I am using autodock tools to create pdbqt file for autodock vina but when i try to save file it warns me that receptor protein contains no non-bonded atoms. I have looked at everything and cannot figure out why this happend or how to prevent it from happening, as to use vina and autodock I need the file as We have a problem when converting PDB file into PDBQT file format for Autodock running. My compound has a doble bond (C=C) in the structure but after.

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Is there a way to save a protein-ligand complex as a PDB file in AutoDock?

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