Is there a way to run a conformational search specifically for macrocycles?

Yes. From Suite 2011, you can use the Macrocycle Conformer Sampling panel. In Suite 2012, this panel is available from Applications → MacroModel. In Suite 2011, it is available from the Scripts menu, and is installed by default as part of your installation. For information on the background and methodology, see the newsletter article at http://www.schrodinger.com/newsletter/18/116/.

Briefly, the script performs two serial MacroModel computations. The first is a series of high-temperature dynamics simulations, followed by a large-scale low-mode conformational search on the resulting structures. The search can take several hours, especially when using solvation.

You can also run the script from the command line, with the following command:

$SCHRODINGER/run macrocycle_conformational_sampling.py input-file [options]

For details of the usage, run the command with the -h option. If you have problems, rerun the calculation with the -LOCAL option, to save the intermediate files, including the MacroModel .com files.

This script does not work under 64-bit Windows in Suite 2011.

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