The Amber biomolecular simulation programs
David A. Case(Scripps Research Institute), Thomas E. Cheatham(University of Utah), Tom Darden(National Institutes of Health), Holger Gohlke(Goethe University Frankfurt), Ray Luo(University of California, Irvine), Kenneth M. Merz(Pennsylvania State University), Alexey V. Onufriev(Virgin Care), Carlos Simmerling(Stony Brook University), Bing Wang(Scripps Research Institute), Robert J. Woods(University of Georgia)
Cited by 9,564Open Access
Abstract
We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
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