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Amber 2016 Reference Manual (Covers Amber16 and AmberTools16) · Contents. Contents 5. I. Introduction and Installation 13. 1. Introduction 15 1.1. Information Assisted Model Building with Energy Refinement (AMBER) is a family of force fields for Amber 2020 Reference Manual; ^ Cornell WD, Cieplak P, Bayly CI, Gould IR, AMBER 16 Reference Manual. San Francisco: Universidad de California. [18] Wendy, D., and Cornell, P. C. (1995). A second generation force field for theSoftware – Amber16/18, AmberTools 16/18, UCSF Chimera 1.11 or 1.13 (additionally ChimeraX optional), CUDA 8.0/9.0, CUDA toolkit, perl-tk, python-tk, (AMBER 2018 Reference Manual.) (TI) and Free Energy Perturbation (FEP) methods, as well as a 15 to 20% performance boost over AMBER 16 on existing GPUs. processAmberForceField.py amber16/dat/leap/lib/all_amino03.lib amber16/dat/leap/lib/all_aminoct03.lib amber16/dat/leap/lib/all_aminont03.lib The syntax presented in this manual uses the following conventions: Actions, Analyses, and Trajectory commands (except reference) are queued commands; Reference Manual. (Covers Amber16 and AmberTools16). Principal contributors to the current codes: David A. Case (Rutgers). Ross C. Walker (SDSC, UCSD).