>pdb</a> file is supplied, residue names might not correspond to
to the GROMACS naming conventions, in which case these residues will
probably not be properly protonated.
<p>
If an index file is specified, please note that the atom numbers
should correspond to the <b>protonated</b> state.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.ht