1Date: Fri, 27 Jul 2001 16:40:50 -0500 2From: Jay Ponder <ponder@dasher.wustl.edu> 3Organization: Biochemistry, Washington University Medical School 4To: chemistry@ccl.net 5Subject: CCL:TINKER 3.9 is Now Available 6Sender: "Computational Chemistry List" <chemistry-request@ccl.net> 7 8Dear CCL, 9 10A new release of the TINKER Molecular Modeling Package, version 113.9 dated June 2001, is available from the TINKER web site at 12http://dasher.wustl.edu/tinker/ or via anonymous ftp download 13> from dasher.wustl.edu in the /pub/tinker area. 14 15TINKER is a modular, general package for molecular mechanics and 16dynamics with some special facilities and parameter sets for 17biopolymers. It supports several common force fields, including 18AMBER, CHARMM, MM2, MM3, OPLS-AA, OPLS-UA, and our own TINKER 19polarizable atomic multipole force field. The package contains 20advanced algorithms for energy minimization, molecular dynamics, 21distance geometry and global search including some methods that 22are not readily available elsewhere. 23 24TINKER version 3.9 contains the following new features and updates 25> from version 3.8: (1) improved nucleic acid building from sequence 26and automated conversion of nucleic acid PDB files to and from the 27TINKER format, (2) a new rigid body dynamics facility, (3) ability 28to handle infinite polymer lattices such as diamond and graphite, 29(4) treatment of intramolecular polarization via the Thole method, 30(5) a new utility program to compute molecular polarization, (6) an 31improved RasMol-based viewer that accepts TINKER coordinate files, 32allows atom selection, etc., (6) an optional Andersen stochastic 33collision thermostat for MD, (7) where appropriate TINKER programs 34such as ANALYZE, SUPERPOSE and SPACEFILL accept multiple coordinate 35set "archive" files as input, (8) updated parameter sets for various 36of the supported force fields. 37 38TINKER is distributed with full source code, a User's Guide, and 39several examples and test molecule files. Directions are supplied 40for building the package on most commonly used CPU/OS combinations. 41Prebuilt executables limited to a maximum of 10000 atoms are also 42provided for Linux, Windows, and Macintosh (currently Mac OS 9, 43OS X executables will be available shortly). 44 45Please see the web site above for further information. Comments, 46questions and suggestions for future improvements can be sent to 47ponder@dasher.wustl.edu. 48 49 Jay Ponder 50 51-- 52Jay W. Ponder Phone: (314) 362-4195 53Biochemistry, Box 8231 Fax: (314) 362-7183 54Washington University Medical School 55660 South Euclid Avenue Email: ponder@dasher.wustl.edu 56St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ 57