AMBER Archive (2005)

Subject: Re: AMBER: How is the origin of the grid defined?(PBSA question)

From: Ray Luo (rluo_at_uci.edu)
Date: Sat Aug 13 2005 - 14:40:54 CDT

Dear Liu,

The origin in fdpb is defined as the center of a rectangular box that is
large enough for all atoms currently considered. You can print out the
center of grid used for each snapshot by setting "pbverb=1" in the pb
portion of your "pbsa.in" file or insert it in the pb section of your
perl script. Do you see any warnings in your output files?

I have turned off the option for end users to define the center of grid
in Amber8, because we have not seen relative standard deviations as
large as yours after implementing the new method to compute reaction
field (solvation) energy using surface charges. This used to be an issue
for pb calculations using only one conformation, not an issue for mmpbsa
type of calculation that uses many conformations.

All the best,
Ray

JunJun Liu wrote:

> Dear AMBER Users:
>
> I obtained 75 snapshots from 750ps to 1500ps every 10ps. The MM-PBSA
> results are shown below.
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -37.81 5.48
> VDW -70.03 3.67
> INT -0.00 0.00
> GAS -107.85 5.00
> PBSUR -6.54 0.27
> PBCAL 76.48 19.28
> PBSOL 69.94 19.30
> PBELE 38.67 18.51
> PBTOT -37.91 18.33
>
> As can be seen, PBCAL is quite inaccurate when compared STD value of
> GAS energy. I got a suggestion that the origin of grids need to be
> checked. If the origin was defined at the center of mass or center of
> charge, then the origins in the complex and free protein are not
> necessarily the same, which will cause inappropriate solvation
> calculations.
>
> If the origin was always defined at the position of the same atom of
> the protein, which means the origins in both the complex and free
> protein should be the same, then what other factors that could cause
> the inappropriately numerical PB solvation? Any suggestions will be
> highly appriecated!
>
> Best Regards!
>
> Liu
> 

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