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, ff99, ff99SB), CHARMM (19, 22, 22CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), 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 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 or improved spherical energy cutoff methods, particle mesh Ewald summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, a new distance geometry metrization method that has greater speed and better sampling than standard methods, Elber's reaction path methods, our potential smoothing and search (PSS) methods for global optimization, an efficient potential surface scanning procedure, and more....

TINKER 5 is a major new release of the Ponder Lab tool set for molecular mechanics and dynamics calculations. Changes from the previous TINKER version include many new and updated force field parameter sets, 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 is neither backward nor forward compatible with earlier versions of TINKER. In particular, earlier versions of parameter files should not be used with TINKER 5 executables and vice versa.

The current release contains an implementation of the Merck Molecular Force Field, MMFF. Since this model requires fairly extensive changes to our standard force field setup procedures, it is being distributed as an add-on feature for TINKER 5. Directions for building MMFF capable executables are provided in the /MMFF area of the source distribution. A separate MMFF package, containing an extensive validation suite is available as a separate download.

At present we are not distributing the Force Field Explorer (FFE) graphical interface to TINKER. We are looking into providing a module for existing visualization package(s) to replace the functionality of FFE. In the meantime, please use the "command line" versions of TINKER for calculations. Some current graphical modeling packages, including VMD and PyMol, are able to directly read and display TINKER coordinate files. And TINKER files can be converted to PDB format for visualization in a wide variety of programs.

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 is 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.

TINKER is provided as a full source distribution via the links below. After unpacking the distribution, you can build a set of TINKER executables on almost any machine with a Fortran compiler. Scripts to compile, build object libraries, and link executables on a wide variety of machine/CPU/OS combinations provided with the distribution. A standard Makefile is also provided.

Pre-built TINKER executables for Linux, Mac OS X, and Windows are also available for download below. These executables should run on most recent vintage machines using these operating systems. You will still need to have a copy of the full TINKER distribution as it contains the parameter sets, examples, benchmarks, test files and documentation needed to use the package.

We have completed much work on the AMOEBA polarizable multipole force field. The AMOEBA parameters for water, small organic, protein and nucleic acids are part of the present distribution. We are providing the original AMOEBA models circa 2004, as well as more recent 2009 sets. Additional ion and small molecule parameters will be made available in due course. We are already planning for improvements and new features in the next release of TINKER. Suggestions and comments regarding other possible additions are always welcome. Of course, offers to provide or help write code are even better....

Starting with the release of TINKER 6, we will switch to a more modern version of Fortran including dynamic memory allocation and parallelization under the OpenMP model. We plan to maintain and update TINKER 5 for some time into the future as the last release of "TINKER Classic" in its current form based on serial, extended Fortran 77.