Abalone (molecular mechanics)
Developer(s) | Agile Molecule |
---|---|
Initial release | 2006 |
Stable release | 2.1.4.2
|
Operating system | Windows XP/7/8/10 |
Platform | x86, Nvidia GPU CUDA |
Available in | English |
Type | Molecular dynamics, molecular graphics |
License | Proprietary |
Website | www |
![](http://upload.wikimedia.org/wikipedia/commons/thumb/6/61/Chaperonin-1AON.png/220px-Chaperonin-1AON.png)
Protein model on Abalone
![](http://upload.wikimedia.org/wikipedia/commons/thumb/8/8b/DNA-ligand-by-Abalone.png/220px-DNA-ligand-by-Abalone.png)
DNA model on Abalone
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.
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[]
- ^ 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.
- ^ 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.
- ^ 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.
External links[]
Categories:
- Monte Carlo software
- Computational chemistry software
- Molecular dynamics software
- Molecular modelling software
- Science software