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 Amber (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), Merck Molecular Force Field (MMFF), 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.

The TINKER package includes a variety of novel algorithms such as a new distance geometry metrization method that has greater speed and better sampling than standard methods, Elber's reaction path methods, several of our Potential Smoothing and Search (PSS) methods for global optimization, an efficient potential surface scanning procedure, a flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, a selection of continuum solvation treatments including several variants of the generalized Born (GB/SA) model, the generalized Kirkwood implicit solvation model for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, an efficient truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, velocity Verlet stochastic dynamics, use of pairwise neighbor lists of an improved spherical energy cutoff method, Particle Mesh Ewald summation for partial charges and regular Ewald for polarizable multipoles, a novel reaction field treatment of long range electrostatics, and more....

The release of TINKER version 5.0 coincides with a greatly improved version of the Force Field Explorer (FFE) visualization program and GUI. This major new release of FFE contains significant improvements in many areas such as stability, feature set and integration with TINKER. The installation kits available for download below contain an integrated version of TINKER with FFE. Further information is available from the FFE web site.

Other changes from the last TINKER version include the initial public release of a complete AMOEBA protein force field parameter set, and numerous minor additions and bug fixes, many of them suggested by users of the package. Please note that as with prior new releases, version 5.0 is neither backward nor forward compatible with earlier versions of TINKER. For example, earlier versions of parameter files should not be used with version 5.0 executables and vice versa.

We have essentially completed work much of the AMOEBA polarizable multipole force field. The AMOEBA water model and protein force field are part of the present distribution. Additional ion and small molecule parameters will be made available on this site in due course. Preliminary work has begun on development of compatible nucleic acid parameters. We are already planning for improvements and new features in the next releases of TINKER and Force Field Explorer. Suggestions and comments regarding other possible additions are always welcome. Of course, offers to provide or help write code are even better....

This distribution version of TINKER, with full source code, is made available free of charge to anyone who wants it. Major new releases of the package with additional features are generally placed on this site during February, June and October. Minor changes and bug fixes are added to the distribution version as we finish testing them. The basic package has been used by the Ponder lab and others at Washington University for several years and should be fairly robust. All we ask is that you notify us of any bugs, features you would like to see implemented, or major code extensions that you add yourself. If you make significant use of the package, please complete and return by regular post the license form available with the full distribution and via a link below. These forms are used to aid in convincing colleagues that TINKER and FFE are used outside of Washington University. They help us justify further development of the programs. We try to respond to email as time allows. Comments and questions are always welcome and should be directed to Jay Ponder at ponder@dasher.wustl.edu.

The easiest way to install TINKER and Force Field Explorer on your computer is to download the self-extracting installation kit for your machine type. Kits for Linux, Windows and Mac OS X are available from the links provided below on this web page. These installation packages are quite large, so make sure you have a stable and fast connection before attempting to download. Note that the Mac OS X kit requires a 10.4 (Tiger) or 10.5 (Leopard) system, and Mac users may need to obtain from Apple and install the Java3D package prior to running TINKER with FFE.

The TINKER executables supplied with the installation kits are intended for use via the Force Field Explorer GUI. These executables have been linked against Java libraries needed for communication between TINKER and FFE. It is possible to run the kit executables stand-alone from the command line, but various Java related environment variables that are normally setup automatically by FFE must be provided manually. For those who do not wish to use the GUI and need only the standard options, we provide sets of prebuilt command line executables for Linux, Windows and Macintosh. See the README files in the command line executable directories.

If you choose not to use the installation kits, you will still need to have a copy of the full distribution containing parameter sets, examples, benchmarks, test files, documentation, source code and instructions for building the package on a variety of machine types. The full distribution is available for download via the links below in two different compressed formats (GNU gzip and Windows ZIP). Please see the README files in the individual directories.