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 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
- 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
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! 