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?
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.
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!
Best wishes
Duan Baogen
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Received on Tue Apr 09 2013 - 00:30:03 PDT
