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I am trying to split to a pdbqt file containing 178 compounds into individual pdbqt files. I have been using the Autodock Vina_split.exe file to split the multiple entry file however I keep running into the following error. What can I do to prevent the error.

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    $\begingroup$ (A) Empty file? Does the file open in PyMol? Also, you can always split it there with split_states. (B) Is the file really called output.pdbqt or is it output.pdbqt.txt and Windows is hiding the extension? $\endgroup$ – Matteo Ferla Sep 22 '20 at 8:00
  • $\begingroup$ There could be many reasons. Maybe lack of permissions or the space in the path. Can you open the file with a different program? Are you on Linux or Windows etc. $\endgroup$ – Sören Sep 23 '20 at 2:22

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