[Pdb2pqr-announce] PDB2PQR 1.4.0 released

[Nathan B. <ba...@bi...>]

Dear PDB2PQR users --

We are pleased to announce the release of PDB2PQR version 1.4.0, which
contains a number of new features including integration of PDB2PQR and APBS
Opal services through remote clusters at NBCR. A complete list of new
features and bug fixes is provided below.

As usual, PDB2PQR can be downloaded from http://pdb2pqr.sourceforge.net/ and
help can be obtained from the PDB2PQR-users mailing list (subscribe:
https://lists.sourceforge.net/lists/listinfo/pdb2pqr-users or browse:
https://sourceforge.net/mailarchive/forum.php?forum_name=pdb2pqr-users).

Thank you for your continuing support of PDB2PQR.

Sincerely,

The PDB2PQR Development Team

 - NEW FEATURES
  * Updated html/master-index.html, deleted html/index.php.
  * Updated pydoc by running genpydoc.sh.
  * Added a whitespace option by by putting whitespaces between atom name
    and residue name, between x and y, and between y and z.
  * Added radius for Chlorine in ligff.py.
  * Added PEOEPB forcefield, data provided by Paul Czodrowski.
  * Updated inputgen.py to write out the electrostatic potential for APBS
    input file.
  * Updated CHARMM.DAT with two sets of phosphoserine parameters.
  * Allowed amino acid chains with only one residue, using --assign-only
    option.
  * Updated server.py.in so that the ligand option is also recorded in
    usage.txt.
  * Updated HE21, HE22 coordinates in GLN according to the results from
    AMBER Leap program.
  * Updated Makefile.am with Manuel Prinz's patch (removed distclean2 and
    appended its contents to distclean-local).
  * Updated configure.ac, pdb2pqr-opal.py; added AppService_client.py and
    AppService_types.py with Samir Unni's changes, which fixed earlier
    problems in invoking Opal services.
  * Applied two patches from Manuel Prinz to pdb2pka/pMC_mult.h and
    pdb2pka/ligand_topology.py.
  * Updated PARSE.DAT with the source of parameters.
  * Created a contrib folder with numpy-1.1.0 package. PDB2PQR will install
    numpy by default unless any of the following conditions is met:
      a. Working version of NumPy dectected by autoconf.
      b. User requests no installation with --disable-pdb2pka option.
      c. User specifies external NumPy installation.
  * Merged Samir Unni's branch. Now PDB2PQR Opal and APBS Opal services are
    available (through --with-opal and/or --with-apbs, --with-apbs-opal
    options at configure stage).
  * Added error handling for residue name longer than 4 characters.
  * Updated hbond.py with Mike Bradley's definitions for ANGLE_CUTOFF and
    DIST_CUTOFF by default.
  * Removed PyXML-0.8.4, which is not required for ZSI installation.
  * Updated propka error message for make adv-test -- propka requires a
    version of Fortran compiler.
  * Updated na.py and PATCHES.xml so that PDB2PQR handles three lettered
    RNA residue names (ADE, CYT, GUA, THY, and URA) as well.
  * Updated NA.xml with HO2' added as an alternative name for H2'', and H5"
    added as an alternative name for H5''.
  * Updated version numbers in html/ and doc/pydoc/ .
  * Updated web server. When selecting user-defined forcefield file from
the
    web server, users should also provide .names file.
  * Removed http://enzyme.ucd.ie/Services/pdb2pqr/ from web server list.
  * Eliminated the need for protein when processing other types (ligands,
    nucleic acids).
  * Updated psize.py with Robert Konecny's patch to fix inconsistent
assignment
    of fine grid numbers in some (very) rare cases.
  * Made whitespace option available for both command line and web server
    versions.
  * Updated inputgen_pKa.py with the latest version.

 -BUG FIXES
  * Fixed a legacy bug with the web server (web server doesn't like ligand
    files generated on Windows or old Mac OS platforms).
  * Fixed a bug in configure.ac, so that PDB2PQR no longer checks for
Numpy.pth at configure stage.
  * Updated pdb2pka/substruct/Makefile.am.
  * Fixed isBackbone bug in definitions.py.
  * Fixed a bug for Carboxylic residues in hydrogens.py.
  * Fixed a bug in routines.py, which caused hydrogens added in LEU and ILE
    in eclipsed conformation rather than staggered.
  * Fixed a bug in configure.ac, now it is OK to configure with double
slashes
    in the prefix path, e.g.,  --prefix=/foo/bar//another/path .
  * Fixed a bug in nucleic acid naming scheme.
  * Fixed a bug involving MET, GLY as NTERM, CTERM with --ffout option.
  * Fixed a bug for PRO as C-terminus with PARSE forcefield.
  * Fixed a bug for ND1 in HIS as hacceptor.
  * Fixed the --clean option bug.
  * Fixed a bug in CHARMM naming scheme.
  * Fixed a bug in test.cpp of the simple test (which is related to recent
    modifications of 1AFS in Protein Data Bank).


-- 
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/