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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_anadock</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
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  15 <H3>Description</H3>
  16 <p>
  17 anadock analyses the results of an Autodock run and clusters the
  18 structures together, based on distance or RMSD. The docked energy
  19 and free energy estimates are analysed, and for each cluster the
  20 energy statistics are printed.<p>
  21 An alternative approach to this is to cluster the structures first
  22 (using <tt><a href="g_cluster.html">g_cluster</a></tt> and then sort the clusters on either lowest
  23 energy or average energy.
  24 <P>
  25 <H3>Files</H3>
  26 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  27 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  28 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">   eiwit.pdb</a></tt> </TD><TD> Input </TD><TD> Protein data bank file </TD></TR>
  29 <TR><TD ALIGN=RIGHT> <b><tt>-ox</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> cluster.pdb</a></tt> </TD><TD> Output </TD><TD> Protein data bank file </TD></TR>
  30 <TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> edocked.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  31 <TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   efree.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  32 <TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> anadock.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
  33 </TABLE>
  34 <P>
  35 <H3>Other options</H3>
  36 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  37 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  38 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  39 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  40 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-[no]free</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use Free energy estimate from autodock for sorting the classes </TD></TD>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-[no]rms</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Cluster on RMS or distance </TD></TD>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-cutoff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.2   </tt> </TD><TD> Maximum RMSD/distance for belonging to the same cluster </TD></TD>
  45 </TABLE>
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