AMBER Archive (2002)

Subject: NMR refinement

From: Jake Isaacs (rjisaa0_at_uky.edu)
Date: Tue May 14 2002 - 14:16:37 CDT

I'd like to get a feel for what you folks think to be the "best" protocol
for structural refinement using NMR-based restraints, specifically for DNA
systems. How do in vacuo, implicit solvent, and explicit solvent methods
compare? How about conventional vs. time-averaged restraints? Restraints
based directly on NOE volumes vs. calculated upper/lower bounds (as with
MARDIGRAS)? How are your simulated annealing runs structured? How are
residual dipolar coupling restraints implemented for DNA?

I would appreciate any input you could provide. Citations would be very
helpful, as well. Thank you for your assistance.

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