docking – Is there any way to handle CONECT records in Autodock Vina?

I have a .pdb file that I modelled myself using Avogadro. Many atoms are CONECT records, so when I prepare the macromolecule in AutoDock Tools and export it as .pdbqt without the CONECT records (since AutoDock Vina can’t handle them), the new .pdbqt file always shows broken bonds.

I’ve tried converting the .pdb file to .pdbqt with OpenBabel, removing all but the largest contiguous fragment, and ignoring CONECT records as well, but nothing works. I’ve also taken a look, and it looks like AutoDock Vina doesn’t have any parameters to handle CONECT records. Isn’t there any way at all to do this?

Thank you in advance.

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