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Model Build

For a given molecule/atoms this procedure adds hydrogen atoms, sets the protonations state, sets the charges and does geometrical optimization.

Select Tools->Model Build under the Main Menu.

Select molecule/atoms

Choose a molecule or its fragment by clicking on it.

Click on the Next button.

Set parameters

The window (Figure 55) appears.

Choose the following Build Model options:

· Add hydrogen atoms filling all valences;

· Fix the protonation state, like carboxil group deprotonization;

· Set the charges by a quantum-mechanical method; and

· Optimize geometry.

All options are on by default.

Figure 55 - Setting Parameters

Note: Switching on all options guarantees that the program works properly. If molecules were already processed by Quantum then options can be switch off. If compounds have the right number of hydrogen atoms, for example, then the add hydrogen atoms box can be turned OFF etc.

If the Optimize Geometry box is ON, then you should choose the structures surrounding the molecule. None is selected by default and means that the molecule will be optimized in vacuum.

To start the Building Model procedure, press the Apply button.

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