MacroModel Reference Manual - ISP

Chapter 1: Capabilities and New Features• Use of FLAP ring vertex reflection algorithm in MCMM and low-mode searches (FLAP).• Use of ring templates for MCMM and low-mode searches (MCRC).1.2.4 Molecular Dynamics and Monte Carlo Simulations• Molecular Dynamics or Stochastic Dynamics.• Multiple timestep acceleration.• Constant temperature or energy.• SHAKE bond length constraints.• Translational and angular momentum constraints.• Simulated annealing.• Internal coordinate and surface area monitoring.• Hydrogen-bond monitoring.• Local conformational searching.• Evaluation of average enthalpy.• Mixed-mode Monte Carlo/Stochastic Dynamics procedure speeds exploration of conformationalspace.• Velocity-Verlet integration scheme for greater efficiency of mixed-mode calculations.• Importance sampling for Monte Carlo or mixed-mode calculations further speeds explorationof conformational space.1.2.5 Coordinate Manipulation• Different molecules may be aligned by center, principal axis, or both, using COPY andALGN.1.2.6 Molecular Association• Embrace (MBAE) Multi-ligand Bimolecular Association with Energetics: A method forautomatically minimizing or performing conformational searches on prepositionedligands in the active site of a protein and obtaining energetic information related to theassociation of the ligands with the protein.6MacroModel 9.7 Reference Manual