NOTE: The ability to run the CHARMM force field inside the Amber program
is not yet functional or supported.  The notes below are for "experts",
who are willing to recompile the code and track down problems!

You should be able to convert CHARMM 22 (and later) all-atom potential files 
(at least for proteins and nucleic acids) to Amber format using the 
following steps:

(1) Edit the *.in files provided here to see that the charges and atom
    types in them match those in the Charmm topology files you are using.
    (Note that atom types are translated from CHARMM to AMBER using the
    name_trans.dna or name_trans.pro files).

(2) run "make" to create an amber-style database (db4.c22.dat) that
    has the CHARMM parameters and atom types.

(3) run c22par_to_amber to create an Amber style parameter file that has
    the CHARMM 22 parameters.  This is a perl script: see the instructions
    at the top for how to run it.

(4) Compile PARM and SANDER with -DCHARMM set in the MACHINE file.

(5) now link-edit-parm-sander using the above database and parameter files
	should give the CHARMM forcefield.  Tell PARM that the nonbonded type is
    "CHAR". Run test cases vs. the real CHARMM program to verify.  Note that
    there could be some (small) diffs if you have large violations of the
    planarity constraints.

Comments/questions to dave case: <case@scripps.edu>  

NOTE #1: this is somewhat old stuff, and I haven't tried this is several
years.  I think it will work, but it certainly is not foolproof.  The
"c22par_to_amber" script relies on pattern matching (rather than parsing) to
read the CHARMM files, so might get fooled if something is different from
the files I used when creating the script.

NOTE #2: The par_all22_*.inp and top_all22_*.inp files here were downloaded
from http://www.pharmacy.umab.edu/~alex/research.html on May 4, 1999.

NOTE #3: look in ../amberff_in_charmm if you want to do the reverse: i.e.,
run the CHARMM program using the Cornell et al. Amber force field.
