> OpenBabel can export this way from a file containing all structures.

Yes, usually. I could give you an example if you told me a bit more  
about the specifics of the formats involved. But let's take this for  
an example:

babel file.sdf -xk "#n B3LYP/6-31G* Opt" -ocom -m

That should split the SDF file into multiple Gaussian input files. You  
can also do something like this in UNIX:

for x in `seq 10 20`; do babel -f $x -l $x file.sdf -xk "#n B3LYP/ 
6-31G* Opt" file-$x.com

This will split out the molecules from 10-20 into separate files: file-10.com 
  ... etc.

Hope that helps,
-Geoff

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