I've been trying replicate the protein design methods from this paper, which uses RosettaScripts. I have been able to replicate most of the data, but I have been struggling to make the last design part t owork. The design_monomer_interface.xml file is used to design the residues of the generated three helical bundle protein (that has desired backbone structure, but not the desired residues) so that the bundles could bind to the target. I wanted to test the design_monomer_interface.xml protocol on a pdb generated through the paper methods, which includes the target protein and the three helix bundle protein. The original paper did not provide any input flags, so we attempted to use some input flags previously used in the paper for a different section, but we still keep running into errors. I uploaded the crash log, and the relevant files are in the Google Drive link below. Can someone please help me navigate through this?
This is the link to the original files used by the paper (also at the bottom of the paper): http://files.ipd.uw.edu/pub/SARS-CoV-2_binder_2020/scripts_models.zip