Well, I'll use about 50 protein conformations so that's an option but can be a mess. I don't know if I merge all the conformations in a single pdb, convert it into a pdbqt file and use it for Vina. I'll see if Vina complains. I was asking because I've read this can be done with GOLD for instance and it's been a common practice in docking for a while.

I dont think autodock will work for ensemble docking. The only to do is to first generate different conformation of protein (alone) and select the representative ones by superimposing them. Use these representative conformations (1-4) and run the usual docking procedure of autodock. Thereafter, select the consensus hits and make the conclusions out of it.

However, this procedure is automated in GOLD and GLIDE.

https://www.ccdc.cam.ac.uk/Community/educationalresources/workshop-materials/GOLD_Ensemble_Docking_TK.pdf

thanks

If you have 50 proteins coformomers against single small molecul, a loop bash scripting should resolve you problem,

for example if you have 50 proteins in pdbqt file can use anything as :

for file in proteinconformomer_*.pdbqt; do

echo "prosseing $File"

mkdir -p $File

./vina --config configure.text --receptor $File --log log.text;

done