From strajbl@silicon.karlov.mff.cuni.cz Tue May 9 04:04:45 1995 Received: from earn.cvut.cz for strajbl@silicon.karlov.mff.cuni.cz by www.ccl.net (8.6.10/930601.1506) id DAA16988; Tue, 9 May 1995 03:53:31 -0400 Received: from ns.karlov.mff.cuni.cz by earn.cvut.cz (IBM VM SMTP V2R1) with TCP; Tue, 09 May 95 09:55:17 MET Received: from silicon.karlov.mff.cuni.cz by ns.karlov.mff.cuni.cz id aa26771; 9 May 95 9:52 MESZ Received: by silicon.karlov.mff.cuni.cz (931110.SGI/930416.SGI) for @NS.KARLOV.MFF.CUNI.CZ:chemistry@ccl.net id AA15724; Tue, 9 May 95 00:27:42 -0700 From: Marek Strajbl Message-Id: <9505090027.ZM15722@silicon.karlov.mff.cuni.cz> Date: Tue, 9 May 1995 00:27:40 -0700 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Visualization of G92 output Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dears, Is there on the net available a simple graphic program (SGI or X-windows) just for visualization and measuring internal coordinates of a molecule (preferably from Gaussian output)? I need the program with the smallest possible memory demands . Thanks a lot to everyone who responds. Marek ---------- Marek Strajbl Institute of Physics of Charles University Ke Karlovu 5, Praha 2, 121 16 Czech Republic e-mail: strajbl@silicon.karlov.mff.cuni.cz ---------- From doherty@msc.edu Tue May 9 08:49:49 1995 Received: from noc.msc.edu for doherty@msc.edu by www.ccl.net (8.6.10/930601.1506) id IAA18957; Tue, 9 May 1995 08:45:33 -0400 Received: from uh.msc.edu by noc.msc.edu (5.65/MSC/v3.0.1(920324)) id AA24900; Tue, 9 May 95 07:45:20 -0500 From: doherty@msc.edu (David C. Doherty) Received: (doherty@localhost) by uh.msc.edu (8.6.8.1/8.6.6) id HAA11895; Tue, 9 May 1995 07:45:26 -0500 Message-Id: <199505091245.HAA11895@uh.msc.edu> Subject: Re: CCL:Visualization of G92 output To: strajbl@silicon.karlov.mff.cuni.cz (Marek Strajbl) Date: Tue, 9 May 1995 07:45:24 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <9505090027.ZM15722@silicon.karlov.mff.cuni.cz> from "Marek Strajbl" at May 9, 95 00:27:40 am X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 533 > >Dears, > >Is there on the net available a simple graphic program (SGI or X-windows) just >for visualization and measuring internal coordinates of a molecule (preferably >from Gaussian output)? I need the program with the smallest possible memory >demands . Thanks a lot to everyone who responds. > Give our program XMol a try. Get: ftp://ftp.msc.edu/pub/xmol/README for downloading and installation instructions. -- David C. Doherty Computational Scientist Cray Research, Inc. doherty@msc.edu 612.337.4302 From michael@argaman.tau.ac.il Tue May 9 09:34:51 1995 Received: from aristo.tau.ac.il for michael@argaman.tau.ac.il by www.ccl.net (8.6.10/930601.1506) id JAA19705; Tue, 9 May 1995 09:27:29 -0400 Received: from argaman.tau.ac.il by aristo.tau.ac.il with SMTP id AA19657 (5.67b/IDA-1.5 for <@aristo.tau.ac.il:CHEMISTRY@ccl.net>); Tue, 9 May 1995 16:27:08 +0300 Received: by argaman.tau.ac.il (931110.SGI/920502.SGI.AUTO) for @aristo.tau.ac.il:CHEMISTRY@ccl.net id AA00332; Tue, 9 May 95 16:27:05 +0300 Date: Tue, 9 May 95 16:27:05 +0300 From: michael@argaman.tau.ac.il (Michael shoken) Message-Id: <9505091327.AA00332@argaman.tau.ac.il> To: CHEMISTRY@ccl.net Subject: molecular modelling software for IBM PC Dear Netters, Is anyone aware of the IBM PC (486 or pentium) commercial software for doing molecular modelling ? Thank you in advance Michael Shokhen E-mail: michael@argaman.tau.ac.il From qftramos@usc.es Tue May 9 11:19:51 1995 Received: from uscmail.usc.es for qftramos@usc.es by www.ccl.net (8.6.10/930601.1506) id LAA21950; Tue, 9 May 1995 11:17:03 -0400 Received: by uscmail.usc.es (5.67b/1.34) id AA18096; Tue, 9 May 1995 17:20:45 +0200 Date: Tue, 9 May 1995 17:20:45 +0200 From: qftramos@usc.es (Antonio Fernandez Ramos) Message-Id: <199505091520.AA18096@uscmail.usc.es> To: chemistry@ccl.net Subject: Intermolecular minimitation I have a dimer intermolecular potential with several parameters; the variables are the distances between atoms. I want to optimize the intermolecular coordinates but keeping the intramolecular coordinates fixed, as well as two intermolecular coordinates, one angle and one distance. Is there any program available which will allow me to introduce the potential depending on the distances and the restrictions, and which will optimize the rest of the coordinates, and be easy to use? Thanks. From sylee@sorak.kaist.ac.kr Tue May 9 11:27:44 1995 Received: from sorak.kaist.ac.kr for sylee@sorak.kaist.ac.kr by www.ccl.net (8.6.10/930601.1506) id LAA21869; Tue, 9 May 1995 11:12:21 -0400 Received: (from sylee@localhost) by sorak.kaist.ac.kr (8.6.9H1/8.6.9) id AAA27731 for chemistry@ccl.net; Wed, 10 May 1995 00:12:23 +0900 Date: Wed, 10 May 1995 00:12:23 +0900 From: sang-yeon lee Message-Id: <199505091512.AAA27731@sorak.kaist.ac.kr> To: chemistry@ccl.net Subject: Seeking IR and Raman spectra simulating program. Dears , I am seeking a simple graphic program (IBM-PC or X-windows) just for simulation of IR and/or Raman spectra using the calculated results ( from Gaussian output ). If you have such a program that you can share with me or can direct me any FTP sites from where such programs can be downloaded, send infomation to sylee@sorak.kaist.ac.kr Thank in advance everyone who responds. Sang Yeon. ---------- Sang Yeon Lee Center for Molecular Science Korea Advanced Institute of Science and Technology. Taejon, 305-701, Rep. of Korea. e-mail: sylee@sorak.kaiat.ac.kr ---------- From choic@gusun.acc.georgetown.edu Tue May 9 11:49:52 1995 Received: from gusun.acc.georgetown.edu for choic@gusun.acc.georgetown.edu by www.ccl.net (8.6.10/930601.1506) id LAA22667; Tue, 9 May 1995 11:42:41 -0400 Received: by gusun.acc.georgetown.edu; (5.0/1.1.8.2/6Jan9518:19pm) id AA18922; Tue, 9 May 1995 11:42:08 +0500 Date: Tue, 9 May 1995 11:42:07 -0400 (EDT) From: Cheol Choi To: CHEMISTRY@ccl.net Subject: MRDCI ?? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII content-length: 166 Hi! Everyone. Is there any program which can do MRDCI calculation? Please, let me know MRDCI and related calculations. Thank you Cheol-Ho Choi Georgetown Univ. From yuan@nka1.med.uc.edu Tue May 9 11:51:33 1995 Received: from nka1.med.uc.edu for yuan@nka1.med.uc.edu by www.ccl.net (8.6.10/930601.1506) id LAA22799; Tue, 9 May 1995 11:45:57 -0400 Received: by nka1.med.uc.edu (920330.SGI/921111.SGI.AUTO) for chemistry@ccl.net id AA06592; Tue, 9 May 95 11:48:27 -0400 Date: Tue, 9 May 1995 11:48:19 -0400 (EDT) From: Jie Yuan To: Computational Chemistry List Subject: MolScript prep program? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers! I heard about a program that composes scripts for MolScript, but I cannot find it by WWW (tried Crawler, Yahoo and some well-known sites). The author(s) was in the Netherlands, I think, but I am not sure. Thanks! Jie -- Dr. Jie Yuan - Pharmacology & Cell Biophysics - U. Cincinnati -- -- Phone: 513-558-2352 -- Fax: x-1169 -- Email: Jie.Yuan@UC.Edu -- -- P.O. Box 670575, 231 Bethesda Ave., Cincinnati, OH 45267-0575 -- From theochem@ctc.com Tue May 9 12:09:14 1995 Received: from server1.ctc.com for theochem@ctc.com by www.ccl.net (8.6.10/930601.1506) id LAA23235; Tue, 9 May 1995 11:57:53 -0400 Received: by server1.ctc.com (5.65/DEC-Ultrix/4.3) id AA16719; Tue, 9 May 1995 11:57:53 -0400 Received: by pauling.ctc.com (931110.SGI/930416.SGI.AUTO) for @server1.ctc.com:chemistry@ccl.net id AA18959; Tue, 9 May 95 12:54:47 -0400 From: theochem@ctc.com (Douglas Smith) Message-Id: <9505091654.AA18959@pauling.ctc.com> Subject: thermochemical reference data To: chemistry@ccl.net (Computational Chemistry List) Date: Tue, 9 May 1995 12:54:46 -0500 (EDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1029 I am looking for some thermochemical data for a variety of compounds. I have checked in the JANAF Thermochemical Tables (second edition, 1971) but cannot find any of the (more exotic) compounds of interest. Is there another source available? The compounds of interest are: nitrocellulose lead azide parathion malathion various PCBs TNT dinitrotoluene RDX (cyclonite, 1,3,5-trinitro-1,3,5-triazocyclohexane) sarin pentaerythritol tetranitrate HMX (1,3,5,7-tetranitro-1,3,5,7-tetraazocyclooctane) Any help or data would be appreciated. Heats of formation, entropy data, and heat capacities are of interest. Doug -- Douglas A. Smith Principal Technical Staff/Theoretical Chemist Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com Stadnard Disclamur: All opinions, comments, mistakes, endorsements and odd noises are my own, not my employer's. I would rather be and optimist and wrong than a pessimist and right. From polowin@hyper.hyper.com Tue May 9 12:19:54 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id MAA23596; Tue, 9 May 1995 12:12:22 -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 MAA00151; Tue, 9 May 1995 12:03:36 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:michael@argaman.tau.ac.il id AA25136; Tue, 9 May 95 12:04:39 -0400 Date: Tue, 9 May 95 12:04:39 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9505091604.AA25136@hyper.hyper.com> To: michael@argaman.tau.ac.il (Michael shoken) Subject: Re: CCL:molecular modelling software for IBM PC Cc: chemistry@ccl.net > Date: Tue, 9 May 95 16:27:05 +0300 > From: michael@argaman.tau.ac.il (Michael shoken) > Subject: CCL:molecular modelling software for IBM PC > > Is anyone aware of the IBM PC (486 or pentium) commercial software > for doing molecular modelling ? There is a great deal of information in the CCL archives about commercial packages of this sort. See: gopher://www.ccl.net:73/00/info/software-packages/* There are, for example, several files there about our HyperChem software, which meets your criteria; or for more information, please contact me. 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 shenkin@still3.chem.columbia.edu Tue May 9 12:50:07 1995 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.10/930601.1506) id MAA24419; Tue, 9 May 1995 12:44:59 -0400 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA16907 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:chemistry@ccl.net>); Tue, 9 May 1995 12:39:53 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:qftramos@usc.es id AA10837; Tue, 9 May 95 12:39:48 -0400 Date: Tue, 9 May 95 12:39:48 -0400 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9505091639.AA10837@still3.chem.columbia.edu> To: chemistry@ccl.net, qftramos@usc.es (Antonio Fernandez Ramos) Subject: Re: CCL:Intermolecular minimitation > From chemistry-request@ccl.net Tue May 9 12:16:47 1995 > From: qftramos@usc.es (Antonio Fernandez Ramos) > Subject: CCL:Intermolecular minimitation > I have a dimer intermolecular potential with several parameters; the > variables are the distances between atoms. I want to optimize the > intermolecular coordinates but keeping the intramolecular coordinates > fixed, as well as two intermolecular coordinates, one angle and one > distance. > Is there any program available which will allow me to introduce the > potential depending on the distances and the restrictions, and which > will optimize the rest of the coordinates, and be easy to use? The 5.0 version of BatchMin (part of the MacroModel suite of fine programs) has facilities for this. You would use FXDI commands to fix as many interatomic distances as you please, then ASET commands to put each molecule into a set, then the ASNT command to turn off all force-field interactions (but not the user-added constraint interactions) between the sets. Once you've done this, you may blithely perform energy minimization, conformational, search, MC, MD, etc., using your choice of MM2, MM3, AMBER or OPLS force-fields, together with the GB/SA solvent model, if you so choose. Coming soon: MMFF (Merck Molecular Force Field). -P. ************************ The secret of life: ************************* *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * ************* If you find a loose thread, don't pull it. ************* From elewars@alchemy.chem.utoronto.ca Tue May 9 13:34:56 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/930601.1506) id NAA25241; Tue, 9 May 1995 13:22:42 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.10/8.6.10) id MAA25541 for chemistry@ccl.net; Tue, 9 May 1995 12:57:05 -0400 Date: Tue, 9 May 1995 12:57:05 -0400 From: "E. Lewars" Message-Id: <199505091657.MAA25541@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: MODELLING SOFTWARE FOR THE PC 1995 May 9 Michael Shokhen asked about modelling software for the IBM PC. Here is some software that will run on the PC and clones thereof: --------------------- Hyperchem from hurst@hyper.com $995, supplementary package $495 Molecular mechanics, a variety of semiempirical (AM1, MNDO and others) routines, and now ab initio. Lots of graphics. Gaussian for Windows from Gaussian Inc., info@gaussian.com $750 Some semiempirical, mainly ab initio and density functional. No graphics of its own. MOPAC; for info' on (almost) free and commercial versions, contact QCPE, qcpe@ucs.indiana.edu (can ask about email searching of their catalog); Fujitsu, kumiko.iguchi@fujitsu.com Semiempirical. No graphics of its own. PCModel from Serena Software, GILBERT@ucs.indiana.edu ca. $400 Molecular Mechanics. You may find it helpful for visual input/output with Gaussian and MOPAC. I would inquire about programs for the PC that will give Gaussian and MOPAC a graphical interface (the book "Exploring Chemistry with Electronic Structure Methods", from Gaussian, has some info' on this). C&EN, 1995 May 1, pp 36- 50 reports on various modelling programs, some of which will run on the PC. From C1790@SLVAXA.UMSL.EDU Tue May 9 13:49:55 1995 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.10/930601.1506) id NAA25686; Tue, 9 May 1995 13:40:19 -0400 Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.3-7 #2503) id <01HQASMK9TKCBSIR3U@SLVAXA.UMSL.EDU>; Tue, 9 May 1995 12:40:34 CDT Date: Tue, 09 May 1995 12:40:34 -0500 (CDT) From: BILL WELSH To: chemistry@ccl.net Message-id: <01HQASMKA37IBSIR3U@SLVAXA.UMSL.EDU> X-VMS-To: in%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT One of my colleagues is giving a presentation to a group for which she needs a good computer-generated image of DNA. I notice that the PDB contains citations to over 250 DNA structures, many of these being clones and fragments. Can someone direct me to a full-length PDB coordinate file for DNA. Thanks ... Bill Welsh Dept. of Chem. Univ. of Missouri-St. Louis c1790@slvaxa.umsl.edu From emcgoran@ewu.edu Tue May 9 13:49:58 1995 Received: from eagle.ewu.edu for emcgoran@ewu.edu by www.ccl.net (8.6.10/930601.1506) id NAA25759; Tue, 9 May 1995 13:43:03 -0400 Received: from [146.187.64.155] (ewu61589.ewu.edu) by ewu.edu (PMDF V4.2-14 #5563) id <01HQAOEZLRJK8Y9326@ewu.edu>; Tue, 9 May 1995 10:39:59 PST Date: Tue, 09 May 1995 10:45:52 -0800 From: emcgoran@ewu.edu (Ernie McGoran) Subject: C-13 NMR/ Ab Initio Calcs To: CHEMISTRY@ccl.net Message-id: <01HQAOF04IOY8Y9326@ewu.edu> X-Envelope-to: CHEMISTRY@ccl.net Content-transfer-encoding: 7BIT X-Sender: emcgoran@eagle.ewu.edu Could anyone point me to references where ab initio calculations/ molecular orbital properties might have been used to account for the different C -13 chemical shifts of carbon atoms whose ligands have different cis/trans or syn/anti dispositions. Since atomic charge, by itself, is not a stand alone C-13 chemical shift predictor, it would seem reasonable that the properties of molecular orbitals might provide a more complete model. Since the compounds I am interested in don't have published C-13 chemical shift parameters for an empirical estimate, and since the data set of published compounds is limited, all I have to buttress a stereochemical assignment is some published C-13 data on somewhat dissimilar compounds. The sterochemical assignments, on these model compounds were based on the anisotropic influence of neighboring (C=C) and distorted cuclobutane rings. I know that Gaussian 94 has a NMR chemical shift prediction module, so it seems reasonable that ab initio calculations would lead to a set of useful predictions. I have carried out ab initio calcuations on these compounds at the 3-21G* level (Spartan), and although there are some differences in the electrostatic charges and the HOMO/density (and other MO) surfaces, translating these into a theoretically sound interpretation escapes me. Thanks for any help you can send my way. Ernie McGoran, Ph. D. | Phone: (509) 359-7931 Dept. of Chem./Biochem. MS 74 | FAX: (509) 359-6937 Eastern Washington University | email: emcgoran@ewu.edu Cheney, WA 99004 From graham@sentex.net Tue May 9 20:04:58 1995 Received: from granite.sentex.net for graham@sentex.net by www.ccl.net (8.6.10/930601.1506) id TAA03318; Tue, 9 May 1995 19:55:29 -0400 Received: from gu-ttyd6.sentex.net (gu-ttyd6.sentex.net [204.50.3.55]) by granite.sentex.net (8.6.5/8.6.9) with SMTP id UAA20792; Tue, 9 May 1995 20:08:13 -0400 Message-Id: <199505100008.UAA20792@granite.sentex.net> X-Sender: graham@mail.sentex.net X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 09 May 1995 19:55:08 -0400 To: "E. Lewars" , chemistry@ccl.net From: graham@sentex.net (Graham Hurst) Subject: Re: CCL:MODELLING SOFTWARE FOR THE PC At 12:57 PM 5/9/95 -0400, E. Lewars wrote: >Michael Shokhen asked about modelling software for the IBM PC. Here is some >software that will run on the PC and clones thereof: >--------------------- >Hyperchem from hurst@hyper.com $995, supplementary package $495 ^^^^^ Try info@hyper.com instead. hurst@hyper.com is my old email address... Cheers, Graham ------- Graham Hurst, PhD or Cambridge, Ontario, Canada From moon@kistmail.kist.re.kr Tue May 9 22:20:00 1995 Received: from garam.kreonet.re.kr for moon@kistmail.kist.re.kr by www.ccl.net (8.6.10/930601.1506) id WAA04677; Tue, 9 May 1995 22:11:25 -0400 Received: from kistmail.kist.re.kr (kistmail.kist.re.kr [161.122.12.3]) by garam.kreonet.re.kr (8.6.9H1/8.6.9) with SMTP id LAA01067 for ; Wed, 10 May 1995 11:13:43 +0900 Received: by kistmail.kist.re.kr (5.65/KISTMAIL-0.1) id AA08782; Wed, 10 May 95 11:10:20 +0900 Date: Wed, 10 May 95 11:10:20 +0900 From: moon@kistmail.kist.re.kr (Moon Tae Sung) Message-Id: <9505100210.AA08782@kistmail.kist.re.kr> To: chemistry@ccl.net Subject: Program for 'Normal Mode Analysis' I am T.S. Moon working at KIST. I am interested in 'Normal Mode Analysis' expecially on protein. Please let me know the program (in workstation level) or the source code. Wait for reply.