MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg7arg8Increment valueThe increment must be nonzero. If arg7 is greater than zero then arg5 must besmaller than arg6, otherwise the drive would never terminate. Similarly, if arg7 isless than zero, arg5 must be greater than arg6.The actual number of steps is given by the formula:N= ABS(arg5–arg6)/arg7 +1The maximum allowable value of N is 100. In the usual use of the DRIV command(i.e., two DRIV commands in a file), N 2 energy minimizations are done.Constraint Force Constant0 Use the default value of 1000>0 Use this valueUnits for the force constant vary with type of drive: kJ mol -1 Å -2 for distances,kJ mol -1 radian -2 for angles, and kJ mol -1 for torsions.SUBS — define a SUBStructure for subsequent minimizationArg1-4 are atom numbers of the substructure: those atoms that are allowed to move withoutrestriction in the environment of anchored atoms. This command is normally used with FXATcommands, which restrain the position of atoms at the periphery of the substructure. Thesubstructure and associated FXAT commands are commonly produced using the substructureeditor of Maestro. There are two principal reasons to do this:• To “tether” part of a molecule in space. This is ordinarily done using FXAT commandsbut no SUBS commands.• To save computing time by ignoring part of the system believed to be irrelevant. If bothSUBS and FXAT commands appear, then atoms that are not specified in either commandare completely ignored in the simulation.Note:When SUBS and FXAT commands appear together, any interaction except a stretchconsisting only of FXAT atoms is eliminated, provided the following conditions hold:• The FXAT atoms in question are not specified by any SUBS command.• The flat-bottom half-width is zero for all the FXAT atoms concerned.• Neither DEBG 17 nor DEBG 28 is specified.The elimination of these interactions saves time, since FXAT atoms will not move much;however, stretches are always included since without them the “fixed” atoms tend to adoptunrealistic relative positions even for rather high tethering potentials.64MacroModel 9.7 Reference Manual