PDB2PQR
Prepare biomolecular structures for electrostatics calculations with charge and radius assignment.
Prepare biomolecular structures for electrostatics calculations with charge and radius assignment.
PDB2PQR prepares biomolecular structures for electrostatics calculations by converting PDB or mmCIF 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 (.pdb or .ent) or mmCIF (.cif or .mmcif) protein, DNA, or RNA structure, or fetch a structure directly from RCSB using a PDB ID. Blank lines at the beginning and end of PDB/ENT files are removed before processing. Structure records and native format are preserved for PDB2PQR. PDB2PQR cannot model large missing regions, so ensure the structure is reasonably complete before processing.
Cryo-EM mmCIF structures can be processed without unit-cell, space-group, or crystallographic transformation metadata. Missing crystallographic headers are recorded in the run log. The same structure preparation, protonation, charge and radius calculations apply.
PDB2PQR 3.7.1 still requires deposition-date metadata (_pdbx_database_status.recvd_initial_deposition_date) when reading mmCIF. Files exported from structure editors or prediction programs may omit this field. ProteinIQ checks for it before submission. If it is missing, export the structure as PDB in the program that created it and upload the PDB file.
You can optionally upload a MOL2 file to parameterize one ligand. The ligand name must match exactly one ligand in each submitted structure. Custom force fields require both the native DAT parameter file and names file.
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 atom rebuilding, debumping, or hydrogen optimization. Use it only with an already complete, explicitly protonated structure.--ffout so residue and atom names follow a selected force-field naming convention..in template generated from the final PQR file..log diagnostics alongside each successful result.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 residue records across TER-separated segments |
| Chains | Number of chain identities or TER-separated segments |
| Total charge | Net charge of the structure in elementary charge units |
| Force field | Which parameter set was used |
For CIF/mmCIF inputs or whitespace-delimited PQR output, residue and chain counts are unavailable unless Keep chain IDs is enabled. In those modes, native PDB2PQR can omit both chain identifiers and TER separators, so the output no longer contains enough information for an accurate count.
When PROPKA is enabled, the pKa values table lists the native summary rows in their original order, including residue/group identity, chain, predicted pKa, model pKa, and applied pH. The Run coverage table pairs PDB2PQR’s own parsed input counts with output counts, total charge, native warning messages, and APBS status. These diagnostics report what the programs emitted; they do not invent a parameterization score or silently classify unsupported chemistry as successful.
Every successful native run also includes a JSON reproducibility manifest with the exact runtime versions, normalized command arguments, applied pH, molecule kind, and SHA-256 digests for the input and returned artifacts. Temporary service paths are excluded.
With Run APBS electrostatics enabled, the Electrostatics result displays the prepared PQR structure together with the native OpenDX potential. Red and blue isosurfaces show −1 and +1 kT/e, respectively. The PQR, OpenDX, APBS input, and APBS log remain independently downloadable for analysis in PyMOL, VMD, or another compatible program.
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 and PROPKA at your pH of interest, then enable Run APBS electrostatics. The result includes the interactive electrostatic view and the native files needed for PyMOL, VMD, or downstream automation.
Enable PROPKA, choose pH series, and set the endpoints and number of points. Compare the pKa and coverage tables by applied pH, inspect total-charge changes, and download each independently prepared PQR. Enabling APBS also produces one potential map per permitted series run.
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 and nucleic-acid 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.
PDB2PQR jobs are limited to 10 structure–pH combinations. APBS jobs are limited to 3 combinations because each calculation generates a three-dimensional grid, and an individual OpenDX map must be no larger than 160 MiB for safe interactive delivery. These limits are checked before dispatch; reduce the number of structures or pH points when a request exceeds them.
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 records by count, target file count, record length, or one sequence per file.
Clean DNA sequences by removing or replacing non-standard nucleotides with IUPAC-aware filters.
Clean protein sequences by removing or replacing non-standard amino acids with configurable filters.
Repair SDF, MOL, and MOL2 ligands for RDKit, Meeko, and docking preparation workflows.
Convert CSV or TSV sequence tables to FASTA with automatic delimiter detection and column mapping.
Paste or upload a sequence file in any common format and download FASTA. The format is detected automatically, and nothing leaves your browser.
Paste or upload DNA, RNA, or protein text and download FASTA. Sequence names, wrapped lines, and tables are detected automatically, and nothing leaves your browser.
Extract CDS, mRNA, gene, rRNA, and tRNA features from GenBank records into FASTA.
Translate DNA sequences into proteins across reading frames and genetic code tables.
Convert coding-strand DNA to RNA notation by replacing thymine with uracil.