[phenixbb] Ligand addition in COOT for later refinement in Phenix.refine

Greetings I am trying to place a ligand (CIT) in a protein model that already have some citrate ligands placed. I am doing this using Coot's option "get monomer", and after the fitting of ligand in the density I tried to refine the model using the ligand and the protein pdb as input models. Refinement did not start and I got an error message in Phenix- "Number of groups of duplicate atom labels:....." Could someone please explain how could I get past this error message and what is the correct way to add a ligand to a model that already has some of the ligands of the same type. Many thanks in advance Regards Manoj Saxena