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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Repeats to create the conjugated double bond of the retinal molecule. The program automatically adds the capping group to this terminal carbon. Tutorials to Help with 8. Sets the operational molecular mechanics conditions and the automatic rotamer search conditions.

Calculates atomic charges for the imine molecule using the single point calculations of a suitable theory balanced with the operational molecular mechanics condition.

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

It only takes about an hour 1 h in our program system, although it takes several days or several weeks in hypeerchem program systems. 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. This tutorial will show how to query a database of molecules for use within HyperChem. Forms the Hyperchsm bond between the prepared retinal molecule and the lysine residue of the protein model using the Intermolecular Bond Setup Wizard.

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. Hypercnem on the top cell of the fourth column, and then selects the “Auto Assign Type” button of the opened dialog box. Performs the procedure of the human Rhodopsin homology modeling tutorial. Determines the best initial rotamer for a residue which differs from the corresponding residue of the template molecule using the batch calculations.


Loads the final alignment table to the program. Homology Modeling Tutorial Membrane Protein: 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.

Tutorials to Help with 8.0

Selects the “Number” label in the Atom Label box. In this case, this retinal molecule is converted to the corresponding imine molecule.

Selects a desired capping group and set a dihedral angle. Assigns the bonding information, hydrogen atoms, and atom types to the incompleted retinal molecule.

Assigns bonding information, tutprial atoms, and atom types for other molecules if extracted. Performs the full optimizations under the operational molecular mechanics condition. Selects the cell corresponding to the retinal terminal carbon, and then clicks on the activated “Set Bond” button in the opened Edit Tool box.

Completed the construction of the retinal Schiff base in the human Rhodopin model. Starts the “Gaussian Interface” program. Clicks on the “Make Job File” button. Sets the target molecule number to “4” original molecule number is 5and then selects the “Select Covalent Unknown” command of the “Selection” menu 4. Clicks on the “Initiate Gaussian” button.

Clicks on the “Gaussian Interface” button. The richness and depth of HyperChem assures that the average user may continue to discover additional features and capabilities long after initial introduction to the program. Selects the “Add H” button of the opened Edit Box. Initiates the “Control Center” by double-clicking on the “HM” icon.

Completed the homology modeling for the human rhodopsin. A few tutorials are available for download on this page. Selects the side chain atoms of the protein model and all hydrogen atoms of all molecules. 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.


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

The HyperChem operations such as the parameter settings of the geometry optimizations and molecular dynamics annealings are also shown in the manual in detail. This tutorial describes the basics of obtaining ray-traced images in HyperChem. Clicks on the top cell of the first column.

Then, selects the activated “Cap Atom” button. Starts the “Restraints” module program. Introduction to the Tutorials. Coordinates a reliable initial structure for the hydrogen atoms of the extracted water molecules. Chooses the “Reverse Selection” command of the “Selection” menu. When the Gaussian job was terminated, clicks on the “Get Data from Gaussian” button to reflect the calculated atomic charges to the molecule in the HyperChem workspace.

Sets the target molecule number to “4”, and then selects the “Delete Target” option of hyperchemm “Option” menu.

Removes all restraint conditions. Uses Gaussian Interface for HyperChem Superposes the structure blue of the template molecule system onto the created 3D structure red.

Assigns protonation state of a histidine residue in the target sequence if necessary. The program automatically assigns the total charges and spin multiplicity for this imine molecule, and calculates single-point atomic hypercuem.

Confirms the precision of the model.

Starts the “Ramachandran Plot” module program. Optimizes the alignment if necessary. Selects two cells in the first column of cells corresponding to the undesired hyperhem hydrogen atoms on the retinal terminal carbon, considering the trans configuration of the potential Schiff base moiety with the lysine residue. Then, the prepared Gaussian input file will appear. Starts the “Interface Selection” module program.