From chemistry-request@www.ccl.net Mon Apr 5 10:20:40 1999 Received: from nickel.camsoft.com ([198.112.109.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA18980 Mon, 5 Apr 1999 10:20:40 -0400 (EDT) Received: from 198.112.109.83 by nickel.camsoft.com with SMTP (QuickMail Pro Server for MacOS 1.0.3); 05 APR 99 10:12:58 UT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: Jonathan Brecher@nickel.camsoft.com Message-Id: In-Reply-To: <001401be7d26$10120c00$320b29d8@camitro.com> Date: Mon, 5 Apr 1999 09:18:01 -0400 To: chemistry@www.ccl.net From: Jonathan Brecher Subject: Re: CCL:Java code for standard orientation transformation? >So does anybody know of (or have) some Java code for transforming molecules >to the standard orientation? I don't have any such code, but could I even one-up the question: Does anybody know of a *definition* of "standard orientation"? Sounds like a useful thing, but I've never heard of it before. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com From chemistry-request@www.ccl.net Mon Apr 5 12:33:10 1999 Received: from quartz.super.arizona.edu (quartz.Super.Arizona.EDU [128.196.131.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA19738 Mon, 5 Apr 1999 12:33:09 -0400 (EDT) Received: from localhost (fan@localhost) by quartz.super.arizona.edu (8.8.7/8.8.7) with SMTP id JAA09042 for ; Mon, 5 Apr 1999 09:33:09 -0700 (MST) X-Authentication-Warning: quartz.super.arizona.edu: fan owned process doing -bs Date: Mon, 5 Apr 1999 09:33:08 -0700 (MST) From: Hua-Jun Fan X-Sender: fan@quartz.super.arizona.edu To: chemistry@www.ccl.net Subject: DSW-Xalpha Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CCL netters, I had question about using DSW-Xalpha methods in calculating Re6 cluster. I have read a paper about it and am interested in repeating the calculations. The authors's email address on the paper is not right. The paper is published by Dr. Arratia-perez on J. Chem.Phy. vol 110, num. 5, 1999 Feb issue about DSW-Xalpha calculation on Re cluster. I wonder if anyone have any suggestion/advice on the software availability, and a bit of detail about it how the calculations are performed, even the priciple about the methods, calculations. (I am quite new to this area, all I knew about it is not very many methods are available to do this kind of cluster) From paper, there is not much information in it. CCL has been a great resource. I will summerize the replies. Thanks in advance. Huajun Fan University of Arizona From chemistry-request@www.ccl.net Mon Apr 5 13:15:46 1999 Received: from sctmg02.sct.ucarb.com (sctmg02.sct.ucarb.com [140.170.101.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA20099 Mon, 5 Apr 1999 13:15:45 -0400 (EDT) Received: by sctmg02.sct.ucarb.com with Internet Mail Service (5.5.2448.0) id ; Mon, 5 Apr 1999 13:16:29 -0400 Message-ID: From: "Smith JA (Jack)" To: "'CCL'" Subject: G98 on an HP V-Class machine Date: Mon, 5 Apr 1999 13:16:17 -0400 X-Mailer: Internet Mail Service (5.5.2448.0) This is a repeat posting of a previous message for those whose mailers don't decode HTML. I was informed that my prior posting was sent (unintentially) in MIME-encoded HTML format. I'm looking for examples of running G98 (or even G94) on an HP Exemplar V-Class machine in parallel. I've found examples for GAUSSIAN on HP SPP-2000 (X/S-Class) machines (under SPP-UX), but I'd like examples using the newer V-Class machines under HP-UX. - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jack A. Smith || Union Carbide || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-4672 P.O. Box 8361 || S. Charleston, WV 25303 || smithja@ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@www.ccl.net Mon Apr 5 13:51:27 1999 Received: from nickel.camsoft.com ([198.112.109.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA20420 Mon, 5 Apr 1999 13:51:26 -0400 (EDT) Received: from 198.112.109.83 by nickel.camsoft.com with SMTP (QuickMail Pro Server for MacOS 1.0.3); 05 APR 99 13:43:32 UT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: Jonathan Brecher@nickel.camsoft.com Message-Id: In-Reply-To: References: <001401be7d26$10120c00$320b29d8@camitro.com> Date: Mon, 5 Apr 1999 13:48:55 -0400 To: chemistry@www.ccl.net From: Jonathan Brecher Subject: SUMM: CCL:Java code for standard orientation transformation? >>So does anybody know of (or have) some Java code for transforming molecules >>to the standard orientation? > >I don't have any such code, but could I even one-up the question: >Does anybody know of a *definition* of "standard orientation"? Sounds like >a useful thing, but I've never heard of it before. Thanks to the folks who have already responded. For those interested, Jen Sorensen provided me the fullest explanation: Excerpted from the Gaussian Programmer's Reference (Chpt 10.6.2) Goals: 1. The molecule is oriented so as to simplify the 3x3 transformation matrix. 2. Two z-matrices differing only in the values of the internal coordinates but which are identical as regards the integer quantities (such as occurs on subsequent points of a geometry optimization) shall produce the same orientation of the molecule. 3. Two different z-matrices for the same molecule shall produce the same coordinates, save for a possible renumbering of the atoms. 4. The number of molecular orbital coefficients zero by symmetry should be maximized. General Considerations: 1. A right-handed coordinate system will be used throughout. 2. The molecule will be translated so that its center of charge is at the origin. 3. Atoms will not be reordered relative to their order upon input. 4. The cartesian axes will be considered to increase in priority in the order x < y < z. *** Neat. Unfortunately, I was hoping for something a little more general-purpose, for example something that said that toluene should be drawn with the methyl group at the 12:00 position rather than the 6:00 position (in 2D space). Seems like everyone was talking about a "standard orientation" defined in terms of 3D space, and in particular in terms of the Gaussian application. Also useful, but not what I was hoping for. Oh, well! Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com From chemistry-request@www.ccl.net Mon Apr 5 16:41:14 1999 Received: from gatekeeper.eastman.com (gatekeeper.eastman.com [164.89.253.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA11201 Mon, 5 Apr 1999 16:41:13 -0400 (EDT) Received: by gatekeeper.eastman.com; id QAA16629; Mon, 5 Apr 1999 16:41:27 -0400 (EDT) Received: from emngw1.eastman.com(164.89.254.2) by gatekeeper.eastman.com via smap (3.2) id xma016585; Mon, 5 Apr 99 16:41:24 -0400 Received: by eastman.com id AA205050 (5.67b/IDA-1.5 for chemistry@www.ccl.net); Mon, 5 Apr 1999 16:40:40 -0400 Received: from ntmcon02.emn.com by eastman.com with SMTP id AA173300 (5.67b/SMI-4.1 for ); Mon, 5 Apr 1999 16:40:40 -0400 Received: by ntmcon02.emn.com with Internet Mail Service (5.5.2232.9) id <2CWA0GRS>; Mon, 5 Apr 1999 16:40:41 -0400 Message-Id: From: "Wilson, Bruce E" To: "'chemistry@www.ccl.net'" Subject: Plotting 2D or 3D data and seeing chemical structure Date: Mon, 5 Apr 1999 16:40:40 -0400 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain We have a need to be able to display some 2D (and preferably 3D) data in a graph and we need to be able to somehow click on a point and see the chemical structure associated with that point. We have a fairly large number of data points, currently in SD files and some in PDB format, so structure import is an issue. The XYZ data is currently in Excel. A robust, commercial solution is preferred, but I'd consider freeware/university-ware if it does this one simple job well. Thanks for any leads and/or information about products you've tried and liked (or tried and despised). ====================================================== Bruce E. Wilson (bewilson@eastman.com) Eastman Chemical Company, Chemicals Research Division Lincoln St, B-150B, Box 1972 Kingsport, TN 37662-5150, USA Office: (423) 229-8886; FAX: (423) 229-4558 From chemistry-request@www.ccl.net Mon Apr 5 18:03:43 1999 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA19834 Mon, 5 Apr 1999 18:03:42 -0400 (EDT) Received: from bilbao.ks.uiuc.edu (bilbao.ks.uiuc.edu [130.126.120.38]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id RAA26853 for ; Mon, 5 Apr 1999 17:03:35 -0500 (CDT) Received: (from johns@localhost) by bilbao.ks.uiuc.edu (980427.SGI.8.8.8/8.6.9)id RAA50727 for chemistry@www.ccl.net; Mon, 5 Apr 1999 17:03:35 -0500 (CDT) From: John Stone Message-Id: <199904052203.RAA50727@bilbao.ks.uiuc.edu> Subject: Announce: VMD 1.3 Release To: chemistry@www.ccl.net Date: Mon, 5 Apr 1999 17:03:35 -0500 (CDT) X-Mailer: ELM [version 2.4ME+ PL14 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit VMD "Visual Molecular Dynamics" 1.3 Announcement ------------------------------------------------ The Theoretical Biophysics group at the Beckman Institute For Advanced Science and Technology, the University of Illinois (U-C), is proud to announce the public release of VMD 1.3. VMD is a package for the visualization and analysis of biomolecular systems. This software is distributed free of charge and includes source code, documentation, and precompiled binaries for HP, Linux, SGI and Sun Unix systems. The documentation includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer. VMD development is supported by the NIH National Center for Research Resources. A full description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ The authors request that any published work which utilizes VMD includes a reference to the VMD web page and/or the following reference: Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. The Theoretical Biophysics group encourages VMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. We are eager to hear from you, and thank you for using our software! The VMD Developers vmd@ks.uiuc.edu April 5, 1999 -- Theoretical Biophysics Group Email: johns@ks.uiuc.edu Beckman Institute http://www.ks.uiuc.edu/~johns/ University of Illinois Phone: (217) 244-3349 405 N. Mathews Ave FAX: (217) 244-6078 Urbana, IL 61801, USA Unix Is Good For You!!! From chemistry-request@www.ccl.net Mon Apr 5 22:39:36 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id WAA20904 Mon, 5 Apr 1999 22:39:36 -0400 (EDT) Received: by bioc1.msi.com (940816.SGI.8.6.9/930416.SGI) for id TAA09046; Mon, 5 Apr 1999 19:38:21 -0700 Received: from unknown(146.202.0.102) by bioc1.msi.com via smap (V2.0) id xma009044; Mon, 5 Apr 99 19:38:04 -0700 Message-Id: <3.0.32.19990405194148.00d28168@146.202.0.225> X-Sender: tvd@146.202.0.225 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Mon, 05 Apr 1999 19:41:52 -0700 To: CHEMISTRY@www.ccl.net From: Ton van Daelen Subject: Cerius2 software developer's kit training workshops Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi to all - MSI will be organizing three two-day C2.SDK training workshops. The C2SDK is MSI's toolkit for the integration and development of modeling applications in the Cerius2 environment. These are the dates and locations: May 4-5 Research Triangle Park, NC June 10-11 Cambridge, England July 15-16 San Diego, CA Seating is limited to 15 people, so please sign up quickly. For details, look at the MSI web site at http://www.msi.com/about/events/training/training_schedule.html and http://www.msi.com/sdk/ or contact Mary Gallo (maryg@msi.com) at MSI in San Diego. Best regards - Ton Ton van Daelen, Ph.D. Product Manager Software Developer's Kit __o E: tvd@msi.com _`\<,_ Molecular Simulations Inc. P: -1-619-799-5329 (*)/ (*) 9685 Scranton Road F: -1-619-458-0136 /\/\/\/\/\/\ San Diego, CA 92121 W: http://www.msi.com The Cerius2 software developer's kit is now available free-of-charge Visit http://www.msi.com/sdk/ to sign up for a copy SDK training courses are coming up in RTP, NC May 4-5, and Cambridge, UK June 10-11. Sign up at http://www.msi.com/about/events/training/training_schedule.html