# Using AutoDock Vina to dock multiple ligands to multiple receptors?

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. • I'm voting to close this question as off-topic because it's about how to use software. – Todd Minehardt Oct 28 '19 at 22:22 • 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. – Martin - マーチン Oct 29 '19 at 14:34 • 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. – Martin - マーチン Oct 29 '19 at 14:42