How to do dockings

Run Autodock Vina

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

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

Split ligands by

python2 split.py

Single receptor

You may find the template vina run script here.

Multiple receptors

You may find the template vina run script (multiple) 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

Get results by

sh get_result_multiple.sh

Move selected directories

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

Looking at the results

Get binding poses

awk '{print gensub (/[^[:blank:]]+/, " ", 11)}'

is useful to remove unwanted columns from a pdb (produced by docking softwares)

adt_split_cluster.sh can be used to split the results from clustering Autodocks.

Combine the ligand with the receptor (proteins)

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.

Rendering

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