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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>make_ndx</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 Index groups are necessary for almost every gromacs program.
  18 All these programs can generate default index groups. You ONLY
  19 have to use make_<a href="ndx.html">ndx</a> when you need SPECIAL index groups.
  20 There is a default index group for the whole system, 9 default
  21 index groups are generated for proteins, a default index group
  22 is generated for every other residue name.<p>
  23 When no index file is supplied, also make_<a href="ndx.html">ndx</a> will generate the
  24 default groups.
  25 With the index editor you can select on atom, residue and chain names
  26 and numbers.
  27 When a run input file is supplied you can also select on atom type.
  28 You can use NOT, AND and OR, you can split groups
  29 into chains, residues or atoms. You can delete and rename groups.<p>
  30 The atom numbering in the editor and the index file starts at 1.
  31 <P>
  32 <H3>Files</H3>
  33 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  34 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  35 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
  36 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt., Mult. </TD><TD> Index file </TD></TR>
  37 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Output </TD><TD> Index file </TD></TR>
  38 </TABLE>
  39 <P>
  40 <H3>Other options</H3>
  41 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  42 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  43 <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>
  44 <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>
  45 <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>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-natoms</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> set number of atoms (default: read from coordinate or index file) </TD></TD>
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