Bioinformatics Molecular Dynamics

Abalone

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Abalone is a general purpose molecular dynamics and molecular graphics program that is used for simulations of biomolecules such as Proteins in explicit or implicit water models. It has been mainly designed to simulate the proteins folding and DNA-ligand complexes in the presence of AMBER force field.

Features

  • 3D molecular graphics
  • Automatic Force Field generator for bioelements: H, C, N, O
  • Building and editing chemical structures
  • Library of building blocks
  • Force fields: Assisted Model Building with Energy Refinement (AMBER)
  • Optimized Potentials for Liquid Simulations (OPLS)
  • Geometry optimization
  • Molecular dynamics with multiple time step integrator
  • Hybrid Monte Carlo
  • Replica exchange
  • Interface with quantum chemistry ORCA, NWChem, Firefly (PC GAMESS), CP2K
  • GPU accelerated molecular modeling

Package of molecular Abalone are;

  • Molecular model building
    • Chain builder
    • Free mouse drawing
    • Geometry editor
    • Bonds detection by distance
    • Overlay
    • Eliminating clashes
  • Force Fields
    • AMBER family
    • AMBER-ii
    • OPLS
    • DREIDING like FF for an arbitrary molecule
    • Semi-automated parameterization
    • Implicit and explicit water models
  • Geometry optimization
    • Conjugate gradients
    • Steepest descent
  • Molecular dynamics
    • Verlet
    • rRESPA
    • OPVL and OVVL fourth-order integrators
    • Replica exchange
  • Hybrid Monte Carlo
    • classical HMC
    • xHMC
    • Adaptive Temperature HMC
  • GPU acceleration
    • MD
    • HMC
  • Interface with quantum chemical programs
    • ORCA
    • NWChem
  • Scripting

Abalone shows molecular models in its separate windows. Each window has two cameras, which allow the model to be simultaneously visualized from two sides and in different graphic modes. The sub-window can be opened by dragging the splitter in the right corner of each graphical window.

Clicking on an atom or bond with the left mouse button slightly changes their color and a brief info about the picked object appears in the status bar. Clicking with the right mouse button selects the object. Double-clicking with the right button inverts the selection. Abalone supports several graphic styles. CPK is the basic style. It gives the most realistic picture of the molecule in space. The Wire frame style is convenient for large molecules, particularly, for proteins. Drawing is very fast for this style. The Stick style is largely for presentations.

The Ball and Stick style is convenient for molecule construction and editing, since atoms and bonds are clearly visible. In addition, the bond color reflects their order. Finally, the CPK Wire frame combines the properties of several above styles.

Chain builder is the main tool to generate molecular models. It allows chain molecules to be constructed from predefined residues. Clearly, this construction mode is not universal. A required residue can be missing in the database or the constructed molecule can be not polymeric. Nevertheless, we believe that it is the principal construction mode due to two reasons. First, it corresponds to the requirements of scientists studying biological molecules. Proteins and nucleic acids are large chain structures. Due to their size, regular structure, and scientific importance, they require special construction tools.

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