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Structure Refinement in Amber

TUTORIAL A4: NMR Refinement of DNA and RNA Duplexes

DNA in xleap 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

"How's that for maxed out?"

Last modified: Oct 4, 2018