Re: [gmx-users] g_rms matrix between wt and mutant

Justin A. Lemkul Mon, 12 Sep 2011 08:21:04 -0700


Shay Teaching wrote:

When I try to work the command on a small portion of the backbone itseems to work just fine. But when I try the entire backbone (which iscomposed 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 wouldcause the problem, but it's possible. In that case, I'd suggest you start witha coordinate file and topology without chain identifiers and generate a new .tprfile (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 <jalem...@vt.edu<mailto:jalem...@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

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Re: [gmx-users] g_rms matrix between wt and mutant

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