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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 30 2010 - 09:30:05 PST
