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

From: Daniel Roe <>
Date: Mon, 29 Jul 2013 10:48:01 -0600


On Mon, Jul 29, 2013 at 10:35 AM, Jason Swails <> wrote:
> 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.

Note that Eq.3 is just the Pearson product-moment coefficient between
Eij and Ekl. A matrix of these coefficients can be calculated for
multiple data sets with the 'crosscorr' command in cpptraj.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Jul 29 2013 - 10:00:03 PDT
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