CAVER

CAVER is a software tool for analysis and visualization of tunnels and channels in protein structures. Tunnels are void pathways leading from a cavity buried in a protein core to the surrounding solvent. Unlike tunnels, channels lead through the protein structure and their both endings are opened to the surrounding solvent. Studying of these pathways is highly important for drug design and molecular enzymology.

Example script slurm-caver-script.sh to run CAVER on 1 node of the cpu partition using 1 cores and at most 16 GB of memory:

slurm-caver-script.sh

#!/bin/bash
 
#SBATCH --time=1-00:00:00
#SBATCH --ntasks-per-node=1
#SBATCH --mem=16GB
#SBATCH --partition=cpu
#SBATCH --qos=cpu
#SBATCH --job-name=run_caver
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
 
echo "JOB NAME    : $SLURM_JOB_NAME"
echo "PARTITION   : $SLURM_JOB_PARTITION"
echo "MEMORY      : $SLURM_MEM_PER_NODE MB"
echo "HOSTNAME    : $HOSTNAME"
 
module load caver
 
# MAX_HEAP_MEM: specification of maximum Java heap size (DON'T CHANGE)
MAX_HEAP_MEM="$(($SLURM_MEM_PER_NODE*90/100))m" #calculated as 90% of slurm memory requested
 
#----------------EDIT BELOW-------------------------------------------------------------------------------------
# PDB_DIR: directory of pdb files (input files)
PDB_DIR="$CAVER_DIR/examples/QUICK_START/md_snapshots"
# OUT_DIR: directory of output files
OUT_DIR="$HOME/out2"
# CONFIG_EXAMPLE: path to the CAVER configuration file (config.txt). This parameter is optional—if not specified
# Path_to_caver_home/config.txt will be used
CONFIG_EXAMPLE="$CAVER_DIR/examples/QUICK_START/inputs/config.txt"
#--------------------------------------------------------------------------------------------------------------
 
mkdir -p "$OUT_DIR"
 
java -Xmx${MAX_HEAP_MEM} -cp "$CAVER_DIR/caver/lib" -jar "$CAVER_DIR/caver/caver.jar" -home "$CAVER_DIR/caver" \
-pdb "$PDB_DIR" -conf "$CONFIG_EXAMPLE" -out "$OUT_DIR"