Direct interaction energies between the solvent and solute would be
difficult to calculate using MM-PBSA. You would have to treat the water
molecules as part of the complex, and this complicates several aspects of
the calculation itself. Plus, you would also probably need to include
solvent-solvent interactions in the calculation, too, and this would
overwhelm the energetics of the system, making the actual binding energy
difficult to discern. MM-PBSA is primarily used as a way to approximate the
binding energy without explicitly taking account the solvent in the energy
calculation.
I hope this helps.
-Bill
On Mon, Aug 23, 2010 at 6:17 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
>
> I am trying to obtain pairwise interaction energies between amino acid
> residues
> from mm_pbsa. The interaction energies obtained (Eele+Evdw+Eint) are the
> gas
> phase energies as suggested in the tutorial. However, a more realistic
> value
> would be the interaction energy taking into consideration the solvent
> effect.
>
> So Eint = Egas+Esolvent
>
> = Eij + Ei-solv + Ej-solv
>
> where i, j are two residues and solv is the solvent.
>
> >From the parameters obtained from the decomposed pairwise interaction
> energies,
> is it possible to derive the above.
> Or is it that I am going wrong somewhere in the basic understanding.
>
> I would be grateful if someone please clarifies my confusion.
> Thanks a lot in advance.
>
> Sincere Regards,
> Moitrayee
>
>
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--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Aug 23 2010 - 04:00:05 PDT
