PDB2PQR An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations
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convert pdb pdb converter PDB to PQR convert protein file protein file

PDB2PQR Description

An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations PDB2PQR is an open source and free Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format.These tasks include:· Adding a limited number of missing heavy atoms to biomolecular structures· Determining side-chain pKas· Placing missing hydrogens· Optimizing the protein for favorable hydrogen bonding· Assigning charge and radius parameters from a variety of force fields Requirements: · Python What's New in This Release: 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).

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