PDB2PQR quickstart
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.
You have a structure and want it docking- and electrostatics-ready — 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
Configure the job
| Parameter | Value |
|---|---|
| PDB ID | 1M17 |
| pH | 7.4 |
| Force field | amber |
| Optimize hydrogens | true |
| Remove water | true |
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.).
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:
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 for all force field and processing options
- See outputs for PQR format details and pKa interpretation
- Use the PQR output with DiffDock for docking with correct protonation
Read next
Was this page helpful?
Interpreting PDB2PQR outputs
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 troubleshooting
Fix PDB2PQR runs: dropped HETATM ligands and non-standard residues, surprising PROPKA pKa values, DEBUMP clash failures, and timeouts above 10,000 atoms.