1To: chemistry@ccl.net
2Subject: CCL:TINKER 3.7 is now available
3From: Jay Ponder <ponder@dasher.wustl.edu>
4Date: Wed, 16 Jun 1999 12:22:12 -0500
5cc: ponder@dasher.wustl.edu
6Sender: "Computational Chemistry List" <chemistry-request@ccl.net>
7
8Dear CCL Subscribers,
9
10     We are pleased to announce TINKER 3.7, a new version of our molecular
11modeling package which is now available from the TINKER Home Page web site
12at http://dasher.wustl.edu/tinker/. Many new features, general improvements
13and bug fixes are incorporated in the new version. We suggest that all
14current users of the package update. Below is some general information
15about the capabilities of TINKER as taken from the web site.
16
17                                 Jay Ponder
18
19--------
20Jay W. Ponder                          Phone:  (314) 362-4195
21Biochemistry, Box 8231                 Fax:    (314) 362-7183
22Washington University Medical School
23660 South Euclid Avenue                Email:  ponder@dasher.wustl.edu
24St. Louis, Missouri 63110  USA         WWW:    http://dasher.wustl.edu/
25--------
26
27              TINKER -- Software Tools for Molecular Design
28
29                        Version 3.7    June 1999
30
31                               Introduction
32
33The TINKER molecular modeling software is a complete and general package
34for molecular mechanics and dynamics, with some special features for
35polypeptides. TINKER has the ability to use any of several common parameter
36sets, such as AMBER-95, CHARMM22, MM2(91), MM3(99), OPLS-AA and OPLS-UA.
37Parameter sets for other standard force fields such as ENCAD, MMFF and UFF
38are in progress, as are our own TINKER polarizable multipole parameters.
39The TINKER package includes a variety of novel algorithms such as a new
40distance geometry metrization method that has greater speed and better
41sampling than standard methods, Elber's reaction path methods, several of
42our Potential Smoothing and Search (PSS) methods for global optimization,
43an efficient potential surface scanning procedure, a Cartesian polytensor
44atomic multipole expansion treatment of electrostatics with explicit
45polarizability, Eisenberg-McLachlan ASP and MacroModel GB/SA solvation,
46our own truncated Newton (TNCG) local optimizer, surface areas and volumes
47with derivatives, a simple free energy perturbation facility, normal mode
48analysis, minimization in Cartesian, torsional or rigid body space,
49velocity Verlet stochastic dynamics, an improved spherical energy cutoff
50method, Particle Mesh Ewald summation for partial charges under periodic
51boundary conditions, a novel reaction field treatment of long range
52electrostatics, and much more....
53
54                             Current Release
55
56The most recent release, version 3.7, contains the following new features
57and updates from version 3.6: (1) further improvements to our Potential
58Smoothing and Search global optimization algorithms, (2) updated parameter
59sets for the CHARMM, AMBER, OPLS and MM3 force fields, further validation
60of each of these parameters sets against their actual programs has resulted
61in some fairly major revisions for CHARMM22 and minor changes to the others,
62(3) a conformational scanning method, SCAN, for use on smoothed potential
63surfaces which efficiently explores the full potential surface, (4) a new
64velocity Verlet stochastic dynamics capability added the TINKER MD program,
65DYNAMIC, (5) Particle Mesh Ewald summation for partial charge electrostatics
66with periodic boundary conditions, (6) prebuilt executables for systems
67with up to 10000 atoms provided for Intel Win9X/NT, Intel Linux and
68Macintosh, and (7) numerous small changes, additions and fixes, many of
69them suggested by users of the package. Please note that as with prior new
70releases, version 3.7 is neither backward nor forward compatible with
71earlier versions of TINKER. For example, version 3.6 parameter files should
72not be used with version 3.7 executables and vice versa.
73
74                               Availability
75
76This distribution version of TINKER, with full source code, is made available
77free of charge to anyone who wants it. New major releases of the package
78with additional features are generally placed on this site each February,
79June and October. Minor changes and bug fixes are added to the distribution
80version as we finish testing them. The basic package has been used by the
81Ponder lab and others at Washington University for several years and should
82be fairly robust. All we ask is that you notify us of any bugs, features you
83would like to see implemented, or major code extensions that you add yourself.
84If you make significant use of the package, please return the enclosed
85license form. Comments and questions are always welcome and should be sent
86to ponder@dasher.wustl.edu. We try to respond to all email as time allows.
87