Mutant Complex Not Launching in HADDOCK (Wild Type Works Fine)

1

Hello everyone,

I am currently performing docking using HADDOCK for a nucleosome–SIRT6 complex with two additional protein partners.

The wild-type complex runs successfully without any issues. However, when I use the mutant version of the same complex, the job does not proceed to launch. The structure uploads without showing any error, but after submission, the docking does not start or move forward.

Here is what I have already checked:

  • Removed water molecules, ions, and heteroatoms

  • Ensured proper chain IDs

  • Verified residue naming format

  • Checked for missing atoms

  • Removed hydrogens before submission

  • Saved as clean PDB file

The mutation was introduced into the third, and the structure appears normal when visualized in Chimera/PyMOL.

Has anyone experienced a similar issue with mutant structures in HADDOCK?
Could this be related to PDB formatting, residue numbering, file size, or structural clashes?

I would greatly appreciate any suggestions or troubleshooting advice.

Thank you in advance.

2

Try simply editing your wild type PDB file and changing the residue name of the residue you want to mutate. HADDOCK will handle the mutation