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mims-harvard / TDC

Therapeutics Commons (TDC-2): Multimodal Foundation for Therapeutic Science
https://tdcommons.ai
MIT License
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About dock：How long does the preparation phase of adding gasteiger charges to peptide take? #200

Open viko-3 opened 1 year ago

viko-3 commented 1 year ago

Thanks to the authors for their excellent work.

image

Is it normal to go on for a long time at this step?

futianfan commented 1 year ago

do you mean to download the oracle? download oracle does not take too much time. or do you mean docking a ligand? docking a ligand requires a couple of minutes mostly, the time also relies on the size of the ligand you dock.

viko-3 commented 1 year ago

do you mean to download the oracle? download oracle does not take too much time. or do you mean docking a ligand? docking a ligand requires a couple of minutes mostly, the time also relies on the size of the ligand you dock.

On the screenshot I provided, I'm just loading the oracal provided in the documentation for dock a ligand. but it still stuck at this step. And, if I use my own protein pdb file to initialize the oracle, it still keep this situation.