I'm coaching an iGEM team at the University of Warwick and they're doing some dock design to try to switch the specificity of a transcription factor to a different ligand. We've been able to run the docking protocol with the protein and it's native ligand and it is able to recapitualte the the native binding. However, when we try the docking protocol with the new ligand we run into this error:
[ ERROR ] UtilityExitException
ERROR: The last residue, residue188 named "ACE" has been indicated to merge with the next residue from the core::io::NomenclatureManager
Looking at the PDB files and the params files there are no obvious differences between the two aside from the different ligand and it's coordinates. I was wondering if you could offer any advice.