AMBER Archive (2005)

Subject: AMBER: How to calculate binding free energy of ligand bound to complex with two active-site water molecules?

From: haixiao jin (jinhx952_at_gmail.com)
Date: Tue Oct 25 2005 - 02:55:46 CDT

dear amber users,
Binding free energy analysis was carried out with MM-PBSA approach. The
complex contains protein, ligand and two active-site water molecules. when
the three prmtop file were prepared, the two active-stie water molecules
should be stay with protein or ligand? Or there is another way to deal with
the active-site water molecules? thank you for your attention!
 haixiao jin

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