AMBER: bending

From: Gustavo Pierdominici Sottile <>
Date: Thu, 12 Aug 2004 17:47:16 -0300

Hi ,
    The problem with Van der Walls energy is not between A and C , if the
angle is A-B-C.
the problem is bewteen to hydrogens that are in different parts of the
molecule. A,B and C are carbon, nitrogen and carbon respectively. I will
re-mention the problem trying to be more specific:

The model has 16 atoms. I have already done an ab initio energy plot for
different values of that angle. Then I calculate the non bonding energy
using Amber Force field, and obtain the potential difference curve(ab
initio - non bonded). When trying to adapt this curve with an harmonic
function, I realized that the difference curve has no minimum (itīs linear).

This has not happended when I parametrized other things. Personally I think
that the difference of Van der Walls energy between conformations that are
close to the equilibrium value is high respect to that one. For example

Units = Kcal
Angle 1_ ab initio 2_ non bonded(predominantly Van der
Walls) 2-1

110 16 397
125 0 (ref. points) 50
140 4 44

The problem is that "2-1" can not be adjusted with an harmonic potential.
Apologizing for non being expecific in the previous mail and/or this one.
Thanking in advance,

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Received on Thu Aug 12 2004 - 22:53:00 PDT
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