PDB2PQR

The PDB2PQR API is organized into several functional groups:

• Forcefield support modules: Handle forcefield definitions and parameters.
• Molecular structure modules: Manage the representation of atoms, residues, biomolecules, ligands, hydrogens, and topologies.
• I/O modules: Handle reading and writing various file formats including PDB and CIF.
• Other modules: Include utilities for configuration, cell handling, and execution control.

The pdb2pqr.hydrogens module provides functionality for handling hydrogen atoms in molecular structures. It is organized into several specialized submodules:

• pdb2pqr.hydrogens: The core module for hydrogen-related operations.
• pdb2pqr.hydrogens.optimize: Contains tools for optimizing hydrogen atom positions.
• pdb2pqr.hydrogens.structures: Provides abstractions and data structures for representing hydrogen configurations within molecular models.

PDB2PQR is a software package used for preparing protein structures for electrostatic calculations. For detailed technical documentation, usage guides, and general information, visit the official resources below:

• Home page: http://www.poissonboltzmann.org/
• Documentation: http://pdb2pqr.readthedocs.io

PDB2PQR supports cumulative mapping in .names files. This is particularly useful for forcefields like CHARMM that use a patch-based naming scheme.

Multiple <residue> sections can share the same canonical <name>. PDB2PQR applies these mappings sequentially. If a subsequent mapping defines specific atom names, those atom names will overwrite the ones defined in previous mappings for that residue. This allows you to define a base residue and then apply specific 'patches' to it.

<!-- Mapping CYX to a base CYS and then applying a DISU patch -->
<residue>
  <name>CYX</name>
  <useresname>CYS</useresname>
</residue>
<residue>
  <name>CYX</name>
  <useresname>DISU</useresname>
  <atom>
    <name>CB</name>
    <useatomname>1CB</useatomname>
  </atom>
  <atom>
    <name>SG</name>
    <useatomname>1SG</useatomname>
  </atom>
</residue>

PDB2PQR supports the MOL2 molecular structure format, which specifies chemical structures including atom types, positions, and bonding.

Limitations: Not all MOL2 bond types are currently supported. Specifically, the following bond types are unsupported:

• am
• du
• un
• nc

For developers who need to integrate PDB2PQR functionality directly into their own Python applications, the core logic is exposed via the pdb2pqr module.

Warning: The API is currently in flux and there is no guarantee of stability between minor releases. Use with caution in production environments.

PDB2PQR is typically used as a preprocessing step for electrostatics calculations, often in conjunction with the APBS software. A standard workflow involves:

1. Input: Start with a PDB ID or a locally generated PDB file.
2. Conversion: Use pdb2pqr to assign titration states and parameters, converting the biomolecule and ligand into PQR format.
3. Calculation: Perform electrostatics calculations using apbs (this can be integrated within the PDB2PQR web server).
4. Visualization: Visualize the results using the PDB2PQR web server or other compatible software.

The PQR format is a modification of the standard PDB format designed to include atomic charge and radius parameters. This allows for electrostatic calculations while remaining compatible with most molecular graphics software.

Unlike the strict column-based formatting required by PDB, APBS uses a whitespace-delimited version of PQR. This liberal formatting allows for atomic coordinates that exceed the standard PDB range of ± 999 Å. While PDB2PQR attempts to preserve PDB-like structure for compatibility, the underlying parser relies on whitespace separation between fields.

To implement a completely new forcefield in PDB2PQR, follow these steps:

1. Generate a forcefield data file: Create a new .DAT file (e.g., myff.DAT).
2. Provide a names file (if necessary): If your forcefield's atom naming scheme differs from the PDB2PQR canonical naming scheme, you must create a .names file (e.g., myFF.names). The format for this file is defined in the /formats/xml-names documentation.
3. Reference existing examples: It is recommended to use the existing .DAT and .names files located in the dat/ directory as templates for your new files.

Once created, these files can be utilized via both the PDB2PQR command line interface and the web server versions.

To use APBS within molecular mechanics and dynamics software, you can use the iAPBS library. iAPBS facilitates the integration of APBS with several major molecular dynamics packages, including:

• NAMD
• AMBER
• CHARMM

Additionally, APBS is used directly by Brownian dynamics software such as SDA and BrownDye.