APBS-PDB2PQR — APBS-PDB2PQR 1.6 documentation

# APBS-PDB2PQR

APBS (Adaptive Poisson-Boltzmann Solver) and PDB2PQR are software packages designed to analyze the solvation properties of small molecules as well as macro-molecules such as proteins, nucleic acids, and other complex systems. This is the documentation for these packages; more information can be found at the APBS-PDB2PQR homepage.

Contents:

- APBS-PDB2PQR overview
  - Why APBS and PDB2PQR?
  - What do I do next?
- How to get the software
  - Web servers
  - Downloads
  - Release histories
- Getting started
  - Using PDB2PQR to prepare structures
- Getting help
  - GitHub issues
  - Announcements
  - Old mailing lists
  - Contacting the authors
- PDB2PQR
  - Installing PDB2PQR
  - Invoking PDB2PQR
  - Extending PDB2PQR
  - PDB2PQR license
- APBS
  - Installing APBS
  - Invoking APBS
  - APBS input files
  - Solvation model background
  - Caveats and sources of error
  - APBS utilities
  - APBS programmer’s guide
  - APBS license
- Other software
  - Calculation setup and visualization
  - Dynamics simulations
- File formats
  - Mesh and scalar data formats
  - Molecular structure formats
  - Matrix formats
- APBS-PDB2PQR examples and tutorials
  - PDB2PQR operations
  - APBS examples
  - Visualizing results
- Support for APBS-PDB2PQR
  - Supporting organizations
  - Please support us by registering
  - Contributors to date
- Citing your use of our software
- Suggested reading for APBS-PDB2PQR
- Documentation TODO list