This is appears to be more of a basic usage issue, and not a parameter issue. Many of the errors arise from initial attempt to read coordinates from a PDB file, which is NOT a native CHARMM format; it can be used for import, but often requires extra steps, esp. if there are any residues missing coordinates. Another issue is the use of BOMLEV -19, which is extreme, and ill-considered.

Suggested reading from the Script Archive: complex PDB input examples

Rick Venable
computational chemist