[gmx-users] g_rms matrix between wt and mutant

[Justin A. Lemkul]

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).

-Justin

> Thanks again,
> -Shay
> 
> 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
>         wt_backbone.ndx
> 
>         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
> 
>     -- 
>     ==============================__==========
> 
>     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
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================