Hi All,
I tried to calculate the binding free energy between molecule A and
molecule B with both MMPBSA and MMGBSA methods. Also I did per-residue
decomposition with both MMPBSA and MMGBSA, and then tried to calculate the
binding free energy from per-residue decomposed energies. The following are
the results.
PBSA
PBSA-decomp
GBSA
GBSA-decomp
Complex
-358.5
-183.2
-400.3
-403.5
A
-305.6
-215.7
-357.0
-361.8
B
-17.9
-20.0
-13.5
-12.9
Binding
-35.0
52.5
-29.8
-28.7
For MMGBSA, the binding free energy from these two approaches is quite
close (-29.8 vs -28.7 kcal/mol).
However, for MMPBSA, the binding free energy calculated from the
per-residue decomposed energies is problematic (positive 52.5 kcal/mol). I
understood that the non-polar solvation free energy cannot be decomposed in
PBSA. But that energy also only makes a minor contribution to the total
energy and binding. And the total energy from adding the per-residue
contribution is far less than the non-decomposed one (take A for example
-215.7 vs. -305.6 kcal/mol). Then what is the main reason leading to this
problem of MMPBSA please?
Could anybody shed some light on this issue please? Any suggestions will be
greatly appreciated.
Regards,
Qiong
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Received on Thu May 10 2012 - 13:30:04 PDT
