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PDBCharges

How to run PDBCharges in Docker container

# build container
docker build -t local/pdbcharges .

# download the Chemical Component Dictionary
curl -s https://files.wwpdb.org/pub/pdb/data/monomers/components-pub.sdf.gz | gunzip -c > components-pub.sdf

# create folder to store results (the folder must be empty)
mkdir results

# run calculation on the 1alf.pdb file from the examples folder
docker run --rm --name PDBcharges \
    -v ./components-pub.sdf:/opt/components-pub.sdf \
    -v ./examples:/opt/PDBCharges/examples \
    -v ./results:/opt/PDBCharges/results \
    local/pdbcharges \
    calculate_charges_workflow.py --CCD_file /opt/components-pub.sdf --PDB_file examples/1alf.pdb --data_dir results

# or you can calculate the charges on another structure from PDB database, e.g.:
curl -O https://files.rcsb.org/download/6wlv.pdb

docker run --rm --name PDBcharges \
    -v ./components-pub.sdf:/opt/components-pub.sdf \
    -v ./6wlv.pdb:/opt/PDBCharges/6wlv.pdb \
    -v ./results:/opt/PDBCharges/results \
    local/pdbcharges \
    calculate_charges_workflow.py --CCD_file /opt/components-pub.sdf --PDB_file 6wlv.pdb --data_dir results