Since the GB model has the parameters for the solvent built-in, the presence
of selected water molecules would affect the overall accuracy of the
implicit model. Personally, I have not attacked this particular question
before, but I know that others have dealt with including explicit waters in
MM-PBSA analysis, and I would be curious to see their use of the dielectric.
You might want to do a literature search on the subject if no one else on
the list has a response for you.
Good luck!
-Bill
On Thu, Aug 26, 2010 at 6:36 AM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
> Thanks Bill for the informative reply.
>
> The DIELEC constant value is equal to 1, for an explicit solvent model.
> What would be the value when selected waters are present in the system? What
> influence the choice of the value ? I have been reading the manual but the
> info is limited.
>
> Amor
>
> --- On Wed, 25/8/10, Bill Miller III <brmilleriii.gmail.com> wrote:
>
> From: Bill Miller III <brmilleriii.gmail.com>
> Subject: Re: [AMBER] MMPBSA.py nmode
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Wednesday, 25 August, 2010, 7:05 PM
>
> The entropy calculations can certainly be done with the 10 water molecules
> included in the calculation, however you will also need to define the
> external dielectric regardless. The entropy program within MMPBSA.py allows
> the user to perform the entropy calculations in either gas phase or with a
> GB implicit solvent model. Furthermore, the calculation will take longer
> with the water molecules, but the extra time should be relatively
> insignificant compared to doing the calculation on the complex, since it is
> significantly larger than the water.
>
> I hope that helps.
>
> -Bill
>
> On Wed, Aug 25, 2010 at 5:40 AM, Amor San Juan <amorsanjuan.yahoo.com
> >wrote:
>
> >
> >
> > Entropy calculation is performed in the gas phase using the nmode program
> > in amber. Does normal mode in MMPBSA.py can do calculations for selected
> 10
> > water molecules (solvent) together with solute (protein+ligand) ? If this
> > current program can do it, it would be great ! Does anybody did an
> > experiment on such case ? If in principle that is doable, the n number of
> > water will take longer entropy calculations, as compared to its gas phase
> > counterpart.
> >
> >
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Thu Aug 26 2010 - 04:00:06 PDT
