I am trying to use AutoDock Vina to do docking however I am getting this error. I would really appreciate any help as I have not been able to resolve this error despite trying numerous times.

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  • $\begingroup$ The error is a bash error from your wrapper script. Which is failing to find vina. What is the detail of line 7 and does it match where you'd expect to find vina (i.e. where you installed it)? $\endgroup$ Aug 9 '20 at 12:24
  • $\begingroup$ Also, I am not a Windows person, but I believe cygwin is highly depracated in favour of the windows 10 dev mode ubuntu kernel. You might want to check for newer options. $\endgroup$ Aug 9 '20 at 12:27
  • $\begingroup$ @+matteo ferla Here is the wrapper script. My co-worker was able to run the script but I performed the exact same steps as him but I couldn't run the script. Do you think AutoDock Vina should be installed or something. The issue seems to be like you stated the script is not able to detect vina. Wrapper Script: "#! /bin/bash for f in ligand_*.pdbqt; do b=basename $f .pdbqt echo Processing ligand $b mkdir -p $b vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt done" $\endgroup$
    – ibio_rep1
    Aug 9 '20 at 14:04
  • $\begingroup$ So you can either use the alias command to tell terminal what vina means, or you can add the vina binary to /usr/bin/. $\endgroup$ Aug 9 '20 at 16:21
  • $\begingroup$ @MatteoFerla will give that a try and get back to you. thank you. $\endgroup$
    – ibio_rep1
    Aug 10 '20 at 10:31

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