dptech-corp / Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program
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Fail to run docking #14

Open Venthaul opened 1 year ago

Venthaul commented 1 year ago

Here is the docking setup and report: GPU: RTX3090 CUDA Version: 11.7 Driver Version: 515.57

receptor = protein.pdbqt gpu_batch = lig765.pdbqt out = lig765_result.pdbqt center_x = 87.603 center_y = 89.271 center_z = 128.509 size_x = 30 size_y = 30 size_z = 30 search_mode = fast num_modes = 1 dir = .


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: protein.pdbqt Grid center: X 87.603 Y 89.271 Z 128.509 Grid size : X 30 Y 30 Z 30 Grid space : 0.375 Exhaustiveness: 128 CPU: 0 Verbosity: 1

Computing Vina grid ... entering done done. exiting done Total ligands: 1 Avaliable Memory = 24004MiB Total Memory = 24268MiB Batch 1 size: 1 Performing docking (random seed: -782310420) ... Segmentation fault (core dumped)

caic99 commented 1 year ago

Hi @VenthaulZI , Would you provide the core dump file and the input files for us to debug? Thanks.