Re: AMBER: transition state

From: Eric Hu <>
Date: Wed, 9 Aug 2006 12:05:14 -0700

Dr. Chuang

You need to use antechamber to generate a frcmod file that calculates
new force parameters for your transition state. Also you need to make
sure that your transition state "looks" like one molecule by adding a
virtual bond in xleap ---- no broken bond in the case of a bimolecular
reaction transition state.


On 8/7/06, John Chuang莊曜遠老師 <> wrote:
> Dear all,
> I am new to the AMBER program. I would like to solvate
> a transition state structure (small organic molecule)
> in the water box and perform MD simulation. However,
> the atomtype and valency of the transition state is
> not found in the force field. Is there any way to
> solve this problem? Does the QM/MM option able to
> handle it?
> Yao-Yuan (John) Chuang
> --
> Yao-Yuan (John) Chuang
> Assistant Professor, Department of Applied Chemistry
> National University of Kaohsiung
> 700 University Road, Nanzih District, Kaohsiung, Taiwan 811
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Received on Sun Aug 13 2006 - 06:07:03 PDT
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