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Article ID: 622 - Last Modified: June 7, 2011

Does the ConfGen Advanced feature "Use n steps per rotatable bond" refer to uniformly distributed torsion values (with a fixed torsion grid increment) or is it something else?

ConfGen generates candidate structures from the combinations of ring conformations for the various rings present, nitrogen atom inversions, and all minima for each rotatable bond in the core with all terminal rotatable bonds in their lowest energy minima. It then reduced the number of conformations to the number specified in the "Maximum number of search moves" text box by uniformly selecting them from the initial collection. If you want to allow more conformations to be kept for more flexible molecules, while keeping the average number of conformations for a database relatively small, you can use the "Use n steps per rotatable bond" text box, which calculates the maximum number of conformations to keep by multiplying the number of rotatable bonds in the molecule by the value given in this text box. (In fact, it is really the number of degrees of freedom, because rings and nitrogen inversions are included.) The maximum number so derived is still limited by the overall number given in the "Maximum number of search moves" text box.

The terminology of "steps" and "search moves" used here comes from the systematic Monte Carlo conformational search methodology, but in this context what is meant is the number of conformations generated or kept overall or per rotatable bond.

Keywords: steps per rotatable bond, conformations, ConfGen

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