MacroModel Reference Manual - ISP

Chapter 4: Operation CodesASL3 — ASL expression for fixed and frozen ligand atoms in Embrace calculationsSpecify ASL syntax for fixed and frozen ligand atoms in Embrace calculations, similar to theFXAT opcode. This command is intended to make it easier to set up standardized substructuresthat can be reused in different calculations on different molecular systems.Note:This special command can only be used in substructure (.sbc) files: it cannot be usedin command (.com) files.The format of this command is similar to that of regular opcodes, starting with a 4-characterstring. The first argument is a floating-point number, and the second argument is a string.arg1Fix or freeze atoms>0 Specify the force constant for the atoms defined by the ASL expression, which are“fixed” atoms−1arg2Freeze the atoms defined by the ASL expression.ASL expressionSee the Maestro Command Reference Manual for information on ASL syntax.FXAT — FiX ATomFix or freeze the position of the atom given in arg1. We use the term “fix” to mean “tether inplace using a constraint”; thus “fixed” atoms can move. We use the term “frozen” to denote“rigidly freeze in place.” Frozen atoms cannot move at all.This command is generally used with the SUBS command to fix or freeze the positions ofcertain atoms at the periphery of the substructure being minimized. See the description of theSUBS command for a description.When doing substructure (SUBS) calculations with FXAT restraints having no free flat bottomregion (arg4 = 0), interactions wholly involving the fixed atoms, other than stretches, are eliminatedfrom the interaction array unless DEBG 17 or 28 is set. This is primarily to improve thespeed of the computation; when the force constant is large, as it is by default, the FXATconstraints, together with the stretch interactions, maintain reasonable local geometries.The constraint potential, E c , for a fixed atom is calculated using the equationE c = 0r ≤ σ= k( r – σ) 2 r > σMacroModel 9.7 Reference Manual 67