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HYPERCHEM Exercise. Part A: Study the electronic structure and vibrational spectrum of formaldehyde. Procedures: Step 1: Build up the structure of the. This site demonstrates a series of the Homology Modeling using the Homology Modeling Professional for HyperChem. TM. A study of molecular structure and reaction mechanism with molecular mechanics and semi-empirical methods using HyperChem. TM molecular modeling.

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Initiates the Peripheral Modeling program, and then selects the “Molecular Modeling” option of the “Modeling” menu.

Tutorials to Help with 8.0

Starts the “Interface Selection” module program. Selects the side chain atoms of the protein model and all hydrogen atoms of all molecules.

Coordinates a reliable initial structure for the hydrogen atoms of the extracted water molecules. Deselects the “Selection Only” option in the View box.

Forms the Schiff-base bond between the prepared retinal molecule and the lysine residue of the protein model using the Intermolecular Bond Setup Wizard. Clicks on the cell corresponding to the retinal terminal carbon. This tutorial will show how to query a database of molecules for use within HyperChem.

Confirms the precision of the model. Sets the target molecule number to hypwrchem fragmented retinal moleculeand then click on the “Edit Molecule” button.

Homology Modeling Professinal for HyperChem The procedure and the parameter settings in the individual module programs are shown in the attached manual in detail. Sets the target molecule number to “4” original molecule number is 5and then selects the “Select Covalent Unknown” command of the “Selection” tutodial 4.


Repeats to create the conjugated double bond of the retinal molecule. At this stage, performs the Estimation of Hydrogen Atoms in Water program. Sets the reference molecule number to “1” and the target molecule number to “Non-Protein”, and then clicks on the “Execute” button of the Distance Selection 4 angstrom between heavy atoms, selection target: Then, selects the activated “Cap Atom” button.

Total Time 9 – Close the Edit Tool box. Starts the “Restraints” module program. Uses Gaussian Interface for HyperChem Common The attached capping group is deleted at this stage. Superposes the structure blue of the template molecule system onto the created 3D structure red. Selects the “Add H” button of the opened Edit Box. The full version of the tutorials is included in the purchased product. Chooses the “Select Proteins” command of the “Selection” menu. Clicks on the top cell of the first column.

Starts the “Ramachandran Plot” module program. Sets the target molecule number to “4” original molecule number is 5and then selects the “Select Covalent Unknown” command of the “Selection” menu.

The richness and depth of HyperChem assures that tutlrial average user may continue to discover additional features and capabilities long after initial introduction to the program. We are excited to announce hypervhem the HyperChem now includes over megabytes of audiovisual tutorials. Moreover, Homology Modeling for HyperChem provides the advanced molecular modeling environment by which the individual researchers can reflect their chemical background to the model, as well.

In addition, Homology Modeling for HyperChem guarantees the logicalness, reproducibility, and comprehensiveness for the model due to the energy basis instead of the knowledge basis of other program systems. Clicks on the “Initiate Gaussian” button. Loads the final alignment table to the program. Determines the best initial rotamer for a hypdrchem which differs from the corresponding residue of the template molecule using the batch calculations.


The Intermolecular Bond Setting Wizard is started. In this case, this retinal molecule is converted to the corresponding imine molecule.

Homology Modeling Professional for HyperChem: Tutorial 1 – Institute of Molecular Function –

Performs the procedure of the human Rhodopsin homology modeling tutorial. It only takes about an hour 1 h in our program system, although it takes several days or several weeks in other program systems. Then, the prepared Gaussian input file will appear. Repeats for the reference molecule number “2” and “3”. The program tuotrial assigns the total charges and spin multiplicity for this imine molecule, and calculates single-point atomic charges.

Homology Modeling Professional for HyperChem: Tutorial 4 – Institute of Molecular Function –

Selects two cells of the first column to set the bond type information to the corresponding atoms of retinal molecule in the HyperChem workspace. Completed the construction of the retinal Schiff base in the human Rhodopin model.

Specifies a sequence of the human rhodopsin as a target sequence. Starts the “Estimation of Hydrogen Atoms in Water” module program.

Welcome Introduction to the Tutorials. Completed the homology modeling for the human rhodopsin.