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?

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 server is usually the best choice. Why? That server hosts more o…

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 o…

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 versi…

Thank You. You was very helpful. Henrrik

Galaxy Community Help

GROMACS initial setup

tool-help, gmx_setup, gromacs

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