prepmd is also accessible via a Python API:
from prepmd.add_modeller_license import setup_license
setup_license("<your license key>") # only needs to be done once
from prepmd.prep import prep
prep("6xov", "6xov.cif", "working_dir")
from prepmd.run import run
run("6xov.cif", traj_out="traj.xtc")