TINKER

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The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as the AMBER forcefield ( ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases.

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References[edit]

  1. J. W. Ponder and F. M. Richards "", Journal of Computational Chemistry 8 pp. 1016-1024 (1987)
  2. C. E. Kundrot, J. W. Ponder and F. M. Richards "", Journal of Computational Chemistry 12 pp. 402-409 (1991)
  3. Michael E. Hodsdon, Jay W. Ponder and David P. Cistola "The NMR Solution Structure of Intestinal Fatty Acid-binding Protein Complexed with Palmitate: Application of a Novel Distance Geometry Algorithm", Journal of Molecular Biology 264 pp. 585-602 (1996)
  4. Rohit V. Pappu, Reece K. Hart, and Jay W. Ponder "Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization", Journal of Physical Chemistry B 102 pp. 9725-9742 (1998)
  5. Pengyu Ren and Jay W. Ponder "Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations", Journal of Computational Chemistry 23 pp. 1497-1506 (2002)
  6. Pengyu Ren and Jay W. Ponder "Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation", Journal of Physical Chemistry B 107 pp. 5933-5947 (2003)