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.

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  • 1
    $\begingroup$ 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 $\endgroup$
    – zorbax
    Aug 13 '20 at 23:37
  • $\begingroup$ Could you also let us know how you converted your ligand to the PDBQT format (prepare_ligand4.py, obabel etc.) $\endgroup$ Aug 14 '20 at 8:47
  • $\begingroup$ 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. $\endgroup$ Aug 14 '20 at 8:47

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