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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Selects the cell corresponding to the retinal terminal carbon, and then clicks on the activated “Set Bond” button in the opened Edit Tool box.

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

Then, selects the activated “Cap Atom” button. 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. Extracts an tutorlal element tutoral to hypercheem model of the template molecule system such as the water molecules and the retinal molecule into the created 3D structure. 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.

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.

Chooses the “Select Proteins” command of the “Selection” menu. Homology Modeling Tutorial Membrane Protein: Optimizes the alignment if necessary.

Tutoriak on the “Initiate Gaussian” button. Starts the “Estimation of Hydrogen Atoms in Water” module program. Assigns the bonding information, hydrogen atoms, and atom types to the incompleted retinal molecule. The full version of the tutorials is included in the purchased product.


Tutorials to Help with 8. Starts the “Ramachandran Plot” module program. CHypercubeInc. Starts the “Protein Superposition” module program. Uses Gaussian Interface for HyperChem Initiates the “Control Center” by double-clicking on the “HM” icon. The richness and depth of HyperChem assures that the average user may continue to discover additional features and capabilities hypercehm after initial introduction to the program.

Forms the Schiff-base bond between the prepared retinal molecule and the lysine tuorial of the protein model using the Intermolecular Bond Setup Wizard. Sets the desired entry boxes using the pop-up list box.

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

hypwrchem 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 “Restraints” module program. This tutorial describes the basics of obtaining ray-traced images in HyperChem. Removes all restraint conditions. Selects two cells in the first column of cells corresponding to the undesired two hydrogen atoms on the retinal terminal byperchem, considering the trans configuration of the potential Schiff base moiety with the lysine residue.

Repeats for tutoorial reference molecule number “2” and “3”. Superposes the structure blue of the template molecule system onto the created 3D structure red.

Selects the side chain atoms of the protein model and all hydrogen atoms of all molecules. This tutorial describes the aspects of rendering available in HyperChem.


Tutorials to Help with 8.0

Deselects the “Selection Only” option in the View box. This tutorial will show how to query a database of molecules for use within HyperChem.

Sets the target molecule number to “4” original molecule number is 5and then hyperchrm the “Select Covalent Unknown” command of the “Selection” menu 4. Assigns bonding information, hydrogen atoms, and atom types for other molecules if extracted. Performs the full optimizations under the operational molecular mechanics condition. Starts the “Interface Selection” module program.

Sets the operational molecular mechanics conditions and the automatic rotamer search conditions. Then, the prepared Gaussian input file will appear. Confirms the precision of the model. Welcome Introduction to the Tutorials.

Sets the target molecule number to “4” original molecule number is 5and then selects the “Select Covalent Unknown” command of the “Selection” menu. Common The attached capping group is deleted at this stage. A few tutorials are available for download on this page. Total Time 9 – Selects two cells of the first column to set the bond type information to the corresponding atoms of retinal molecule in the HyperChem workspace.

Coordinates a reliable initial structure for the hydrogen atoms of the extracted water molecules. Starts the “Gaussian Interface” program.

Starts the “Side Chain Rotamer Modeling” module program.