I think that your ligands are named the same in the params and protein file. The default residue name is LG1. Open your params file and rename the name and the IO_STRING line to a different name than LG1. Also, you need to edit your pdb file so that it corresponds to the changed name in your params file. Alternatively, you can run molfile_to_params.py with the flag -n letter name> to create the params file and pdb file with different names.
I have attached a documentation file on the parameters file for your reference. This file was created for the purpose of the Rosetta Workshop. This article along with full tutorials on several applications will be made public next week on the Meiler Lab website.