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?
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?
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?
Many thanks!
Mu Xia,
Zhejiang University, China
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Received on Mon Aug 26 2013 - 21:00:02 PDT
