Update CCTools version to 4.1.3
Small fix in install-cctools-41
Merge branch 'master' of github.com:leeping/forcebalance
Clean up printout
Made PDB.py more standalone

Conflicts:

	src/amberio.py
Merge branch 'master' of github.com:leeping/forcebalance
Bonds were sometimes incorrectly determined using PBC
Merge branch 'master' of github.com:leeping/forcebalance
Fix parsing of total molecular polarizability
Protocol for pickle was too high
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