[gmx-users] g_rms matrix between wt and mutant
Justin A. Lemkul
jalemkul at vt.edu
Mon Sep 12 17:20:00 CEST 2011
Shay Teaching wrote:
> 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.
> Any workaround for that, so I can use the entire backbone?
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).
> Thanks again,
> On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> Shay Teaching wrote:
> Hi all,
> (Gromacs 4.0.7): I am trying to make rms matrix between one Wt
> trajectory and one mutant trajectory using the following command:
> g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
> The file wt_backbone.ndx contains the backbone of the protein
> (Backbone indices are identical between wt and mutant).
> 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):
> Fatal error:
> Second trajectory (76128 atoms) does not match the first one
> (76129 atoms)
> So the question becomes: Is there a (convenient) way to produce
> rms-matrix between wt and mutant?
> Or perhaps circumvent this problem in some other way?
> 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.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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