[gmx-users] g_rms matrix between wt and mutant

[Justin A. Lemkul]

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

-- 
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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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