We will use  xleap to draw the molecules and to generate pdb files. First type “xleap” at the command prompt to bring up a window like this one:

Next, we will create our first unit, by typing at the xleap command prompt:

This will create an “BF4” object, and a graphical interface will open pop up. Drawing a molecule is fairly intuitive: select “draw” in the “Manipulation” box, select an appropriate element, click to draw an atom, and drag to draw a bond. For BF4, select “Boron” from “other elements,” and left click to draw a single boron atom.

Next, select “Fluorine” from “other elements,” and drag your mouse from the boron atom to the desired fluorine position.

Draw three more fluorine atoms in the same manner, roughly in a tetrahedral geometry. The geometry need not be perfect at this stage–rough estimations will suffice.

Note: Hold control and move the mouse to rotate the view. Hold control and the right mouse while moving the mouse upwards to zoom in or downwards to zoom out. If you click an atom and select it, hold shift and click anywhere in the drawing space to deselect.

Xleap will optimise the geometry for us. Select all atoms by dragging your mouse over the molecule (or by clicking each atom). Select “Relax selection” under the “Edit” menu.

Note: The menu may not work properly if the NUM/CAPS Lock is turned on.

Exit out of this window.  Note: Do NOT use the “X” button, as xleap will quit in entirety and your work will not be saved. Instead, select “Close” under unit.