Question: example code for setting up MD simulation of protein-ligand complexes

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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Question: example code for setting up MD simulation of protein-ligand complexes #135

Closed mganahl closed 1 year ago

mganahl commented 1 year ago

Hi! Thanks for the great work here!

I'm be interested in running an MD simulation of a protein-ligand complex, using espaloma for the ligand FF and a standard FF for the protein (e.g. one of the amber ff). Is there any example code to help me get started? (I'm a newcomer to the field :)!).

Thanks!

yuanqing-wang commented 1 year ago

Hi @mganahl

Sorry for the delayed response. We are using OpenMMForceFields https://github.com/openmm/openmmforcefields to assign parameters to different regions of protein-ligand complex.