Re: [AMBER] Question about NAB package usage in AMBER

From: David A Case via AMBER <>
Date: Thu, 1 Sep 2022 15:42:08 -0400

On Tue, Aug 30, 2022, Qinsi Xiong via AMBER wrote:
>I’m trying to find a way to construct a superhelix A-form DNA structure
>(or say nucleosome-like structure) with relative short basepairs (less than
>I know NAB can do this ($AMBERHOME/ AmberTools/examples/nab/
>, but the tricky part is that NAB only supports to construct
>a nucleosome model based on B-form DNA, and what I want is to construct a
>nucleosome model based on A-form DNA.
> 1. I tried to modify the code by changing the input parameter of wc_helix() from
>“m1 = wc_helix( sbase, "", "dna", abase, "", "dna", 2.25, -4.96, 0.0, 0.0, "" );”
>“m1 = wc_helix( sbase, "", "dna", abase, "", "dna", -6.0, 20.0, 0.0, 0.0, "" );”
> And I failed in getting a right A-type geometry, which
> is predictable, as it is mentioned in the manual that
> wc_helix() is not a generic method for constructing
> different types of helixes.

This seems like the approach I would use. Try experimenting with the
wc_helix parameters to get a feeling for how things change. It's not clear
what you obtained, other than not the "right A-type geometry".

[Aside: how much superhelical twist are you trying to impose? Do you think
(guess) that the structure would not quick relax back to a B-form geometry,
as would happen for linear duplexes.]


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Received on Thu Sep 01 2022 - 13:00:30 PDT
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