MacroModel Reference Manual - ISP

Chapter 1: Capabilities and New Features• Torsional potentials for highly strained conformations in which three of the atoms at oneend of the torsion become collinear can cause problems during minimizations. The torsionalpotential is damped as either triplet of atoms at the end of the torsion becomes linear.The strength of the damping can be controlled via arg8 of FFLD.1.2.2 Energy Minimization Methods• Large and small molecules.• Single or multiple structures.• Full structure or substructure.• Substructures can be specified using ASL expressions.• Positional, distance, and angular constraints.• Choice of steepest descent (SD), Powell-Reeves conjugate gradient (PRCG), truncated-Newton conjugate-gradient (TNCG), Oren-Spedicato variable metric (OSVM), fullmatrixNewton-Raphson (FMNR), and Limited Broyden-Fletcher-Goldfarb-Shanno(LBFGS) minimization methods.• Enhanced saddle-point searching (see the MINI command on page 52).• Eigenvalue minimum testing and vibrational frequencies.• Visualization of normal modes (VIBR and VBR2 ).• Harmonic-entropy free-energy calculations.• Greater control over intermediate output during minimization: see MINI command.• Explicit saddle-point search method (see the SDLP command on page 61).• The FXAT command has facilities which allow constraints to be relaxed in a stepwisemanner. Minimization may be performed at each stage. This is useful in refining poorlyinitialized structures which may have been derived from NMR or low-resolution crystallography,or from homology modelling.• The LCPO method, our accurate analytical surface-area computation method, is parameterizedfor metal atoms. DEBG 91 uses the old surface area method.• Additional LCPO parameters allow use of LCPO surface-area calculation with a broadervariety of atom types.• Automatic sequential minimization using multiple minimizer methods (MWRT).4MacroModel 9.7 Reference Manual