MSL
http://dx.doi.org/10.1002/jcc.22968
... modeling or design).
MSL is developed in the Senes Lab at the University of Wisconsin-Madison and by a team of developers/users from other research laboratories.
Reference:
Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A.
Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).
J Comput Chem. 2012 vol. 33 pages 1645-61
Download article at http://dx.doi.org/10.1002/jcc.22968