Error: could not open "" for reading.

[yanze039]

Scripts:

Unidock --receptor 1ipb_protein_only.pdbqt \
        --ligand_index ligands.idx \
        --reference ligands/M7G.sdf \
        --scoring vina \
        --center_x 10.671 \
        --center_y -73  \
        --center_z 22.  \
        --size_x 20  \
        --size_y 20 \
        --size_z 20 \
        --search_mode balance  \
        --dir results

Output:

.....
.....
ligand output_15345 preperation successful
ligand output_15295 preperation successful
ligand output_15347 preperation successful
ligand output_15322 preperation successful
ligand output_15343 preperation successful
ligand output_15352 preperation successful
ligand output_15320 preperation successful
ligand output_15296 preperation successful
ligand output_15301 preperation successful
ligand output_15346 preperation successful
ligand output_15353 preperation successful
ligand output_15310 preperation successful
15335 sdf format ligands have been prepared successfully in total 15354
command_ligand:  --ligand_index results/ligands.dat
command: unidock --scoring  vina --ligand_index results/ligands.dat --receptor 1ipb_protein_only.pdbqt --center_x 10.671 --center_y -73.0 --center_z 22.0 --size_x 20.0 --size_y 20.0 --size_z 20.0 --dir results --cpu 0 --seed 0 --num_modes 9 --min_rmsd 1 --energy_range 3 --spacing 0.375 --verbosity 1 --max_step 0 --refine_step 5 --max_gpu_memory 0 --search_mode balance --multi_bias
Uni-Dock v0.1.0

If you used Uni-Dock in your work, please cite:               

Yu, Y., Cai, C., Wang, J., Bo, Z., Zhu, Z., & Zheng, H. (2023). 
Uni-Dock: GPU-Accelerated Docking Enables Ultralarge Virtual Screening. 
Journal of Chemical Theory and Computation.                    
https://doi.org/10.1021/acs.jctc.2c01145                       

Tang, S., Chen, R., Lin, M., Lin, Q., Zhu, Y., Ding, J., ... & Wu, J. (2022). 
Accelerating autodock vina with gpus. Molecules, 27(9), 3041. 
DOI 10.3390/molecules27093041                                 

J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli  
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force      
Field, and Python Bindings, J. Chem. Inf. Model. (2021)       
DOI 10.1021/acs.jcim.1c00203                                  

O. Trott, A. J. Olson,                                        
AutoDock Vina: improving the speed and accuracy of docking    
with a new scoring function, efficient optimization and        
multithreading, J. Comp. Chem. (2010)                         
DOI 10.1002/jcc.21334                                         

Please refer to https://github.com/dptech-corp/Uni-Dock/ for  
bug reporting, license agreements, and more information.      

Scoring function : vina
Rigid receptor: 1ipb_protein_only.pdbqt
Grid center: X 10.671 Y -73 Z 22
Grid size  : X 20 Y 20 Z 20
Grid space : 0.375
Exhaustiveness: 384
CPU: 0
Verbosity: 1

Computing Vina grid ... done.
Total ligands: 15335
Avaliable Memory = 32188MiB   Total Memory = 32500MiB
Batch 1 size: 116

Error: could not open "" for reading.

[pkuyyj]

@YNYuan Maybe the output of unidock_tools is "" which causes the failure of reading in unidock?

[yanze039]

how to exaimine the output of unidock_tools?

[pkuyyj]

@YNYuan Maybe the output of unidock_tools is "" which causes the failure of reading in unidock?

Sorry, I found that multi_bias option is on. The bias file is not generated I suppose.