Thanks a lot for the information..
Asfa.
On Wed, Aug 4, 2010 at 6:57 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
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> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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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Received on Wed Aug 04 2010 - 07:00:03 PDT
