AMBER Archive (2009)
Subject: Re: [AMBER] average torsional energy
From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Sun Jun 07 2009 - 11:09:14 CDT
Francesco and all.
I am not fully sure I understand your question, but I will give a more
My very strong opinion, shared by most practitioners, is that the DIHED
term (torsions) can never be interpreted in ANY way.
I also personally believe that one should be very careful in
interpreting the other terms also (vdw, elec,etc) but that is a more
Why is DIHED particularly bad? because it is a clear fudge term. While
one can assign a physical interpretation to the other terms (after all,
we have the 'idea' of a bond in our heads), the torsional potential
could be thought as if if comes from the electrostatics and vdw terms
only. The torsional term itself is simply a correction to get the force
field to match a QM torsional potential.
In short, the torsional term is NOT the torsional potential ! The
torsional potential, from where minima and barriers are extracted, comes
from the total energy vs torsional angle: a scan.
This usual confusion has some troublesome uses in the literature. Some
people will set the torsional term to ZERO, and call the new potential
one with 'reduced barriers'. This is non-sense. Setting a torsional term
to ZERO could do a number of things including: changing the location of
the minima, changing the number of minima, increasing the barriers,
decreasing the barriers, etc etc.
Just my three cents' worth of opninion.
Francesco Pietra wrote:
> My I ask about the practice of correctly evaluating from the DIHED
> term (with Amber 9 or 10) the average torsional energy for an alpha
> helical stretch where a major bending at a GLY residue is observed?
> francesco pietra
> AMBER mailing list
Dr. Adrian E. Roitberg
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
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