# Troubleshooting Generate MD topologies for small molecules **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** tool-help, gromacs, ambertools\_acpype\ **Created:** [October 29, 2024, 11:26am UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780 "2024-10-29T11:26:30Z")\ **Posts on this page:** 9\ **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 29, 2024, 11:26am UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780/1 "2024-10-29T11:26:30Z")
Dear Friends I’m studying “High Throughput Molecular Dynamics and Analysis,” and several 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).” ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/3639503a2a798ed8638d9a0fa08c05df85f27b97.png) I appreciate any help from You. 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 29, 2024, 5:53pm UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780/2 "2024-10-29T17:53:09Z")
Xref: [GROMACS initial setup - #4 by jennaj](https://help.galaxyproject.org/t/gromacs-initial-setup/13725/4) Hi @henrrik_prendushi Did the tutorial work? Just curious! 🙂 Then, if you need more help, please share back your history so we can check if this is a server problem, or something with your data itself. The most common reason for errors with this tool is missing annotation inside the PDB and the logs will note that, but it is a bit complicated, and we can try to help to diagnose that. How to share is in the banner at this forum, or see here directly → [How to get faster help with your question](https://help.galaxyproject.org/docs?topic=11469). A shared history link is best for this since we’ll need access to all of the job logs, and that is difficult to capture with screenshots. But you decide how quickly you want this to be resolved. Thanks! 🙂 ---
**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 30, 2024, 8:00am UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780/3 "2024-10-30T08:00:32Z")
First of all, thank you very much. The guide is very interesting and instructive but I believe there are problems with the app. This is the link to my History [https://usegalaxy.eu/u/henrrik/h/high-prova](https://usegalaxy.eu/u/henrrik/h/high-prova) 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:** [October 30, 2024, 5:51pm UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780/4 "2024-10-30T17:51:54Z")
Ok, thanks for posting back your history. The input file to the tool you are asking about what empty. This is a screenshot from the job information view [using the i-icon](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_icons.html) on the failed red dataset. This is always the place to check how the job was run, even if successful and you just forgot what parameters were used or whatever. ![Screen Shot 2024-10-30 at 10.43.41 AM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/f/fac386533d94c0f008bffef9a1a2047b270631e6.png) Then, if I look at the jobs that generated that input, it seems the problem was introduced at the start. This is what I was talking about in the other topic about the most common problem being missing annotation in the original PDB file. I think that is what is going on with your problem, too. More screenshots, this time just of the history share link to show the status of the files along the chain. Notice how dataset 3 is empty. ![Screen Shot 2024-10-30 at 10.47.38 AM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/9/97511bfea21c45d098ba34708bdb33390fca0dab.png) ![Screen Shot 2024-10-30 at 10.49.18 AM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/35cbf820d2deb59bddb0c4cec8d4e6ca8d4a44cf.png) For a comparison, I started up that simple training workflow. It is still chomping through the data, so give it time to complete. - [https://usegalaxy.eu/u/jenj/h/gromacs-training-workflow-1](https://usegalaxy.eu/u/jenj/h/gromacs-training-workflow-1) Hope this helps! 🙂 ---
**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:** [November 1, 2024, 8:51am UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780/5 "2024-11-01T08:51:03Z")
Thank you very much. Now, I will try “High Throughput Molecular Dynamics and Analysis” again. Henrrik ---
**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:** [November 1, 2024, 10:05am UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780/6 "2024-11-01T10:05:43Z")
Dear Jennaj I tried several times, with different parameter combinations, to extract the ligand file from the shared history. I haven’t had any success. It seems that the system does not recognize just AGSE or BGSE. It extracts HETATM (a mixing of AGSE, BGSE, and other HETATM). I believe I need just the ligand A (AGSE) or the ligand B (BGSE). Can you help me? Thank you 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:** [November 4, 2024, 6:48pm UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780/7 "2024-11-04T18:48:56Z")
> [@henrrik\_prendushi](#): > > HETATM Hi @henrrik_prendushi The first step in the protocol is _excluding_ HETATM specifically. You can customize what you want to review with the options on the form. Also keep in mind: tools available in the Galaxy website are still the original tool, exactly how the original authors wrote them. If the underlying tool cannot process a certain type of data, then that same tool as available in Galaxy cannot process it. Now, I don’t think that is what is going on with your data (yet). I do see that your history is now private, and that you have run the first step several times. For now I’ll just say – compare to the tutorial example and notice the “Don’t Match” option set at the very top. That means that if found, that line is not printed out into the output. You will need to customize what to keep and what to exclude to fit your own data: use the terms in your PDB to guide what to input on the form. If you have a term that you are not sure how to format for the perl regex, we can probably help, but will need to see those specific lines here and what your expression looks like now. Thanks! 🧑‍🔬 ---
**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:** [November 7, 2024, 5:31pm UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780/8 "2024-11-07T17:31:02Z")
Thank You I solved the problem. You were very clear. 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:** [April 8, 2026, 1:00am UTC](https://help.galaxyproject.org/t/troubleshooting-generate-md-topologies-for-small-molecules/13780/9 "2026-04-08T01:00:59Z")
Closed on April 8, 2026, 1:00am UTC