Dear Prof. Jason,
What you suppose is exatly accurate, that the nonpolar free energy
contribution were very different between PBSA and GBSA.
I already performed the free energy calculation using inp=1 for &pb section,
and it works.
Thanks so much for your help.
best regards,
Nafiva
On Sun, Jan 11, 2015 at 11:04 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Sat, Jan 10, 2015 at 10:55 PM, asdda asa <nadaafiva.gmail.com> wrote:
>
> > Dear Amber users,
> > I have problem with the result of MMPBSA and MMGBSA calculation.
> > Previously, I performed three md simulations, each consisted of a ligand
> > bound to the same protein. The three systems differ in ligand structures
> > only.
> > I noticed that there were significantly different results of binding
> > energies calculated by MMPBSA and those by MMGBSA.
> > The final binding energies calculated by GB were about -50 kcal/mol for
> > each system, while those are from PB were about +10 kcal/mol for each
> > system.
> > Please anyhelp how could these difference occured?
> >
>
> Look at the breakdown of the binding free energy contributions. I suspect
> that the nonpolar free energy contribution (ENPOLAR+EDISPER for PB and
> ESURF for GB) are very different from each other. They use different
> models by default. I suspect that you can account for almost the entire 60
> kcal/mol difference between PB and GB binding energies simply through this
> contribution.
>
> It's unclear to me which is "better", but in this case I would probably go
> with the simple model used by GB. You can use this model in the PB code by
> setting inp=1 in the &pb section of the input file.
>
> Also make sure you are using the most up-to-date version of AmberTools.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sun Jan 11 2015 - 01:30:02 PST
