In collaboration with the NIH Research Resource for Multiscale Modeling Tools in Structural Biology we continue to develop the MMTSB Tool Set. The current version (1.5) can be downloaded here.

MMTSB NIH resource @University of Michigan
MMTSB Tool Set
MMTSB Tool Set Documentation Wiki @MSU
MMTSB Forum

Protein Structure Prediction and Multi-Scale Modeling (PSC, 2003)
Theory and Computation in Molecular Biological Physics (UCSD, 2004)
Modeling Proteins and Nucleic Acids with Amber, VMD and the MMTSB Toolkit (PSC, 2005)
Molecular simulation and structure prediction using CHARMM and the MMTSB Tool Set (UCSD, 2006)