APBS 0.2.3 (2002-10) — APBS-PDB2PQR 1.6 documentation

# APBS 0.2.3 (2002-10)

- Fixed bugs in salt-dependent Helmholtz/nonlinear term of PBE affecting both LPBE and NPBE calculations. While this bug fix only changes most energies by < 2 kJ/mol, it is recommended that all users upgrade. Many thanks to Michael Grabe for finding and carefully documenting this bug!

- A parameter (chgm) has been added which controls the charge discretization method used. Therefore, this version contains substantial changes in both the API and input file syntax. Specifically:

  > - PBEparm has two new members (chgm, setchgm)
  > - Vpmg_fillco requires another argument
  > - Vpmg_*Force functions require additional arguments
  > - Input files must now contain the keyword “chgm #” where # is an integer
  > - Please see the documentation for more information.

- Fixed problems with “slicing” off chunks of the mesh during I/O of focused calculations

- Updated authors list

- New CHARMM parameters – Robert Konecny

- Created enumerations for common surface and charge discretization methods

- Added Vmgrid class to support easy manipulation of nested grid data

- Added more verbosity to error with NPBE forces

- Added working Python wrappers – Todd Dolinksy

- Modified VMD scripts read_dx and loadstuff.vmd