Dear AMBER
One of my projects is dealing with the binding affinity calculation of some ligands with a certain protein.
When I calculated the binding energies using MMPBSA, I got a good correlation with the experimental data, but when I analyzed the simulation trajectory, I found the binding mode of the ligand with the receptor is not correct for most of the studied ligands comparing to the crystal structure according to the binding mode with the metal ion at the active site.
I repeated the calculation again (using on modified parameters for the metal ion), I got a very good trajectory comparing to the crystal structural. But the binding energies were horrible.
So how does it give good correlation with giving wrong binding mode with the active site? It is a luck or a black box.
Thanks and happy new year
Eliac
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Received on Thu Dec 30 2010 - 21:00:04 PST
