[AMBER] Help regarding appropriate analysis for correlated motion using cpptraj

From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
Date: Mon, 30 Mar 2015 22:44:39 +0300

Dear Users,

I have MD trajectories of a protein-ligand complex. During closer
inspection of MD movie, I found that the rotation of one of phenyl ring of
Phe causes ligand dynamics. It is quite obvious in MD movies. However, I am
unable to show this correlated motion in 2D picture. The calculation of
Chi2 dihedral clearly shows the rotation of phenyl ring but I have no idea
to show the dynamics of ligand during MD.
   I will be very thankful if someone can suggest me the appropriate type
of analysis using cpptraj such that this correlated motion between rotation
of phenyl ring and ligand dynamics can be pictorially represented.

Thanks in advance.

Best Regards
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Received on Mon Mar 30 2015 - 13:00:04 PDT
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