AMBER Archive (2005)

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

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Tue Aug 23 2005 - 03:46:03 CDT

Dear Dr.Luo

Thank you very much! The patch works! But I don't know why they(results
 from pbsa/Delphi) are so different? Which program performs better? Here's
my results:

# DELTA
# -----------------------
# MEAN STD
# =======================
PBTOT -37.91 18.33 # pbsa, unpatched
PBTOT -57.31 4.23 # pbsa, patched
PBTOT -38.26 5.56 # DelPhi

By the way, it seems a dot was missed in the modified code,
> At line 558 in pb_force.f:
>
> change:
>
> if ( abs(totcrg) > smallcrg ) then
>
> to:
>
> if ( .false. and. abs(totcrg) > smallcrg ) then
                  ^^^^^^
Here I believe it should be .and.

Best Regards!

Liu

On Tue, 16 Aug 2005 17:03:04 +0800, Ray Luo <rluo_at_uci.edu> wrote:

> Dear Liu,
>
> Most likely this is due to the surface charge scaling for nearly neutral
> molecules in pbsa. After removing this feature, the energies will become
> stable. i.e.
>
> At line 558 in pb_force.f:
>
> change:
>
> if ( abs(totcrg) > smallcrg ) then
>
> to:
>
> if ( .false. and. abs(totcrg) > smallcrg ) then
>
> A patch will be posted at "AMBER Bug fixs" today.
>
> Thanks a lot for letting us know.
>
> Ray
>
> JunJun Liu wrote:
>
>> Dear Dr.Luo:
>>
>> Thank you for response! I find STD value decreased to about 5kcal/mol
>> when using DelPhi program. I'd like to find out what the problem is,
>> but I have to leave for about one week. I hope I still can get help
>> from you one week later when I come back to this issue.
>>
>> Best Regards!
>>
>> Liu
>>
>> On Sun, 14 Aug 2005 03:40:54 +0800, Ray Luo <rluo_at_uci.edu> 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
>>>>
>>>
>>
>>
>>
> 

-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu