From slee@ccl.net Tue Jan 25 00:52:53 1994 Received: from mail.uunet.ca for slee@ccl.net by www.ccl.net (8.6.4/930601.1506) id AAA01306; Tue, 25 Jan 1994 00:04:36 -0500 Received: from hyper by mail.uunet.ca with UUCP id <128182(5)>; Mon, 24 Jan 1994 19:05:46 -0500 Received: by hyper.hyper.com (920330.SGI/890607.SGI) (for ccl.net!chemistry) id AA28404; Mon, 24 Jan 94 16:40:52 -0500 From: slee@ccl.net (Thomas Slee) Message-Id: <9401242140.AA28404@hyper.hyper.com> Subject: Re: HyperChem 3.0 To: chemistry@ccl.net Date: Mon, 24 Jan 1994 16:40:51 -0500 X-Mailer: ELM [version 2.3 PL9] Dear Netters, I answered Joe Landman's recent question about the HyperChem Release 3 snapshot file format offline to avoid bombarding this group with details that are of limited general interest. Anybody else who is interested in this reply please contact me directly. Tom Slee P.S. I also sent this message a few days ago, but we had mail problems (poor posties get blamed for everything). Sorry for the delay. -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 From slee@ccl.net Tue Jan 25 00:54:40 1994 Received: from mail.uunet.ca for slee@ccl.net by www.ccl.net (8.6.4/930601.1506) id XAA01272; Mon, 24 Jan 1994 23:58:16 -0500 Received: from hyper by mail.uunet.ca with UUCP id <127972(6)>; Mon, 24 Jan 1994 18:52:53 -0500 Received: by hyper.hyper.com (920330.SGI/890607.SGI) (for ccl.net!chemistry) id AA28325; Mon, 24 Jan 94 16:26:01 -0500 From: slee@ccl.net (Thomas Slee) Message-Id: <9401242126.AA28325@hyper.hyper.com> Subject: Re: MM+ in new HYPERCHEM To: chemistry@ccl.net Date: Mon, 24 Jan 1994 16:26:01 -0500 In-Reply-To: <3985.sfilipek@zoolook.chem.uw.edu.pl_POPMail_3.1.8>; from "Slawomir Filipek" at Jan 24, 94 6:44 am X-Mailer: ELM [version 2.3 PL9] Slawomir Filipek writes... | | When I used MM+ in the new version 3.0 of HyperChem I got the following: | O | compound: R1-N-C-N-R2 R1=R2 (identical topology and charges) | H H | results (single point of energy for part of molecule): | | MM+ (bond dipoles) MM+ (atomic charges) AMBER OPLS | ------------------------------------------------------------ | R1 -1. -5. -37. -40. | R2 -3. -437. -39. -46. | HyperChem questions may be better dealt with on the HyperChem e-mail group (join at hyperchem-request@autodesk.com). The energy for the atomic charges calculation depends on how those charges are generated. Did you assign charges manually, or from an SCF calculation, or from ChemPlus? Please let me know details via e-mail (better not to the whole list) and I'll look into it further for you. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 From yam@crystal.pc.uec.ac.jp Tue Jan 25 04:52:56 1994 Received: from les.pc.uec.ac.jp for yam@crystal.pc.uec.ac.jp by www.ccl.net (8.6.4/930601.1506) id DAA02191; Tue, 25 Jan 1994 03:59:35 -0500 Received: from crystal.pc.uec.ac.jp by les.pc.uec.ac.jp (5.61/6.4J.6-pcgwy.pc.uec.ac.jp-2.4) id AA18866; Tue, 25 Jan 94 17:59:24 +0900 Received: by crystal.pc.uec.ac.jp (4.1/6.4J.6) id AA04244; Tue, 25 Jan 94 17:57:09 JST Date: Tue, 25 Jan 94 17:57:09 JST From: yam@crystal.pc.uec.ac.jp (Norimasa Yamazaki) Message-Id: <9401250857.AA04244@crystal.pc.uec.ac.jp> To: CHEMISTRY@ccl.net Subject: ORTEP Mac version Dear netters; For those who are using my version of ORTEP for Macintosh and for those who are looking for it, here is the updated version. ftp.cc.uec.ac.jp: ortep/ortep15.mac.sit.hqx Best regards, Norimasa Yamazaki University of Electro-Communications, Tokyo, Japan yam@crystal.pc.uec.ac.jp P.S. There is another ORTEP for Macintosh. It is called 'MacOrtep', written by French colleagues. It has much Macintosh-like feature than my ortep has. You can find it on some anonymous ftp sites, for example, www.ccl.net: pub/chemistry/software/ORTEP directory. From ferenc@rchsg8.chemie.uni-regensburg.de Tue Jan 25 07:52:59 1994 Received: from rrzs1.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id HAA03045; Tue, 25 Jan 1994 07:20:05 -0500 Received: from rchsg8.chemie.uni-regensburg.de by rrzs1.rz.uni-regensburg.de (4.1/URRZ-relay (1.4)) id AA28829; Tue, 25 Jan 94 13:19:56 +0100 Received: by rchsg8.chemie.uni-regensburg.de (920330.SGI/BelWue-1.0SG(subsidiary)) (for CHEMISTRY@ccl.net) id AA18440; Tue, 25 Jan 94 13:21:21 +0100 Date: Tue, 25 Jan 94 13:21:21 +0100 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9401251221.AA18440@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: C6H5O2 Dear Netters: I post this to the net because I cannot reach Dr. Stewart through email (jstewart@fai.com does not work, user unknown). Would anybody, who can reach him, forward this mail. Thanks a lot. Ferenc Dr. Stewart: I tried an optimization of the geometry you posted. The direct route was not possible, so I decided to optimize with UHF first. I used the achieved geometry as an input to the RHF calculation. The AM1 Hamiltonian was used but not MOPAC. I personally prefer VAMP (vectorized derivate of early AMPAC). If you are interested I will send you both the files of the UHF and RHF calculation. The RHF calculation had a gnorm of about 2.4 and indicates a non-planar structure. Yours Sincerely, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): ferenc@rchsg8.chemie.uni-regensburg.de c5071@rchs1.chemie.uni-regensburg.de ferenc@rchnw2.ngate.uni-regensburg.de --------------------------------------------------------------------------- :-) There is more to live than increasing its speed. -- Ghandi ;-) --------------------------------------------------------------------------- From jwcnmr@watson.ibm.com Tue Jan 25 08:53:11 1994 Received: from watson.ibm.com for jwcnmr@watson.ibm.com by www.ccl.net (8.6.4/930601.1506) id IAA03395; Tue, 25 Jan 1994 08:15:14 -0500 Received: from WATSON by watson.ibm.com (IBM VM SMTP V2R3) with BSMTP id 3863; Tue, 25 Jan 94 08:15:06 EST Received: from YKTVMH by watson.vnet.ibm.com with "VAGENT.V1.0" id 5788; Tue, 25 Jan 1994 08:14:52 EST Received: from FLAHDO.watson.ibm.com by yktvmh.watson.ibm.com (IBM VM SMTP V2R3) with TCP; Tue, 25 Jan 94 08:12:47 EST Received: by FLAHDO.watson.ibm.com (IBM OS/2 SENDMAIL 1.2.10/) id AA0253; Tue, 25 Jan 94 08:12:58 -0500 Message-Id: <9401251312.AA0253@FLAHDO.watson.ibm.com> Date: Tue, 25 Jan 94 08:12:00 EST From: "James W. Cooper, Ph.D." To: chemistry@ccl.net Subject: abstract forms X-External-Networks: yes I have made up a color AmiPro style sheet file which can be used as a template for ACS abstracts. You can request it from me. James W. Cooper Manager of Programming and Scientific Solutions We're not opening old Windows, we're opening new doors: to Fibber McGee's Closet! From J_BROWN@uvmvax.uvm.edu Tue Jan 25 08:54:24 1994 Received: from uvmvax for J_BROWN@uvmvax.uvm.edu by www.ccl.net (8.6.4/930601.1506) id IAA03613; Tue, 25 Jan 1994 08:48:21 -0500 From: Received: from uvmvax.uvm.edu by uvmvax.uvm.edu (PMDF #12059) id <01H83DPQUPLC001UMN@uvmvax.uvm.edu>; Tue, 25 Jan 1994 08:45 EST Date: Tue, 25 Jan 1994 08:45 EST Subject: Requesting code to convert MM2 input file into MM3 input file To: chemistry@ccl.net Message-id: <01H83DPQUPLC001UMN@uvmvax.uvm.edu> X-VMS-To: IN%"chemistry@ccl.net" Has anyone developed code that will convert MM2(87) input files into MM3 format. I understand that MM3 will read MM2(87) format, however, MM3 also strips away the lone pairs and renumbers the atoms. We are studying systems with multiple nitrogens and keeping tract of the renumbered atoms has become very difficult, especially for complex driver calculations. Thank you, Jay Brown From kcross@cas.org Tue Jan 25 09:53:02 1994 Received: from srv01s4.cas.org for kcross@cas.org by www.ccl.net (8.6.4/930601.1506) id JAA03967; Tue, 25 Jan 1994 09:21:03 -0500 Date: Tue, 25 Jan 94 09:20:31 EST From: kcross@cas.org (Kevin P. Cross Ext. 3192) Message-Id: <9401250920.AA20906@cas.org> Subject: Re: ACS abstract form In-Reply-To: Your message of Mon, 24 Jan 94 18:19:39 -0500 To: friedman@tammy.harvard.edu Cc: chemistry@ccl.net Dawn and list folks: There is no online source for ACS abstracts but you can get them from the ACS. It includes instructions. It would be difficult to create an online version of this form as it includes "blue lines" for aligning text that do not show up when photographed. This allows the abstracts to be in camera-ready format when submitted (i.e. not retyped). Send me your address and I will send you as many as you like. However, keep in mind that the deadline for abstract submissions for the Spring ACS meeting has past. Division chairs had to submit their sessions for publication last December. These deadlines are published in C&E news. The Spring ACS program should be published in one of the next issues of C&E News. It will include titles and speakers but not abstracts. Sincerely, Kevin P. Cross, Ph.D. ================================================ Kevin P. Cross, Ph.D. Senior Associate Research Scientist Systems Development Chemical Abstracts Service (American Chemical Society) 2540 Olentangy River Road P.O. Box 3012 Columbus, OH 43210 kcross@cas.org (800)-848-6538 Ext. 3192 FAX:(614)-447-3750 ================================================ From chemistry-request@ccl.net Mon Jan 24 19:00:30 1994 Errors-To: jkl@ccl.net Errors-To: jkl@ccl.net Date: Mon, 24 Jan 94 18:19:39 -0500 From: friedman@tammy.harvard.edu (Dawn Friedman) Message-Id: <9401242319.AA01554@tammy.harvard.edu> To: chemistry@ccl.net Subject: ACS abstract form Cc: friedman@tammy.harvard.edu Sender: chemistry-request@ccl.net Errors-To: jkl@ccl.net Precedence: bulk Is there an online submission process for abstracts for posters at upcoming ACS conferences? Is there an online source for abstract forms? Is there an online source for abstract instructions? Is there a FAST real-world source for abstract forms? They're like hens' teeth around here, and the only one I could find was from 1984 and looks like an income tax sheet. Thanks, Dawn ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net (port 70 or 73) Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search From ackerman@theochem.tu-muenchen.de Tue Jan 25 10:53:12 1994 Received: from theo1.theochem.tu-muenchen.de for ackerman@theochem.tu-muenchen.de by www.ccl.net (8.6.4/930601.1506) id KAA04506; Tue, 25 Jan 1994 10:02:25 -0500 Received: from theo80.theochem.tu-muenchen.de by theo1.theochem.tu-muenchen.de (5.64/1.34) id AA01727; Tue, 25 Jan 94 16:02:41 +0100 Received: by theo80.theochem.tu-muenchen.de (4.1/SMI-4.1) id AA10655; Tue, 25 Jan 94 16:02:39 +0100 Date: Tue, 25 Jan 94 16:02:39 +0100 From: ackerman@theochem.tu-muenchen.de (Lutz Ackermann) Message-Id: <9401251502.AA10655@theo80.theochem.tu-muenchen.de> To: CHEMISTRY@ccl.net Subject: molecular modelling of guanidinium/carboylate interaction Dear Netters! A biochemist, who uses Insight/Discover and Macromodel came along with an interesting question concerning molecular modelling. I pass it on to the net, hoping to find experts in this field. Here is the problem: The interaction of a guanidinium function and a carboxylate fnc was modelled using the software cited above (I do not know, which force fields they used). N---H - - - O / \ / \ R---N---C + - C---R \ / \ / N---H - - - O In either case they did not obtain a planar geometry. Indeed, the COO turns out to be almost perpendicular to the C(NH)2 plane, which is not, what one would intuitively assume to be realistic. So what might have gone wrong? They don't have any idea, and I (as a new- comer to the field of MM) only have some vague assumptions. If you have any experience with such systems, please contact me! Thank you! L. Ackermann ***************************************************** * * * Dr. Lutz Ackermann * * * * Lehrstuhl fuer Theoretische Chemie (TU Munich) * * Lichtenbergstr. 4 * * 85747 Garching * * Germany * * * * room Nr. 63103 * * Tel. (+49 +89) 3209 3602 * * Fax (+49 +89) 3209 3622 * * e-mail ackerman@theo1.theochem.tu-muenchen.de * * * ***************************************************** From hongma@mcnc.org Tue Jan 25 11:06:22 1994 Received: from robin.mcnc.org for hongma@mcnc.org by www.ccl.net (8.6.4/930601.1506) id KAA04753; Tue, 25 Jan 1994 10:31:03 -0500 Received: by robin.mcnc.org (5.59/MCNC/8-10-92) id AA13590; Tue, 25 Jan 94 10:31:00 -0500 for chemistry@ccl.net Date: Tue, 25 Jan 94 10:31:00 -0500 From: Hong Ma Message-Id: <9401251531.AA13590@robin.mcnc.org> To: chemistry@ccl.net Subject: Gaussian 92/DFT workshop ************************************************************************* INTRODUCTION TO GAUSSIAN: THEORY AND PRACTICE April 26-29, 1994 Presented by The North Carolina Supercomputing Center and Gaussian Inc. MCNC North Carolina Supercomputing Center 3021 Cornwallis Road Research Triangle Park, NC 27709-2889 North Carolina Supercomputing Center (NCSC) is pleased to offer "Introduction to Gaussian: Theory and Practice." This four day workshop will be presented in conjunction with Gaussian, Inc., on April 26-29, 1994 at NCSC in Research Triangle Park, North Carolina. The workshop provides an overview of the Gaussian software package and introduces participants to electronic structure methods. This workshop will also provide an exellent review for researchers currently active in the field. Attendance is open to researchers at all levels of academic, government and industrial research. Gaussian 92/DFT is a user-friendly set of programs for performing ab initio, density functional, and semi-empirical molecular orbital calculations. This workshop provides an introduction to the underlying theory along with practical pointers. All of the ab initio and density functional methods available in Gaussian 92 will be covered, along with discussion on choosing methods appropriate to the chemistry being studied. Additional topics will include estimating computer resource requirements and dealing with computational difficulties. INSTRUCTORS: Dr. Michael J. Frisch Lorentzian, Inc. Prof. H. Bernard Schlegel Wayne State University Prof. John A. Pople Northwestern University Dr. Douglas J. Fox Gaussian, Inc. AGENDA: o Building Gaussian Input Decks o Model Chemistries (basis sets, level of theory) o SCF Methods (RHF/UHF/ROHF, GVB, MCSCF) o Stability and Convergence of SCF Wavefunctions o Geometry Optimization: Techniques for Finding Energy Minima o Studying Transition States: Optimization and Reaction Paths o Electron Correlation Methods o Excited States via CI Singles o Interpretation of Results and Molecular Properties o Solvent Effects on Molecular Electronic Structure o Gaussian Utilities o Guidelines for Choosing Algorithms and Estimating Resources o Density Functional Methods TRAINING MATERIALS There will be hands-on sessions each day between the morning and afternoon lectures. Additional hands-on sessions will be available until the building closes at 5:00pm. Workshop participants will be provided with a class computer account, of limited allocation, on NCSC's CRAY Y-MP for use during the hands-on workshop sessions. Each workshop participant will also be provided a copy of the lecture notes, a copy of the Gaussian 92 User's Guide, and a copy of "Exploring Chemistry with Electronic Structure Methods: A Guide to Using Gaussian." THE TRAINING FACILITY Our training facility has 15 DEC Alpha AXP (OSF/1) workstations equipped with color monitors for state of the art graphics training. The number of students must be limited to allow adequate training to all attendees. GAUSSIAN 92/DFT AVAILABILITY Gaussian software is available on our CRAY Y-MP supercomputor to North Carolina academic and licensed commercial users. For account information, people from North Carolina academic institutions should send electronic mail to to request account information; interested corporate users should contact our Business Development Office at 919-248-1133. REGISTRATION Registration is first-come-first-served based upon receipt of payment and the completed registration form. Please fill out a separate form for each attendee and mail it to MCNC--Gaussian Workshop North Carolina Supercomputing Center Attn: Course Registrar P.O. Box 12889 3021 Cornwallis Road Research Triangle Park, NC 27709-2889 Cancellations must be made at least 2 weeks prior to course starting date to receive a refund. Hotel selections will be mailed to conference participants. Hotel, travel, and meals are at the separate expense of participants, except for lunches and refreshments which will be provided. DEADLINES: Receipt of Registration Materials: March 25, 1994 Receipt of Registration Fee: April 8, 1994 Receipt of Cancellations to receive refund: April 15, 1994 Receipt of Notification of Substitution: April 22, 1994 REGISTRATION FEE: $ 1,400 General Registration $ 1,200 Government or Nonprofit Organization $ 1,200 MCNC Partner* and For-Profit Company $ 1,000 MCNC Partner* and Government/Nonprofit Organization $ 150 Academic * Attendees employed and enrolled by a company having a partnership agreement with MCNC. This includes sponsors of the IAC, Supercomputing Collaborative Research Partnerships, and MCNC affiliated companies. REGISTRATION FORM: Name: Affiliation: Address: Telephone: Facsimile: E-Mail Address: Please indicate your Research Status (check one): Faculty _______ University Research Staff _______ Postdoctorate ______ University Non-Research Staff ______ Graduate Student ______ Government _______ Undergraduate Student _______ Industrial ______ Other ______ Payment method: -- Check or Money Order ( make payable to MCNC) -- Purchase Order (please attach) This notice is sent without warranty of any kind, expressed or implied by Gaussian, Inc. or MCNC. Gaussian and Gaussian 92 are trademarks of Gaussian, Inc. **************************************************************************** From mizan@rz.engin.umich.edu Tue Jan 25 11:44:22 1994 Received: from rz.engin.umich.edu for mizan@rz.engin.umich.edu by www.ccl.net (8.6.4/930601.1506) id LAA05266; Tue, 25 Jan 1994 11:00:59 -0500 Received: by rz.engin.umich.edu (5.67/1.35) id AA45443; Tue, 25 Jan 94 16:00:58 GMT Date: Tue, 25 Jan 94 16:00:58 GMT From: "Tahmid I. Mizan" Message-Id: <9401251600.AA45443@rz.engin.umich.edu> To: CHEMISTRY@ccl.net Subject: Summary on tape drives Here is a summary of the reply I received to my question about using tape drives for data storage Original question: ******************************************************************************* Hi Netters, I am thinking of buying a tape drive to backup my md simulation data from an IBM RS6000 machine. I would appreciate input and insight from any of you on the following: What make of tape drive is most reliable ? Are 4mm or 8mm tape drives better ? Which vendors are reputable in the market ? How can you get most out of the vendor in terms of after sales service ? Have you had any good/bad experiences with a particular kind of tape/drive? Any problems using unix archiving commands with the drives ? Any problems configuring the machine to recognize the device ? Loss of data during transfer or in storage ? Is it possible to read directly from the tape into an analysis program ? ******************************************************************************* From: nittoli@pokey.chem.sunysb.edu (Thomas Nittoli) We have been using Peripheral Solutions' 4 Gbyte tape drive (6 months) and their 1.2 Gbyte hard drive (~ 1 year). There have been no problems to date. They were very helpful with customizing the hard drive, which was useful. Thomas Nittoli Dept. of Chemistry State University of NY Stony Brook, NY 11794 Phone:(516)632-7854 FAX:(516)632-7960 nittoli@pokey.chem.sunysb.edu ******************************************************************************* m.sunysb.edu ******************************************************************************* From: Thomas Weimar hi, in my old lab we had a exabyte (8mm video) drive. at the beginning there were no problems. but sometimes it was not possible to extract big files (several hundret megabytes). now it is not working any more and we dont know why! so all of my old nmr and monte-carlo data on this tapes are gone! as far as i know, the so called DAT-drives are supposed to be much more saver. and they are faster and cheaper too. thats all i knew about this. thomas --------------------------------------------------------- * Thomas Weimar (Ph. D.) voice: 604 291 5650 * * Department of Chemistry fax : 604 291 3765 * * Simon Fraser University * * Burnaby, B.C. * * V5A 1S6, Canada e-mail: thomas_weimar@sfu.ca * --------------------------------------------------------- ******************************************************************************* From: Michael Sennett Hi, This is in response to your posting on the net re: tape drives. *****Official Disclaimer******* The following information is my opinion only and does not reflect the position of the US Government, US Army, or any other organization or person. ************ My advice would be not to use tape for your application. The problem with backing up MD runs to tape, in my experience, is that the data is not terribly accessible after you get it off of the disk. A better, albeit more costly solution, is read-write capable CD storage or WROM (write-read optical memory). We have one of these units that holds 650 Mb per disk (325/side) and appears to the system just like a hard disk. With the random access capability of the CD, it is much easier to get to your data. Write time is slow (compared to a hard disk) because the system makes a verification pass after writing, but reading data >from the disk is virtually indistinguishable from the hard drive despite a published access time of something like 50 ns. The cost of this unit was about $8000 in 1991 and the optical disks were about $300 ea. Costs may have come down. I have seen ads for WROM systems for the PC going for around $3000 recently. I don't know if workstation compatible drives cost more. Good luck. Mike Sennett ******************************************************************************* From: SBPM Marc GINGOLD With 4mm you can use the r flag of the tar command. They models which directly compress the archives => UP to 8GBytes ******************************************************************************* From: bayard@pixies.univ-lyon1.fr (BAYARD Francois) We have an old DAT from HP (1.3 Gigabytes), we bought it from another laboratory and it still work well (backup every day (incremental) and a full backup evry week. I hope this could be helpfull Francois BAYARD | e-mail bayard@pixies.univ-lyon1.fr | COMS - CNRS | tel (+33) 72 44 53 21 CPE - ESCIL - Bat 308 | 43 Bd du 11 Novembre 1918 | fax (+33) 72 44 28 52 F-69616 VILLEURBANNE - FRANCE | -------------------------------------------------------------------------- HP: means of course Hewlett Packard ******************************************************************************* END ******* T. Mizan , U of Michigan ************************************** From ferenc@rchsg8.chemie.uni-regensburg.de Tue Jan 25 12:58:24 1994 Received: from rrzs1.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id LAA05898; Tue, 25 Jan 1994 11:58:17 -0500 Received: from rchsg8.chemie.uni-regensburg.de by rrzs1.rz.uni-regensburg.de (4.1/URRZ-relay (1.4)) id AA01003; Tue, 25 Jan 94 17:57:58 +0100 Received: by rchsg8.chemie.uni-regensburg.de (920330.SGI/BelWue-1.0SG(subsidiary)) (for CHEMISTRY@ccl.net) id AA19250; Tue, 25 Jan 94 17:59:25 +0100 Date: Tue, 25 Jan 94 17:59:25 +0100 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9401251659.AA19250@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: solid state physics Dear netters, does anybody know about a forum discussing problems related to solid state physics?! I would appreciate some details on how to join. Thanks a lot. Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): ferenc@rchsg8.chemie.uni-regensburg.de c5071@rchs1.chemie.uni-regensburg.de ferenc@rchnw2.ngate.uni-regensburg.de --------------------------------------------------------------------------- :-) There is more to live than increasing its speed. -- Ghandi ;-) --------------------------------------------------------------------------- From burkhart@goodyear.com Tue Jan 25 13:01:08 1994 Received: from goodyear.com for burkhart@goodyear.com by www.ccl.net (8.6.4/930601.1506) id MAA05978; Tue, 25 Jan 1994 12:04:51 -0500 Received: from rdsrv2 (rdsrv2.goodyear.com) by goodyear.com (4.1/SMI-4.1) id AA23620; Tue, 25 Jan 94 12:04:49 EST Received: from rds325 by rdsrv2 (4.1/SMI-4.1) id AA09216; Tue, 25 Jan 94 12:04:48 EST Received: by rds325 (920330.SGI/920502.SGI.AUTO) for @rdsrv2:chemistry@ccl.net id AA10192; Tue, 25 Jan 94 12:04:21 -0500 Date: Tue, 25 Jan 94 12:04:21 -0500 From: burkhart@goodyear.com (Craig W. Burkhart) Message-Id: <9401251704.AA10192@rds325> To: chemistry@ccl.net Subject: Spartan in a Queued Environment... Dear netters: I'm looking to install a set of batch queues to execute Spartan jobs. I do all of my Spartan building/setup on an SGI 4D/35, but perform all the large-scale calculations on a pair of HP 735's. I need to install queues to allocate the resources on the HP 735's better than I'm doing now. Has anyone on the net modified the Spartan shell scripts to accomodate batch operation? If so, I would like to hear from you... Please send your responses directly to me at "cburkhart@goodyear.com", and I'll summarize for the net. Thanks in advance. -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D. Senior Research Chemist E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.3163 Research Center Fax: 216.796.3304 142 Goodyear Boulevard Akron, OH 44305 -------------------------------------------------------------------------- For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled - Feynman -------------------------------------------------------------------------- From vis@genny.gensia.com Tue Jan 25 13:44:21 1994 Received: from genny.gensia.com for vis@genny.gensia.com by www.ccl.net (8.6.4/930601.1506) id NAA06458; Tue, 25 Jan 1994 13:09:01 -0500 From: Received: by genny.gensia.com (930416.SGI/920502.SGI) for chemistry@ccl.net id AA08247; Tue, 25 Jan 94 09:07:46 -0800 Date: Tue, 25 Jan 1994 09:06:42 -0800 (PST) Subject: Quantum Chemistry Short Course To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Everybody, I received several responses (about the same workshop) for my query on Quantum Chemical Methods workshop held in Florida. It is coming up in May and is conducted by Quantum Theory Project (Univ. Florida). Please contact Yanke@qtp.ufl.edu if you are interested in attending the workshop (or shortcourse). vis@gensia.com From jkl@ccl.net Tue Jan 25 14:58:30 1994 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id NAA06730; Tue, 25 Jan 1994 13:46:39 -0500 From: Jan Labanowski Received: from localhost for jkl@ccl.net by krakow.ccl.net (8.6.4/920428.1525) id NAA04982; Tue, 25 Jan 1994 13:46:38 -0500 Date: Tue, 25 Jan 1994 13:46:38 -0500 Message-Id: <199401251846.NAA04982@krakow.ccl.net> To: ferenc@rchsg8.chemie.uni-regensburg.de Subject: electronic forums In-Reply-To: Mail from 'ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar)' dated: Tue, 25 Jan 94 17:59:25 +0100 Cc: CHEMISTRY@ccl.net, jkl@ccl.net ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) writes: >does anybody know about a forum discussing problems >related to solid state physics?! For the general information, in the archives of CCL on the www.ccl.net there is a directory: /pub/chemistry/info/academic-lists which collects the electronic conferences on various topics. Though there is no e-mail list specifically on solid state physics, some of them come close... Jan Labanowski jkl@ccl.net From tudor@wucmd.wustl.edu Tue Jan 25 15:44:24 1994 Received: from wugate.wustl.edu for tudor@wucmd.wustl.edu by www.ccl.net (8.6.4/930601.1506) id PAA08403; Tue, 25 Jan 1994 15:40:44 -0500 Received: by wugate.wustl.edu (5.67b+/WUSTL-0.3) with SMTP id AA08761; Tue, 25 Jan 1994 14:39:59 -0600 Received: by wucmd (911016.SGI/911001.SGI) for @wugate.wustl.edu:CHEMISTRY@ccl.net id AA08982; Tue, 25 Jan 94 19:21:56 GMT Date: Tue, 25 Jan 1994 12:58:35 -0600 (CST) From: Tudor Oprea Subject: Re: molecular modelling of guanidinium/carboylate interaction To: Lutz Ackermann Cc: CHEMISTRY@ccl.net In-Reply-To: <9401251502.AA10655@theo80.theochem.tu-muenchen.de> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 25 Jan 1994, Lutz Ackermann wrote: > Dear Netters! > > A biochemist, who uses Insight/Discover and Macromodel came along > with an interesting question concerning molecular modelling. I pass > it on to the net, hoping to find experts in this field. Here is > the problem: > > The interaction of a guanidinium function and a carboxylate fnc > was modelled using the software cited above (I do not know, which > force fields they used). > > > > N---H - - - O > / \ > / \ > R---N---C + - C---R > \ / > \ / > N---H - - - O > > In either case they did not obtain a planar geometry. Indeed, the > COO turns out to be almost perpendicular to the C(NH)2 plane, which > is not, what one would intuitively assume to be realistic. So what > might have gone wrong? They don't have any idea, and I (as a new- > comer to the field of MM) only have some vague assumptions. If > you have any experience with such systems, please contact me! > Thank you! > > > L. Ackermann > > * e-mail ackerman@theo1.theochem.tu-muenchen.de * I have tried to model this using the following molecules: CH3CH2CH2NHC(NH2)2 +1 CH3CH2CH2COO -1 I used the docking procedure from Cosmic, which centers the target molecule inside a sphere of 10 A radius (this case), and from uniformly spaced points (204 in total) sends the mobile molecule towards the center. The 'bullet' is initially oriented by simplex (rotations @ 60 degrees in all 3 axes), and the optimal orientation is simplexed towards the target. Butanoic acid was used as mobile molecule. The results favor slightly the perpendicular geometry, as shown with Insight & Macromodel. In this case, four hydrogen bonds are formed (each carboxyl oxygen is allowed to interact at less than 2.3 A with the two hydrogens depicted in the figure above). However, 1scf for the perpendicular and the planar geometries favors the planar one (using VAMP, the AM1 hamiltonian, and 0 formal charge on a closed shell system). I did not investigate further with QM. Statistics are given below (energies in kcal/mol, dist in A): E(Cosmic) E(AM1) dCg-Cc Hbonds # & dist NC--CO angle perpend -32.22 -79.11 3.51 4: 2.03, 1.94 78.3 1.85, 2.25 planar -31.60 -82.09 4.12 2: 1.88, 1.92 3.4 Tudor ========================== Tudor-Ionel Oprea = Tel. (1-314) 935 4672 = Research Associate = Fax. (1-314) 935 4979 = Washington University Center for Molecular Design = Email: = Lopata 510, Box 1099, One Brookings Drive = tudor@wucmd.wustl.edu = St.Louis MO 63130 ========================== From Jeffrey.Nauss@UC.Edu Tue Jan 25 16:44:23 1994 Received: from ROCK.SAN.UC.EDU for Jeffrey.Nauss@UC.Edu by www.ccl.net (8.6.4/930601.1506) id QAA09470; Tue, 25 Jan 1994 16:40:17 -0500 Received: from ucmodl.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.2-14 #4918) id <01H83UBGT36O94GAF9@UCBEH.SAN.UC.EDU>; Tue, 25 Jan 1994 16:40:04 EST Received: by ucmodl.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:ackerman@theochem.tu-muenchen.de id AA02269; Tue, 25 Jan 94 16:45:57 -0500 Date: Tue, 25 Jan 1994 16:45:57 -0500 From: Jeffrey.Nauss@UC.Edu (Jeffrey L. Nauss) Subject: Re: molecular modelling of guanidinium/carboylate interaction To: ackerman@theochem.tu-muenchen.de (Lutz Ackermann) Cc: CHEMISTRY@ccl.net Message-id: <9401252145.AA02269@ucmodl.che.uc.edu> Content-transfer-encoding: 7BIT Could these perpendicular arrangments be similar to the bifurcated hydrogen bonds observed in some x-ray crystal structures of DNA? I think they might be. Two references which come to mind are Fritsch and Westhof, JACS, vol 113, pg 8271 (1991) for a crystal structure and Mohan and Yathindra, J. Biomol. Struc. and Dyn. vol 9, pg 113 (1991) for a theoretical study of possible bifurcated hydrogen binds. Jeff Nauss ************************************************************************ * Dr. Jeffrey L. Nauss * Telephone: 513-556-0148 * * Department of Chemistry * Fax: 513-556-9239 * * University of Cincinnati * e-mail: Jeffrey.Nauss@UC.Edu * * Cincinnati, OH 45221-0172 * nauss@ucmodl.che.uc.edu * ************************************************************************ From palres.dnet.sandoz.com!bowlus@sandoz.com Tue Jan 25 19:44:25 1994 Received: from tigger.jvnc.net for palres.dnet.sandoz.com!bowlus@sandoz.com by www.ccl.net (8.6.4/930601.1506) id TAA10983; Tue, 25 Jan 1994 19:11:11 -0500 Received: from sndzeh.UUCP by tigger.jvnc.net with UUCP id AA23335 (5.65c/IDA-1.4.4); Tue, 25 Jan 1994 18:40:28 -0500 Message-Id: <199401252340.AA23335@tigger.jvnc.net> Date: Tue, 25 Jan 94 18:13:37 -0500 From: bowlus@palres.dnet.sandoz.com (Steve Bowlus) To: "ackerman@theochem.tu-muenchen.de"@SNDZEH.dnet.sandoz.com Cc: "chemistry@ccl.net"@SNDZEH.dnet.sandoz.com, BOWLUS@sandoz.com Subject: Guanidinium carboxylates 1. In MM, there are several ways to treat hydrogen bonds, and some of these do not give physically/biologically "real" models, although the energies work out fine. For instance, Sybyl's treatment of the HB is (I believe) purely electrostatic, with no directionality at all. So an argininium carboxylate can have all manner of geometries, so long as at least one N-H--O distance is reasonable. I address the problem by constraining the system to a desired (biologically reasonable ?) geometry. But this may just give me garbage, since I've told the forcefield that is what it is to produce. One might examine (or ask the vendor's tech support ) how the HB is modeled in the software. 2. At the semi-empirical level, I have gotten some truly wonderful geom- etries. . .I wonder where they came from. Full relaxation of a guanidin- ium carboxylate has given everything from the "standard model" hydrogen bonds, to systems in which the guanidinium is concave, and the carboxylate points into this dish (this latter with AM1). In this case, we decided a lysine would do just as well for the model we were developing. . . sb =========================================================================== Stephen B. Bowlus 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 ===========================================================================