AMBER Archive (2005)

Subject: Re#2:Re: AMBER: Solute-solvent boundary in pbsa

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed May 25 2005 - 15:03:47 CDT

Hi Prof. Luo,

I have one more question regarding application 1 you
have described below.

Let us assume that pbsa has computed electrostatic
potentials for solvent, solute interior and
solute-solvent boundary in some way. What procedure
does pbsa follow to compute Ges? Would that be similar
to EQ 20 in Lu&Luo(2003)JCP,119,11035.

best regards,

jenk

--- Ray Luo <rluo_at_uci.edu> wrote:
> Jenk,
>
> 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
> >interior.
> >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 ?
> >
> >epsboundary=epsout.epsin/(epsin.d+epsout(1-d))
> >
> >where d is the fraction of the grid line that is
> >solvent.
> >
> >
>
> 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
> >program?
> > 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.
>
> Best,
> Ray
>
> --
> ====================================================
> 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: rluo_at_uci.edu
> Home page: http://rayl0.bio.uci.edu/rayl/
> ====================================================
>

                
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