AMBER Archive (2004)

Subject: AMBER: mutation of Tyr to Leu with TI

From: Oliver Hucke (
Date: Tue Aug 24 2004 - 18:56:47 CDT

Dear amber users/developers,

is it possible to "mutate" a Tyr to a Leu within one thermodynamic
integration simulation with sander?
My understanding is that this would involve the following:
o conversion of the OH in the Tyr sidechain and the carbon atom bound to
it to dummies,
o conversion of the CE carbons to hydrogens (HC) and of the H's bound to
them to dummies,
o conversion of the CD bound H's from HA to HC,
o conversion of the CD carbon types from CA to CT,
o letting a third hydrogen (HC) appear at each of the CD carbons.

How can I achieve especially the last step?

Thanks very much in advance,


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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