Re: [AMBER] stacking energy calculation

From: Jiri Sponer <>
Date: Wed, 16 Mar 2011 12:02:39 +0100 (MET)


it is not fully clear what kind of calculations
you wish exactly to do, however, look for example at
this study where we monitored stacking via
QM along MD trajectory.

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

Best wishes Jiri

Jiri Sponer
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 Wed, 16 Mar 2011, hari krishna wrote:

> Date: Wed, 16 Mar 2011 15:36:36 +0530
> From: hari krishna <>
> Reply-To: AMBER Mailing List <>
> To: AMBER <>
> Subject: [AMBER] stacking energy calculation
> Hi all:
> Initially I did a simulation for 20ns for a DNA and ligand system. I
> want to calculate the stacking energy between the Ligand and DNA, I removed
> the atoms of backbone and bases except the bases contributing to the
> stacking with the ligand. Then I calculated the sinlge point energy using
> the Gaussian, how can i remove the energy contributed from electrostatics or
> H-bond except from stacking energy. Is there is any way to calcluate using
> the MD trajectory files from simulation.
> HariKrishna. S
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Mar 16 2011 - 04:30:04 PDT
Custom Search