AMBER Archive (2004)

Subject: AMBER: which atoms are H's for SHAKE?

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Tue Apr 06 2004 - 12:32:12 CDT

Dear All,

can somebody tell me how the SHAKE algorithm in sander determines which
atoms actually are hydrogens?
Does the assignment of the element "H" to a new atom type in Leap with

addAtomTypes {{"X" "H" "sp3"}}

mean that SHAKE will treat the new type as hydrogen?

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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