---
title: PDB2PQR quickstart
description: Protonate a structure at pH 7.4 with the amber force field, read the predicted pKa and histidine states, then download the PQR file for docking or APBS.
tags:
  - pdb2pqr
  - quickstart
---

You have a structure and want it docking- and electrostatics-ready — [PDB2PQR](/docs/pdb2pqr) does it in a few steps: point it at a PDB ID (or uploaded file), set the pH, run it, then review the predicted pKa values and download the protonated PQR file.

## PDB2PQR quickstart

This guide walks through protonating a protein at physiological pH and reviewing the predicted pKa values.

## Workflow 1: Protonate a PDB structure

### Step 1: Open PDB2PQR

Navigate to **Tools > PDB2PQR** in .bloom*, or ask Ivy:

```
Prepare PDB 1M17 for electrostatics at pH 7.4
```

### Step 2: Configure the job

| Parameter | Value |
|-----------|-------|
| PDB ID | `1M17` |
| pH | `7.4` |
| Force field | `amber` |
| Optimize hydrogens | `true` |
| Remove water | `true` |

### Step 3: Review pKa predictions

The pKa table shows predicted values for titratable residues:

| Residue | Chain | Predicted pKa | Model pKa | Protonated? |
|---------|-------|---------------|-----------|-------------|
| ASP-32 | A | 3.2 | 3.8 | No |
| GLU-51 | A | 4.8 | 4.5 | No |
| HIS-64 | A | 6.8 | 6.5 | No (HIE) |
| HIS-94 | A | 7.9 | 6.5 | Yes (HIP) |
| LYS-125 | A | 10.8 | 10.5 | Yes |

Residues with pKa shifted far from the model value may be in unusual local environments (buried, salt bridges, etc.).

### Step 4: Download the PQR file

Click **Download PQR** to get the protonated structure file for use in APBS, docking tools, or MD setup.

## Workflow 2: Explore histidine protonation

Histidine protonation is especially important for active sites and metal-binding sites. To focus on histidines:

```
Run PDB2PQR on 4HHB at pH 7.4 and show me all histidine protonation states
```

The output identifies each histidine as HID (delta), HIE (epsilon), or HIP (double):

| Residue | State | pKa | Rationale |
|---------|-------|-----|-----------|
| HIS-20 | HIE | 5.2 | Below pH, neutral, epsilon-protonated for H-bond to Asp-22 |
| HIS-87 | HIP | 8.1 | Above pH, doubly protonated, coordinating iron |
| HIS-143 | HID | 6.0 | Below pH, neutral, delta-protonated for H-bond to backbone |

## Workflow 3: Prepare for APBS electrostatics

Use the PARSE force field, which is tuned for Poisson-Boltzmann calculations:

| Parameter | Value |
|-----------|-------|
| PDB ID | `1M17` |
| Force field | `parse` (optimized for PB) |

The job produces the protonated PQR file — build your APBS run from that output; PDB2PQR does not generate an APBS input file itself.

## Next steps

- See [inputs](/docs/pdb2pqr/inputs) for all force field and processing options
- See [outputs](/docs/pdb2pqr/outputs) for PQR format details and pKa interpretation
- Use the PQR output with DiffDock for docking with correct protonation

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