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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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Aug 25 2010 - 04:30:03 PDT
