We're trying to incorporate a nonanonical amino acid (3, 5-Difluorotyrosine) in my enzyme design protocol. We've been using the molfile_to_params_polymer.py script provided in the demos folder; however, the params file isn't generating correctly (the file is attached below as DFT.params). When running enzyme design protocol, we get the following error:
"Only the third ICOOR atom in a topology file should list itself as its own dihedral atom"
We suspect that it is because the CB (on the 4th line of the params file) is referencing itself during creation; however, we don't know how to change the file so that this does not happen. We ran the example files provided in the /main/demos/protocol_capture/using_ncaas_protein_peptide_interface_design/HowToMakeResidueTypeParamFiles/ path, and the script seemed to run correctly and generated the params file expected in the output. Does anyone know what is causing our particular structure to generate incorreclty, and how does one resolve this issue? (The molfile is also attached, in case that is where the issue is arising)