Re: AMBER: Problem finding transition state using NMODE

From: David A. Case <>
Date: Thu, 22 Sep 2005 07:56:59 -0700

On Thu, Sep 22, 2005, Peter Anderson wrote:
> I am trying to use the nmode program of AMBER 8 in
> order to find the energy and transition state
> separating two minimum-energy structures of a
> four-residue peptide in vacuum.

The transition state search moves from one local minimum to *some* nearby
transition state. It will not try to find a transition state that "connects"
two minima.

> I entered the following command:
> nmode -O -i -o nmode.out -c min1.restrt -p
> -r nmode.restrt
> where "min1.restrt" contains the coordinates of one of
> the minima.

But your starting coordinates are not at a minimum. I don't know how much of
an impact this has, but you should certainly make sure that you can minimize
your system (using ntrun=4), before trying to find transition states.

I'm not sure why you are getting bad energies. You should know that this
procedure for finding transition states has not been used very much in a long

....good luck...dac
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Received on Thu Sep 22 2005 - 16:53:01 PDT
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