With the proper mpif90 in your path you should be able to install a parallel CHARMM executable using:
install.com gnu xxlarge M MPIF90 X86_64

The X86_64 flag is needed with c35 on most modern (64-bit) machines; if you are installing on a 32-bit system you should leave it out.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden