This protocol implements a calculation of atomic charges (this fucntionality must be supported by the interface used)
In addition to the individual charges, their sums over user-defined fragments can be printed if the defintion of the fragments is presented in the input (see the example).
The following examples, along with all other files needed to run them, can be found in the directory cuby4/protocols/atomic_charges/examples
#=============================================================================== # Atomic charges protocol example #=============================================================================== job: atomic_charges # System specification geometry: S66:water_dimer # Water dimer from the built-in S66 data set charge: 0 # Method of calculation - the interface and must support the calculation # of atomic charges. interface: turbomole method: hf basisset: SVP # Type of charges (some interfaces support multiple options) atomic_charges: mulliken # Optional defintion of the fragments - in this case the individual molecules # in the dimer fragment_1: selection: "1-3" fragment_2: selection: "4-6"
_______ /\______\ / / / / / Cuby / Atomic charges calculation \/______/ Energy: -95338.454957 kcal/mol Atomic charges (Mulliken charges): O -0.3880 H 0.1645 H 0.1815 O -0.3392 H 0.1906 H 0.1906 Charge on fragments: 1 -0.0420 2 0.0420