TINKER

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This article is about a molecular dynamics application and force field. For more meanings of the word Tinker, see Tinker (disambiguation).

TINKER is a molecular modeling program with a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. The heart of the TINKER package is a modular set of callable routines which allow the manipulation of coordinates and evaluation of potential energy and derivatives in a straightforward fashion.

TINKER works on Windows, Mac, and Unix/Linux and is source code is available free of charge to anyone who wants it (see: External links). The code was written in Fortran77 with common extensions and some C. The code is maintained by Jay Ponder at the Washington University School of Medicine.

Contents 1 Features 2 See also 3 References 4 External links

[edit] Features

Programs are provided to perform many functions including:

1. energy minimization over Cartesian coordinates, torsional angles or rigid bodies via conjugate gradient, variable metric or a truncated Newton method;
2. molecular, stochastic, and rigid body dynamics with periodic boundaries and control of temperature and pressure;
3. normal mode vibrational analysis;
4. distance geometry including an efficient random pairwise metrization;
5. building protein and nucleic acid structures from sequence;
6. simulated annealing with various cooling protocols;
7. analysis and breakdown of single point potential energies;
8. verification of analytical derivatives of standard and user defined potentials;
9. location of a transition state between two minima;
10. full energy surface search via a "Conformation Scanning" method;
11. free energy calculations via free energy perturbation or weighted histogram analysis;
12. fitting of intermolecular potential parameters to structural and thermodynamic data; and
13. global optimization via energy surface smoothing including a own "Potential Smoothing and Search" (PSS) method.

[edit] See also

• Molecular dynamics
• Molecular geometry

[edit] References

• P. Ren and J. W. Ponder, Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation, J. Phys. Chem. B, 107, 5933-5947 (2003).
• R. V. Pappu, R. K. Hart and J. W. Ponder, Analysis and Application of Potential Energy Smoothing for Global Optimization, J. Phys. Chem. B, 102, 9725-9742 (1998).
• Y. Kong and J. W. Ponder, Reaction Field Methods for Off-Center Multipoles, J. Chem. Phys., 107, 481-492 (1997).
• M. J. Dudek and J. W. Ponder, Accurate Modeling of the Intramolecular Electrostatic Energy of Proteins, J. Comput. Chem., 16, 791-816 (1995).
• C. E. Kundrot, J. W. Ponder and F. M. Richards, Algorithms for Calculating Excluded Volume and Its Derivatives as a Function of Molecular Conformation and Their Use in Energy Minimization, J. Comput. Chem., 12, 402-409 (1991).
• J. W. Ponder and F. M. Richards, An Efficient Newton-like Method for Molecular Mechanics Energy Minimization of Large Molecules, J. Comput. Chem., 8, 1016-1024 (1987).

[edit] External links

• TINKER website