pdb2pqr_1.8-1_amd64.deb


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Description

pdb2pqr - Preparation of protein structures for electrostatics calculations

Distribution: Debian 7 (Wheezy)
Repository: Debian Main amd64
Package name: pdb2pqr
Package version: 1.8
Package release: 1
Package architecture: amd64
Package type: deb
Installed size: 2.33 KB
Download size: 456.48 KB
Official Mirror: ftp.br.debian.org
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides 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 This package also includes PropKa, a tool to modify the protonation state of protein structures in the Protein Data Bank (PDB) format to match a given pKa value. It can also be used to refine NMR structures, which often yield inaccurate pKa values for some residues.

Alternatives

Provides

  • propka

Conflicts

  • propka

Replaces

  • propka

    Download

    Binary package: pdb2pqr_1.8-1_amd64.deb
    Source package: pdb2pqr

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install pdb2pqr deb package:
      # sudo apt-get install pdb2pqr

    Files

    • /usr/bin/pdb2pqr
    • /usr/bin/propka
    • /usr/bin/psize
    • /usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so
    • /usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so
    • /usr/share/doc/pdb2pqr/AUTHORS
    • /usr/share/doc/pdb2pqr/ChangeLog
    • /usr/share/doc/pdb2pqr/NEWS.gz
    • /usr/share/doc/pdb2pqr/README
    • /usr/share/doc/pdb2pqr/README.Debian
    • /usr/share/doc/pdb2pqr/changelog.Debian.gz
    • /usr/share/doc/pdb2pqr/changelog.gz
    • /usr/share/doc/pdb2pqr/copyright
    • /usr/share/man/man1/pdb2pqr.1.gz
    • /usr/share/man/man1/propka.1.gz
    • /usr/share/man/man1/psize.1.gz
    • /usr/share/pdb2pqr/main.py
    • /usr/share/pdb2pqr/main_cgi.py
    • /usr/share/pdb2pqr/pdb2pqr.py
    • /usr/share/pdb2pqr/dat/AA.xml
    • /usr/share/pdb2pqr/dat/AMBER.DAT
    • /usr/share/pdb2pqr/dat/AMBER.names
    • /usr/share/pdb2pqr/dat/CHARMM.DAT
    • /usr/share/pdb2pqr/dat/CHARMM.names
    • /usr/share/pdb2pqr/dat/HYDROGENS.xml
    • /usr/share/pdb2pqr/dat/NA.xml
    • /usr/share/pdb2pqr/dat/PARSE.DAT
    • /usr/share/pdb2pqr/dat/PARSE.names
    • /usr/share/pdb2pqr/dat/PATCHES.xml
    • /usr/share/pdb2pqr/dat/PEOEPB.DAT
    • /usr/share/pdb2pqr/dat/PEOEPB.names
    • /usr/share/pdb2pqr/dat/SWANSON.DAT
    • /usr/share/pdb2pqr/dat/SWANSON.names
    • /usr/share/pdb2pqr/dat/TOPOLOGY.xml
    • /usr/share/pdb2pqr/dat/TYL06.DAT
    • /usr/share/pdb2pqr/dat/TYL06.names
    • /usr/share/pdb2pqr/extensions/README
    • /usr/share/pdb2pqr/extensions/__init__.py
    • /usr/share/pdb2pqr/extensions/chi.py
    • /usr/share/pdb2pqr/extensions/contact.py
    • /usr/share/pdb2pqr/extensions/hbond.py
    • /usr/share/pdb2pqr/extensions/rama.py
    • /usr/share/pdb2pqr/extensions/resinter.py
    • /usr/share/pdb2pqr/extensions/salt.py
    • /usr/share/pdb2pqr/extensions/summary.py
    • /usr/share/pdb2pqr/extensions/template
    • /usr/share/pdb2pqr/pdb2pka/NEWligand_topology.py
    • /usr/share/pdb2pqr/pdb2pka/__init__.py
    • /usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
    • /usr/share/pdb2pqr/pdb2pka/apbs.py
    • /usr/share/pdb2pqr/pdb2pka/charge_mon.py
    • /usr/share/pdb2pqr/pdb2pka/example.py
    • /usr/share/pdb2pqr/pdb2pka/inputgen_pKa.py
    • /usr/share/pdb2pqr/pdb2pka/ligand_topology.py
    • /usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py
    • /usr/share/pdb2pqr/pdb2pka/pKa_base.py
    • /usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py
    • /usr/share/pdb2pqr/pdb2pka/pMC_mult.py
    • /usr/share/pdb2pqr/pdb2pka/pka.py
    • /usr/share/pdb2pqr/pdb2pka/pka_help.py
    • /usr/share/pdb2pqr/pdb2pka/pka_routines.py
    • /usr/share/pdb2pqr/pdb2pka/prepare_pKa_ligand.py
    • /usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py
    • /usr/share/pdb2pqr/pdb2pka/ligandclean/ligff.py
    • /usr/share/pdb2pqr/pdb2pka/ligandclean/lookuptable.py
    • /usr/share/pdb2pqr/pdb2pka/ligandclean/peoe_PDB2PQR.py
    • /usr/share/pdb2pqr/pdb2pka/ligandclean/templates.py
    • /usr/share/pdb2pqr/pdb2pka/ligandclean/trial_templates.py
    • /usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so
    • /usr/share/pdb2pqr/pdb2pka/substruct/__init__.py
    • /usr/share/pdb2pqr/propka30/__init__.py
    • /usr/share/pdb2pqr/propka30/compare.py
    • /usr/share/pdb2pqr/propka30/experiment.py
    • /usr/share/pdb2pqr/propka30/propka.py
    • /usr/share/pdb2pqr/propka30/propka_det.py
    • /usr/share/pdb2pqr/propka30/propka_gui.py
    • /usr/share/pdb2pqr/propka30/propka_mut.py
    • /usr/share/pdb2pqr/propka30/propka_pdb.py
    • /usr/share/pdb2pqr/propka30/Source/__init__.py
    • /usr/share/pdb2pqr/propka30/Source/bonds.py
    • /usr/share/pdb2pqr/propka30/Source/calculator.py
    • /usr/share/pdb2pqr/propka30/Source/chain.py
    • /usr/share/pdb2pqr/propka30/Source/compare.py
    • /usr/share/pdb2pqr/propka30/Source/corresponding_atoms.py
    • /usr/share/pdb2pqr/propka30/Source/coupled_residues.py
    • /usr/share/pdb2pqr/propka30/Source/debug.py
    • /usr/share/pdb2pqr/propka30/Source/determinant.py
    • /usr/share/pdb2pqr/propka30/Source/determinants.py
    • /usr/share/pdb2pqr/propka30/Source/ions.list
    • /usr/share/pdb2pqr/propka30/Source/iterative.py
    • /usr/share/pdb2pqr/propka30/Source/lib.py
    • /usr/share/pdb2pqr/propka30/Source/ligand.py
    • /usr/share/pdb2pqr/propka30/Source/mutate.py
    • /usr/share/pdb2pqr/propka30/Source/output.py
    • /usr/share/pdb2pqr/propka30/Source/parameters.py
    • /usr/share/pdb2pqr/propka30/Source/parameters_new.py
    • /usr/share/pdb2pqr/propka30/Source/parameters_std.py
    • /usr/share/pdb2pqr/propka30/Source/pdb.py
    • /usr/share/pdb2pqr/propka30/Source/protein.py
    • /usr/share/pdb2pqr/propka30/Source/protein_bonds.dat
    • /usr/share/pdb2pqr/propka30/Source/protonate.py
    • /usr/share/pdb2pqr/propka30/Source/protonator.py
    • /usr/share/pdb2pqr/propka30/Source/residue.py
    • /usr/share/pdb2pqr/propka30/Source/rotate.py
    • /usr/share/pdb2pqr/propka30/Source/vector_algebra.py
    • /usr/share/pdb2pqr/propka30/Source/version.py
    • /usr/share/pdb2pqr/src/__init__.py
    • /usr/share/pdb2pqr/src/aa.py
    • /usr/share/pdb2pqr/src/aconf.py
    • /usr/share/pdb2pqr/src/aconf.py.in
    • /usr/share/pdb2pqr/src/definitions.py
    • /usr/share/pdb2pqr/src/forcefield.py
    • /usr/share/pdb2pqr/src/hydrogens.py
    • /usr/share/pdb2pqr/src/inputgen.py
    • /usr/share/pdb2pqr/src/na.py
    • /usr/share/pdb2pqr/src/pdb.py
    • /usr/share/pdb2pqr/src/protein.py
    • /usr/share/pdb2pqr/src/psize.py
    • /usr/share/pdb2pqr/src/quatfit.py
    • /usr/share/pdb2pqr/src/routines.py
    • /usr/share/pdb2pqr/src/server.py
    • /usr/share/pdb2pqr/src/server.py.in
    • /usr/share/pdb2pqr/src/structures.py
    • /usr/share/pdb2pqr/src/topology.py
    • /usr/share/pdb2pqr/src/utilities.py
    • /usr/share/python/runtime.d/pdb2pqr.rtupdate

    Changelog

    2012-06-21 - Manuel Prinz <manuel@debian.org> pdb2pqr (1.8-1) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Add publication information [ Manuel Prinz ] * New upstream version. Updated debian/copyright. * Updated Standards-Version to 3.9.3. No changes needed. * Changed Maintainer to Debian Med team. * Pass -fPIC to CXXFLAGS. Thanks to Konstantinos Margaritis for the patch! Closes: 654240. LP: 935357. * Updated PROPKA packaging to new version. (It's written in Python now.) * Added fix-hashbangs.patch. * Merged pdb2pqr and propka packages as they are more interconnected since this upstream version. Updated README.Debian accordingly.

    2011-08-31 - Manuel Prinz <manuel@debian.org> pdb2pqr (1.7-2) unstable; urgency=low * Pass -fPIC to compiler on all architectures. Closes: 636204. LP: 791313. * Bumped Standards-Version to 3.9.2. No changes needed.

    2011-01-30 - Manuel Prinz <manuel@debian.org> pdb2pqr (1.7-1) unstable; urgency=low * New upstream release. Closes: #416269, #420734.

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