AMBER Archive (2007)

Subject: AMBER: Best way to apply WC basepair restraints during MD

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Sun Feb 25 2007 - 14:24:40 CST

Dear Amber Community,

I would like to run an MD simulation on a NA molecule and hold the bases paired
and fixed with one another while allow the backbone to move. What would be the
best way to apply this? Would I follow a similar procedure as the NMR
refinement tutorial?

Thanks,
Seth
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