Hi All,
I have performed thermodynamic integration calculations for the
complex(protein+ligand) system under explicit solvent conditions using ff99
forcefield and amber8. The binding energy was -9.2 kcal/mol. There is no
experiment value avaliable in the literature. So to cross check TI
calculations, I have perfomed MM-GBSA and PBSA using amber11 and ff99 for
250 snapshots. The binding enthaplies value for GBSA was found to be -11.85
kcal/mol. Further I have performed NAB calculations using AmberTools 1.5
for 10 snapdhots, the entropy contribution was -19.59 kcal/mol. The net
binding free energy for GBSA is 7.74 kcal/mol. Which is quite close to the
TI value but with opposite sign.
The PBSA binding enthaply value is nearly same as that of NAB entropy value.
Techanically entropy value has to be far less than the present value.
Does AmberTools1.5 typically report high entropy values? How should I
interpet my values?
Any suggesstions???
Thanks,
mani
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Received on Tue Sep 13 2011 - 18:00:02 PDT
