GMMX Conformer Calculation
The GMMX Conformer Calculation dialog is used to set up and run a GMMX calculation. This dialog will let you specify how you want the calculation set up. It is illustrated below.
The GMMX Conformer Calculation Window
The Force Field dropdown menu allows you to choose what type of force field to use for the Conformer Calculation. The default force field is MMFF94, a general purpose organic force field designed primarily for small, drug like organic molecules. The other two force fields, MMX and MM3, come from the Allinger group and differ from MMFF94 in the treatment of extended conjugation.
The Method dropdown menu specifies what kind of calculation to run:
The Energy Window field specifies the tolerance level of the energy difference between the results and the lowest energy conformer (in kcal/mol). When the calculation is run, conformers that fall outside of this range will be discarded.
The Max Search field specifies the maximum number of structures that will be minimized.
When checked, the Epimers checkbox says to include all epimers of the current structutre in the search. Epimers are stereoisomers whose configurations differ only at a single stereo center.When checked, the Double Bonds checkbox will search for conformations via bond rotations involving double bonds as well as single bonds.
The Search Method options allow you to choose how you want GaussView to search for conformations. You can choose from , , or at the same time:
The two lists in the bottom of the window specify the bonds and rings to use in the search for conformers. The top list has three columns:
, and . Clicking on the grey dot in the column will highlight that bond in the view window. The column lists the atom numbers for each identified bond. The checkbox controls whether the bond is used during the calculation. The column displays the increment in degrees for rotations about that bond.The bottom list contains the parameters used when the molecular structure contains ring(s). In this case, the information specified is the ring angle and the bond to be broken. The checkbox again controls whether the item is active during the conformational search.
When you click on the icon in the
column, GaussView will select the atoms and highlight them in the view window, giving a visual indication of the bond you are selecting. An example of this is included below.
A Grid Search specifies the rotation angle when rotating about the specified bonds. For example a value of 120° means that rotation angles of 0°, 120° and 240° will be used. Hence, a lower value will generate more structures for examination during the grid search. The Grid Search dialog is illustrated below:
The GMMX Conformer Calculation Window Grid Search method
The
column lists the atom numbers for each identified bond.The Energy Window field specifies the tolerance level of the energy difference between the results and the lowest energy conformer (in kcal/mol). When the calculation is run, conformers that fall outside of this range will be discarded.
The Number of Structures shows how many structures are present in the molecule.
When checked, the Epimers checkbox says to include all epimers of the current structutre in the search. Epimers are stereoisomers whose configurations differ only at a single stereo center.
When checked, the Double Bonds checkbox will search for conformations via bond rotations involving double bonds as well as single bonds.