Using AutoDock Vina to dock multiple ligands to multiple receptors?

Question

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.

Answer 1

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.