Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions...

From: Stéphane Téletchéa <>
Date: Tue, 05 Jun 2007 10:01:10 +0200

Sophie Barbe a écrit :
> Dear amber users,
> I am performing molecular dynamics simulations of DNA fragments ( with AMBER9).
> I use the amber force field refined for nucleic acids : parmbsc0.
> I want to analyse several parameters of the nucleic acid during the simulation
> such :
> - the average backbone torsions
> - the average base pair parameters
> - the average pair step parameters
> - the average puckers
> Could you indicate to me which tool can I use to make these analyses?
> In several plucations, I noted that a carnal module found in previous amber
> versions was used.
> It seems me that there is not a similar module in amber9.
> So, I need some help.
> Thank you for advance for your answers
> Sophie

I think i've setup something that could be helpfull for you, the basic
idea is calculating first the parameters, then averaging them (so you
can easily average them in a different manner).

The whole procedure is described here:

My ISP had a problem yesterday and is planning to fix it within hours.
don't hesitate to contact me privately (in French if you wish) during
this reconstruction period.


Stéphane Téletchéa, PhD.        
Unité Mathématique Informatique et Génome
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901
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Received on Wed Jun 06 2007 - 06:07:27 PDT
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