File: pdb2pqr.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 pdb2pqr "<command>pdb2pqr</command>">
]>
<refentry>
  <refentryinfo>
    <title>PDB2PQR Manual</title>
    <!-- "date" should be the date of the latest change -->
    <date>2008-06-04</date>
    <productname>pdb2pqr</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>pdb2pqr</refentrytitle>
    <manvolnum>1</manvolnum>
  </refmeta>
  <refnamediv>
    <refname>pdb2pqr</refname>
    <refpurpose>Generate <acronym>PQR</acronym> files for use in electrostatics calculations</refpurpose>
  </refnamediv>
  <refsynopsisdiv>
    <cmdsynopsis>
      <command>pdb2pqr</command>
      <arg choice="opt"><option>--nodebump</option></arg>
      <arg choice="opt"><option>--noopt</option></arg>
      <arg choice="opt"><option>--chain</option></arg>
      <arg choice="opt"><option>--assign-only</option></arg>
      <arg choice="opt"><option>--clean</option></arg>
      <arg choice="opt"><option>--ffout=<replaceable>name</replaceable></option></arg>
      <arg choice="opt"><option>--with-ph=<replaceable>ph</replaceable></option></arg>
      <arg choice="opt"><option>--apbs-input</option></arg>
      <arg choice="opt"><option>--ligand=<replaceable>path</replaceable></option></arg>
      <group choice="opt">
	<arg><option>--verbose</option></arg>
	<arg><option>-v</option></arg>
      </group>
      <arg choice="plain"><option>--ff=<replaceable class="option">forcefield</replaceable></option></arg>
      <arg choice="plain"><option><replaceable>path</replaceable></option></arg>
      <arg choice="plain"><option><replaceable>output-path</replaceable></option></arg>
    </cmdsynopsis>
    <cmdsynopsis>
      <command>pdb2pqr</command>
      <group choice="req">
	<arg choice="plain"><option>--help</option></arg>
	<arg choice="plain"><option>-h</option></arg>
      </group>
    </cmdsynopsis>
  </refsynopsisdiv>
  <refsect1 id="description">
    <title>DESCRIPTION</title>
    <para>
      &pdb2pqr; automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a utility for converting protein files in <acronym>PDB</acronym> format (<replaceable>path</replaceable>) to <acronym>PQR</acronym> format (<replaceable>output-path</replaceable>). These tasks include:</para>
      <itemizedlist>
	<listitem><para>Adding a limited number of missing heavy atoms to biomolecular structures</para></listitem>
	<listitem><para>Determining side-chain pKas</para></listitem>
	<listitem><para>Placing missing hydrogens</para></listitem>
	<listitem><para>Optimizing the protein for favorable hydrogen bonding</para></listitem>
	<listitem><para>Assigning charge and radius parameters from a variety of force fields</para></listitem>
      </itemizedlist>
  </refsect1>
  <refsect1 id="options">
    <title>OPTIONS</title>
    <para>&pdb2pqr; accepts the following options:</para>
    <variablelist>
      <varlistentry>
	<term><option>--ff=<replaceable class="option">forcefield</replaceable></option></term>
	<listitem>
	  <para>The <replaceable class="option">forcefield</replaceable> to use. Current values are <option>amber</option>, <option>charm</option>, <option>parse</option> and <option>tyl06</option>.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--help</option></term>
	<term><option>-h</option></term>
	<listitem>
	  <para>Print a help message and exit.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--nodebump</option></term>
	<listitem>
	  <para>Do not perform debumping operation.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--noopt</option></term>
	<listitem>
	  <para>Do not perform hydrogen optimization.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--chain</option></term>
	<listitem>
	  <para>Keep the chain ID in the output PQR file.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--assign-only</option></term>
	<listitem>
	  <para>Only assigns charges to add atoms, debump, or optimize.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--clean</option></term>
	<listitem>
	  <para>Do no optimization, atom addition, or parameter assignment, just return
	  the original <acronym>PDB</acronym> file in alligned format.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--ffout=<replaceable>name</replaceable></option></term>
	<listitem>
	  <para>Instead of using the standard caninical naming scheme for
	  residue and atom names, use the names from the given forcefield.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--with-ph=<replaceable>ph</replaceable></option></term>
	<listitem>
	  <para>Use <command>propka</command> to calculate pKas and apply
	  them to the molecule given the pH value. Actual PropKa results will
	  be output to <filename><replaceable>output-path</replaceable>.propka</filename>.
	  </para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--apbs-input</option></term>
	<listitem>
	  <para>Create an APBS input file based on the generated
	  PQR file. Also create a Python pickle for using these
	  parameters in other programs.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--ligand=<replaceable>path</replaceable></option></term>
	<listitem>
	  <para>Calculate the parameters for the ligand in MOL2 format at
	  the given <replaceable>path</replaceable>. Pdb2pka must be compiled.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--verbose</option></term>
	<term><option>-v</option></term>
	<listitem>
	  <para>Print additional information to screen.</para>
	</listitem>
      </varlistentry>
    </variablelist>
  </refsect1>
  <refsect1 id="extensions">
    <title>EXTENSIONS</title>
    <para>Extensions add functionality to PDB2PQR and are called by passing a parameter
    to &pdb2pqr;. They put their results into files located in <replaceable>output-path</replaceable>.</para>
    <para>The following extensions can be used by &pdb2pqr;:</para>
    <variablelist>
      <varlistentry>
	<term><option>--phi</option></term>
	<listitem>
	  <para>Print the per-residue backbone phi angle to 
	  <filename><replaceable>output-path</replaceable>.phi</filename>.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--psi</option></term>
	<listitem>
	  <para>Print the per-residue backbone psi angle to
	  <filename><replaceable>output-path</replaceable>.phi</filename>.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--hbond</option></term>
	<listitem>
	  <para>Print a list of hygrogen bonds to
	  <filename><replaceable>output-path</replaceable>.hbond</filename>.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--chi</option></term>
	<listitem>
	  <para>Print the per-residue backbone chi angle to
	  <filename><replaceable>output-path</replaceable>.chi</filename>.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--contact</option></term>
	<listitem>
	  <para>Print a list of contacts to
	  <filename><replaceable>output-path</replaceable>.con</filename>.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--hbondwhatif</option></term>
	<listitem>
	  <para>Print a list of hydrogen bonds to
	  <filename><replaceable>output-path</replaceable>.hbo</filename>.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--salt</option></term>
	<listitem>
	  <para>Print a list of salt bridges to
	  <filename><replaceable>output-path</replaceable>.salt</filename>.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
	<term><option>--rama</option></term>
	<listitem>
	  <para>Print the per-residue phi and psi angles to
	  <filename><replaceable>outpath-path</replaceable>.rama</filename>.</para>
	</listitem>
      </varlistentry>
    </variablelist>
  </refsect1>
  <refsect1 id="citing">
    <title>CITING PDB2PQR</title>
    <para>Please acknowledge your use of &pdb2pqr; by citing:</para>
    <para>Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research, 32, W665-W667 (2004).</para>
  </refsect1>
  <refsect1 id="seealso">
    <title>SEE ALSO</title>
    <para><citerefentry><refentrytitle>psize</refentrytitle><manvolnum>1</manvolnum></citerefentry></para>
  </refsect1>
</refentry>