Software for molecular mechanics modeling
From DrugPedia: A Wikipedia for Drug discovery
(Difference between revisions)
Revision as of 20:11, 11 August 2008
Short list of molecular mechanics programs
Min - Optimization,
MD - Molecular Dynamics,
MC - Monte Carlo,
QM - Quantum mechanics.
HA - Hardware accelerated.
Y - Yes.
I - Has interface.
| View
3D | Model
Builder | Min | MD | MC | QM | HA | Comments | License | |
|---|---|---|---|---|---|---|---|---|---|
| AGM Build | Y | Y | Model building with charges and MM atom types | Free (GPL) | |||||
| AMBER | Y | Y | Y | ||||||
| Ascalaph | Y | Y | Y | I | Y | Molecular building (DNA, proteins, hydrocarbons, nanotubes). Molecular dynamics. GPU acceleration. | |||
| BOSS | Y | Y | Y | OPLS | |||||
| CHARMM | Y | Y | Y | Y | I | ||||
| ChemSketch | Y | Y | Y | Fast 2-D graphical molecule builder and 3-D viewer. Contains simplified CHARMM for fast stable inaccurate optimization of single molecules up to 1000 atoms | |||||
| GROMACS | Y | ? | High performance MD | ||||||
| GROMOS | Y | Y | Geared towards biomolecules | ||||||
| LAMMPS | Y | Has potentials for soft and solid-state materials and coarse-grain systems | |||||||
| MCCCS Towhee | Y | Originally designed for the prediction of fluid phase equilibria | |||||||
| MDynaMix | Y | Parallel MD | |||||||
| MOE | Y | Y | Y | Y | I | Molecular Operating Environment | |||
| MOIL | Y | Y | Y | Y | Also includes action-based algorithms (Stochastic Difference Equation in Time and Stochastic Difference Equation in Length) and locally enhanced sampling. | ||||
| MOLDY | Y | Parallel, only pair-potentials, Cell lists, modified Beeman's algorithm | |||||||
| NAB | Y | Generation of Models for "Unusual" DNA and RNA | |||||||
| Packmol | Y | Builds complex initial configurations for Molecular Dynamics | |||||||
| Protein Local Optimization Program | Y | Y | Y | Y | Helix, loop, and side chain optimization. Fast energy minimization. | ||||
| QMOL | Y | Protein viewer | |||||||
| RasMol | Y | Fast viewer | |||||||
| Raster3D | Y | High quality raster images | |||||||
| STR3DI32 | Y | Y | Y | Y | Software for molecular design, bio-molecular simulations, docking of ligands, studying host-guest complexes | ||||
| TINKER | I | Y | Y | Y | Y | I | Software Tools for Molecular Design | ||
| UCSF_Chimera | Y | Visually appealing viewer | |||||||
| VMD + NAMD | Y | Y | Y | Y | ? | Fast, parallel MD | |||
| WHAT IF | Y | Y | I | I | I | Visualizer for MD. Interface to GROMACS. | |||
| xeo | Y | Y | open project management for nanostructures | ||||||
| YASARA | Y | Y | Y | Y | Molecular-graphics, -modeling and -simulation program | ||||
| Zodiac | Y | Y | Y | Drug design suite |
