Abalone (molecular mechanics)

This article is about a computer program for molecular dynamics. For other uses, see Abalone (disambiguation).

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 release	2006; 19 years ago (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.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

• Comparison of software for molecular mechanics modeling
• Molecular design software
• Ascalaph Designer
• MDynaMix
• Tinker (software)
• NAMD
• GROMACS
• SAMSON