# Uncategorized **URL:** https://ask.bioexcel.eu/c/uncategorized/1.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [Welcome to ask.bioexcel.eu](https://ask.bioexcel.eu/t/welcome-to-ask-bioexcel-eu/8)
**Author:** [@system](https://ask.bioexcel.eu/u/system)\ **Replies:** 0\ **Last updated:** [February 16, 2016, 4:26pm UTC](https://ask.bioexcel.eu/t/welcome-to-ask-bioexcel-eu/8 "2016-02-16T16:26:08Z")
Welcome to ask.bioexcel.eu! This forum supports the community for computational biomolecular research in academia and industry, with particular focus on biomolecular simulation and modelling and using high-performance c… --- ## [Account not activated,confirmed the activation email more than 24 hours ago](https://ask.bioexcel.eu/t/account-not-activated-confirmed-the-activation-email-more-than-24-hours-ago/6245)
**Author:** [@Zcjalex](https://ask.bioexcel.eu/u/Zcjalex)\ **Replies:** 0\ **Last updated:** [September 5, 2026, 10:43am UTC](https://ask.bioexcel.eu/t/account-not-activated-confirmed-the-activation-email-more-than-24-hours-ago/6245 "2026-09-05T10:43:15Z")
Dear HADDOCK support team, I registered for a HADDOCK account and confirmed the activation email more than 24 hours ago, but my account has still not been activated. The portal keeps showing “Your account has not been a… --- ## [Covalent CL in small molecule is not supported](https://ask.bioexcel.eu/t/covalent-cl-in-small-molecule-is-not-supported/6238)
**Author:** [@Bahaa\_Ali](https://ask.bioexcel.eu/u/Bahaa_Ali)\ **Replies:** 0\ **Last updated:** [August 25, 2026, 12:59pm UTC](https://ask.bioexcel.eu/t/covalent-cl-in-small-molecule-is-not-supported/6238 "2026-08-25T12:59:55Z")
I am trying to dock my small molecule, but each time covalent CL is replaced with CH3. is there a way to solve other than running local haddock with my generated parameters? --- ## [Powerfit error:Request not submitted](https://ask.bioexcel.eu/t/powerfit-error-request-not-submitted/6224)
**Author:** [@bharti04](https://ask.bioexcel.eu/u/bharti04)\ **Replies:** 4\ **Last updated:** [August 6, 2026, 9:07am UTC](https://ask.bioexcel.eu/t/powerfit-error-request-not-submitted/6224 "2026-08-06T09:07:24Z")
@honoratorv I am using powerfit to do a fitting of a cryomap density. after submitting the reuest, it shows “Request not submitted, contact to the support”. How to fix this? --- ## [HADDOCK 2.4 — batch of 8 jobs pending since 21 July](https://ask.bioexcel.eu/t/haddock-2-4-batch-of-8-jobs-pending-since-21-july/6209)
**Author:** [@om894](https://ask.bioexcel.eu/u/om894)\ **Replies:** 1\ **Last updated:** [July 25, 2026, 12:38pm UTC](https://ask.bioexcel.eu/t/haddock-2-4-batch-of-8-jobs-pending-since-21-july/6209 "2026-07-25T12:38:17Z")
Hi, I’ve seen the recent comments about the current backlog and the ~800 jobs/day throughput, so I appreciate the queue is busy — but I wanted to flag mine in case it’s the “unusual” case you mentioned rather than norma… --- ## [All the docking is in queued](https://ask.bioexcel.eu/t/all-the-docking-is-in-queued/6206)
**Author:** [@Abhimanyu](https://ask.bioexcel.eu/u/Abhimanyu)\ **Replies:** 1\ **Last updated:** [July 24, 2026, 1:22pm UTC](https://ask.bioexcel.eu/t/all-the-docking-is-in-queued/6206 "2026-07-24T13:22:06Z")
Yesterday i put the docking but till now it shown in queued, does it going to happen or not --- ## [HADDOCK account confirmation link certificate error](https://ask.bioexcel.eu/t/haddock-account-confirmation-link-certificate-error/6178)
**Author:** [@Murphy](https://ask.bioexcel.eu/u/Murphy)\ **Replies:** 1\ **Last updated:** [June 24, 2026, 10:21am UTC](https://ask.bioexcel.eu/t/haddock-account-confirmation-link-certificate-error/6178 "2026-06-24T10:21:32Z")
Dear HADDOCK team, I registered for a HADDOCK web server account, but the confirmation link redirects to rascar.science.uu.nl and Chrome reports NET::ERR\_CERT\_COMMON\_NAME\_INVALID. I cannot complete the email confirmati… --- ## [Support for O-Linked Serine and GalNAc-OMe](https://ask.bioexcel.eu/t/support-for-o-linked-serine-and-galnac-ome/6167)
**Author:** [@keeankawamoto](https://ask.bioexcel.eu/u/keeankawamoto)\ **Replies:** 0\ **Last updated:** [June 12, 2026, 8:37pm UTC](https://ask.bioexcel.eu/t/support-for-o-linked-serine-and-galnac-ome/6167 "2026-06-12T20:37:59Z")
Hello, can you please add support for O-Linked Serine and GalNAc-OMe? Thank you so much! --- ## [Poster Abstract: Marc El Hasbany](https://ask.bioexcel.eu/t/poster-abstract-marc-el-hasbany/6140)
**Author:** [@marc](https://ask.bioexcel.eu/u/marc)\ **Replies:** 0\ **Last updated:** [May 27, 2026, 12:17pm UTC](https://ask.bioexcel.eu/t/poster-abstract-marc-el-hasbany/6140 "2026-05-27T12:17:56Z")
Deciphering the molecular basis for activation and inhibition of olfactory receptors. Marc El Hasbany;1Chulwon Choi;2 Marie-Charlotte Dumargne;3 Romain Barrès;3 Hee-Jung Choi;2 Jérémie Topin1 Institut de Chimie … --- ## [Problems with queued dockings](https://ask.bioexcel.eu/t/problems-with-queued-dockings/6108)
**Author:** [@Charliep53](https://ask.bioexcel.eu/u/Charliep53)\ **Replies:** 2\ **Last updated:** [May 14, 2026, 4:37pm UTC](https://ask.bioexcel.eu/t/problems-with-queued-dockings/6108 "2026-05-14T16:37:52Z")
Hello estimated HADDOCK support team, i have a question: my submit requests are in a permanent queued state, and the past week the jobs were completed in the range of 2 to 4 hours. Is there any problem with my account or… --- ## [Saving docked files](https://ask.bioexcel.eu/t/saving-docked-files/6102)
**Author:** [@KarthikIITG](https://ask.bioexcel.eu/u/KarthikIITG)\ **Replies:** 1\ **Last updated:** [May 6, 2026, 9:53am UTC](https://ask.bioexcel.eu/t/saving-docked-files/6102 "2026-05-06T09:53:20Z")
Hi. I am about to submit a manuscript for publication. I have docked around 100 models and I will be using the data for about 40-50 models in my paper. But I just checked, the runs have been deleted my server and I am n… --- ## [NOE constrains C-C vs H-H](https://ask.bioexcel.eu/t/noe-constrains-c-c-vs-h-h/6094)
**Author:** [@csadim](https://ask.bioexcel.eu/u/csadim)\ **Replies:** 0\ **Last updated:** [April 27, 2026, 8:21am UTC](https://ask.bioexcel.eu/t/noe-constrains-c-c-vs-h-h/6094 "2026-04-27T08:21:17Z")
Hi, I am calculating a CSP, NOE guided protein/peptide complex. I am getting better results when using heavy atom to heavy atom constrains (only one cluster, lower energy ) than when using H-H constrains. I have two q… --- ## [advanced settings](https://ask.bioexcel.eu/t/advanced-settings/6090)
**Author:** [@Mami](https://ask.bioexcel.eu/u/Mami)\ **Replies:** 1\ **Last updated:** [April 26, 2026, 3:28pm UTC](https://ask.bioexcel.eu/t/advanced-settings/6090 "2026-04-26T15:28:46Z")
I am currently using HADDOCK to study interactions between proteasome variants and an MHC peptide. While running docking calculations, I tried an option that I believe was labeled something like “advanced” or “expert” s… --- ## [Visual Artifacts in PyMOL Following GROMACS Trajectory Post-Processing](https://ask.bioexcel.eu/t/visual-artifacts-in-pymol-following-gromacs-trajectory-post-processing/6086)
**Author:** [@holly](https://ask.bioexcel.eu/u/holly)\ **Replies:** 0\ **Last updated:** [April 23, 2026, 9:42am UTC](https://ask.bioexcel.eu/t/visual-artifacts-in-pymol-following-gromacs-trajectory-post-processing/6086 "2026-04-23T09:42:03Z")
Hello, after running MD production for my antigen and Fv complex using GROMACS 2025.4, I applied the following preprocessing commands and exported a specific frame conformation (colored green). When viewing the ori… --- ## [Problem work submission](https://ask.bioexcel.eu/t/problem-work-submission/6057)
**Author:** [@ioannis](https://ask.bioexcel.eu/u/ioannis)\ **Replies:** 2\ **Last updated:** [March 29, 2026, 2:50pm UTC](https://ask.bioexcel.eu/t/problem-work-submission/6057 "2026-03-29T14:50:48Z")
Dear HADDOCK Support, I am contacting you because, although the platform indicates that my account is being activated, I am still unable to access HADDOCK and use the service. I have already completed the registration … --- ## [Error installing haddock3](https://ask.bioexcel.eu/t/error-installing-haddock3/6038)
**Author:** [@Rainer.Lilischkis](https://ask.bioexcel.eu/u/Rainer.Lilischkis)\ **Replies:** 3\ **Last updated:** [March 23, 2026, 11:00am UTC](https://ask.bioexcel.eu/t/error-installing-haddock3/6038 "2026-03-23T11:00:03Z")
while installing haddock3 I get the following: Created wheel for haddock3: filename=haddock3-2025.11.0-cp313-cp313-linux\_x86\_64.whl size=15023319 sha256=5804a7e45a5ba804f4b803cc7b566a2eb89b0f1185fb72b971943297da4fbb9b … --- ## [Molecular dynamics parameters (.mdp options)](https://ask.bioexcel.eu/t/molecular-dynamics-parameters-mdp-options/6049)
**Author:** [@holly](https://ask.bioexcel.eu/u/holly)\ **Replies:** 0\ **Last updated:** [March 22, 2026, 7:14am UTC](https://ask.bioexcel.eu/t/molecular-dynamics-parameters-mdp-options/6049 "2026-03-22T07:14:13Z")
I am performing molecular dynamics (MD) simulations on a complex system composed of a protein antigen and the Fv fragment of a monoclonal antibody using GROMACS 2024.3, and I have been running into persistent errors thro… --- ## [Introduction: Marc El Hasbany](https://ask.bioexcel.eu/t/introduction-marc-el-hasbany/6043)
**Author:** [@marc](https://ask.bioexcel.eu/u/marc)\ **Replies:** 0\ **Last updated:** [March 19, 2026, 10:31am UTC](https://ask.bioexcel.eu/t/introduction-marc-el-hasbany/6043 "2026-03-19T10:31:52Z")
Hello everyone! My name is Marc El Hasbany, I am a PhD candidate in theoretical chemistry at the Institut de Chimie de Nice. Originally from Lebanon, I moved to Paris, where I lived for two years to complete my training… --- ## [Mutant Complex Not Launching in HADDOCK (Wild Type Works Fine)](https://ask.bioexcel.eu/t/mutant-complex-not-launching-in-haddock-wild-type-works-fine/6004)
**Author:** [@GouravChoudhir](https://ask.bioexcel.eu/u/GouravChoudhir)\ **Replies:** 1\ **Last updated:** [February 11, 2026, 5:52pm UTC](https://ask.bioexcel.eu/t/mutant-complex-not-launching-in-haddock-wild-type-works-fine/6004 "2026-02-11T17:52:19Z")
Hello everyone, I am currently performing docking using HADDOCK for a nucleosome–SIRT6 complex with two additional protein partners. The wild-type complex runs successfully without any issues. However, when I use the m… --- ## [Issue with submission of Haddock run](https://ask.bioexcel.eu/t/issue-with-submission-of-haddock-run/6003)
**Author:** [@RashmiPanigrahi](https://ask.bioexcel.eu/u/RashmiPanigrahi)\ **Replies:** 1\ **Last updated:** [February 10, 2026, 2:36pm UTC](https://ask.bioexcel.eu/t/issue-with-submission-of-haddock-run/6003 "2026-02-10T14:36:42Z")
Hello, I am new to this club. I am trying perform protein-protein interaction studies. I am not able to find the submission interface. Is the server not active? Thank you --- ## [ARCTIC-3d is not working](https://ask.bioexcel.eu/t/arctic-3d-is-not-working/5999)
**Author:** [@Juan.Cardenas](https://ask.bioexcel.eu/u/Juan.Cardenas)\ **Replies:** 3\ **Last updated:** [February 5, 2026, 2:40am UTC](https://ask.bioexcel.eu/t/arctic-3d-is-not-working/5999 "2026-02-05T02:40:08Z")
Hello, I have been trying to use ARCTIC-3D, but every time I try, I get an error message: =========================================================================== command: arctic3d --full P06756 --threshold 0.866 --l… --- ## [Modified amino acid](https://ask.bioexcel.eu/t/modified-amino-acid/5986)
**Author:** [@dkarunat](https://ask.bioexcel.eu/u/dkarunat)\ **Replies:** 0\ **Last updated:** [January 28, 2026, 2:28am UTC](https://ask.bioexcel.eu/t/modified-amino-acid/5986 "2026-01-28T02:28:49Z")
Hi! I’m trying to dock the peptide Cilengitide onto the human avb3 integrin. However, this peptide has a modified valine (cyclo\[Arg-Gly-Asp-D-Phe-N(Me)Val\]) which isn’t currently in the list of modified amino acids permi… --- ## [Ligand conformer generator](https://ask.bioexcel.eu/t/ligand-conformer-generator/5964)
**Author:** [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Replies:** 7\ **Last updated:** [January 6, 2026, 10:12am UTC](https://ask.bioexcel.eu/t/ligand-conformer-generator/5964 "2026-01-06T10:12:06Z")
Hi all, I need advise on an open-source web based reliable conformer generator for small molecule sugar ligands. I understand this platform is haddock related, but I have hit a roadblock in finding a good one. I have tr… --- ## [Suitable tool for docking stapled peptide and protein](https://ask.bioexcel.eu/t/suitable-tool-for-docking-stapled-peptide-and-protein/5962)
**Author:** [@Sumaiya](https://ask.bioexcel.eu/u/Sumaiya)\ **Replies:** 1\ **Last updated:** [December 10, 2025, 3:41pm UTC](https://ask.bioexcel.eu/t/suitable-tool-for-docking-stapled-peptide-and-protein/5962 "2025-12-10T15:41:47Z")
Hi, I am a first year PGR, I need to know which software to choose to draw the stapled peptide and which one for docking the stapled peptide with protein? Thanks a ton. --- ## [Need to dock 1000 peptide for one protein in HPC. Is there is any way to do that in one job?](https://ask.bioexcel.eu/t/need-to-dock-1000-peptide-for-one-protein-in-hpc-is-there-is-any-way-to-do-that-in-one-job/5959)
**Author:** [@fow028](https://ask.bioexcel.eu/u/fow028)\ **Replies:** 5\ **Last updated:** [December 8, 2025, 9:06pm UTC](https://ask.bioexcel.eu/t/need-to-dock-1000-peptide-for-one-protein-in-hpc-is-there-is-any-way-to-do-that-in-one-job/5959 "2025-12-08T21:06:29Z")
Hello, I want to dock 1000 peptide against one protein. Is that any efficient way to do that other than one json for each. Also, I have to use HPC installation for this. Can I generate the output in the same format as t… --- ## [Z-score is zero](https://ask.bioexcel.eu/t/z-score-is-zero/5954)
**Author:** [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Replies:** 2\ **Last updated:** [November 19, 2025, 10:26am UTC](https://ask.bioexcel.eu/t/z-score-is-zero/5954 "2025-11-19T10:26:21Z")
Hi, I run a protein ligand docking on haddock and this is the result I got. Z-score is returned as zero, does it mean the ligand does not bind to the protein? Also, is clustering 400 structures in 1 cluster incorre… --- ## [Unusual bonds in -OSO3 of ligand after docking](https://ask.bioexcel.eu/t/unusual-bonds-in-oso3-of-ligand-after-docking/5951)
**Author:** [@ef25](https://ask.bioexcel.eu/u/ef25)\ **Replies:** 3\ **Last updated:** [November 14, 2025, 8:26am UTC](https://ask.bioexcel.eu/t/unusual-bonds-in-oso3-of-ligand-after-docking/5951 "2025-11-14T08:26:25Z")
Hello! I made my ligand molecule using Chemdraw and Chem3D. Before docking, I made sure that the pdb file has the correct format for docking. However, after docking, all my ligands have this unusual bond formed which I a… --- ## [TIP in my pdb file](https://ask.bioexcel.eu/t/tip-in-my-pdb-file/5943)
**Author:** [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Replies:** 2\ **Last updated:** [November 9, 2025, 12:37pm UTC](https://ask.bioexcel.eu/t/tip-in-my-pdb-file/5943 "2025-11-09T12:37:15Z")
Hi, I am running a protein-small molecule docking and there is an error in my pdb file. My water molecule is defined as TIP. What should I change TIP into? I have attached the pdb file and error given by HADDOCK for your… --- ## [Haddock Queued for a long time](https://ask.bioexcel.eu/t/haddock-queued-for-a-long-time/5929)
**Author:** [@Samantha\_Alyssa](https://ask.bioexcel.eu/u/Samantha_Alyssa)\ **Replies:** 0\ **Last updated:** [November 3, 2025, 10:10am UTC](https://ask.bioexcel.eu/t/haddock-queued-for-a-long-time/5929 "2025-11-03T10:10:27Z")
Hi, good day! I would just like to ask if it’s normal that my molecular docking submission has been queued for so long already. For the past week, I have not encountered this issue. I have only encountered this after I … --- ## [Docking with protein embedded in a bacterial membrane](https://ask.bioexcel.eu/t/docking-with-protein-embedded-in-a-bacterial-membrane/5925)
**Author:** [@ef25](https://ask.bioexcel.eu/u/ef25)\ **Replies:** 1\ **Last updated:** [October 31, 2025, 7:33am UTC](https://ask.bioexcel.eu/t/docking-with-protein-embedded-in-a-bacterial-membrane/5925 "2025-10-31T07:33:30Z")
Good day! I would like to ask if I can dock my protein embedded in a bacterial membrane using haddock2.4? I built the system using charmm gui membrane builder. Thank you [Next page](https://ask.bioexcel.eu/c/uncategorized/1.md?page=1)