how to minimize energy and save in mol2 format

Hi,

How can I minimize the energy of my compound and save it in a mol2 format?

Thanks!!

Hi,

 

GUI: open/draw your compound in Marvin Sketch, select Structure - Clean 3D - Clean in 3D then save it ( File - Save As ) in "Tripos mol2 format".

 

Command line: Use molconvert command line tool. Example:

molconvert mol2 -3 -s "C1CCCCC1" -o out.mol2

Regards,

Gabor