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.teach...@gmail.com <mailto:shay.teach...@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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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
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Virginia Tech
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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
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