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Administrator Intermediate status messages may appear in the Output window. A message appears if the minimization terminates abnormally, usually due to a poor starting conformation. To interrupt a minimization that is in progress: • Click Stop in the Computing dialog box. The minimization and recording stops. Queuing Minimizations You can start to minimize several models without waiting for each model to finish minimizing. If a computation is in progress when you begin minimizing a second model, the minimization of the second model is delayed until the first minimization stops. If you are using other applications, you can run minimization with Chem3D in the background. You can perform any action in Chem3D that does not change the position of an atom or add or delete any part of the model. For example, you can move windows around during minimization, change settings, or scale your model. 3. Drag in the model window. A model of Ethane appears. 4. Choose Show Serial Numbers on the Model Display submenu of the View menu. You might also want to set the Model Display Mode to Ball and Stick or Cylindrical Bonds. 5. On the Calculations menu, point to MM2 and choose Minimize Energy. 6. Click Run on the Minimize Energy dialog box. The calculation is performed. Messages appear in the Output Window. To view all the messages: • Scroll in the Output Window. You can also “tear off ” the window and enlarge it to make it easier to view. Minimizing Ethane Ethane is a particularly straightforward example of minimization, because it has only one minimum-energy (staggered) and one maximum-energy (eclipsed) conformation. To minimize energy in ethane: 1. From the File menu, choose New. An empty model window appears. 2. Click the Single Bond tool. The Total Steric Energy for the conformation is 0.8181 kcal/mol. The 1,4 VDW term of 0.6764 dominates the steric energy. This term is due to the H-H repulsion contribution. NOTE: The values of the energy terms shown are approximate and can vary slightly based on the type of processor used to calculate them. 150•MM2 and MM3 Computations CambridgeSoft Minimize Energy
To view the value of one of the dihedral angles that contributes to the 1,4 VDW contribution: 1. Select the atoms making up the dihedral angle as shown below by Shift+clicking H(7), C(2), C(1), and H(4) in that order. To force a minimization to converge on the transition conformation, set the barrier to rotation: 1. In the Measurements table, type 0 in the Optimal column for the selected dihedral angle and press the Enter key. 2. On the MM2 submenu of the Calculations menu, choose Minimize. The Minimize Energy dialog box appears. 3. Click Run. The model conforms to the following structure: 2. From the Structure menu, point to Measurement, and select Set Dihedral Measurement. The following measurement appears. The 60 degree dihedral represents the lowest energy conformation for the ethane model. Select the Trackball tool: 1. Reorient the model by dragging the X- and Y- axis rotation bars until you have an end-on view. Entering a value in the Optimal column imposes a constraint on the minimization routine. You are increasing the force constant for the torsional term in the steric energy calculation so that you can optimize to the transition state. When the minimization is complete, the reported energy values are as follows. The energy for this eclipsed conformation is higher relative to the ChemOffice 2005/Chem3D MM2 and MM3 Computations • 151 Minimize Energy
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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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Chapter 31: Changes and Audit Trail
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Administrator Tutorial 7: Docking M
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Administrator Connection Table . .
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Administrator Specifying Properties
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Administrator Undoing Changes . . .
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Administrator Chapter 28: Introduci
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Administrator Atom Properties . . .
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CAMBRIDGESOFT ChemOffice Desktop to
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CHEMICAL Chemical Databases Referen
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CONSULTING & Consulting & Services
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CS Software Problem Report For fast
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