AMBER Archive (2003)

Subject: characteristics of nucleic acids homopolymers

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue Apr 08 2003 - 13:33:03 CDT

Hi amber users,

I am sorry if my question sounds naive but I've been looking through the
literature and could not find a very clear answer.

I did dynamics for a single stranded nucleic acid homopolymer in water
with the initial configuration being helical and the final sort of bulky.
I was thinking that a way to characterize the "distortion" is to follow
during the dynamics the values of the minor/major grooves and also the
helicity.
I have two questions:
1. Between which atoms exactly one should measure the minor/major grooves
2. What is the best way to calculate the helicity of a strand?

Any advice on this matter would be appreciated.
Thanks in advance,
Ioana