Autogrow4: tutorial failure

[Taylor]

HI! We are running autogrow4 on Linux cluster with python 3.7.6 and mgltools. When running the tutorial with the correct paths, we keep getting an error with the input files.No changes have been made to the RunAutogrow.py file or user_vars.py file.

running:
python /home/witte.t/autogrow4/RunAutogrow.py -j /home/witte.t/autogrow4/tutorial_variables.json

Error:
File "/home/witte.t/autogrow4/RunAutogrow.py", line 657, in <module>
vars, printout = load_in_commandline_parameters(INPUTS)
File "/home/witte.t/autogrow4/autogrow/user_vars.py", line 964, in load_in_commandline_parameters
check_for_required_inputs(json_vars)
File "/home/witte.t/autogrow4/autogrow/user_vars.py", line 438, in check_for_required_inputs
"Receptor file can not be found. File must be a .PDB file."
NotImplementedError: Receptor file can not be found. File must be a .PDB file.

JSON file
{
"filename_of_receptor": "./home/witte.t/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": "./home/witte.t/autogrow4/source_compounds/naphthalene_smiles.smi",
"root_output_folder": "./home/witte.t/autogrow4/de_novo_design/autogrow4_results/",
"number_of_mutants_first_generation": 10,
"number_of_crossovers_first_generation": 10,
"number_of_mutants": 3,
"number_of_crossovers": 3,
"number_elitism_advance_from_previous_gen": 3,
"top_mols_to_seed_next_generation": 5,
"diversity_mols_to_seed_first_generation": 3,
"diversity_seed_depreciation_per_gen": 0,
"num_generations": 1,
"mgltools_directory": "./home/witte.t/autogrow4/mgltools_x86_64Linux2_1.5.6",
"number_of_processors": -1,
"selector_choice": "Rank_Selector",
"max_variants_per_compound": 1,
"filter_source_compounds": false,
"use_docked_source_compounds": false,
"LipinskiLenientFilter": true,
"docking_exhaustiveness": 1,
"start_a_new_run": true,
"generate_plot": true,
"rescore_lig_efficiency": true,
"scoring_choice": "VINA",
"dock_choice": "QuickVina2Docking",
"gypsum_timeout_limit": 1,
"debug_mode": false,
"rxn_library": "all_rxns"
}

[ikk6]

hello. What are the permissions of the receptor.pdb? I.e.
ls -l /home/witte.t/autogrow4/tutorial/PARP/4r6eA_PARP1_prepared.pdb

[Taylor]

Hi! Thank you! Changing the access to the folder did help! However it came up with another error in plotting.

Finished generation 1

Plotting

Overall Scoring Average for all Compounds

Traceback (most recent call last):

File "/home/witte.t/autogrow4/RunAutogrow.py", line 675, in <module>

AutogrowMainExecute.main_execute(vars) 

File "/home/witte.t/autogrow4/autogrow/autogrow_main_execute.py", line 140, in main_execute

plot.generate_figures(vars) 

File "/home/witte.t/autogrow4/autogrow/plotting/generate_line_plot.py", line 442, in generate_figures

dict_of_averages = print_data_table(infolder, folder_list) 

File "/home/witte.t/autogrow4/autogrow/plotting/generate_line_plot.py", line 388, in print_data_table

average_affinity_dict = get_average_score_per_gen(infolder, folder_list) 

File "/home/witte.t/autogrow4/autogrow/plotting/generate_line_plot.py", line 104, in get_average_score_per_gen

gen_affinity_average = gen_affinity_sum / num_lines_counter 

ZeroDivisionError: float division by zero

[ikk6]

Still looks like a permission error to me. It’s either the ranked file(s) that was not created or it’s empty. Would you mind checking?
ls -lR | grep "_ranked.smi"

[Taylor]

Hi
The smi files only allow the user to write which could be leading to an issue. However to hault this from happening on all codes. Where in the code would you suggest i put the "chmod u=rwx,g=rwx,o=rwx $PATH/generation1_ranked.smi" to change the permissions errors.

I also noticed that the code is failing to "Convert Ligand to PDBQT format Begun" on all of the files.

Failed to convert 0 times: /home/witte.t/autogrow4/de_novo_design/autogrow4_results/Run_4/generation_1/PDBs/naphthalene_60__1.pdb

Thank you for your help!
Best,
Taylor

[ikk6]

I wouldn’t suggest doing this, to begin with. Yet if no other solution is available, I would assume it makes sense to change the perms before the files are accessed. For example, in:
/home/witte.t/autogrow4/autogrow/plotting/generate_line_plot.py
You could add
import os
after line 8
Then, after line 86 (after the loop for rank_file in ranked_file:)
os.chmod(rank_file , 0777)
Disclaimer: I’m not the author of autogrow project. This all looks like a poor man’s solution. Ideally would be to deal with the OS setup, so that the files would be accessible with no tweaks.
Let’s try and call someone else to help you.

[Jacob Durrant]

Hi all. I noticed in your JSON file that "filename_of_receptor" is set to "./home/witte.t/autogrow4/tutorial/PARP/4r6eA_PARP1_prepared.pdb". Did you mean to include the initial "."? I suspect that’s the problem. Take care.

[Jacob Durrant]

Re. the second error, can you confirm that your ""*_ranked.smi" files exist, and that they are not empty? It may be that rerunning AutoGrow with the corrected JSON file with correct this second issue as well.

[Author]

Posts