MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg1Number of Monte Carlo steps to be carried out before stopping0 Carry out the search until arg2 structures have been found. We do not recommendthe use of this default.arg2Maximum number of structures to retain while running0 The maximum number of conformations to retain while running is the value specifiedin arg1 or 10,000, whichever is greater.>0 This is the maximum number of conformations to retain while running.arg3arg4Number of variables altered in each stepThe number of torsional angles varied and/or molecules moved in each step(default: 3). The value specified is randomly varied by +/–1 to prevent concentrationof the search in local areas of conformational space. The default (3) thus alters 2–4variables at each step.Greater control over this parameter may be obtained using the MCNV command; thisis the most common procedure.Search mode0 Global search (each Monte Carlo step begins with the preceding Monte Carlo structure,providing the structure is within 100 kJ of the global minimum). This is equivalentto MCSS (arg1=0, arg2=0, arg4=100.0).1 Local search (each Monte Carlo step begins with the original structure). Generallyused with small coordinate variations in TORS or MOLS to find other minima whichare closely related to the starting structure.arg6Allowable interatomic approach distanceFraction of sum of van der Waals radii which is used as a closest atomic approachlimit (default: 0.25).SPMC — Systematic Pseudo-Monte Carlo searchSimilar to MCMM, but invokes systematic search in place of random search. The search begins atlow torsional resolution (120˚), searches all angles without duplicating coverage, then doublesthe resolution, etc. This method has the advantage of not retracing its path and consequentlyconverges the final stages of the conformational search more efficiently than MCMM. Like MCMM,the method is effectively open-ended: it will search conformational space until stopped by theuser or with arg1.102MacroModel 9.7 Reference Manual