PDB2PQR 1.4.0 (2009-03) — APBS-PDB2PQR 1.6 documentation

# 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).