ligand flies away from binding pocket

From: Osman Yogurtcu (karmatech_at_yahoo.co.uk)
Date: Thu Feb 12 2009 - 11:39:04 CST

Hi, I have a 300 K water NPT simulation of a ligand (one aminoacid) bound to a receptor. After I do minimization and equilibration (for 1 ns), I do an MD run. I observe that my ligand leaves the binding pocket after 2 ns. My question: is there a trick that I can make sure that my ligand sits in the binding pocket all the time or should I define bonds artificially and fix the ligand? thank you, Osman

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