From CHARMM tutorial
Installation of CHARMM
CHARMM runs on a variety of UNIX-like systems, although most installations currently are being done on Linux. With a little bit of work, the program can be installed on Windows machines via the CYGWIN emulation layer.
There are many options for installing CHARMM, many of which the beginning user need not touch. It is highly recommended that the user read install.doc and the installation board on the CHARMM forums before trying to install CHARMM.
CHARMM must be installed through a command line. The general format is:
./install.com <host machine type> [ <CHARMM_size> <install switches> ]
It is recommended that you type "./install.com" with no arguments to see all of the possible machine types, sizes, and install switches. It is usually a good idea to build CHARMM at the large or xlarge sizes, although very large systems may require the "huge" size. Be careful with huge, though, as several people have reported problems with it. If building a huge version you should run your binary on the test cases (found in the test subdirectory of the CHARMM source) and carefully compare the results with known good runs (sets of known-good results may be found on charmm.org). This is a good idea with any new binary you build! Note that very small numeric differences in test case output are to be expected, but otherwise results should agree. If compiling CHARMM to perform QM/MM calculations in conjunction with a different QM package, consult the output of "./install.com" to determine the correct flag to use (e.g. QC for Q-CHEM). Additional flags must also be given to compile parallel versions using MPI; again consulting "./install.com" is necessary.
Note: Compiling with the gcc/gfortran 4.0 as your compiler may result in installation problems. It is recommended that gcc 4.1.1 or later be used. Currently gcc version 4.2 or greater is recommended due to trajectory file compatibility issues with gcc 4.1. If gcc 4.1 must be used, a workaround is available (consult the Installation board mentioned above for details). CHARMM is being updated to Fortran 95, so versions c36 and later require gcc version 4.3 or later. Relatively recent versions of the Intel, Pathscale, and PGI compilers may also be used.