Dear sir,
I'm dealing with simulations of structurally similar ligands (~100 atoms) bound at the surface of a receptor (~ 2600 atoms). I calculated binding free energies with MM-GBSA method and performed entropy calculations with Nmode module of Amber 9. GB calculation was applied for 1000 snapshots while Nmode calculation was applied for 20 snapshots. One ligand remained rigid at the binding interface, and the absolute binding free energy was close to the experimental value (less than 0.5 kcal/mol). Another ligand fluctuated over the interface and not bound as tightly as the former, but its absolute binding free energy was lower than the former's and deviated from its experimental value by almost 2 kcal/mol. Is it because that Nmode calculation failed to give reasonable estimation for the latter ligand-receptor complex?
Thanks a lot...
caobb
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Received on Wed Jun 08 2011 - 17:30:03 PDT
