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 - 06:00:12 PDT
