sokrypton / sokrypton/ColabFold
Relax_amber notebook
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- Dominant language
- Jupyter Notebook
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Description
I have been trying to use this notebook to relax some predicted models but the notebook stuck in for hours after the warning that reads " Warning:root: importing 'simtk.openmm' is deprecated. Import 'openmm' instead."
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the Relax_amber notebook and run the relaxation cells until the deprecation warning appears. Identify the cell and output where execution stops, then verify whether relaxation completes for a predicted model without remaining stuck for hours.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100