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pengxingang / Pocket2Mol

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
MIT License
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Issues about the vina score #7

Closed Layne-Huang closed 1 year ago

Layne-Huang commented 1 year ago

Hi,

I have used your vina score script "docking.py" recently. However, I have met the following error,

Traceback (most recent call last): File "/sample_geo.py", line 519, in g_vina_score = vina_task.run_sync() File "/evaluation/docking.py", line 168, in run_sync while self.get_results() is None: File "/evaluation/docking.py", line 182, in get_results self.results = parse_qvina_outputs(self.docked_sdf_path) File "/evaluation/docking.py", line 24, in parse_qvina_outputs suppl = Chem.SDMolSupplier(docked_sdf_path) OSError: File error: Invalid input file /tmp/olzbpempbkdjotcpxfbqvwjfnxltvc_ligand_out.sdf

I found that error was caused by the missing script “prepare_receptor4.py ”.

Could you please help me solve it or provide this script?

Thank you for your attention.

pengxingang commented 1 year ago

Hi, to use docking.py you should install conda environment defined in adt.yml. When you installed the environment, the prepare_receptor4.py file were automatically installed. You can check whether you have successfully installed the environment by directly tapping prepare_receptor4.py and qvina2 in the terminal .