Re: [AMBER-Developers] Langridge B-DNA vs Arnott B-DNA

From: David A Case <>
Date: Thu, 5 Sep 2019 08:29:33 -0400

On Wed, Sep 04, 2019, Pengfei Li wrote:
>I am going to build a B-DNA using nucleic acid builder (NAB) in
>AmberTools. For building a right-handed B-DNA, there are two
>options: Langridge and Arnott. Does anyone know the difference between
>them? Thanks!

You can just look at the helical parameters to see any detailed
differences. The "Arnott" values are by far the most commonly used, and
would correspond to what most people would think of as "canonical"

As Tom points out, if you run a simulation, you will quickly move to
what the force field wants, which will be sequence dependent, but really
quite good for B DNA: differences from the canonical form are generally
pretty good (although actual evidence for this statement is sparse.)


AMBER-Developers mailing list
Received on Thu Sep 05 2019 - 05:30:02 PDT
Custom Search