Optional Parameters

-method {option}

Selects the charging method to be applied to the input molecule(s). Choose one of the following recommended options:

am1bccsym applies AM1BCC charges as published, including partial semiempirical AM1 geometry optimization and averaging bond-topologically symmetric charges. It requires a 3D geometry associated with an input structure. These are good-quality charges for pharmaceutical organic molecules for intermolecular interactions.

mmff applies MMFF94 charges. It will work with only a 2D geometry. This method is the best choice for use with the MMFF forcefield and these charges are of passable quality for intermolecular interactions. This is the default method.

amberff99sb applies to proteins the RESP charge set used for Amber forcefields ff94, ff96, ff98, ff99, ff99sb, and ff99sbc0 (the same charge set is used in all these cases). This method only works for standard amino acids. These are very good-quality charges for proteins for intermolecular interactions.

gasteiger applies gasteiger charges (a charge-equilibration method). NOTE: This method should not be used for intermolecular interactions. This method was intended for comparing relative reactivity of related organic chemical functional groups within different molecular contexts. It will work with only a 2D geometry.

There are a number of other options for charge methods, but none are recommended. They are listed in the molcharge appendix.


The argument for this flag is the name of a file containing control parameters. The control parameter file acts to either replace or augment the command line interface. All parameters necessary for program execution may be provided in the control parameter file, although any command given explicitly on the command line will supersede options found in the parameter file. molcharge generates a new parameter file containing the full set of execution parameters upon every execution. The name of the parameter file written by molcharge is created by combining the prefix base name with the ‘.parm’ extension.


The filename for the output parameter file can be set with this flag and it overrides -prefix flag for the name of parameter file.


The argument for this flag defines the prefix to be used for parameter and log files. The parameter and log files will be written to what follows this flag plus the extension .param or .log. [default = molcharge]