AMBER Archive (2007)

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

From: Sophie Barbe (sbarbe_at_insa-toulouse.fr)
Date: Mon Jun 04 2007 - 16:16:48 CDT

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

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