Chem3D Users Manual - CambridgeSoft

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Administrator In the Results In text box, specify the path to the directory where results are stored by typing or browsing. Save a customized job to appear as a Gaussian submenu item as follows: 1. In the Menu Item Name text box, type the name of the job description. 2. Click Save As. The Save dialog box appears. 3. Browse to the Gaussian Job folder in the \Chem3D\C3D Extensions folder. NOTE: The file must be saved in the Gaussian Job folder in order for it to appear in the menu. 4. Select the file type to save. For more information, see “Job Description File Formats” on page 202. 5. Click Save. Job Description File Formats .jdf Format The .jdf format is a file format for saving job descriptions. Clicking Save within the dialog box saves modifications without the appearance of a warning or confirmation dialog box. Saving either format within the Gaussian Job folder adds it to the Gaussian submenu for convenient access. Computing Properties To specify the parameters for computations to predict properties of a model: • From the Calculations menu, point to Gaussian and choose Compute Properties. The Compute Properties dialog box appears and displays the Properties tab with the top property of the menu preselected. Job description files are like Preferences files; they store the settings of the dialog box. You may save the file as either a .jdf or a .jdt type. You modify and save .jdf files more easily than .jdt files. .jdt Format The .jdt format is a template format intended to serve as a foundation from which other job types may be derived. The Minimize Energy and Compute Properties job types supplied with Chem3D are examples of these. To discourage modification of these files, the Save button is deactivated in the dialog box of a template file. Creating a Gaussian Input File A Gaussian Input file contains the coordinates and geometry of the model and the Gaussian keywords taken from the settings of the dialog box. 202•Gaussian Computations CambridgeSoft Job Description File Formats
To create a Gaussian Input file: 1. From the Gaussian submenu, choose Create Input File. The Create Input File dialog box appears. To run a Gaussian input file: 1. From the Gaussian submenu, choose Run Input File. The Run Gaussian Input file dialog box appears. 2. Type the full path of the Gaussian file or Browse to location. 3. Select the appropriate options. If you want to … Then click … 2. Click Create. An input file saves in Gaussian’s native .GJF format. NOTE: The .GJF Gaussian Input File is not the same as the .GJC Gaussian Input File. The .GJC file stores only the model coordinates and not the Gaussian keywords specifying computational parameters. Running a Gaussian Input File If you have a previously created .GJF Gaussian input file, you can run the file from within Chem3D. watch the minimization process “live” at each iteration in the calculation record each iteration as a frame in a movie for later replay track a particular measurement Display Every Iteration NOTE: Displaying or recording each iteration adds significantly to the time required to minimize the structure. Record Every Iteration Copy Measurements to Output 4. Click Run. A new model window is created and the initial model appears. The Gaussian job runs and the results will appear. All properties requested for the job appear in the *.out file. Only iteration messages appear for Gaussian Input File jobs. ChemOffice 2005/Chem3D Gaussian Computations • 203 Running a Gaussian Input File
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • CambridgeSoft
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Administrator the activation each t
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Administrator The following table d
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator • In the Model Sett
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Administrator 30 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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3. Move the pointer over the C-C bo
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Administrator Add serial numbers an
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Administrator 5. Press the Enter ke
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. Administrator b. From the Structu
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Administrator In the Measurements t
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A molecule of Epinephrine appears.
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Administrator Tutorial 7: Docking M
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Administrator To save the iteration
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The allyl radical, CH 2 =CHCH 2·,
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Administrator Determine the raw spi
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To change the structural display ty
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• Select Parallel to rotate the r
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Administrator 2. Adjust the slider
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator To use the same text
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Administrator Example 2. Building a
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Administrator 3. Type the atom type
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Setting Serial Numbers this step, y
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Administrator New in Chem3D version
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To position a plane in your model p
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Administrator For example, consider
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Administrator If you want to displa
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Administrator Example: To examine t
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Administrator Chem3D provides two o
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Administrator change a property. By
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Administrator To add to a group: 1.
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To stop spinning: • On the Movie
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Administrator If you want to … Th
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If you want the file to … Then cl
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Molecular Design Limited MolFile (.
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Method Type Advantages Disadvantage
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Administrator constant), while θ 0
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the same wave function and a consta
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Administrator A variety of other ba
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Administrator activation barriers.
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Parameter Table Use Parameter Table
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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