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OptiMaL-PSE-Lab / DeepDock

Code related to : O. Mendez-Lucio, M. Ahmad, E.A. del Rio-Chanona, J.K. Wegner, A Geometric Deep Learning Approach to Predict Binding Conformations of Bioactive Molecules
MIT License
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Error when using another Ligand #12

Open nohandsomewujun opened 2 years ago

nohandsomewujun commented 2 years ago

I tried to use different ligands to dock with the proteins in the repo .According to the files in your examples, when I tried to dock with 2br1_protein.pdb and 2wtv_protein.pdb, it worked .But when I tried to dock with 1z6e_protein.pdb, it failed. And error msg:

Traceback (most recent call last):
  File "test.py", line 7, in <module>
    compute_inp_surface(target_filename, ligand_filename, dist_threshold=10)
  File "/DeepDock/deepdock/prepare_target/computeTargetMesh.py", line 70, in compute_inp_surface
    structure = structures[0] # 'structures' may contain several proteins in this case only one.
  File "/opt/conda/lib/python3.6/site-packages/Bio/PDB/Entity.py", line 45, in __getitem__
    return self.child_dict[id]
KeyError: 0

It seems like something wrong when generating 1z6e_protein_15A.pdb. And my Ligand file: new1.mol2.zip Thank you!

Chemwzd commented 1 year ago

I got the seem message when I tried to dock new ligand, have you solve this error yet?

nohandsomewujun commented 1 year ago

I got the seem message when I tried to dock new ligand, have you solve this error yet?

Well, I didn't solve the problem and go looking for a new tool.