APBS 0.2.1 (2002-04) — APBS-PDB2PQR 1.6 documentation

# APBS 0.2.1 (2002-04)

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