AutoDock GPU
Description¶
The AutoDock-GPU Suite is a growing collection of methods for computational docking and virtual screening, for use in structure-based drug discovery and exploration of the basic mechanisms of biomolecular structure and function. The source code is available at the GitHub page.
It is highly recommended to run AutoDock GPU within its container using the Singularity utility.
Available Versions¶
The following versions of AutoDock GPU are currently available:
- Runtime dependencies:
- singularity/ce-3.11.0
AutoDock GPU is available as a container; use singularity to build or run the applications. First load the singularity module with the following command:
module load singularity/ce-3.11.0
User guide¶
You can find the software documentation and user guide at the official website and for running in Singularity at the NVIDIA NGC catalog.
Example run script¶
You can copy and modify this script as autodock_singularity.sh and submit the job to a GPU node with the command sbatch autodock_singularity.sh. Values for the number of GPUs, ntasks and CPUs per task have been tested and optimized for best performance on the Devana cluster.
#!/bin/bash
#SBATCH -J "AD_GPU" # name of job in SLURM
#SBATCH --account=p70-23-t # project number
#SBATCH --partition=gpu # selected partition
#SBATCH --gres=gpu:1 # runs on one gpu
#SBATCH --ntasks=1 # number of parallel tasks
#SBATCH --cpus-per-task=8 # number of cpus per task
#SBATCH --time=01:00:00 # time limit for a job
#SBATCH -o stdout.%J.out # standard output
#SBATCH -e stderr.%J.out # error output
# Modules
module load singularity/ce-3.11.0
# Shortcuts
Container_loc=/storage-apps/software/containers/autodock
Script_loc=$HOME
# Execute AD_GPU_sing.sh script within the container
singularity exec --nv $Container_loc/autodock_gpu_zinc_latest.sif "$Script_loc/AD_GPU_sing.sh"
The second script, started within the container, loops over the desired directory and can be modified to specify targets or loop over a list of ligands (see the AutoDock Vina page).
#!/bin/bash
# Shortcuts
Ligands_location=$HOME/ligands
Proteins_location=$HOME/proteins
Outputs=$HOME/results
# Loop over compounds
Ligands=$(ls "$Ligands_location"/*.pdbqt)
for ligand in $Ligands; do
# autodock_gpu_128wi -lfile $ligand -ffile $Proteins_location/6WQF_clean.maps.fld -nrun 50 -resnam $Outputs/$ligand.dlg
autodock_gpu_128wi -lfile $ligand -ffile $Proteins_location/6WQF_clean.maps.fld -nrun 50
done