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
Fixed issue with toppbc

Conflicts:

	src/molecule.py
Merge branch 'master' of github.com:leeping/forcebalance

Conflicts:
	src/molecule.py
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