An example run of the molcharge program is given below.
prompt> molcharge -method mmff drugs.sdf drugs.mol2
This executes molcharge with the default parameters, to sprout explicit hydrogens and assign MMFF94 partial charges. The file drugs.sdf is opened in SD format for input, and the output is written to the file drugs.mol2 in Sybyl .mol2 format.
prompt> molcharge -method amberff99sb 2iko_prot.pdb 2iko_prot.oeb
In this sample execution, a protein is charged using the Amber charge set and written to OEB format.