From thomas_w@btm2x2.mat.uni-bayreuth.de Thu Apr 27 03:01:01 1995 Received: from btr0x1.hrz.uni-bayreuth.de for thomas_w@btm2x2.mat.uni-bayreuth.de by www.ccl.net (8.6.10/930601.1506) id DAA11671; Thu, 27 Apr 1995 03:00:40 -0400 Received: from btm2x2.mat.uni-bayreuth.de by btr0x1.hrz.uni-bayreuth.de (4.1/btr0x1 (UBTGW/btr0x1-2.4.7)) id AA16080; Thu, 27 Apr 95 08:42:24 +0200 Received: by btm2x2.mat.uni-bayreuth.de (4.1/SMI-4.1) id AA06521; Thu, 27 Apr 95 08:41:53 +0200 Date: Thu, 27 Apr 95 08:41:53 +0200 From: thomas_w@btm2x2.mat.uni-bayreuth.de (Thomas Wieland) Message-Id: <9504270641.AA06521@btm2x2.mat.uni-bayreuth.de> To: chemistry@ccl.net Subject: Methods for converting internal to external coordinates A colleague of mine is looking for conversion methods from internal to external 3D-coordinates. Given a set of points, their distances, angles and dihedral angles, he wants to compute Cartesian coordinates in space. We know that this routine is implemented in many packages and to avoid reinventing the wheel we wondered if somebody out there could point us to a description of the method (no code or complete program since it shall be adapted to our own data structure). What we already know is MOPAC on the one hand, which, however, has a slightly different approach, and BABEL on the other hand, which also tells nothing about the underlying methods. Thanks a lot, Thomas From davide@stinch0.csmtbo.mi.cnr.it Thu Apr 27 04:46:02 1995 Received: from stinch0.csmtbo.mi.cnr.it for davide@stinch0.csmtbo.mi.cnr.it by www.ccl.net (8.6.10/930601.1506) id EAA12794; Thu, 27 Apr 1995 04:41:49 -0400 Received: by stinch0.csmtbo.mi.cnr.it (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@ccl.net id AA23389; Thu, 27 Apr 95 10:33:54 +0200 Date: Thu, 27 Apr 95 10:33:54 +0200 From: davide@stinch0.csmtbo.mi.cnr.it (Davide Proserpio) Message-Id: <9504270833.AA23389@stinch0.csmtbo.mi.cnr.it> To: CHEMISTRY@ccl.net Subject: QSAR and electrophilicity Dear Netters: I am interested in correlating (QSAR) the electrophilicity of a carbonly in a series of alpha-keto compounds to their biological activity. Does anyone know if there have been any theorectical studies on the electrophilicity of a carbonyl in a nucleophilic attack reaction? Thank you Davide ------------------------------------------------------------------- Davide M. Proserpio Dipartimento di Chimica Strutturale e Stereochimica Inorganica Universita' di Milano, Via Venezian, 21 - 20133 Milano, Italy phone +39-2-70635120 fax 70635288 - davide@stinch.csmtbo.mi.cnr.it ------------------------------------------------------------------- From iaapeorm@vp.ehu.es Thu Apr 27 05:46:02 1995 Received: from vphx00.vp.ehu.es for iaapeorm@vp.ehu.es by www.ccl.net (8.6.10/930601.1506) id FAA13017; Thu, 27 Apr 1995 05:35:06 -0400 Received: by vphx00.vp.ehu.es (1.37.109.4/16.2) id AA23361; Thu, 27 Apr 95 11:44:12 +0200 Date: Thu, 27 Apr 1995 11:42:15 +0200 (METDST) From: Perez Ortiz de Elguea Miguel Angel Subject: looking for Chemical *engineer* software To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thu 27 April 1995 Dear netters, I'm a Chemical Engineer that I have 'listening' the messages of CCL list since March. I joined this list because I was looking for Chemical Engineer Software (free of charge or shareware). I have discovered that in this list the people speak about chemical software and not Ch. Engineer software.(*) So, any body out there know a place (list) where I can found matters about chemical _Engineer_ sotware (PC computers), especially programs for material and energy balance? (*) This is not a criticism I think the job maded by the netters in this list is excellent. Any information is welcome, thanks in advance Miguel Angel Perez \\////// .-------------------------------------------. \\ / \ .oOO| "Quibus vivere est cogitare" (Ciceron) | C C C `-------------------------------------------' \ > Miguel Angel Perez -- an engineer from Spain \ _ iaapeorm@vp.ehu.es (Internet) ----------\_|--------------------------------------------------- From SIEW@vms.huji.ac.il Thu Apr 27 08:01:04 1995 Received: from VMS.HUJI.AC.IL for SIEW@vms.huji.ac.il by www.ccl.net (8.6.10/930601.1506) id HAA14129; Thu, 27 Apr 1995 07:57:45 -0400 Received: by HUJIVMS (HUyMail-V7b); Thu, 27 Apr 95 14:57:42 +0200 Received: by HUJIVMS (HUyMail-V7b); Thu, 27 Apr 95 14:46:38 +0200 Date: Thu, 27 Apr 95 14:46 +0200 Message-id: <27040095144625@HUJIVMS> From: To: chemistry@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: hydrophobicity profile Dear CCLers, When doing a hydrophobicity profile for a protein, it is recommended to use a smoothing window. What are the advantages in using different window sizes? How do I interpret the results I get from using a 19 residue long window compared with a 5 residues long one? Thank-you for your help, Naomi Siew siew@vms.huji.ac.il From Karl.F.Moschner@urlus.sprint.com Thu Apr 27 08:31:04 1995 Received: from sprintf.merit.edu for Karl.F.Moschner@urlus.sprint.com by www.ccl.net (8.6.10/930601.1506) id IAA14473; Thu, 27 Apr 1995 08:16:31 -0400 X400-Received: by mta merit in /PRMD=internet/ADMD=telemail/C=us/; Relayed; Thu, 27 Apr 1995 08:14:35 -0400 X400-Received: by /ADMD=TELEMAIL/C=US/; Relayed; Thu, 27 Apr 1995 08:12:08 -0400 X400-Received: by /PRMD=SMXFL2/ADMD=TELEMAIL/C=US/; Relayed; Thu, 27 Apr 1995 08:18:03 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 27 Apr 1995 08:17:00 -0400 Date: Thu, 27 Apr 1995 08:17:00 -0400 X400-Originator: Karl.F.Moschner@urlus.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Thu Apr 27 08:17:54 199500] X400-Content-Type: P2-1984 (2) Content-Identifier: Internal-Cartess From: Karl.F.Moschner@urlus.sprint.com Message-ID: <"Thu Apr 27 08:17:54 199500*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: CHEMISTRY@ccl.net, thomas_w@btm2x2.mat.uni-bayreuth.de Subject: Internal-Cartessian Coordinate Interconversion Try QCPE. It's a nice place to "shop". There are a series of programs for calculation of atomic coordinates. The most likely candidate is COORD QCPE#419, but there may also be a newer version. QCPE Creative Arts Building 181 Indiana University Bloomington, IN 47405 USA Phone: (812) 855-4784 FAX: (812) 855-5539 E-mail: qcpe@ucs.indiana.edu For information and catalogues: login: anonymous@qcpe6.chem.indiana.edu password: guest _______________________________________________________________________ / \ | 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 | \_______________________________________________________________________/ From osawa@cochem.tutkie.tut.ac.jp Thu Apr 27 08:46:06 1995 Received: from cochem2.cochem2.tutkie.tut.ac.jp for osawa@cochem.tutkie.tut.ac.jp by www.ccl.net (8.6.10/930601.1506) id IAA15250; Thu, 27 Apr 1995 08:41:12 -0400 Received: from [133.15.160.31] (cochem3.tutkie.tut.ac.jp [133.15.160.31]) by cochem2.cochem2.tutkie.tut.ac.jp (8.6.9+2.4Wb/3.3W9) with SMTP id VAA06359 for ; Thu, 27 Apr 1995 21:44:25 +0900 Date: Thu, 27 Apr 1995 21:44:25 +0900 Message-Id: <199504271244.VAA06359@cochem2.cochem2.tutkie.tut.ac.jp> To: chemistry@ccl.net From: osawa@cochem.tutkie.tut.ac.jp (Eiji Osawa) X-Sender: osawa@cochem2.tutkie.tut.ac.jp Subject: Dr. Raghavachari's address MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8-J13) Dear Netters: Does anyone knows Dr. K. Raghavachari's e-mail address? With thanks in advance, Eiji Osawa /************************************************* * Eiji Osawa * Department of Knowledge-based Information Engineering * Toyohashi University of Technology * Aichi 441, Japan * Phone: x-81-532-47-0111(ex. 853) * FAX: x-81-532-48-5588 * E-mail: osawa@cochem.tutkie.tut.ac.jp *************************************************/ From gotwals@mcnc.org Thu Apr 27 08:46:11 1995 Received: from robin.mcnc.org.mcnc.org for gotwals@mcnc.org by www.ccl.net (8.6.10/930601.1506) id IAA15280; Thu, 27 Apr 1995 08:43:23 -0400 Received: from [128.109.178.10] by robin.mcnc.org.mcnc.org (8.6.9/MCNC/8-10-92) id IAA01123; Thu, 27 Apr 1995 08:43:20 -0400 for Date: Thu, 27 Apr 1995 08:43:20 -0400 Message-Id: <199504271243.IAA01123@robin.mcnc.org.mcnc.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemconf@umdd.umd.edu, chemistry@ccl.net From: gotwals@mcnc.org (Bob Gotwals) Subject: Computational Chemistry Course online The North Carolina Supercomputing Center (NCSC), with funding support from Glaxo/Wellcome in Research Triangle Park, NC, is pleased to offer an on-line course entitled "Computational Chemistry for Chemistry Educators". This course is intended for secondary, community college and undergraduate educators of chemistry. The course interface (minus the sessions!) can be viewed by setting your World Wide Web browser to this URL: http://tfnet.ils.unc.edu/~gotwals/cc.html Description of the workshop: The goal of this course is to introduce chemistry educators to computational techniques in quantum chemistry. The course is intended as an enrichment activity, designed to help educators understand the use of high-performance computing tools and their role in chemical research. Educators are not expected to integrate these technologies into their teaching activities, but the course will offer discussions on how this might be accomplished for those educators interested in doing so. Using commercial third-party software (Gaussian94) resident on the North Carolina Supercomputing Center's Cray T3D supercomputer (and a cluster of workstations), educators will investigate, using computational tools, techniques, and technologies, a number of chemical properties, such as single-point energies, geometry optimizations, and frequency calculations. Participants will also have the opportunity to complete a number of case studies Prerequisites: Educators must have access to the Internet via the World Wide Web (WWW), preferably using Netscape 1.1. Text-based access (i.e., via lynx) is inadequate. Access assumes electronic mail capabilities. Educators should also have a basic background in quantum chemistry and atomic structure. Completion of a basic course in physical chemistry at the undergraduate level is the appropriate level. A solid mathematics background, particularly in calculus, is helpful but not mandatory. Participants should also have basic computer literacy skills: use of a word processor, basic understanding of the concepts of an operating system, keyboarding skills, etc. A UNIX background is helpful but not required. No programming skills are required. Workshop Logistics: The course is designed as a self-paced "seminar" series, consisting of 15 sessions. Each week, a new topic and assignment will be posted to the World Wide Web. Students need to complete the reading and assignment, ask questions via electronic mail, and submit their work via email to the course instructor. Students will be able to interact via an email discussion list (listserv). All reading materials and resources are available electronically, although the use of a basic physical chemistry textbook (Atkins is recommended) is strongly advised. Access to the lessons and the supercomputer will begin on May 30, 1995, and will close on October 6, 1995. The course instructor will be available for electronic support during that period. The fee for this activity is $50. Tuition will be used to defray the costs of computing time on the supercomputer. As there is limited enrollment, participants are asked to give considerable consideration to their commitment PRIOR to registering for this activity. The course will require time (roughly four to five hours per week), effort, and intellectual energy. To register for this course, complete the form below and email it to Robert R. Gotwals (gotwals@mcnc.org). There is limited enrollment in this course. Registration is on a first-come, first-serve basis. Please feel free to send questions about this course to gotwals@mcnc.org Tentative Schedule: Session 1: Overview of Computational Chemistry Session 2: Using Gaussian94 on the Cray supercomputer; creating and submitting G94 input files Session 3: Basis sets and approximations; Input file options; Calculating Single Point Energies Session 4: Single Point Energies. Analyzing output files Session 5: Case Study: Energies of Isomers Session 6: Geometry Optimizations Session 7: Geometry Optimizations Session 8: Potential Energy Scans Session 9: Frequency Calculations Session 10: Frequency Calculations Session 11: Case Study 1 Session 12: Case Study 2 Session 13: Case Study 3 Session 14: Overview of other tools for computational chemistry; Classroom integration Session 15: "Final Exam"; Course Wrap-up / Evaluation ****************************************************************** "Computational Chemistry for Chemistry Educators" Registration Form Last Name: First Name: Position: Phone: Curriculum Area: Primary Courses Taught (intro, AP Chem., etc.) School: District( if appropriate): School Address: FAX: E-mail Address: Degree(s): BS [ ] MS [ ] Doctorate [ ] Other [ ] Subject area(s) of degree(s): Years of Teaching Experience: 1-5 [ ] 6-10 [ ] 11-15 [ ] >16 [ ] Years of Technology Experience: 1-5 [ ] 6-10 [ ] 11-15 [ ] Do you own your own computer system? Yes [ ] No [ ] If yes, indicate the hardware platform: Describe the hardware you will use to access the Web lessons: Describe your chemistry, mathematics, and computing background (coursework, workshops, experiences, etc.) Return this registration form to Robert R. Gotwals, Jr. (gotwals@mcnc.org) or by FAX (919) 248-1101. Send tuition check or PO to: Faye McLean Ellis Course Registrar North Carolina Supercomputing Center 3021 Cornwallis Road Research Triangle Park, NC 27709 From polowin@hyper.hyper.com Thu Apr 27 10:46:07 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id KAA17448; Thu, 27 Apr 1995 10:34:15 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id KAA09522 for <@www.hyper.com:CHEMISTRY@ccl.net>; Thu, 27 Apr 1995 10:28:02 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@ccl.net id AA03879; Thu, 27 Apr 95 10:46:58 -0400 Date: Thu, 27 Apr 95 10:46:58 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9504271446.AA03879@hyper.hyper.com> To: CHEMISTRY@ccl.net Subject: Re: Nine bits v. Eight > Date: Tue, 25 Apr 1995 17:08:57 -0400 (EDT) > From: Friedman > Subject: CCL:Nine bits v. Eight > > We are purchasing a pentium 100MHZ PC to speed up our runs using Hyperchem > and Gaussian 92W/DFT. I was alerted by several people that many of the newer > PCs use 8 bit SIMMs now. I've gotten differing opinions on whether parity > checking is needed. I would appreciate hearing from anyone with an informed > opinion as to the risks (no pun) involved. Hypercube and Gaussian boffins > especially welcome. I relayed the question to our hardware expert, Edmund Lam. He responded: --------- In the past, PC used 9 bit wide RAM. This architecture was used to ensure detection of RAM errors. In recent times, the quality of RAM and mainboards have curved the need for parity detection. MACs have always run 8 bit wide RAM. Workstations such as the Sparcs also use 8 bit wide RAM. The extra bit can be used to detect a memory error, but is not sufficient to correct it. ---------- My own experience with parity checking was a PC that I ended up lugging back and forth to and from the shop for nearly a year because it kept giving me "Parity error -- system halted" crashes at home but worked fine at the shop. Shop kept claiming it was a problem with the RAM, and replacing the chips. Took them a year to clue in that the problem was actually with the motherboard; after they replaced *that*, the machine gave no more trouble. Whether that little story argues FOR or AGAINST the merits of parity-checking is something I'll leave for others to sort out. :-) Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From umcshah@uxa.ecn.bgu.edu Thu Apr 27 13:16:09 1995 Received: from ecom3.ecn.bgu.edu for umcshah@uxa.ecn.bgu.edu by www.ccl.net (8.6.10/930601.1506) id NAA29737; Thu, 27 Apr 1995 13:02:28 -0400 Received: by ecom3.ecn.bgu.edu id AA23837 (5.67a/IDA-1.5 for chemistry@ccl.net); Thu, 27 Apr 1995 12:01:06 -0500 Date: Thu, 27 Apr 1995 12:01:05 -0500 (CDT) From: Milan Shah Subject: Hyperchem and intermediates To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Is it possible to model an intermediate for an organic reaction through the use of Hyperchem? Send any observations or commentary to Milan C. Shah at ( umcshah@uxa.ecn.bgu.edu ). A summary will be provided. Thanks beforehand. From gotwals@mcnc.org Thu Apr 27 14:01:09 1995 Received: from robin.mcnc.org.mcnc.org for gotwals@mcnc.org by www.ccl.net (8.6.10/930601.1506) id NAA01459; Thu, 27 Apr 1995 13:59:41 -0400 Received: from [128.109.178.10] by robin.mcnc.org.mcnc.org (8.6.9/MCNC/8-10-92) id NAA26105; Thu, 27 Apr 1995 13:59:40 -0400 for Date: Thu, 27 Apr 1995 13:59:40 -0400 Message-Id: <199504271759.NAA26105@robin.mcnc.org.mcnc.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@ccl.net From: gotwals@mcnc.org (Bob Gotwals) Subject: Clarification on CompChem Online Course Friends, The course description for "Computational Chemistry for Chemistry Educators" should have said that Gaussian94 is on the Cray Y-MP, **NOT** on the T3D. There IS no Gaussian94 on the T3D at this time....I've been working on T3D training materials, so I have T3D on the brain....apologies for any confusion. Appropriate flames sent this way (but NOT to the list) gladly accepted! From polowin@hyper.hyper.com Thu Apr 27 15:31:09 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id PAA03129; Thu, 27 Apr 1995 15:24:43 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id PAA10265 for <@www.hyper.com:CHEMISTRY@ccl.net>; Thu, 27 Apr 1995 15:18:28 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@ccl.net id AA05553; Thu, 27 Apr 95 15:37:25 -0400 Date: Thu, 27 Apr 95 15:37:25 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9504271937.AA05553@hyper.hyper.com> To: CHEMISTRY@ccl.net Subject: Re: Hyperchem and intermediates > Date: Thu, 27 Apr 1995 12:01:05 -0500 (CDT) > From: Milan Shah > Subject: CCL:Hyperchem and intermediates > > Is it possible to model an intermediate for an organic > reaction through the use of Hyperchem? Send any observations or > commentary to Milan C. Shah at ( umcshah@uxa.ecn.bgu.edu ). A > summary will be provided. Thanks beforehand. There are a couple of ways of doing such things. For example, it is possible to run semi-empirical molecular dynamics calculations on two organic units such that they collide and react, giving products that separate from the site of reaction. By using the 'snapshot' option, the coordinates of the atoms are saved periodically during the simulation; then one can retrieve the configuration of the system at any point, including the period when the system is rearranging. The system could also be set up with a reasonable set of internal vibrations and rotations at the beginning of the simulation to give an appropriately complex model. One can also do semi-empirical minimization of the static system, with bond distances constrained to values that indicate the partial bonds of an intermediate. This sort of everything-minimized-but-partial-bonds model may or may not be a realistic description of a real chemical species; *I* tend to think not, since I favour a dynamic picture, but that's merely my personal opinion. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/