APBS 0.3.0 (2004-02)¶
News¶
APBS is now supported by the NIH via NIGMS grant GM69702-01.
Changes that affect users¶
New version of the documentation
New directory structure in tools/
Finished fe-manual mode for ELEC calculations – this is the adaptive finite element solver
Added documetnation for fe-manual
New apbs/tools/manip/inputgen.py script to automatically generate input APBS files from PQR data
Added new asynchronous mode in mg-para parallel calculations to enable running on-demand and/or limited resources
Added new script (tools/manip/async.sh) to convert mg-para calculations in mg-async calculations
Added following aliases for some of the more obscure parameters in the input files:
chgm 0 ==> chgm spl0
chgm 1 ==> chgm spl2
srfm 0 ==> srfm mol
srfm 1 ==> srfm smol
srfm 2 ==> srfm spl2
bcfl 0 ==> bcfl zero
bcfl 1 ==> bcfl sdh
bcfl 2 ==> bcfl mdh
bcfl 4 ==> bcfl focus
calcenergy 0 ==> calcenergy no
calcenergy 1 ==> calcenergy total
calcenergy 2 ==> calcenergy comps
calcforce 0 ==> calcforce no
calcforce 1 ==> calcforce total
calcforce 2 ==> calcforce comps
Example input files have been updated to reflect this change. NOTE: the code is backward-compliant; i.e., old input files WILL still work.
Added new READ options “PARM” and “MOL PDB”, see documentation for more information. These options allow users to use unparameterized PDB files together with a parameter database.
Updated the documentation
Now include support for chain IDs and other optional fields in PQR/PDB files
Added support for parsing PDB files
Renamed:
amber2charmm -> amber2charmm.sh
pdb2pqr -> pdb2pqr.awk
qcd2pqr -> qcd2pqr.awk
Added a new Python-based pdb2pqr (tools/conversion/pdb2pqr) script that allows users to choose parameters from different forcefields.
Updated Python wrappers (tools/python) and added the python directory to autoconf/automake.
Reformatted examples/README.html for readability.
Bug fixes¶
Fixed bug in PQR parsing that can cause PDB/PQR files to be mis-read when they contain residues with numbers in their names (Thanks to Robert Konecny and Joanna Trylska)
Fixed bug when writing out number/charge density: unrealistic densities reported inside iVdW surface.
Fixed bug in VMD read_dx utility
Invalid map IDs now result in an error message instead of a core dump (thanks to Marco Berrera)
Modified mechanism for cubic-spline output, fixing a bug associated with zero-radius atoms
Fixed omission of srfm in sections of documentation (thanks to Sameer Varma)
Made autoconf/automake configure setup more robust on Solaris 8 platforms (thanks to Ben Carrington)
Changes that affect developers¶
New docuemtnation setup
New tools/ directory structure
Changed Vgreen interface and improved efficiency
Changed Vopot interface to support multiple grids
Added several norm and seminorm functions to Vgrid class
Altered –with-blas syntax in configure scripts and removed –disable-blas
Documented high-level frontend routines
Cool new class and header-file dependency graphs courtesy of Doxygen and Graphviz
Added substantial mypde.c-based functionality to Vfetk
Moved chgm from PBEparm to MGparm
Minor changes to Vfetk: removed genIcos and added genCube
FEM solution of RPBE working again (see test/reg-fem) and is probably more up-to-date than test/fem
Updated API documentation
Changed many NOsh, FEMparm, MGparm variables to enums
Changes to Valist and Vatom classes
Fixed minor bugs in documentation formatting
Made Vopot more robust
Created Vparam class for parameter file parsing
Added vparam* parameter database flat files to tools/conversion/param