This menu contains commands that
Fix Distance: Fix a distance between any two atoms.
Fix Angle: Fix an angle. Up to 10;
Fix Torsions: Fix a dihedral angle
Mark Pi Atoms: Pi atoms.
Mark Metal Atoms: Set electron count, charge and coordination of metal atoms.
Hydrogen Bonding: Hydrogen Bonds
Reset: Reset any of the above.
The Fix_Distances option is used to fix the distance between two atoms.. The two atoms whose distance is to be fixed should be selected using the SELA button on the TOOLS menu, then Fix Distances can be selected from the MARK menu. A dialog box will appear listing the two atoms, the current distance and two edit boxes, one for the distance to fix at, and the other for a force constant (default 5.0 mdyne/angstrom ). The distance is fixed by creating a bond between the two atoms with the default distance set at the fixed distance, and with a force constant input. The default force constant works for most cases. Fixed distances can be combined with energy minimization or dynamics to build large structures with specific interactions, for example, folded peptides (where the fixed distances come from NMR experiments).
The Fix Angle option is used to fix the angle made by three atoms and up to ten angles can be fixed at one time. The three atoms of the angle should be selected first using the SELA button, and then Fix Angle from the Mark menu. A dialog box will appear giving the atom numbers of the atoms of the angle, the current angle and edit boxes for the angle and the force constant to use.
The Fix Torsions options is used to fix up to ten dihedral angles. The four atoms defining the dihedral angle must first be selected using the SELA button in the TOOLS menu. The Fix Torsion option will then present a dialog box listing the four atoms, the current angle, and an edit box for entering the angle and force constant. The fixed torsions are treated separately from the dihedral driver torsions.
The MM2 and MM3 force field only contains one atom type to describe alkenes (atom type 2), which is used to describe all types of unsaturation. The default parameters for atom type 2 are set to reproduce the geometry of an isolated double bond, such as ethylene, and will not accurately represent the geometry or energy of a conjugated system such as butadiene or benzene. The solution to this problem is to do a simple pi vescf calculation on conjugated systems. This calculation gives the bond orders of all the bonds in the conjugated system, and these bond orders are used to adjust the stretching and torsional parameters for those atoms in the conjugated system. The pi atom marking is used to tell PCMODEL which atoms belong to the conjugated system and that a pi calculation should be done. Selecting the Pi atom marking brings up a dialog box where you can mark some of the pi atom, all the pi atoms or unmark all the pi atoms Unmarking can also be done with. Reset. When Pi atoms are marked and minimize is selected PCMODEL will first do a pi calculation on the conjugated system, the parameters will be adjusted and then 15 iterations of geometry optimization will be done. A pi calculation is then done on the updated geometry, the parameters are again adjusted, and a complete minimization is done. When the minimization is complete another pi calculation is done, followed by another minimization. The minimization ends when no change in the geometry is observed after a pi calculation.
The Mark Metal Coordindation option is used for coordinating pi systems to a metal atom, setting the electron count and geometry of a metal, and setting the charge on the metal. The metal atom of interest and any coordinated atoms must first be selected using the SELA button on the TOOLS menu. After selecting Mark Metal Coordination a dialog box will be presented showing the metal atom symbol, the current charge if any, and a set of radio buttons describing the electron count and geometry. The force field model was designed with no charges on the metal atoms (default charge is 0). Setting a charge will turn on electrostatic interactions with other atoms and should be treated with caution. The electrostatic model within molecular mechanics is widely used and it has been found that formal charges do not work well. You should check your calculations against known compounds as you make modifications.
If the Metal Coord option is not used, all metals are assumed to be coordinately saturated, and there will be no attractive potential between the metal and the pi atoms of ligands which were not explicitly bonded during the DRAW phase of the input. Atoms coordinated to the metal will be shown with a yellow line between the atom and the metal. Metal atoms may be bonded to heteroatoms as an alternative to metal coordination.
The MMX force field contains an extra term to correct deficiencies (in the original MM2 force field) in describing hydrogen bonds. This term is turned on or off depending upon whether the hydrogen bonds are marked. The default is not to automatically mark hydrogen bonds and not to turn on the extra term in the force field. If the hydrogen bond marking is turned off using the Reset option (see below), then the H_Bond option is used to turn on the hydrogen bond term again.
The Reset option brings up a dialog box which allows resetting all the options given above.