Both are approximations for real solvent effects. I would suggest
consulting the literature about this, as people typically report both.
MM/PBSA in itself is a significant approximation, so you really need
experimental data to compare to (and only relative binding free energies are
typically comparable).
Good luck!
Jason
On Wed, Aug 4, 2010 at 9:19 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> So for reporting the mm_pbsa values, should one use only the PB values or
> both can be given ?
>
> On Wed, Aug 4, 2010 at 6:06 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > Because they are different solvent models solving different equations.
> You
> > would never expect to get the same result, though one would hope that
> > delta-energies would be similar (since a single-point energy is
> meaningless
> > in molecular mechanics). GB models are parameterized to reproduce PB
> > results, but are much faster to solve. If the answers were always the
> > same,
> > there would never be any point in using PB. The corresponding parts of
> the
> > amber/ambertools manual gives decent background into the PB and GB
> methods.
> >
> > Hope this helps,
> > Jason
> >
> > On Wed, Aug 4, 2010 at 2:50 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> >
> > > Hi,
> > >
> > > I have one basic question :
> > >
> > > Why is there a discrepancy in the energy values obtained by PB ang GB ?
> > >
> > > e.g.
> > >
> > > For a DNA-lig complex , I get :
> > >
> > > PBTOT = -36.26 kcal/mol
> > > GBTOT = -38.88 kcal/mol
> > >
> > > Thanks in advance..
> > > Asfa.
> > > _______________________________________________
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> > > AMBER.ambermd.org
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> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Aug 04 2010 - 06:30:06 PDT
