[gmx-users] %hbond number problem

[gromacs564]

Dear Justin
      I download the script "plot_hbmap.pl" and input "perl $0 -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n",

but the output info is "Unrecognized switch: -bash  (-h will show valid options).";

      then,I input "perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n",and the output info is nothing?

     So, could you tell me the correct usage? Very thanks!

There are protein and sol in b4md.pdb file.The hbond.ndx file only contain the [ hbonds_Protein ] section:
      1      2    603
      1      2    619
      1      2    634
      1      2    635
      1      2   1299
   1942   1943   1917
   1937   1939    113
   1937   1939    114

-------------------------------------

 xiaodu



My simulation system contains protein, dna and water.
I used your script already for obtaining %exist hydrogen bonds between
protein and dna
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110323/85c0daa8/attachment.html>