GROMACS Solvation Step High Throughput Molecular Dynamics and AnalysisTutorial

[liz_wright]

I am getting an error message when I run the GROMACS solvation step for the tutorial on High Throughput Molecular Dynamics and Analysis. The log file for this step indicates that the error is Fatal error:
number of coordinates in coordinate file (solv.gro, 1988)
does not match topology (./top_input.top, 5237)

Here is my history for the tutorial Galaxy

Any help is appreciated.

[jennaj]

Welcome @liz_wright

Thanks for sharing the history! It looks like the inputs were a bit mixed up in an upstream tool.

Reviewing the job details using the i-icon (or navigating to this view from most of the other icons!) is how to see all the inputs and parameters in a small table view.

The repeated structure file was only for the ligand, so the full TOP file isn’t a match.

I have a version of the tutorial workflow modified to accept an input file from the history (instead of the PDB term query). Maybe useful? You can get a copy and modify it too!

• https://usegalaxy.org/u/jen-galaxyproject/w/gromacs-training-worklow----modified-for-general-custom-input

Hope this helps!

[liz_wright]

Thanks I managed to fix it starting from scratch