MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg6Maximum value for the Gaussian, A0 use 1> 0 use this valuearg7Relative penalty cutoff, P cutoff0 use 0.25> 0 use this valueCGO6 — Additional ConfGen Options for rejecting conformations with closecontacts between nonhydrogen atomsCGO6 allows the user to activate and adjust enhanced ConfGen capabilities for rejectingconformations that have too many nonhydrogen atoms in close proximity. CGO6 is one of anumber of opcodes (CGOP, CGO2, CGO3, CGO4, CGO5, CGO6) that provide access to additionaloptions for the ConfGen facility.Bioactive conformations tend to be relatively extended. ConfGen can generate conformationsin which topologically distant parts of the ligand lie close to each other. These conformationsmay end up being saved in the output structure file. CGO6 turns on a penalty mechanism thatcan exclude such conformations within ConfGen itself particularly if the groups approachingeach other are rings. The penalty for conformation k is calculated using the expression:P k=∑ijp ijwhere the sum runs over all all pairs of nonhydrogen atoms i and j that are at least three bondsaway from each other. The penalty term is defined by2p ij = A exp( – r ij ⁄ 2s 2 )A and s are constants and r Xj is the distance between atoms X 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 2.5 ÅMacroModel 9.7 Reference Manual 163