AMBER: About protein-ligand binding

From: Francesco Pietra <>
Date: Fri, 21 Dec 2007 06:52:00 -0800 (PST)

Unable to calculate free energy of binding protein-non_standard_ligand per
residues in explicit medium (gaff ff for the ligand), I would appreciate
suggestions how to best approach the problem of detecting the protein residues
most responsible for the binding under such conditions.

EPTOT is absolutely flat so that there is no point to continue to accumulate

If I map the residues most close to the ligand (which allows the most
straightforward comparison with experimental data), which snapshot should I
best consider in the "best" family of snapshots? The one for the minimum
potential energy or rather the average structure, or which else? The minimum
potential energy if for the whole (complex and surrounding medium), so that I
guess it is not useful to my purpose.


francesco pietra

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Received on Sun Dec 23 2007 - 06:07:31 PST
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