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The Amber biomolecular simulation programs
TLDR
The development, current features, and some directions for future development of the Amber package of computer programs, which 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. Expand
Development and testing of a general amber force field
TLDR
A general Amber force field for organic molecules is described, designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. Expand
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvationExpand
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of
TLDR
The development, current features, and some directions for future development of the AMBER package of computer programs are described, embodying a number of the powerful tools of modern computational chemistry-molecular dynamics and free energy calculations. Expand
A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS
We present the development of a force field for simulation of nucleic acids and proteins. Our approach began by obtaining equilibrium bond lengths and angles from microwave, neutron diffraction, andExpand
Automatic atom type and bond type perception in molecular mechanical calculations.
TLDR
Anautomatic algorithm of perceiving atom types that are defined in a description table, and an automatic algorithm of assigning bond types just based on atomic connectivity are presented. Expand
An all atom force field for simulations of proteins and nucleic acids
TLDR
An all atom potential energy function for the simulation of proteins and nucleic acids and the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach is presented. Expand
RNAMotif, an RNA secondary structure definition and search algorithm.
TLDR
A new computational motif search algorithm that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements is described and its utility is demonstrated. Expand
Force fields for protein simulations.
TLDR
The chapter focuses on a general description of the force fields that are most commonly used at present and gives an indication of the directions of current research that may yield better functions in the near future. Expand
Exploring protein native states and large‐scale conformational changes with a modified generalized born model
TLDR
A popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large‐scale conformational transitions, such as protein folding. Expand
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