ligand problem

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    • #34068
      xiaoqing Gong
      Guest

      Hello! I was running autogrow4 on Linux with python 3.7.6 and mgltools. I failed when I was running the tutorial, and an error showed that there was a problem with the ligand file. I used the naphthalene_smiles.smi file of the tutorial.
      Traceback (most recent call last):
      File "RunAutogrow.py", line 675, in <module>
      AutogrowMainExecute.main_execute(vars)
      File "/home/cuda/gx/autogrow4-4.0.3/autogrow4-4.0.3/autogrow/autogrow_main_execute.py", line 83, in main_execute
      smile_file_new_gen, new_gen_ligands_list = operations.populate_generation(vars, current_generation_number)
      File "/home/cuda/gx/autogrow4-4.0.3/autogrow4-4.0.3/autogrow/operators/operations.py", line 75, in populate_generation
      vars, generation_num
      File "/home/cuda/gx/autogrow4-4.0.3/autogrow4-4.0.3/autogrow/operators/operations.py", line 691, in get_complete_list_prev_gen_or_source_compounds
      raise Exception(printout)
      Exception:
      There were no available ligands in previous generation ranked ligand file.
      Check formatting or if file has been moved.

    • #37849
      Jacob Durrant
      Keymaster

      Hi Xiaoqing. Much thanks for your interest in AutoGrow. I suspect you’re getting this error because you are using AutoGrow settings that are too restrictive. AutoGrow appears to be unable to generate any compounds given those settings. It could also be that your initial starting compound(s) do not have any chemical moieties compatible with AutoGrow’s reaction library. This posting could also be helpful: https://durrantlab.pitt.edu/forums/topic/not-creating-ranked-ligand-file-during-lead-optimization-in-generation-0/

      Hope this answer helps. ~Jacob

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