A PQR file with partial charge and radius in the occupancy and B-factor columns, a PROPKA pKa table with HID, HIE and HIP assignments, and a net charge.

PDB2PQR returns a PQR coordinate file — the same atoms as your input, now carrying partial charges and radii — plus a per-residue pKa table and any processing warnings. The PQR file is what you carry forward: use it directly in APBS electrostatics, as a correctly protonated receptor for docking, or as the starting point for MD setup, while the pKa table tells you which residues (especially histidines) sit in unusual environments.

Interpreting PDB2PQR outputs

PQR file

The primary output is a PQR coordinate file. PQR format is similar to PDB but replaces the occupancy and B-factor columns with partial charge and atomic radius:

ATOM      1  N   ALA A   1      27.340  24.430   2.614  -0.4157  1.8240
ATOM      2  CA  ALA A   1      26.266  25.413   2.842   0.0337  1.9080
ATOM      3  C   ALA A   1      26.913  26.639   3.531   0.5973  1.9080

Column	PDB Meaning	PQR Meaning
Column 55-60	Occupancy	Partial charge (e)
Column 61-66	B-factor	Atomic radius (A)

pKa predictions

Field	Type	Description
`titratable_residues`	array	Per-residue pKa predictions
`titratable_residues[].residue_name`	string	Three-letter residue code (e.g., "ASP")
`titratable_residues[].residue_number`	integer	Residue sequence number
`titratable_residues[].chain_id`	string	Chain identifier
`titratable_residues[].predicted_pka`	number	PROPKA-predicted pKa
`titratable_residues[].model_pka`	number	Model compound pKa (reference)
`titratable_residues[].pka_shift`	number	Shift of the predicted pKa from the model value
`titratable_residues[].protonation_state`	string	Assigned protonation state

Titratable residues

Residue	Model pKa	Typical Range
ASP (Aspartate)	3.8	2.0-7.0
GLU (Glutamate)	4.5	2.5-7.5
HIS (Histidine)	6.5	4.0-9.0
CYS (Cysteine)	9.0	6.0-12.0
TYR (Tyrosine)	10.0	8.0-13.0
LYS (Lysine)	10.5	8.0-12.0
N-terminus	8.0	6.0-9.5
C-terminus	3.6	2.0-5.5

Histidine protonation states

PDB2PQR distinguishes three histidine states:

State	Name	Description
HID	delta-protonated	Hydrogen on N-delta
HIE	epsilon-protonated	Hydrogen on N-epsilon
HIP	doubly-protonated	Both nitrogens protonated (positive charge)

At pH 7.4, histidines with pKa > 7.4 are assigned HIP; others are assigned HID or HIE based on hydrogen bond optimization.

Processing summary

Field	Type	Description
`atoms_processed`	integer	Atom count in the output structure
`residues_processed`	integer	Number of residues processed
`total_charge`	number	Net estimated charge of the system at the target pH
`warnings`	string[]	Processing warnings (missing atoms, clashes)
`processing_time_seconds`	number	Total processing time

PDB2PQR does not generate an APBS input file — its output is the PQR (or PQR + PDB) structure plus the pKa table above. To run APBS electrostatics, use the "parse" or "peoepb" force field (optimized for Poisson-Boltzmann) and build the APBS run from the resulting PQR file.

Downloading artifacts

PQR file (pqr_content / pqr_s3_uri): primary output, downloadable from the job panel
pKa table: per-residue predictions from titratable_residues
Log file: processing log with warnings and statistics

Interpreting PDB2PQR outputs