-1
$\begingroup$

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
 done
done

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.

$\endgroup$
3
  • 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
-1
$\begingroup$

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.

$\endgroup$
1

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.