AMBER Archive (2006)

Subject: Re: AMBER: transition state

From: Eric Hu (list.eric_at_gmail.com)
Date: Mon Aug 21 2006 - 19:06:22 CDT

John,

If antechamber does not recognize the paremeters such as bond, angle
or dihedral angle, it will list their values as zero along with
something like NEED REVISION. You really have to modify them according
to the closest known values. By the way it will be helpful if you can
post your frcmod file next time when you ask for help.

Good luck!
-Eric

On 8/14/06, John Chuang$Bh7MK1sO7;U(B <yaoyuan.chuang_at_gmail.com> wrote:
> Eric,
>
> Thanks for your help. I have connected the atoms that having longer bond
> distances than the stationary molecules. However, I run into problem of
> assigning the force field parameters for the extra torsions and bends, I
> wonder if you have any suggestions on this?
>
> thanks
>
> John Chuang
>
> 2006/8/9, Eric Hu <list.eric_at_gmail.com>:
> >
> Dr. Chuang
>
> You need to use antechamber to generate a frcmod file that calculates
> new force parameters for your transition state. Also you need to make
> sure that your transition state "looks" like one molecule by adding a
> virtual bond in xleap ---- no broken bond in the case of a bimolecular
> reaction transition state.
>
> Eric
>
> On 8/7/06, John Chuang$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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>
>
> --
>
> 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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