Begin working on AMBER engine
Updating AMBER setup
Merged over changes from master
Improved onefile()
Merge branch 'master' into amber

Conflicts:
	src/openmmio.py
Merge branch 'master' into amber
AMBER engine is able to prepare a simulation
Made PDB.py more standalone
Implemented evaluate_ method in amberio.py
Clean up printout
Fixed some issues with AMBER engine
AMBER energies and forces now work. Replaced qm_forces with qm_grads in molecule.py .
Merge branch 'master' of github.com:leeping/forcebalance into amber
Fixed issue with toppbc
Allow selection of force fitting atoms by comma and dash list
Merge branch 'master' into amber
Improve file management with AMBER
Merge pull request #66 from leeping/amber

AMBER engine