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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Common The attached capping group is deleted at this stage. Repeats for the reference molecule number “2” and “3”. Confirms the precision of the model. Starts the “Ramachandran Plot” module program. Initiates the “Control Center” by double-clicking on the “HM” icon. 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.

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.

The procedure and the parameter settings in the individual module programs are shown in the attached manual in detail. It only takes about an hour 1 h in our program system, although it takes several days or several weeks in other program systems.

Rendering This tutorial describes the aspects of rendering available in HyperChem. Optimizes the alignment if necessary. Starts the “Restraints” module program. Sets the target molecule number to “30” fragmented retinal moleculeand hutorial click on the “Edit Molecule” button.


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

Optimizes these atoms under the operational molecular mechanics condition. Selects the side chain atoms of the protein model and all hydrogen atoms of all molecules. Clicks on the “Initiate Gaussian” button.

Forms the Schiff-base bond between the prepared retinal molecule and the lysine residue of the protein model using the Intermolecular Bond Setup Wizard. Starts the “Protein Superposition” module program.

Sets a desired calculation condition for modeling the insertion sequences. Completed the homology modeling for the human rhodopsin.

Clicks on the “Delete H” button in the Edit Tool box. Tutorials to Help with 8. Then, selects the activated “Cap Atom” button. Uses Gaussian Interface for HyperChem This tutorial describes the basics of obtaining ray-traced images in HyperChem.

Tutorials to Help with 8.0

Performs the full optimizations under the operational molecular mechanics condition. Starts the “Gaussian Interface” program.

Coordinates a reliable initial structure for the hydrogen atoms of the extracted water molecules. This tutorial describes the aspects of rendering available in HyperChem. Homology Modeling Tutorial Membrane Protein: 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.


Starts the “Interface Selection” module program.

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

Chooses a desired semi-empirical method from the “Calculation” menu, and then click on the “Calculate Charge” button. Loads the structure of the bovine rhodopsin as a template into the HyperChem workspace. Assigns bonding information, hydrogen atoms, and atom types for other molecules if extracted.

Deselects the “Selection Only” option in the View box. Selects two cells of the first column to hyprchem the bond type information to the corresponding atoms of retinal molecule in the HyperChem workspace. Chooses a desired molecular mechanics force field from the “Calculation” menu. Starts the “Estimation of Hydrogen Atoms in Water” module program. Chooses the “Complement Selection” command of the “Selection” menu, and then selects the “Delete Selection” command of the “Option” menu.

The program automatically assigns the total charges and spin multiplicity for this imine molecule, and calculates single-point atomic charges. Follows the instruction of this wizard steps. We are excited to announce hypsrchem the HyperChem now includes over megabytes of audiovisual tutorials. Repeats to tutoriial the conjugated double bond of the retinal molecule.