Dear Dr. Adrian
Thanks so much, your reply was faster than I can imagine.
In fact, in some drugs, the inhibition caused by the stacking of the benzene ring of the inhibitor with an aromatic ring of amino acid.
How AMBER manage the stacking here? is there an implemented function in the code to account for this stacking?
Thanks again for your help
Eliac
--- On Tue, 11/30/10, Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
> From: Adrian Roitberg <roitberg.qtp.ufl.edu>
> Subject: Re: [AMBER] Benzene Stacking in AMBER
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Tuesday, November 30, 2010, 5:12 PM
> Dear Eliac,
>
> This is just my personal opinion on this.
>
> First, the ONLY possible definition of stacking energy I
> can imagine is
> what one would call dimerization energy. Basically, it is
> the energy of
> the dimer, minus the energy of a single benzene alone (this
> last one
> multiplied by two of course). This could be done in
> solution or
> in-vacuo, etc
>
> I am not sure what the values really are, but there is not
> 'stacking'
> energy per se anywhere in the force field.
>
> Another point of importance. It is a common
> misunderstanding to think of
> a benzene dimer as 'stacked'. In fact, in vacuum, the most
> stable
> conformation is a T-shape, not the stacked one. The second
> most stable
> is a displaced stacked conformation, and what one usually
> calls 'staked'
> comes in third place. The T-shaped conformation is around 2
> kcal/mol
> stable at most.
>
> See recent paper by David Sherill on this issue. It
> requires some very
> heavy QM calculation to get it right.
>
> Adrian
>
>
> On 11/30/10 6:04 PM, Eliac Brown wrote:
> > Dear All
> > I was wondering if you could direct me to how the
> stacking energy of the benzene rings implemented in
> AMBER? all what I need is a start point.
> > Thanks
> > Eliac
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
>
> Dr. Adrian E.
> Roitberg
>
> Associate
> Professor
>
> Quantum Theory Project, Department of Chemistry
>
> University of
> Florida
>
> Senior Editor. Journal of Physical
> Chemistry.
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
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Received on Tue Nov 30 2010 - 09:30:04 PST
