OpenBabel vs pdbqt

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    • #15945
      Christian Le Gouill


      Just a correction for your readme file…

      When you use Openbabel to convert an SD file to a pdbqt file, you need to add this argument to the cmd line: –partialcharges gasteiger for ex: obabel -isdf gypsum_output.sdf -O gypsum_output.pdbqt –partialcharges gasteiger . Openbabel automatically calculates partial charges for mol2 files but not for pdbqt files.


    • #16243
      Jacob Durrant

      Hi Christian. Much thanks for this careful reading of the file. It’s interesting that Open Babel calculates partial charges for MOL2 files but not PDBQT files. In this case, though, I don’t think it much matters, because I believe AutoDock Vina (surprisingly) doesn’t care about the partial charges listed in the PDBQT file:,needed

      Since Webina is based on the Vina codebase, I don’t think it cares about the partial charges either.

      Take care,

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