Hi Jason,
Thanks for your prompt reply. As you mentioned that AmberTools 1.5 uses the two equations to calculate the non-polar term in MM/PBSA and MM/GBSA, I found that the SASA values also differs a lot when binding free energy is obtained by MMPBSA.py in AmberTools 1.5.
So, regarding to AmberTools 1.5, can I simplely deduce that the methods for estimating the SASA values are different in the cases of MM/PBSA and MM/GBSA?
If so, are there some references or information about the methods implemented to calculate SASA in MM/PBSA and MM/GBSA (AmberTools 1.5)? I have googled a lot, but nothing valuable.
Many thanks!
Mu Xia,
Zhejiang University, China
At 2013-08-27 20:38:40,"Jason Swails" <jason.swails.gmail.com> wrote:
>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
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Received on Tue Aug 27 2013 - 07:00:03 PDT
