MacroModel Reference Manual - ISP

Chapter 4: Operation Codeswhere r = R–R 0 , R is the current position and R 0 is the desired position (arg6-arg8), k isthe force constant (arg5), and σ is the half-width of the flat-bottomed potential (arg4).When using low force constants to “gently” constrain atomic positions, local geometriesbecome unreasonable unless debug switch 17 is set. Also, unless mutual interactions betweenFXAT atoms are active, solvation energies for systems involving FXAT have no absolutemeaning, although comparisons between conformers are still meaningful.When using FXAT commands in molecular dynamics (e.g., doing substructure moleculardynamics), it is appropriate to use substantially reduced force constants (arg5, e.g., 50-100) sothat realistic flexibility and rapid thermal equilibration is possible.If two FXAT commands specify the same atom, the second replaces the first.A FXAT command must come after READ commands.Note that for MBAE calculations, FXAT commands should be placed in a .sbc file.arg1Fixed atom number0 Clear or modify fixed and/or frozen atom constraints, depending on the values of theother arguments. A typical use for this facility is in homology modeling, when onemight want to perform a minimization with frozen or “tight” fixed constraints, thenrepetitively diminish the constraints and reminimize. When arg1 is 0, the other argsare interpreted as follows.If arg2 is 0, all fixed and frozen atoms become unconstrained. If arg2 is positive,then all fixed atoms are affected according to the values of arg4 and arg5; if arg2 isnegative, then all frozen atoms are so affected. For arg2 nonzero, then, if arg4 andarg5 are zero, all fixed or frozen atoms are simply unconstrained; if either arg4 orarg5 is nonzero, then the behavior is as follows.If arg2 is positive, fixed-atom constraints are modified. If arg5 is negative, all fixedatoms are frozen. Otherwise, if arg5 is positive, all fixed atoms have their force constantsmultiplied by arg5 (e.g., arg5=0.1 lowers the fixed-atom force constants to 1/10 their current values). If arg4 is 0, the current flat-bottom half widths are unmodified;if arg4 is negative, any flat bottoms are removed; if arg4 is positive, then thecurrent flat-bottom half widths are multiplied by arg4/10 (e.g., arg4=1 lowers theflat-bottom half widths to 1/10 their current values).If arg2 is negative, then frozen-atom constraints are modified. If arg5 is positive, allfrozen atoms become fixed, instead, with a force constant of arg5. If arg4 is positive,they receive a flat-bottom half width of arg4/10.68MacroModel 9.7 Reference Manual