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Gamess+Tinker http://cfm.ehu.es/ricardo/master/intranet_ESCMAN/WinGAMESS/manuals/simomm.pdf (advantages: free, disadvantages: might not run well 
)
Gaussian+Gromacs http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM (advantages: will work well, Scuzeria Scuseria will likely help; disadvantages: will likely be limited to Rice U comp. resources.)
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