CCDC

Description

The CCDC (Cambridge Crystallographic Data Centre) develops software for chemistry and crystallography, including GOLD (protein-ligand docking), CSD (Cambridge Structural Database), and analysis tools.

Available Versions

  • ccdc/2024.3

Components

  • CSD: Cambridge Structural Database

  • GOLD: Protein-ligand docking

  • Mercury: Structure visualization and analysis

  • Hermes: System preparation for docking

  • SuperStar: Intermolecular interaction mapping

Job Submission with GOLD

submit_gold.sh
#!/bin/bash
#SBATCH -J gold_docking
#SBATCH -N 1
#SBATCH -c 8
#SBATCH -t 48:00:00
#SBATCH --mem=16G

export INPUT="protein.mol2 ligand.mol2 gold.conf"
export OUTPUT="gold_results/"

module load ccdc/2024.3

job-nanny gold_conf gold.conf

Example GOLD Configuration File

gold.conf
GOLD CONFIGURATION FILE
AUTOMATIC SETTINGS

PROTEIN DATA FILENAME protein.mol2
LIGAND DATA FILENAME ligand.mol2
SITE ATOM RADIUS 10.0
CAVITY DETECTION METHOD SPHERES
FLOOD FILL RADIUS 10.0
FLOOD FILL ORIGIN X 0.0 0.0 0.0

GENETIC ALGORITHM
POPULATION SIZE 100
SELECTION PRESSURE 1.1
NUMBER OF OPERATIONS 100000
NUMBER OF ISLANDS 5
NICHING PRESSURE 1.1
MUTATION RATE 30
CROSSOVER RATE 95

TERMINATION
TOP SOLUTIONS 10
RMS THRESHOLD 1.5

OUTPUT OPTIONS
LOG FILE gold.log
SAVE RANKED LIGANDS YES
SAVE BINDING ENERGIES YES
SAVE INTERACTIONS YES

Job Submission with GOLD (MPI)

submit_gold_mpi.sh
#!/bin/bash
#SBATCH -J gold_mpi
#SBATCH -N 2
#SBATCH --ntasks-per-node=28
#SBATCH -t 48:00:00
#SBATCH --mem-per-cpu=2G

export INPUT="protein.mol2 ligands/ gold.conf"
export OUTPUT="gold_mpi_results/"

module load ccdc/2024.3
module load openmpi/4.1.5

job-nanny mpirun gold_conf_mpi gold.conf

Batch Processing of Multiple Ligands

submit_gold_batch.sh
#!/bin/bash
#SBATCH -J gold_batch
#SBATCH --array=1-100
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 24:00:00
#SBATCH --mem=8G
#SBATCH --output=gold_%A_%a.out

export INPUT="protein.mol2"
export OUTPUT="results_${SLURM_ARRAY_TASK_ID}/"

module load ccdc/2024.3

# Specific ligand for this array
LIGAND="ligand_${SLURM_ARRAY_TASK_ID}.mol2"

# Create specific configuration file
cat > gold_${SLURM_ARRAY_TASK_ID}.conf << EOF
GOLD CONFIGURATION FILE
PROTEIN DATA FILENAME protein.mol2
LIGAND DATA FILENAME $LIGAND
SITE ATOM RADIUS 10.0
OUTPUT DIRECTORY results_${SLURM_ARRAY_TASK_ID}
EOF

job-nanny gold_conf gold_${SLURM_ARRAY_TASK_ID}.conf

Accessing the CSD (Cambridge Structural Database)

To access the CSD database:

# Configure environment variables
module load ccdc/2024.3
export CSDHOME=$CCDC_CSD

# Search structures
csdsearch -q "benzene" -o benzene.csds

# Convert to common formats
csd2cif benzene.csds benzene.cif
csd2mol2 benzene.csds benzene.mol2

Analysis with Mercury (text mode)

submit_mercury.sh
#!/bin/bash
#SBATCH -J mercury
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 02:00:00
#SBATCH --mem=4G

export INPUT="structure.cif"
export OUTPUT="analysis.txt"

module load ccdc/2024.3

# Hydrogen bond analysis
job-nanny mercury -s structure.cif -o analysis.txt -c "hbonds"

# Distance and angle calculation
job-nanny mercury -s structure.cif -o geometry.txt -c "geometry"

Preparation with Hermes

submit_hermes.sh
#!/bin/bash
#SBATCH -J hermes
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 02:00:00
#SBATCH --mem=4G

export INPUT="protein.pdb ligand.mol2"
export OUTPUT="protein_prepared.mol2 ligand_prepared.mol2"

module load ccdc/2024.3

# Add hydrogens
job-nanny hermes -p protein.pdb -o protein_prepared.mol2 -addh

# Prepare ligand
job-nanny hermes -l ligand.mol2 -o ligand_prepared.mol2 -addh -charges

Mapping with SuperStar

submit_superstar.sh
#!/bin/bash
#SBATCH -J superstar
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 04:00:00
#SBATCH --mem=8G

export INPUT="protein.mol2"
export OUTPUT="superstar_map.grd"

module load ccdc/2024.3

# Map interaction-prone regions
job-nanny superstar -p protein.mol2 -o superstar_map.grd -probe "water"

References

See also