# Latest **URL:** https://ask.bioexcel.eu/latest.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… --- ## [Haddock 2.4 webserver - Protein/Small molecule docking](https://ask.bioexcel.eu/t/haddock-2-4-webserver-protein-small-molecule-docking/6275)
**Author:** [@marianvincenzi](https://ask.bioexcel.eu/u/marianvincenzi)\ **Replies:** 7\ **Last updated:** [September 23, 2026, 8:59pm UTC](https://ask.bioexcel.eu/t/haddock-2-4-webserver-protein-small-molecule-docking/6275 "2026-09-23T20:59:15Z")
Dear All, I have some doubts related to the docking analysis of small moelcules vs Protein. As my habit from Protein/Protein and Protein/peptide docking analyses, I set true value Sample 180 degrees rotated solutions d… --- ## [Glycan chains becoming monomers](https://ask.bioexcel.eu/t/glycan-chains-becoming-monomers/6271)
**Author:** [@mccals](https://ask.bioexcel.eu/u/mccals)\ **Replies:** 1\ **Last updated:** [September 23, 2026, 11:45am UTC](https://ask.bioexcel.eu/t/glycan-chains-becoming-monomers/6271 "2026-09-23T11:45:25Z")
Is there a way to refine glycan chains and maintain glycosidic bonds in 2.4? Oligos are disassociating and becoming monomers in docking schemes between a circular glycan chain and small molecule ligand despite them havin… --- ## [HADDOCK account not activated](https://ask.bioexcel.eu/t/haddock-account-not-activated/6273)
**Author:** [@18332008013](https://ask.bioexcel.eu/u/18332008013)\ **Replies:** 0\ **Last updated:** [September 23, 2026, 9:24am UTC](https://ask.bioexcel.eu/t/haddock-account-not-activated/6273 "2026-09-23T09:24:03Z")
Hello, I registered on the WeNMR portal and received the e-mail “Your HADDOCK account is now active, welcome to the platform!”. However, when I log in to the HADDOCK web server ( HADDOCK Web Server ) the following ba… --- ## [HADDOCK2.4 jobs stuck in Queued status for several hours](https://ask.bioexcel.eu/t/haddock2-4-jobs-stuck-in-queued-status-for-several-hours/6267)
**Author:** [@karen.vara.b](https://ask.bioexcel.eu/u/karen.vara.b)\ **Replies:** 1\ **Last updated:** [September 20, 2026, 7:12pm UTC](https://ask.bioexcel.eu/t/haddock2-4-jobs-stuck-in-queued-status-for-several-hours/6267 "2026-09-20T19:12:49Z")
Hello, I currently have three protein–protein docking jobs on the HADDOCK2.4 web server that have remained in Queued status with it0 = 0.0% for approximately 10 hours: CD36\_0115700\_ALTA — Job ID 766957 CD36\_1041300\_IN… --- ## [Freezing previously-mutated residues in a staged/sequential multi-mutation pmx workflow](https://ask.bioexcel.eu/t/freezing-previously-mutated-residues-in-a-staged-sequential-multi-mutation-pmx-workflow/6264)
**Author:** [@Sankalp](https://ask.bioexcel.eu/u/Sankalp)\ **Replies:** 1\ **Last updated:** [September 17, 2026, 10:45am UTC](https://ask.bioexcel.eu/t/freezing-previously-mutated-residues-in-a-staged-sequential-multi-mutation-pmx-workflow/6264 "2026-09-17T10:45:28Z")
Hi all, I’m running a sequential (staged) multi-mutation alchemical calculation with pmx + GROMACS: I mutate one residue per stage (e.g. T2V), equilibrate both end states, then use the state-B equilibrated structure as … --- ## [CSBPortal account inactive (403) and HADDOCK3 reproducible workflow inquiry](https://ask.bioexcel.eu/t/csbportal-account-inactive-403-and-haddock3-reproducible-workflow-inquiry/6260)
**Author:** [@ysp87940255](https://ask.bioexcel.eu/u/ysp87940255)\ **Replies:** 2\ **Last updated:** [September 15, 2026, 1:30pm UTC](https://ask.bioexcel.eu/t/csbportal-account-inactive-403-and-haddock3-reproducible-workflow-inquiry/6260 "2026-09-15T13:30:35Z")
Dear BonvinLab/WeNMR support team, I can log in to CSBPortal and view the user dashboard, but requesting elevated \`Guru\` permissions returns HTTP 403 with the API response \`{“error”:“user is not active”}\`. The account t… --- ## [Account not activated- Shengnan Wang-Yangzhou Univerisity](https://ask.bioexcel.eu/t/account-not-activated-shengnan-wang-yangzhou-univerisity/6262)
**Author:** [@wangshengnanwsnj](https://ask.bioexcel.eu/u/wangshengnanwsnj)\ **Replies:** 0\ **Last updated:** [September 15, 2026, 7:22am UTC](https://ask.bioexcel.eu/t/account-not-activated-shengnan-wang-yangzhou-univerisity/6262 "2026-09-15T07:22:09Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab Dear HADDOCK Support Team, I have registered and confirm,but it shows "Your acco… --- ## [Unable to submit a new job — account not activated](https://ask.bioexcel.eu/t/unable-to-submit-a-new-job-account-not-activated/6258)
**Author:** [@ksz910](https://ask.bioexcel.eu/u/ksz910)\ **Replies:** 1\ **Last updated:** [September 15, 2026, 7:14am UTC](https://ask.bioexcel.eu/t/unable-to-submit-a-new-job-account-not-activated/6258 "2026-09-15T07:14:33Z")
Hello HADDOCK support team, I can log in to the HADDOCK web portal at HADDOCK Web Server, but it displays “Your account has not been activated yet.” When I click “Submit a new job,” I am returned to the home page instea… --- ## [Intramolecular interactions](https://ask.bioexcel.eu/t/intramolecular-interactions/6250)
**Author:** [@hyunseo.kang](https://ask.bioexcel.eu/u/hyunseo.kang)\ **Replies:** 1\ **Last updated:** [September 14, 2026, 1:04pm UTC](https://ask.bioexcel.eu/t/intramolecular-interactions/6250 "2026-09-14T13:04:56Z")
Dear community, I am trying to optimize orientations of two domains within one protein (AF3 structure) using CSP. Does the webserver allow this without splitting a protein into two? Comments would be appreciated! Hans… --- ## [Account not activated - 汪予诺, 中国热带农业科学院](https://ask.bioexcel.eu/t/account-not-activated/6255)
**Author:** [@847932379](https://ask.bioexcel.eu/u/847932379)\ **Replies:** 0\ **Last updated:** [September 13, 2026, 1:30pm UTC](https://ask.bioexcel.eu/t/account-not-activated/6255 "2026-09-13T13:30:37Z")
Dear HADDOCK support team, My account is activated by e-mail, but after logging in the portal still reports that it is not activated / restricted to team members, and I cannot submit jobs. Registered e-mail: 847932379… --- ## [Change account email](https://ask.bioexcel.eu/t/change-account-email/6246)
**Author:** [@audreybelinda](https://ask.bioexcel.eu/u/audreybelinda)\ **Replies:** 4\ **Last updated:** [September 8, 2026, 12:23pm UTC](https://ask.bioexcel.eu/t/change-account-email/6246 "2026-09-08T12:23:01Z")
Hello HADDOCK Support Team, I already have a HADDOCK account, and I would like to change the email address associated with my account. Could you please help me update the email address associated with my HADDOCK accoun… --- ## [HADDOCK account has not been activated](https://ask.bioexcel.eu/t/haddock-account-has-not-been-activated/6247)
**Author:** [@Anan](https://ask.bioexcel.eu/u/Anan)\ **Replies:** 1\ **Last updated:** [September 8, 2026, 8:21am UTC](https://ask.bioexcel.eu/t/haddock-account-has-not-been-activated/6247 "2026-09-08T08:21:01Z")
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 … --- ## [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… --- ## [DisVis: Server error](https://ask.bioexcel.eu/t/disvis-server-error/6244)
**Author:** [@lpp1](https://ask.bioexcel.eu/u/lpp1)\ **Replies:** 0\ **Last updated:** [September 3, 2026, 7:41am UTC](https://ask.bioexcel.eu/t/disvis-server-error/6244 "2026-09-03T07:41:16Z")
I have been trying to generate a DisVis output for several weeks now. But every time I submit a job I get an “Internal Server Error” message saying, “The server encountered an internal error and was unable to complete yo… --- ## [HADDOCK account activation](https://ask.bioexcel.eu/t/haddock-account-activation/6243)
**Author:** [@isapargi](https://ask.bioexcel.eu/u/isapargi)\ **Replies:** 5\ **Last updated:** [September 1, 2026, 11:18am UTC](https://ask.bioexcel.eu/t/haddock-account-activation/6243 "2026-09-01T11:18:55Z")
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 … --- ## [Account not activated — urgent request due to limited project timeline](https://ask.bioexcel.eu/t/account-not-activated-urgent-request-due-to-limited-project-timeline/6241)
**Author:** [@ChoiSeoyeon](https://ask.bioexcel.eu/u/ChoiSeoyeon)\ **Replies:** 1\ **Last updated:** [August 29, 2026, 7:40pm UTC](https://ask.bioexcel.eu/t/account-not-activated-urgent-request-due-to-limited-project-timeline/6241 "2026-08-29T19:40:22Z")
Hello, I registered for the HADDOCK2.4 web server with the email address 2xx4x217@inha.edu, but my account still shows the “not activated yet” banner and I am unable to access the service. I am an undergraduate researc… --- ## [HADDOCK3 workflow definition](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628)
**Author:** [@holly](https://ask.bioexcel.eu/u/holly)\ **Replies:** 20\ **Last updated:** [August 29, 2026, 8:18am UTC](https://ask.bioexcel.eu/t/haddock3-workflow-definition/5628 "2026-08-29T08:18:22Z")
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 HAD… --- ## [Small molecule chlorines](https://ask.bioexcel.eu/t/small-molecule-chlorines/4458)
**Author:** [@JHlatt](https://ask.bioexcel.eu/u/JHlatt)\ **Replies:** 3\ **Last updated:** [August 25, 2026, 5:41pm UTC](https://ask.bioexcel.eu/t/small-molecule-chlorines/4458 "2026-08-25T17:41:16Z")
Hi, I’m trying to dock a small molecule that has 2 chlorine atoms within it. Whenever I run webserver the resulting docked small molecule always swaps these chlorines for carbon atoms. I have tried to edit the input pdb … --- ## [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? --- ## [Follow-up on pending GURU access request for HADDOCK2.4](https://ask.bioexcel.eu/t/follow-up-on-pending-guru-access-request-for-haddock2-4/6237)
**Author:** [@Ehsanbm](https://ask.bioexcel.eu/u/Ehsanbm)\ **Replies:** 2\ **Last updated:** [August 24, 2026, 8:43am UTC](https://ask.bioexcel.eu/t/follow-up-on-pending-guru-access-request-for-haddock2-4/6237 "2026-08-24T08:43:11Z")
I recently requested GURU access for my HADDOCK account, but my access level is still shown as EASY. I require GURU access to configure advanced docking parameters, particularly random-patch restraints, for unbiased pro… --- ## [Account not activated](https://ask.bioexcel.eu/t/account-not-activated/6235)
**Author:** [@Mint](https://ask.bioexcel.eu/u/Mint)\ **Replies:** 1\ **Last updated:** [August 19, 2026, 6:02pm UTC](https://ask.bioexcel.eu/t/account-not-activated/6235 "2026-08-19T18:02:15Z")
Dear BonvinLab support, I have registered a HADDOCK account at \[wenmr.science.uu.nl/haddock2.4\]( HADDOCK Web Server ) with my email address 3306468382@qq.com. However, my account remains unactivated up to now. Could you… --- ## [HADDOCK account still pending service activation after email confirmation](https://ask.bioexcel.eu/t/haddock-account-still-pending-service-activation-after-email-confirmation/6233)
**Author:** [@Angleylca](https://ask.bioexcel.eu/u/Angleylca)\ **Replies:** 0\ **Last updated:** [August 19, 2026, 4:30pm UTC](https://ask.bioexcel.eu/t/haddock-account-still-pending-service-activation-after-email-confirmation/6233 "2026-08-19T16:30:18Z")
Dear HADDOCK support team, My registered account email: ngzhang@chimebiologics.com I have finished email confirmation and received the welcome‑active email from BonvinLab. Nevertheless, after logging into the web port… --- ## [PRODIGY Error possible issue with ions?](https://ask.bioexcel.eu/t/prodigy-error-possible-issue-with-ions/6216)
**Author:** [@nyyount](https://ask.bioexcel.eu/u/nyyount)\ **Replies:** 2\ **Last updated:** [August 16, 2026, 11:13pm UTC](https://ask.bioexcel.eu/t/prodigy-error-possible-issue-with-ions/6216 "2026-08-16T23:13:10Z")
Hi I’m getting the following error after submitting several files to PRODIGY. These responses are for the same file. Output not found, please report this error and the id: 1748643 Output not found, please report this… --- ## [Account not activated-DM](https://ask.bioexcel.eu/t/account-not-activated-dm/6227)
**Author:** [@DMMMMM](https://ask.bioexcel.eu/u/DMMMMM)\ **Replies:** 1\ **Last updated:** [August 16, 2026, 6:52am UTC](https://ask.bioexcel.eu/t/account-not-activated-dm/6227 "2026-08-16T06:52:04Z")
Dear HADDOCK team, I registered for a HADDOCK account at wenmr.science.uu.nl/haddock2.4 using the email 3014798539@qq.com but my account has not been activated yet. Could you please activate my account?Thank you very mu… --- ## [Error in generating DISVIS output; job Id 1743432](https://ask.bioexcel.eu/t/error-in-generating-disvis-output-job-id-1743432/6211)
**Author:** [@bharti04](https://ask.bioexcel.eu/u/bharti04)\ **Replies:** 8\ **Last updated:** [August 6, 2026, 9:08am UTC](https://ask.bioexcel.eu/t/error-in-generating-disvis-output-job-id-1743432/6211 "2026-08-06T09:08:43Z")
@honoratorv I tried to run DisVis for my protein. It always showed this error “Output not found, please report this error and the id: 1743432”. --- ## [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? --- ## [Positive HADDOCK score for glycosylated protein–protein docking](https://ask.bioexcel.eu/t/positive-haddock-score-for-glycosylated-protein-protein-docking/5948)
**Author:** [@s.bulut2018](https://ask.bioexcel.eu/u/s.bulut2018)\ **Replies:** 9\ **Last updated:** [August 5, 2026, 1:17pm UTC](https://ask.bioexcel.eu/t/positive-haddock-score-for-glycosylated-protein-protein-docking/5948 "2026-08-05T13:17:53Z")
Hello, I performed protein–protein docking using HADDOCK2.4. My system includes one glycosylated protein (prepared via CHARMM-GUI) and another non-glycosylated protein (antibody). After docking, I noticed that all top c… --- ## [Prodigy webserver not working/loading](https://ask.bioexcel.eu/t/prodigy-webserver-not-working-loading/6223)
**Author:** [@Theomorf](https://ask.bioexcel.eu/u/Theomorf)\ **Replies:** 1\ **Last updated:** [August 5, 2026, 11:15am UTC](https://ask.bioexcel.eu/t/prodigy-webserver-not-working-loading/6223 "2026-08-05T11:15:37Z")
Hello, I have been trying to use the PRODIGY webserver during the last two days, but it does not seem to work. Even the sample data provided on the website are not loading. Could you please let me know if the server is … --- ## [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… [Next page](https://ask.bioexcel.eu/latest.md?page=1)