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