[Amber]: Peptide torsions in Parm99.dat

From: Warren DeLano <warren_at_sunesis-pharma.com>
Date: Thu 25 Jan 2001 14:53:15 -0800

Amber Parameter Jocks:

I noticed a puzzling set of parameters for amide torsions in the
parm99.dat file (directly from the Amber web site, Jun-mei Wang's work -
lines 534-538)

C -N -CT-C 1 0.850 180.000 -2.
C -N -CT-C 1 0.800 0.000 1.
C -CT-N -C 1 0.50 180.0 -4.
C -CT-N -C 1 0.15 180.0 -3.
C -CT-N -C 1 0.53 0.0 1.

There seems to be a doubling up on the C-CT-N-C torsion with a set each
for both the forward and reverse directions. Are both of these in
effect, or just one? What is intended?

If we only want one, which one does Amber normally use given the
ordering of the parameter file? (I don't have access to Amber, so I
can't test this myself.) Does the first entry take precedence?

I'm asking because I am converting these parameters for use with Python
code that autogenerates parameters requirements for any molecular system
and then applies a standard Amber-format parameter file to fill those
requirements (part of PyMOL/Tinker -- the goal: a free/open-source
replacement for Macromodel or Insight/Discover).


- Warren

Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
3696 Haven Ave., Suite C
Redwood City, CA 94063
(650)-562-3106 fax: (650)-556-8824
Received on Thu Jan 25 2001 - 14:53:15 PST
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