TINKER Molecular Modeling


TINKER - Software Tools for Molecular Design

Current Major Version: TINKER 6.3

Major Version Date: February 2014

Minor Revision: 6.3.3 on March 21, 2014


Introduction

    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, 2013) 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, free energy calculations via the Bennett Acceptance Ratio (BAR) method, normal mode vibrational 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....

Current Release

    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, 2009 and 2013 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.

    Starting with TINKER 6.3, Cartesian coordinate files optionally contain periodic system dimensions on a line immediately following the title line, in addition to their previous location in the system key file. This facilitates study of crystal structures and simplifies analysis of constant pressure molecular dynamics simulations.

Availability

    This distribution version of TINKER, with full source code, is made available free of charge to anyone who wants it. Download links are provided in the bottom section of this web page. 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.

Installation

    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, and can handle a maximum of 100,000 atoms (25000 on 32-bit systems). These 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. On Windows systems a dynamic library, libiomp5md.dll, is required by the pre-built executables. This DLL is provided with the Windows binaries and should be kept in the same directory as the binaries.

    Since a few portions of TINKER still make partial use of static memory allocation, some of the executables require a large available memory (i.e., total of actual RAM and swap space/virtual memory) to run. Some of the programs may require 8 GB of total memory or more in order to handle large molecular systems. There are instructions available on the internet for increasing the size of the swap space/virtual memory under various versions of Linux and Windows. If a program fails with the message "insufficient virtual memory", "resource temporarily unavailable" or a "segmentation fault", then you may need to add swap space. Mac OSX increases the size of the swap space automatically as needed, and such modifications are not needed to use TINKER on a Macintosh.

Future Development

    We have big plans for the TINKER package going forward. The next version of TINKER already in the early design stage, and will include new software programs for free energy calculations, major new sampling methods, 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.

Force Field Explorer and Visualization

    Force Field Explorer (FFE) is a Java-based GUI for the TINKER package. The original version was written by Michael Schnieders, now in Biomedical Engineering at the University of Iowa. FFE for Linux and Mac OS X can be downloaded from the lower section of this web page as "installation kits" containing the FFE GUI and an FFE-enabled version of TINKER. There is no version of FFE for Windows available at this time.

    There are two additional issues specific to use of FFE on Mac OS X. First, OS X 10.8 and later has a security feature called Gatekeeper that keeps applications not obtained from the App Store or Apple identified developers from being opened. Gatekeeper is enabled by default, and will result in the (incorrect!) error message: "Molecular Tools Installer.app" is damaged and can't be opened. To turn off Gatekeeper, go to the panel System Preferences > Security & Privacy > General, and set "Allow apps downloaded from:" to "Anywhere". This will require an Administrator account, and must be done before downloading the FFE installer kit. Once FFE is installed and has been launched for the first time, you can set the System Preference back to its prior value.

    One additional change is needed to use FFE on Mac OS X. FFE packages its own Java JRE and version of Java3D. The older Apple-supplied Java3D is not compatible with FFE. This causes FFE to hang immediately after display of the opening splash screen. To get FFE to work on Macs, you will need to disable the Apple Java3D version found in the directory /System/Library/Java/Extensions. In this directory, you must move, delete or rename the following files: j3daudio.jar, j3dcore.jar, j3dutils.jar, libJ3D.jnilib, libJ3DAudio.jnilib, libJ3DUtils.jnilib and vecmath.jar. Once these files are out of the way, FFE will use its packaged Java3D and should work correctly.

    We note that other visualization programs (such as VMD, MOLDEN, and some versions of PyMOL) can also read and display TINKER structure and MD trajcetory files. For serious work, we recommend using the latest "command line" version of TINKER for numerical calculations, and then using FFE or another visualization program to view the results.


TINKER Downloads

TINKER Summary Sheet

PDF

TINKER License Agreement

PDF

TINKER Wiki Site

WEB SITE

TINKER User's Guide

PDF

TINKER Logo Illustration

GIF

TINKER Distribution Directory

DIRECTORY

Force Field Parameter Sets

DIRECTORY

TINKER Source Code Directory

DIRECTORY

TINKER Complete Distribution (GNU gzip, 20.5 Mb)

DOWNLOAD

TINKER Complete Distribution (Windows zip, 22.8 Mb)

DOWNLOAD

Validation Suite for MMFF in TINKER (GNU gzip, 5.7 Mb)

DOWNLOAD

TINKER Executables for 64-bit Linux (GNU gzip, 102.2 Mb)

DOWNLOAD

TINKER Executables for 32-bit Linux (GNU gzip, 85.9 Mb)

DOWNLOAD

TINKER Executables for Mac OS X (GNU gzip, 100.4 Mb)

DOWNLOAD

TINKER Executables for 64-bit Windows (Windows zip, 100.9 Mb)

DOWNLOAD

TINKER Executables for 32-bit Windows (Windows zip, 63.8 Mb)

DOWNLOAD

Previous Release (TINKER 5.1.9, GNU gzip, 14.1 Mb)

DOWNLOAD

Previous Release (TINKER 4.3, GNU gzip, 7.5 Mb)

DOWNLOAD

Force Field Explorer for 64-bit Linux (GNU gzip, 292.5 Mb)

DOWNLOAD

Force Field Explorer for Mac OS X (DMG Image, 275.0 Mb)

DOWNLOAD




    TINKER's "Molecular Mechanics" Logo Illustration by Jay Nelson. Courtesy of Prof. Robert Paine, Chemistry Department, University of New Mexico.

    Prior development of TINKER was supported by Awards DBI 9808317, MCB 0344670 and CHE 0535675 from the National Science Foundation, and NIH R01 GM58712 from the United States National Institutes of Health. Continued development of the TINKER software and AMOEBA polarizable force field is funded by NSF Awards CHE 1152823 and CHE 1265731, and by NIH R01 GM106137.

    Any opinions, findings, and conclusions or recommendations expressed in the TINKER Molecular Modeling package are those of the authors and do not reflect the views of either the National Science Foundation or the National Institutes of Health.



Last Update: March 25, 2014
Maintainer: ponder@dasher.wustl.edu (sendmail)