[AMBER] assess which structures are similar between two MD-trajectories

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Thu, 15 Oct 2020 09:21:04 +0530

Dear All,
I have two trajectories for which I want to estimate electrostatics E
differences but only for structures which are very similar i.e. low
pair-wise backbone rmsd.
I'm getting large (unrealistic E differences) for some and realistic E
differences for other pairs, thus I'm guessing that the bad ones are due to
large differences in backbone/side-chain rmsd.

I think I need to calculate an nD-rmsd plot/data between two MD
trajectories (after stripping water/ions) for this.
Is this correct, if yes, how can I use AmberTools for this purpose? Then I
will also need a mechanism to record the snapshot numbers with lowest rmsd
and pass them on to the electrostatics program.

Or is it better to cluster the trajectories first and then compare the
nD-rmsd only for the representative structures generated by clustering
algorithm?

Other suggestions to approach this problem are also highly appreciated.
Looking forward to receiving valuable suggestions form the list.
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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VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
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Received on Wed Oct 14 2020 - 21:00:02 PDT
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