APBS¶

Contents

  • Installing APBS
    • Binary installation
    • Source installation
    • What’s in the box?
  • Invoking APBS
    • APBS input files
  • APBS input files
    • READ input file section
    • ELEC input file section
    • APOLAR input file section
    • PRINT input file section
  • Solvation model background
    • Solvation Models
    • Further Reading
  • Caveats and sources of error
    • Model error
    • Parameter set errors
    • Structure-based errors
    • Discretization error
    • Solver and round-off error
  • APBS utilities
    • amber2charmm.sh
    • del2dx
    • dx2mol
    • dx2uhbd
    • qcd2pqr.awk
    • uhbd_asc2bin
    • WHATIF2AMBER.sed
    • benchmark
    • analysis
    • born
    • coulomb
    • dxmath
    • inputgen.py
    • mergedx and mergedx2
    • mgmesh
    • multivalue
    • psize.py
    • similarity
    • smooth
  • APBS programmer’s guide
  • APBS license

APBS-PDB2PQR

Navigation

Contents:

  • APBS-PDB2PQR overview
  • How to get the software
  • Getting started
  • Getting help
  • PDB2PQR
  • 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
  • File formats
  • APBS-PDB2PQR examples and tutorials
  • Support for APBS-PDB2PQR
  • Citing your use of our software
  • Suggested reading for APBS-PDB2PQR
  • Documentation TODO list

Related Topics

  • Documentation overview
    • Previous: PDB2PQR license
    • Next: Installing APBS

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