Re: [AMBER] Transition state

From: Jason Swails <>
Date: Thu, 13 Nov 2014 08:24:30 -0500

On Thu, 2014-11-13 at 09:43 +0000, Mahmood Jasim wrote:
> Hi AMBER users
> I am trying to simulate a chemical reaction that involves the formation of
> a covalent bond between the sulphur atom (SG) of a cysteine residue and an
> electrophilic carbon of a ligand that is connected to a sulfonium ion (red
> carbon in the figure)
> [image: Inline images 4]
> The reaction involves the liberation of the sulfonium ion.
> I have tried steered MD with QM treatment of the ligand and the cysteine
> residue. I have used an LCOD varaible for the steered MD with the two
> distances being the distance of the bond being formed and the bond being
> broken.
> The reaction happens, but the problem is that once the new bond forms, the
> bond between the electrophilic carbon and the sulfonium ion breaks, the ion
> leaves and LCOD value remains unchanged after that. Therefore I could not
> get the curve as the one in the SMD tutorial, between the work and CV, from
> which to obtain the transition state structure.
> Any advice would be greatly appreciated

A couple things that may be going wrong: it is possible that your LCOD
restraint is poorly formulated. For example, if the LCOD is the sum of
the two distances, it will probably change very little over the course
of the reaction, and you will have a hard time resolving any aspects of
the reaction this way.

Additionally, the QM Hamiltonian that you are using may not be
appropriate for your system. It certainly wouldn't be the first time
that a more approximate/parametrized QM model predicted ridiculous
chemistry (if indeed that is what it's doing here).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 13 2014 - 05:30:03 PST
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