** Use PDB2PQR web service directly instead of this tool **

As of 4/30/2020, the PDB2PQR web service from the National Biomedical Computation Resource (NBCR) has been discontinued. This Chimera tool will no longer work unless you have an older version of PDB2PQR locally installed on your own computer (it does not work with the current version) and then in this tool, you change the Executable location to Local and enter its location.

Instead, we recommend using the PDB2PQR web service at server.poissonboltzmann.org (directly, not from Chimera). The resulting PQR file can be opened in Chimera if you wish.

The PDB2PQR tool is an interface for running PDB2PQR, which prepares structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files. Several of the force field options were developed specifically for Poisson-Boltzmann calculations, and thus, a primary use is to prepare structures for APBS (Adaptive Poisson-Boltzmann Solver). Users should cite:

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W522-5.
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W665-7.
Results are opened as a new model in Chimera, with charge and radius attributes assigned to the atoms. ** Any residues not handled by the designated force field will be omitted. Conversely, any unwanted residues such as waters should be deleted beforehand to ensure they do not appear in the result. **

PDB2PQR and Dock Prep overlap in functionality, but only partially, and even the seemingly shared functions (e.g., repairing truncated sidechains, adding hydrogens) are done differently. It may be useful to run certain parts of Dock Prep beforehand, for example, to delete solvent. However, only the charge and radius assignments from PDB2PQR, not those from Chimera or other Chimera tools, can be written to a PQR file. See also: AddH, Add Charge, FindHBond, Coulombic Surface Coloring

There are several ways to start PDB2PQR, a tool in the Structure Editing category. It is also implemented as the command pdb2pqr.

Options (see the documentation at the PDB2PQR site for details): Executable location: OK initiates the calculation and dismisses the dialog, whereas Apply initiates the calculation without dismissing the dialog. The job will be run in the background; clicking the information icon in the Chimera status line will bring up the Task Panel, in which the job can be canceled if desired. Close dismisses the dialog, and Help opens this manual page in a browser window.

The processed structure will be opened as a new model in Chimera, with charge and radius attributes assigned to the atoms.

UCSF Computer Graphics Laboratory / May 2021