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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Starts the “Gaussian Interface” program. Then, selects the activated “Cap Atom” button.

A calculated alignment table will appear The program automatically performs a pairwise alignment using the Blosum62 score matrix in default, and assigns the secondary structure parts for the template sequence.

Sets the target molecule number to “4”, and then selects the “Delete Target” option of the “Option” menu. This tutorial will show how to query a database of molecules for use within HyperChem. tutoriql

Tutorials to Help with 8.0

Starts the “Restraints” module program. Uses Gaussian Interface for HyperChem Initiates the Peripheral Modeling program, and then selects the “Molecular Modeling” option of the “Modeling” menu. Total Time 9 – Confirms the precision of the model. Assigns the bonding information, hydrogen atoms, and atom types to the incompleted retinal molecule. Sets the target molecule number to “30” fragmented retinal moleculeand then click on the “Edit Molecule” button.

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

Selects the “Add H” button of the opened Edit Box. Completed the construction of the retinal Schiff base in the human Rhodopin model. Sets the target molecule number to “4” original molecule number is 5and then selects the “Select Covalent Unknown” command of the “Selection” menu. Starts the “Ramachandran Hypeechem module program.


Creates a preliminary 3D structure, i. Chooses a desired semi-empirical method from the “Calculation” menu, and then click on the “Calculate Charge” button. Loads the final alignment table to the program. This tutorial describes the aspects of rendering available in HyperChem.

It only takes about an hour 1 h in our program system, although it takes several days or several weeks in other program systems.

Clicks on the “Make Job File” button. Selects the cell corresponding to the retinal terminal carbon, and then clicks on the activated “Set Bond” button in the opened Edit Tool box. 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: Performs the full optimizations under the operational molecular mechanics condition.

Sets the desired entry boxes using the pop-up list box. Close the Edit Tool box. Clicks on the “Delete H” button in the Edit Tool box.

Completed the homology modeling for the human rhodopsin. Loads the structure of the bovine rhodopsin as a template into the HyperChem workspace. Assigns structure of an insertion sequence in the target sequence with a secondary structure information obtained from the secondary structure prediction or assigned by a certain method.

Chooses the “Complement Selection” command of the “Selection” menu, and then selects the “Delete Selection” command of the “Option” menu. Chooses a desired molecular mechanics force field from the “Calculation” menu.

Starts the “Protein Superposition” module program. Sets the operational molecular mechanics conditions and the automatic rotamer search conditions. A few tutorials are available for download on this page.


The HyperChem operations such as the parameter settings of the geometry optimizations and molecular dynamics annealings are also shown in the manual in detail. Chooses the “Reverse Selection” command of the “Selection” menu. Starts the “Interface Selection” module program. Selects two cells of the first column to set the bond type information to the corresponding atoms of retinal molecule in the HyperChem workspace. Selects a desired capping group and set a dihedral angle.

Starts the “Side Chain Rotamer Modeling” module program.

HyperChem Tutorials

When the Gaussian job was terminated, clicks on the “Get Data from Gaussian” button to reflect the calculated atomic charges to the molecule in hyperfhem HyperChem workspace. CHypercubeInc. Tutorials to Help with 8.

Sets the restraint condition to all heavy atoms. Introduction to the Tutorials. Determines the best initial rotamer for a residue which differs from the corresponding residue of the template molecule using the batch calculations. Decides a suitable template molecule from the protein molecules which formed the homo-dimer, comparing their respective thermal factors and amino-acid identities with the target sequence.

At this stage, performs the Estimation of Hydrogen Atoms in Water program. Superposes the structure blue of the template molecule system onto tutogial created 3D structure red. In turorial, 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.

Optimizes the alignment if necessary.