The message indicates that CHARMM was not compiled with the G09 keyword. If you include the PREF keyword in CHARMM input, the program will list any special features such as G09.
Perhaps your compile attempt did not succeed; did you check the log files after the build?
The correct syntax is ./install.com gnu G09
Be sure to clean up first by doing the following:
- Rename (via mv) or delete (rm) exec/gnu/charmm
- rm -rf lib/gnu build/gnu
If you have a working executable you want to keep, you should rename it. The directory deletion gets rid of debris from previous attempts, which can create conflicts.