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AutoDock Vina

AutoDock Vina is an open-source program for doing molecular docking.

AutoDock Vina is available as a module on Apocrita.

Usage

To run the default installed version of AutoDock Vina, simply load the autodock-vina module:

$ module load autodock-vina
$ vina --help
AutoDock Vina vX.Y.Z

Input:
  --receptor arg             rigid part of the receptor (PDBQT)
  --flex arg                 flexible side chains, if any (PDBQT)
  --ligand arg               ligand (PDBQT)
  --batch arg                batch ligand (PDBQT)
  --scoring arg (=vina)      scoring function (ad4, vina or vinardo)
(etc.)

For usage documentation, run vina --help.

Example jobs

Serial jobs

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load autodock-vina

vina --ligand 1iep_ligand.pdbqt \
     --maps 1iep_receptor --scoring ad4 \
     --exhaustiveness 32 \
     --out 1iep_ligand_ad4_out.pdbqt

Here is an example job running on 8 cores and 8GB of memory:

Core Usage

Please set the --cpu argument to the value of ${NSLOTS} (number of cores requested by the job script), to avoid overloading the compute nodes.

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 8
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load autodock-vina

vina --ligand 1iep_ligand.pdbqt \
     --maps 1iep_receptor --scoring ad4 \
     --exhaustiveness 32 \
     --out 1iep_ligand_ad4_out.pdbqt \
     --cpu $NSLOTS

References