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