It ain’t easy.  You would need to modify Chimera’s Python code.  First you would need to squirrel the “frcmod" file computed by parmchk away so it could be used later.  You can find the file by looking at the Reply Log and in the parmchk command it’s the file after the “-o” parmchk option.  Probably some horrible path to a file in a temporary folder (for example on my Mac it was "/var/folders/mz/q5nthjsn13gcb04mw0xnxkcc0000gn/T/tmpLLQnFV/frcmod.0-1”).  Then you would need to change line 471 of <your chimera>/share/MMMD/MMTKinter.py from:

rtype2frcmod = {}

to:

rtype2frcmod = { ‘your-res-name’: ‘full-path-to-squirreled-frcmod’ }

(e.g. rtype2frcmod = { ‘GLC’: ‘/Users/pett/frcmods/GLC.frcmod’ })

On a Mac, “<your chimera>” is Chimera.app/Contents/Resources.

—Eric