Re: [AMBER] Interaction energy-based residue-residue correlation matrix

From: Jason Swails <>
Date: Mon, 29 Jul 2013 12:35:09 -0400

On Mon, Jul 29, 2013 at 2:36 AM, anu chandra <> wrote:

> Dear Amber users,
> Sorry that I couldn’t attach the article with last mail. Please excuse me.

In general, it's probably better to either provide a link to the article on
the publisher's website or the necessary citation information unless you're
citing an open journal.

Does PTRAJ or MMPBSA module in Amber have an option to do the interaction
> energy-based residue-residue correlation analysis. Please see the Equations
> 1 - 6 in the methodology section in the attached article for the details of
> interaction energy based correlation analysis.

The 'difficult' part of those equations is getting the pairwise energy
terms (eq. 2). can do this (or you can do it directly with
sander) using the pairwise residue decomposition scheme. From there, you
can write a Python script to read in the energy terms printed by
(or use the Python API to get direct access to the data), and
implement Eqs. 3 through 6 yourself.

There is no single action that does all of it to my knowledge.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jul 29 2013 - 10:00:02 PDT
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