Abalone (molecular mechanics)

Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model[1]) or in implicit water models.[2] Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field.

Abalone
Developer(s)Agile Molecule
Initial release2006 (2006)
Stable release
2.1.4.2
Operating systemWindows XP/7/8/10
Platformx86, Nvidia GPU CUDA
Available inEnglish
TypeMolecular dynamics, molecular graphics
LicenseProprietary
Websitewww.biomolecular-modeling.com/Abalone
Protein model on Abalone
DNA model on Abalone

Key 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) 94, 96, 99SB, 03; Optimized Potentials for Liquid Simulations (OPLS)
  • Geometry optimizing
  • Molecular dynamics with multiple time step integrator
  • Hybrid Monte Carlo
  • Replica exchange[3]
  • Interface with quantum chemistry - ORCA, NWChem, Firefly (PC GAMESS), CP2K
  • GPU accelerated molecular modeling

See also

References
  1. Toukan K & Rahman A (1985). "Molecular-dynamics study of atomic motions in water". Physical Review B. 31 (5): 2643–2648. Bibcode:1985PhRvB..31.2643T. doi:10.1103/PhysRevB.31.2643.
  2. Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990). "Semianalytical treatment of solvation for molecular mechanics and dynamics". J Am Chem Soc. 112 (16): 6127–6129. doi:10.1021/ja00172a038.
  3. Y. Sugita & Y. Okamoto (1999). "Replica-exchange molecular dynamics method for protein folding". Chemical Physics Letters. 314: 141–151. Bibcode:1999CPL...314..141S. doi:10.1016/S0009-2614(99)01123-9.
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