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.
>
>
>
>
>
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 26 2010 - 04:00:03 PDT
