AMBER: which atoms are H's for SHAKE?

From: Oliver Hucke <>
Date: Tue, 06 Apr 2004 10:32:12 -0700

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:
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Apr 06 2004 - 18:53:00 PDT
Custom Search