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Autodock Vina not recognizing Chloride ion in ligand.pqbqt file

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:

enter image description here

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

vina
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updated by Mensur Dlakic Mensur Dlakic • written by Sanjukta • Sanjukta

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.

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written by Mensur Dlakic Mensur Dlakic

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