Do you mean getting the interaction energy between two solvent-exposed amino
acid residues? You should be able to do this by simply defining the print
residue option in your mm_pbsa.pl input file (COMPRI, RECPRI, and LIGPRI) to
print only those two residues.
-Bill
On Mon, Aug 23, 2010 at 7:15 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Thanks a lot for your email.
>
> I am using mm-pbsa for obtaining the pairwise interaction energies between
> the
> different amino acid residues in the complex.
>
> Can you please suggest me how I can realistically obtain the interaction
> energies (ele+vdw) of a residue pair in solvent.
>
> Thanks once again.
>
> Sincere Regards,
> Moitrayee
>
> > 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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> >>
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> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
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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 - 04:30:07 PDT
