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

From: George Tzotzos <>
Date: Wed, 19 Aug 2015 18:57:09 +0300

I’m jumping in because I’m dealing with a similar situation.

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. Generate topologies for ligand, receptor and complex using and then run to calculate deltaG of subunit B. Then repeat the 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?

> On 18 Aug 2015, at 16:08, Jason Swails <> wrote:
> 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?
> ​One 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
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Aug 19 2015 - 09:00:02 PDT
Custom Search