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
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?
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
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
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).
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!
Thank You.
You was very helpful.
Henrrik