Pi stacking is usually well described by atom-centered charges force field
with AMBER-type ESP charges. (depending on system, systems with quadrupole
moment benzen-like distribution could be more difficult.)
Thus the name "pi-pi" is somewhat misleading in most cases.
J. Sponer, J. Leszczynski, P. Hobza: On the nature of nucleic acid base
stacking. Nonempirical ab initio and empirical potential characterization
of 10 stacked base pairs. Comparison of stacked and H-bonded base pairs.
Journal of Physical Chemistry 100, 1996, 5590-5596.
P. Hobza, J. Sponer: Structure, energetics, and dynamics of the nucleic
acid base pairs: Nonempirical ab initio calculations. Chemical Reviews 99,
1999, 3247-3276.
As far as simulations is concerned, the best way is to monitor the Lennard
Jones term (without electrostatics) of potential energy between the
stacked systems.
Note that the term "hydrophobic interaction" is complex, since it is
context dependent.
J. Sponer, K. E. Riley, P. Hobza: Nature and magnitude of aromatic
stacking of nucleic acid bases. Physical Chemistry Chemical Physics 10,
2008,
2595-2610.
J. Sponer, J. E. Sponer, A. Mladek, P. Jurecka, P. Banas, M. Otyepka:
Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum
chemistry, molecular mechanics and experiment. Biopolymers, 2013, 99,
978-988.
Note that while van der Waals potential energy can be easily monitored
along the simulation run, hydrophobic interaction cannot be monitored, as the later is a free
energy term pertinent to a thermodynamics state. In that
case binding free energy would have to be calculated, which is exceptionally difficult
and not always doable with a meaningful accuracy.
Jiri
-------------------------------------------------------
Jiri Sponer
Professor of Biochemistry
Head of Department of Structure and Dynamics of Nucleic Acids
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer.ncbr.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/
http://www.ibp.cz/en/departments/structure-and-dynamics-of-nucleic-acids/
-----------------------------------------------------------
On Fri, 24 Feb 2017, Chris Neale wrote:
> Date: Fri, 24 Feb 2017 15:46:58 -0700
> From: Chris Neale <candrewn.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] pi-pi interaction and hydrophobic
>
> Atomistic force fields don't have pi electrons ;)
>
> On Fri, Feb 24, 2017 at 3:17 PM, Kenneth McGuinness <
> kenneth.mcguinness.gmail.com> wrote:
>
>> Hi Abhishek, the paper below is a good reference for calculating Pi-Pi
>> interactions
>>
>> https://www.ncbi.nlm.nih.gov/pubmed/3892686
>>
>> ~Kenneth
>>
>>
>> On Fri, Feb 24, 2017 at 3:59 PM, Thakur, Abhishek <axt651.miami.edu>
>> wrote:
>>
>>> Hi,
>>>
>>> I have MD for my receptor, ligand complex.
>>>
>>> Now I want to do analysis like pi-pi interaction and hydrophobic
>>> interaction.
>>>
>>> can anyone suggest me how to do that.
>>>
>>>
>>>
>>>
>>> With regards,
>>>
>>> -AT
>>> _______________________________________________
>>> 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
>>
> _______________________________________________
> AMBER mailing list
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Received on Sat Feb 25 2017 - 01:30:02 PST
