cannot run toturial

  • This topic has 5 replies, 1 voice, and was last updated 5 months ago by Wenchang.
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    • #59614 Reply
      Wenchang
      Guest

      Hi,

      Thank you so much for sharing autogrow4 which is super fun to play with, I could follow all the installation guide but got the error when I run the tutorial Can you take a look and guide me from their? Thanks!

      The error is here,
      autogrow4/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/dimorphite_dl/dimorphite_dl.py:744: SyntaxWarning: "is not" with a literal. Did you mean "!="?
      if line is not "":
      Traceback (most recent call last):
      File "autogrow4/RunAutogrow.py", line 675, in <module>
      AutogrowMainExecute.main_execute(vars)
      File "autogrow4/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 "autogrow4/autogrow/operators/operations.py", line 74, in populate_generation
      source_compounds_list = get_complete_list_prev_gen_or_source_compounds(
      File "autogrow4/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.

      the command I used is:
      python RunAutogrow.py \
      –filename_of_receptor ./autogrow4/tutorial/PARP/4r6eA_PARP1_prepared.pdb \
      –center_x -70.76 –center_y 21.82 –center_z 28.33 \
      –size_x 25.0 –size_y 16.0 –size_z 25.0 \
      –source_compound_file ./autogrow4/source_compounds/naphthalene_smiles.smi \
      –root_output_folder . \
      –number_of_mutants_first_generation 50 \
      –number_of_crossovers_first_generation 50 \
      –number_of_mutants 50 \
      –number_of_crossovers 50 \
      –top_mols_to_seed_next_generation 50 \
      –number_elitism_advance_from_previous_gen 50 \
      –number_elitism_advance_from_previous_gen_first_generation 10 \
      –diversity_mols_to_seed_first_generation 10 \
      –diversity_seed_depreciation_per_gen 10 \
      –num_generations 5 \
      –mgltools_directory ./mgltools_x86_64Linux2_1.5.7/ \
      –number_of_processors -1 \
      –scoring_choice VINA \
      –LipinskiLenientFilter \
      –start_a_new_run \
      –rxn_library robust_rxns \
      –selector_choice Rank_Selector \
      –dock_choice VinaDocking \
      –max_variants_per_compound 5 \
      –redock_elite_from_previous_gen False \
      –generate_plot True \
      –reduce_files_sizes True \
      –use_docked_source_compounds True \
      > test_file.txt 2> test_errormessage_file.txt

    • #60141 Reply
      Wenchang
      Guest

      It seemed the PDB to PDBQT conversion failed:

      Running Filter on the Compounds from last generation/Source
      GET SOME LIGANDS FROM THE LAST GENERATION
      GOT LIGANDS FROM THE LAST GENERATION
      Not all ligands in source compound list are scored. We will convert and redock them all.
      CONVERTING SMILES TO SDF
      CONVERTING SMILES TO SDF COMPLETED
      CONVERTING SDF TO PDB
      CONVERTING SDF TO PDB COMPLETED
      ####################
      Convert Ligand to PDBQT format Begun
      Failed to convert 0 times: ./Run_1/generation_0/PDBs/naphthalene_96__3.pdb
      Failed to convert 1 times: ./Run_1/generation_0/PDBs/naphthalene_96__3.pdb
      Failed to convert 2 times: ./Run_1/generation_0/PDBs/naphthalene_96__3.pdb
      COMPLETELY FAILED TO CONVERT: ./Run_1/generation_0/PDBs/naphthalene_96__3.pdb
      …….

    • #60166 Reply
      ikk6
      Keymaster

      Can you please check that the PDB file is properly formatted?

    • #60171 Reply
      Wenchang
      Guest

      Thanks @ikk6, I checked the receptor PDB (./autogrow4/tutorial/PARP/4r6eA_PARP1_prepared.pdb) which looks fine to me, this receptor PDB is from the original autogrow4 release.

      The later generated ones like this (./Run_1/generation_0/PDBs/naphthalene_96__3.pdb) did not get saved, so I don’t know how to check them.

    • #60182 Reply
      ikk6
      Keymaster

      Well, I am not the project maintainer. I will let somebody from the lab know.

    • #60317 Reply
      Wenchang
      Guest

      @ikk6, thanks very much for directing this topic, can I get to know the project maintainer? I’m very excited to try to play it, would be great if I can talk to this person.

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