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dptech-corp / Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program
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ERROR：Empty ligland list #6

Closed Ljs1016 closed 1 year ago

Ljs1016 commented 1 year ago

My ligands.index have some records, but when I run the command "./unidock --receptor Uni-Dock/example/screening_test/indata/def.pdbqt --ligand_index def_ligands.index --center_x -36.01 --center_y 25.63 --center_z 67.49 --size_x 17.20 --size_y 14.38 --size_z 12.24 --scoring vinardo --refine_step 3 --num_modes 1 --seed 5 --search_mode fast --dir results/def-fast " Then will have some erros “ERROR：Empty ligland list”

pkuyyj commented 1 year ago

Please check your ligand file and make sure the paths are correct. If ligand parsing fails, this error can happen.

Zehui7Zhou commented 1 year ago

I also came across this error "ERROR：Empty ligland list" when I ran the example codes:

cp config_def.json config.json python run_dock.py

pkuyyj commented 1 year ago

The global memory of the GPU should be larger than about 8GB, otherwise the ligands cannot be processed.