software for preparing input file for large molecule!



 Dear CCL members,
     I have a question about the preparation of input file for large molecules.
  It is hard to use z-matrix input for a large molecule. So I decided to use
  some drawing software to draw the molecule and then extract the coordinates
  using 'BABEL'. I have been using ISIS Draw 2.2.1. However, all structures
  drawn by me are coming as planar  i.e. Z-coordinates are all zero.
  My question is
      Am I making some mistake or is it intrinsic to ISIS?
         and
      is there any other software, which can do the things better?
        and
      what is the standard way of generating input file for a large molecule
     (say, has 100 atoms) i.e. my way is correct or not?
  Thanks for your help. I will summarize the replies.
                                           Pradipta
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                *   Dr. Pradipta Bandyopadhyay          *
                *   AMES LAB                            *
                *   Department of Chemistry             *
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