I am not familiar with CHARMm, but I've worked with JUMNA and X-PLOR and
had some problems with PDB files. I had generated a PDB file with JUMNA
and wanted to make a molecular dynamics simulation with X-PLOR, but
X-PLOR coouldn't read my JUMNA PDB becaude nucleotide libraries are
different between JUMNA and X-PLOR.
If you can, get an example of a CHARMm PDB file and make sure yours can
be red. If not you'll have to modify it....
Raphael