AMBER Archive (2004)

Subject: Re: AMBER: Amber Transition State Output

From: David A. Case (
Date: Wed Jun 09 2004 - 20:54:23 CDT

On Wed, Jun 09, 2004, Johnson Agbo wrote:

> I am using nmode to find a transition state structure(coordinates) and the
> energy barrier between my input structure or mininum structure and that of
> the transition state. My input structure has 24.0 kcal/mol of energy. The
> output file I am looking at has as its last part for the transition state
> search as :
> step = 56
> F = -0.488232E+01 GRDMAX = 0.662498E-03 GNORM = 0.132406E-03

The energy at the transtion state is -4.88 kcal/mol ("F"); it is not clear
that you "input structure" is a minimum energy structure; you might
investigate that if you want the difference in energy between the transition
state and some other state.


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