docking for objectives

[fdaqin-v]

Great work！ Currently, I have a problem like this. In the example of Enamine50k, I just change the objective type from lookup to docking in the Enamine50k_retrain.ini, and I also updated the docking.ini file (4nuu, center = [6.69, 17.69, -7.07], size = [40, 40, 40]).However, it seems that the docking does not work properly. I saw someone asked a similar question, but I don’t know how to deal with it, thank you！

(prepare_and_run pid=201507) Information (optional): (prepare_and_run pid=201507) --help display usage summary (prepare_and_run pid=201507) --help_advanced display usage summary with advanced options (prepare_and_run pid=201507) --version display program version (prepare_and_run pid=201507) (prepare_and_run pid=201507) Docking: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 503/503 [00:08<00:00, 59.15ligand/s] Exception raised! Intemediate state saved to "molpal_50k/chkpts/iter_0_2021-12-21_18-02-39/state.json" Traceback (most recent call last): File "run.py", line 71, in main() File "run.py", line 55, in main explorer.run() File "/home/fgq/molpal-main/molpal/explorer.py", line 317, in run self.explore_initial() File "/home/fgq/molpal-main/molpal/explorer.py", line 363, in explore_initial self.write_scores(include_failed=True) File "/home/fgq/molpal-main/molpal/explorer.py", line 542, in write_scores top_m = self.top_explored(m) File "/home/fgq/molpal-main/molpal/explorer.py", line 473, in top_explored if k / len(self.scores) < 0.8: ZeroDivisionError: division by zero (prepare_and_run pid=201492) ERROR: docking failed. Message: Command line parse error: unrecognised option '--log=/tmp/pyscreener/session_2021-12-21_18-02-29/outputs/vina_4unn_receptor_ligand_493_0.log' (prepare_and_run pid=201492) (prepare_and_run pid=201492) Correct usage: (prepare_and_run pid=201492) (prepare_and_run pid=201492) Input: (prepare_and_run pid=201492) --receptor arg rigid part of the receptor (PDBQT) (prepare_and_run pid=201492) --flex arg flexible side chains, if any (PDBQT) (prepare_and_run pid=201492) --ligand arg ligand (PDBQT) (prepare_and_run pid=201492) --batch arg batch ligand (PDBQT) (prepare_and_run pid=201492) --scoring arg (=vina) scoring function (ad4, vina or vinardo)

[davidegraff]

Which version of Vina are you using?

[fdaqin-v]

vina_1.2.3_linux_x86_64

[davidegraff]

Pyscreener is designed to work with vina 1.1.2

[fdaqin-v]

OK, thanks! I will try again.

[fdaqin-v]

Vina version was changed to 1.1.2(vina_1.1.2-boost-new_linux_x86_64), and it really works for me. Thanks very much!

ITER: 5/5 | TOP-105 AVE: -4.920 | BUDGET: 530/10560. Continuing... Inference: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 1.91smi/s] Docking: 0%| | 0/106 [00:00<?, ?ligand/s](prepare_and_run pid=267840) ERROR: docking failed. Message: (prepare_and_run pid=267840) (prepare_and_run pid=267840) Parse error on line 106 in file "/tmp/pyscreener/session_2021-12-22_09-21-27/inputs/ligand_532_0.pdbqt": Unknown or inappropriate tag (prepare_and_run pid=267840) Docking: 21%|█████████████████████████████████▏ | 22/106 [01:46<06:47, 4.85s/ligand](prepare_and_run pid=267866) ERROR: docking failed. Message: (prepare_and_run pid=267866) (prepare_and_run pid=267866) Parse error on line 113 in file "/tmp/pyscreener/session_2021-12-22_09-21-27/inputs/ligand_565_0.pdbqt": Unknown or inappropriate tag (prepare_and_run pid=267866) Docking: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 106/106 [06:15<00:00, 3.55s/ligand] Finished exploring! FINAL TOP-105 AVE: -4.910 | FINAL BUDGET: 636/10560. Final averages

TOP-0.01%: -4.000 TOP-0.05%: -4.160 TOP-0.10%: -4.280 TOP-0.50%: -4.698 Total time for exploration: 0d 0h 37m 37.68s Thanks for using MolPAL!

[davidegraff]

Glad to see it’s working! Remember to add the —minimize flag to your docking objective config so that you can identify the best docking scores

[fdaqin-v]

Thanks! I will check this option.