AMBER: Nucleic acid : nonplanarity

From: Sophie Barbe <>
Date: Wed, 04 Jul 2007 14:37:26 +0200

Dear amber users,

I am performing molecular dynamics simulations of DNA double-strands( with
AMBER9). I use the amber force field refined for nucleic acids : parmbsc0.
My procedure is the following one :
- preparation of MD : initial minimization followed by slow heating to 310K at
constant volume over a period of 100 ps using harmonic restraints (25 kcal...)
on the solute atoms. These restraints are slowly relaxed from 10 to 1 kcal.. :
- first during an equilibration at constant volume
- secondly during 8 segments of equilibration using constant temperature (310 K)
and pressure (1 bar) conditions via the Berendsen algorithm with a coupling
constant of 0.2 ps for both parameters.
The final segment consists of 50ps unrestrained equilibration.
The simulations are then continuing at constant temperature and pressure
conditions, using Beredsen algorithm with a coupling constant of 2 ps for both
I notice that the nucleic bases are not planar. The substituents of the bases
are out of plane (dihedral angle > 10 deg).

Thank you for advance for your answers


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Received on Sun Jul 08 2007 - 06:07:08 PDT
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