<div dir="ltr">Thanks, I'll try that, and post again if it works.<br><br><div class="gmail_quote">On Mon, Sep 12, 2011 at 6:20 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Shay Teaching wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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 _separate_ chains) I am getting segmentation fault.<br>
Any workaround for that, so I can use the entire backbone?<br>
</blockquote>
<br></div>
Are there chain identifiers separating the proteins? I don't know if that would cause the problem, but it's possible. In that case, I'd suggest you start with a coordinate file and topology without chain identifiers and generate a new .tpr file (and then take the backbone atoms only with tpbconv).<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks again,<br>
-Shay<div><div></div><div class="h5"><br>
<br>
On Mon, Sep 12, 2011 at 5:29 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>
Shay Teaching wrote:<br>
<br>
Hi all,<br>
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt<br>
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<br>
wt_backbone.ndx<br>
<br>
The file wt_backbone.ndx contains the backbone of the protein<br>
(Backbone indices are identical between wt and mutant).<br>
<br>
The result is that I am getting a well deserved error saying<br>
that wt.xtc and mutant.xtc has different number of atoms (the<br>
tpr itself):<br>
Fatal error:<br>
Second trajectory (76128 atoms) does not match the first one<br>
(76129 atoms)<br>
<br>
So the question becomes: Is there a (convenient) way to produce<br>
rms-matrix between wt and mutant?<br>
Or perhaps circumvent this problem in some other way?<br>
<br>
<br>
Use trjconv to write out new trajectories containing only backbone<br>
atoms of each protein, then use tpbconv to write a .tpr file with<br>
only backbone atoms in it (using index groups, if necessary). Then<br>
run g_rms again with these new trajectories and .tpr file.<br>
Everything should match if the indices are chosen correctly.<br>
<br>
-Justin<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></div></div>
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==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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