I am running Jaguar and want to do a conformational search. How do I do this?

You can use MacroModel in conjunction with Jaguar to perform a conformational search and obtain high quality conformers. First, run a MacroModel conformational search. We recommend using either the mixed torsional/low mode method, or a ligand torsional search. When this job finishes, examine the results in the Project Table and check the log file to see if any conformers need further minimization. If so, run a MacroModel multiple minimization job. Next, select the conformers in the Project Table that you want to optimize with Jaguar, and run a Jaguar optimization job. Finally, use the MacroModel redundant conformer elimination facility to ensure that you have unique structures. An example of this kind of conformational search is given in the Jaguar Quick Start Guide.

Keywords: Jaguar, conformations

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