AMBER: with two water molecules in active site, how to calculate the free energy of ligand bound to complex?

From: haixiao jin <>
Date: Mon, 31 Oct 2005 14:27:08 +0800

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!

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Oct 31 2005 - 06:53:02 PST
Custom Search