About

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 PQR files are PDB files where the occupancy and B-factor columns have been replaced by per-atom charge and radius.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.

This is a clone of PDB2PQR server(Dolinsky et.al 2004). Original server you can access from Here

Please enter either:
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
Use PROPKA to assign protonation states at pH
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)
PDB2PQR References:

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]