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carbonsilicon-ai / CarsiDock

Official repo of "CarsiDock: a deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training" proposed by CarbonSilicon AI.
http://dx.doi.org/10.1039/D3SC05552C
Apache License 2.0
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Run failed to compute RMSD. Very little info to debug. #9

Open agarrubio opened 4 months ago

agarrubio commented 4 months ago

The test command works:

docker run --gpus all --shm-size=2g  -v /home/alejandro/CarsiDock:/Docking carsidock:v1 python /Docking/run_docking_inference.py --pdb_file example_data/4YKQ_hsp90_40_water.pdb --sdf_file example_data/4YKQ_hsp90_40.sdf --cuda_convert

But my command fails:

docker run --gpus all --shm-size=2g  -v /home/alejandro/CarsiDock:/Docking carsidock:v1 python /Docking/run_docking_inference.py --pdb_file input/rec7_4.pdb --sdf_file input/rec7_4.sdf --cuda_convert

The only output is:

@> 2886 atoms and 1 coordinate set(s) were parsed in 0.02s.
read data...
docking...0
fail to compute rmsd
rmsd: None

Both my pdb and sdf work well with gnina and DiffDock. These are here https://drive.google.com/drive/folders/1AOjhhStJ_QN8U5aGyi-i0bfwRaKpfJiN?usp=drive_link

Can you help me to debug this? Many thanks!

gitabtion commented 3 months ago

It means the docking has failed. Like custom docking methods, there are a few cases of docking failures in CarsiDock. Currently, there is no solution available, but based on our analysis, the ligands that fail to dock have a low probability of being active.

agarrubio commented 3 months ago

Many thanks!