I am trying to use enzyme design application to predict favorable mutations for my research. I am only specifying a refile and no constraint file. The input pdb is what was predicted from the ligand dock application. I am working with a heme protein, so the input pdb has multiple ligands (heme and substrate). The ligand dock application worked great after keeping the substrate as the last entry in the pdb. However, the enzyme design application is giving error saying that it does not support multiple ligands. Since the documentation for enzyme design states that it is based on the ligand dock functionality, I am wondering if I am doing something wrong.
Also, if it is indeed impossible to use the enzyme design application with multiple ligands, what other options do I have? Would rosetta scripts be useful for this?
Thanks in advance!