---
title: Interpreting PDB2PQR outputs
description: '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.'
tags:
  - pdb2pqr
  - outputs
---

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

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