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

From: pengfei li <>
Date: Wed, 18 Dec 2019 11:52:23 -0500

Hi Dave and Tom,

Do you know any research (experimental or computational) that has been done about the sequence dependence of DNA duplex structures? Thanks!

Best regards,

> On Sep 5, 2019, at 8:29 AM, David A Case <> wrote:
> 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"
> B-DNA.
> 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.)
> ....dac
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Received on Wed Dec 18 2019 - 09:00:01 PST
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