MacroModel Reference Manual - ISP

Chapter 4: Operation Codesfrom within the ranges specified in arg5-6 and arg7-8. MOLS has the same relationship to LIGBas TORS has to RCA4: the bonds specified in a LIGB command are broken before the MOLSspecifiedmolecular motion is carried out, then the LIGB bonds are remade prior to minimizationof the resulting structure.Note:arg1-4During a long enough search, if pair-list cutoffs are in effect, as is normal (see EXNB),one molecule may eventually wander far enough away from another that nononbonded energies between them exist anymore. In this situation, further searchingjust explores random spatial dispositions of this pair with no energetic contributionfrom their mutual interaction. Unless already-found binding conformations are lowerin energy by at least the DEMX-specified energy, this will lead to essentially an infiniteand fruitless search of conformational space. To avoid this, use FXDI to constrain thedistance between atom pairs spanning pairs of molecules to some maximum distance.This maximum distance should be specified as the half-width of an FXDI potential. Inpractice, we do this only if we encounter difficulties without doing so.Atom in a molecule to be movedEach nonzero atom given specifies independent motion of the entire molecule containingthe atom. Thus, to specify independent motion of two molecules, put anatom number from the first in arg1 and an atom number from the second in arg2.0 Perform rotations about the center of mass of the molecule containing the atom.arg5arg6arg7arg8Minimum rotational variationAngle in degrees (default: 0.0).Maximum rotational variationAngle in degrees (default: 0.0, i.e., no rotation). 180˚ is a reasonable value.Minimum translational variationMovement in Angstroms (default: 0.0).Maximum translational variationMovement in Angstroms (default: 0.0). A value in the range 3-5 Å is reasonablevalue.MacroModel 9.7 Reference Manual 113