You have tried many things, and still it seems that you are not getting a parallel MPI executable.
Can you compile and run a small MPI test program? This is a basic step to master when installing CHARMM on a new platform - the same compiler and runtime options should then be used for installing and running CHARMM. Is your mpif90 set up for use with the same compiler as you have been trying to use for the CHARMM installation?
It would be easier to help if you could post the following from a clean installation:
1/ The command line used for the installation (install.com ....)
2/ The Makefile that was used (ie, the one that was produced from Makefile_gnu)
3/ The last part of the logfile, showing the linking step
You could also try to use the selfcontained socket library instead of MPI, just to get going with a parallel CHARMM version:
install.com gnu large S EFC