MacroModel Reference Manual - ISP

Chapter 4: Operation Codesd = 0d 0 – σ ≤ r ≤ d 0 + σd = r – ( d 0 – σ)r < d 0 – σd = r – ( d 0 + σ)r < d 0 + σr = R i – R j , R i and R j are the positions of the atoms i and j that define the distance, d 0 is thedesired position (arg6), k is the force constant (arg5) and σ is the half width of the flatbottomedpotential (arg7).Note:With hydrogens bound to carbon in force fields MM2 and MM3, the restraint isapplied between the van der Waals positions of the hydrogen (e.g., with a (C)H inMM2, the hydrogen is treated as if it were at a position shifted 8.5% of the C-H bondlength toward the C).If two FXDI commands specify the same atoms, the second replaces the first.Note that for MBAE calculations, FXDI commands should be placed in a .sbc file.arg1 Atom 10 Clear all existing FXDI constraintsarg2 Atom 2arg4Nonbonded control1 The corresponding nonbonded interaction is eliminated from the interaction array.Used to allow fixed distances for atoms which are close in space.arg5 Force constant (default = 100 kJ/mol·Å 2 )arg6Desired distance (Å)0 Use initial value.>0 Use this value.arg7Half-width of flat bottom part of the potential wellFXBA — FiX Bond AnglesThis command supplies energetic restraints to planar angles defined by the locations of tripletsof atoms.70MacroModel 9.7 Reference Manual