MacroModel Reference Manual - ISP

Chapter 4: Operation CodesTCMP — Torsional CoMParisonUsed during importance sampling to define the torsions for torsional RMS calculation and forthe torsional check during the assignment of the simulated structure to one of the input structures.Can be used either with torsional RMS calculations (both functions) or with CartesianRMS calculations (second function only).arg1-4Atom numbers defining the torsional angleZMAT — Z-MATrixDefines the internal degrees of freedom (Z-matrix variables) to be sampled during all degreesof freedom MMC or MC(JBW) runs (also used in MCSD and MC(JBW)/SD). In a Z-matrix,each atom (except the first three specified) is defined with a bond length, bond angle, andtorsional angle with respect to atoms previously defined. The first atom is defined with respectto itself, the second by a bond length to the first, and the third by a bond length to the secondand a bond angle to the first.Also defined in this command are the ranges of change/randomization for each degree offreedom. Typical ranges are 0-0.1 Å for bond lengths and 5 for bond angles. In course of anMMC simulation, backbone torsions should be changed by large ranges to allow for acomplete sampling of the entire potential energy surface. With the above definition ofZ-matrix, torsions to branched atoms should be changed by a small amount (0-5 ) to avoiddistorted bond angles. For MC(JBW) and MC(JBW)/SD simulations, typical randomizationranges are 0-0.1A for bond angles and 0-5 for bond and torsion angles. Large randomizationsreduce the acceptance rate and the number of conformational interconversions, and have theeffect of reducing the JBW procedure to an MMC one.arg1-4arg5arg6arg8Atom numbersSpecify two for bond lengths, three for bond angles, four for torsions.Minimum change/randomization rangeNo default values are supplied; zero means zero.Maximum change/randomization rangeNo default values are supplied; zero means zero.Atom-connectivity sanity checkCheck to make sure the atoms specified in arg1-4 are connected.0 Default: Perform this test.134MacroModel 9.7 Reference Manual