On Mon, Aug 26, 2013 at 11:46 PM, Mu Xia <muxiachuixue.163.com> wrote:
> Hi all,
>
>
> I am using Amber11 and AmberTools12 for the binding free energy
> calculation. MMPBSA.py was implemented. The following is the input file:
>
>
> Input file for running PB and GB
> &general
> verbose=1, interval=5,
> strip_mask=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:Na+:Rb+",
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
>
> I noted that MMPBSA.py uses the following equations to calculate the
> non-polar solvation free energy:
>
>
> MM/PBSA: Delta(Gnp) = cavity_surften * SASA + cavity_offset
> MM/GBSA: Delta(Gnp) = surften * SASA + surfoff
>
>
> in which cavity_surften = 0.0378, cavity_offset = -0.5692, surften =
> 0.0072, surfoff = 0 for the default value in AmberTools12, respectively.
>
>
> It seems that MMPBSA.py uses the LCPO method in sander to obtain the SASA
> values both in the cases of MM/PBSA and MM/GBSA. Strangely, when I tried to
> reckon the value of SASA according to the values of ESURF and ECAVITY
> shown in the final output file, I found that the values of SASA were
> different in MM/PBSA (SASA = 952) and MM/GBSA (SASA = 904).
>
>
> I have three questions:
>
>
> 1. Are the above equations for calculating the non-polar solvation free
> energy by MMPBSA.py correct or not?
>
It depends on the version that you are using. For AmberTools 1.5, you are
correct. For AmberTools 12 and 13, PBSA implements a new non-polar
solvation term that has a (repulsive) cavitation term and a (attractive)
dispersion term -- the 'nonpolar solvation' free energy is a sum of the
two. Since this is a fundamentally different model than the simple
SASA-scaling you showed above, the results are frequently quite different.
(I've found the difference in _binding_ energy to be ca. 30 kcal/mol
typically).
> 2. If MMPBSA.py uses the same method to calculate SASA in MM/PBSA and
> MM/GBSA, why are the values so different? Or different methods are
> conducted?
>
As mentioned above -- different methods.
3. From AmberTools1.5 to AmberTools12, why did the Amber developers update
> the default values for PB variables in MMPBSA.py, especially cavity_surgten
> and cavity_offset?
>
Presumably because the new values were found to produce better results,
although I'm not the definitive source on these changes.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 27 2013 - 06:00:02 PDT
