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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dyndom</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 g_dyndom reads a <a href="pdb.html">pdb</a> file output from DynDom
  18 http://www.cmp.uea.ac.uk/dyndom/
  19 It reads the coordinates, and the coordinates of the rotation axis
  20 furthermore it reads an index file containing the domains.
  21 Furthermore it takes the first and last atom of the arrow file
  22 as command line arguments (head and tail) and
  23 finally it takes the translation vector (given in DynDom info file)
  24 and the angle of rotation (also as command line arguments). If the angle
  25 determined by DynDom is given, one should be able to recover the
  26 second structure used for generating the DynDom output.
  27 Because of limited numerical accuracy this should be verified by
  28 computing an all-atom RMSD (using <tt><a href="g_confrms.html">g_confrms</a></tt>) rather than by file
  29 comparison (using diff).<p>
  30 The purpose of this program is to interpolate and extrapolate the
  31 rotation as found by DynDom. As a result unphysical structures with
  32 long or short bonds, or overlapping atoms may be produced. Visual
  33 inspection, and energy minimization may be necessary to
  34 validate the structure.
  35 <P>
  36 <H3>Files</H3>
  37 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  38 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  39 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">  dyndom.pdb</a></tt> </TD><TD> Input </TD><TD> Protein data bank file </TD></TR>
  40 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rotated.xtc</a></tt> </TD><TD> Output </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> </TD></TR>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> domains.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
  42 </TABLE>
  43 <P>
  44 <H3>Other options</H3>
  45 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  46 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  47 <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>
  48 <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>
  49 <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>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-firstangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Angle of rotation about rotation vector </TD></TD>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-lastangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Angle of rotation about rotation vector </TD></TD>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-nframe</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>11</tt> </TD><TD> Number of steps on the pathway </TD></TD>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-maxangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> DymDom dtermined angle of rotation about rotation vector </TD></TD>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-trans</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Translation (Aangstroem) along rotation vector (see DynDom info file) </TD></TD>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-head</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> First atom of the arrow vector </TD></TD>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-tail</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Last atom of the arrow vector </TD></TD>
  57 </TABLE>
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