MacroModel Reference Manual - ISP

Chapter 4: Operation Codes2 retain the original carboxylic acid bond geometry3 make carboxylic acid bond geometry transarg3Method for estimating the number of degrees of freedomWhen AUOP arg5 is greater than zero, the number of conformations to sample isgiven by the product of this value and the number of degrees of freedom. This argumentcontrols which method is used to estimate the number of degrees of freedom.0, 2 Use ConfGen’s internal estimate for the number of degrees of freedom, which isgiven by the number of rotatable bonds + log 2 (number of ring conformation-nitrogenatom inversion combinations)1 Use the number of rotatable bonds given by MacroModel.arg4arg5Include the most extended conformersWhen selecting a subset of conformers from those produced by ConfGen includethe arg4 most extended conformers first. In each conformer the largest distancebetween any two heavy atoms is calculated. The ratio of this value to the largestsuch distance amongst all of the conformations for this molecule is used as a measurefor how extended the conformer is.Van derWaals radius scaling factor for close atomic approachesConfGen rejects conformations with atoms closer than this factor times the sum oftheir van der Waals radii.≤0 use default value of 0.6>0 use this valuearg6Scaling factor for close atom gradientsConfGen internally minimizes structures on a simple potential function thatincludes a penalty term for close approaches of atoms. This argument specifies thescaling factor for this penalty term.≤0 use default value of 1.0>0 use this value158MacroModel 9.7 Reference Manual