AMBER Archive (2007)

Subject: AMBER: protein-ligand binding affinity

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Dec 13 2007 - 08:00:17 CST

I would like to calculate the binding affinities to a protein of non-standard
non-polymeric ligands. Ideally, free energies. At worst, relative energies.

The complex is in a hydrated POPC membrane and I could continue current MD
(Amber9, sander.MPI) to several ns.

I wonder whether there is in Amber9 anything similar to Q-program linear
interaction energy methodology, or if this can be imitated. Of course, unless
there is anything better in Amber9, provided that the environment is maintained
for both the ligand alone and the complex to be compared.

Thanks

francesco pietra

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