# HADDOCK **URL:** https://ask.bioexcel.eu/c/haddock/6.md?page=1 [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) **Page:** 2 --- ## [CNS License Issues for Using HADDOCK3](https://ask.bioexcel.eu/t/cns-license-issues-for-using-haddock3/6218)
**Author:** [@ben1992](https://ask.bioexcel.eu/u/ben1992)\ **Replies:** 2\ **Last updated:** [August 5, 2026, 1:06am UTC](https://ask.bioexcel.eu/t/cns-license-issues-for-using-haddock3/6218 "2026-08-05T01:06:43Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab I inquired with Biovia (3DS) about licensing in accordance with haddock3/DISCLAIM… --- ## [Modeling protein-protein-ligand complexes -- adding unambiguous restraints](https://ask.bioexcel.eu/t/modeling-protein-protein-ligand-complexes-adding-unambiguous-restraints/6199)
**Author:** [@RichikNeogi](https://ask.bioexcel.eu/u/RichikNeogi)\ **Replies:** 5\ **Last updated:** [July 29, 2026, 12:37pm UTC](https://ask.bioexcel.eu/t/modeling-protein-protein-ligand-complexes-adding-unambiguous-restraints/6199 "2026-07-29T12:37:20Z")
Hi all, I posted a topic previously regarding the protein complex I am trying to model. Essentially I am trying to model the complex between an RGS protein and a G-protein alpha subunit (GTP and Mg-bound). In order for … --- ## [Job status on HADDOCK web server](https://ask.bioexcel.eu/t/job-status-on-haddock-web-server/6212)
**Author:** [@Sachithra](https://ask.bioexcel.eu/u/Sachithra)\ **Replies:** 1\ **Last updated:** [July 29, 2026, 6:52am UTC](https://ask.bioexcel.eu/t/job-status-on-haddock-web-server/6212 "2026-07-29T06:52:08Z")
When a job is submitted to the HADDOCK web server, the job status shows as processed. What does this mean? Is this normal? This is my first time using HADDOCK. --- ## [WHISCY error, Can not read sequence number](https://ask.bioexcel.eu/t/whiscy-error-can-not-read-sequence-number/6190)
**Author:** [@F-Mars](https://ask.bioexcel.eu/u/F-Mars)\ **Replies:** 5\ **Last updated:** [July 28, 2026, 7:45am UTC](https://ask.bioexcel.eu/t/whiscy-error-can-not-read-sequence-number/6190 "2026-07-28T07:45:58Z")
I have run into a problem with WHISCY: set -euo pipefail export MUSCLE\_BIN=/home/fabian/software/muscle3.8.1551/muscle MUSCLE\_BIN=/home/fabian/software/muscle3.8.1551/muscle export FREESASA\_BIN=/home/fabian/software/f… --- ## [100.00% of output was not generated for this module and tolerance was set to 5.00%](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202)
**Author:** [@Anupama1](https://ask.bioexcel.eu/u/Anupama1)\ **Replies:** 8\ **Last updated:** [July 23, 2026, 6:25am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202 "2026-07-23T06:25:34Z")
I am facing the error during protein peptide docking in haddock V3. My protein contains two domains defined as chainA and chainB. Both chains are reported to have functional role in ligand binding and activity. PDB file … --- ## [HADDOCK jobs remain in "Queued" status for over a day](https://ask.bioexcel.eu/t/haddock-jobs-remain-in-queued-status-for-over-a-day/6195)
**Author:** [@HYjeong](https://ask.bioexcel.eu/u/HYjeong)\ **Replies:** 3\ **Last updated:** [July 22, 2026, 10:59am UTC](https://ask.bioexcel.eu/t/haddock-jobs-remain-in-queued-status-for-over-a-day/6195 "2026-07-22T10:59:16Z")
Dear HADDOCK Support Team, I am experiencing an issue with the HADDOCK web server. My jobs submitted on July 15 have all remained in “Queued” status and have not started running. In addition, my colleague also submitte… --- ## [Missing active residues](https://ask.bioexcel.eu/t/missing-active-residues/6200)
**Author:** [@emreynaud](https://ask.bioexcel.eu/u/emreynaud)\ **Replies:** 3\ **Last updated:** [July 20, 2026, 10:32am UTC](https://ask.bioexcel.eu/t/missing-active-residues/6200 "2026-07-20T10:32:12Z")
I submitted a docking job (protein-ligand) by specifying a list of active residues (binding sites). The run completed successfully, but after downloading the results and inspecting the active residues, I noticed that som… --- ## [Refinement with HADDOCK3](https://ask.bioexcel.eu/t/refinement-with-haddock3/6197)
**Author:** [@Lucas](https://ask.bioexcel.eu/u/Lucas)\ **Replies:** 2\ **Last updated:** [July 16, 2026, 3:22pm UTC](https://ask.bioexcel.eu/t/refinement-with-haddock3/6197 "2026-07-16T15:22:50Z")
My question concerns how to implement refinement using HADDOCK3. Starting with an ensemble of protein-protein interaction complexes that received the highest scores from LightDock, I proceeded with a refinement workflow … --- ## [Request to kill my stuck running job which blocks new queued submission](https://ask.bioexcel.eu/t/request-to-kill-my-stuck-running-job-which-blocks-new-queued-submission/6193)
**Author:** [@tfjhbkvf](https://ask.bioexcel.eu/u/tfjhbkvf)\ **Replies:** 1\ **Last updated:** [July 16, 2026, 10:09am UTC](https://ask.bioexcel.eu/t/request-to-kill-my-stuck-running-job-which-blocks-new-queued-submission/6193 "2026-07-16T10:09:17Z")
Dear HADDOCK admin team, One of my jobs has been stuck in Running status for 2 full days with no further log output, it becomes a zombie process and occupies cluster resource. Since this running job cannot be cancelled … --- ## [Docking of small molecule to a binding site consists of nucleic acids and protein](https://ask.bioexcel.eu/t/docking-of-small-molecule-to-a-binding-site-consists-of-nucleic-acids-and-protein/6185)
**Author:** [@mushroom\_ali](https://ask.bioexcel.eu/u/mushroom_ali)\ **Replies:** 1\ **Last updated:** [July 2, 2026, 8:11am UTC](https://ask.bioexcel.eu/t/docking-of-small-molecule-to-a-binding-site-consists-of-nucleic-acids-and-protein/6185 "2026-07-02T08:11:25Z")
Hello! I have a small molecule that I would like to dock to a receptor site. The receptor site, however, includes nucleobases from RNA and amino acids from protein. I know some of the bases are important in establishing … --- ## [Docking of small ssDNA on proteins](https://ask.bioexcel.eu/t/docking-of-small-ssdna-on-proteins/6183)
**Author:** [@BioMarc](https://ask.bioexcel.eu/u/BioMarc)\ **Replies:** 3\ **Last updated:** [June 29, 2026, 9:01pm UTC](https://ask.bioexcel.eu/t/docking-of-small-ssdna-on-proteins/6183 "2026-06-29T21:01:01Z")
Hello, I am trying to do a docking of multiple small (6 nts) single-stranded DNAs on a protein. I am wondering if I am using the right parameters. I would like to dock blindly. Here is a part of my cfg file with the par… --- ## [Clustering failure - IMPROPER tag in topology](https://ask.bioexcel.eu/t/clustering-failure-improper-tag-in-topology/6181)
**Author:** [@josephjpark](https://ask.bioexcel.eu/u/josephjpark)\ **Replies:** 1\ **Last updated:** [June 26, 2026, 2:52pm UTC](https://ask.bioexcel.eu/t/clustering-failure-improper-tag-in-topology/6181 "2026-06-26T14:52:25Z")
Hello, I am running into some issues with the clustering of my HADDOCK3 run where clusters are forming, but they comprise of exactly four identical models. Additionally, I am finding some atoms under the IMPROPER tag wi… --- ## [Long Queuing Durations and Appearance of "Unknown" Job Status](https://ask.bioexcel.eu/t/long-queuing-durations-and-appearance-of-unknown-job-status/6180)
**Author:** [@LJY](https://ask.bioexcel.eu/u/LJY)\ **Replies:** 1\ **Last updated:** [June 25, 2026, 4:55am UTC](https://ask.bioexcel.eu/t/long-queuing-durations-and-appearance-of-unknown-job-status/6180 "2026-06-25T04:55:28Z")
Dear HADDOCK Support Team, I am a postgraduate student using the HADDOCK 2.4 web server to run simulations. I notice the jobs that I submitted is taking much longer than usual to completed, it usually takes 3-5 hours fo… --- ## [Inquiry About Job Status – HADDOCK Job Submission (36 Hours in Queue)](https://ask.bioexcel.eu/t/inquiry-about-job-status-haddock-job-submission-36-hours-in-queue/6176)
**Author:** [@peitao](https://ask.bioexcel.eu/u/peitao)\ **Replies:** 1\ **Last updated:** [June 24, 2026, 7:11am UTC](https://ask.bioexcel.eu/t/inquiry-about-job-status-haddock-job-submission-36-hours-in-queue/6176 "2026-06-24T07:11:10Z")
I am writing to kindly inquire about the status of my submitted docking job, which has been queued for approximately 36 hours. I wanted to check whether this delay is due to an issue with my specific submission, or if it… --- ## [Add support for O-Linked Serine and GalNAc-OMe](https://ask.bioexcel.eu/t/add-support-for-o-linked-serine-and-galnac-ome/6172)
**Author:** [@keeankawamoto](https://ask.bioexcel.eu/u/keeankawamoto)\ **Replies:** 2\ **Last updated:** [June 16, 2026, 6:32pm UTC](https://ask.bioexcel.eu/t/add-support-for-o-linked-serine-and-galnac-ome/6172 "2026-06-16T18:32:27Z")
Hello, can you please add support for O-Linked Serine and GalNAc-OMe? Thank you so much! --- ## [Modeling protein-protein-ligand complexes](https://ask.bioexcel.eu/t/modeling-protein-protein-ligand-complexes/6168)
**Author:** [@RichikNeogi](https://ask.bioexcel.eu/u/RichikNeogi)\ **Replies:** 1\ **Last updated:** [June 12, 2026, 9:20pm UTC](https://ask.bioexcel.eu/t/modeling-protein-protein-ligand-complexes/6168 "2026-06-12T21:20:53Z")
Hello, I am attempting to dock a G-protein with a protein that accelerates GTPase activity of the G-protein. I have conducted runs with the GTP and Magnesium-free structure – however I feel that the next step would be t… --- ## [How to model antibody-antigen complexes with partial experimental data?](https://ask.bioexcel.eu/t/how-to-model-antibody-antigen-complexes-with-partial-experimental-data/6164)
**Author:** [@mberksoz](https://ask.bioexcel.eu/u/mberksoz)\ **Replies:** 3\ **Last updated:** [June 5, 2026, 2:04pm UTC](https://ask.bioexcel.eu/t/how-to-model-antibody-antigen-complexes-with-partial-experimental-data/6164 "2026-06-05T14:04:43Z")
Dear Haddock team, I have been using a local version of Haddock3 to dock antibody clones that we have partial epitope for. Clone X is shown to share an overlapping epitope with a reference antibody on SPR epitope binnin… --- ## [Refinement jobs failing on Haddock 2.4 web server](https://ask.bioexcel.eu/t/refinement-jobs-failing-on-haddock-2-4-web-server/6160)
**Author:** [@Pietro](https://ask.bioexcel.eu/u/Pietro)\ **Replies:** 6\ **Last updated:** [June 5, 2026, 5:34am UTC](https://ask.bioexcel.eu/t/refinement-jobs-failing-on-haddock-2-4-web-server/6160 "2026-06-05T05:34:55Z")
Hi, In the last 4/5 days I cannot get my refinement jobs done on haddock 2.4. I can see each job going through the it0, it1 and itw and reaching the 100%, then they freeze and the job status becomes: unknown. I am using… --- ## [Support for glucosamine (GCS) in HADDOCK?](https://ask.bioexcel.eu/t/support-for-glucosamine-gcs-in-haddock/6158)
**Author:** [@Magnus](https://ask.bioexcel.eu/u/Magnus)\ **Replies:** 10\ **Last updated:** [June 4, 2026, 12:02pm UTC](https://ask.bioexcel.eu/t/support-for-glucosamine-gcs-in-haddock/6158 "2026-06-04T12:02:35Z")
Is it possible to get support for glucosamines/chito-oligos in HADDOCK? --- ## [The data uploaded by HADDOCK2.4 has been continuously showing as being in the queue.](https://ask.bioexcel.eu/t/the-data-uploaded-by-haddock2-4-has-been-continuously-showing-as-being-in-the-queue/6145)
**Author:** [@xiebiyu](https://ask.bioexcel.eu/u/xiebiyu)\ **Replies:** 1\ **Last updated:** [May 28, 2026, 12:30pm UTC](https://ask.bioexcel.eu/t/the-data-uploaded-by-haddock2-4-has-been-continuously-showing-as-being-in-the-queue/6145 "2026-05-28T12:30:19Z")
The data uploaded by HADDOCK2.4 has been continuously showing as being in the queue. Is this normal? --- ## [Urgent: Stuck jobs in queue and water refinement (itw) - HIV-1 Tat/Receptor docking](https://ask.bioexcel.eu/t/urgent-stuck-jobs-in-queue-and-water-refinement-itw-hiv-1-tat-receptor-docking/6138)
**Author:** [@shaughn](https://ask.bioexcel.eu/u/shaughn)\ **Replies:** 1\ **Last updated:** [May 27, 2026, 8:27am UTC](https://ask.bioexcel.eu/t/urgent-stuck-jobs-in-queue-and-water-refinement-itw-hiv-1-tat-receptor-docking/6138 "2026-05-27T08:27:31Z")
Dear HADDOCK Support Team, I am an MD-PhD student conducting in silico research on HIV-1 Tat structural variants. I currently have six (6) active docking jobs that have stalled significantly at different stages of the p… --- ## [Live runtime statistics](https://ask.bioexcel.eu/t/live-runtime-statistics/6125)
**Author:** [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Replies:** 0\ **Last updated:** [May 22, 2026, 7:50am UTC](https://ask.bioexcel.eu/t/live-runtime-statistics/6125 "2026-05-22T07:50:21Z")
Hi there Some maintenance and other issues outside our control had created a long queue of jobs. The situation is now back to normal. Note that you can always get an idea of the average (+min/max) times from submission… --- ## [Account not activated — Khan Sibghat Ullah, Northeastern University China](https://ask.bioexcel.eu/t/account-not-activated-khan-sibghat-ullah-northeastern-university-china/6117)
**Author:** [@Sibghat203](https://ask.bioexcel.eu/u/Sibghat203)\ **Replies:** 1\ **Last updated:** [May 18, 2026, 10:28am UTC](https://ask.bioexcel.eu/t/account-not-activated-khan-sibghat-ullah-northeastern-university-china/6117 "2026-05-18T10:28:04Z")
Dear HADDOCK team, I registered for a HADDOCK account at wenmr.science.uu.nl/haddock2.4 using the email 2429016@stu.neu.edu.cn but my account has not been activated yet. I tried sending an email to haddock.support@uu.nl … --- ## [Almost 24 hrs since job in queue](https://ask.bioexcel.eu/t/almost-24-hrs-since-job-in-queue/6110)
**Author:** [@Sumayya7](https://ask.bioexcel.eu/u/Sumayya7)\ **Replies:** 1\ **Last updated:** [May 14, 2026, 8:30am UTC](https://ask.bioexcel.eu/t/almost-24-hrs-since-job-in-queue/6110 "2026-05-14T08:30:56Z")
I’m wondering why? Is the problem at my end? Job name is rage-hm, ID 683822. Thank you. --- ## [Protein Protein docking without restraint definitions](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545)
**Author:** [@ajaniharesh](https://ask.bioexcel.eu/u/ajaniharesh)\ **Replies:** 8\ **Last updated:** [May 14, 2026, 8:17am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-without-restraint-definitions/1545 "2026-05-14T08:17:12Z")
Hi Prof. Bonvin, I have experienced with bound ligand protein-protein docking with restraint definition with 5A active site residue from the ligand. HADDOCK generated almost similar poses as reference. Now, assume if I … --- ## [Issue with account activation email](https://ask.bioexcel.eu/t/issue-with-account-activation-email/6104)
**Author:** [@Yuxinxx](https://ask.bioexcel.eu/u/Yuxinxx)\ **Replies:** 2\ **Last updated:** [May 14, 2026, 5:35am UTC](https://ask.bioexcel.eu/t/issue-with-account-activation-email/6104 "2026-05-14T05:35:36Z")
Hi! I was trying to create an account to use haddock2.4, but I could not receive the activation email. The email address I use is an academic email: yx592@cornell.edu. I also checked junk email, but still couldn’t find i… --- ## [What are the units of this](https://ask.bioexcel.eu/t/what-are-the-units-of-this/6105)
**Author:** [@itsPriyanka](https://ask.bioexcel.eu/u/itsPriyanka)\ **Replies:** 2\ **Last updated:** [May 13, 2026, 6:16am UTC](https://ask.bioexcel.eu/t/what-are-the-units-of-this/6105 "2026-05-13T06:16:53Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab Cluster 2 HADDOCK score -72.5 +/- 2.9 Cluster size … --- ## [Preserving peptide secondary structure during cyclization/docking](https://ask.bioexcel.eu/t/preserving-peptide-secondary-structure-during-cyclization-docking/6098)
**Author:** [@Jameel9](https://ask.bioexcel.eu/u/Jameel9)\ **Replies:** 3\ **Last updated:** [May 6, 2026, 8:57am UTC](https://ask.bioexcel.eu/t/preserving-peptide-secondary-structure-during-cyclization-docking/6098 "2026-05-06T08:57:23Z")
Hello everyone, I am wondering if there is a way to preserve the secondary structures of the input peptide during the cyclization and subsequent docking in Haddock3. Of course it needs to undergo 3D changes for the dock… --- ## [Doubt regarding uploading the topology and the parameter files for the ligand in Haddock 2.4V](https://ask.bioexcel.eu/t/doubt-regarding-uploading-the-topology-and-the-parameter-files-for-the-ligand-in-haddock-2-4v/6101)
**Author:** [@Sidharth](https://ask.bioexcel.eu/u/Sidharth)\ **Replies:** 1\ **Last updated:** [May 5, 2026, 5:24pm UTC](https://ask.bioexcel.eu/t/doubt-regarding-uploading-the-topology-and-the-parameter-files-for-the-ligand-in-haddock-2-4v/6101 "2026-05-05T17:24:27Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab . I am not able to find and option on this server to upload the topology and the pa… --- ## [Registered e-mail](https://ask.bioexcel.eu/t/registered-e-mail/6097)
**Author:** [@KKH](https://ask.bioexcel.eu/u/KKH)\ **Replies:** 1\ **Last updated:** [April 28, 2026, 6:44am UTC](https://ask.bioexcel.eu/t/registered-e-mail/6097 "2026-04-28T06:44:20Z")
I signed up a while ago, but when I try to do anything, “Your account has not been activated yet, you won’t be able to use the services until it is activated. If your request is pending for more than 24h, please send an … [Previous page](https://ask.bioexcel.eu/c/haddock/6.md) [Next page](https://ask.bioexcel.eu/c/haddock/6.md?page=2)