Subject: TINKER 3.7 is now available

From: Jay Ponder <[email-masked]>
Date: Wed, 16 Jun 1999 12:22:12 -0500

Dear CCL Subscribers,

      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:  [email-masked]
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 [email-masked]. We try to respond to all email as time allows.

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