9 NMR Refinement
9.1 NMR Refinement of DNA
and RNA Duplexes
This
tutorial provides a basic introduction to using AMBER for NMR refinement of a
DNA duplex. It makes use of LEaP and Sander.
[Related information: Mike Summers has prepared a
set of scripts for RNA
refinement. It contains descriptions, examples, and scripts that were
used to generate initial structures with cyana and refined with Amber. Nearly
all steps (file conversions, etc.) are written into scripts so that the
process can be followed. Some scripts may need tweaking, depending on your
operating system. The work is described in: J. Biomol. NMR 47,
205-219 (2010).] By Vickie Tsui and Rhonda Torres
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