AMBER Archive (2004)

Subject: AMBER: mutation of Tyr to Leu with TI

From: Oliver Hucke (ohucke_at_u.washington.edu)
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,
AND
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 

-- 
_______________________________________________________________

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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