#60 chain capping doesn't work with terminal PRO

[Raik Gruenberg]

In PDBCleaner and AmberParmBuilder, capping of N-terminal Proline residues doesn't work. The ACE is placed for a trans peptide bond which doesn't work for Pro. The problem is that the code runs through without error. If used as an input for tleap, leap will not recognize the connection and place an additional hydrogen at the end of the Pro.