#!/bin/sh
#SBATCH --partition=normal
#SBATCH   --job-name=ligand_pocket
#SBATCH   --output=pocket-%j.out
#SBATCH   --error=pocket-%j.err
#SBATCH   --time=0-20:00:00
#SBATCH   --nodes=5
#SBATCH   --ntasks-per-node=6
#SBATCH   --mem-per-cpu=2GB

module load rosetta
NUM=1
srun mpirun rosetta_scripts.mpi.linuxgccrelease
        -ex1 \
        -ex2 \
        -linmem_ig 10 \
        -restore_pre_talaris_2013_behavior \
        -parser:protocol design.xml \
        -extra_res_fa ribose.sdf.params \
        -s "protein.pdb ligand.pdb" \
        -nstruct $NUM --out:prefix $SLURM_ARRAY_TASK_ID \
        -out:file:scorefile pocket.out