Re: [AMBER] Ligand movement in protein cavatiy

From: Jason Swails <>
Date: Mon, 02 Jun 2014 07:25:24 -0400

On Mon, 2014-06-02 at 04:20 +0200, Jurgens de Bruin wrote:
> Hi All,
> Firstly I am new to AMBER and MD of proteins. I have been working on
> Homology Modeling and Docking for 2years now and would like to start using
> AMBER for MD purposes.
> I do hope someone can be of assistance, I would like to know if it would be
> possible to track the movement of a ligand within a protein cavity using
> AMBER and if so point me in the correct direction?

You have to apply a geometric definition of what you mean by "movement".
For example, certain distances or angles between atoms or centers of
mass of different atom groups. Or a root mean squared deviation of the
ligand atoms following a RMSD-based fit of the protein.

All of this trajectory analysis can be run with the "cpptraj" program of
AmberTools, but you must first devise a rigorous definition of what you
want to quantify (or qualify).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 02 2014 - 04:30:04 PDT
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