AMBER Archive (2009)

Subject: Re: [AMBER] average torsional energy

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Jun 07 2009 - 11:14:17 CDT

I add my 2 cents in support of Adrian's 3- clearly the DIHED energy is not
the energy for rotating around a bond. I also see this misinterpreted in the
literature quite often. As Adrian says, the DIHED is an empirical correction
term in most cases.

On Sun, Jun 7, 2009 at 12:09 PM, Adrian Roitberg <roitberg_at_qtp.ufl.edu>wrote:

> Francesco and all.
> I am not fully sure I understand your question, but I will give a more
> general answer.
>
> 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 complex discussion.
> 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.
>
> Adrian
>
>
>
> 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?
>>
>> thanks
>> francesco pietra
>>
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> --
> Dr. Adrian E. Roitberg
> Associate Professor
> 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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