HyperChem is a desktop molecular modeling program. It has modules based on
Molecular Mechanics (MM) methods with several force fields and also modules for
electronic structure calculations at semiempirical and ab initio levels.
It is easy to set-up an input for the desirable system (molecules, macromolecule and
extended systems) to compute and analyze the results with Hyperchem’s inbuilt graphical
user interface. We will explore the world of molecules with HyperChem molecular
modeling suit. Let us start with the simple MMX method.
Molecular Mechanics: Computing the structure and stability of molecules using MMX
method, HyperChem allows us to choose four types of force fields namely MM+,
AMBER, OPLS, and BIO+.
Please follow the list of instructions given below to compute structure and stability of a
molecule using MMX.
1.
Run the HyperChem with a series of mouse clicks on the START button
(located at left lower corner of the Tabletop of Microsoft Windows opening
page), then Programs, then HyperChem release 7.5 and lastly click on
HyperChem Professional. It will open a HyperChem window, which in
general looks like this.
2.
Using this 3D graphical user interface we can build our models with the vast
availability of the built-in tools. Use the building tools and model your
molecule or even periodic system. By keeping the mouse on the tool icons it
will display the use of the icon like draw, select, rotate etc. Using the menu
bar we can almost model the molecules the way we want.
3.
Assuming that we have the molecule to start the MMX calculation. Choose
Molecular Mechanics on the Setup of the menu bar. Then a dialog box
appears with the four verities of force fields, options and components. Choose
the required force filed. [MM+ is appropriate for non-biological species,
AMBER appropriate for polypeptides and nucleic acids, OPLS also designed
fro the polypeptides and nucleic acids along with the solvent and BIO+ is
designed for macromolecules.] Click on the options tab and it will ask to
choose the type of electrostatic and the cutoff value for the interactions.
[Choose bond dipole for the polar systems and we can choose the cutoff
“none” option for small molecules] Click on the components tab and it will
allow you to choose the type of components that we want to include in the
calculations. Lastly choose the select parameter set on the setup menu bar. We
will find out only one parameter mmplus for the MM+ type of calculations.
4.
Choose the type of computation (single point, optimization) that you wanted
to perform from the Compute setup menu bar. It will start to compute for the
required information now. A set of brief results can be seen in the lower part
of the HyperChem window called status line and the results are stored in the
chem.log file which is located in the HyperChem program installed directory
or before initiation of the calculation we can specify the path of the log file
filed from the menu bar option.
5.
When the computing process is going on the fields in the menu bar will
disappear. When the job gets complete, the fields in the menu bar will activate
again.