Computer-Aided Drug Design at the Durrant Lab › Forums › Webina › OpenBabel vs pdbqt
- This topic has 1 reply, 1 voice, and was last updated 2 years, 8 months ago by Jacob Durrant.
- September 23, 2020 at 2:55 pm #15945Christian Le GouillGuest
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.
- September 27, 2020 at 3:01 am #16243Jacob DurrantKeymaster
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.
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