<div dir="ltr">Ok I tried that and it doesn't work:<br>There's a fundamental difference between chains/no-chains topology, namely the existence of peptide bond between chains, and the different protonation state on the termini.<br>
In the chain-based topology there are several termini, and less peptide bonds.<br><br>This causes the no-chains-tpr to have different number of atoms, and different protonation states.<br>I tried using tpbconv to make a backbone-tpr, but it still gets me to segmentation fault.<br>
<br>So thanks, but I don't think it would work.<br>-SA<br><br><div class="gmail_quote">On Mon, Sep 12, 2011 at 11:47 PM, Shay Teaching <span dir="ltr"><<a href="mailto:shay.teaching@gmail.com">shay.teaching@gmail.com</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 dir="ltr">Thanks, I'll try that, and post again if it works.<div><div></div><div class="h5">
<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" target="_blank">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><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;">
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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks again,<br>
-Shay<div><div></div><div><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>
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==============================<u></u>==========<br>
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Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
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Virginia Tech<br>
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