This is the input file. This file can contain molecules in a wide-variety of molecular formats. Some of the partial charging models, such as AM1 and AM1BCC require coordinates in order to calculate charges. While the input file is required, the -in flag is optional. If no -in flag is specified, the first unflagged parameter is used as the input file.
This is the output file and it is a required parameter. Since the object of molcharge is to generate partial charges, it will only write to formats that can specify a partial charge. These formats currently include only .mol2, .mol2H and .oeb. While the output file is required, the -out flag is optional. If no -out flag is specified, the second unflagged parameter is used as the output file.