Hello everyone,
I may have found a potential bug in the refinement step. I am using HADDOCK 2.4 to refine (protein–ligand)-protein interactions. Before starting the refinement, I download the .json file in order to add restraints. Occasionally (around 20% of cases in a small sample), my first protein (protein–ligand) is defined in the .json file as “Ligand” or “Nucleic,” even though it was correctly identified as a protein–ligand on the website beforehand.
Of course, I can manually check and correct this in the .json file, but it is a bit confusing when the file is flagged as invalid upon upload.