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 and add workarounds for SGI compiler bugs. 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 coordinate with our AMBER collborators and users using Internet access available through the Resource.
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