HADDOCK job clustering error during run

HADDOCK
1

I’ve tried:

Reviewing the output logs for clues Checking the docking parameters to ensure they’re set correctly Searching the HADDOCK docs and discussion group for similar “clustering error” cases

But I’m stuck! Could anyone help with:

Possible reasons for clustering failures in HADDOCK (e.g., input data issues, parameter conflicts)?Steps to troubleshoot or fix this (e.g., adjusting clustering settings, verifying inputs)?Any similar experiences or documentation I might have missed?

HADDOCK - Run bos_NDUFB11_szbz3_ND5_1 HADDOCK - Run bos_NDUFB11_szbz3_ND5_2

Thanks so much for your time—any advice would be really appreciated!

2

You should download the full archive of the run and look at some models from the structures/it1/water directory.
Their ranking is provided in the file.list file in that folder.

They are simply all over the place and do not cluster.

Also it looks like you are using input structures with a lot of disordered regions… This will only cause problems.
If using AlphaFold model, best to remove all the poorly predicted parts.

3

Thank you very much for your insights and suggestions, which have helped me better understand the problem.