AMBER Archive (2004)

Subject: Re: AMBER: bending

From: David A. Case (
Date: Thu Aug 12 2004 - 14:48:30 CDT

On Thu, Aug 12, 2004, Gustavo Pierdominici Sottile wrote:

> Trying to reproduce the ab initio energy for a bending I found that the
> difference between the ab initio energy and the non bonded, can not be
> adjusted with an harmonic potential.
> This difference potencial is linear with a negative slope. I think that this
> problem is due to the high increment of Van der Walls interaction as the
> angle decreases.
> In this model, two hydrogens get closer as the angle decreases.
> If someone knows why this happens, please write me

If by "bending" you mean "angle bending" (that is, changing the A-B-C angle,
where A and C are both bonded to B), molecular mechanics force fields always
ignore any nonbonded interactions (such as van der Waals) between atoms A
and C. But is sounds like you might not be doing this(?).

If I am mis-reading your question, then you will probably have to be more
specific, probably giving an actual example of what is not working the way you
want it to.


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