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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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<title>Basic Molecular Mechanics Modelling</title>
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<body>
<h2> </h2>
<h1>2. User's Manual</h1>
<h1>2.1 Molecular Mechanics Modelling</h1>
<h1>2.1.1 Quick Start : modelling Ethane</h1>
<p>This section covers the features required to build a simple molecule (Ethane)
using ghemical.</p>
<h3>Step 1</h3>
<p>After starting ghemical you must open a new project. To do this, click
on the file menu and select "mm1pg - molecular mechanics"</p>
<img src="images/new_mm.png"
alt="A Screenshot of the creation of a new gpr project.">
<h3>Step 2</h3>
<p>Select Draw from the toolbar on the left hand side. The Draw tool is the
method that all bonds and atoms are added with.</p>
<img src="images/draw_button.png"
alt="Screenshot of selecting the draw tool in ghemical.">
<h3>Step 3</h3>
<p>Now begin to add atoms and bonds to your molecule. The default atom type
is carbon. To add a single atom to the molecule, single click on the location
you would like to put the atom. </p>
<img src="images/first_atom.png"
alt="Screenshot of the first atom being added to the molecule.">
<p> To draw a bond between two atoms, single left click on the first atom
in the bond, drag the mouse over to the second atom and then release the
mouse button. You may also create atoms and bonds at the same time by left
clicking on an existing atom, dragging the mouse to where you want to place
the second atom and then releasing the mouse button.</p>
<img src="images/2atoms_bond.png" width="495" height="629"
alt="Screenshot of two carbon atoms bonded together.">
<h3>Step 4</h3>
<p> Now that the carbon backbone is created, we can now add the hydrogens.
To do this, we must first change the atom type from carbon to hydrogen.
This is done selecting the periodic table button from the top toolbar.</p>
<img src="images/periodic_button.png"
alt="Screenshot of Set current element button.">
<p> A dialog box of the periodic table will appear. To select an element,
simply click on the button corresponding to it. All further atoms drawn
on the molecule will be of this element until it is changed by the same
method. In this example, hydrogen is selected. This menu can also be opened
by right clicking on the view windows, selecting Settings from the popup
menu and then selecting Set Current Element.</p>
<img src="images/periodic_table.png" width="541" height="258"
alt="Screenshot of the periodic table dialog box.">
<h3>Step 5</h3>
<p>In this step additional hydrogens are added to the molecule in same way
the second carbon atom was added. This process can be simplified using
the Add Hydrogens tool.</p>
<img src="images/draw_hydrogens.png" width="496" height="627"
alt="Screenshot of hydrogens being added to the carbon atoms.">
<p>Although the all the correct atoms and bonds are present, the molecule
is not in the most stable conformation. Ghemical can attempt to do this
for you using the Geometry Optimization tool.</p>
<p>You can also change the bond type by clicking on the "Set the current
bond type" button on the top tool bar.</p>
<img src="images/change_bond_select.png" width="325" height="238"
alt="Screenshot of the selection of the change bond type option.">
<p>This button will launch a dialog box that lets you select the bond type
from a list of single, conjugated double and triple. All further bonds
that you create will be on the type that you select until you change the
bond type again. Conjugated bonds are drawn as a single solid tube with
a second dashed tube parallel to it. Double bonds and triple bonds are
drawn as two and three parallel tubes respectively. This menu can also
be opened by right clicking on the view windows, selecting Settings from
the popup menu and then selecting Set Current Bond. </p>
<img src="images/change_bond_dialog.png" width="122" height="155"
alt="Screenshot of the change bond type dialog box.">
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