An all atom force field for simulations of proteins and nucleic acids

@article{Weiner1986AnAA,
  title={An all atom force field for simulations of proteins and nucleic acids},
  author={Scott J. Weiner and Peter A. Kollman and Dzung T. Nguyen and David A. Case},
  journal={Journal of Computational Chemistry},
  year={1986},
  volume={7}
}
We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n−butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin… 
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References

SHOWING 1-10 OF 59 REFERENCES
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, and…
An approach to computing electrostatic charges for molecules
We present an approach for deriving net atomic charges from ab initio quantum mechanical calculations using a least squares fit of the quantum mechanically calculated electrostatic potential to that…
Molecular dynamics of native protein. I. Computer simulation of trajectories.
  • M. Levitt
  • Physics
    Journal of molecular biology
  • 1983
Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms
An improved force field for molecular mechanics calculations of the structures and energies of hydrocarbons is presented. The problem of simultaneously obtaining a sufficiently large gauche butane…
Experimental studies of molecular interactions between nitrogen bases of nucleic acids
TLDR
New experimental results concerning molecular interactions between the nitrogen bases of nucleic acids in the crystalline phase and in vacuo are reported and the energy gain in the formation of trimers of identical molecules was shown to be larger than that for dimers.
Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water
Transferable intermolecular potential functions (TIPS) suitable for use in liquid simulation are reported for water, alcohols, and ethers. Interaction sites are located on oxygens, hydroxyl…
A molecular dynamics simulation of double-helical B-DNA including counterions and water.
TLDR
An atomic level molecular dynamical simulation of a 5-base-pair fragment of double-helical DNA with inclusion of water and sodium counterions and a complete description of their electrostatic interactions finds the most flexible conformational angles in the structure are the glycosidic angle and the sugar pucker.
Planar and nonplanar vibrations of cytosine
The formalism developed in the preceding article is used in a normal coordinate analysis of the pyrimidine base cytosine. The results of both planar and nonplanar vibrations are reported. The model…
Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.
  • B. Brooks, M. Karplus
  • Physics, Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 1983
TLDR
The analysis demonstrates that, in spite of the anharmonic contributions to the potential, a normal mode description can provide useful results concerning the internal motions of proteins.
Calculation of the crystal structures of hydrocarbons by molecular packing analysis
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