From rochus@felix.anorg.chemie.tu-muenchen.de Thu Aug 17 04:03:33 1995 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.6.10/950810.1506) id DAA29759; Thu, 17 Aug 1995 03:57:35 -0400 Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) id JAA01541; Thu, 17 Aug 1995 09:56:22 +0200 From: "Rochus Schmid" Message-Id: <9508170956.ZM1539@felix> Date: Thu, 17 Aug 1995 09:56:22 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Transf. from 6D to 5D Cc: rochus@felix.anorg.chemie.tu-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Netters, Can anyone of you tell me, or point me to a reference, how to transform the MO coefficients of cartesian d-functions into those of spherical d-functions properly. I will summarize to the list. Thank you very much in advance. Greetings to all, Rochus -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 3209 3140 Anorganisch Chemisches Institut 1 Fax. ++49 89 3209 3473 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From jkl@ccl.net Thu Aug 17 05:03:33 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id EAA00107; Thu, 17 Aug 1995 04:58:43 -0400 Received: from chamber.cco.caltech.edu for news@nntp-server.caltech.edu by bedrock.ccl.net (8.6.10/930601.1506) id EAA17848; Thu, 17 Aug 1995 04:58:42 -0400 Received: from gap.cco.caltech.edu by chamber.cco.caltech.edu with ESMTP (8.6.12/DEI:4.41) id BAA20833; Thu, 17 Aug 1995 01:58:40 -0700 Received: by gap.cco.caltech.edu (8.6.7/DEI:4.41) id BAA21646; Thu, 17 Aug 1995 01:58:39 -0700 To: mlist-chemistry@nntp-server.caltech.edu Path: blt From: blt@wag.caltech.edu (Bao-Liang Tsai) Newsgroups: mlist.chemistry Subject: G92 symmetry question Date: 17 Aug 1995 08:58:38 GMT Organization: California Institute of Technology, Pasadena, CA Lines: 8 Message-ID: <40v0bu$l4c@gap.cco.caltech.edu> NNTP-Posting-Host: teijin.wag.caltech.edu How does Gaussian 92 recognize molecular symmetry? I have a molecular geometry with perfect C2v symmetry in Z-matrix, but G92 just won't acknowledge it. Is there any trick to solve the problem? Advices will be very much appreciated. -Bao From tieleman@chem.rug.nl Thu Aug 17 05:33:34 1995 Received: from rugch4.chem.rug.nl for tieleman@chem.rug.nl by www.ccl.net (8.6.10/950810.1506) id FAA00333; Thu, 17 Aug 1995 05:27:02 -0400 From: Received: from rugmd10.chem.rug.nl by rugch4.chem.rug.nl with SMTP (1.38.193.4/16.2) id AA13425; Thu, 17 Aug 1995 11:26:13 +0200 Received: by rugmd10 (940816.SGI.8.6.9/930416.SGI) id LAA08207; Thu, 17 Aug 1995 11:26:02 +0200 Date: Thu, 17 Aug 1995 11:26:02 +0200 Message-Id: <199508170926.LAA08207@rugmd10> To: chemistry@www.ccl.net Subject: G94 on Cray: summary of responses Yesterday I asked for help installing G94 on a Cray J-16. Within a couple of hours I got almost a dozen reactions, including reactions from Cray and someone from Gaussian. Thank you all for your help. This is what I've understood from the reactions: We have a workstation academic license. To run G94 on a J-16 Cray, you need supercomputer support. This is available for Crays, and G94 has been installed on J-types Crays before. However, someone told me supercomputer support costs approx. $20000. Currently, I don't happen to have $20000, but I'll forward the information I received to the bosses. If they're still interested they can contact Gaussian :) (info@gaussian.com) Best regards, Peter Tieleman -- email: tieleman@chem.rug.nl address: Dept. of Biophysical Chemistry telephone: 31-50-634338 Nijenborgh 4 fax: 31-50-634800 9747 AG Groningen From jkl@ccl.net Thu Aug 17 07:03:35 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id GAA00929; Thu, 17 Aug 1995 06:48:59 -0400 Received: from Mailer.Uni-Marburg.DE for SERGEI@ps1515.chemie.uni-marburg.de by bedrock.ccl.net (8.6.10/930601.1506) id GAA18961; Thu, 17 Aug 1995 06:48:55 -0400 Received: from ps1515.Chemie.Uni-Marburg.DE by Mailer.Uni-Marburg.DE (AIX 3.2/UCB 5.64/20.07.94) id AA42235; Thu, 17 Aug 1995 12:47:25 +0200 Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.20); 17 Aug 95 12:47:37 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.20); 17 Aug 95 12:47:21 GMT+2 To: blt@wag.caltech.edu, chemistry@ccl.net From: "Sergei Vyboishchikov" Date: 17 Aug 95 12:47:16 MDT Subject: Re:G92 symmetry question Priority: normal X-Mailer: Pegasus Mail v2.3 (R5). Message-Id: <4CBF5296DB0@ps1515.chemie.uni-marburg.de> Dear Bao-Liang, As far as I know, the Gaussian - takes the molecular geometry - calculates the tensor of inertia - diagonalizes it - determines the principal axes of inertia and the type of top: -- asymmetrical, which can occur only in C1 and Ci point groups -- symmetrical, which can occur only in subgroups of D2d (e.g., in C2v) -- spherical, which can occur only in high symmetric groups (e.g., in Oh or Td) - transforms the geometry to the coordinate system of axes of inertia (so-called "standard orientation") - finally, determines the point group Note that all this actions are done with the actual molecular geometry regardless of the Z-matrix. Normally, Gaussian does it perfectly. However, it can unfortunately occur that the particular molecule is by occasion a spherical top (i.e. all three components of traceless inertia tensor are occasionally equal within the thresholds used by Gaussian) but it does not belong to any high symmetric group. In this case, the Gaussian gives a corresponding error message. If it is really the case, one can try to change the atomic weights of some atoms to avoid this difficulty. If you do not receive any error message, it means most likely that your Z-matrix is wrong and the molecule has no C2v symmetry. Regards, Sergei Vyboishchikov Universitaet Marburg From jkl@ccl.net Thu Aug 17 08:33:36 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id IAA01673; Thu, 17 Aug 1995 08:29:52 -0400 Received: from msi.com for Don_Gregory@msi.com by bedrock.ccl.net (8.6.10/930601.1506) id IAA20044; Thu, 17 Aug 1995 08:29:48 -0400 Received: from qmail-gw.msi.com by msi.com (4.1/SMI-4.1) id AA06737; Thu, 17 Aug 95 08:25:19 EDT Message-Id: Date: 17 Aug 1995 06:41:53 -0400 From: "Don Gregory" Subject: Biosym/MSI Merger Announcem To: "Cerius2 BBS" , "CHARMM BBS" , "PDB BBS" , "Quanta BBS" , "Comp. Chem. Listserver" X-Mailer: Mail*Link SMTP-QM 3.0.2 Subject: Time:6:35 AM OFFICE MEMO Biosym/MSI Merger Announcement Date:8/17/95 BIOSYM Technologies Inc. and Molecular Simulations Inc. Agree to Merge SAN DIEGO, Calif. August 15, 1995 - BIOSYM Technologies Inc. and Molecular Simulations Inc. (MSI) announce a merger between BIOSYM, a wholly-owned Corning subsidiary, and MSI, a privately held company. Under an agreement signed today Corning will receive approximately 55% of the outstanding equity in the new company, which will operate independently. The two companies had combined revenues exceeding $45 million in 1994 and will continue to pursue the development and marketing of scientific software and services designed to improve the efficiency of the research, development and production processes in both Life Sciences and Materials industries. Mr. Michael Savage, the current CEO of Molecular Simulations Inc., will become the CEO of the new company. Mr. Savage says, "This merger creates a new company with greater depth and economies of scale that will be able to create innovative technologies, delivered in ways that provide more immediate value to customers." Dr. C. Derek Statham, a Corning executive and CEO of BIOSYM Technologies Inc., will become Chairman of the new company. Dr. Statham says, "Corning has often used equity ventures to create stronger, more successful businesses, and believes that this venture will be well placed to advance this very exciting technology." The new company headquarters will be in San Diego, California, at the current headquarters of BIOSYM Technologies Inc. It will manage its European operations in Cambridge, England, the current European headquarters of Molecular Simulations Inc. BUSINESS OVERVIEW The business strategy of the new company includes several elements that will broaden the practical impact of modeling and simulation on industrial research, development and production. A full suite of software products will build on a rigorous scientific foundation and use innovative software engineering approaches to ensure accelerated development, reduced time to market, product ease of use, and intercompatibility. The new company will continue a strong customer commitment, emphasizing cooperative relationships with industry in consortia and solutions through simulation services. A focus on customer support and training will be strengthened further to ensure that customers can apply the company's products and services more rapidly and with greater impact. Together, BIOSYM and MSI can deliver better solutions faster, for the mutual success of customers and the new company. The new company will continue to provide modeling and simulation software products and services worldwide through its existing direct and indirect sales channels. The senior management of the new company comprises: Michael J. Savage - President and CEO Saiid Zarrabian - Chief Operating Officer David Hiatt - Chief Financial Officer Lissa Goldenstein - Sr. V. P., Worldwide Sales Chris Herd - V. P. and General Manager, Life Sciences Dr. John Newsam - V. P. and General Manager, Materials Technology Dr. Patrick Coulter - V. P. Materials Products and General Manager, Europe COMPANY BACKGROUNDS BIOSYM was founded in 1984 by Dr. Arnold T. Hagler, a biophysicist who helped pioneer computational chemistry technology. Corning acquired BIOSYM in 1992, and Dr. Derek Statham has been President and CEO since January of 1995. MSI is the result of the 1991 mergers of BioDesign (founded in 1984 with a Life Sciences focus), Cambridge Molecular Design (founded in 1989 with a Materials focus), and Polygen (founded in 1984 with a Life Sciences focus). In 1994, MSI acquired BioCAD, a Life Sciences company with strengths in database technology and hypothesis generation. Michael Savage has been President and CEO of MSI since its forming in 1991. BIOSYM has achieved a leading position in both Life Sciences and Materials Sciences computational chemistry, and is noted for the breadth and scientific depth of its modeling and simulation technology. BIOSYM is also known for its successful consortium approach, which entails team relationships with leading industrial, academic and government research organizations, with the aim of developing advanced modeling and simulation technologies for specific application segments. MSI has achieved a leading position in Materials computational chemistry and advanced software engineering using Cerius2, an open architecture computing environment for scientific simulation for materials and life science applications. Cerius2 allows for more streamlined integration of software application programs, and is also noted for its easy-to-use graphical interface. MSI is also an established innovator in drug discovery technology for the life sciences marketplace. BENEFITS TO INDUSTRY AND CUSTOMERS As a result of this merger customers will get the best of both companies. This, combined with the economies of scale that can be achieved, will benefit the industry and customers by providing: o Rapid technology advancement o Better customer support and training o Broader and deeper product offerings and services o The ability to invest more resources in new products, R&D, applications and training Mr. Savage adds, "This merger creates a dynamic new company and signifies the beginning of a new era in this industry. We are reinforcing our commitment to serving customers' needs in computational chemistry and related fields for the long run." MEDIA CONTACTS: Jo Ellen Collins Brenda Pfeiffer Molecular Simulations Inc. BIOSYM Technologies Inc. (617) 229-9800 x220 (619) 546-5319 From oreola@chem.QueensU.CA Thu Aug 17 09:48:37 1995 Received: from QUCDN.QueensU.CA for oreola@chem.QueensU.CA by www.ccl.net (8.6.10/950810.1506) id JAA02534; Thu, 17 Aug 1995 09:47:34 -0400 Received: from quchem.chem.QueensU.CA by QUCDN.QueensU.CA (IBM VM SMTP V2R2) with TCP; Thu, 17 Aug 95 09:44:14 EDT Received: by quchem.chem.QueensU.CA (4.1/SMI-4.0) id AA10853; Thu, 17 Aug 95 09:54:31 EDT Date: Thu, 17 Aug 95 09:54:31 EDT From: oreola@chem.QueensU.CA (Oreola Donini) Message-Id: <9508171354.AA10853@quchem.chem.QueensU.CA> To: chemistry@www.ccl.net Subject: K+ basis sets Hello, Netters, I am in need of basis sets for K+. I already know of the Wachters/Clementi 6-31G basis set ( J.Chem Phys, 52, 1033 (1970); Gaz.Chim.It., 108, 181 (1978)) and the basis sets in the book by Huzinaga et.al.(Gaussian basis sets for molecular calculations; 1984 Elsevier). Any other suggestions would be most welcome. I will summarize all the answers I get. Thank-you, Oreola Donini oreola@chem.queensu.ca From gbaudoux@quick.cc.fundp.ac.be Thu Aug 17 10:18:38 1995 Received: from hermes.fundp.ac.be for gbaudoux@quick.cc.fundp.ac.be by www.ccl.net (8.6.10/950810.1506) id KAA03351; Thu, 17 Aug 1995 10:17:42 -0400 From: Received: by hermes.fundp.ac.be; id AA12043; Thu, 17 Aug 1995 16:26:33 +0200 Received: from quick.cc.fundp.ac.be by hermes.fundp.ac.be; id AA12043; Thu, 17 Aug 1995 16:26:33 +0200 Date: Thu, 17 Aug 1995 16:11:58 +0100 Message-Id: <95081716115842@quick.cc.fundp.ac.be> To: chemistry@www.ccl.net Subject: maximal cliques in a graph X-Vms-To: SMTP%"chemistry@www.ccl.net" Hello! I am searching for a fortran routine finding all maximal cliques in a graph, using the Bron-Kerbosch algorithm or any other. Thanks in advance! Guy Baudoux Facultes Universitaires de Namur rue de Bruxelles, 61 5000 Namur, Belgium e-mail: gbaudoux@quick.cc.fundp.ac.be From jkl@ccl.net Thu Aug 17 10:33:38 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id KAA03462; Thu, 17 Aug 1995 10:21:32 -0400 Received: from Mailer.Uni-Marburg.DE for SERGEI@ps1515.chemie.uni-marburg.de by bedrock.ccl.net (8.6.10/930601.1506) id KAA22114; Thu, 17 Aug 1995 10:21:15 -0400 Received: from ps1515.Chemie.Uni-Marburg.DE by Mailer.Uni-Marburg.DE (AIX 3.2/UCB 5.64/20.07.94) id AA14428; Thu, 17 Aug 1995 16:17:33 +0200 Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.20); 17 Aug 95 16:17:37 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.20); 17 Aug 95 16:17:21 GMT+2 To: blt@wag.caltech.edu, chemistry@ccl.net From: "Sergei Vyboishchikov" Date: 17 Aug 95 16:17:20 MDT Subject: Re-2:G92 symmetry question Priority: normal X-Mailer: Pegasus Mail v2.3 (R5). Message-Id: <4CF754917DC@ps1515.chemie.uni-marburg.de> Answering Bao-Liang's question, I wrote .......... - Gaussian determines the principal axes of inertia and the type of top: -- asymmetrical, which can occur only in C1 and Ci point groups -- symmetrical, which can occur only in subgroups of D2d (e.g., in C2v) -- spherical, which can occur only in high symmetric groups (e.g., in Oh or Td) .......... I am sorry. It is wrong, of course. The correct formulation is following: - Gaussian determines the principal axes of inertia and the type of top: -- asymmetrical, which can occur only in subgroups of D2h (e.g., in C2v) -- symmetrical, which can occur only in groups which contain only one axis of higher order (e.g., C3v or D6h) -- spherical, which can occur only in highly symmetric groups (e.g., in Oh or Td) The rest of the message should be correct. I express my apology for this mistake and regret that some of the netters wasted their time reading my message. Greetings, Sergei Vyboishchikov Universitaet Marburg From jbrown@indigo17.carb.nist.gov Thu Aug 17 10:48:38 1995 Received: from ENH.NIST.GOV for jbrown@indigo17.carb.nist.gov by www.ccl.net (8.6.10/950810.1506) id KAA04287; Thu, 17 Aug 1995 10:46:13 -0400 Received: from indigo17.carb.nist.gov by ENH.NIST.GOV (PMDF V5.0-4 #10952) id <01HU6DFRO1JK00RJ1A@ENH.NIST.GOV> for chemistry@www.ccl.net; Thu, 17 Aug 1995 10:36:56 -0400 (EDT) Received: by indigo17.carb.nist.gov (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id KAA09255; Thu, 17 Aug 1995 10:34:41 -0400 Date: Thu, 17 Aug 1995 10:34:40 -0400 From: "Dr. James Brown" Subject: Parameters for Mn To: chemistry@www.ccl.net Message-id: <9508171034.ZM9253@indigo17.carb.nist.gov> MIME-version: 1.0 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Anyone know of any forcefield parameters for Mn other than the UFF? Thanks, James -- ------------------------------------------------------------- | James Brown, Ph.D | I swear by my life and my | | Center for Advanced | love of it that I will | | Research in Biotechnology | never live for the sake of | | 9600 Gudelsky Dr. | another man, nor ask another | | Rockville, MD 20850 | man to live for mine. | | jbrown@iris7.carb.nist.gov | -- John Galt | ------------------------------------------------------------- From toukie@zui.unizh.ch Thu Aug 17 10:49:53 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950810.1506) id KAA04095; Thu, 17 Aug 1995 10:38:11 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA10510; Thu, 17 Aug 95 16:38:03 +0200 X-Nupop-Charset: Swiss Date: Thu, 17 Aug 1995 16:38:04 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <59884.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Standalone sim. annealing for PC? Dear Colleagues; I wish to know if there exist any (standalone) programmes for either a DOS and/or Windows-based PC that can perform conformational energy minimisa- tions via simulated annealing. Such a programme would be able to take the structure of a small molecule (using one or more of the various commonly used structural file formats) as input and, after a computational analysis, return a structural file corresponding to a (the?) conformer having an energy minimum. It would also be beneficial if the computation can take into ac- count the dielectric constant of the medium, rather than being good only in vacuo or in an aqueous milieu. Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Zuerich toukie@zui.unizh.ch From toukie@zui.unizh.ch Thu Aug 17 10:51:49 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950810.1506) id KAA04097; Thu, 17 Aug 1995 10:38:15 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA10517; Thu, 17 Aug 95 16:38:07 +0200 X-Nupop-Charset: Swiss Date: Thu, 17 Aug 1995 16:38:07 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <59887.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Question about Babel for DOS Dear Colleagues; After performing a MOPAC run, I wished to convert the resultant geome- try-optimised internal Cartesian coordinate output to a .hin file using the DOS version Babel. The input file, "mopacout.dat", is as follows: 1 C .0000 .0000 .0000 2 C 1.4005 .0000 .0000 3 C -.7170 1.2162 .0000 4 C 2.0977 1.2028 -.0013 5 C .0020 2.4110 -.0031 6 C 1.3972 2.4078 -.0021 7 O -.7313 -1.1648 .0019 8 C -2.2030 1.1536 .0036 9 C -2.8977 2.4978 .0011 10 C -4.4029 2.3313 .0138 11 C -5.1029 3.6650 -.0049 12 H 1.9443 -.9592 -.0007 13 H 3.1993 1.2031 -.0027 14 H -.5343 3.3759 -.0029 15 H 1.9482 3.3615 -.0019 16 H -.1074 -1.9129 .0226 17 H -2.5330 .5611 -.8947 18 H -2.5289 .5664 .9070 19 H -2.5797 3.0966 .8949 20 H -2.5970 3.0768 -.9123 21 H -4.7176 1.7265 -.8786 22 H -4.7117 1.7562 .9258 23 H -6.2106 3.5226 .0026 24 H -4.8202 4.2717 .8897 25 H -4.8268 4.2421 -.9207 After loading this file into my Babel subdirectory, I typed babel -iac mopacout.dat -ohin geom.hin but instead of performing the desired conversion I got a message "Unable to allocate memory for 0 bonds require 0 bytes" Can anyone tell me just what this message means, and how I can "alter the situation" such that I can get Babel to make the desired file format conver- sion? Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Zuerich toukie@zui.unizh.ch From dave@wh.bayer.com Thu Aug 17 11:18:38 1995 Received: from wh.bayer.com for dave@wh.bayer.com by www.ccl.net (8.6.10/950810.1506) id LAA04774; Thu, 17 Aug 1995 11:10:34 -0400 From: Received: from mrcs1 ([140.250.41.24]) by wh.bayer.com (8.6.12/8.6.12) with SMTP id LAA07468 for ; Thu, 17 Aug 1995 11:07:43 -0400 Received: by mrcs1 (5.64/X1.00) id AA29825; Thu, 17 Aug 95 11:07:49 -0400 Date: Thu, 17 Aug 95 11:07:49 -0400 Message-Id: <9508171507.AA29825@mrcs1> To: CHEMISTRY@www.ccl.net Subject: PM3 for phosphates Does anyone have any info regarding the accuracy of PM3 for phosphates (in particular ATP but any phosphate will do)? I have looked in JCC 10 (1989) 221-264 and cannot seem to find anything regarding this. Any info would be greatly appreciated.... Dave ---------------------------------------------------------------- David Hartsough dave@wh.bayer.com Structural Chemistry Bayer Research Center 400 Morgan Lane Phone: (203)937-2982 West Haven CT 06516 Fax: (203)937-2650 ---------------------------------------------------------------- The opinions expressed herein are solely those of the author and are not necessarily those of Bayer ---------------------------------------------------------------- From dave@wh.bayer.com Thu Aug 17 11:20:02 1995 Received: from wh.bayer.com for dave@wh.bayer.com by www.ccl.net (8.6.10/950810.1506) id LAA04752; Thu, 17 Aug 1995 11:08:58 -0400 From: Received: from mrcs1 ([140.250.41.24]) by wh.bayer.com (8.6.12/8.6.12) with SMTP id LAA07463 for ; Thu, 17 Aug 1995 11:06:06 -0400 Received: by mrcs1 (5.64/X1.00) id AA29785; Thu, 17 Aug 95 11:06:13 -0400 Date: Thu, 17 Aug 95 11:06:13 -0400 Message-Id: <9508171506.AA29785@mrcs1> To: CHEMISTRY@www.ccl.net Subject: Mg++2 parameters I am searching for vdW parameters for Mg++2 suitable for use in AMBER. We are trying to simulate a Mg containing protein and I have not been able to find any parameters yet. My apologies to the list if the location of said parameters is screamingly obvious and I have not seen them..... Dave ---------------------------------------------------------------- David Hartsough dave@wh.bayer.com Structural Chemistry Bayer Research Center 400 Morgan Lane Phone: (203)937-2982 West Haven CT 06516 Fax: (203)937-2650 ---------------------------------------------------------------- The opinions expressed herein are solely those of the author and are not necessarily those of Bayer ---------------------------------------------------------------- From huang@mazda.wavefun.com Thu Aug 17 11:48:41 1995 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by www.ccl.net (8.6.10/950810.1506) id LAA05125; Thu, 17 Aug 1995 11:33:56 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA02477; Thu, 17 Aug 95 08:34:15 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma002475; Thu Aug 17 08:34:07 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@www.ccl.net id AA23001; Thu, 17 Aug 95 08:33:55 -0700 From: "Wayne Huang" Message-Id: <9508170833.ZM22999@mazda.wavefun.com> Date: Thu, 17 Aug 1995 08:33:54 -0700 In-Reply-To: "Dr. James Brown" "CCL:Parameters for Mn" (Aug 17, 10:34am) References: <9508171034.ZM9253@indigo17.carb.nist.gov> Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Dr. James Brown" Subject: Re: CCL:Parameters for Mn Cc: chemistry@www.ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Aug 17, 10:34am, Dr. James Brown wrote: > Subject: CCL:Parameters for Mn > > Anyone know of any forcefield parameters for Mn other than the UFF? > > Thanks, > James > In respond to your quest for Mn parameter, we have just finished the parameterization of Mn on PM3(tm) module which is available on Spartan 4.0. Let me know if you need additional information. --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+ From godbout@CHIMCN.UMontreal.CA Thu Aug 17 13:03:41 1995 Received: from condor.CC.UMontreal.CA for godbout@CHIMCN.UMontreal.CA by www.ccl.net (8.6.10/950810.1506) id MAA06646; Thu, 17 Aug 1995 12:59:07 -0400 Received: from chims1.CHIMCN.UMontreal.CA (chims1.CHIMCN.UMontreal.CA [132.204.11.106]) by condor.CC.UMontreal.CA with ESMTP id MAA12554 (8.6.11/IDA-1.6 for ); Thu, 17 Aug 1995 12:57:46 -0400 Received: by chims1.CHIMCN.UMontreal.CA (940816.SGI.8.6.9/5.17) id NAA03950; Thu, 17 Aug 1995 13:00:36 -0400 From: godbout@CHIMCN.UMontreal.CA (Godbout Nathalie) Message-Id: <199508171700.NAA03950@chims1.CHIMCN.UMontreal.CA> Subject: normal modes visualisation To: CHEMISTRY@www.ccl.net Date: Thu, 17 Aug 1995 13:00:36 -0400 (EDT) MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 780 Hello CCL members, I am in need of a program that will help me visualize the nature of the calculated normal modes of molecules. Specifically, the commonly found illustrations of arrows along bonds would be helpful. The molecules contain between 20-25 atoms, hence the difficulty in interpreting the results of the vibrational analysis. Many thanks in advance for your help. Nathalie -- ------------------------------------ |Nathalie Godbout | |Universite de Montreal | |Departement de chimie | |C.P. 6128, Succ. Centre-ville | |Montreal, Quebec H3C 3J7 | |Canada | |Tel: (514) 343-6111 ext. 3949 | |godbout@chimcn.umontreal.ca | ------------------------------------ From smb@smb.chem.niu.edu Thu Aug 17 14:33:41 1995 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.10/950810.1506) id OAA08249; Thu, 17 Aug 1995 14:28:36 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA12691 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net>); Thu, 17 Aug 1995 13:28:46 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA22189; Thu, 17 Aug 95 12:16:48 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA09201; Thu, 17 Aug 95 12:16:47 -0500 Date: Thu, 17 Aug 95 12:16:47 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9508171716.AA09201@smb.chem.niu.edu> To: CHEMISTRY@www.ccl.net Subject: Chemistry on the Infobahn Electronic Session At the Chicago ACS Meeting to be held next week, the Computers in Chemistry Division and Division of Chemical Information are sponsoring the symposium "Chemistry on the Infobahn". Part of this session will be electronic, and we would like to officially invite everyone to "attend" the electronic poster session. The session is available now at the URL http://hackberry.chem.niu.edu/Infobahn Thomas Pierce Henry Rzepa Steve Bachrach organizers of the Chemistry on the Infobahn symposium Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From nauss@ucmod2.che.uc.EDU Thu Aug 17 14:37:43 1995 Received: from phem3 for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.10/950810.1506) id OAA08198; Thu, 17 Aug 1995 14:19:13 -0400 Received: from UCBEH.SAN.UC.EDU (SMTPUSER@UCBEH) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HU6L7BGQHC9FN4ON@phem3.acs.ohio-state.edu>; Thu, 17 Aug 1995 14:19:08 EDT Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-4 #7238) id <01HU6L6RY952HV2NWJ@UCBEH.SAN.UC.EDU> for chemistry@www.ccl.net; Thu, 17 Aug 1995 14:18:44 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:chemistry@www.ccl.net id AA05385; Thu, 17 Aug 1995 14:24:34 -0400 Date: Thu, 17 Aug 1995 14:24:34 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Concerns with the Biosym/MSI merger To: chemistry@www.ccl.net Reply-to: nauss@ucmod2.che.uc.EDU Message-id: <9508171824.AA05385@ucmod2.che.uc.EDU> Content-transfer-encoding: 7BIT I am assuming that most people are aware of the merger between Biosym and MSI. When I heard of that I immediately had some concerns which I would like to share with you. 1) Pricing of software - we will now have a single company owning the two largest software pacakages in at least North America (or pretty close to it). Competition will be reduced and that usually means prices will go up. 2) What happens to CHARMm? - IMHO a big advantage for MSI was that they sold CHARMm. CHARMm has some deep roots in academia (including NIH) and I found there was ample help available for CHARMm from the non-commercial sources. In addition, the academic version of the CHARMm source code was available for innovations. With certain limitations, the academic version was compatible with the MSI software. So now what will happen? Will Discover and CHARMm merge to form a new proprietary package which will be as much of a black box as ESFF? Personally, I would rather use CHARMM than Discover. I feel that CHARMm is much more versatile, user-friendly, and stable than Discover. I would hate to see it get ruined. 3) Will the CHARMM forcefield become incorporated into Discover? - Not really a concern, actually, but rather a good idea IMO. 4) Will the reduced competition diminish the incentive to improve the software? - Could the corporate attitude found at large companies like IBM dominate Biosym/MSI so that improvements and innovations are made grudingly, sporatically, and not in touch with customer desires? Healthy competition usually means better products. As I see it, that competition is significantly reduced. So what incentive is there for continued product development? Biosym already has a reputation (at least in my circle of aquintances) as being somewhat buggy. What will happen now? Just some of my thoughts. Alternate viewpoints are welcomed. Jeff Nauss **************************************************************************** * Jeffrey L. Nauss, PhD * telephone: 513-556-0148 * * Director, Molecular Modeling Services * fax: 513-556-9239 * * Department of Chemistry * e-mail: nauss@ucmod2.che.uc.edu * * University of Cincinnati * URL http:/www.che.uc.edu/~nauss * * Cincinnati, OH 45221-0172 * * **************************************************************************** * "Once in awhile you get shown the light * * in the strangest places if you look at it right." * * * * Jerry Garcia (1942-1995) * * from "Scarlet Begoonias" * **************************************************************************** From jbrown@indigo17.carb.nist.gov Thu Aug 17 16:03:42 1995 Received: from ENH.NIST.GOV for jbrown@indigo17.carb.nist.gov by www.ccl.net (8.6.10/950810.1506) id PAA09228; Thu, 17 Aug 1995 15:53:31 -0400 Received: from indigo17.carb.nist.gov by ENH.NIST.GOV (PMDF V5.0-4 #10952) id <01HU6OE9LF9S00SNRM@ENH.NIST.GOV> for chemistry@www.ccl.net; Thu, 17 Aug 1995 15:50:15 -0400 (EDT) Received: by indigo17.carb.nist.gov (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id PAA10249; Thu, 17 Aug 1995 15:48:14 -0400 Date: Thu, 17 Aug 1995 15:48:13 -0400 From: "Dr. James Brown" Subject: Biosym/MSI...antitrust? To: chemistry@www.ccl.net Message-id: <9508171548.ZM10247@indigo17.carb.nist.gov> MIME-version: 1.0 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT > 1) Pricing of software - we will now have a single company owning the > two largest software pacakages in at least North America (or pretty > close to it). Competition will be reduced and that usually means > prices will go up. I sent mail to Biosym asking this question...are there any anti-trust issues surrounding this merger? James -- ------------------------------------------------------------- | James Brown, Ph.D | I swear by my life and my | | Center for Advanced | love of it that I will | | Research in Biotechnology | never live for the sake of | | 9600 Gudelsky Dr. | another man, nor ask another | | Rockville, MD 20850 | man to live for mine. | | jbrown@iris7.carb.nist.gov | -- John Galt | ------------------------------------------------------------- From palres.dnet.sandoz.com!bowlus@sandoz.com Thu Aug 17 16:33:43 1995 Received: from tigger.jvnc.net for palres.dnet.sandoz.com!bowlus@sandoz.com by www.ccl.net (8.6.10/950810.1506) id QAA09455; Thu, 17 Aug 1995 16:21:03 -0400 Received: from sndzeh.UUCP by tigger.jvnc.net with UUCP id AA27828 (5.65c/IDA-1.4.4 for CHEMISTRY@www.ccl.net); Thu, 17 Aug 1995 16:20:59 -0400 Message-Id: <199508172020.AA27828@tigger.jvnc.net> Date: Thu, 17 Aug 95 16:06:07 -0400 From: bowlus@palres.dnet.sandoz.com (Steve Bowlus) To: "CHEMISTRY@www.ccl.net"@SNDZEH.dnet.sandoz.com Cc: BOWLUS@sandoz.com Subject: Mg Parameters for AMBER David Hartsough (dave@wh.bayer.com) wrote: I am searching for vdW parameters for Mg++2 suitable for use in AMBER. We are trying to simulate a Mg containing protein and I have not been able to find any parameters yet. My apologies to the list if the location of said parameters is screamingly obvious and I have not seen them..... There are some parameters reported in Mertz et al., JACS, _1992_, 114, 4762 -4769. These are for Mg bound in a porphyrin, so I don't have any clue how generally useful they are. If the whereabouts of a repository or collection of AMBER parameters (outside the original articles) is screamingly obvious, I guess I was standing behind the door with you when the word was passed. Will one of the cognoscenti share this information with the list? A partial search of the archives (painfully, by mailserver) has given me few clues. sb =========================================================================== Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 =========================================================================== From kotelyan@che.udel.edu Thu Aug 17 16:35:44 1995 Received: from che.udel.edu for kotelyan@che.udel.edu by www.ccl.net (8.6.10/950810.1506) id QAA09532; Thu, 17 Aug 1995 16:26:40 -0400 Received: by che.udel.edu (AIX 3.2/UCB 5.64/4.03) id AA24656; Thu, 17 Aug 1995 16:26:35 -0400 Date: Thu, 17 Aug 1995 16:25:06 +22305241 (EDT) From: Mike Kotelyanski Subject: Re: CCL:Concerns with the Biosym/MSI merger To: "Jeffrey L. Nauss" Cc: chemistry@www.ccl.net In-Reply-To: <9508171824.AA05385@ucmod2.che.uc.EDU> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I share the concerns about CHARMm, and let's hope, that AMBER will be still around before it becomes a black box. Michael Kotelyanskii PhD Department of Chemical Engineering University of Delaware kotelyan@che.udel.edu Newark DE 19716 On Thu, 17 Aug 1995, Jeffrey L. Nauss wrote: > I am assuming that most people are aware of the merger between Biosym > and MSI. When I heard of that I immediately had some concerns which I > would like to share with you. > > 1) Pricing of software - we will now have a single company owning the > two largest software pacakages in at least North America (or pretty > close to it). Competition will be reduced and that usually means > prices will go up. > > 2) What happens to CHARMm? - IMHO a big advantage for MSI was that > they sold CHARMm. CHARMm has some deep roots in academia (including > NIH) and I found there was ample help available for CHARMm from the > non-commercial sources. In addition, the academic version of the CHARMm > source code was available for innovations. With certain limitations, > the academic version was compatible with the MSI software. So now > what will happen? Will Discover and CHARMm merge to form a new > proprietary package which will be as much of a black box as ESFF? > > Personally, I would rather use CHARMM than Discover. I feel that > CHARMm is much more versatile, user-friendly, and stable than > Discover. I would hate to see it get ruined. > > 3) Will the CHARMM forcefield become incorporated into Discover? - Not > really a concern, actually, but rather a good idea IMO. > > 4) Will the reduced competition diminish the incentive to improve the > software? - Could the corporate attitude found at large companies like > IBM dominate Biosym/MSI so that improvements and innovations are made > grudingly, sporatically, and not in touch with customer desires? > Healthy competition usually means better products. As I see it, that > competition is significantly reduced. So what incentive is there for > continued product development? Biosym already has a reputation (at > least in my circle of aquintances) as being somewhat buggy. What will > happen now? > > Just some of my thoughts. Alternate viewpoints are welcomed. > > Jeff Nauss > > **************************************************************************** > * Jeffrey L. Nauss, PhD * telephone: 513-556-0148 * > * Director, Molecular Modeling Services * fax: 513-556-9239 * > * Department of Chemistry * e-mail: nauss@ucmod2.che.uc.edu * > * University of Cincinnati * URL http:/www.che.uc.edu/~nauss * > * Cincinnati, OH 45221-0172 * * > **************************************************************************** > * "Once in awhile you get shown the light * > * in the strangest places if you look at it right." * > * * > * Jerry Garcia (1942-1995) * > * from "Scarlet Begoonias" * > **************************************************************************** > > > -------This is added Automatically by the Software-------- > -- Original Sender From: Address: nauss@ucmod2.che.uc.EDU > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From jkl@ccl.net Thu Aug 17 17:03:43 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id RAA09920; Thu, 17 Aug 1995 17:00:06 -0400 Received: from earth.ox.ac.uk for Keith.Refson@earth.ox.ac.uk by bedrock.ccl.net (8.6.10/930601.1506) id RAA29982; Thu, 17 Aug 1995 17:00:00 -0400 Received: from rahman.earth.ox.ac.uk by earth.ox.ac.uk; Thu, 17 Aug 1995 22:01:47 +0100 Date: Thu, 17 Aug 95 22:01:44 BST Message-Id: <15129.9508172101@rahman.earth.ox.ac.uk> From: Keith Refson Subject: Re: CCL:Concerns with the Biosym/MSI merger To: chemistry@ccl.net Organisation: Earth Sciences Department, Oxford University. The question that immediately sprang to my mind on reading about the Biosym/MSI merger is "why?". What is the motivation for the two most direct competitors in this field to combine? The content-free managementese of the announcement certainly didn't give a clue. I imagine there must be a pretty strong motive for a step like this, since there are pretty strong disincentives for all kinds of reasons. Is the market not big enough for both of them, or is either in trouble? Or has some financial backer pulled a plug? Can anyone familiar with their balance sheets suggest a reason and comment on the financial stability of the new company? sincerely Keith Refson From stoutepf@chemsci5.dmpc.com Thu Aug 17 18:18:44 1995 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci5.dmpc.com by www.ccl.net (8.6.10/950810.1506) id SAA11071; Thu, 17 Aug 1995 18:04:57 -0400 Received: by gatekeeper.es.dupont.com; id AA14658; Thu, 17 Aug 95 18:04:53 -0400 Received: from [158.117.153.76] (esm153076) by chemsci5.dmpc.com (5.0/SMI-SVR4) id AA03542; Thu, 17 Aug 1995 18:03:52 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Organization: The DuPont Merck Pharmaceutical Company X-Mailer: Eudora Pro 2.1.3 for Macintosh X-Url: http://www.halcyon.com/stouten/index.html Date: Thu, 17 Aug 1995 18:06:48 -0400 To: chemistry@www.ccl.net From: stoutepf@chemsci5.dmpc.com (Pieter Stouten) Subject: Re: CCL:Concerns with the Biosym/MSI merger Content-Length: 892 How many different user interfaces will we get: Insight, Cerius2, Quanta, ....? Will all the functionality that is available under Insight be redistributed over the different interfaces? The real problem with MSI's software, IMHO, has always been that it is a collection of unrelated, not-integrated tools. I sure hope it won't get worse. -- ** Please note my new e-mail address: stoutepf@chemsci5.dmpc.com ** ** The old address (chemsci1) has stopped working on 7 August 1995 ** Pieter Stouten || Nothing shocks me; Computer Aided Drug Design Group || The DuPont Merck Pharmaceutical Company || I am a scientist! P.O. Box 80353, Wilmington, DE 19880-0353 || Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 2813 || Internet: stoutepf@chemsci5.dmpc.com || Indiana Jones From Karl.F.Moschner@urlus.sprint.com Thu Aug 17 19:18:45 1995 Received: from merit-mx1.telemail.net for Karl.F.Moschner@urlus.sprint.com by www.ccl.net (8.6.10/950810.1506) id TAA11917; Thu, 17 Aug 1995 19:16:49 -0400 From: X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 17 Aug 1995 18:04:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 17 Aug 1995 18:04:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 17 Aug 1995 18:04:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 17 Aug 1995 18:04:00 -0400 Date: Thu, 17 Aug 1995 18:04:00 -0400 X400-Originator: Karl.F.Moschner@urlus.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Thu Aug 17 18:04:20 199500] X400-Content-Type: P2-1984 (2) Content-Identifier: Biosym/MSI Merge Message-ID: <"Thu Aug 17 18:04:20 199500*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: chemistry@www.ccl.net Subject: Biosym/MSI Merger MIME-version: 1.0 Content-type: multipart/mixed; boundary="23T9LlajP0KsMg888TTzeawo3qh7nCjD" --23T9LlajP0KsMg888TTzeawo3qh7nCjD Content-type: text/plain; charset="us-ascii" While I share many of Dr. Jeff Nauss' concerns it will be a while before we can tell if the MSI-Biosym merger gives birth to a monster molecular modeling company. Clearly they represent the lions share of the $$ market, I'd guess 60%, but I doubt that reflects the relative usage of their offerings. Thus there will be needs that MSI-Biosym don't satisfy though there is obvious pressure to stick with a market leader particularly in an industrial setting. Obviously the announcement presages further clarifications at next weeks ACS meeting in Chicago (some may recall the fuss over the MS-Polgen merger during the ACS meeting in NYC several years ago). It also signals smaller, less well positioned companies that they had better stick to niche markets or seek alliances which will let them survive. But neither mergers nor specialization will guarantee success and further growth. Cutbacks in real chemical R&D spending, both academic and industrial, along with reductions in chemical employment require molecular modeling companies to improve the overall cost-effectiveness of their offerings. This is part icularly crucial if companies wish to expand the user base since the newer users are unlikely to spend $100K for software to run on a $5-20K workstation, yet they demand a wide range of capabilities. At the moment, I'm curious what MSI-Biosym will offer current customers and what their proposed future merged product (and company) will look like. I have my suspicions that they will eventually streamline the company significantly more than their product. On the whole, I think most users, particularly existing customers, will be winners in the deal. If they sense that they're being taken advantage of, they'll look for other opportunities. To ensure the best outcome, users will have to provide their input. So "offer encouraging suggestions" either at next weeks ACS meeting in Chicago or through your local sales rep. Just be a bit patient because, right now, the phones lines and e-mail routes are probably jammed. And remember, keep demanding data portability (we're not there yet) so you can move to another application...if pushed! Best of luck! Karl _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ --23T9LlajP0KsMg888TTzeawo3qh7nCjD Content-type: text/plain; charset="us-ascii" --23T9LlajP0KsMg888TTzeawo3qh7nCjD-- From adler@pulsar.cs.wku.edu Thu Aug 17 20:03:45 1995 Received: from WKUVX1.WKU.EDU for adler@pulsar.cs.wku.edu by www.ccl.net (8.6.10/950810.1506) id UAA12434; Thu, 17 Aug 1995 20:01:42 -0400 Received: from pulsar.cs.wku.edu by WKUVX1.WKU.EDU (MX V4.1 VAX) with SMTP; Thu, 17 Aug 1995 19:03:12 CDT Received: by pulsar.cs.wku.edu (5.0/SMI-SVR4) id AA12525; Thu, 17 Aug 1995 19:00:14 -0500 From: adler@pulsar.cs.wku.edu (Allen Adler) Message-ID: <9508180000.AA12525@pulsar.cs.wku.edu> Subject: Merger To: chemistry@www.ccl.net Date: Thu, 17 Aug 1995 19:00:13 -0500 (CDT) X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 584 The recent discussion on the significance of the merger of two companies which market molecular modeling software has rekindled my interest in a certain question, namely: why is everyone bothering with canned commercial software? I much prefer to see free software, distributed with complete source code according to the GNU public license agreement and supported by its user community. It just seems as though anything less than that standard amounts to buying a pig in a poke. From that standpoint, who cares if these companies merge or not? Allan Adler adler@pulsar.cs.wku.edu From ross@cgl.ucsf.EDU Thu Aug 17 22:18:47 1995 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.6.10/950810.1506) id WAA13441; Thu, 17 Aug 1995 22:14:13 -0400 From: Received: (from ross@localhost) by socrates.ucsf.EDU (8.6.12/GSC4.24) id TAA03813 for chemistry@www.ccl.net; Thu, 17 Aug 1995 19:14:12 -0700 Date: Thu, 17 Aug 1995 19:14:12 -0700 Message-Id: <199508180214.TAA03813@socrates.ucsf.EDU> To: chemistry@www.ccl.net Subject: merging & black boxes and let's hope, that AMBER will be still around before it becomes a black box. Michael Kotelyanskii PhD To allay any such fears: we have no intention of making AMBER a black box - one of its major strengths has been that source code is provided, and this has helped attract excellent feedback and collaborations from the user community, as well as drawing requests from hardware vendors to include it in the SPEC benchmarks (it is now at the 'candidate' level and we don't know if it will actually be included). When we drew up an agreement with Oxford Molecular to allow them to also distribute AMBER, one of the first stipulations was that they would provide source in addition to their executables. Incidentally, we don't provide executables ourselves (although we can ship the OM CD), but AMBER includes a very portable compilation scheme for FORTRAN - the user just chooses a machine compatibilty file - which we have put in the public domain. See http://www.amber.ucsf.edu/amber/amber.html. Bill Ross Kollman lab University of California, San Francisco