AMBER Archive (2004)

Subject: AMBER: cap waters always flexible?

From: Oliver Hucke (ohucke_at_u.washington.edu)
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 

-- 
_______________________________________________________________

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: ohucke_at_u.washington.edu
_______________________________________________________________

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