[AMBER] Transition state

From: Mahmood Jasim <ddfd09.gmail.com>
Date: Thu, 13 Nov 2014 09:43:51 +0000

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

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

Mahmood Jasim

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(image/png attachment: image.png)

Received on Thu Nov 13 2014 - 02:00:02 PST
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