MEGADOCK 4.x
Megadock is a structural bioinformatics software for FFT-grid-based protein-protein docking that takes advantage of the massively parallel CUDA architecture of NVIDIA GPUs and/or multiple computation nodes.
Slurm Script
#!/bin/bash #SBATCH -J mega_job # Job name #SBATCH -o mega_job.o%j # Name of stdout output file (%j expands to jobId) #SBATCH -p CUIQue # Queue name, the default Que #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) # Everything below here should be Linux commands echo "starting at:" date ## The Megadock module, U need to load it always module load megadock/4.0.3 ## Receptor = 1gcq_r.pdb ## Ligand = 1gcq_l.pdb mpirun megadock -R 1gcq_r.pdb -L 1gcq_l.pdb echo "ending at:" date
Submit the job to the scheduler as
sbatch YourMegadock.slurm
For managing your “job” , refer to this guide.
For more on Mega-dock, refer to their official documentation