# Possible Bug in HADDOCK 2.4 Refinement (.json Restraint File)

**URL:** <https://ask.bioexcel.eu/t/possible-bug-in-haddock-2-4-refinement-json-restraint-file/5946>\
**Category:** HADDOCK\
**Created:** [November 10, 2025, 9:46am UTC](https://ask.bioexcel.eu/t/possible-bug-in-haddock-2-4-refinement-json-restraint-file/5946 "2025-11-10T09:46:11Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![JonesLeo](https://avatars.discourse-cdn.com/v4/letter/j/ee59a6/32.png) [@JonesLeo](https://ask.bioexcel.eu/u/JonesLeo)\
**Post date:** [November 10, 2025, 9:46am UTC](https://ask.bioexcel.eu/t/possible-bug-in-haddock-2-4-refinement-json-restraint-file/5946/1 "2025-11-10T09:46:11Z")

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Hello everyone,

I may have found a potential bug in the refinement step. I am using HADDOCK 2.4 to refine (protein–ligand)-protein interactions. Before starting the refinement, I download the `.json` file in order to add restraints. Occasionally (around 20% of cases in a small sample), my first protein (protein–ligand) is defined in the `.json` file as “Ligand” or “Nucleic,” even though it was correctly identified as a protein–ligand on the website beforehand.

Of course, I can manually check and correct this in the `.json` file, but it is a bit confusing when the file is flagged as invalid upon upload.

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [November 10, 2025, 9:47am UTC](https://ask.bioexcel.eu/t/possible-bug-in-haddock-2-4-refinement-json-restraint-file/5946/2 "2025-11-10T09:47:15Z")

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We would need an explicit example where this happens to investigate