I used pdb_selaltloc to deal with multiple occupancy side-chain conformations in my pdb file.
Resulting output file gives me this error: The following error occurred when processing one of your PDB file: Unable to generate topology for ligand UNX. PRODRG did not create the required output: PRODRG> Found unsupported atom type U (atom ’ UNK’) in your coordinates.
You seem to have some ligands in your PDB file with a uranium atom??? Not supported.
Check if this is the case. And / or remove that ligand if not relevant.
Hi there, it seems that your input contains some HETATMs as well as solvent used during crystallography, are you using a structure directly from the PDB database?
In most cases you will need to remove atoms that are not essential to your analysis, please check How to prepare structures for HADDOCK?