# HDOCK refinement **URL:** https://ask.bioexcel.eu/t/hdock-refinement/6069 **Category:** HADDOCK **Tags:** haddock, support **Created:** [April 10, 2026, 9:51am UTC](https://ask.bioexcel.eu/t/hdock-refinement/6069 "2026-04-10T09:51:56Z") **Posts on this page:** 4 **Page:** 1
### Author: ![F-Mars](https://avatars.discourse-cdn.com/v4/letter/f/f1d935/32.png) [@F-Mars](https://ask.bioexcel.eu/u/F-Mars) #### Post date: [April 10, 2026, 9:51am UTC](https://ask.bioexcel.eu/t/hdock-refinement/6069/1 "2026-04-10T09:51:56Z")
Could HADDOCK be used to refine a docking complex made by HDOCK? And if so, which refinement method would work best? ---
### Author: ![AKravchenko](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/akravchenko/32/1168_2.png) [@AKravchenko](https://ask.bioexcel.eu/u/AKravchenko) #### Post date: [April 10, 2026, 10:37am UTC](https://ask.bioexcel.eu/t/hdock-refinement/6069/2 "2026-04-10T10:37:49Z")
I am not familiar with HDOCK output, but in principle, if it’s a regular PDB file, then HADDOCK3 should be able to refine it. You can check input file requirements here: [Haddock3 requirements - HADDOCK3 User Manual](https://www.bonvinlab.org/haddock3-user-manual/structure_requirements.html) And the choice of the module depends on the level of refinement you would like to apply: [Refinement - HADDOCK3 User Manual](https://www.bonvinlab.org/haddock3-user-manual/modules/refinement.html) Typical choice would be _flexref_ for the semi-flexible interface refinement. If you’re looking for a quick refinement to eliminate small clashes, then _emref_ is better. ---
### 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: [April 10, 2026, 11:19am UTC](https://ask.bioexcel.eu/t/hdock-refinement/6069/3 "2026-04-10T11:19:16Z")
For only refinement purposes, I would recommend `emref` or `mdref` if you want a bit more flexibility. The HADDOCK2.4 server also offers a refinement mode with different options. Which one works better will depend on the quality of your initial conformation. Check the following paper about refining complexes: - T Neijenhuis, S.C. van Keulen and A.M.J.J. Bonvin. [Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4](https://doi.org/10.1016/j.str.2022.02.001). _Structure_ _30_, 476-484 (2022). ---
### Author: ![F-Mars](https://avatars.discourse-cdn.com/v4/letter/f/f1d935/32.png) [@F-Mars](https://ask.bioexcel.eu/u/F-Mars) #### Post date: [April 13, 2026, 7:32am UTC](https://ask.bioexcel.eu/t/hdock-refinement/6069/4 "2026-04-13T07:32:44Z")
Thanks, will do