During CHARMM33b1 compilation with gfortran 4.1.1 I could see some warning/error messages in gnu.log regarding mismatch of ##IF and ##ENDIF directives.
1. source/energy/afm.src: The ##ENDIF directive at the end of the file should have "(afm_outter)" instead of "(afm_outer)".
2. source/misc/scpism.src: The subroutine SCPPARSE was missing the closing ##ENDIF (scpism_main) directive.