AutoGrow 4: Failed to run the given json example

[Christian Grunwald]

Hello,
after installing AutoGrow 4 and all of its dependencies within ubuntu, I tried out the sample json file "sample_submit_autogrow.json" with only minor adaptions (paths were changed, gypsum_timeout_limit was set to 15). The run seemed to start correctly, but the conversion PDBQT format failed in all cases (see below). I would be very happy if somebody could help me to find the error.
Thank you very much in advance
Christian

Here is a part of the log output:
…
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: /home/osboxes/programs/autogrow4/test_out/Run_3/generation_1/PDBs/naphthalene_70__1.pdb
Failed to convert 0 times: /home/osboxes/programs/autogrow4/test_out/Run_3/generation_1/PDBs/Gen_1_Mutant_11_789365__1.pdb
Failed to convert 1 times: /home/osboxes/programs/autogrow4/test_out/Run_3/generation_1/PDBs/naphthalene_70__1.pdb
Failed to convert 1 times: /home/osboxes/programs/autogrow4/test_out/Run_3/generation_1/PDBs/Gen_1_Mutant_11_789365__1.pdb
Failed to convert 2 times: /home/osboxes/programs/autogrow4/test_out/Run_3/generation_1/PDBs/naphthalene_70__1.pdb
COMPLETELY FAILED TO CONVERT: /home/osboxes/programs/autogrow4/test_out/Run_3/generation_1/PDBs/naphthalene_70__1.pdb
PDBQT not generated: Deleting naphthalene_70__1.pdb…
…

[Christian]

There is some progress here: I changed the conversion method by adding the following lines to the json file:
"conversion_choice": "ObabelConversion",
"obabel_path": "/usr/bin/obabel",
Now AutoGrow runs without an error message.
Interestingly, the ""mgltools_directory"" variable was needed in addition in the json file to be able to run AutoGrow.
Regards
Christian

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