AMBER Archive (2006)

Subject: AMBER: MMPBSA: magnitude of PB calculation

From: sishi.tang_at_utoronto.ca
Date: Fri Feb 03 2006 - 17:34:10 CST

Hi all,

I'm calculating the binding energy of a protein with a nonpolar ligand using
MMPBSA, the results that I obtained are as follows:

ELE -27.41 3.62
VDW -52.37 2.66
INT 0.00 0.00
GAS -79.78 4.73
PBSUR -3.37 0.22
PBCAL -573.75 28.49
PBSOL -577.12 28.40
PBELE -601.16 27.46
PBTOT -656.90 26.82

I also performed entropy calculation using nmode, which results in an entropy
contribution of around -5 kcal/mol (T=298) If that's the case, the overall
absolute binding energy amounts to -650 kcal/mol,which is obviously
non-physical. Is there any obvious anormaly in my PB results? Any
suggestions/advice will be more than welcome.

Thanks,
Sishi.

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