I am trying to carry out virtual screening using autodock vina. I have all the files necessary in my directory as suggested by literatures and tutorials. But when I run the command
./vina_vs.sh, I get the error message
'vina: command not found'. It's my first time running a virtual screening. What could be the reason for this error?
Assuming you are using Linux and the bash shell:
Look at the shell script vina_vs.sh in a text editor. In there is a call to the program vina, something like:
vina --config conf_vs.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt
Is the path to the vina executable listed in the PATH variable? (type echo$PATH in the terminal) If not, you need to add it or use the explicit path within the shell script
https://linuxhint.com/path_in_bash/
It looks like it might be a wrapper that someone wrote for using the tool. Try "sudo apt install autodock-vina", and the above recommendation to run it. Worked for me in Ubuntu 19.10 and 20
In linux, vina is not usually installed like other programs. So you have to keep the vina in some directory and set that path to your linux environment. Or you can simply keep the vina executable in your working directory along with your ligand and receptor files to run vina. I hope this will work for you.
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