MacroModel Reference Manual - ISP

Chapter 4: Operation CodesConfGen inherently generates conformations without considering electrostatics. This canoccasionally lead to conformations that have functional groups with a formal charge of thesame sign lying near each other. If minimization or energy filtering of conformations is notdone inside MacroModel itself (CGEN arg3 = −1 or−2, respectively) these conformations mayend up being saved in the output structure file. CGO4 turns on a penalty mechanism that canexclude such conformations within ConfGen itself. The penalty for conformation k is calculatedfrom the fractional formal charges q i on the atoms using the expressionP k=∑ijp ijwhere the sum runs overall all pairs of atoms i and j that are separated by at least 3 bonds, andp ij = 0,q i q j ≤ 0=2Aq i q j exp( – r ij ⁄ 2s 2 ), q i q j > 0where A and s are constants and r ij is the distance between atoms i and j.If P k – P min > P cutoff where P min is the smallest penalty for any of the conformations then theconformation is eliminated within ConfGen.arg5Standard deviation of the Gaussian penalty, s0 use 5 Ang> 0 use this value (Ang)arg6Maximum value for the Gaussian, A0 use 2.5> 0 use this valuearg7Relative penalty cutoff, P cutoff0 use 0.75> 0 use this valueMacroModel 9.7 Reference Manual 161