MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg1Sampling symmetric terminal groups+Terminal – CH 3 , – NH 2 and – NH 3 groups are never sampled by ConfGen. Samplingthe conformations of other types of symmetric terminal groups is sometimesnot useful. The identification of such groups is complex but boils down to an atomwith identical groups attached to it. These groups can be monoatomic or composedof atoms with only 2 or 3 hydrogen atoms bonded to them. Checks for rotationalsymmetry are also imposed (e.g. if there are two groups but they do not lie 180˚apart from each other, they would need to be sampled). Typical examples include–+– SO 3 , – NCH ( 3 ) 3, and – NO 2 .0 do not sample these symmetric terminal groups1 sample such terminal groupsarg2Ring conformation samplingRing sampling is done by matching the rings in the molecules with templates forwhich the low-energy conformers have been previously identified. Two such templatematching systems are supported:• one using general forms for flexible 5 and 6 atom rings.• one employing an extensive collection of specific templates for a large varietyof ring systems (ring_conf utility).The specific templating system has broader coverage (several hundred templates)and the template conformations were generated using MacroModel searchesemploying the MMFFs force field.0 or 2 use the specific templating system (ring_conf)1 use the general templating system3 do not sample ring conformationsarg3Minimization of generated structures0 minimize generated conformations using at most the number of iterations in theMINI command−1−2do not minimize the generated conformations, but estimate the current energy,superimpose the generated conformations, and eliminate redundant conformationsdo not post process the conformations provided by ConfGen156MacroModel 9.7 Reference Manual