AMBER Archive (2005)

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

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu May 26 2005 - 15:58:55 CDT

Prof. Luo,

Information you have provided has been helpful. Thank
you.

I guess I'll have one last question about
determination of solvent/solute boundary by pbsa,
invoked by mm_pbsa.
I know that mm_pbsa uses mosurf to compute SASA and
G(non-electrostatic). I was wondering if pbsa uses the
SASA information to determine solute-solvent boundary,
or it has just its own codes to do that (any
literature?) ?

best regards,

jenk

--- Ray Luo <rluo_at_uci.edu> wrote:
> Hi Jenk,
>
> To discuss properties of dielectric in electrostatic
> field, it is very
> useful to use the concept of induced surface charge.
> Suppose there are M
> atomic charges, Q_1, ..., Q_M. After solving
> Poisson's equation, the
> electrostatic potential distribution around these
> charges can be obtained.
>
> Inversely, we can recover these charges according to
> Gauss' Law:
>
> \nabla E = 4 \pi \rho,
>
> where E is electrostatic field and \rho is charge
> density. Note that
> \rho is non-zero apparently at atomic centers
> because we put charges
> there. However, \rho is non-zero also at the
> dielectric boundary. This
> is due to the discontinuity of E when there is a
> discontinuity of
> dielectric constant at the boundary. E is very easy
> to obtain given
> electrostatic potential according to the
> finite-difference method. So it
> is straightforward to obtain \rho at the dielectric
> boundary.
>
> Now suppose there are N included surface charges,
> q_1, ..., q_N at the
> boundary. An interesting finding is that the
> reaction field energy is
> equal to
>
> 1/2 \sum_{i=1, M} \sum_{j=1, N} Q_i q_j
>
> This is equivalent to
>
> 1/2 \sum{{i=1, M} Q_i \phi_i^{reac}
>
> where \phi_i^{reac} is reaction field potential at
> atomic charge Q_i.
> The latter equation is used in Lu and Luo, JCP. The
> equivalence of the
> two relations can be proven based on Poisson's
> equation and Green's
> Theorem, or just divergence theorem.
>
> The induced surface charge approach is more
> intuitive but slower. We are
> replacing the nonuniform dielectric media by induced
> boundary charges.
> So electrostatic interactions between solute and
> solvent can be
> described by pairwise interactions between atomic
> solute charges and
> induced boundary solvent charges.
>
> All the best,
> Ray
>
> Cenk Andac wrote:
>
> >Dear Prof. Luo,
> >
> >I do not have any versions of Delphi. Would you
> >possibly provide me with an equation for
> electrostatic
> >potential at the solute-solvent boundary that
> >is coded in pbsa for single-point Poisson
> computations
> >at zero salt concentrations?
> >
> >Best regards,
> >
> >Jenk
> >
> >
> >
>
> --
> ====================================================
> 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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