1To: chemistry@ccl.net 2Subject: CCL:TINKER 3.8 is Now Available 3From: Jay Ponder <ponder@dasher.wustl.edu> 4Date: Fri, 27 Oct 2000 11:45:20 -0500 5Organization: Biochemistry, Washington University Medical School 6Sender: "Computational Chemistry List" <chemistry-request@ccl.net> 7 8Dear CCL, 9 10A new release of the TINKER Molecular Modeling Package, version 113.8 dated October 2000, is available from the TINKER web site at 12http://dasher.wustl.edu/tinker/ or via anonymous ftp download 13from 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, distance geometry 21and global search that are not readily available elsewhere. 22 23TINKER version 3.8 contains the following new features and updates 24from version 3.7: (1) replacement of previous conjugate gradient 25minimizer with a more efficient L-BFGS algorithm, (2) updated 26parameter sets for several distributed 3rd-party force fields, 27(3) a new nucleic acid building module for generating DNA or RNA 28structures from sequence, (4) "final" parameters for the TINKER 29polarizable atomic multipole water model, (5) faster and more 30flexible GB/SA continuum solvation models including several 31literature variants, (6) Ewald summation for polarizable multipole 32electrostatics, (7) new programs to compute radial distribution 33functions, diffusion constants and power spectra from MD simulations. 34 35TINKER is distributed with full source code, a User's Guide, and 36several examples and test molecule files. Directions are supplied 37for building the package on most commonly used CPU/OS combinations. 38Prebuilt executables limited to a maximum of 10000 atoms are also 39provided for Linux, Windows, and Macintosh. 40 41Please see the web site above for further information. Comments, 42questions and suggestions for future improvements can be sent to 43ponder@dasher.wustl.edu. 44 45 Jay Ponder 46 47-- 48Jay W. Ponder Phone: (314) 362-4195 49Biochemistry, Box 8231 Fax: (314) 362-7183 50Washington University Medical School 51660 South Euclid Avenue Email: ponder@dasher.wustl.edu 52St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ 53