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Article ID: 892 - Last Modified:

I want to do a transition state search with Jaguar, but the atom numbering for my product and reactant entries is different, and I can't run the calculation. How do I change the atom numbering?

The matching of the atoms for a transition state search is done on the order of the atoms in the Jaguar input file. This means that the atom names and atom numbers must match. As Maestro automatically sets the atom numbers in a structure, you cannot simply renumber the atoms. However, you can reorder the atoms in the Jaguar Edit panel, then rename them, as follows:

  1. Display the structure in the Workspace.
  2. Open the Jaguar panel (a single point calculation will do).
  3. Click and hold the Settings (gear) button on the Job toolbar, and choose Edit. The Edit Job panel opens, showing the input file.
  4. Cut and paste the lines of the input file to reorder the atoms (CTRL+X, CTRL+V).
  5. Click OK in the Edit Job panel. The structure in the Workspace is updated with new atom numbers.
  6. Open the Atom Properties tab of the Build panel (Edit → Build → Atom Properties).
  7. Choose Atom Name from the Property option menu.
  8. Under Canonical names, ensure that Composition is set to Element & Atom Number, then click Apply to All Atoms.

To check that the atom names match:

  1. Display the structures in the Workspace.
  2. Choose Atom Name from the Label All button menu on the Label toolbar.
  3. Click the Tile button on the View toolbar.

The structures are placed in separate "tiles" in the Workspace, and you can compare the labels on each structure to make sure that the correspondence of the atoms is correct.

In general, we recommend building one of the structures, then duplicating it in the Project Table and editing it to produce the other structures. In this way, the atom names and numbers are guaranteed to be the same.

Related Articles:

#416: How should I prepare reactant, product, and transition state guess structures for a transition state search?

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