PDB2PQR

PDB2PQR prepares an existing protein structure for electrostatics, docking, and molecular dynamics: it assigns protonation states at a chosen pH, adds missing hydrogens, and applies force-field charges and radii. Reach for it after you already have a structure — it is a preparation step, not a source of structures. Get the structure first by downloading it from the PDB, fetching it with AlphaFold, or predicting it with ESMFold, then run PDB2PQR to make it docking-ready. See what you can achieve for the full set.

PDB2PQR overview

PDB2PQR automates the preparation of protein structures for electrostatics calculations, molecular dynamics, and docking. It assigns protonation states at a specified pH using PROPKA pKa prediction, adds missing hydrogen atoms, and assigns partial charges and atomic radii from the chosen force field. The output PQR file can be used directly with APBS for Poisson-Boltzmann electrostatics.

How it works

Rendering diagram…

Key capabilities

Supported force fields

When to use PDB2PQR

Use PDB2PQR when:

• You need to prepare a protein structure for electrostatics calculations (APBS)
• You need correct protonation states at a specific pH for docking
• You want to identify which histidines are protonated (HID, HIE, or HIP)
• You need to add hydrogens to a crystal structure that lacks them
• You are setting up molecular dynamics simulations and need force field parameters

Use other tools instead when:

• You need full MD system setup (solvation, ions, topology files): use GROMACS or AmberTools
• You need small-molecule protonation: use server-side cheminformatics tools
• You need only 3D structure prediction: use ESMFold

Limitations

• Non-standard residues (modified amino acids, ligands) may not have force field parameters in all force fields
• PROPKA assumes a static structure; conformational flexibility is not accounted for
• Very large structures (> 10,000 atoms) may take longer to process
• Membrane proteins may have inaccurate pKa predictions due to the implicit solvent model

Citations

Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 2004;32(Web Server issue):W665-W667. doi: 10.1093/nar/gkh381

Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 2007;35(Web Server issue):W522-W525. doi: 10.1093/nar/gkm276

Olsson MHM, Sondergaard CR, Rostkowski M, Jensen JH. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. J Chem Theory Comput. 2011;7(2):525-537. doi: 10.1021/ct100578z

Chat Usage

Example Prompts

• "Prepare PDB 1M17 for electrostatics calculation at pH 7.4"
• "Add hydrogens to this protein structure with AMBER force field"
• "Run PDB2PQR on my uploaded PDB and show me the histidine protonation states"

Workflow Chaining

• Feeds into: APBS electrostatics, DiffDock (protonated receptor), molecular dynamics setup
• Accepts from: PDB Search (crystal structures), ESMFold (predicted structures), Biotite (processed structures)

FAQ

Read next