The system command should return control to the CHARMM script when it completes. If you want to pass some data back to CHARMM, the python script should write a stream file, which can then be read by a subsequent CHARMM command.

In principle, you can use Fortran to call system() under Linux, but you'd still have an issue with using any data produced, as Fortran cannot read python data objects directly.
Rick Venable
computational chemist