Article ID: 416 - Last Modified: October 10, 2011
How should I prepare reactant and product structures for a transition state search?
We recommend that you start with one structure, duplicate it in the Project Table and then change the duplicate into the other structure by making and breaking the appropriate bonds. Before you do this, you should ensure that the preference "Adjust number of hydrogens following build operations" in the Builder tab of the Preferences panel is turned off. Building the reactant from the product (or vice versa) ensures that the atom numbers and labels remain the same, which is important for the transition state search.
If you can, you should duplicate the structure again and try to construct your best guess at the transition state, and use this guess with the QST method in your transition state search.
Keywords: atom numbers, renumber, Maestro, Jaguar
#892: I want to do a transition state search with Jaguar, but the atom numbering for my product and reactant entries is dif...
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