File: propka.1.xml

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<?xml version="1.0"?>
<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN" "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
<!ENTITY propka "<command>propka</command>">
]>
<refentry>
  <refentryinfo>
    <title>PROPKA Manual</title>
    <!-- "date" should be the date of the latest change -->
    <date>2008-06-15</date>
    <productname>propka</productname>
    <authorgroup>
      <author>
	<firstname>Manuel</firstname><surname>Prinz</surname>
	<contrib>Wrote this manpage for the Debian System.</contrib>
	<address><email>debian@pinguinkiste.de</email></address>
      </author>
    </authorgroup>
    <copyright><year>2008</year><holder>Manuel Prinz</holder></copyright>
  </refentryinfo>
  <refmeta>
    <refentrytitle>propka</refentrytitle>
    <manvolnum>1</manvolnum>
  </refmeta>
  <refnamediv>
    <refname>propka</refname>
    <refpurpose>Protonate <acronym>PDB</acronym> files based on pKa</refpurpose>
  </refnamediv>
  <refsynopsisdiv>
    <cmdsynopsis>
      <command>propka</command>
      <arg choice="plain"><option><filename>PROPKATMP1</filename></option></arg>
    </cmdsynopsis>
  </refsynopsisdiv>
  <refsect1 id="description">
    <title>DESCRIPTION</title>
    <para>
      &propka; automates the protonation (positioning of hydrogen ions) to a structure in <acronym>PDB</acronym> format for any given pKa value. The file to use has to be named <filename>PROPKATMP1</filename> in the directory where propka is run.</para>
      <para>&propka; will generate two output files named <filename>PROPKATMP2</filename> and <filename>PROPKATMP3</filename>. <filename>PROPKATMP2</filename> contains the resulting structure in <acronym>PDB</acronym> format. <filename>PROPKATMP3</filename> contains a summary of the &propka; run.</para>
  </refsect1>
  <refsect1 id="citing">
    <title>CITING PROPKA</title>
    <para>Please acknowledge your use of &propka; by citing:</para>
    <para>Hui Li, Andrew D. Robertson, and Jan H. Jensen: Very Fast Empirical Prediction and Interpretation of Protein pKa Values, Proteins, 2005, 61, 704-721.</para>
  </refsect1>
  <refsect1 id="webservice">
    <title>WEB SERVICE</title>
    <para>PropKa can be used via a web interface at <ulink url="http://propka.ki.ku.dk/">http://propka.ki.ku.dk/</ulink>.</para>
  </refsect1>
  <refsect1 id="seealso">
    <title>SEE ALSO</title>
    <para><citerefentry><refentrytitle>pdb2pqr</refentrytitle><manvolnum>1</manvolnum></citerefentry></para>
  </refsect1>
</refentry>