[AMBER] similarity of quasi-harmonic modes dependent on reference conformation

From: Jose Borreguero <borreguero.gmail.com>
Date: Tue, 29 Jun 2010 22:34:52 -0400

Dear Amber users,

In ptraj, using *matrix mwcovar* produces very different set of modes if one
uses different reference conformations to remove translations and rotations.
Does anyone know why is this the case? I had assume that being the same
trajectory, the modes would be very similar. If the modes are to be a
property of the protein, they should be quite independent of the reference

This is the ptraj input file. Here I used the first conformation as
*trajin mdcrd
reference first.rst
rms reference :.CA
matrix mwcovar name pca :.CA out evecs_first.dat
I also have another input file using the last conformation as reference (*
last.rst* produces *evecs_last.dat*)

As it turns out, modes in *evecs_first.dat *and *evecs_last.dat *are very
different! I compare the modes using the Hess metric:
*similarity = 1/N * Sum_i Sum_j (v_i w_j)^2,*
where *v_i* are the first *N* modes from *evecs_first.dat *and *w_j* are the
first *N *modes from *evecs_last.dat*. There is a dot product between the

Has anybody encountered such situation?

Best regards,
-Jose M. Borreguero
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Received on Tue Jun 29 2010 - 20:00:03 PDT
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