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:
http://www.steletch.org/spip.php?article32
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.
Cheers,
Stéphane
--
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
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
