Unfortunately, the current script doesn't support a non-unity interior
dielectric constant. However, this is quite straightforward to do as you
pointed from the cited paper in your email. You simple divide all the
intramolecular EEL energies by the interior dielectric constant by hand.
The scaled EEL energies are then consistent with the EPB energies computed
with the same interior dielectric constant.
This also comes to the Dave's original suggestion of not treating any
automatic script as a black box. Try to understand each step of the
calculations and make sure you can do these calculations by hand. If you
fully understand the script, it's quite straightforward to tailor the
output to suit your specific project at hand.
All the best,
Ray
On Wed, Jul 25, 2012 at 7:36 AM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote:
> 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
>> _______________________________________________
>> 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 Wed Jul 25 2012 - 10:00:03 PDT
