PDB2PQR

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). The interface can use either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy of the program. 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.

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.

• Molecule - the structure of interest (choose from pulldown menu of models in Chimera)
  
  
• Force field - source of charge and radius information; residues not handled by the designated force field will be omitted
  
  
  • AMBER - AMBER ff99 (Wang, Cieplak, and Kollman, J Comput Chem 21:1049 (2000))
  • CHARMM - CHARMM27 (MacKerell et al., J Phys Chem B 102:3586 (1998))
  • PARSE (default) - PARameters for Solvation Energy (Sitkoff, Sharp, and Honig, J Phys Chem 98:1978 (1994) and Tang et al., J Mol Biol 366:1475 (2007))
  • PEOEPB - a version of Gasteiger-Marsili Partial Equalization of Orbital Electronegativities, optimized for Poisson-Boltzmann calculations (Czodrowski et al., Proteins 65:424 (2006))
  • SWANSON - AMBER ff99 charges with optimized radii (Swanson et al., J Chem Theory Comput. 3:170 (2007))
  • TYL06 - a Poisson-Boltzmann-optimized force field (Tang, Yang, and Luo, J Phys Chem B 110:18680 (2006))
  
  
• PQR output file (optional) - name and location of output PQR file; if not specified, a temporary name and location will be used.

• Use PROPKA to predict protonation states (true/false) - whether to use PROPKA (version 3.0) to predict the pKa values of ionizable groups in protein. 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.

• pH value to use with PROPKA (default 7.0) - set protonation states based on the PROPKA-predicted pKa values and the specified pH
• Make protein N-terminus neutral (PARSE only) (true/false) - only available for the PARSE force field
• Make protein C-terminus neutral (PARSE only) (true/false) - only available for the PARSE force field
• Debump added atoms (true/false) - ensure that new atoms are not rebuilt too close to existing atoms
• Optimize hydrogen bonds (true/false) - adjust hydrogen positions and flip certain sidechains (His, Asn, Glu) as needed to optimize hydrogen bonds
• Hydrogen bond distance cutoff (default 3.4 Å)
• Hydrogen bond angle cutoff (default 30.0°)
• Report hydrogen bonds in Reply Log (true/false) - whether to send hydrogen bond information to the Reply Log
• Assign charges to ligands (true/false) - 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
• Display APBS control file in Reply Log (true/false) - whether to generate an example APBS input file and show it in the Reply Log; however, such a file is not needed for running the Chimera APBS tool

• Opal web service (default)
  • Server - URL of web service implemented using Opal; clicking Reset restores the URL for the service provided by the NBCR
• Local
  • Path - pathname of locally installed executable

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