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I try to gnina docking tool for protein-ligand docking

But I can get output file just included ligand. (there is no protein in pdb)

Is there problem at openbabel in gnina? Or at input file format?

Command is

gnina -r 6vl4/6vl4.pdb -l ligand/structure.sdf --autobox_ligand 6vl4/6vl4_B_QY1.sdf --device 0 --minimize_single_full --pose_sort_order CNNaffinity -o ../gnina_output/6vl4_structure_docked.pdb --seed 0

The Error

*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

enter image description here

[Env]
Ubuntu 18.04
python 2.7

JeongSoo Na
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1 Answers1

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There is no problem, the output file of gnina just show the orientation of the ligands. However, you just need to open your receptor original file (-r file) and the output file (-o file) together in a visualiser to see the ligand in the pocket of the receptor.

Charlt
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