Chimera Commands Index

pdb2pqrmolecule  atom-spec ]  options

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

As of 4/30/2020, the PDB2PQR web service from the National Biomedical Computation Resource (NBCR) has been discontinued. The pdb2pqr command 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 you use the backend local and location options of the command.

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

Like the Chimera PDB2PQR tool, the pdb2pqr command runs 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. 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.
If more than one molecule model is present, the molecule option should be used to specify which to act upon. 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. **

Although Dock Prep has a similar function, the overlap is only partial 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, addcharge, findhbond, coulombic


Option keywords for pdb2pqr can be truncated to unique strings and their case does not matter. A vertical bar “|” designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.

See the documentation at the PDB2PQR site for details on specific options.

molecule  atom-spec
Limit the calculation to the specified model (the entire molecule model containing the specified atoms). Only one model should be specified. If atom-spec includes any spaces, it must be enclosed in single or double quote marks.
forcefield  ff
Which charge and radius parameters to use, where ff can be: Note: residues not handled by the designated force field will be omitted.
pqr  file
Pathname (name and location) of the output PQR file; if not specified, a temporary name and location will be used.
propkaph  pH
Use PROPKA to predict the pKa values of ionizable groups in protein at the specified pH. Users should cite:
Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values. Søndergaard CR, Olsson MHM, Rostkowski M, Jensen JH. J Chem Theory Comput. 2011;7(7):2284-95.
Very fast empirical prediction and rationalization of protein pKa values. Li H, Robertson AD, Jensen JH. Proteins. 2005 Dec 1;61(4):704-21.
neutralN true | false
Whether to make the protein N-terminus neutral (only available for the PARSE force field).
neutralC true | false
Whether to make the protein C-terminus neutral (only available for the PARSE force field).
debump true | false
Whether to ensure that new atoms are not rebuilt too close to existing atoms.
optHbond true | false
Whether to adjust hydrogen positions and flip certain sidechains (His, Asn, Glu) as needed to optimize hydrogen bonds.
distCutoff  d
Hydrogen bond distance cutoff (default 3.4 Å).
angleCutoff  a
Hydrogen bond angle cutoff (default 30°).
hbonds true | false
Whether to send hydrogen bond information to the Reply Log.
ligands true | false
Whether to use the PEOEPB approach (see above) to assign charges to any ligand residues, after protonation and conversion to Mol2 format (by Chimera) as currently required by the program; the residue(s) will be renamed LIG and placed in chain L.
apbs true | false
Whether to generate an example APBS input file and show it in the Reply Log; however, such a file is not needed to run the program from Chimera (using the APBS tool or apbs command).
backend  opal | local
Whether to use an Opal web service (default) or a locally installed executable.
location  opal-URL | local-path
Depending on the backend setting, the URL of the web service (default is the URL for the service provided by the NBCR) or the pathname of the local executable. Since the NBCR web service has been retired, users need to download PDB2PQR and use both the backend local and location options.
wait true | false
Whether to wait for the calculation to finish before starting to execute any subsequent commands.