My guess is that INDI and EXDI for PB also must be redefined for MMPBSA with
selected explicit waters. You should be able to find values others have used
in the literature.
-Bill
On Thu, Aug 26, 2010 at 7:18 AM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
> Thanks for the feedback.
>
> I got the point. NMODE namelist "dielc' needs a suitable numerical value,
> not the default one.
>
> So, PB calculation needs to define INDI (internal dielectric) and EXDI
> (external dielectric). You would agree that both INDI and EXDI namelist
> variables should also be redefined into suitable values ?
>
>
> Amor
>
>
> --- On Thu, 26/8/10, 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: Thursday, 26 August, 2010, 6:51 PM
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 - 04:30:06 PDT
