> 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?
They are both old and canonical and there is citable literature. In
reality, with modern force fields for DNA (and WC basepaired structures
either from crystal, NMR, or canonical) the DNA will relax fairly quickly
to what the force field "wants" noting that complete convergence of a DNA
duplex takes on the order or 2-5 microseconds, however you can get
approximations "quicker" than that. There is a livecoms article that just
came out, however, that discusses convergence and how shorter simulations
can be misleading depending on what you want to look at.
https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-simulation-of-double-stranded-dna-solvation-and-salt-concerns-article-v1-0
--tec3
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Received on Wed Sep 04 2019 - 13:00:02 PDT
