sokrypton / sokrypton/ColabFold
Amber relaxation of already predicted structure in local
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- Jupyter Notebook
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Description
Is there an available script to relax already predicted structure on our HPC? i tried to transfer the code of the notebook https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/relax_amber.ipynb#scrollTo=PCvpws3iNmFc
but i received error for the location of the modules.
I need this script because if I use amber on GPU I get always errors, and if I use CPU is to slow using only the cores dedicated to GPU on our system and therefore i want to do the relaxation step separately.
thank you
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 beta/relax_amber.ipynb from the linked ColabFold notebook and compare its module locations with the HPC environment. The work is complete when the relaxation step can be run separately on the HPC without the reported module-location errors.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics, hpc
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100