AMBER Archive (2007)

Subject: AMBER: applying restraints

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Thu Feb 22 2007 - 10:40:59 CST

Dear Amber Users,

I am attempting to apply different NMR restraints and am following the method
outlined in the "NMR refinement of a DNA Duplex" tutorial. For example, one of
the structures I am interested in is a regular DNA duplex but with an increased
distance between the bases, moving the strands farther apart. I applied WC
restraints with increased distances only and structure after annealing was very
folded and unordered. What other restraints should I apply to ensure the other
parameters remain the same (basepairing, etc.)? What would be the best way to
go about doing this?

Thanks,
Seth
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