Hydrated Docking - Dry.py error

[jfair32]

All, I am following the directions in Autodock Vina Read the Docs on hydrated docking. I am able to reproduce all steps except the post-processing using dry.py. I can split and open my raw vina results (receptor_5HT1A_7e2y_SRO_ad4_out.pdbqt) in Pymol and see that the ligand has docked with explicit waters. I tried to view the options in dry.py, but I get the same error as below. This leads me to lean toward an error in the dry.py script (at least my version). Has anyone else seen this issue?

When I run the dry.py command, this is the error I get:

File "dry.py", line 237 if not QUIET: print(" [ %d docking pose(s) found ] " % len(models), end=' ') ^ SyntaxError: invalid syntax

Here is a copy of the cmd line history: C:\Users\xxxx\Desktop\VinaRuns\5HT1A_ad4maps\Hydrated\5HT1A_7e2y_SRO>vina --ligand SRO.pdbqt --maps receptor_5HT1A_7e2y --scoring ad4 --exhaustiveness 1200 --num_modes 10 --out receptor_5HT1A_7e2y_SRO_ad4_out.pdbqt AutoDock Vina v1.2.3 #################################################################

If you used AutoDock Vina in your work, please cite:

J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force

Field, and Python Bindings, J. Chem. Inf. Model. (2021)

DOI 10.1021/acs.jcim.1c00203

O. Trott, A. J. Olson,

AutoDock Vina: improving the speed and accuracy of docking

with a new scoring function, efficient optimization and

multithreading, J. Comp. Chem. (2010)

DOI 10.1002/jcc.21334

Please see https://github.com/ccsb-scripps/AutoDock-Vina for

more information.

#################################################################

Scoring function : ad4 Ligand: SRO.pdbqt Exhaustiveness: 1200 CPU: 0 Verbosity: 1

Reading AD4.2 maps ... done. Performing docking (random seed: -2060840117) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----|

---

mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -7.567 0 0 2 -7.523 1.158 2.251 3 -7.465 1.242 2.114 4 -7.44 2.525 4.587 5 -7.44 2.926 6.37 6 -7.436 2.892 6.318 7 -7.368 2.523 4.92 8 -7.305 2.355 5.092 9 -7.271 2.351 5.732 10 -7.27 2.284 4.865

C:\Users\xxxx\Desktop\VinaRuns\5HT1A_ad4maps\Hydrated\5HT1A_7e2y_SRO>python dry.py -c -r receptor_5HT1A_7e2y.pdbqt -m receptor_5HT1A_7e2y.W.map -i receptor_5HT1A_7e2y_SRO_ad4_out.pdbqt File "dry.py", line 237 if not QUIET: print(" [ %d docking pose(s) found ] " % len(models), end=' ') ^ SyntaxError: invalid syntax

[jfair32]

I was able to get dry.py to run but had to switch to Anaconda to do it rather than CMD line in windows. I have been able to run all the basic, flexible, and hydrated commands in CMD except for dry.py and mk_prepare_ligand.py.

[domiko96]

Hey jfair32 can you maybe mention your exact environment - anaconda/python version and numpy version

[domiko96]

I also tried it with anaconda but no luck yet

[GuidoSanche5]

Tienes que separar con vina_split y, uno por uno usar el dry.py Exitos

[marktan1990]

This is due to the Python version. Python 2.7 could not recognize the end=' ' as correct grammer. Just use Python3