Running smina on PyRx 0.9.2

[Phung Hien Le]

Hi Team,

I have tried to run smina in PyRx 0.9.2, by replacing the vina binaries with smina.static in PyRx and rename. It does work (with smina.static only).

   _______  _______ _________ _        _______ 
  (  ____ \(       )\__   __/( (    /|(  ___  )
  | (    \/| () () |   ) (   |  \  ( || (   ) |
  | (_____ | || || |   | |   |   \ | || (___) |
  (_____  )| |(_)| |   | |   | (\ \) ||  ___  |
        ) || |   | |   | |   | | \   || (   ) |
  /\____) || )   ( |___) (___| )  \  || )   ( |
  \_______)|/     \|\_______/|/    )_)|/     \|


smina is based off AutoDock Vina. Please cite appropriately.

Weights      Terms
-0.035579    gauss(o=0,_w=0.5,_c=8)
-0.005156    gauss(o=3,_w=2,_c=8)
0.840245     repulsion(o=0,_c=8)
-0.035069    hydrophobic(g=0.5,_b=1.5,_c=8)
-0.587439    non_dir_h_bond(g=-0.7,_b=0,_c=8)
1.923        num_tors_div

Using random seed: -2141829263

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
******************

However, the logger shows error and does not display the score ranking.

Open /mnt/d/PyRx/Docking/Macromolecules/protein_name/ligand_name.pdbqt for details.
Protein instance has no attribute 'vina_results'

I'm not sure what is the scoring function being used? Is it Vinardo or something else?

And I just wonder if you can consider making a PyRx compatible version of smina that only modify the scoring function?

Thank you very much.

Best regards.

[David Koes]

Wouldn't it make more sense to modify PyRx to look for the appropriate output fields in smina/gnina?