2.4 Input Files

HBPLUS.EXE requires a "clean" brookhaven (PDB) file, where all the atoms are
accurately named and ordered, and no atoms have alternate locations.
I expect that most "uncleaned" brookhaven files will work with HBPLUS, but
if you want to be certain of your results, run a program to clean up the
PDB file.

HBPLUS will also attempt to find the an original "unclean" PDB file which
contains the CONECT records, but will run the program anyway if that
fails.  If two files are named in the command line, then the second file is
taken as being the old PDB file.  If no such file is named, HBPLUS looks
for a file with the name "p" + brookhaven code + ".pdb" in the current
directory.

If two files are named in the command line, then the first file is a
"cleaned" file