# \#community **URL:** https://ask.bioexcel.eu/tag/community/10.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [Troubleshooting prodigy results](https://ask.bioexcel.eu/t/troubleshooting-prodigy-results/6184)
**Author:** [@philipeh](https://ask.bioexcel.eu/u/philipeh)\ **Replies:** 1\ **Last updated:** [July 1, 2026, 1:33pm UTC](https://ask.bioexcel.eu/t/troubleshooting-prodigy-results/6184 "2026-07-01T13:33:07Z")
Hello Everyone, I’ve issue. When I analyse the results of my docking with GRAMM-X in PRODIGY to study the molecular interactions, the tool tells me that no contact has been detected. However, visualisation with PyMOL … --- ## [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… --- ## [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… --- ## [Threshold value](https://ask.bioexcel.eu/t/threshold-value/6042)
**Author:** [@itsPriyanka](https://ask.bioexcel.eu/u/itsPriyanka)\ **Replies:** 3\ **Last updated:** [March 19, 2026, 11:27am UTC](https://ask.bioexcel.eu/t/threshold-value/6042 "2026-03-19T11:27:10Z")
I have done the HADDOCK docking. I am getting the results for Cluster 1. HADDOCK score -100.5 +/- 2.7 Cluster size 62 RMSD from the overall lowest-energy structure 1.… --- ## [NVT vs NPT for Non-Equilibrium Switching in pmx/GROMACS](https://ask.bioexcel.eu/t/nvt-vs-npt-for-non-equilibrium-switching-in-pmx-gromacs/5980)
**Author:** [@EidRashed](https://ask.bioexcel.eu/u/EidRashed)\ **Replies:** 1\ **Last updated:** [January 26, 2026, 11:19am UTC](https://ask.bioexcel.eu/t/nvt-vs-npt-for-non-equilibrium-switching-in-pmx-gromacs/5980 "2026-01-26T11:19:35Z")
I’m using pmx + GROMACS to run non-equilibrium alchemical free energy calculations for large protein–protein interactions (e.g., ~150 k atoms, like Fc–FcRn). My workflow is essentially: Equilibrate both end states (st… --- ## [Binding affinity and Kd prediction](https://ask.bioexcel.eu/t/binding-affinity-and-kd-prediction/5930)
**Author:** [@Hadeeqa](https://ask.bioexcel.eu/u/Hadeeqa)\ **Replies:** 1\ **Last updated:** [November 3, 2025, 4:54pm UTC](https://ask.bioexcel.eu/t/binding-affinity-and-kd-prediction/5930 "2025-11-03T16:54:51Z")
Hi, I am trying to find binding affinity for two of my proteins. The file is okay, the run was successful. However the message I got is ‘\[+\] Executing 1 task(s) in total Error processing model: No contacts found for sel… --- ## [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… --- ## [Cannot select both chains of MHC II complex for docking](https://ask.bioexcel.eu/t/cannot-select-both-chains-of-mhc-ii-complex-for-docking/5558)
**Author:** [@sauda07](https://ask.bioexcel.eu/u/sauda07)\ **Replies:** 1\ **Last updated:** [April 2, 2025, 7:19am UTC](https://ask.bioexcel.eu/t/cannot-select-both-chains-of-mhc-ii-complex-for-docking/5558 "2025-04-02T07:19:09Z")
Hello, I want to dock peptide with mhcii complex with both chains, ie. A and B but after uploading the pdb file in haddock webserver, How do I involve both chains for docking? Thanks!! --- ## [Disassociation of synthetic amino acid after docking](https://ask.bioexcel.eu/t/disassociation-of-synthetic-amino-acid-after-docking/5557)
**Author:** [@sauda07](https://ask.bioexcel.eu/u/sauda07)\ **Replies:** 1\ **Last updated:** [April 2, 2025, 7:18am UTC](https://ask.bioexcel.eu/t/disassociation-of-synthetic-amino-acid-after-docking/5557 "2025-04-02T07:18:04Z")
Hi, I ran a protein-peptide docking in Haddock webserver, In result the synthetic amino acid showing disassociation with the peptide . Can I know the reason and how do I solve this problem? Thanks! --- ## [PMX Ligand Preparation from Scratch - Atom Types and Parameter Discrepancies](https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429)
**Author:** [@jinurajkr](https://ask.bioexcel.eu/u/jinurajkr)\ **Replies:** 2\ **Last updated:** [February 28, 2025, 11:49am UTC](https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429 "2025-02-28T11:49:21Z")
Dear All We are writing to you regarding the preparation of ligands from scratch for running in PMX. We obtained the SDF file for the ligand from the following reference: \[https://pubs.acs.org/doi/10.1021/ja512751q\] Ou… --- ## [2 Protein-1 DNA Docking](https://ask.bioexcel.eu/t/2-protein-1-dna-docking/5389)
**Author:** [@pranav0903](https://ask.bioexcel.eu/u/pranav0903)\ **Replies:** 1\ **Last updated:** [January 2, 2025, 10:34am UTC](https://ask.bioexcel.eu/t/2-protein-1-dna-docking/5389 "2025-01-02T10:34:19Z")
I went through the basic Protein-DNA tutorial on HADDOCK2.4 website and followed all the steps. I applied symmetry restraints too. I did not apply any ambiguous or unambiguous restraints as I specified the active resid… --- ## [Protein and cell membrane docking](https://ask.bioexcel.eu/t/protein-and-cell-membrane-docking/5379)
**Author:** [@xander](https://ask.bioexcel.eu/u/xander)\ **Replies:** 2\ **Last updated:** [December 26, 2024, 10:38am UTC](https://ask.bioexcel.eu/t/protein-and-cell-membrane-docking/5379 "2024-12-26T10:38:26Z")
I have anti-microbial peptide structure, and then i obtained a fungal membrane structure for a particular database, i want to perform docking between the anti-microbial peptide, as a ligand, and then the membrane as a re… --- ## [How to add body restraints in haddock3?](https://ask.bioexcel.eu/t/how-to-add-body-restraints-in-haddock3/5180)
**Author:** [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\ **Replies:** 0\ **Last updated:** [July 8, 2024, 10:24am UTC](https://ask.bioexcel.eu/t/how-to-add-body-restraints-in-haddock3/5180 "2024-07-08T10:24:31Z")
This question and answers are detailed in our haddock3 git hub repo (issues 923) --- ## [Example for General Feedback](https://ask.bioexcel.eu/t/example-for-general-feedback/5177)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [July 5, 2024, 1:22pm UTC](https://ask.bioexcel.eu/t/example-for-general-feedback/5177 "2024-07-05T13:22:37Z")
Topic: Feedback for BioExcel activities Feedback: Write your ideas for new or better tutorials, workshops and webinars, how to better engage with the community. Login to post, select the sub-category general feedback, …