Autodock Vina not recognizing Chloride ion in ligand.pqbqt file

Question

[Sanjukta]

Hi there, I am performing AutoDock Vina using command prompt, and running it for 10 ligands. My code is not able to run Ligands that have Chloride ions present in the structure, and is showing an error like this:

Parse error on line 21 in file ".IM...78.pdbqt": Unknown or inappropriate tag

When the minimized IM..78.pdbqt file was opened in notepad, the following was displayed:

I am not sure what is means and how this can be troubleshot. Any help will be much appreciated. :)

[Mensur Dlakic]

The message is clear:

Parse error on line 21 in file ".IM...78.pdbqt": Unknown or inappropriate tag

That's your second ROOT line and something seems to be wrong there rather than the CL ion.