AMBER Archive (2004)

Subject: AMBER: cap waters always flexible?

From: Oliver Hucke (
Date: Thu May 06 2004 - 15:41:19 CDT

Dear amber users,

I am attempting to calculate protein ligand binding free energies for a
partially solvated system (solvateCap). I would like to consider only a
region of 15A around the inhibitor as flexible. From the literature it
is not completely clear to me if I should consider all water molecules
as flexible at every stage of the simulation. Or are the water molecules
outside the 15A shell supposed to be fixed at some stage?

Thanks very much,



Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: _______________________________________________________________

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