I am trying do that what the title depicts, but I keep running into errors creating the executable script. Is it even possible to automate the docking of multiple ligands to multiple receptors?

Below is the script that I have. Right now I tried to get it to read from a configuration file, because the software could not read all of the arguments when they were in the executable. I am using

#! /bin/bash -i
for f in *lig.pdbqt ; do
  for n in nolig* ; do
    b=`basename $f .pdbqt`
    echo "Processing ligand $b"
    #(commented since I already have a directory for it)
    # mkdir -p $b
    vina --ligand $f --config avppar_conf.txt --out outputs/${b}_out.pdbqt --log outputs/${b}_log.txt

This is the configuration file as it currently is:

--receptor $n (I thought this would not work, but I had to try anyway). 

--center_x = -36.456

--center_y = 51.1

--center_z = 47.157

--size_x = 70

--size_y = 70

--size_z = 70

--num_modes = 9

--exhaustiveness = 8

I understand this looks messy; I would even appreciate it if I was directed to a more appropriate forum if needed.

  • 1
    $\begingroup$ I'm voting to close this question as off-topic because it's about how to use software. $\endgroup$ – Todd Minehardt Oct 28 '19 at 22:22
  • 1
    $\begingroup$ Please read the manual, there is an example of the configuration. Your bash script also needs some love; it contains some deprecated code and mistakes. See shellcheck (shellcheck.net/#) for testing it. $\endgroup$ – Martin - マーチン Oct 29 '19 at 14:34
  • 1
    $\begingroup$ I have tried to fix your script although I'm pretty sure it still won't work. You are not using $n. You should also try to use more descriptive variable names. this was very hard to decipher, and the done were missing completely. $\endgroup$ – Martin - マーチン Oct 29 '19 at 14:42

I actually found the answer to my question. In order to link configuration and script files the way I wanted, I needed the 'seb' command.


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