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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The program automatically assigns the total charges and spin multiplicity for this imine molecule, and calculates single-point atomic charges. A few tutorials are available for download on this page.
Tutorials to Help with 8.0
Sets the reference molecule number to “1” and the tugorial molecule number to “Non-Protein”, and then clicks on tutoiral “Execute” button of the Distance Selection 4 angstrom between heavy atoms, hypetchem target: Selects the “Number” label in the Atom Label box. Introduction to the Tutorials. Sets the target molecule number to “4”, and then selects the “Delete Target” option of the “Option” menu.
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.
Performs the procedure of the human Rhodopsin homology modeling tutorial. Close the Edit Tool box. The full version of the tutorials is included in the purchased product.
This tutorial will show how to query a database of molecules for use within HyperChem. Then, selects the activated “Cap Atom” button.
Homology Modeling Professional for HyperChem: Tutorial 1 – Institute of Molecular Function –
Starts the “Side Chain Rotamer Modeling” module program. Assigns bonding information, hydrogen atoms, and atom types for other molecules if extracted. Chooses a desired molecular mechanics force field from the “Calculation” menu. Loads the final alignment table to the 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. Confirms the precision of the model.
Decides a suitable template molecule from the protein molecules which formed the homo-dimer, comparing their hyperche thermal factors and amino-acid identities with the target sequence. CHypercubeInc. Chooses a desired semi-empirical method from the “Calculation” menu, and then click on the “Calculate Charge” button.
Determines the best initial rotamer for a residue which differs from the corresponding residue of the template molecule using the batch calculations. Sets the target molecule number to “30” fragmented retinal moleculeand then click on the “Edit Molecule” button. This tutorial describes the aspects of rendering available in HyperChem.
These tutorials are intended to help the new user become acclimated to HyperChem, tutoriao well as to provide training in some of the advanced features of HyperChem that the seasoned user may have yet to discover.
Chooses the “Reverse Selection” command of the “Selection” menu. Deselects the “Selection Only” option in the View box.
The HyperChem operations such as the parameter settings of the geometry optimizations and molecular dynamics annealings are also shown in the manual in detail. Superposes the structure blue of the template molecule system onto the created 3D structure red. Homology Modeling Professinal for HyperChem The procedure and the parameter settings in the individual module programs are shown in the attached manual in detail.
Optimizes these atoms under the operational molecular mechanics condition. Optimizes the alignment if necessary. Starts the “Estimation of Hydrogen Atoms in Water” module program. Assigns protonation state of a histidine residue in the target sequence if necessary.
Removes all restraint conditions. Completed the homology modeling for the human rhodopsin. The program automatically adds the capping group to this terminal carbon. Uses Gaussian Interface for HyperChem Clicks on the “Make Hyperchrm File” button. Assigns the bonding information, hydrogen atoms, and atom types to the incompleted retinal molecule.
In this hypercuem, this retinal molecule is converted to the corresponding imine molecule. Starts the “Ramachandran Plot” module program. 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.
Starts the “Gaussian Interface” program. The procedure and the parameter settings in the individual module programs are shown in the attached manual in detail.