Converting AutoDock-Vina PDBQTs to PDB files

Question

[Ricard]

Hello bioinformaticians,

I am working with AutoDock Vina, actually using it inside a workflow, and my input files are in the PDB file format. I am docking some ligands into my receptor protein using Vina and then I receive back some PDBQT files. The problem here is that my workflow needs again PDB files to continue its execution, not PDBQTs.

So my question is simple, does anyone know a way to convert these PDBQT files back to PDB in a programatically way? Ideally using a Python API, but it can also be using directly the CLI (by means of the Python subprocess module I would be able to run it anyways). I have tried Open babel to do this, but the resulting PDB file does not look that properly formatted.

Thanks in advance. Regards,

NOTE: I have found some answers regarding this topic in other posts, but they imply using some software's GUI, which in this case would not be possible, so please abstain from proposing this as a solution.

Answer 1

[Mensur Dlakic]

I have tried Open babel to do this, but the resulting PDB file does not look that properly formatted.

Open Babel is a go-to tool for conversions between different macromolecular formats. The ultimate criterion of its PDBQT-> PDB conversion is whether the downstream programs can use the resulting PDB files rather than whether those files look properly formatted to the eye. In case the PDB files are not properly formatted, I would consider a possibility that something is wrong with the upstream applications rather than with Open Babel.

PDBQT and PDB formats are very similar, and it wouldn't be too difficult to write a parser. In case you want to give it a try, here is a PDB file format description:

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html

I have read somewhere that this line alone will do the conversion, at least for the lines with ATOM records:

cut -c-66 file.pdbqt > file.pdb