Article ID: 892 - Last Modified: May 2, 2012
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 actually done on the atom name, not the atom number. You cannot in any case renumber the atoms in Maestro, because the number is determined by the order the atoms appear in the structure file (or by the order of addition when building). However, you can change the atom names so that they match. To do so, choose Edit → Build → Atom Properties, and choose Atom Name from the Property option menu. You can then use the tools in this panel to set the atom name for atoms in your structure. To help match the atoms between the structures, display both structures, label them with the atom names, and then tile the Workspace (from Suite 2010 on, this does not change the atom coordinates). You can then see which atoms should correspond between the structures.
In general, we recommend that you build either the reactant or product, then do the necessary bond breaking and making and structural adjustments to create the product, and if possible, a guess at the transition state. In this way, the atom names are guaranteed to be the same.
Keywords: Atom numbering, transition state, Jaguar
#416: How should I prepare reactant and product structures for a transition state search?
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