<P>Dear Justin<BR> I download the script "plot_hbmap.pl" and input "perl $0 -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n",</P>
<P>but the output info is "Unrecognized switch: -bash (-h will show valid options).";</P>
<P> then,I input "perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n",and the output info is nothing?</P>
<P> So, could you tell me the correct usage? Very thanks!</P>
<P>There are protein and sol in b4md.pdb file.The hbond.ndx file only contain the [ hbonds_Protein ] section:<BR> 1 2 603<BR> 1 2 619<BR> 1 2 634<BR> 1 2 635<BR> 1 2 1299<BR> 1942 1943 1917<BR> 1937 1939 113<BR> 1937 1939 114</P>
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<P> xiaodu</P>
<P><BR><BR>My simulation system contains protein, dna and water.<BR>I used your script already for obtaining %exist hydrogen bonds between<BR>protein and dna</P><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span>