AMBER Archive (2004)

Subject: Re: AMBER: question on mm-pbsa

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Sep 01 2004 - 13:55:50 CDT

cailliez schrieb:
>
> Dear AMBER users,
>
> I have questions about nonpolar contribution calculated in mm-pbsa.
> If I use Delphi to calculate the electrostatics. Is this contribution
> calculated in Delphi
> or in Sander (I do not use Molsurf).

The nonpolar part is calculated by sander (using the LCPO method for
determining the solvent accessible surface).

> In the example given in the manual of AMBER7, the parameters SURFTEN and
> SURFOFF
> used to calculate this nonpolar contribution are different between PB
> and GB :
> For Delphi : SURFTEN=0.00542 and SURFOFF=0.092
> For GB : SURFTEN=0.0072 and SURFOFF=0.00
> What is the reason for this difference ?

The reason is that different parameters exist in the literature for the
contribution of the nonpolar part to solvation free energy. When
parameterizing the electrostatic part to get the total solvation free
energy, one needs to make a choice as to which nonpolar parameters to
use. This somehow "links" the electrostatic and nonpolar parameters of a
given method.

Please note that the SURFOFF value in the case of Delphi should read
0.92 (not 0.092)!

Best regards

Holger
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