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I am trying to run : python vina_dock.py -i smiles.smi --no_protonation -o/ --output output.txt

Traceback (most recent call last):
File "/home/ubuntu/Desktop/rdkit-scripts/vina_dock.py", line 473, in
main()
File "/home/ubuntu/Desktop/rdkit-scripts/vina_dock.py", line 453, in main
add_protonation(args.output)
File "/home/ubuntu/Desktop/rdkit-scripts/vina_dock.py", line 54, in add_protonation
protonate, done = list(cur.execute('SELECT protonation, protonation_done FROM setup'))[0]
sqlite3.OperationalError: no such table: setup

Could you please help me resolve it or do I have to give more information while running it ?

Thanks in advance,
Navya

hello Dr Pavel,
I chanced across your repo and found it useful to parse docked pdbqt files back to RDKit mol for further analysis. However, sometimes the pdbqt2mol() function fails as RDKit is not happy with the "G" atom type.

giving:

****
Post-condition Violation
Element 'G' not found
Violation occurred on line 93 in file /project/build/temp.linux-x86_64-cpython-310/rdkit/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****

This "G" atom type is generated by meeko at macrocycles during ligand preparation for docking with Autodock Vina, see: forlilab/Meeko#10

I saw in your in-line code comments about this issue, but I didn't manage to modify the fix_pdbqt() function successfully:

Please note that I didn't use your script to run docking; it was prepared slightly differently. I am just using your code to parse back the docked .pdbqt files
I also saw your comment on build_macrocycle=:

Do you have any idea how to fix this issue?
I've attached a sample offending .pdbqt file: https://gist.github.com/linminhtoo/5949437ae066fdd136709971dcc36220#file-bad-pdbqt-L26-L27
As you can see, some lines have either "G" (macrocycle), and also "CG0" (not sure if this will also cause problems). I tried brute forcing by replacing "G" with "C" but the template bond order assignment step failed (seems RDKit fails to parse the ring correctly)

Thanks,
Min Htoo

This will help to avoid the issue with missing Hs in input template mol, which are stripped during Chem.MolFromSmiles operation. so a user will be able to construct a molecules as needed.