Reputation: 27
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
[Env]
Ubuntu 18.04
python 2.7
Upvotes: 0
Views: 1177
Reputation: 17
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.
Upvotes: 0