AMBER Archive (2004)

Subject: Re: AMBER: Amber Transition State Output

From: Johnson Agbo (agboj_at_chem.unr.edu)
Date: Fri Jun 11 2004 - 00:28:05 CDT

Hi Amber;
Thank you Dr. David Case for the help. My problem with the barrier
height is now fully resolved.

On Jun 9, 2004, at 6:54 PM, David A. Case wrote:

> 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.
>
> ...dac
>
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