We are pleased to announce TINKER 3.7, a new version of our
molecular modeling package which is now available from the TINKER
Home Page web site at http://dasher.wustl.edu/tinker/. Many new
features, general improvements and bug fixes are incorporated in
the new version. We suggest that all current users of the package
update. Below is some general information about the capabilities
of TINKER as taken from the web site.
Jay Ponder
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Jay W. Ponder Phone: (314) 362-4195
Biochemistry, Box 8231 Fax: (314) 362-7183
Washington University Medical School
660 South Euclid Avenue Email: ponder at dasher.wustl.edu
St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/
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TINKER -- Software Tools for Molecular Design
Version 3.7 June 1999
Introduction
The TINKER molecular modeling software is a complete and general
package for molecular mechanics and dynamics, with some special
features for polypeptides. TINKER has the ability to use any of
several common parameter sets, such as AMBER-95, CHARMM22, MM2(91),
MM3(99), OPLS-AA and OPLS-UA. Parameter sets for other standard
force fields such as ENCAD, MMFF and UFF are in progress, as are
our own TINKER polarizable multipole parameters. 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 Cartesian polytensor atomic multipole expansion
treatment of electrostatics with explicit polarizability, Eisenberg-
McLachlan ASP and MacroModel GB/SA solvation, our own 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, an improved spherical
energy cutoff method, Particle Mesh Ewald summation for partial
charges under periodic boundary conditions, a novel reaction field
treatment of long range electrostatics, and much more....
Current Release
The most recent release, version 3.7, contains the following new
features and updates from version 3.6: (1) further improvements to
our Potential Smoothing and Search global optimization algorithms,
(2) updated parameter sets for the CHARMM, AMBER, OPLS and MM3 force
fields, further validation of each of these parameters sets against
their actual programs has resulted in some fairly major revisions
for CHARMM22 and minor changes to the others, (3) a conformational
scanning method, SCAN, for use on smoothed potential surfaces which
efficiently explores the full potential surface, (4) a new velocity
Verlet stochastic dynamics capability added the TINKER MD program,
DYNAMIC, (5) Particle Mesh Ewald summation for partial charge
electrostatics with periodic boundary conditions, (6) prebuilt
executables for systems with up to 10000 atoms provided for Intel
Win9X/NT, Intel Linux and Macintosh, and (7) numerous small changes,
additions and fixes, many of them suggested by users of the package.
Please note that as with prior new releases, version 3.7 is neither
backward nor forward compatible with earlier versions of TINKER.
For example, version 3.6 parameter files should not be used with
version 3.7 executables and vice versa.
Availability
This distribution version of TINKER, with full source code, is made
available free of charge to anyone who wants it. New major releases
of the package with additional features are generally placed on this
site each 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 return the enclosed
license form. Comments and questions are always welcome and should
be sent to ponder at dasher.wustl.edu. We try to respond to all email
as time allows.
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