Re: [AMBER] amber/gaussian find the transition state

From: Jason Swails <>
Date: Wed, 13 Aug 2014 08:07:08 -0400

On Wed, 2014-08-13 at 17:03 +0800, 王珍 wrote:
> Hi all,
> I am working with QM/MM using the Amber and gaussian,I want to
> find the transition state. the file I wrote did not work,the file is
> following;

"did not work" is a poor description of your problem. If you want us to
help you solve your actual problem, you'll need to tell us exactly what
you tried and what went wrong. This means copying exact input _and_
output so we can see the relevant error message with the necessary
context. Making us guess is an unreliable way to elicit helpful advice.
> &cntrl
> imin=1, maxcycle=200,
> ntb=0,
> cut=20,
> ifqnt=1
> &end
> &qmmm
> iqatom=1 2 3 4 5 6 7 8 9 10

This won't work for two reasons. The variable name is "iqmatoms", not
"iqatom". Second, it needs to be a comma-separated list of integers, as
described in the Amber manual.

> qm_theory='EXTERN',
> qmcut=20.0,
> qmcharge=0,
> spin=2,
> &end
> &gau
> num_threads=8
> method= 'B3LYP'
> basis= 6-31G,

This is a string, and needs to have quotes around it.

> opt=ts,

Same with this.

However, I don't think you can do a transition state optimization with
Amber. I know you can with Gaussian, but Amber does not have such an
optimization scheme. And in this case, Amber is the driver and all
Gaussian is used to do is provide energies, gradients, and charges for
use in the total QM/MM calculation. It doesn't know the whole potential
(since it doesn't know the QM/MM and MM parts), and so it cannot
possibly find a minimum energy or transition state structure. You will
have to find another way to find your transition state.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Aug 13 2014 - 05:30:02 PDT
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