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luwei0917 / DynamicBind

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
MIT License
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LM embeddings for complex did not have the right length for the protein #38

Open liyue9129 opened 1 week ago

liyue9129 commented 1 week ago

Hi ! Great work ! I have encountered several issues during the docking process. And I am seeking to determine whether the issue originate from the protein structure or the ESM employed, and to pinpoint the exact nature of the problem. LM embeddings for complex did not have the right length for the protein

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Thank you ! best wishes!

patjiang commented 6 days ago

Hello! Rather than a screenshot of the code itself, could you also provide the associated stderr output? That is, if the code generates a print statement or a .out file, could you please show that as well?

From what I've seen with working in this package, I think this should not be an endemic issue, rather, this might happen sometimes in the "pseudo-dynamics" timesteps of the model-- that being said, I do believe that this issue might be moreso due to the structure rather than the esm embeddings. I hope this helps!