Bioinformatics Molecular Dynamics

MacroModel

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MacroModel is a computer program for molecular modeling of organic compounds and biopolymers. Its features include force fields coupled with energy minimization algorithms for the prediction of geometry and relative  conformational energies of molecules. It carries out simulations in the framework of classical mechanics, the so-called “molecular mechanics”. MacroModel also has the ability to perform molecular dynamics simulations to model systems at finite temperatures using stochastic dynamics and mixed Monte Carlo algorithms. MacroModel supports Windows, Linux, Mac, SGI/ IRIX and IBM/ AIX.

Force field-based molecular modeling is routinely used to examine molecular conformations, molecular motion, and intermolecular interactions for a wide range of different materials including organic and inorganic molecules and oligomers, organometallic complexes as well as complex biological systems.

Features

  • Implicit solvation (continuum solvation) model
  • Generalized Born model augmented with the hydrophobic solvent accessible surface area (SA) term (GBSA) 

The Advantages of Force Field-based Molecular Modeling

The energy and properties of a chemical system depend on the exact three-dimensional molecular structure. Subtle variations in functional groups can result in dramatic differences in behavior. Force field methods that show the potential energy of a molecule as simple functions of distances and angles between atoms have proven to be an efficient and effective approach to obtaining accurate relative energies for chemical systems. The efficiency of force field-based calculations allows the exploration of large portions of the conformational space, revealing the detailed relationship between structure and energy.

MacroModel’s combination of high-quality force fields and GB/SA effective solvation model leads to reliably accurate estimations of energies.
MacroModel supports a wide range of conformational searching methods, capable of handling systems ranging from small molecules to entire proteins. Investigating conformational space is important for understanding structural-property dependence, and for constructing initial models for Molecular Dynamics simulations. MacroModel supports all leading force fields, including MM2, MM3, AMBER, AMBER94, MMFF, MMFFs, OPLS, OPLS_2005 and OPLS3, to support a wide range of research applications.

MacroModel is a general purpose, force-field-based molecular modeling program with applicability to a broad range of chemical systems. MacroModel provides multiple advanced methods to help in the understanding of chemical structure, energetics, and dynamics. A large selection of force fields is included, along with the latest technical advances introduced into the OPLS force fields. Certain minimization methods are available, enabling geometry optimizations for a broad selection of structural classes. A wide range of methods is available for conformational searching, which allows efficient sampling of the potential energy surface for low-energy structures, including entire proteins. Solvation effects can be accounted for using the efficient continuum solvation model in MacroModel. Additional advanced features include molecular dynamics simulations, free-energy perturbation simulations, and pure- and mixed ensemble sampling methods.

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