On Wed, Jul 25, 2012 at 9:15 AM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote:
> I am using Amber11/AT1.5. Could anyone point to me how can I get
> electrostatic energies in gas phase scaled by dielectric constant with
> MMPBSA.py or which variable should I use please? I've read the related part
> for MMPBSA.py in the manual, but have not found it.
> With the following input, only the polar solvation energy is scaled, while
> the electrostatic energies in gas phase stays unaffected.
>
This is expected behavior, as far as I understand. The effect of the
internal dielectric constant is reflected in the polar solvation term
(EPB), not the gas-phase electrostatic interactions (EEL), but this doesn't
change the nature of that difference.
Note that the division of what constitutes 'EPB' and 'EEL' is rather
arbitrary and artificial (they are calculated together and decomposed
after-the-fact, I think), and terms involving the dielectric constant
(either the internal or external) are rolled into EPB.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 25 2012 - 07:30:05 PDT
