MacroModel Reference Manual - ISP

Appendix D: Force-Field File FormatD.3.2Adding New ParametersNew parameters generally come from one of three possible sources: new published work,quantum-mechanical calculations and educated guesses based on analogy to systems similar tothat being parameterized. Some examples of parameters based on quantum-mechanical calculationsare given in the MacroModel Technical Manual.New parameters from MM2, MM3, and OPLSA publications may be added directly to theforce field files without modification. If specific charges are desired, you may convert thedesired charges to a dipole entry in the stretch section of the field using the following formula:µ = L 0 * Q / 0.2082Here, µ is the dipole moment in debyes, L 0 is the natural length of the bond (in Angstroms, Å)given in the force field and Q is the desired charge (+ on one end and – on the other).A positive dipole moment means that the first main atom in the force field entry will have thepositive charge and the second atom will get an equal but negative charge. For the oppositepolarity, use a negative dipole moment. Again, test by doing an energy calculation on a structurewith MacroModel via Maestro, and then using the Electrostatics panel to display theresulting partial charges. The Electrostatics panel can be displayed by choosing Force-FieldViewer from Maestro’s Analysis menu, then clicking the Electrostatics button.For stretches and bends, new values may be assigned to fit experimental data as far as bondlengths and angles are concerned. Such data commonly comes from high quality x-ray crystalstructures. Force constants can be approximated by analogy with similar structures in the forcefield or from infrared stretching frequencies:K(stretch-MM2,MM3) = 5.3x10 –7 ν 2 M 1M 2/ (M 1+M 2)K(stretch-AMBER) = 3.0x10 –5 ν 2 M 1M 2/ (M 1+M 2)where ν is the IR frequency in wave numbers (cm -1 ), and M 1and M 2are the atomic masses ofthe atoms involved in the stretch. Alternatively, you may transfer force constants from one fieldto another. AMBER stretching force constants are approximately 60 times those of MM2 orMM3.For bending, infrared frequencies may also be used (if they are available for the scissoringmode) from the following approximate expression:K(bend-MM2,MM3) = 3.0x10 –7 ν 2 M 1M 3/ (M 1+M 3)K(bend-AMBER) = 3.4x10 –5 ν 2 M 1M 3/ (M 1+M 3)206MacroModel 9.7 Reference Manual