> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 29 2010 - 15:00:03 PDT
