APBS 0.2.1 (2002-04)ΒΆ

This version requires the latest version of MALOC to work properly!

  • Syntax changes

    • The writepot and writeacc keywords have been generalized and new I/O features have been added. The syntax is now:

      • write pot dx potential
      • write smol dx surface
      • etc. Please see the User’s Manual for more information
    • The read keywords has been generalized and new I/O features have been added which support the use of pre-calculated coefficient grids, etc. The correct syntax for reading in a molecule is now “read mol pqr mol.pqr end”; please see the User’s Manual for more information.

    • The “mg” keyword is no longer supported; all input files should use “mg-manual” or one of the other alternatives instead.

  • A change in the behavior of the “calcenergy” keyword; passing an argument of 2 to this keyword now prints out per-atom energies in addition to the energy component information

  • A new option has been added to tools/manip/acc to give per-atom solvent-accessible surface area contributions

  • A new option has been added to tools/manip/coulomb to give per-atom electrostatic energies

  • Added tools/mesh/dxmath for performing arithmetic on grid-based data (i.e., adding potential results from two calculations, etc.)

  • Added tools/mesh/uhbd_asc2bin for converting UHBD-format grid files from ASCII to binary (contributed by Dave Sept)

  • Improvement of VMD visualization scripts (contributed by Dave Sept)

  • The API has changed significantly; please see the Programmer’s Manual.

  • Working (but still experimental) Python wrappers for major APBS functions.

  • More flexible installation capabilities (pointed out by Steve Bond)

  • Added ability to use vendor-supplied BLAS

  • Brought up-to-date with new MALOC