[gmx-users] g_rms matrix between wt and mutant

Shay Teaching shay.teaching at gmail.com
Thu Sep 15 07:52:18 CEST 2011 

Thanks Mark and Justin for your input. it works. For progeny, here's how:

1. In case of multiple, separate chains of protein, generate a *new* tpr X
that does not include chain information.
2. From X generate a new tpr file Y, consisting now only of the group under
scrutiny (for example, backbone. Use tpbconv).
3. Make new index file for Y.
4. Now use trjconv to make xtc1  and xtc2 that consist only on that group.
5. Use g_rms with Y tpr, the generate xtcs, and the new index group.

This should work and avoid the notorious segmentation fault (as long as you
make sure the group you choose, backbone for example, has identical number
of atoms in both xtc1 and xtc2).

-SA
On Tue, Sep 13, 2011 at 11:17 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 13/09/2011 6:11 PM, Shay Teaching wrote:
>
> Ok I tried that and it doesn't work:
> There's a fundamental difference between chains/no-chains topology, namely
> the existence of peptide bond between chains, and the different protonation
> state on the termini.
> In the chain-based topology there are several termini, and less peptide
> bonds.
>
> This causes the no-chains-tpr to have different number of atoms, and
> different protonation states.
> I tried using tpbconv to make a backbone-tpr, but it still gets me to
> segmentation fault.
>
>
> The idea behind Justin's original solution is still right. You need to
> provide two sets of corresponding atoms and those sets have to have the same
> size. So you need to construct two index groups that suit what you actually
> want to compare - say, the backbone atoms that are common to the two forms.
> That will require some thought, and playing around with make_ndx (or a text
> editor). Then use those to create subset .tpr and trajectory files as Justin
> suggested. Each form is likely to need its own customized index group to
> make the subset that is correct for it.
>
> Mark
>
>
>
> So thanks, but I don't think it would work.
> -SA
>
> On Mon, Sep 12, 2011 at 11:47 PM, Shay Teaching <shay.teaching at gmail.com>wrote:
>
>> 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<%28540%29%20231-9080>
>>>>    <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 <%28540%29%20231-9080>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
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