Re: AMBER: Modeling of a radical

From: David A. Case <>
Date: Thu, 14 Jul 2005 08:48:54 -0700

On Thu, Jul 14, 2005, L Jin wrote:
> Is it possible to model a radical with AMBER 7? The unpaired electron is on
> the place of N-O'. How can I represent this when preparing this residue in
> leap? And can I just set the net charge of this residue to zero when
> calculating the atom charge for the structure? Many thanks for any
> suggestion in advance.

It's possible for some purposes. You can't represent the position of the
unpaired electron, since force fields have no concept of electrons. For a
relatively rigid spin label, you can treat it is an a special residue: you
will have to come up with a charge distribution, bond force constants, and so
on. You should look for published papers on force field models for nitroxide
spin labels, and see how things were handled there.


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Received on Thu Jul 14 2005 - 16:53:00 PDT
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