Run vina

Prepare all ligands (.pdbqt) in a directory ligand/pdbqt.

Prepare all receptors (.pdbqt) in a directory receptor.

Split ligands by

python2 make_vina_split.py

Single receptor

You may find the template vina run script here.

Define path to receptors (RECP), configuration file (CONF), and output directory (OUTPUT).

The basic run command is

vina --config <config> --receptor <pdbqt> --ligand <pdbqt> --out out.pdbqt --log log.txt

You may find the template job script here.

Prepare (and submit) the vina run scripts by

sh make_vina_rec.sh

Make a namelist

head -25 sort | awk '{print $1}' | cut -d/ -f1-5 > tmp

Move the directories

for ii in $(cat tmp); do cp -r $ii res; done

Make a namelist

find res -type d | tail -n +2 > namelist

Combine ligands and receptors

sh make_combine.sh

Now you will have a combined.pdb to look at.

Here is a sample vmd visualization file for TBL1: render.vmd

The render command is

sh make_render_vmd.sh

You may use

sh make_render.sh

or just uncomment lines in make_combine.sh

Gather the pictures

sh cp_jpg.sh