TINKER

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 molecular 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.

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TINKER works on Windows, Mac, and Unix/Linux and its 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.

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 an own "Potential Smoothing and Search" (PSS) method.

See also

• Molecular dynamics
• Molecular geometry

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).