LE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 18 Jan 2009</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<tt>protonate</tt> reads (a) conformation(s) and adds all missing
hydrogens as defined in <tt>ffgmx2.<a href="hdb.html">hdb</a></tt>. If only <tt>-s</tt> is
specified, this conformation will be protonated, if also <tt>-f</tt>
is specified, the conformation(s) will be read from this file
which can be either a single conformation or a trajectory.
<p>
If a <a href="pdb.html"