Subject: TINKER 3.9 is Now Available

From: Jay Ponder <[email-masked]>
Date: Fri, 27 Jul 2001 16:40:50 -0500

Dear CCL,

A new release of the TINKER Molecular Modeling Package, version
3.9 dated June 2001, is available from the TINKER web site at
http://dasher.wustl.edu/tinker/ or via anonymous ftp download
> from dasher.wustl.edu in the /pub/tinker area.

TINKER is a modular, general package for molecular mechanics and
dynamics with some special facilities and parameter sets for
biopolymers. It supports several common force fields, including
AMBER, CHARMM, MM2, MM3, OPLS-AA, OPLS-UA, and our own TINKER
polarizable atomic multipole force field. The package contains
advanced algorithms for energy minimization, molecular dynamics,
distance geometry and global search including some methods that
are not readily available elsewhere.

TINKER version 3.9 contains the following new features and updates
> from version 3.8: (1) improved nucleic acid building from sequence
and automated conversion of nucleic acid PDB files to and from the
TINKER format, (2) a new rigid body dynamics facility, (3) ability
to handle infinite polymer lattices such as diamond and graphite,
(4) treatment of intramolecular polarization via the Thole method,
(5) a new utility program to compute molecular polarization, (6) an
improved RasMol-based viewer that accepts TINKER coordinate files,
allows atom selection, etc., (6) an optional Andersen stochastic
collision thermostat for MD, (7) where appropriate TINKER programs
such as ANALYZE, SUPERPOSE and SPACEFILL accept multiple coordinate
set "archive" files as input, (8) updated parameter sets for various
of the supported force fields.

TINKER is distributed with full source code, a User's Guide, and
several examples and test molecule files. Directions are supplied
for building the package on most commonly used CPU/OS combinations.
Prebuilt executables limited to a maximum of 10000 atoms are also
provided for Linux, Windows, and Macintosh (currently Mac OS 9,
OS X executables will be available shortly).

Please see the web site above for further information. Comments,
questions and suggestions for future improvements can be sent to
[email-masked].

                             Jay Ponder

-- 
Jay W. Ponder                          Phone:  (314) 362-4195
Biochemistry, Box 8231                 Fax:    (314) 362-7183
Washington University Medical School
660 South Euclid Avenue                Email:  [email-masked]
St. Louis, Missouri 63110  USA         WWW:    http://dasher.wustl.edu/