Autodock

Autodock Vina

AutoDock is a molecular modeling simulation software. It is especially effective for protein-ligand docking.  It is also parallel aware.

Slurm script

#!/bin/bash
#SBATCH -J vina_job # Job name
#SBATCH -o vina_job.o%j # Name of stdout output file (%j expands to jobId)
#SBATCH -p CUIQue # Queue name
#SBATCH -N 8 # Total number of nodes requested (16 cores/node)
#SBATCH -n 16 # Total number of mpi tasks requested
#SBATCH -t 00:50:00 # Run time (hh:mm:ss)
###SBATCH -A CTLS2017 # <-- Allocation name to charge job against

# Everything below here should be Linux commands

echo "starting at:"
date

module load autodock-vina/1.1.2

mpirun vina --config conf.txt --out myoutput_ligands.pdbqt

echo "ending at:"
date

Submit the job to the scheduler as

sbatch YourautodockVinaScript.slurm

For managing your “job” , refer to this guide.

For more on Autodock-Vina, refer to their official documentation
https://vina.scripps.edu/