MolProbity could not guess the protonation state of histidine

Hi! I’m using HADDOCK web server to dock a dismutase with a list of peptides. In the first try, I had removed all the metal ions from the protein (1 Cu+2 & 1 Zn+2 in every chain of the dimer) and everything worked fine. Now I’m trying to add these ions and redo the docking and I’m facing this error
"The following error occurred when processing one of your PDB file: There was an error while calling Reduce. MolProbity could not guess the protonation state of histidine 218 in the PDB file " during the input submission and also a similar error when using MolProbity locally from haddock-tools.
I figured out that the problem occurs only when the Zn atom of one specific chain is present, so I guess it interacts somehow with that histidine… Is there something I could do to fix the above problem?
Thank you in advance!

That’s a tricky one.

You could try to run reduce locally (not using our scripts) on your computer to see if there is a more specific error message.
E.g. is reduce failing to generate the PDB? If it works, then it could be there is an issue on our side on the parsing of the generated PDB file with all hydrogens added.

And is the culprit histidine any close to the binding site (if you know it). If remote from it simply remove the zinc…

Thank you for the suggestions!
I ran reduce locally and it generates the PDB with no errors but I noticed that if I maintain the default distance for the option -METALBump (H ‘bumps’ metals at radius plus this (default=0.865)), it skips some H -including one of the problematic HIS. I tried to reduce the default distance, just for checking the output, and all the above generated PDB files raise the same error in HADDOCK web-server.
I am thinking about just removing this ion, but it has a structural role in the protein so I thought it would be better to include it.
I have attached the terminal output of reduce, in case it adds any useful information I missed.

reduce_output.txt (13.7 KB)

If not at the interface, you can safely remove it and add it again later.