# \#tutorials **URL:** https://ask.bioexcel.eu/tag/tutorials/9.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 … --- ## [HADDOCK3 User Manual issue](https://ask.bioexcel.eu/t/haddock3-user-manual-issue/6072)
**Author:** [@F-Mars](https://ask.bioexcel.eu/u/F-Mars)\ **Replies:** 3\ **Last updated:** [April 14, 2026, 1:05pm UTC](https://ask.bioexcel.eu/t/haddock3-user-manual-issue/6072 "2026-04-14T13:05:26Z")
In the haddock3 manual, in 8.7. Complexes refinement protocols, the openMM simulation\_timesteps is set to 5000000; however, when trying this, an error: Value “5000000” is not in the allowed boundaries ranging from 0 to 1… --- ## [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.… --- ## [About the pair to active/passive selection set numbers](https://ask.bioexcel.eu/t/about-the-pair-to-active-passive-selection-set-numbers/5769)
**Author:** [@yashika](https://ask.bioexcel.eu/u/yashika)\ **Replies:** 1\ **Last updated:** [August 12, 2025, 1:07pm UTC](https://ask.bioexcel.eu/t/about-the-pair-to-active-passive-selection-set-numbers/5769 "2025-08-12T13:07:56Z")
I want to dock 2 siRNAs with single protein one at position near 184 and other near 440 but in active/passive selection set numbers box i am facing problem. In pair to active/passive selection set number box of molecule … --- ## [Why it is not accepting the specified active/passive residues?](https://ask.bioexcel.eu/t/why-it-is-not-accepting-the-specified-active-passive-residues/5793)
**Author:** [@JoseAcuna](https://ask.bioexcel.eu/u/JoseAcuna)\ **Replies:** 0\ **Last updated:** [July 9, 2025, 9:23pm UTC](https://ask.bioexcel.eu/t/why-it-is-not-accepting-the-specified-active-passive-residues/5793 "2025-07-09T21:23:44Z")
Hi there, I am trying to dock 4 same beta subunits to a transmembrane protein complex (integrated by 4 alfa subunits). I upload these 5 files and fill out the required data, including the active/passive residues which a… --- ## [Protein-protein docking parameters](https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776)
**Author:** [@Negin](https://ask.bioexcel.eu/u/Negin)\ **Replies:** 2\ **Last updated:** [July 1, 2025, 9:48am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776 "2025-07-01T09:48:29Z")
Hello I would like to perform protein-protein docking, and I do not have any experimental data showing how they are interacting and what is the binding interface of them. But, I used PesTo webserver and other online too… --- ## [Variability between HADDOCK runs for protein–DNA docking (wild-type vs mutant comparison)](https://ask.bioexcel.eu/t/variability-between-haddock-runs-for-protein-dna-docking-wild-type-vs-mutant-comparison/5645)
**Author:** [@EPIGENOME](https://ask.bioexcel.eu/u/EPIGENOME)\ **Replies:** 5\ **Last updated:** [May 5, 2025, 11:41am UTC](https://ask.bioexcel.eu/t/variability-between-haddock-runs-for-protein-dna-docking-wild-type-vs-mutant-comparison/5645 "2025-05-05T11:41:05Z")
Hello everyone, I’m currently working on a protein–DNA docking study comparing the wild-type and mutant forms of the same protein. To perform this, I’m using HADDOCK2.4 (web server). The DNA structure used in the docki… --- ## [Failure to write antibody-antigen-ambig.tbl](https://ask.bioexcel.eu/t/failure-to-write-antibody-antigen-ambig-tbl/5564)
**Author:** [@valerio](https://ask.bioexcel.eu/u/valerio)\ **Replies:** 8\ **Last updated:** [April 10, 2025, 9:20am UTC](https://ask.bioexcel.eu/t/failure-to-write-antibody-antigen-ambig-tbl/5564 "2025-04-10T09:20:59Z")
Dear Developer, I am using a local version of Haddock2.4 and following the ab-antigen tutorial where the paratope is known and the epitope is not.(Tutorial describing the use of a local version of HADDOCK2.4 – Bonvin La… --- ## [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… --- ## [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, …