AMBER Archive (2005)

Subject: AMBER: intramolecular nonbonded interactions in AMBER force field

From: John Silvio Vieceli (john_at_zymeworks.com)
Date: Wed Apr 20 2005 - 17:06:48 CDT

Hi,

Are intramolecular nonbonded interactions applied to atoms separated by
more than three bonds in the AMBER force field? I understand that 1,4
LJ and Coulomb interactions are calculated and scaled by 1/2 and 1/1.2,
respectively. But what about 1,5 and beyond? Are these interactions
included and, if so, scaled by any factor? Thank you. 

-- 
John S. Vieceli, Ph.D.
Zymeworks, Inc.
201-1401 West Broadway Avenue
Vancouver, B.C. V6H 1H6
(604) 678-1388 ext. 25
john_at_zymeworks.com
www.zymeworks.com

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