The structure that you built with the Maestro Builder or MOLDEN Z-Matrix editor is likely to be somewhat different from the actual structure of a particular conformer. The Maestro Builder helps to get reasonable structures by using the Geometry Cleanup function that does a good job fixing errors such as inappropriate bond lengths and angles, and can relieve some steric crowding. However, the Geometry Cleanup uses a Universal Force Field (UFF) that, while universally applicable, has limited quantitative accuracy. The quality of the structure that you built with MOLDEN's Z-matrix editor is determined by the built-in standard bond length and angle parameters unless you manually alter these values. If you did not change the geometry based on known experimental or high-level quantum chemical structure, the structure built by MOLDEN is not a minimum energy structure.
In general, you should minimize your molecule further with an appropriate force field before further analysis. There is a large number of force fields available and it is often difficult to decide which force field is the most appropriate. The choice is guided by both the type of molecule and the type of application. For example, while both the MMFF and OPLS-AA (OPLS2003) force fields are generally applicable for organic and biological molecules, the MMFF typically produces more accurate structures and conformational energies. On the other hand, the functional form of the OPLS-AA force field is much simpler, and this force field may be a good choice if simulation of a very large system is desired.
This tutorial illustrates how to perform molecular mechanics geometry minimization with the program Macromodel, which is integrated with the Maestro graphical interface. Build or open your molecule and follow these steps to minimize and analyze the results of minimization:
The results of calculations have become part of the current project and the geometry on the screen now corresponds to the minimized geometry. The geometry can be analyzed by selecting Measurements from the Tools menu. By default, Distances Folder opens allowing to measure distances by clicking on two atoms. Write down one distance between any two bonded atoms in your molecule, one angle between any three binded atoms, and one dihedral between any four bonded atoms.
Repeat the minimization and analysis with the OPLS2003 force field but this time choose Append new entries for Incorporate Output option when launching the calculation. This will keep the MMFF minimized structure as well as the new, OPLS2003 minimized structure, in the project database. You can toggle between the two structures using the Show Table command from the Project menu. Compile a table that lists the total energy of the minimized structure, and the three structural parameters for these two force fields. Comment on the meaning of the Total Energy in the context of these calculations.
Try to build the same molecule with MOLDEN's Z-matrix editor. Make sure that you build the same conformer that you studied with MacroModel. If your molecule is too complex to be built with MOLDEN's Z-matrix editor, you may export it from Maestro and then import to MOLDEN. To do this:
Molden allows minimization using an external minimizer. One such minimizer is provided by the TINKER Molecular Modeling Package. MOLDEN can minimize structures using TINKER's MM3, CHARMM, or AMBER force fields. To minimize a molecule in MOLDEN:
MOLDEN also provides convenient point-and-click tools for measurement of distances, angles and dihedrals. Append a column in your table that reports the MM3*-optimized values for the distance, angle, and dihedral that you studied previously. You can get the energy (labeled Final Function Value) for the minimized structure from the molin.log file.
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