This project consists of a collection of Python modules to aid in the preparation of molecular mechanics systems for popular molecular simulation packages, such as gromacs and AMBER. It draws on tools such as MCCE (Gunnar lab) for prediction of protonation states, UCSF Modeller (Sali lab) for building in missing loops and residues, ACPYPI for conversion of topology file formats, and Amber's AmberTools for setup of proteins and small molecules.

THIS PROJECT HAS BEEN MIGRATED TO GITHUB:
http://github.com/choderalab/mmtools