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pdb2pqr

Preparation of protein structures for electrostatics calculations

Variants:
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.

Homepage:
Package version:1.8-1
Architecture:amd64
Distribution:Debian
Filename:pdb2pqr_1.8-1_amd64.deb

/usr/share/doc/pdb2pqr/README

Please see doc/userguide.html for the documentation index and COPYING for license information.

Please see doc/programmerguide.html for information on working with the PDB2PQR code. 

/usr/share/doc/pdb2pqr/README.Debian

PROPKA
======

PDB2PQR can use PROPKA to protonate the structure it converts. PROPKA is
packaged along with the PDB2PQR in this package.

 -- Manuel Prinz  Thu, 21 Jun 2012 15:57:01 +0200


Web Service
===========

The Debian package of PDB2PQR currently does not provide the parts that are
necessary to run PDB2PQR as a web service. If you think that the PDB2PQR
web service should be available as a
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/usr/share/pdb2pqr/extensions/README

Please see the programmer's guide (doc/programmerguide.html) for a discussion on how to add your own functionality to PDB2PQR.

Additionally, the "template" file is a template for interfacing with PDB2PQR.

/usr/share/doc/pdb2pqr/NEWS.gz

Please visit the PDB2PQR SourceForge project page (http://sourceforge.net/projects/pdb2pqr) for the 
more»

/usr/share/man/man1/pdb2pqr.1.gz

PDB2PQR(1)                 PDB2PQR Manual                 PDB2PQR(1)



NAME
       pdb2pqr - Genera
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/usr/share/man/man1/propka.1.gz

PROPKA(1)                   PROPKA Manual                  PROPKA(1)



NAME
       propka - Protona
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/usr/share/man/man1/psize.1.gz

PSIZE(1)                   PDB2PQR Manual                   PSIZE(1)



NAME
       psize - Get dime
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/usr/share/doc/pdb2pqr/ChangeLog

Please see http://www.poissonboltzmann.org/pdb2pqr/release-history

# These are notes for the curren
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