this problem in some other way?<br>
</blockquote>
<br></div>
Use trjconv to write out new trajectories containing only backbone atoms of each protein, then use tpbconv to write a .tpr file with only backbone atoms in it (using index groups, if necessary). Then run g_rms again with these new trajectories and .tpr file. Everything should match if the indices are chosen correctly.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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