Re: [AMBER] rmsd of a subunit I w.r.t subunit II

From: Thomas Cheatham III <tec3.utah.edu>
Date: Wed, 29 Sep 2010 15:33:47 -0600 (Mountain Daylight Time)

> Is it possible to compute the rmsd of one subunit of a protein w.r.t another
> using PTRAJ module in amber ?

Yes, but not directly. What I would do is use the "strip" command to
write out in-vacuo trajectories, separately, for each subunit. Then you
could do the RMSd; unless looking for symmetric movement, likely you do
not want to compare subunit 1 to subunit 2 at time 1, 2, 3, ... however.
What you could do is compare all frames to all frames using a 2D-RMSd
approach (although if the trajectories are large likely you will not be
able to do the all-to-all comparison since it will take too long).

trajin subunit-1.strip 50 9999999 50
trajin subunit-2.strip 50 9999999 50

2drms out 2drms.dat raw mass .CA

--tec3

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Received on Wed Sep 29 2010 - 15:00:03 PDT
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