share/html/online/protonate.html

   1 <HTML>
   2 <HEAD>
   3 <TITLE>protonate</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>protonate</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 4.0<br>
  13 Sun 18 Jan 2009</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 <tt>protonate</tt> reads (a) conformation(s) and adds all missing
  18 hydrogens as defined in <tt>ffgmx2.<a href="hdb.html">hdb</a></tt>. If only <tt>-s</tt> is
  19 specified, this conformation will be protonated, if also <tt>-f</tt>
  20 is specified, the conformation(s) will be read from this file
  21 which can be either a single conformation or a trajectory.
  22 <p>
  23 If a <a href="pdb.html">pdb</a> file is supplied, residue names might not correspond to
  24 to the GROMACS naming conventions, in which case these residues will
  25 probably not be properly protonated.
  26 <p>
  27 If an index file is specified, please note that the atom numbers
  28 should correspond to the <b>protonated</b> state.
  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>-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>
  34 <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, Opt. </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>
  35 <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>
  36 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">protonated.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>
  37 </TABLE>
  38 <P>
  39 <H3>Other options</H3>
  40 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  41 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  43 <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>
  44 <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>
  45 <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>
  46 <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>
  47 </TABLE>
  48 <P>
  49 <hr>
  50 <div ALIGN=RIGHT>
  51 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
  52 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
  53 </div>
  54 </BODY>