My understanding for adding the ligand is to use the molfile_to_params script to generate XXX.cen.params, XXX.fa.params, XXX.tors files.
My ligand is just a one atom Zn. When molfile_to_params script is used, I got this error
ValueError: Fragment 1 has 1 atoms; merge with another fragment or add virtual atoms to make 3 total
which seems to indicate the ligand must be 3 or more than 3 atoms, is that correct?
If so, how to add virtual atoms, or is there an alternative way to add Zn atom during RosettaCM?