# HADDOCK3 workflow definition
**URL:** https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628
**Category:** HADDOCK
**Created:** [April 24, 2025, 5:59am UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628 "2025-04-24T05:59:37Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@holly](https://ask.bioexcel.eu/u/holly)
#### Post date: [April 24, 2025, 5:59am UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/1 "2025-04-24T05:59:37Z")
For antibody antigen modeling using the native version of HADDOCK3, I refer to the Antibody Antigen Modeling Using the Native Version of HADDOCK3 tutorial ([Antibody-antigen modelling tutorial using a local version of HADDOCK3 – Bonvin Lab](https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-antibody-antigen/)). Creating a HADDOCK3 profile for defining the docking workflow, no reference is given, how do I set up the caprieval step(s)?
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### Author:  [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)
#### Post date: [April 24, 2025, 6:22am UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/2 "2025-04-24T06:22:18Z")
Hi holly,
The `[caprieval]` module is mostly used for benchmarking purposes (if you have a reference file), or will use as reference the best scoring models.
Tt also allows to generate the final plots during the post-processing steps (in the `analysis` directory).
If you do not provide any reference file, just run `[caprieval]` using default parameters.
Cheers
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### Author:  [@holly](https://ask.bioexcel.eu/u/holly)
#### Post date: [May 6, 2025, 1:06pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/3 "2025-05-06T13:06:08Z")
Is it sufficient to leave the next line under [caprieval] empty and unprocessed as shown in the picture?
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### Author:  [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)
#### Post date: [May 6, 2025, 1:21pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/4 "2025-05-06T13:21:03Z")
Yes, if you do not have a reference structure.
In that case, the lowest energy structure will be used as reference for the plots
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### Author:  [@holly](https://ask.bioexcel.eu/u/holly)
#### Post date: [May 6, 2025, 2:18pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/5 "2025-05-06T14:18:46Z")
Thank you very much for your explanation, it has helped me a lot
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### Author:  [@jay\_14](https://ask.bioexcel.eu/u/jay_14)
#### Post date: [September 19, 2025, 1:01pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/6 "2025-09-19T13:01:13Z")
Hii! I have a doubt! I have done the same but the output files show no scores for i-RMSD, Fnat and DOCKQ and I have got the entries as ‘nan’. Can you please help me with this?
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [September 19, 2025, 1:18pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/7 "2025-09-19T13:18:42Z")
What kind of system are you docking?
Looking at the lrmsd is looks like your molecules are not docked, i.e. no interface can be defined for the analysis.
Visualize a few PDBs to confirm
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### Author:  [@jay\_14](https://ask.bioexcel.eu/u/jay_14)
#### Post date: [September 19, 2025, 2:00pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/8 "2025-09-19T14:00:49Z")
I am doing antibody antigen modelling. I did get some errors stating ‘capri WARNING] No reference contacts found’ and ‘[libparallel WARNING] Exception in task execution: list index out of range’. But I still got the scores. And when I visualised the pdb, the results were not a complex, but the Ag and Ab were present as separate chains. I did not get any other warnings too. So I am a bit unsure as where is the mistake!
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [September 19, 2025, 2:12pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/9 "2025-09-19T14:12:55Z")
Probably an issue in your restraints definition.
Did you follow first our haddock3 antibody-antigen tutorial?
[https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-antibody-antigen/](https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-antibody-antigen/)
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### Author:  [@jay\_14](https://ask.bioexcel.eu/u/jay_14)
#### Post date: [September 19, 2025, 5:39pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/10 "2025-09-19T17:39:44Z")
Yeah I did! Thank you! I will try troubleshooting the errors
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### Author:  [@holly](https://ask.bioexcel.eu/u/holly)
#### Post date: [September 22, 2025, 7:39am UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/11 "2025-09-22T07:39:34Z")
I am very happy to see that you have solved the issue of not having antigen-antibody complexes after this docking, but instead having them appear separately. I encountered a similar situation when I first started using it.
jay\_14 via BioExcel \<[notifications@bioexcel.discoursemail.com](mailto:notifications@bioexcel.discoursemail.com)\> 于2025年9月20日周六 01:49写道：
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### Author:  [@jay\_14](https://ask.bioexcel.eu/u/jay_14)
#### Post date: [September 27, 2025, 7:42pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/12 "2025-09-27T19:42:50Z")
Thank you for helping me out! It was actually an issue with the restraints definition!
I have another doubt! Where will I be able to find the Z scores after docking? I am running Haddock locally, so once I get the result files, I am not able to find the Z scores. Can you please help me with that?
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [September 27, 2025, 8:00pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/13 "2025-09-27T20:00:08Z")
Forget about the z-score. Use simply the HADDOCK score.
The caprieval modules together with the final analysis in haddock3 will generate html reports files
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### Author:  [@jay\_14](https://ask.bioexcel.eu/u/jay_14)
#### Post date: [September 28, 2025, 6:50am UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/14 "2025-09-28T06:50:19Z")
I have got 4 models in each cluster, so basically I have to consider the model that has the least negative HADDOCK score right? Or is there any other parameter that I should consider additionally?
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [September 28, 2025, 12:31pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/15 "2025-09-28T12:31:49Z")
The most negative score is the best - but clusters might overlap in score when you consider the standard deviation of the scores.
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### Author:  [@jay\_14](https://ask.bioexcel.eu/u/jay_14)
#### Post date: [October 3, 2025, 2:12pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/16 "2025-10-03T14:12:47Z")
Noted!
I have a doubt! If the epitope information is not available in my case, then how can I define the active and passive residues in the local HADDOCK version for the antigen?
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [October 4, 2025, 7:25am UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/17 "2025-10-04T07:25:05Z")
You can use the haddock-restraints tool to define automatically all solvent exposed residues.
Check:
[https://www.bonvinlab.org/haddock-restraints/configuration\_file.html](https://www.bonvinlab.org/haddock-restraints/configuration_file.html)
There is an option for selecting the solvent accessible residues (surface\_as\_passive)
Those should be defined as passive.
Also do increase the sampling in this case, e.g. 10000 for rigidbody and 400 for further refinement.
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### Author:  [@jay\_14](https://ask.bioexcel.eu/u/jay_14)
#### Post date: [October 5, 2025, 12:51pm UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/18 "2025-10-05T12:51:30Z")
For docking, I have given sampling size as 200 and 50 for further refinement mainly because of my computational requirement. Is it possible to reduce the sampling size than the number you mentioned for me to go with surface\_as\_passive option?
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [October 6, 2025, 7:20am UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/19 "2025-10-06T07:20:52Z")
> For docking, I have given sampling size as 200 and 50 for further refinement mainly because of my computational requirement. Is it possible to reduce the sampling size than the number you mentioned for me to go with surface\_as\_passive option?
Well don’t expect fantasist results with limited sampling…
If you are limited in computational resources, you could try using instead of HADDOCK2.4 web server.
[http://wenmr.science.uu.nl/haddock2.4](http://wenmr.science.uu.nl/haddock2.4)
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### Author:  [@holly](https://ask.bioexcel.eu/u/holly)
#### Post date: [August 29, 2026, 12:57am UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628/20 "2026-08-29T00:57:52Z")
I noticed that the official HADDOCK3 antibody-antigen tutorial performs docking using the antibody Fv region. I now have a requirement to perform docking using the full‑length antibody. Is it possible to adapt the approach from this tutorial ([Antibody-antigen modelling tutorial using a local version of HADDOCK3 – Bonvin Lab](https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-antibody-antigen/))? Is this an allowed operation in this tool?
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