AMBER Archive (2000)

Subject: Improper Dihedrals

From: Ryan H. Lilien (Ryan.H.Lilien_at_Dartmouth.EDU)
Date: Mon Nov 06 2000 - 14:38:49 CST

Hello,
  I'm emailing to ask about the implementation of improper dihedrals in the AMBER force-field. I have read through the parm.dat (http://www.amber.ucsf.edu/amber/formats.html#parm.dat) webpage file format description but have been unable to determine which atoms I,J,K, and L refer to. In some forcefields I is the central atom and in others, J is the central atom. So I essentially have two questions:

1. Which atoms are I, J, K, and L in the improper dihedrals

2. Is the standard cos terms used for these dihedrals or is another approach used.

Thanks,
Ryan Lilien
--------------------
Department of Computer Science
Dartmouth College
Hanover, NH 03755
USA