Conversion of mol2 file to sdf using babel

11 August, 2005
Conversion of mol2 file to sdf using Open Babel

babel -imol2 file.mol2 -osdf file.sdf

Conversion of .mdb (Molecular data base format, ex. Sybyl also uses this format) to sdf

.mdb generally contains multiple mol2 files for converting to sdf first
catinate all the mol2 files to single mol2 file. Now use babel to convert mol2 to sdf
Following commands will be useful:

cat `find ./ -name "*.mol2"` > all_mol.mol2
babel -imol2 all_mol.mol2 -osdf all_mol.sdf
rm -rf all_mol.mol2

Note: put the above set of commands in to a file (say "mol2sdf") in ~/bin directory
and use it inside the .mdb (database) directory.

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