AMBER Archive (2006)

Subject: Re: AMBER: transition state

From: John Chuang莊曜遠老師 (yaoyuan.chuang_at_gmail.com)
Date: Mon Aug 14 2006 - 17:20:20 CDT

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莊曜遠老師 <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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
Yao-Yuan (John) Chuang
Assistant Professor, Department of Applied Chemistry
National University of Kaohsiung
700 University Road, Nanzih District, Kaohsiung, Taiwan 811
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu