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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> >
>
>
>
> --
> 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 - 06:30:05 PDT
