PDB2PQR prepares protein structures for electrostatics calculations by converting PDB files to PQR format. The PQR format extends PDB by replacing the occupancy and B-factor columns with atomic partial charge and radius values—the two parameters required for solving the Poisson-Boltzmann equation.
Continuum electrostatics methods like Poisson-Boltzmann calculations reveal how charge distribution influences protein stability, binding affinity, and molecular recognition. However, PDB files from X-ray crystallography lack hydrogen atoms and contain no charge or radius information. PDB2PQR automates the preparation pipeline: reconstructing missing atoms, predicting protonation states at your target pH, and assigning force field parameters.
The output is a PQR file ready for electrostatics solvers like APBS (Adaptive Poisson-Boltzmann Solver). For general structure repair before molecular dynamics, consider PDB Fixer instead—it offers more extensive modeling capabilities including loop reconstruction and solvent box construction.
PDB2PQR operates as a multi-step pipeline that analyzes, corrects, and parameterizes protein structures.
Steric clashes between residues are resolved by systematically rotating dihedral angles. The algorithm uses distance cutoffs of 1.0 Å for hydrogen-hydrogen collisions, 1.5 Å for hydrogen-heavy atom interactions, and 2.0 Å for heavy atom pairs. When conflicts are detected, dihedral angles are adjusted in 5-degree increments until a non-clashing configuration is found.
Missing hydrogen atoms are added and then optimized to improve the hydrogen bonding network. The optimization includes:
PROPKA predicts pKa values for all titratable residues based on the local protein environment—nearby charges, hydrogen bonds, and solvent accessibility shift pKa values from their reference values. At your specified pH, residues are assigned appropriate protonation states.
For example, a buried glutamate forming a salt bridge might have its pKa shifted upward, remaining protonated (neutral) at physiological pH where surface glutamates would be deprotonated (charged).
After determining the structure and protonation states, PDB2PQR assigns atomic partial charges () and radii () from the selected force field. These parameters define the inputs to the Poisson-Boltzmann equation:
Where is the dielectric function (determined by atomic radii), is the electrostatic potential, and is the charge density (from atomic charges).
Upload a PDB file (.pdb or .ent) or fetch directly from RCSB using a PDB ID. PDB2PQR cannot model large missing backbone regions—ensure your structure is reasonably complete before processing.
The force field determines which charge and radius parameters are assigned to each atom. This choice significantly affects your electrostatics results.
PARSE is the recommended choice for standalone electrostatics calculations. Use AMBER or CHARMM when you need consistency with MD simulation parameters.
7.0 for physiological conditions, 4.5 for endosomal/lysosomal compartments, 2.0 for gastric conditions.--nodebump.--noopt.--assign-only to assign charges and radii without PROPKA, atom rebuilding, debumping, or hydrogen optimization. Use it only with an already complete, explicitly protonated structure. Disable it when ProteinIQ needs to predict protonation states or add missing atoms.--ffout so residue and atom names follow a selected force-field naming convention..in template generated from the final PQR file.PDB2PQR outputs a PQR file containing atomic coordinates, charges, and radii. The results summary shows structure statistics:
| Metric | Description |
|---|---|
| Atoms | Total atoms in the output (increases when hydrogens are added) |
| Residues | Number of amino acid residues |
| Chains | Number of protein chains |
| Total charge | Net charge of the structure in elementary charge units |
| Force field | Which parameter set was used |
The total charge should match your expectations based on the amino acid composition and pH:
The PQR file can be used directly with APBS for calculating:
Use PARSE for pure electrostatics work. This force field was designed specifically for Poisson-Boltzmann calculations and provides the most accurate results for solvation energies and potential surfaces.
Match your pH to experimental conditions. If studying enzyme activity at pH 5, use pH 5.0 for protonation—the charge distribution at different pH values can dramatically alter electrostatic properties.
Inspect unusual total charges. If the net charge seems unexpected, examine the PROPKA output for residues with shifted pKa values. A buried aspartate might remain protonated when you expected it to be charged.
Keep crystallographic waters for binding studies. Waters at interfaces often mediate important electrostatic interactions. Remove them only when computing surface potentials for visualization.
Prepare the structure with PARSE force field and PROPKA at your pH of interest. The PQR file can then be processed by APBS to generate dx grid files for 3D electrostatic potential visualization in tools like PyMOL or VMD.
Process both structures with identical settings (same force field, pH, options). The difference in electrostatic potential reveals how mutations alter the charge distribution and local environment—useful for understanding effects on binding or stability.
For structures that need both repair and electrostatics preparation, run PDB Fixer first to add missing residues and atoms, then process the fixed structure through PDB2PQR for charge assignment.
PDB2PQR works with protein structures but has limited support for non-standard molecules. Ligands, cofactors, and modified residues may not be parameterized in the standard force fields.
Some protonation states predicted by PROPKA may not be supported by all force fields. PARSE supports the widest range of protonation states including neutral termini, while AMBER and CHARMM have more limited options.
The debumping algorithm finds the first acceptable configuration rather than the optimal one. For structures with severe clashes, additional energy minimization may be needed.
Split FASTA files into record-based chunks by sequence count, target file count, maximum residues per file, or one file per sequence.
Clean and filter protein sequences by removing or replacing non-standard amino acid characters. Supports multiple filter modes including standard 20 amino acids, IUPAC codes, and custom character sets.
Clean and filter DNA sequences by removing or replacing non-standard nucleotide characters. Supports multiple filter modes including standard 4 bases, IUPAC ambiguity codes, and custom character sets.
Fix ligand files that fail RDKit, Meeko, or docking preparation. Repair SDF, MOL, and MOL2 inputs, apply safe chemistry cleanup, and export docking-ready SDF files.
PDBFixer is an OpenMM-based tool used for fixing problems in protein/DNA/RNA structure files, including adding missing atoms, adding missing residues, and fixing improper formatting.
Convert Protein Data Bank files to Crystallographic Information File format
Convert Protein Data Bank files to FASTA sequence format
Convert Protein Data Bank files to MOL2 molecular format
Download BindingDB binding record files by BindingDB monomer ID.
Convert CSV and TSV files containing sequence data to FASTA format with flexible column mapping and automatic delimiter detection
PDB2PQR prepares protein structures for electrostatics calculations by converting PDB files to PQR format. The PQR format extends PDB by replacing the occupancy and B-factor columns with atomic partial charge and radius values—the two parameters required for solving the Poisson-Boltzmann equation.
Continuum electrostatics methods like Poisson-Boltzmann calculations reveal how charge distribution influences protein stability, binding affinity, and molecular recognition. However, PDB files from X-ray crystallography lack hydrogen atoms and contain no charge or radius information. PDB2PQR automates the preparation pipeline: reconstructing missing atoms, predicting protonation states at your target pH, and assigning force field parameters.
The output is a PQR file ready for electrostatics solvers like APBS (Adaptive Poisson-Boltzmann Solver). For general structure repair before molecular dynamics, consider PDB Fixer instead—it offers more extensive modeling capabilities including loop reconstruction and solvent box construction.
PDB2PQR operates as a multi-step pipeline that analyzes, corrects, and parameterizes protein structures.
Steric clashes between residues are resolved by systematically rotating dihedral angles. The algorithm uses distance cutoffs of 1.0 Å for hydrogen-hydrogen collisions, 1.5 Å for hydrogen-heavy atom interactions, and 2.0 Å for heavy atom pairs. When conflicts are detected, dihedral angles are adjusted in 5-degree increments until a non-clashing configuration is found.
Missing hydrogen atoms are added and then optimized to improve the hydrogen bonding network. The optimization includes:
PROPKA predicts pKa values for all titratable residues based on the local protein environment—nearby charges, hydrogen bonds, and solvent accessibility shift pKa values from their reference values. At your specified pH, residues are assigned appropriate protonation states.
For example, a buried glutamate forming a salt bridge might have its pKa shifted upward, remaining protonated (neutral) at physiological pH where surface glutamates would be deprotonated (charged).
After determining the structure and protonation states, PDB2PQR assigns atomic partial charges () and radii () from the selected force field. These parameters define the inputs to the Poisson-Boltzmann equation:
Where is the dielectric function (determined by atomic radii), is the electrostatic potential, and is the charge density (from atomic charges).
Upload a PDB file (.pdb or .ent) or fetch directly from RCSB using a PDB ID. PDB2PQR cannot model large missing backbone regions—ensure your structure is reasonably complete before processing.
The force field determines which charge and radius parameters are assigned to each atom. This choice significantly affects your electrostatics results.
PARSE is the recommended choice for standalone electrostatics calculations. Use AMBER or CHARMM when you need consistency with MD simulation parameters.
7.0 for physiological conditions, 4.5 for endosomal/lysosomal compartments, 2.0 for gastric conditions.--nodebump.--noopt.--assign-only to assign charges and radii without PROPKA, atom rebuilding, debumping, or hydrogen optimization. Use it only with an already complete, explicitly protonated structure. Disable it when ProteinIQ needs to predict protonation states or add missing atoms.--ffout so residue and atom names follow a selected force-field naming convention..in template generated from the final PQR file.PDB2PQR outputs a PQR file containing atomic coordinates, charges, and radii. The results summary shows structure statistics:
| Metric | Description |
|---|---|
| Atoms | Total atoms in the output (increases when hydrogens are added) |
| Residues | Number of amino acid residues |
| Chains | Number of protein chains |
| Total charge | Net charge of the structure in elementary charge units |
| Force field | Which parameter set was used |
The total charge should match your expectations based on the amino acid composition and pH:
The PQR file can be used directly with APBS for calculating:
Use PARSE for pure electrostatics work. This force field was designed specifically for Poisson-Boltzmann calculations and provides the most accurate results for solvation energies and potential surfaces.
Match your pH to experimental conditions. If studying enzyme activity at pH 5, use pH 5.0 for protonation—the charge distribution at different pH values can dramatically alter electrostatic properties.
Inspect unusual total charges. If the net charge seems unexpected, examine the PROPKA output for residues with shifted pKa values. A buried aspartate might remain protonated when you expected it to be charged.
Keep crystallographic waters for binding studies. Waters at interfaces often mediate important electrostatic interactions. Remove them only when computing surface potentials for visualization.
Prepare the structure with PARSE force field and PROPKA at your pH of interest. The PQR file can then be processed by APBS to generate dx grid files for 3D electrostatic potential visualization in tools like PyMOL or VMD.
Process both structures with identical settings (same force field, pH, options). The difference in electrostatic potential reveals how mutations alter the charge distribution and local environment—useful for understanding effects on binding or stability.
For structures that need both repair and electrostatics preparation, run PDB Fixer first to add missing residues and atoms, then process the fixed structure through PDB2PQR for charge assignment.
PDB2PQR works with protein structures but has limited support for non-standard molecules. Ligands, cofactors, and modified residues may not be parameterized in the standard force fields.
Some protonation states predicted by PROPKA may not be supported by all force fields. PARSE supports the widest range of protonation states including neutral termini, while AMBER and CHARMM have more limited options.
The debumping algorithm finds the first acceptable configuration rather than the optimal one. For structures with severe clashes, additional energy minimization may be needed.
Split FASTA files into record-based chunks by sequence count, target file count, maximum residues per file, or one file per sequence.
Clean and filter protein sequences by removing or replacing non-standard amino acid characters. Supports multiple filter modes including standard 20 amino acids, IUPAC codes, and custom character sets.
Clean and filter DNA sequences by removing or replacing non-standard nucleotide characters. Supports multiple filter modes including standard 4 bases, IUPAC ambiguity codes, and custom character sets.
Fix ligand files that fail RDKit, Meeko, or docking preparation. Repair SDF, MOL, and MOL2 inputs, apply safe chemistry cleanup, and export docking-ready SDF files.
PDBFixer is an OpenMM-based tool used for fixing problems in protein/DNA/RNA structure files, including adding missing atoms, adding missing residues, and fixing improper formatting.
Convert Protein Data Bank files to Crystallographic Information File format
Convert Protein Data Bank files to FASTA sequence format
Convert Protein Data Bank files to MOL2 molecular format
Download BindingDB binding record files by BindingDB monomer ID.
Convert CSV and TSV files containing sequence data to FASTA format with flexible column mapping and automatic delimiter detection