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

From: David A Case <>
Date: Wed, 19 Aug 2015 12:22:16 -0400

On Wed, Aug 19, 2015, George Tzotzos wrote:
> Assuming a GB calculation, would it be legitimate to treat one of the
> subunits (say subunit A) as a receptor and the other as ligand.

Yes: the terms "ligand" and "receptor" are just labels. Any problem that has
A + B interacting non-covelently can in principle to addressed by these

> Generate
> topologies for ligand, receptor and complex using and
> then run to calculate deltaG of subunit B.

This gets you the free energy of interaction, not the free energy of
interaction "of subunit B". It doesn't matter which subunit you call "ligand"
and which one you call "receptor".

> Repeat same procedure (using subunit B as receptor) to calculate deltaG of
> subunit A. Would adding the deltaGs of the two subunits correspond to
> the total interaction energy?

There is no need to repeat anything. The two calculations you describe are
identical. [If not, them I am not understanding what you are proposing to


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Received on Wed Aug 19 2015 - 09:30:03 PDT
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