# Parse Error while using AutoDock Vina

I am trying to dock ligands with proteins to estimate the docking potential however, I am facing this error while docking. Any help will be highly appreciated.

• could you share the content of the line 574 of the Spike_C.pdbqt file? You can use sed for select one line after and one before of the 574 specific line sed -n '573,575p' Spike_C.pdbqt Aug 13 '20 at 23:37
• Could you also let us know how you converted your ligand to the PDBQT format (prepare_ligand4.py, obabel etc.) Aug 14 '20 at 8:47
• Also (minor point), having the grid box the size of your protein (270_000 Å) is not a good idea: you may know where the ligand binds —i.e. receptor binding domain. In the case of a VLS you want scores for it to bind there. Otherwise a lot will stick to the energetically unhappy transmembrane domain doing nothing. Aug 14 '20 at 8:47