Hi Eliac,
To follow up on what Adrian says you may want to take a look at the
following manuscript:
Sherrill C.D., Sumpter B.G., Sinnokrot M.O., Marshall M.S., Hohenstein E.G.,
Walker R.C., Gould I.R., "Assessment of standard force field models against
high-quality ab initio potential curves for prototypes of -, CH/, and SH/
interactions", J. Comp. Chem, 2009, 30, 2187-2193.
http://www.wmd-lab.org/papers/JCompChem_2009_Sherrill_paper.pdf
In here we compared interaction energies for benzene benzene stacks in
multiple configurations as well as CH4-Benzene and H2S-Benzene interactions
for AMBER FF99SB and CHARMM ALL 27 against complete basis set CCSD(T)
calculations. Interestingly for Benzene 'sandwiches' the AMBER force field
is actually pretty good, due mostly to the VDW parameters and the
electrostatic term. As opposed to PM3/PDDG which gives a totally repulsive
curve with no minima. Not surprisingly it does not do as good when the two
rings are displaced or in a T-configuration.
All the best
Ross
> -----Original Message-----
> From: Adrian Roitberg [mailto:roitberg.qtp.ufl.edu]
> Sent: Tuesday, November 30, 2010 9:22 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Benzene Stacking in AMBER
>
> There is no particular stacking energy term, but it should come out as
> the sum of electrostatic and vdw terms. Warning: These are SMALL terms
> and with high errors. I personally do not trust them in terms of the
> details of the energies, but you see the effect you call stacking very
> often.
>
> Adrian
>
>
> On 11/30/10 6:17 PM, Eliac Brown wrote:
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> >
> > _______________________________________________
> > 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 - 18:00:04 PST
