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, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA (2004, 2009) polarizable atomic multipole force field. Parameter sets for other widely-used force fields are under consideration for future releases.

The TINKER package contains a variety of interesting algorithms such as: flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments including several generalized Born (GB/SA) models, generalized Kirkwood implicit solvation for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, efficient truncated Newton (TNCG) local optimization, surface areas and volumes with derivatives, simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better sampling than standard methods, Elber's reaction path algorithm, our potential smoothing and search (PSS) methods for global optimization, Monte Carlo Minimization (MCM) for efficient potential surface scanning, and more....

TINKER 6 is a major new release of the Ponder Lab tool set for molecular mechanics and dynamics calculations. An important difference is a move toward the Fortran 95 standard and dynamic memory allocation. TINKER 6 also supports OpenMP parallelization for particle mesh Ewald (PME) calculations using neighbor lists, such as molecular dynamics, minimization and conformational sampling. This provides enhanced performance on shared memory, multi-core machines. Other 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 6 is neither backward nor forward compatible with earlier versions of TINKER. In particular, earlier versions of parameter files should not be used with TINKER 6 executables and vice versa.

New features for TINKER 6 include expanded parameter files for the 2004 and 2009 releases of the AMOEBA force field. A new RESPA integrator for molecular dynamics allows use of 2 femtosecond time steps for fully flexible force fields with excellent energy conservation. RESPA MD steps at 3 fs are suitable for thermostated MD used in sampling. A variety of additional MD integrators, thermostats and barostats are also included. Enhanced programs for force field parameterization (VALENCE, POTENTIAL and POLEDIT) are available in TINKER 6, as well as a new torsional parameter fitting program (TORSFIT). As of TINKER 6.0.05, the MMFF force field is available in the main distribution. The MMFF validation suite for TINKER is provided as a separate download.

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 6 is provided as a complete 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-operating system combinations are included with the distribution. A standard Makefile is also provided, as well as configure scripts for use with GNU autoconf.

If you wish to build the OpenMP-capable parallel version of TINKER, object libraries from the FFTW 3.3 Fourier transform package are required. Support for APBS Poisson-Boltzmann calculations within TINKER requires object libraries from the APBS 1.3 software package.

Pre-built TINKER executables for Linux, Mac OS X, and Windows are also available for download below. They should run on most recent vintage machines using the above operating systems. The executables are OpenMP capable, but do not support APBS or the TINKER FFE interface. You will still need to have a copy of the complete TINKER distribution as it contains the parameter sets, examples, benchmarks, test files and documentation needed to use the package.

We have big plans for the TINKER package going forward. TINKER 7 is already in the early design stage, and will include new software programs for free energy calculations, enhanced crystal modeling capability, more and better tools for force field parameterization, and some anticipated new energy components to enhance the accuracy and generality of AMOEBA. Suggestions and comments regarding other possible additions to TINKER are always welcome. Of course, offers to provide or help write code are even better....

While we strongly suggest users switch to TINKER 6 with its many important new features and bug fixes, we provide download links below for two stable prior versions, TINKER 5.1.09 and TINKER 4.3. Both these earlier releases are written in serial, extended Fortran 77.