Re: [AMBER] Total interaction energy between monomeric units of a dimer

From: Jason Swails <>
Date: Tue, 18 Aug 2015 09:08:12 -0400

On Tue, Aug 18, 2015 at 7:55 AM, anu chandra <> wrote:

> Dear Amber users,
> I am working with protein A-protein B dimer system. I wish to calculate
> the total interaction energy between protein A and protein B. Though the
> can do the pair-wise decomposition of energy, how can I get the
> total interaction energy between the two monomeric units of a dimeric
> protein?

‚ÄčOne way is to do pairwise energy decomposition and add up all of the
contributions between residue pairs that are in different monomers. That
would work if you're doing a GB calculation.

Other approaches will involve some clever tricks to arrive at the energy
result you want. For example, the A-B interaction energies should be
strictly non-bonded in nature, unless there is a covalent link between the
two proteins. If there is, then *most* of the interaction is non-bonded,
with a (typically tiny) amount coming from the bonded interaction where
they are connected.

Think of the total energy as the "internal" energy of each monomer A and B,
the interaction energy of each monomer A and B with the solvent, and the
interaction energy between monomers A and B. If you can compute the
"internal" energy of monomers A and B as well as the interaction of
monomers A and B with the solvent, then you can subtract that from the
total energy and get the interaction energy you are looking for.

There is no built-in way of doing this automatically in Amber. You would
basically have to create "new" topology files (either with the charges and
van der Waals set to zero on the monomer you are excluding, or having them
stripped out completely via cpptraj) and run three separate calculations.

NAMD *does* have a pairInteraction command that basically automates this
procedure for you in explicit solvent (I'm not sure if it works for GB or
not). If you are familiar with NAMD, this may be an easier route to try.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 18 2015 - 06:30:06 PDT
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