PDB2PQR Server

Currently using PDB2PQR Version 2.0.0

Return to the PDB2PQR homepage.


This server enables a user to convert PDB files into PQR files. PQR files are PDB files where the occupancy and B-factor columns have been replaced by per-atom charge and radius.

pKa calculations are performed by PROPKA.

For more information on PDB2PQR please see the:

If you use the PDB2PQR service in a publication, please cite:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32 W665-W667 (2004). [Link]

Note: This server uses automatic refreshing to update the status of your PDB2PQR submission.

Please enter either:
a PDB ID:
upload a PDB file:

Pick a forcefield to use:

AMBER
CHARMM
PARSE
PEOEPB
SWANSON
TYL06
User-defined forcefield (help):


Pick an output naming scheme to use (help):
Internal naming scheme (What's this?)
AMBER
CHARMM
PARSE
PEOEPB
SWANSON
TYL06
Available options:
Ensure that new atoms are not rebuilt too close to existing atoms
Optimize the hydrogen bonding network
Assign charges to the ligand specified in a MOL2 file:
Create an APBS input file (this also enables the option to run APBS and visualize your results through the web interface, if it has been installed)
Add/keep chain IDs in the PQR file
Insert whitespaces between atom name and residue name, between x and y, and between y and z
Create Typemap output
Make the protein's N-terminus neutral (requires PARSE forcefield)
Make the protein's C-terminus neutral (requires PARSE forcefield)
Remove the waters from the output file
pKa Options:
Use pH
No pkA calculation
Use PROPKA to assign protonation states at provided pH
Use PDB2PKA to parametrize ligands and assign pKa values (requires PARSE forcefield) at provided pH


The PDB2PQR application and web server was written by:
Jens Erik Nielsen
Todd Dolinsky
Nathan Baker
Kyle Monson

PDB2PQR Opal integration by:
Wes Goodman
Samir Unni
Yong Huang

JMol visualization scripts and applets provided by:
Robert Hanson

PDB2PQR is supported by NIH grant GM069702-01 to NAB, the NPACI Alpha Project program, and the National Biomedical Computation Resource.

Before sending a bug report you may want to check the pdb2pqr-users mailing list archives to make sure your question has not already been addressed.

For additional support, feature requests, and bug reports you may contact the pdb2pqr-users mailing list.