OpenBabel vs pdbqt

[Christian Le Gouill]

Hi,

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.

Best,
Christian

[Jacob Durrant]

Hi Christian. Much thanks for this careful reading of the README.md 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: http://vina.scripps.edu/manual.html#:~:text=assigning%20atom,needed

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

Take care,
Jacob

[Author]

Posts