AMBER Archive (2005)

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

From: Ray Luo (rluo_at_uci.edu)
Date: Wed May 25 2005 - 00:56:08 CDT

Jenk,

See my reply to your previous email.

Ray

Cenk Andac wrote:

>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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>.
>
>
> 

-- 
====================================================
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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