As I known from the Examples in mm_pbsa, the std of PB is always
larger than GB, such as
Amber7/src/mm_pbsa/Examples/03_MMPBSA_Binding
PBTOT: -21.68 std: 14.41
GBTOT: -42.67 std: 5.52
Amber8/src/mm_pbsa/Examples/03_MMPBSA_Binding
PBTOT: -64.87 std: 14.88
GBTOT: -51.43 std: 3.78
I also want to know the large std of PB and how to deal with it.
Any suggestion about it.
Best Regards
Suxin
On Aug 13, 2005, at 12:40 PM, Ray Luo wrote:
> 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.uci.edu
> Home page: http://rayl0.bio.uci.edu/rayl/
> ====================================================
>
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Received on Tue Aug 16 2005 - 22:53:00 PDT
