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Article ID: 1265 - Last Modified: June 3, 2011

How do I find information about atomic charges used in MacroModel calculations?

Usually, the partial atomic charges used in a computation are obtained from information stored with the force-field. However, MacroModel uses the charges that appear in the structure input file if the CHGF command appears in the command file. After a computation is complete, the charges (as determined by the force field in use) appear in the output structure file.

When the force-field file is used as the charge source, there are three types of information that affect the partial charges: bond dipoles, formal charges, and explicit substructure charges.

Bond Dipoles

Bond dipoles are stored in the stretch part of the force field. The following example is from the AMBER* force field:

1  CT - H1                1.0900   331.0000   -0.6597   N400 0000
                                              ^^^^^^^

The highlighted number is the bond dipole (D, in debye) that is applied between types CT and H1. Partial charges Q and -Q (in units of e) would be assigned to the atoms CT and H1 respectively based upon the relation:

Q = 0.2082 * Dipole/ L0

where L0 is the "natural" bond length in angstroms.

The charge for atoms which have more than one bonded attachment is the sum of all the contributions from the bond dipoles. This method of charge accounting has the significant advantage that it is guaranteed to maintain charge neutrality.

Formal Charges

Some atom types (like OM: O-) have a "formal" charge which is added to the partial atomic charge calculated by the bond dipole method.

Substructure Charges

Charge distribution information for substructures may be stored either as atomic charge or bond dipoles. There are a few cases where atomic charges are stored directly in the substructure part of the force field. In general, however, we have attempted to avoid this and most charges come from bond dipoles.

See the appendix entitled "The BMFF Protocol" in the MacroModel Reference Manual for further details.

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