Problems in Molecular Docking in Autodock vina

Question

[Nibedita]

How can I resolved this error in vina? Parse error on line 29 in file "ligand.pdbqt": ATOM syntax incorrect: "B" is not a valid AutoDock type?

Answer 1

[Anonsirs]

Try to re run the command by first starting meeko and rdkit . to convert PDB files to PDQT files. It can help vina recognize the atom . assuming B for Boron atom, autodock vina cannot handle boron, due to the scoring function.