share/html/online/g_confrms.html

   1 <HTML>
   2 <HEAD>
   3 <TITLE>g_confrms</TITLE>
   4 <LINK rel=stylesheet href="style.css" type="text/css">
   5 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
   6 <TABLE WIDTH="98%" NOBORDER >
   7 <TR><TD WIDTH=400>
   8 <TABLE WIDTH=400 NOBORDER>
   9 <TD WIDTH=116>
  10 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_confrms</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>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 g_confrms computes the root mean square deviation (RMSD) of two
  18 structures after LSQ fitting the second structure on the first one.
  19 The two structures do NOT need to have the same number of atoms,
  20 only the two index groups used for the fit need to be identical.
  21 With <tt>-name</tt> only matching atom names from the selected groups
  22 will be used for the fit and RMSD calculation. This can be useful
  23 when comparing mutants of a protein.
  24 <p>
  25 The superimposed structures are written to file. In a <tt>.<a href="pdb.html">pdb</a></tt> file
  26 the two structures will be written as separate models
  27 (use <tt>rasmol -nmrpdb</tt>). Also in a <tt>.<a href="pdb.html">pdb</a></tt> file, B-factors
  28 calculated from the atomic MSD values can be written with <tt>-bfac</tt>.
  29 <P>
  30 <H3>Files</H3>
  31 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  32 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  33 <TR><TD ALIGN=RIGHT> <b><tt>-f1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   conf1.gro</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>
  34 <TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   conf2.gro</a></tt> </TD><TD> Input </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>
  35 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">     fit.pdb</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
  36 <TR><TD ALIGN=RIGHT> <b><tt>-n1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">    fit1.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  37 <TR><TD ALIGN=RIGHT> <b><tt>-n2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">    fit2.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  38 <TR><TD ALIGN=RIGHT> <b><tt>-no</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   match.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
  39 </TABLE>
  40 <P>
  41 <H3>Other options</H3>
  42 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  43 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  44 <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>
  45 <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>
  46 <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>
  47 <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>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Only write the fitted structure to file </TD></TD>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Mass-weighted fitting and RMSD </TD></TD>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Try to make molecules whole again </TD></TD>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Do least squares superposition of the target structure to the reference </TD></TD>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-[no]name</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Only compare matching atom names </TD></TD>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-[no]label</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Added chain labels A for first and B for second structure </TD></TD>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-[no]bfac</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Output B-factors from atomic MSD values </TD></TD>
  55 </TABLE>
  56 <P>
  57 <hr>
  58 <div ALIGN=RIGHT>
  59 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
  60 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
  61 </div>
  62 </BODY>