If you really wanted to, you could use molfile_to_params to make a parameter file for it, though if you’re doing “abinitio”, you probably don’t care about that residue.
I’m assuming you’re using the file with NO3 as the -in:file:native in your abinitio run. As the native in abinitio is only used for calculating Calpha rmsd, the presence/absence of ligands will have no effect on the results.
In addition to manually deleting those ligand lines, or using the clean_pdb.py script, you can also pass the commandline flag “-ignore_unrecognized_res” to the Rosetta program. This will cause Rosetta to ignore (delete) any residue it doesn’t recognize. (Be a little careful with it, in case there’s an unrecognized residue you somehow do want to keep.)
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