---
title: PDB2PQR inputs and parameters
description: 'PDB structures, pH settings, force field options, and processing flags.'
tags:
  - pdb2pqr
  - inputs
---

You provide a protein structure — as a PDB ID, raw PDB data, or an S3 URI — plus a target pH. The pH is the parameter that most affects your result: it drives which titratable residues get protonated, so set it to the environment you care about (7.4 for physiological, lower for endosomal or gastric contexts).

## PDB2PQR inputs and parameters

## Structure input

| Parameter | Type | Required | Description |
|-----------|------|----------|-------------|
| `pdb_id` | string | One of three (chat only) | Four-character PDB accession code (e.g., `"1M17"`). The platform resolves this to the structure before dispatch — it is not a field the backend API accepts directly. |
| `pdb_content` | string | One of three | PDB file contents as a string |
| `pdb_s3_uri` | string | One of three | S3 URI to an already-uploaded or previously-downloaded PDB file |

Exactly one of `pdb_content` or `pdb_s3_uri` must reach the backend job (the chat tool also accepts `pdb_id`, which the platform resolves to one of the other two first).

## Core parameters

| Parameter | Type | Default | Description |
|-----------|------|---------|-------------|
| `ph` | number | `7.4` | Target pH for protonation state assignment (0.0-14.0) |
| `forcefield` | string | `"amber"` | Force field for charge/radius assignment |

pKa prediction always uses PROPKA — there is no user-selectable titration-state method.

### Force field options

| Value | Description |
|-------|-------------|
| `"amber"` (default) | AMBER ff14SB, general purpose / MD preparation |
| `"charmm"` | CHARMM36 parameters |
| `"parse"` | Optimized for Poisson-Boltzmann electrostatics |
| `"swanson"` | Extended AMBER for nucleic acid-protein complexes |
| `"peoepb"` | PB-optimized partial charges for APBS |
| `"tyl06"` | Tyrosine-focused parameters |

## Processing options

| Parameter | Type | Default | Description |
|-----------|------|---------|-------------|
| `include_hydrogens` | boolean | `true` | Add missing hydrogens to the structure |
| `optimize_hydrogen_bonds` | boolean | `true` | Optimize the hydrogen-bonding network |
| `assign_charges` | boolean | `true` | Assign partial charges from the chosen force field |
| `debump` | boolean | `true` | Resolve steric clashes introduced by added hydrogens |
| `remove_water` | boolean | `true` | Remove crystallographic water molecules |
| `chain_ids` | string[] | `null` (all chains) | Process only the listed chain IDs (e.g., `["A"]`) |

## Output options

| Parameter | Type | Default | Description |
|-----------|------|---------|-------------|
| `output_format` | string | `"pqr"` | `"pqr"` (charges and radii) or `"pdb"` (also writes a companion PDB file) |
| `include_propka_output` | boolean | `true` | Include the full PROPKA pKa-prediction output |
| `pdb_filename` | string | `"input.pdb"` | Filename recorded for tracking; has no effect on processing |

## Common pH values

| pH | Context |
|----|---------|
| 7.4 | Physiological (blood, most in vitro assays) |
| 7.0 | Standard neutral |
| 5.0 | Endosomal/lysosomal pH |
| 6.5 | Tumor microenvironment |
| 4.5 | Gastric pH |

## Input validation rules

- PDB ID must be a valid four-character alphanumeric code
- pH must be between 0.0 and 14.0
- PDB content must contain valid ATOM/HETATM records
- Force field name must be lowercase (`"amber"`, not `"AMBER"`)

## Input from previous jobs

| Source Tool | Extracted Field |
|-------------|-----------------|
| PDB Search | PDB ID or structure file |
| ESMFold | Predicted PDB structure |
| Biotite | Processed structure file |

## Read next