Hi,
I am investigating the binding free energy of a pentapeptide to a receptor
with Steered MD and GBSA . For SMD I have used,
"Constant velocity SMD simulation with force constant k=7 and velocity
0.00001 Å/ps until work graphics are converged. "
For GBSA the following is done,
Internal dielectric constant is taken 2 and external dielectric constant is
80. Bondi radii is used as 2 Ǻ for GB analysis. LCPO method is used with γ
value taken as 0.005 and β value taken as 0 for nonpolar
contributions.Entropy terms are calculated by NMODE module with ε = 4Ri.
For SMD binding free energy is found to be -3,5 kcal/mole ; but from GBSA it
is found -7,33 kcal/mol.
Can anybody help for the reason of this difference?
Thanks in advance,
Mehmet Ali Öztürk
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Received on Sat Sep 18 2010 - 13:00:04 PDT
