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   introduction

Tinker


1. Introduction to the TINKER Package

Welcome to the TINKER molecular modeling package! TINKER is designed to be an easily used and flexible system of programs and routines for molecular mechanics and dynamics as well as other energy-based and structural manipulation calculations. It is intended to be modular enough to enable development of new computational methods and efficient enough to meet most production calculation needs. Rather than incorporating all the functionality in one monolithic program, TINKER provides a set of relatively small programs that interoperate to perform complex computations. New programs can be easily added by modelers with only limited programming experience. The series of major programs included in the distribution system perform the following core tasks:
  1. build protein and nucleic acid models from sequence
  2. energy minimization and structural optimization
  3. analysis of energy distribution within a structure
  4. molecular dynamics and stochastic dynamics
  5. simulated annealing with a choice of cooling schedules
  6. normal modes and vibrational frequencies
  7. conformational search and global optimization
  8. transition state location and conformational pathways
  9. fitting of energy parameters to crystal data
  10. distance geometry with pairwise metrization
  11. molecular volumes and surface areas
  12. free energy changes for structural mutations
  13. advanced algorithms based on potential smoothing

Many of the various energy minimization and molecular dynamics computations can be performed on full or partial structures, over Cartesian, internal or rigid body coordinates, and including a variety of boundary conditions and crystal cell types. Other programs are available to generate timing data and allow checking of potential function derivatives for coding errors. Special features are available to facilitate input and output of protein and nucleic acid structures, the basic core routines have no knowledge of biopolymer structure and can be used for general molecular systems.

Due to its emphasis on ease of modification, TINKER differs from many other currently available molecular modeling packages in that the user is expected to be willing to write simple ‘‘front-end'' programs and make some alterations at the source code level. The main programs provided should be considered as templates for the users to change according to their wishes. All subroutines are internally documented and structured programming practices are adhered to throughout. The result, it is hoped, will be a calculational system which can be tailored to local needs and desires.

The core TINKER system consists of about 110,000 lines of source written entirely in a portable Fortran77 superset. Use is made of only some very common extensions that aid in writing highly structured code. The current version of the package has been ported to a wide range of computers with no or extremely minimal changes. Tested machines include: Compaq Alphas under Tru64 Unix or OpenVMS; Hewlett- Packard, IBM RS/6000, Silicon Graphics and Sun workstations under the vendor's Unix; Apple Macintosh; and Intel PCs under Windows9X/NT/2000 and Linux. At present, our new code is written on Compaq Alpha platforms, and occasionally tested for compatibility on various of the machine and OS combinations listed above. At present, we are in the process of converting our primary development efforts from Fortran77 to a more modern Fortran dialect. A machine-translated C version of TINKER is currently available, and a hand-translated optimized C version of a previous TINKER version is available for inspection. Conversion to C or C++ is under consideration, but not being actively pursued at this time.

The basic design of the energy function engine used by the TINKER system allows usage of several different parameter sets. At present we are distributing parameters that implement AMBER-95, CHARMM22, MM2, MM3, OPLS-AA, OPLS-UA and our own TINKER parameters. In most cases, the source code separates the geometric manipulations needed for energy derivatives from the actual form of the energy function itself. Several other literature parameter sets are being considered for future development (ENCAD, MMFF-94, UFF, etc.), and many of the alternative potential function forms reported in the literature can be implemented directly or after minor code changes.

Much of the software in the TINKER package has been heavily used and well tested, but some modules are still in a fairly early stage of development. Further work on the TINKER system is planned in three main areas: (1) extension and improvement of the potential energy parameters including further development of our polarizable multipole TINKER force field, (2) coding of new computational algorithms including additional methods for free energy determination, torsional Monte Carlo and molecular dynamics sampling, advanced methods for long range interactions, better transition state location, and further application of the potential smoothing paradigm, (3) a friendlier user interface for protein/nucleic acid/polysaccharide computations including direct input/output of Protein Data Bank files, and (4) a simple GUI front-end to tie together the TINKER programs using RasMol as a molecule viewer.

Questions and comments regarding the TINKER package, including suggestions for improvements and changes should be made to the author:

Professor Jay William Ponder
Biochemistry & Molecular Biophysics
North Building, Room 2811, Box 8231
Washington University School of Medicine
660 South Euclid Avenue
Saint Louis, MO 63110 U.S.A.
phone: (314) 362-4195
fax: (314) 362-7183
email: ponder@dasher.wustl.edu

In addition, an Internet web site containing an online version of this User's Guide, the most recent distribution version of the full TINKER package and other useful information can be found at http://dasher.wustl.edu/tinker, the Home Page for the TINKER Molecular Modeling Package.




© Goodman Group, 2005-2017; privacy; last updated November 16, 2017

department of chemistry University of Cambridge