AMBER Archive (2004)

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

From: Oliver Hucke (
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 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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