Re: [AMBER] regarding pi-pi interaction

From: Jiri Sponer <>
Date: Tue, 7 Jun 2011 12:28:00 +0200 (MEST)

See for example the following.

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps
in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability
by Quantum-Chemical Calculations?
Author(s): Svozil D, Hobza P, Sponer J
Source: JOURNAL OF PHYSICAL CHEMISTRY B Volume: 114 Issue: 2 Pages:
1191-1203 Published: JAN 21 2010

The best way from physical chemistry point of view is
to monitor the vdW part of stacking energy.
In case of protein core you may also consider
adding the elstat term, when it is not exposed to solvation.
Geometry definitions are always problematic and often

When you use MD trajectories, then it is smooth.
Be careful with medium to low resolution atomistic
X-ray structures, data and refinements error
could hamper energy evalulations (some spurious
steric clashes etc).

The force field is qualitatively OK.

Best wishes, 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
fax: 420 5412 12179
phone: 420 5415 17133

On Tue, 7 Jun 2011, Hirdesh Kumar wrote:

> Date: Tue, 7 Jun 2011 15:49:32 +0530
> From: Hirdesh Kumar <>
> Reply-To: AMBER Mailing List <>
> To: AMBER Mailing List <>
> Subject: [AMBER] regarding pi-pi interaction
> Hi All,
> I am interested in calculating the pi-pi interaction between two aromatic
> rings of protein residues. The use of distance between two centroid or the
> dihedral angle between the two ring does not solve the problem. Please
> suggest me how should I proceed further to check whether two rings are
> actually making making pi-pi interaction or not..
> Thanks in advance.
> Hirdesh Kumar
> _______________________________________________
> AMBER mailing list

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Received on Tue Jun 07 2011 - 03:30:05 PDT
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