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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>do_dssp</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 do_dssp
  18 reads a trajectory file and computes the secondary structure for
  19 each time frame
  20 calling the dssp program. If you do not have the dssp program,
  21 get it. do_dssp assumes that the dssp executable is
  22 /usr/local/bin/dssp. If this is not the case, then you should
  23 set an environment variable <b>DSSP</b> pointing to the dssp
  24 executable, e.g.: <p>
  25 <tt>setenv DSSP /opt/dssp/bin/dssp</tt><p>
  26 The structure assignment for each residue and time is written to an
  27 <tt>.<a href="xpm.html">xpm</a></tt> matrix file. This file can be visualized with for instance
  28 <tt>xv</tt> and can be converted to postscript with <tt><a href="xpm2ps.html">xpm2ps</a></tt>.
  29 Individual chains are separated by light grey lines in the <a href="xpm.html">xpm</a> and
  30 postscript files.
  31 The number of residues with each secondary structure type and the
  32 total secondary structure (<tt>-sss</tt>) count as a function of
  33 time are also written to file (<tt>-sc</tt>).<p>
  34 Solvent accessible surface (SAS) per residue can be calculated, both in
  35 absolute values (A^2) and in fractions of the maximal accessible
  36 surface of a residue. The maximal accessible surface is defined as
  37 the accessible surface of a residue in a chain of glycines.
  38 <b>Note</b> that the program <tt><a href="g_sas.html">g_sas</a></tt> can also compute SAS
  39 and that is more efficient.<p>
  40 Finally, this program can dump the secondary structure in a special file
  41 <tt>ssdump.<a href="dat.html">dat</a></tt> for usage in the program <tt><a href="g_chi.html">g_chi</a></tt>. Together
  42 these two programs can be used to analyze dihedral properties as a
  43 function of secondary structure type.
  44 <P>
  45 <H3>Files</H3>
  46 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  47 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
  50 <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. </TD><TD> Index file </TD></TR>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-ssdump</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">  ssdump.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-map</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="map.html">      ss.map</a></tt> </TD><TD> Input, Lib. </TD><TD> File that maps matrix data to colors </TD></TR>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">      ss.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-sc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  scount.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">    area.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-ta</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> totarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-aa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">averarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  58 </TABLE>
  59 <P>
  60 <H3>Other options</H3>
  61 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  62 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  63 <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>
  64 <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>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
  71 <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>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-sss</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>HEBT</tt> </TD><TD> Secondary structures for structure count </TD></TD>
  73 </TABLE>
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