[AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Mon, 11 Jan 2021 15:59:49 +0900

Dear All,
I have simulated two protein structures in which only one residue was
mutated and thus backbone sequence is the same.
I'm guessing it must be possible to use cpptraj to align the backbone
coordinates frame-by-frame, and estimate rmsd to check if the mutants
sample the same conformational space.
Can you please suggest to me what is the best combination of cpptraj action
commands to achieve this?
Using the following I will load the trajectories, but then I'm not sure
which commands can help me analyse if the trajectories are similar or not
and in which regions of the protein they are the largest variation in
motion.
Looking forward to getting valuable suggestions from the list.

parm prot-top
trajin prot.nc
reference prot.inpcrd
parm prot1-top [top1]
trajin prot1.nc parm [top1]
align :1-141 ???

thank you and best regards

-- 
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Received on Sun Jan 10 2021 - 23:30:02 PST