Issue generating ligand

[paul-goldsmith]

Hi, I am running through the tutorial example using PDB: 1OL5 but keep getting an error when clicking "Generate Ligand". All steps up to that point are fine. I have configured and installed everything as in the User Guide.

Traceback (most recent call last):
File "C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\docking_program_gui\tabs.py", line 2183, in generate_ligand_func
generated_ligand = Generate_Object(self, dict = self.docking_programs_child_tabs.docking_programs.vina_ligands_dict,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\Functions\general_docking_func.py", line 284, in init
self.generate_receptor()
File "C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\Functions\general_docking_func.py", line 306, in generate_receptor
self.generate_checked_object()
File "C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\Functions\general_docking_func.py", line 412, in generate_checked_object
os.rename(old_name, new_name)
FileNotFoundError: [WinError 2] The system cannot find the file specified: 'obj01.pdbqt' -> '01_obj01_Vina.pdbqt'

DockingPie

• Version: 1.2.1
• Plugin path: C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main
• Config directory: C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\Lib\site-packages\pmg_tk\startup\DockingPie1\lib\docking_program_main\config

PyMOL

• Version: 2.6.0a0
• Path: C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\pythonw.exe
• Qt: PyQt5
• Has Conda: False

Python

• Version: 3.11.7 | packaged by Anaconda, Inc. | (main, Dec 15 2023, 18:05:47) [MSC v.1916 64 bit (AMD64)]
• Arch: 64
• Path: C:\Users\pgoldsmith\AppData\Local\anaconda3\envs\pymol_311\pythonw.exe

Operating system

• Platform: win32
• Arch: 64

Python libs

• PyQt5: 5.15.10
• Conda version: -
• Numpy version: 1.26.4
• Biopython version: 1.83

[SerenaRosi]

Please double check that the plugin is properly configured for all dependencies in the CONFIGURATION tab.

[paul-goldsmith]

They all appear to be OK, the status by each of them is:
RxDock is not available for this OS
Vina already installed
Smina is not available for this OS
ADFR already installed
Openbabel already installed
sPyRMSD already installed
sdsorter is not available for this OS

[paul-goldsmith]

I get the error for generating ligands in both Vina and ADFR tabs

[SerenaRosi]

We have recently become aware of unexpected issues reported by multiple users, which we believe may be stemming from recent updates to PyMOL and/or other external libraries. These issues were not encountered previously and are likely a result of incompatibilities introduced by these updates. As a result, we have temporarily placed DockingPie under maintenance mode while we work diligently to resolve these issues. Once these issues are resolved, we will promptly update our GitHub page to inform users of the fixes and any necessary instructions. Thank you for your understanding and cooperation during this period.

Best,
Serena

[paiardin]

We have just released an updated version of DockingPie, which should fix this issue.