MacroModel Reference Manual - ISP

Chapter 4: Operation Codes−1arg5Do not use templates in conformational searchProbability of using templatesSpecify the fraction of conformational search steps that will use templates. If usedin conjunction with FLAP, the sum of the FLAP and template probabilities must notbe greater than 1.0 Use the default value of 0.5>0 Use this value. Should be between 0 and 1.MCTS — Monte Carlo Torsion SelectionExperience has shown that this command is not terribly useful.Use in conjunction with MCMM to favor torsion angle selection near local torsional minima forthe angles being varied. One MCTS command is required for each torsion which is to beeffected. Arg1-4 are the atoms defining a particular torsion angle (i.e., arg2-3 should appear asa rotatable bond in a TORS command). Arg5-7 are 1-fold, 2-fold, and 3-fold torsional barrierswhich are used to compute local torsional energies as part of the test for an allowable value ofthe randomly selected Monte Carlo angular change. After a Monte Carlo variation of a torsionangle described by arg1-4 of this command is performed, a local torsional energy (E T )iscomputed based on the value of the dihedral angle, τ, using the usual MM2 formula:E T = (V 1 /2)(1+cos τ) + (V 2 /2)(1–cos 2τ) + (V 3 /2)(1+cos 3τ) – E T,minwhere E T,min is the minimum possible value of E T .IfE T is greater than 1, the torsion is rejectedand a new random torsion angle is chosen. Otherwise, E T is compared with a random numberbetween 0 and 1 and, if E T is larger than that number, a new random torsion angle is chosen.This scheme selects for local torsions which are low in energy. For sp3-sp3 linkages, one canfavor the gauche and anti conformers (the minima) by using a V 1 (arg5) and V 3 (arg7)of 0.25.This will cause totally eclipsed (0-degree torsion) torsions to be strongly disfavored, 120-degree torsions to be moderately disfavored and the gauche and anti conformations to befavored. By choosing V 1 -V 3 with care and using a random number for comparison, even highenergy geometries are occasionally explored.arg1-4arg5arg6Atoms defining the torsionV 1 (positive number gives anti minima)V 2 (positive number gives eclipsed minima)MacroModel 9.7 Reference Manual 107