# HADDOCK **URL:** https://ask.bioexcel.eu/c/haddock/6.md?page=3 [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) **Page:** 4 --- ## [Bidentate ligand docking](https://ask.bioexcel.eu/t/bidentate-ligand-docking/5927)
**Author:** [@GGTheophall](https://ask.bioexcel.eu/u/GGTheophall)\ **Replies:** 2\ **Last updated:** [November 14, 2025, 4:12pm UTC](https://ask.bioexcel.eu/t/bidentate-ligand-docking/5927 "2025-11-14T16:12:30Z")
Good afternoon, TLDR; How do I dock a bidentate ligand in which one site is known with atomic resolution and the other is only characterized by AIRs and UIRs. Full; I am trying to dock a bidentate protein ligand to an… --- ## [Interpreting a large, highly converged cluster in AIR-guided docking](https://ask.bioexcel.eu/t/interpreting-a-large-highly-converged-cluster-in-air-guided-docking/5949)
**Author:** [@henryhardigan](https://ask.bioexcel.eu/u/henryhardigan)\ **Replies:** 1\ **Last updated:** [November 13, 2025, 4:12pm UTC](https://ask.bioexcel.eu/t/interpreting-a-large-highly-converged-cluster-in-air-guided-docking/5949 "2025-11-13T16:12:51Z")
I am docking two protein fragments that I suspect interact via short linear motifs. I used default docking parameters and two models taken from reviewed UniProtKB entries. For this run I defined AIRs on a 12-residue stre… --- ## [Error during protein/DNA docking with mutated nucleotide](https://ask.bioexcel.eu/t/error-during-protein-dna-docking-with-mutated-nucleotide/5944)
**Author:** [@LBCVini](https://ask.bioexcel.eu/u/LBCVini)\ **Replies:** 7\ **Last updated:** [November 13, 2025, 12:33pm UTC](https://ask.bioexcel.eu/t/error-during-protein-dna-docking-with-mutated-nucleotide/5944 "2025-11-13T12:33:07Z")
To the HADDOCK support team, I would like to express my compliments to your team for your work. I am attempting to dock a modified DNA strand containing a deoxyuracil in place of a standard thymine using HADDOCK 2.4. H… --- ## [Desolvation-energy](https://ask.bioexcel.eu/t/desolvation-energy/5941)
**Author:** [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Replies:** 4\ **Last updated:** [November 10, 2025, 10:01pm UTC](https://ask.bioexcel.eu/t/desolvation-energy/5941 "2025-11-10T22:01:54Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab Hi, I recently run a protein ligand docking in haddock 2.4 webserver. The result ga… --- ## [Question about vizualization of docking protein-DNA (2.4 tutorial / own data)](https://ask.bioexcel.eu/t/question-about-vizualization-of-docking-protein-dna-2-4-tutorial-own-data/5854)
**Author:** [@ldrahnik](https://ask.bioexcel.eu/u/ldrahnik)\ **Replies:** 4\ **Last updated:** [November 10, 2025, 11:41am UTC](https://ask.bioexcel.eu/t/question-about-vizualization-of-docking-protein-dna-2-4-tutorial-own-data/5854 "2025-11-10T11:41:14Z")
Hello, I am interested in generating the same image as is https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-protein-DNA-advanced/PyMol.jpg so I would like to generate the same image according to tutorial first, th… --- ## [Possible Bug in HADDOCK 2.4 Refinement (.json Restraint File)](https://ask.bioexcel.eu/t/possible-bug-in-haddock-2-4-refinement-json-restraint-file/5946)
**Author:** [@JonesLeo](https://ask.bioexcel.eu/u/JonesLeo)\ **Replies:** 1\ **Last updated:** [November 10, 2025, 9:47am UTC](https://ask.bioexcel.eu/t/possible-bug-in-haddock-2-4-refinement-json-restraint-file/5946 "2025-11-10T09:47:15Z")
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 … --- ## [HADDOCK2.4 Job Stuck in 'Queued' Status for Several Days - Seeking Assistance](https://ask.bioexcel.eu/t/haddock2-4-job-stuck-in-queued-status-for-several-days-seeking-assistance/5935)
**Author:** [@wengh](https://ask.bioexcel.eu/u/wengh)\ **Replies:** 6\ **Last updated:** [November 10, 2025, 9:46am UTC](https://ask.bioexcel.eu/t/haddock2-4-job-stuck-in-queued-status-for-several-days-seeking-assistance/5935 "2025-11-10T09:46:45Z")
Dear HADDOCK Support Team and Community, I am a Master’s student currently using the HADDOCK web server (specifically HADDOCK2.4) for my research on protein-glycan docking simulations. I have been successfully utilizin… --- ## [Help understanding HADDOCK's different refinement methods](https://ask.bioexcel.eu/t/help-understanding-haddocks-different-refinement-methods/5924)
**Author:** [@sgaray](https://ask.bioexcel.eu/u/sgaray)\ **Replies:** 2\ **Last updated:** [October 30, 2025, 10:09pm UTC](https://ask.bioexcel.eu/t/help-understanding-haddocks-different-refinement-methods/5924 "2025-10-30T22:09:25Z")
Hi all. I got this result from AlphaFold2 for a heterotrimer, and I want to check out different binding options using the ‘refinement’ method. I see the interface gives me four different choices: ‘water refinement (defau… --- ## [How do I choose the active residues?](https://ask.bioexcel.eu/t/how-do-i-choose-the-active-residues/5923)
**Author:** [@girish23](https://ask.bioexcel.eu/u/girish23)\ **Replies:** 1\ **Last updated:** [October 30, 2025, 10:46am UTC](https://ask.bioexcel.eu/t/how-do-i-choose-the-active-residues/5923 "2025-10-30T10:46:09Z")
Hello, I have two proteins (X and Y); X has 2 chains (A and B), and Y has 1 chain. I want to dock Y with the B chain of X. I don’t understand how to choose the active residues, as the protein structure is not published y… --- ## [The DNA structure error during Protein-DNA docking](https://ask.bioexcel.eu/t/the-dna-structure-error-during-protein-dna-docking/5918)
**Author:** [@Takashibobbob](https://ask.bioexcel.eu/u/Takashibobbob)\ **Replies:** 4\ **Last updated:** [October 28, 2025, 11:35am UTC](https://ask.bioexcel.eu/t/the-dna-structure-error-during-protein-dna-docking/5918 "2025-10-28T11:35:25Z")
Dear HADDOCK developers, I am following the Protein–DNA docking tutorial with HADDOCK3 (https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-protein-DNA-basic/) and obtained docking results consistent with the precompu… --- ## [Multi protein docking on the web server](https://ask.bioexcel.eu/t/multi-protein-docking-on-the-web-server/5921)
**Author:** [@girish23](https://ask.bioexcel.eu/u/girish23)\ **Replies:** 1\ **Last updated:** [October 27, 2025, 1:34pm UTC](https://ask.bioexcel.eu/t/multi-protein-docking-on-the-web-server/5921 "2025-10-27T13:34:11Z")
Hey, I am trying to dock 5 proteins (1 main + 4 small proteins) with each other to create a protein scaffold, but the parameter page keeps getting reloaded and not showing any error (I am using the web portal). Could you… --- ## [Charge of modified lysines after refinement run](https://ask.bioexcel.eu/t/charge-of-modified-lysines-after-refinement-run/5917)
**Author:** [@ef25](https://ask.bioexcel.eu/u/ef25)\ **Replies:** 1\ **Last updated:** [October 25, 2025, 6:51am UTC](https://ask.bioexcel.eu/t/charge-of-modified-lysines-after-refinement-run/5917 "2025-10-25T06:51:04Z")
Hello! I ran my WT protein in HADOOCK2.4 and wants to know the effect of modifying the lysines into different methylation status in the complex structure. So, after docking the WT, I changed the names of the LYS in my pd… --- ## [HADDOCK3 Webserver issue when launching Protein-Ligand docking run](https://ask.bioexcel.eu/t/haddock3-webserver-issue-when-launching-protein-ligand-docking-run/5919)
**Author:** [@RuiAlmeida999](https://ask.bioexcel.eu/u/RuiAlmeida999)\ **Replies:** 1\ **Last updated:** [October 25, 2025, 6:39am UTC](https://ask.bioexcel.eu/t/haddock3-webserver-issue-when-launching-protein-ligand-docking-run/5919 "2025-10-25T06:39:15Z")
Hi, community. I tried to launch a few protein-small ligand runs in the HADDOCK3 Server, but they never launched. No error message appeared on screen, either. Using Chrome’s Developer Tools, I found a few errors in the… --- ## [HADDOCK 2.4 server not progressing (0.0% for all stages)](https://ask.bioexcel.eu/t/haddock-2-4-server-not-progressing-0-0-for-all-stages/5913)
**Author:** [@amandacgn](https://ask.bioexcel.eu/u/amandacgn)\ **Replies:** 2\ **Last updated:** [October 9, 2025, 1:54pm UTC](https://ask.bioexcel.eu/t/haddock-2-4-server-not-progressing-0-0-for-all-stages/5913 "2025-10-09T13:54:26Z")
I would like to ask if the HADDOCK 2.4 web server is currently functioning properly. I submitted a few RNA–ligand docking jobs several hours ago, but none of them have shown any progress — the status remains: it0: 0.0% … --- ## [Access to the full results of Haddock runs](https://ask.bioexcel.eu/t/access-to-the-full-results-of-haddock-runs/5912)
**Author:** [@lequestel-jy](https://ask.bioexcel.eu/u/lequestel-jy)\ **Replies:** 4\ **Last updated:** [October 2, 2025, 8:32am UTC](https://ask.bioexcel.eu/t/access-to-the-full-results-of-haddock-runs/5912 "2025-10-02T08:32:55Z")
Dear all, I use the Haddock server to run protein protein docking simulations and I really find it very useful. However, I would like to check some results locally. I have downloaded the results of the complete run as a… --- ## [Haddock 2.4 Vs 3](https://ask.bioexcel.eu/t/haddock-2-4-vs-3/5910)
**Author:** [@Sabrina](https://ask.bioexcel.eu/u/Sabrina)\ **Replies:** 3\ **Last updated:** [September 29, 2025, 7:51pm UTC](https://ask.bioexcel.eu/t/haddock-2-4-vs-3/5910 "2025-09-29T19:51:19Z")
What is the difference between Haddock 2.4 and 3? I have currently been using Haddock2.4 for protein-peptide docking but want to know if Haddock 3 is a more comprehensive software? Although Haddock scores can’t be correl… --- ## [Problem with restraints file in haddock2.4](https://ask.bioexcel.eu/t/problem-with-restraints-file-in-haddock2-4/5898)
**Author:** [@ef25](https://ask.bioexcel.eu/u/ef25)\ **Replies:** 1\ **Last updated:** [September 25, 2025, 9:15am UTC](https://ask.bioexcel.eu/t/problem-with-restraints-file-in-haddock2-4/5898 "2025-09-25T09:15:58Z")
I have a set of restraints from an NMR experiment. My distance restraint is formatted as follows: assign (resid \<\> and name \<\>) (resid \<\> and name \<\>) while my dihedral restraint is like this: assign (resid 1 and na… --- ## [Something is wrong with the config file](https://ask.bioexcel.eu/t/something-is-wrong-with-the-config-file/5895)
**Author:** [@ef25](https://ask.bioexcel.eu/u/ef25)\ **Replies:** 9\ **Last updated:** [September 24, 2025, 9:03am UTC](https://ask.bioexcel.eu/t/something-is-wrong-with-the-config-file/5895 "2025-09-24T09:03:06Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab I have been trying to dock heparan sulfate with my protein. I set it as an ordinary… --- ## [Rigid-body step fails with 100% output not generated (tolerance 5%)](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889)
**Author:** [@Yashpawar](https://ask.bioexcel.eu/u/Yashpawar)\ **Replies:** 16\ **Last updated:** [September 22, 2025, 6:00pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889 "2025-09-22T18:00:26Z")
Hello everyone, I’m facing a significant issue with the HADDOCK3 rigid-body docking step. The process fails completely, and I receive the following error: RuntimeError: 100.00% of output was not generated for this modu… --- ## [Peptide Energy Minimization Prior to Docking](https://ask.bioexcel.eu/t/peptide-energy-minimization-prior-to-docking/5893)
**Author:** [@Sabrina](https://ask.bioexcel.eu/u/Sabrina)\ **Replies:** 1\ **Last updated:** [September 19, 2025, 9:01am UTC](https://ask.bioexcel.eu/t/peptide-energy-minimization-prior-to-docking/5893 "2025-09-19T09:01:32Z")
Hi, I have just some questions. Some of the peptides I am making are modified from estasablished PDBs, however some monocyclic ones I am making the sequence on ChimeraX. However, there is no way to do energy minimizatio… --- ## [How to do peptide water refinement/energy minimization before docking](https://ask.bioexcel.eu/t/how-to-do-peptide-water-refinement-energy-minimization-before-docking/5894)
**Author:** [@Sabrina](https://ask.bioexcel.eu/u/Sabrina)\ **Replies:** 1\ **Last updated:** [September 18, 2025, 9:00pm UTC](https://ask.bioexcel.eu/t/how-to-do-peptide-water-refinement-energy-minimization-before-docking/5894 "2025-09-18T21:00:37Z")
I want to do energy minimization before docking for accuracy. However, when I use the refinement tool and do water refinement I notice that my bond to make my peptide cyclic breaks, so it becomes linear. Is there a way t… --- ## [Usage of cross-link MS-derived distance constraints in HADDOCK 3.0](https://ask.bioexcel.eu/t/usage-of-cross-link-ms-derived-distance-constraints-in-haddock-3-0/5890)
**Author:** [@DiT](https://ask.bioexcel.eu/u/DiT)\ **Replies:** 4\ **Last updated:** [September 17, 2025, 10:02am UTC](https://ask.bioexcel.eu/t/usage-of-cross-link-ms-derived-distance-constraints-in-haddock-3-0/5890 "2025-09-17T10:02:11Z")
Dear HADDOCK developers, I’m trying to use the HADDOCK 3 webserver (Haddock3) to dock antibody to antigen with experimental cross-link distance constraint. I have some confusion that would be nice to have some input fr… --- ## [HADDOCK on multi-chain receptor: how to approach?](https://ask.bioexcel.eu/t/haddock-on-multi-chain-receptor-how-to-approach/5885)
**Author:** [@haddock\_newbie](https://ask.bioexcel.eu/u/haddock_newbie)\ **Replies:** 3\ **Last updated:** [September 16, 2025, 5:40am UTC](https://ask.bioexcel.eu/t/haddock-on-multi-chain-receptor-how-to-approach/5885 "2025-09-16T05:40:02Z")
Hi Bonvin Lab people! First of all, let me tell you that I am very new to this topic and I might be quite wrong in some of the formulations here. Please don’t mind that and correct me if I am wrong! I am setting up a d… --- ## [Cannot submit “Request elevated access → Guru” on HADDOCK](https://ask.bioexcel.eu/t/cannot-submit-request-elevated-access-guru-on-haddock/5884)
**Author:** [@ziyi](https://ask.bioexcel.eu/u/ziyi)\ **Replies:** 2\ **Last updated:** [September 8, 2025, 8:22am UTC](https://ask.bioexcel.eu/t/cannot-submit-request-elevated-access-guru-on-haddock/5884 "2025-09-08T08:22:36Z")
Title: Cannot submit “Request elevated access → Guru” on HADDOCK server Body: Hello HADDOCK team, I created a new account today and I am trying to request Guru access from my profile page (Profile → Request elevated a… --- ## [Guru and Expert privileges](https://ask.bioexcel.eu/t/guru-and-expert-privileges/2600)
**Author:** [@jenaros](https://ask.bioexcel.eu/u/jenaros)\ **Replies:** 2\ **Last updated:** [September 8, 2025, 7:36am UTC](https://ask.bioexcel.eu/t/guru-and-expert-privileges/2600 "2025-09-08T07:36:01Z")
Hi Everyone, I am a graduate student from the University of California, Irvine. I am attempting to model Protein-DNA docking. I came across a great tutorial by Dr. Marc van. Through the tutorial I have learned that I re… --- ## [O-linked glycosylation](https://ask.bioexcel.eu/t/o-linked-glycosylation/5875)
**Author:** [@pmer](https://ask.bioexcel.eu/u/pmer)\ **Replies:** 10\ **Last updated:** [September 5, 2025, 1:05pm UTC](https://ask.bioexcel.eu/t/o-linked-glycosylation/5875 "2025-09-05T13:05:41Z")
Dear Bonvin lab, I am trying to model an O-glycosylated protein ligand binding to a protein in Haddock3 locally. My understanding is that since the O-glycan linkage is not recognised in the topo step the linkage is cut … --- ## [Multiple jobs submitted but no email sent](https://ask.bioexcel.eu/t/multiple-jobs-submitted-but-no-email-sent/5879)
**Author:** [@janeshen91](https://ask.bioexcel.eu/u/janeshen91)\ **Replies:** 1\ **Last updated:** [September 4, 2025, 6:57am UTC](https://ask.bioexcel.eu/t/multiple-jobs-submitted-but-no-email-sent/5879 "2025-09-04T06:57:16Z")
submitted several jobs of Haddock 2.4. Received emails for the first 3 but not the next 3. Is there a place I can go to look at jobs I have running if I didn’t receive an email with a link to the results? Thanks. --- ## [Protein and peptide ligand docking](https://ask.bioexcel.eu/t/protein-and-peptide-ligand-docking/5877)
**Author:** [@Eugeneng991031](https://ask.bioexcel.eu/u/Eugeneng991031)\ **Replies:** 5\ **Last updated:** [September 4, 2025, 6:16am UTC](https://ask.bioexcel.eu/t/protein-and-peptide-ligand-docking/5877 "2025-09-04T06:16:05Z")
Hi, sorry for once again for bothering , I am now interested in docking the HLA-E nonamer peptide , VMAPRTLFL, with the receptor proteins of NKG2A/CD94. Is it wise to have the docking parameters setup as mentioned in htt… --- ## [ProABC2 - error. log file](https://ask.bioexcel.eu/t/proabc2-error-log-file/5878)
**Author:** [@Sura](https://ask.bioexcel.eu/u/Sura)\ **Replies:** 2\ **Last updated:** [September 3, 2025, 12:12pm UTC](https://ask.bioexcel.eu/t/proabc2-error-log-file/5878 "2025-09-03T12:12:51Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab Dear Dr. Alexandre Bonvin When I use PROABC2 to identify the paratope following t… --- ## [Haddock semi-flexibility?](https://ask.bioexcel.eu/t/haddock-semi-flexibility/5872)
**Author:** [@Eugeneng991031](https://ask.bioexcel.eu/u/Eugeneng991031)\ **Replies:** 2\ **Last updated:** [September 1, 2025, 12:45pm UTC](https://ask.bioexcel.eu/t/haddock-semi-flexibility/5872 "2025-09-01T12:45:39Z")
Hi, good day to everyone , if for example, from literature, I know my protein-protein interaction is rigid body interaction, in HADDOCK, during the “input parameter”, is it right if i set the semi-flexible region as rigi… [Previous page](https://ask.bioexcel.eu/c/haddock/6.md?page=2) [Next page](https://ask.bioexcel.eu/c/haddock/6.md?page=4)