PDB2PQR 1.4.0 (2009-03)¶
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:
Working version of NumPy dectected by autoconf.
User requests no installation with –disable-pdb2pka option.
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).