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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Removes all restraint conditions.

Uses Gaussian Interface for HyperChem Performs the hpyerchem molecular dynamics annealings under the operational molecular mechanics condition. Starts the “Side Chain Rotamer Modeling” module program. Chooses the “Reverse Selection” command of the “Selection” menu. Selects the “Number” label in the Atom Label box.

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.

In this case, this retinal molecule is converted to the corresponding imine molecule. Sets the target molecule number to “4” original molecule number is 5and then selects the “Select Covalent Unknown” command of the “Selection” menu. Repeats for the reference molecule number “2” and “3”. Sets a desired calculation condition for modeling the insertion sequences.

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

Welcome Introduction to the Tutorials. Homology Modeling Tutorial Membrane Protein: Clicks on the “Initiate Gaussian” button.


Creates a preliminary 3D structure, i. 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.

Loads the final alignment table to the program. Chooses the “Select Proteins” command of the “Selection” menu. Starts the “Ramachandran Plot” module program. Starts the “Restraints” module program.

Selects the side chain atoms of the protein model and all hydrogen atoms of all molecules. Optimizes the alignment if necessary.

Tutorials to Help with 8.0

Optimizes these atoms under the operational molecular mechanics condition. Performs the full optimizations under the operational molecular mechanics condition. We are excited to announce that the HyperChem now includes over megabytes of audiovisual tutorials. The program automatically adds the capping group to this terminal carbon. The procedure and the parameter settings in the individual module programs are shown in the attached manual in detail. 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.

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

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

Calculates atomic charges for the imine molecule using the single point calculations of a suitable theory balanced with the operational molecular mechanics condition. Tutorials to Help with 8. Selects two cells in the first column of cells corresponding to the undesired two hydrogen atoms on the retinal terminal carbon, considering the trans configuration tutoriall the potential Schiff base moiety with the lysine residue. Sets the target molecule number to “30” fragmented retinal moleculeand then click on the “Edit Molecule” button.


Coordinates a reliable initial structure for the hydrogen atoms of the extracted water molecules.

These tutorials are intended to help the new user become acclimated to HyperChem, as well as to provide training in some of the advanced features of HyperChem that the seasoned user may have yet to discover.

Selects the “Add H” button of the opened Edit Box. Starts the “Protein Tutoorial module program. Forms the Schiff-base bond between the prepared retinal molecule and the lysine residue of the protein model using the Intermolecular Bond Setup Wizard.

Specifies a sequence of the human rhodopsin as a target sequence. Assigns the bonding information, hydrogen atoms, and atom types to the incompleted retinal molecule. Initiates the Hhperchem Modeling program, and then selects the “Molecular Modeling” option of the “Modeling” menu.

Clicks on the “Make Job File” button. 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.

Rendering This tutorial describes the aspects of rendering available in HyperChem.