To: chemistry@ccl.net Subject: CCL:TINKER 3.7 is now available From: Jay Ponder Date: Wed, 16 Jun 1999 12:22:12 -0500 cc: ponder@dasher.wustl.edu Sender: "Computational Chemistry List" 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 -------- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ -------- 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 ponder@dasher.wustl.edu. We try to respond to all email as time allows.