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Article ID: 411 - Last Modified:

How can I generate a dimer from a given conformation of a monomer, without any information from a crystal structure?

You can use the general procedure below, for any molecule, to create a dimer structure by manually positioning the monomers.

  1. Duplicate your structure: select it in the Project Table and press Ctrl+D. The duplicate should be selected and displayed in the Workspace.
  2. Select Molecule from the Transform toolbar button menu, and click on the molecule in the Workspace. Some markers should appear on the molecule.
  3. Move the molecule somewhere else. This is so that it's not on top of the other copy.
  4. Include the original conformation in the Workspace (control-click the In column). Note that the duplicate still has the markers.
  5. Now rotate and translate the duplicate so that it is at the desired position relative to the original. You can hold down the space bar to temporarily exit local transformation mode and rotate the view. This will allow you to translate the duplicate in another plane.
  6. When you are satisfied with the positions of the two molecules, click the Create Entry toolbar button, to create a new entry for the dimer. Alternatively, you can select both entries in the Project table and choose Entry → Merge to merge the two entries into a new entry.

Keywords: intermolecular dimer, Maestro

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