From cbas25@strath.ac.uk Fri Nov 28 06:37:53 1997 Received: from lismore.cc.strath.ac.uk for cbas25@strath.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA29007; Fri, 28 Nov 1997 06:07:07 -0500 (EST) Received: from skye.cc.strath.ac.uk [130.159.248.9] by lismore.cc.strath.ac.uk with esmtp (Exim 1.61 #3) id 0xbOFB-0000fd-00; Fri, 28 Nov 1997 11:05:57 +0000 Received: from sunflower (dialup-08.cc.strath.ac.uk [130.159.96.150]) by skye.cc.strath.ac.uk (SMI-8.6/8.6.12) with SMTP id LAA24556; Fri, 28 Nov 1997 11:05:15 GMT Sender: cbas25@ccsun.strath.ac.uk Message-ID: <347EA621.41C6@strath.ac.uk> Date: Fri, 28 Nov 1997 11:08:17 +0000 From: Peter Bladon Organization: University of Strathclyde X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: New version of INTERCHEM software Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit A new version of the INTERCHEM molecular modelling software is now available from QCPE and direct from Interprobe Chemical Services. For more details take a look at the website:- http://interchem.chem.strath.ac.uk/inter/interprobe.html Peter Bladon (cbas25@strath.ac.uk) From mry@cartan.gmd.de Fri Nov 28 07:37:55 1997 Received: from mail.gmd.de for mry@cartan.gmd.de by www.ccl.net (8.8.3/950822.1) id GAA29083; Fri, 28 Nov 1997 06:49:12 -0500 (EST) Received: from cartan (cartan [129.26.8.171]) by mail.gmd.de (8.8.7/8.8.7) with SMTP id MAA14235 for ; Fri, 28 Nov 1997 12:49:00 +0100 (MET) Received: from fermat by cartan with SMTP id AA06598 (5.67b/IDA-1.5 for ); Fri, 28 Nov 1997 12:48:54 +0100 Message-Id: <199711281148.AA06598@cartan> Date: Fri, 28 Nov 1997 12:48:54 +0100 (MET) From: Matthias Rarey Reply-To: Matthias Rarey Subject: FlexX -- software for automatic ligand docking available To: CHEMISTRY@www.ccl.net Cc: mry@cartan.gmd.de Mime-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-Md5: fHP3RKqxn2nyo0orChwffw== X-Mailer: dtmail 1.2.0 CDE Version 1.2 SunOS 5.6 sun4u sparc Dear Colleague, FlexX is a fully automated receptor-ligand docking program, whose development started approximately five years ago in a cooperation between pharmaceutical industry in Germany and GMD. The FlexX method and some results obtained with the software have been published in a series of four papers: Rarey, Wefing, Lengauer; J.Comput.-Aided Mol.Design 10 pages 41--54, 1996 Rarey, Kramer, Lengauer, and Klebe; J.Mol.Biol. 261 pages 470--489, 1996 Rarey, Kramer, Lengauer; J.Comput.-Aided Mol.Design 11 pages 369--384, 1997 Kramer, Rarey, Lengauer; PROTEINS: Struct., Funct., and Genet., in press (CASP-2 issue) Currently and for a limited time period, GMD-SCAI offers a demo license for evaluating FlexX free-of-charge. The license covers the full functionality of FlexX and will be valid until 1st February 1998. More information can be found on: http://cartan.gmd.de/FlexX.html Matthias Rarey From laaksone@csc.fi Fri Nov 28 07:43:26 1997 Received: from voxopm.minedu.fi for laaksone@csc.fi by www.ccl.net (8.8.3/950822.1) id HAA29113; Fri, 28 Nov 1997 07:04:33 -0500 (EST) Received: from laaksonen.csc.fi (laaksonen.csc.fi [193.166.1.75]) by voxopm.minedu.fi (8.8.8/8.8.8/CSC/Svrs-3.02) with SMTP id OAA28424 for ; Fri, 28 Nov 1997 14:04:22 +0200 (EET) Date: Fri, 28 Nov 1997 14:07:15 +0200 (GFT Standard Time) From: Leif Laaksonen To: chemistry@www.ccl.net Subject: gOpenMol 1.0 available Message-ID: X-X-Sender: laaksone@laaksonen.csc.fi MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, The version 1.0 of the molecular display and analysis program gOpenMol is now available at: http://laaksonen.csc.fi/gopenmol/ gOpenMol is now available for: * Windows 95/NT * SGI IRIX 6.x with MESA * IBM AIX 4.x with MESA and (hopefully next week) for * LINUX with MESA * DEC/OSF with MESA This release has added input coordinate filters for Gromos96, Tinker and UHBD qcd input coordinate files. gOpenMol can also now read and analyse the Gromos96 and Tinker formatted coordinate trajectories. Several help programs are also available in the utility/ directory. There are programs for: * formatting and unformatting of CHARMM trajectories * formatting and unformatting of plt files (gOpenMol plot files) * conversion of UHBD formatted and unformatted .psi files to plt files to be displayed by gOpenMol * unformatting of formatted AMBER trajectories * and many more Please report all bugs and comments directly to me. Have fun! Regards, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- From shenkin@still3.chem.columbia.edu Fri Nov 28 12:37:56 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id MAA00242; Fri, 28 Nov 1997 12:07:27 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id MAA18788; Fri, 28 Nov 1997 12:07:26 -0500 (EST) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id MAA20867; Fri, 28 Nov 1997 12:07:25 -0500 From: "Peter Shenkin" Message-Id: <9711281207.ZM20865@still3.chem.columbia.edu> Date: Fri, 28 Nov 1997 12:07:25 -0500 In-Reply-To: Rick Venable "CCL:Help in Mathematical methods." (Nov 27, 12:24pm) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Re: CCL:Help in Mathematical methods. Cc: Rick Venable Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Nov 27, 12:24pm, Rick Venable wrote: > Subject: CCL:Help in Mathematical methods. ... > First, let me highly recommend that you look at the code available at NETLIB; Yes. ... > It is public domain code, with no restrictions on re-use ... Not! Many of the modules, routines and packages contain re-use limitations. Here's an example from random.c/README. Though in this case the contributors place their own code in the public domain, the package is not usable without the ACM code that they also incorporate. random.c is far from the only package with such reuse restrictions. Of the approximately 10 netlib packages I've looked at seriously, nearly all contains such provisions. Some indeed do not, but if this kind of thing is an issue for you, you had better look carefully. By the way, it's not clear to me whether the re-use restriction quoted below pertains to selling the source code, selling a product that incorporates the restricted routines, or both. --------------------- from random.c/README -------------------------- LEGALITIES Code that appeared in an ACM publication is subject to their algorithms policy: Submittal of an algorithm for publication in one of the ACM Transactions implies that unrestricted use of the algorithm within a computer is permissible. General permission to copy and distribute the algorithm without fee is granted provided that the copies are not made or distributed for direct commercial advantage. The ACM copyright notice and the title of the publication and its date appear, and notice is given that copying is by permission of the Association for Computing Machinery. To copy otherwise, or to republish, requires a fee and/or specific permission. Krogh, F. Algorithms Policy. ACM Tran. Math. Softw. 13(1987), 183-186. We place the Ranlib code that we have written in the public domain. ------------------------------------------------------------------- -P. -- ****************** Sir Isaiah Berlin, 1909 - 1997, RIP ******************** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From huixiao@helix.nih.gov Fri Nov 28 17:37:57 1997 Received: from helix.nih.gov for huixiao@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id RAA01016; Fri, 28 Nov 1997 17:14:59 -0500 (EST) Received: (from huixiao@localhost) by helix.nih.gov (8.8.5/8.8.5) id RAA03354; Fri, 28 Nov 1997 17:14:59 -0500 (EST) Date: Fri, 28 Nov 1997 17:14:59 -0500 (EST) From: Huixiao Hong To: chemistry@www.ccl.net Subject: De Novo Design Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues: I am going to work on De Novo design. Could you tell me are there this kind of software somewhere (demo or commercial) and references on this topic. I very appreciate and will summary all answers. Huixiao Hong, Ph.D. Lab. of Med. Chem. National Cancer Institute National Institutes of Health Bethesda, MD 20892, USA Tel: 301-402-3111 Fax: 301-496-5839 Email: huixiao@helix.nih.gov From wtang@rainbow.uchicago.edu Fri Nov 28 17:53:00 1997 Received: from rainbow.uchicago.edu for wtang@rainbow.uchicago.edu by www.ccl.net (8.8.3/950822.1) id QAA00961; Fri, 28 Nov 1997 16:47:03 -0500 (EST) Received: (from wtang@localhost) by rainbow.uchicago.edu (8.8.6/8.8.6) id PAA08784 for CHEMISTRY@www.ccl.net; Fri, 28 Nov 1997 15:47:03 -0600 (CST) From: Wilfred Tang Message-Id: <199711282147.PAA08784@rainbow.uchicago.edu> Subject: CCL:Help in Mathematical methods. To: CHEMISTRY@www.ccl.net Date: Fri, 28 Nov 1997 15:47:03 -0600 (CST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > On Wed, 26 Nov 1997, Norge Cruz Hernandez wrote: > > I am trying to solve the minimization of a function whith non linear > > constrained. > > First, let me highly recommend that you look at the code available at NETLIB; > it has the following attributes: > > o It is mature, well tested, stable code; the linear algebra library (BLAS) > is the basis for most vendor implementations, and the LINPACK suite used > to benchmark floating point performance is also here > > o It is public domain code, with no restrictions on re-use > > o It is highly efficient, well optimized code; for inversion of large > matrices, I observed a ca. 50-fold speedup in switching from N.R. > routines to those in NETLIB > > o The web site is fairly well organized, and allows you to download just the > source files you need > > http://www.netlib.org Another good place to look is NIST Guide to Available Mathematical Software http://gams.nist.gov/ It has software organized by both problem type and package name. Wilfred Tang