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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Sets a desired calculation condition for modeling the insertion sequences.

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

Loads the final alignment table to the 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 the cell corresponding to the retinal terminal carbon, and then clicks on the activated “Set Bond” button in the opened Edit Tool box. Removes all restraint conditions. The full version of the tutorials is included in the purchased product. Total Time hyperchdm – We are excited to announce that the HyperChem now includes over megabytes of audiovisual tutorials.

Specifies a sequence of the human rhodopsin as a target sequence. Clicks on the top cell of the first column. Close the Edit Tool box. Sets the target molecule number to “4”, and then selects the “Delete Target” option of the “Option” menu.

Initiates the “Control Center” by double-clicking on the “HM” icon.

Optimizes the alignment if necessary. Starts the “Side Chain Rotamer Modeling” module program. 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 of the potential Schiff base moiety with the lysine residue.


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

Tutorials to Help with 8. Then, selects the activated “Cap Atom” button.

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. Sets the target molecule number to “30” fragmented retinal molecule hutorial, and then click on the “Edit Molecule” button. 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.

Selects the “Number” label in the Atom Label box. Starts the “Ramachandran Plot” module program. It only takes about an hour 1 h in our program system, although it takes several days or several weeks in other program systems. This tutorial will show how to query a database of molecules for use within HyperChem. Clicks on the “Delete H” button in the Edit Tool box.

Chooses hyperchm “Reverse Selection” command of the “Selection” menu. Sets the operational molecular mechanics conditions and the automatic rotamer search conditions. CHypercubeInc.

Starts the “Homology Modeling” module program. Loads the structure of the bovine rhodopsin as a template into the HyperChem workspace. Clicks on the “Make Job File” button. 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.


Completed the construction of the retinal Schiff base in the human Rhodopin model. Clicks on the top cell of the fourth column, and then selects the “Auto Assign Type” button of the opened dialog box. Coordinates a reliable initial structure for the hydrogen atoms of the extracted water 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.

Chooses the “Select Proteins” command of the “Selection” menu. Then, the prepared Gaussian input file will appear.

Performs the full optimizations under the operational molecular mechanics condition. Starts the “Gaussian Interface” program. Chooses the “Complement Selection” command of the “Selection” menu, and then selects the “Delete Selection” command of the “Option” menu.

Repeats for the reference molecule number “2” and “3”. Starts the “Protein Superposition” module program. Performs the procedure tutoriap the human Rhodopsin homology modeling tutorial.

Tutorials to Help with 8.0

Confirms the precision of the model. This tutorial describes the aspects of rendering available in HyperChem.

In this case, this retinal molecule is converted to the corresponding imine molecule.