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 “Restraints” module program. Starts the “Side Chain Rotamer Modeling” module program. The HyperChem operations such as the parameter settings of the geometry optimizations and molecular dynamics annealings are also shown in the manual in detail. Sets an operational molecular mechanics condition.

HyperChem Tutorials

Sets the target molecule number to “4” original molecule number is 5and then selects the “Select Covalent Unknown” command of the “Selection” menu.

Sets the target molecule number to “30” fragmented retinal moleculeand then click on the “Edit Molecule” button. Uses Gaussian Interface for HyperChem Sets the target molecule number to “4” original molecule number is 5and then selects the “Select Covalent Unknown” command of the “Selection” menu 4. Sets the target molecule number to “4”, and then selects the “Delete Target” option of the “Option” menu.

Homology Modeling Tutorial Membrane Protein: Starts the “Ramachandran Plot” module program. Starts the “Interface Selection” module program. 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. Forms the Schiff-base bond between the prepared retinal molecule and the lysine residue of the protein model using the Intermolecular Bond Setup Wizard.


Performs the low-temperature molecular dynamics annealings under the operational molecular mechanics condition.

Clicks on the top cell of the fourth column, and then selects the “Auto Assign Type” button of the opened dialog box. Sets a desired calculation condition for modeling the insertion sequences.

This tutorial describes the aspects of rendering available in HyperChem. Selects the “Number” label in the Atom Label box. Common The attached capping group is deleted at this stage.

Starts the “Gaussian Interface” program. Tutorials to Help with 8.

Tutorials to Help with 8.0

Creates a preliminary 3D structure, i. Chooses the “Reverse Selection” command of the “Selection” menu. 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.

Total Time 9 – Optimizes the alignment if necessary. Chooses a desired molecular mechanics force field from the “Calculation” menu. The program automatically adds the capping group to this terminal carbon. Welcome Introduction to the Tutorials. Sets the restraint condition to all heavy atoms.

Superposes hypercehm structure blue of the template molecule system onto the created 3D structure red. Chooses the “Complement Selection” command of the “Selection” menu, and then selects the “Delete Selection” command of the “Option” menu.

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

Sets the desired entry boxes using the pop-up list box. Initiates the Peripheral Modeling program, and then selects the “Molecular Modeling” option of the “Modeling” menu.

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.


This tutorial describes the basics of obtaining ray-traced images in HyperChem.

Assigns the bonding information, hydrogen atoms, and atom types to the incompleted retinal molecule. Introduction to the Tutorials. Specifies a sequence of the human rhodopsin as a target sequence.

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. Confirms the precision of the model. Calculates atomic charges for the imine molecule using the single point calculations of a suitable theory balanced with the operational molecular mechanics condition. Deselects the “Selection Only” option in the View box.

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

Follows the instruction of this wizard steps. In this case, this retinal molecule is converted to the corresponding imine molecule. Performs the procedure of the human Rhodopsin homology modeling tutorial. 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 hyperchrm sequence. Clicks on the cell corresponding to the retinal terminal carbon.

Starts the “Estimation of Hydrogen Atoms in Water” module program.