Re: [AMBER] About interaction energy over time

From: <>
Date: Wed, 21 Dec 2011 04:12:29 -0500 (EST)


> I would like to calculate the interaction energy between ligand and
> protein for each frame of the trajectory.

Do you really want the interaction energy or the free energy? The later is
what you normally want to judge binding phenomena, but it is more
difficult to compute.

Either way, the MM-PBSA method is what you need. It will split your system
up into ligand, receptor and solvent parts and compute the (free) energies
for each. Tutorial A3 may be what you want to look at.

Amber comes both with the tools, as well as their
reimplementation in python form, They (try to) do the same
thing, see which one would be best for you.

> program could do it. I wonder if there is just a one line code instead.

That would still be a very long line of code ;-)

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Dec 21 2011 - 01:30:02 PST
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