Hi Jason,
Thanks for the reply.
I read the paper on J. Chem. Inf. Model. 2011, 51, 69–82. It shows how
dielectric constant affects the binding free energy calculated by MMPBSA.
When I looked closely at their data (Table S2) the gas-phase electrostatic
interactions (EEL) are also scaled by solute dielectric constant.
Indi=1
deltaEEL deltaEPB
-133.38±1.13 193.46±0.23
Indi=2
deltaEEL deltaEPB
-66.69±0.56 93.87±0.16
I found in this thread
http://archive.ambermd.org/201106/0170.html, Prof.
Luo has commented that:
"In general, a higher dielectric constant should reduce the contribution of
electrostatic interactions (both Coulombic and solvation electrostatic,
i.e. PB/GB) in the final binding free energies. "
"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)".
I thought they are calculated separately. As far as I understood, for "EEL"
part, it is calculated directly by Coulombic law; while for 'EPB' is
calculated by solving the PB equations. So for "EEL" part, it should be
divided by the dielectric constant when solute dielectric constant is not
equal 1. Please correct me if I am wrong here.
Whether gas-phase electrostatic interactions should be scaled by the solute
dielectric constant or not if one would like to see how the dielectric
constant affects the binding free energy?
Please help to shed more lights on it. Thanks!
Best,
Qiong
On Wed, Jul 25, 2012 at 10:11 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 - 08:00:04 PDT
