Article ID: 1213 - Last Modified: April 9, 2014
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 on each conformer.
Finally, use the MacroModel redundant conformer elimination facility on the Jaguar optimized structures to ensure that you have unique structures. Use the Jaguar energy as the criterion for eliminating redundancies. This step is needed because conformers generated by MacroModel as different conformers can collapse to the same conformer when optimized with Jaguar.
An example of this kind of conformational search is given in the Jaguar Quick Start Guide.
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