If it does not recognize your CA yet, try playing with the spacing. There are two letters in a four-column field, so there are 3 ways to space it. I’ve replaced spaces with dashes to illustrate:
I don’t know which one is correct.
I don’t know anything more about molfile_to_params than is in its help (molfile_to_params.py -h). It’s in src/python/apps/public.
I’ve emailed the guy who knows about making rotamer libraries to see if it’s possible in 3.2.