Open WesleyAC opened 2 weeks ago
Hi @WesleyAC
The ligand's PDBQT file doesn't have valid 3D coordinates. With obabel, a quick fix would be:
obabel -ismiles methylphenidate.smiles -opdbqt -Omethylphenidate.pdbqt --gen3d
Let us know if that works for you
Ah, that makes complete sense in retrospect! And fixes the issue. Should I close this and open a separate issue to improve the error message?
Hi @WesleyAC Yes, PR is welcome to the develop branch if you're able to provide some fixes to catch similar problems in ligand PDBQT files. Otherwise, you could leave this open or open an issue. It would be tremendously helpful if we could find out underlying problems with input files (like when angles become zero), skip the instances in batch and/or print useful help messages.
I am getting started using AutoDock Vina, trying to check the binding of methylphenidate to the DAT receptor to check that everything is working. I am running into the following error:
methylphenidate.pdbqt
was generated with OpenBabel:obabel -ismiles methylphenidate.smiles -opdbqt -Omethylphenidate.pdbqt
.methylphenidate.smiles
containedCOC(=O)C(c1ccccc1)C1CCCCN1
. Link to generated PDBQT filesdat.pdbqt
was generated with OpenBabel from the AlphaFold-predicted PDB file (probably not ideal but I just grabbed it because it was simple):obabel AF-Q01959-F1-model_v4.pdb -xr -Odat.pdbqt
. Link to generated PDBQT filesMy assumption is that my preperation of the PDBQT files is incorrect, but if that's the case, there's still a bug here, as the error message should be something better.