AMBER is a suite of programs and a force field for molecular mechanics-based simulation. It is designed primarily for proteins and nucleic acids, and is being extended for small molecules. It includes: energy minimization, dynamics, NMR restrained dynamics, and free energy and normal mode calculations, as well as a graphical model builder X-windows program called Leap. It is developed and maintained by the Kollman group with collaborators at other sites and distributed worldwide by Oxford Molecular. The Research Resource for Biomolecular Graphics helps support the AMBER development effort by providing access to high performance workstations (Digital Equipment and Silicon Graphics) to run verification suites to ensure correct compilation. We use the Purify program (Centerline Software), which our group purchased jointly with the Computer Graphics Lab, to do basic debugging of the Leap system. We also depend on the Resource for stable email service, and system management and programming/algorithmic advice related to graphics and 3D modeling.
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