From: KIRTANA S (skirtana4_at_gmail.com)
Date: Thu May 21 2009 - 12:32:35 CDT

If I use topotools plugin with scripts as suggested in your mail ,what
should I replace for the index numbers . I am a first time user and non able
to decide on it .Can you suggest an example if my psf file is :

PSF

       1 !NTITLE
 REMARKS VMD generated structure x-plor psf file

      24 !NATOM
       1 2 MOL AU13 AU13 0.000000 196.9666 0
       2 2 MOL AU14 AU14 0.000000 196.9666 0
       3 2 MOL AU17 AU17 0.000000 196.9666 0
       4 2 MOL AU17 AU17 0.000000 196.9666 0
       5 2 MOL AU18 AU18 0.000000 196.9666 0
       6 2 MOL AU18 AU18 0.000000 196.9666 0
       7 2 MOL AU18 AU18 0.000000 196.9666 0
       8 2 MOL AU19 AU19 0.000000 196.9666 0
       9 2 MOL AU1 AU1 0.000000 196.9666 0
      10 2 MOL AU1 AU1 0.000000 196.9666 0
      11 2 MOL AU1 AU1 0.000000 196.9666 0
      12 2 MOL AU1 AU1 0.000000 196.9666 0
      13 2 MOL S13 S13 0.000000 32.0650 0
      14 2 MOL C38 C38 0.000000 12.0107 0
      15 2 MOL C40 C40 0.000000 12.0107 0
      16 2 MOL C41 C41 0.000000 12.0107 0
      17 2 MOL C42 C42 0.000000 12.0107 0
      18 2 MOL C43 C43 0.000000 12.0107 0
      19 2 MOL C44 C44 0.000000 12.0107 0
      20 2 MOL H51 H51 0.000000 1.0079 0
      21 2 MOL H53 H53 0.000000 1.0079 0
      22 2 MOL H55 H55 0.000000 1.0079 0
      23 2 MOL H57 H57 0.000000 1.0079 0
      24 2 MOL H59 H59 0.000000 1.0079 0

      13 !NBOND: bonds
       6 13 13 14 14 19 14 15
      15 20 15 16 16 17 16 21
      17 18 17 22 18 23 18 19
      19 24

       0 !NTHETA: angles

       0 !NPHI: dihedrals

       0 !NIMPHI: impropers

       0 !NDON: donors

       0 !NACC: acceptors

       0 !NNB

       0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0

       1 0 !NGRP
       0 0 0

I need to add the bond for Au and bond angles in the file .

Thanks and regards
kirtana