How to fix error output of gromacs solvation and adding ions?
Welcome, @SALSABILA_AQILAPUTRI
We have a tutorial that you can follow to learn how these tools work. Once you complete the tutorial, you can compare your custom input to the example data, and using that context, you will probably be able to learn what may be going wrong so that you can make adjustments.
The most common issue is the original PDB file missing the annotation that these tools need. You can learn if that is the problem by reviewing the job logs from the tool. The logs can be found by using the i-icon in any dataset output from a tool. This includes both successful and failed results.
Tutorial
Try running the workflow inside the tutorial to create your “answer key” example. Everything is contained in that workflow, so just create a new history, give it a unique name, then load up the workflow and run it. Do this at UseGalaxy.eu, since the older tool versions in the workflow will fail at UseGalaxy.org.
Then, once you understand the processing, you can swap in your own PDB and process the data at either server – just be sure to use the most current tool versions when working at UseGalaxy.org. Or, you can work at UseGalaxy.eu with the tutorial workflow and your own data.
Hope this helps, and if you get stuck, you can come back and we can try to help more. How to share your work is in the banner at this forum, and also here. → How to get faster help with your question
Thanks! 