Article ID: 768 - Last Modified: December 4, 2010
If I want to get 10-20 diverse conformations for Glide, how do I set the parameters for MacroModel CSearch or ConfGen?
First, you can use the duplicate-elimination feature within MacroModel CSearch or ConfGen itself. Set the number of structures to save to 20, but increase the cutoff for eliminating redundant conformations to ensure greater diversity in the results. Alternatively, you can generate many conformations and then reduce them to a diverse set with MacroModel's Redundant Conformer Elimination. Another approach is to cluster the conformations and choose a representative from each cluster.
Keywords: diverse conformations, Csearch, MacroModel
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