AMBER Archive (2008)

Subject: Re: AMBER: question about dihedral angles

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Sep 15 2008 - 10:10:55 CDT

> I noticed that in the force field file, in dihedral angle part, for example,
> there are entries like:
> X - CT - OS - X 3 1.15 0.0 3.
> CT - CT - OS - CT 1 0.383 0.0 -3.
> CT - CT - OS - CT 1 0.1 180.0 2.
> So, when assign the parameters to dihedral angle CT - CT - OS - CT to
> calculate the energy, are all three entries used or just the latter two
> used? Thank you.

In this format, the last two entries will define the torsional energy
for CT - CT - OS - CT. The first entry is the generic definition; for
instance if you have dihedrals of H -CT-OS-H, then that entry is used to
define the torsional energy. 

-- 
  Ilyas Yildirim, Ph.D.
  ---------------------------------------------------------------
  = Hutchison Hall B#10          - Department of Chemistry      =
  =                              - University of Rochester      =
  = 585-275-6766 (office)        -                              =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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