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dptech-corp / Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program
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Unidock seems to be not progressing. #59

Open majumderS opened 10 months ago

majumderS commented 10 months ago

Hi I have run unidock before using the run_dock.py script, it successfully ran. But it has not been running since after that. I have checked the path of unidock : /usr/local/unidock/unidock and checked path of receptor and ligands as well. It just stops at the following screen even for 4-5 ligands.

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/usr/local/unidock/unidock --receptor ./test_files/2eh9.pdbqt --ligand_index def_ligands2.txt --center_x 4.48 --center_y -2.42 --center_z 2.14 --size_x 22 --size_y 22 --size_z 22 --dir ./result2/2eh9 --exhaustiveness 200 --max_step 40 --num_modes 10 --scoring vina --refine_step 3 --seed 5

majumderS commented 10 months ago

GPU hows at 100% . Any help would be appreciated.

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ysyecust commented 10 months ago

Hi I have run unidock before using the run_dock.py script, it successfully ran. But it has not been running since after that. I have checked the path of unidock : /usr/local/unidock/unidock and checked path of receptor and ligands as well. It just stops at the following screen even for 4-5 ligands.

image

/usr/local/unidock/unidock --receptor ./test_files/2eh9.pdbqt --ligand_index def_ligands2.txt --center_x 4.48 --center_y -2.42 --center_z 2.14 --size_x 22 --size_y 22 --size_z 22 --dir ./result2/2eh9 --exhaustiveness 200 --max_step 40 --num_modes 10 --scoring vina --refine_step 3 --seed 5

If the number of exhaustiveness is reduced, for example, set to 128, 64. Can the process be completed successfully?

majumderS commented 10 months ago

No, it didnt run successfully. It's stuck for one ligand also at Performing docking (random seed: 5) ...

ysyecust commented 9 months ago

@majumderS We have updated the code. You can try again. If it still fails, is it convenient to provide the failed source file?