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From: Cenk Andac <cenk_andac.yahoo.com>

Date: Thu, 26 May 2005 13:58:55 -0700 (PDT)

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.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.uci.edu
*

*> Home page: http://rayl0.bio.uci.edu/rayl/
*

*> ====================================================
*

__________________________________

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Received on Thu May 26 2005 - 22:53:00 PDT

Date: Thu, 26 May 2005 13:58:55 -0700 (PDT)

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.uci.edu> wrote:

__________________________________

Do you Yahoo!?

Yahoo! Small Business - Try our new Resources site

http://smallbusiness.yahoo.com/resources/

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Received on Thu May 26 2005 - 22:53:00 PDT

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