Incorporating Metal Atoms and Building Complexes

go back to Main Page, Computational Codes, MACROMODEL

extracted from http://www.scripps.edu/rc/softwaredocs/macromodel/mm7/html/primer/prmrchp2.htm

MacroModel allows the introduction of metal atoms and energy calculations on the resulting molecules. Prior to Version 4.5, only one special atom type was available for assigning to a metal, and it was given in the force field as a type Z0 atom (referred to in documentation as type Z). In Version 7.0, this mechanism still exists; however, we have added a new mechanism whereby users can create additional atom types with appropriate names (such as Li, Na or Fe), and define parameters for these types in the force field. Such additional types have "equal status" with the traditional MacroModel types in energetic calculations, but they are not handled automatically by the builder.

The characteristics of the atom types (old as well as new) are given in a file called "atom.typ", which is read in at run time. The default version of this file resides in the directory $MMOD_ROOT/run/mmdat; however, as with force fields, a local version overrides the default. Thus, a user wishing to add a new atom type for personal use can make a copy of the default file and modify it accordingly. The file contains a lengthy header describing the file format and the meaning of the various entries. We supply entries for Li+ and Na+ in the default atom.typ file. The first 64 atom types however are fixed and changes made in the atom.typ file for these atoms will not be reflected in MacroModel.

Metals can be introduced as ionic or covalent complexes. Ionic complexes are easily created and modeled, but coordination complexes are not generally well handled.

To create an ionic complex, input the desired ligand and then select the DRAW button of the ORGANI submode and point to the location on the screen where the metal atom is to appear. The cursor will deposit a "C0" symbol on the screen signifying that an unattached carbon atom has been created. Convert the "C" to a metal by pointing to the "*" in the atom menu. The program will provide a scrolling list of all the atom types given in the atom.typ file currently in use. Selecting from the scrolling list turns the C into the selected type. You may use the M XY button to move the ion around the screen as desired. Alternatively, use the TRMol button in 3D MacroModel to pick and move the ion. With ionic complexes, electrostatic and other nonbonded interactions will be created between the ion in question and all other proximate atoms. These interactions are all that is necessary to hold the ion in place.

Covalent complexes are modeled by zero-order bonds between the metal atom and the ligating atoms. As described earlier, zero-order bonds are created by drawing normal single bonds and then using the DELET button to pick the bond one time. Such zero-order bonds are displayed as dark green bonds. The procedure for selecting the desired metal atom type are exactly as described above for selecting the type when forming an ionic complex. Energy calculations on such coordination complexes generally require the addition of new parameters to the force field file. We do not supply such parameters; however, users who do have such parameter sets may incorporate them.