Hi I am trying to convert a mol2 file to params file using mol2genparams.py script. The mol2params conversion appears to work (please see attached log file) but when I run rosetta_scripts to perform GAliganddocking, it throws up an error "dont add residue bonds more than once". I have looked at the params file but can't see any obvious duplications. I am following the protocol outlined for generating mol2 file for GAliganddocking at this location. https://www.rosettacommons.org/docs/latest/GALigandDock-Preprocessing
The .params file is uploaded as a txt file. I would deeply appreciate any help. I have been at it for a long time now and just can't seem to find a work around. I have tried to generate mol2 file from different sources, also tried starting from SMILES, pdb and mol but ended up with the same result.