Error associated with metal ion

I am trying to carry out protein-ligand docking in HADDOCK 2.4. The preparation of the PDB file of the receptor (protein) was satisfactory, however, problems have arisen with the ligand. The source of the ligand structure is a CIF file that I transformed to PDB using Pymol to obtain a single chain. So when I submit the ligand’s structure, it returns an error associated with a metal ion, specifically iron (II), belonging to its structure. I have already reviewed the library and the supported ions, in conclusion, I have made multiple changes in the writing of the file based on the examples and tutorials and it keeps returning the same error.
I would appreciate some advice on this. Maybe my problem is in the conversion from CIF to PDB, or directly in writing the PDB.

Hi Peter

Ions in a ligand are not supported unfortunately - has to do with the ligand topo/param generation.

Only ions associated with a protein/nuclei acids are supported.

Thank you very much for the quick answer. The software has offered me very good results in protein-protein interactions, it is a shame not to be able to use it in this context. If you have any suggestions for this type of procedure I would appreciate it.

You could try to parametrize your ligand with e.g. acpype and then run HADDOCK locally.

Check for example:


The git repo contains an example of parametrisation for CNS (used by HADDOCK)