Merge pull request #66 from leeping/amber

AMBER engine
Added runamber.sh
Merge branch 'master' of github.com:leeping/forcebalance into amber
TINKER fixes
Merge branch 'master' of github.com:leeping/forcebalance
Added amber_nbcut option
Merge branch 'master' of github.com:leeping/forcebalance into amber