Re: AMBER: Solute-solvent boundary in pbsa

From: Ray Luo <>
Date: Tue, 24 May 2005 01:48:10 -0700


There are two different applications of pbsa: 1) You can use pbsa for
single-structure energy and electrostatic potential map calculation. The
pb implementation for this application is very similar to DelphiII. 2)
You can also use pbsa for MD simulations (only with cap water in
amber8). The pb implementation is according to Lu and Luo.

Since the original purpose in packaging pbsa was to support mmpbsa, the
2nd application was not described in the pbsa section of the manual even
if it is fully supported in the code. You can find relevant description
in the sander section of the manual. Now answers to your specific questions.

>As far as I understand, the Poisson-Boltzman equation
>(EQ 10. in Luo's paper)coded in the pbsa module is
>used to compute electrostatic potentials on
>finite-difference grid points (to which partial atomic
>charges are mapped) assigned in the continuum high
>dielectric (solvent) and the low dielectric (the
>solute interior). I guess this information is already
>provided in the AMBER8 manual.
This is correct.

>However, I have not seen any information in the manual
>about how the solute-solvent boundary is treated by
>the pbsa program. Looking at fortran codes in
>$AMBERHOME/src/pbsa/pb_force.f , I see that definition
>of the electrostatic potential for boundary conditions
>is different than that of the solvent or the solute
>Considering that the solute-solvent boundary is
>treated differently, I will have two questions:
>1) How does the pbsa program determine dielectric at
>the solute-solvent boundary ?
> -- Is it identical to the smoothing function below
>which is used in the UHBD program ?
>where d is the fraction of the grid line that is

Now suppose you refer to the first application. The pbsa program does
not smooth dielectric at the solvent/solute boundary by default. This is
to mimic the DelphiII behavior. However, you can turn this on, but the
result will be more different from DelphiII.

>2) How is the electrostatic potential at the
>solute-solvent boundary determined by the pbsa
> Is it like EQ 11,12,13&14 provided in Luo's paper?
> If so, which of the equations in Luo's paper is
>used in the pbsa program?
For the first application, the energy calculation in pbsa does not use
the method in Lu and Luo, JCP, 2003, but use the method in DelphiII,
i.e. the included surface charge method. This method reduces the
dependence of solvation energy upon grid position. This is also why we
do not use smooth boundary dielectric by default.

We should publish a new method paper to better document pbsa's different
functions and methods.


Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail:
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Received on Tue May 24 2005 - 21:53:00 PDT
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