Error: No ranked file from generation 0

[Christian]

Hello,
I used
"use_docked_source_compounds": true
to calculate affinities for my starter set. Affinities were calculated succesfully (there were *_docking_output.txt files in folder PDBs), but at the end of generation 0 I got the following:

Begin Ranking and Saving results
Completed Ranking and Saving results
Deleting temporary files and directories
Finished generation 0
/home/osboxes/programs/autogrow4/psx/results/Run_5/generation_1/
There were no available ligands in previous generation ranked ligand file.
Check formatting or if file has been moved.

There were three result files in folder generation_0:
generation_0.smi 596 bytes
generation_0_ranked.smi 0 bytes
generation_0_to_convert.smi 596 bytes

What could be the reason for this empty ranked flle? I use python3. Could it be the same problem reported by Yash?

Can you help me to fix this? Thank you very much!
Christian

[Jacob Durrant]

Hi Christian. I checked with my lab’s AutoGrow4 expert, and he said he’d need more information to be able to debug the issue. If possible, please send 1) the parameters used; 2) the version of AutoGrow4; 3) the operating system; and 4) either the source compound list and/or what the *_docking_output.txt (files in folder PDBs) read.

His guess is that either there is something wrong with the input smiles (e.g., they are misformatted somehow), or there is an OS error. I see osboxes in the pathing. Perhaps you’re using a less common flavor of Linux via Virtualbox? Could cause issues with the Vina compilation. But that’s just speculation.

Take care.

[Christian]

Hi Jacob, thank you very much for these suggestions! To test it I used the first ten SMILES strings from naphthalene_smiles.smi with my receptor and my parameters. And this time, the "generation_0_ranked.smi" file was filled with docking results. Thus there doesn’t seem to be an issue with the OS or the parameters or the installation of AutoGrow4.
Regarding the generation of SMILES strings: I used OpenBabel 3.0.0 for this task. Would you recommend another method?
Best regards
Christian
Here is the requested information:

1) Parameters used: Attached below.
2) Version of AutoGrow4: 4.0.1
3) Operating system: Ubuntu 20.04 LTS 64-bit
4) Example of source compound (this is one line from the SMILES file):
C(=O)(C(CCC(=O)O)N)O Glutamate
Glutamate__1.pdbqt_docking_output.txt: Attached below.

————– Parameters used —————–
"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": 3,
"conversion_choice": "ObabelConversion",
"obabel_path": "/usr/bin/obabel",
"mgltools_directory": "/home/osboxes/programs/mgltools_x86_64Linux2_1.5.6/",
"number_of_processors": 3,
"selector_choice": "Rank_Selector",
"max_variants_per_compound": 3,
"filter_source_compounds": false,
"use_docked_source_compounds": true,
"LipinskiLenientFilter": false,
"docking_exhaustiveness": 8,
"docking_timeout_limit": 300,
"start_a_new_run": true,
"generate_plot": true,
"rescore_lig_efficiency": false,
"scoring_choice": "VINA",
"dock_choice": "QuickVina2Docking",
"gypsum_timeout_limit": 15,
"debug_mode": false,
"rxn_library": "all_rxns"

————– Glutamate__1.pdbqt_docking_output.txt —————–
############################################################################

If you used Quick Vina 2 in your work, please cite:

…
############################################################################
WARNING: The search space volume > 27000 Angstrom^3 (See FAQ)
Reading input … done.
Setting up the scoring function … done.
Analyzing the binding site … done.
Using random seed: 75724026
Performing search …
0% 10 20 30 40 50 60 70 80 90 100%
|—-|—-|—-|—-|—-|—-|—-|—-|—-|—-|

---

done.
Refining results …
searching finished in 51.789 seconds
done.

mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
—–+————+———-+———-
1 -6.8 0.000 0.000
2 -5.6 5.757 7.270
3 -5.5 5.631 7.193
4 -5.3 6.422 7.034
5 -5.2 7.904 9.285
6 -5.2 7.443 8.388
7 -5.1 7.963 8.450
8 -5.1 6.873 7.955
9 -5.0 6.793 8.248
Writing output … done.

[Rajeev Gangal]

Any progress on this issue ? I tried looking into code but this issue of 0 size smiles in generation 1 persists despite no filters. All precursor actions happen just as discussed here. Tried on 2 diff computers and several pdb files, smiles inputs. Something goes wrong , maybe the path to the prev file?

Please check get_complete_list_prev_gen_or_source_compounds

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