How to save "saperate" molecules in a SDF file?

I drew abount 54 chemical structures with ChemSketch and saved as .sdf file format. However, when this file loaded into the docking program, it cannot be recognized as 54 "different" compounds. Shall I draw one compound at one time and save each one, then pull together??? It seems a stupid way.

Hi,





If you draw your structures into the same sketch, certainly they will be saved as one record. There is nothing surprising in it; just imagine that you draw a salt: would you expect Marvin to save the positive and the negative ions to separate records?


There are several ways to create SDFiles, but the easiest way is to use InstantJChem (http://www.chemaxon.com/product/ijc.html). On the other hand, if you want to use Marvin only, you have to do draw the structures one by one, and add them always to the end of the SDFile (if you select an existing filename at the Save (or Save As) action, you will be asked whether to overwrite the content of the file, or add the structure to it as a new record).