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choderalab / espaloma

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196
https://docs.espaloma.org/en/latest/
MIT License
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Deployment of espaloma-0.3 for a protein-ligand system #212

Open OleinikovasV opened 3 months ago

OleinikovasV commented 3 months ago

Hi! Looking at the blogpost here (Applications - at the end): https://openforcefield.org/community/news/science-updates/espaloma-03/

Seems like there is a possibility to deploy espaloma force-field assignment to the biomolecules, eg. proteins - as given in the example. However, I cannot find examples of how to do deploy that for the protein system. Is it done identically, i.e. reading a protein from a file as a small-molecule graph, or is there another procedure?

Thanks for the help! Super excited to try it!

ijpulidos commented 3 months ago

Hello!

I way to do this could be adjusted from the work in https://github.com/choderalab/vanilla-espaloma-experiment/blob/main/experiment/script/create_system.py , which requires OpenEye as far as I can tell. It is possible to refactor this code to use RDkit instead, but we don't have a sample script with it. I hope this helps answering the questions, please let us know if you encounter any other blockers.