Body: <p>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.</p>
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Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-09T12:24:56.270Z
Comments.Text: 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)?
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-09T12:27:21.350Z
Comments.Text: 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.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-09T14:04:08.640Z
Comments.Text: @+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"
Comments.UserDisplayName: ibio_rep1
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-09T16:21:20.890Z
Comments.Text: So you can either use the alias command to tell terminal what `vina` means, or you can add the vina binary to `/usr/bin/`.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-10T10:31:09.903Z
Comments.Text: @MatteoFerla will give that a try and get back to you. thank you.
Comments.UserDisplayName: ibio_rep1
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-10T13:44:21.723Z
Comments.Text: @MatteoFerla i added the vina application files to the "bin" folder but I am getting the same error. Which file in the screenshot below is the vina binary you are referring to. Any additional recommendations on what might be causing the error. 
  Image: https://ibb.co/ZzMV2Vp
Comments.UserDisplayName: ibio_rep1
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-10T15:34:53.037Z
Comments.Text: You can edit your original post to add extra data btw —including SE image upload. If you run the command `./vina` in the bin folder it should work and it's just cygwin oddity —which best left alone. 
  If so, modify your script to call `/usr/bin/vina` as opposed to simply `vina`.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-11T15:06:29.547Z
Comments.Text: @MatteoFerla
  I added the vina files and wrapper script to the usr/bin folder and retried on Linux but I am getting the same error. I added the screenshots to my original post above. Any suggestions.
Comments.UserDisplayName: ibio_rep1
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-12T09:48:46.617Z
Comments.Text: `.exe`? That is a **Windows** binary, whereas you are trying in **Linux**, please download the appropriate one or change your bash script to a batch script and run in normal DOS terminal —for 6 ligands you don't need a for-loop though. However, however... may I suggest before embarking on a computational biochemistry task that you read around or watch a few videos about using the terminal?
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-12T11:30:27.413Z
Comments.Text: @Matteo Ferla thank you, which videos would you suggest going through before embarking on the task.
Comments.UserDisplayName: ibio_rep1
Tags: <protein-structure><bash><docking><computational-biochemistry>
Title: Issues with AutoDock Vina
ThreadText: # Issues with AutoDock Vina
  
  (Asked by: username_0 on 2020-08-09)
  
  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.
  
  [![enter image description here](https://i.sstatic.net/c5yR4.png)](https://i.sstatic.net/c5yR4.png)
  
  [![enter image description here](https://i.sstatic.net/4uwpM.png)](https://i.sstatic.net/4uwpM.png)
  
  **Tags:** protein-structure, bash, docking, computational-biochemistry
  
  > **Comments:**
  > **username_1**: 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)?  
  > **username_1**: 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.  
  > **username_0**: @+username_1 username_1 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"  
  > **username_1**: So you can either use the alias command to tell terminal what `vina` means, or you can add the vina binary to `/usr/bin/`.  
  > **username_0**: @username_1 will give that a try and get back to you. thank you.  
  > **username_0**: @username_1 i added the vina application files to the "bin" folder but I am getting the same error. Which file in the screenshot below is the vina binary you are referring to. Any additional recommendations on what might be causing the error.  Image: https://ibb.co/ZzMV2Vp  
  > **username_1**: You can edit your original post to add extra data btw —including SE image upload. If you run the command `./vina` in the bin folder it should work and it's just cygwin oddity —which best left alone.  If so, modify your script to call `/usr/bin/vina` as opposed to simply `vina`.  
  > **username_0**: @username_1 I added the vina files and wrapper script to the usr/bin folder and retried on Linux but I am getting the same error. I added the screenshots to my original post above. Any suggestions.  
  > **username_1**: `.exe`? That is a **Windows** binary, whereas you are trying in **Linux**, please download the appropriate one or change your bash script to a batch script and run in normal DOS terminal —for 6 ligands you don't need a for-loop though. However, however... may I suggest before embarking on a computational biochemistry task that you read around or watch a few videos about using the terminal?  
  > **username_0**: @username_1 thank you, which videos would you suggest going through before embarking on the task.  
  
  ---
  
  ## 0 answers
  
  