[gmx-users] g_rms matrix between wt and mutant

[Shay Teaching]

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?
Thanks again,
-Shay

On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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