# GROMACS initial setup **URL:** \ **Category:** Uncategorized\ **Tags:** tool-help, gmx\_setup, gromacs\ **Created:** [October 20, 2024, 11:08pm UTC](https://help.galaxyproject.org/t/gromacs-initial-setup/13725 "2024-10-20T23:08:46Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![henrrik\_prendushi](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/henrrik_prendushi/32/6226_2.png) [@henrrik\_prendushi](https://help.galaxyproject.org/u/henrrik_prendushi)\ **Post date:** [October 20, 2024, 11:08pm UTC](https://help.galaxyproject.org/t/gromacs-initial-setup/13725/1 "2024-10-20T23:08:46Z")
Hi I’m in “GROMACS initial setup of topology and GRO structure file” I have specified the necessary parameters and uploaded my PDB file to the history. It is green. I try to run the app but it says “No pdb datasets available”! Can you help me? ---
**Author:** ![tcollins2011](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/tcollins2011/32/4111_2.png) [@tcollins2011](https://help.galaxyproject.org/u/tcollins2011)\ **Post date:** [October 23, 2024, 6:56pm UTC](https://help.galaxyproject.org/t/gromacs-initial-setup/13725/2 "2024-10-23T18:56:56Z")
Hi @henrrik_prendushi, How did you upload your file? If you let galaxy guess your file’s datatype format what is the result? Does galaxy detect that it is a PDB file or is it recognizing it as something else? Let us know and if you need more help feel free to share your history! If you need help on how to upload your history check out the pinned posts on the top of the forum. Best, Tyler Collins ---
**Author:** ![henrrik\_prendushi](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/henrrik_prendushi/32/6226_2.png) [@henrrik\_prendushi](https://help.galaxyproject.org/u/henrrik_prendushi)\ **Post date:** [October 27, 2024, 3:50pm UTC](https://help.galaxyproject.org/t/gromacs-initial-setup/13725/3 "2024-10-27T15:50:24Z")
Thank you, Tyler. It was my mistake. Now I’m studying the guides. By the way. I’m studying “High Throughput Molecular Dynamics and Analysis” and three times, using the recommended data, I have the results (in my history) in red (Error) for “Generate MD topologies for small molecules ( Galaxy version 21.3+galaxy0)”. I don’t believe that again is my mistake. What do you think? Best Henrrik Prendushi ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [October 28, 2024, 5:36pm UTC](https://help.galaxyproject.org/t/gromacs-initial-setup/13725/4 "2024-10-28T17:36:00Z")
Hi @henrrik_prendushi Glad you sorted out the first part. Now, for the current error, I wondering which server you are working at. I’m also wondering if you tried to use the tutorial example yet. **For these tutorials, the [UseGalaxy.eu](http://UseGalaxy.eu) server is usually the best choice.** Why? That server hosts more of the proteomics tools you will probably want to use later anyway. If you try the introduction tutorial there, does it work? You can just load up the tutorial’s workflow and run it to see what happens since it doesn’t have any inputs to select. This is super quick when I try it. Then you can use that example history when including your own PDB data. The comparison will show what is happening at each step. (this is sort of how we help with troubleshooting too) As a reference, these are the **GROMACS** tutorials, starting with the first tool’s linked tutorials (find these at the bottom of the tool form). - **GROMACS initial setup** : of topology and GRO structure file → [linked tutorials](https://training.galaxyproject.org/training-material/by-tool/chemteam/gmx_setup.html) - And this is the introduction tutorial with the workflow that automatically fetches the example data, and processes it with a single click. → [Hands-on: Running molecular dynamics simulations using GROMACS / Running molecular dynamics simulations using GROMACS / Computational chemistry](https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html) Please give that a try. If you were working somewhere else, please know that having an account at each of the servers is expected and common, and grants you access to the different resources, including more data storage space! 🙂 ---
**Author:** ![henrrik\_prendushi](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/henrrik_prendushi/32/6226_2.png) [@henrrik\_prendushi](https://help.galaxyproject.org/u/henrrik_prendushi)\ **Post date:** [October 29, 2024, 11:17am UTC](https://help.galaxyproject.org/t/gromacs-initial-setup/13725/5 "2024-10-29T11:17:03Z")
Thank You. You was very helpful. Henrrik ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [December 2, 2024, 5:27pm UTC](https://help.galaxyproject.org/t/gromacs-initial-setup/13725/6 "2024-12-02T17:27:33Z")
A post was split to a new topic: [PDB format versus PDQ](https://help.galaxyproject.org/t/pdb-format-versus-pdq/14041) ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [December 2, 2024, 5:27pm UTC](https://help.galaxyproject.org/t/gromacs-initial-setup/13725/7 "2024-12-02T17:27:53Z")