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Gaussian+Gromacs http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM (advantages: will work well, Scuseria will likely help; disadvantages: will likely be limited to Rice U comp. resources.)
Mechanistic Insight into Catalytic Activity of BBA-Metallonucleases (This model system, Vibrio vulnificus, is thought to have the same cleavage mechanism as the HNH domain)
RNA coarse grain models:
http://pubs.acs.org/doi/abs/10.1021/jp104926t
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