Hey.
Using cpptraj, I am interested in how to get the RMSD of a certain
region within two structures after fitting these structures using
another region. The same question was already answered for ptraj:
http://archive.ambermd.org/201102/0128.html
Quote by Dan:
"
reference refstruct.rst7
rms reference :1-100
rms reference :50-55 nofit out rmsd.dat
The first rms command performs the best fit, then the second rms
command calculates the rmsd you want without changing the fit from the
first rms command.
"
This is what I propose for cpptraj (for my system):
parm topology.top
trajin traj1.mdcrd
rmsd :1-150 first
rmsd :151-161 first nofit out rmsd.dat
Would that for each frame
1) align the residues 1-150 of the current frame to the residues 1-150
of the first frame and then
2) calculate the RMSD for residues 151 to 161 with the alignment from
(1) (again current frame vs. first frame)?
I could just try, but I do not want to do a mistake that would lead to a
"good-looking" but wrong result.
Thanks!
Jan-Philip
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Received on Tue Aug 30 2011 - 08:00:03 PDT
