MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg6Allowable interatomic approach distanceFraction of sum of van der Waals radii used as a closest atomic approach limit. If avan der Waals pair comes closer together than this as the result of an LMCS move,the move is rejected before minimization.0 Default: 0.25>0 Other fraction.arg7Minimum distance (Å)In an LMCS move, a random total travelling distance is selected between the specifiedminimum and maximum values. The distances specified here and in arg6correspond to the motion of the fastest-moving atom.It is often useful to perform a short conformational search with the default values ofarg7 and arg8, and, based on the results, adjust these arguments accordingly. Ifmany conformations minimize back to the starting conformation, increase arg7 (andperhaps arg8). If many conformations are ruled out because of distorted sp 3 carbons,decrease arg8 (and perhaps arg7). The information needed to make these choiceswill become visible by specifying MCOP arg1=1.0 Default: 3 Å>0 Other value to be used.arg8Maximum distance (Å)0 Default: 6 Å>0 Other value to be used.LMC2 — Low-Mode Conformational search for large moleculesThis method, termed LLMOD, is described by Kolossváry and Keseru [29]. LLMOD has beendeveloped for large-scale conformational searching, such as protein loop optimization,homology model refinement, and fully flexible docking for induced fit modeling, only tomention a few applications [30]. LLMOD is very similar to LMOD, which is implemented inMacroModel as the LMCS command, but LLMOD utilizes the ARPACK package to computelow-mode eigenvectors of a Hessian matrix that is only referenced implicitly, through itsproduct with a series of vectors. The Hessian × vector product can be calculated by a numberof methods. LLMOD is the first conformational search method that can be applied to fully flexible,unconstrained protein structures.90MacroModel 9.7 Reference Manual