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Administrator Tutorial 7: Docking Models The Dock command enables you to position a fragment into a desired orientation and proximity relative to a second fragment. Each fragment remains rigid during the docking computation. The Dock command is available when two or more distances between atoms in one fragment and atoms in a second fragment are specified. These distances are entered into the Optimal field in the Measurements table. You can use docking to simulate the association of regions of similar lipophilicity and hydrophilicity on two proximate polymer chains. There are four steps: A. Build a polymer chain: 1. Open a new Model window and select the Text Building tool. 2. Click in the model window. A text box appears. 3. Type (AA-mon)3(C2F4)4(AA-mon)3H in the text box. 4. Press the Enter key. A polyacrylic acid/polytetrafluoroethylene block copolymer appears in the model window. The text, (AA-mon)3, is converted to a polymer segment with three repeat units of acrylic acid. The text, (C2F4)4, is converted to a polymer segment with four repeat units of tetrafluoroethylene. B. Build a copy of the chain: Double-click in the model window well above and to the right of the first polyacrylic acid/polytetrafluoroethylene block copolymer molecule. A second polymer molecule appears above the first polyacrylic acid/polytetrafluoroethylene block copolymer molecule. C. Orient the chains: 1. Click in the empty space in the model window to deselect any atoms in the model window. 2. Click the arrow on the Trackball tool to open the Rotation Dial tool. 3. Select the Y axis, and drag the dial to show 55°. TIP: To get exactly 55° you will probably have to edit the value in the number box. After editing, you must press the Enter key. The value displayed in the right corner of the dial should be the same as in the number box. The resulting model appears as shown in the following illustration (the second model may appear in a different position on your computer): D. set optimal distances between atoms in the two fragments: The Optimal distance determines how closely the molecules dock. In this tutorial, you will set the distance to 5Å. 42 •Chem3D Tutorials <strong>CambridgeSoft</strong> Tutorial 7: Docking Models
1. In the Model Explorer, select C(6) in Fragment 1. Hint: It’s in the AA-mon 2 group. 2. Locate the C(98) atom in Fragment 2 (AA-mon 12 group) and Ctrl-click to select it also. 3. In the Structure menu, point to Measurements and choose Set Distance Measurement. The Measurements table opens, (if it is already open as a tabbed window, it becomes active) displaying the C(98)-C(6) pair. 4. Click the Optimal cell. 5. Type 5 and press the Enter key. The optimal distance between C(6) and C(98) is specified as 5.000Å. To have a reasonable dock, you must specify at least four atom pairs. Repeat steps 1 through 5 for matching atom pairs throughout the fragments. For example, if you choose one pair from each group your list might look like the following: Atoms Actual Optimal C(34)-C(126) 20.1410 5.0000 C(133)-C(41) 20.3559 5.0000 C(45)-C(137) 20.3218 5.0000 C(50)-C(142) 20.4350 5.0000 Ignore the distances in the Actual cell because they depend on how the second polymer was positioned relative to the first polymer when the second polymer was created. To begin the docking computation: 1. From the Structure menu, choose Dock. The Dock dialog box appears. Atoms Actual Optimal C(1)-C(93) 21.2034 5.0000 C(98)-C(6) 21.1840 5.0000 C(104)-C(12) 21.2863 5.0000 C(108)-C(16) 21.1957 5.0000 C(22)-C(114) 20.6472 5.0000 C(28)-C(120) 20.7001 5.0000 2. Type 0.100 for the Minimum RMS Error value and 0.010 for the Minimum RMS Gradient. The docking computation stops when the RMS Error or the RMS Gradient becomes less than the Minimum RMS Error and Minimum RMS Gradient value. 3. Click Display Every Iteration. This allow you to see how much the fragments have moved after each iteration of the docking computation. <strong>ChemOffice</strong> 2005/Chem3D Chem3D Tutorials • 43 Tutorial 7: Docking Models
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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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