On Tue, Apr 9, 2013 at 3:24 AM, dbaogen <dbaogen.gmail.com> wrote:
> Dear all,
>
> I have met a problem in calculation binding free energy using
> MMPBSA.py script in two versions of AmberTools. one is Amber 11 combined
> with AmberTools 1.5. The nonpolar solvation energy (ECAVITY ) is -3.4672
> kcal/mol. And the input file is as follow:
>
> MMPBSA input file for Amber 11 and AmberTools 1.5
> &general
> startframe=1, endframe=100, interval=1,
> keep_files=0,strip_mdcrd=0,verbose=1,
> /
> &pb
> istrng=0.1,
> /
> Searching in the AmberTools 1.5 Manual, the nonpolar solvation energy is
> calculated by using the equation G(np) = SurfTen*SASA+SurOFF = G(cavity)
> under the above parameter settings.
>
> The other is Amber 11 and AmberTools 12. The input file:
>
> MMPBSA input file for Amber 11 and AmberTools 12
> &general
> startframe=1, endframe=100, interval=1,
> keep_files=2,search_path=1,verbose=1,
> /
> &pb
> istrng=0.1, sander_apbs=1,radiopt=0
> /
> In this condition, according to the manual, the nonpolar solvation
> free energy is calculated by using G(np)=G(disp)+G(cavity), and the value
> (ENPOLAR) is -31.1906 kcal/mol. In addition, the AmberTools 12 manual
> mentions that the default parameters must be INP=2 with radiopt =1.
> whether did it mean that I set the wrong parameters for MMPBSA.py script?
>
This is not right, I don't think. The dispersion/cavitation decomposition
of the non-polar solvation free energy is only available via the PBSA
source code, _not_ via sander.APBS. Therefore, I think that the surface
area term here is the simple term G(np) = surften*SASA+offset.
>
> If I changed the "radiopt" to 1, the error message is "CalcError:
> sander.APBS failed with prmtop" when sander_apbs is set to 1. If the
> parameter radiopt=1 and sander_apbs=0, the error message is " PB Bomb in
> pb_aaradi(): No radius assigned for atom 3 C5' CI ". The program is
> normally ended only when radiopt is set to 0.
>
You must either add the missing atom types to the PBSA source code and
recompile, or settle with the inp=1 model for non-polar solvation free
energy term.
Would you like to give me some help about large difference of nonpolar
> solvation energy and radii selection of nonpolar energy calculation? Thanks
> in advance!
>
I didn't see any numbers, and have no idea what differences you are
referring to. Note that inp=2 requires AmberTools to be fully patched (at
least up to bugfix.27) in order to get the correct values for the
dispersion energy.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 09 2013 - 15:00:02 PDT
