Re: CCL:software for preparing input file for large molecul

["Tamas Gunda" <tamasgunda(-(at)-)tigris.klte.hu>]

 > From:          Pradipta Bandyopadhyay
 <pradipta(-(at)-)si.fi.ameslab.gov>
 >  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
 Dear Pradipta,
 ISIS Draw is a sketch program, so you can create only "flat"
 molecules in 2D. You need something to convert them into
 real 3D molecules. There are a lot of modeling
 programs for this. As a quick solution, you can download
 from the ACD LAbs homepage (www.acdlabs.com) a free plug-in
 for ISIS/Draw, which can make this conversion. You can
 then export the molecule as a 3D molfile into other programs
 Hope this helps
 best regards
 Tamas Gunda
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