[gmx-users] g_rms matrix between wt and mutant

[Shay Teaching]

Thanks, I'll try that, and post again if it works.

On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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://vt.edu/Pages/Personal/justin>
>>    <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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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