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

From: anu chandra <>
Date: Tue, 18 Aug 2015 15:17:19 +0100

Thanks Daniel and Jason. BTW, I feel the 'Anal' in the older version of
Amber could be a better utility for this calculation.

Many thanks

On Tue, Aug 18, 2015 at 2:08 PM, Jason Swails <>

> 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.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Aug 18 2015 - 07:30:05 PDT
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