AMBER Archive (2005)

Subject: Solute-solvent boundary in pbsa ..Re: AMBER: Copyright for PBSA

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Tue May 24 2005 - 13:48:26 CDT

Hello Prof. Case,

I have read Luo's paper published at J. Chem. Phys.
119, 11035-11047.

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.

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.

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?

my best regards,

jenk.

--- "David A. Case" <case_at_scripps.edu> wrote:
> On Sat, May 21, 2005, Cenk Andac wrote:
>
> > I used the PBSA module of AMBER8 to complete my
> thesis
> > work. Hence, I would like to cite PBSA in my
> thesis in
> > some way.
>
> The manual section on "Poisson-Boltzmann dynamics"
> (section 5.16) has
> references to papers that describe in detail the
> methods used. The paper
> by Lu and Luo is probably the most informative.
>
> > I have read the following copyright notice:
> >
> >
>
> > This software provided pursuant to a license
> > agreement containing restrictions on its
> > disclosure, duplication, and use. This
> > software contains confidential and proprietary
> > information, and may not be extracted or
> > distributed, in whole or in part, for any purpose
> > whatsoever, without the express written permission
> > of the authors....
> >
> > I was wondering if users are allowed to divulge
> the PB
> > equations (implemented in the PBSA module) with a
> > permission.
>
> The license refers to redistributing the _code_, not
> to referring to the
> equations that are used. You may of course discuss
> the PB equations that are
> the basis for the computer code.
>
> ...dac
>

                
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