AMBER Archive (2005)

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

From: Ray Luo (rluo_at_uci.edu)
Date: Tue Aug 16 2005 - 08:46:01 CDT

Suxin,

See my last reply to Liu ... please patch "pb_force.f" under src/pbsa
with the attached bugfix file and recompile pbsa. I'm uploading the
bugfix to Amber 8 web site.

Best,
Ray

Suxin Zheng wrote:

> 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_at_uci.edu
>> Home page: http://rayl0.bio.uci.edu/rayl/
>> ====================================================
>>
>> ---------------------------------------------------------------------- -
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> .
> 

-- 
====================================================
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/
====================================================

*** pb_force.f 2004-03-13 22:21:24.000000000 -0800
--- pb_force.f 2005-08-16 14:54:39.133342846 -0700
***************
*** 555,561 ****
     anaeelr = DHALF*frcfac*anaeelr
     !tmpeelr = DHALF*frcfac*tmpeelr
     !grdeelr = DHALF*frcfac/h*grdeelr
! if ( abs(totcrg) > smallcrg ) then
        scalfact = abs( totcrg/srfcrg*(ONE/epsin - ONE/epsout)*eps0 )
     else
        scalfact = ONE
--- 555,561 ----
     anaeelr = DHALF*frcfac*anaeelr
     !tmpeelr = DHALF*frcfac*tmpeelr
     !grdeelr = DHALF*frcfac/h*grdeelr
! if ( .false. .and. abs(totcrg) > smallcrg ) then
        scalfact = abs( totcrg/srfcrg*(ONE/epsin - ONE/epsout)*eps0 )
     else
        scalfact = ONE

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu