AMBER Archive (2006)

Subject: Re: AMBER: transition state

From: Eric Hu (list.eric_at_gmail.com)
Date: Wed Aug 09 2006 - 14:05:14 CDT

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.

Eric

On 8/7/06, John Chuang$Bh7MK1sO7;U(B <yaoyuan.chuang_at_gmail.com> 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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