From chemistry-request@www.ccl.net Thu Aug 27 04:00:26 1998 Received: from mail.gmd.de (mail.gmd.de [129.26.8.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA20597 Thu, 27 Aug 1998 04:00:25 -0400 (EDT) Received: from cartan (cartan.gmd.de [129.26.8.171]) by mail.gmd.de (8.8.8/8.8.8) with SMTP id KAA27307 for ; Thu, 27 Aug 1998 10:00:21 +0200 (MET DST) Received: from fermat by cartan with SMTP id AA03472 (5.67b/IDA-1.5 for ); Thu, 27 Aug 1998 10:00:17 +0200 Message-Id: <199808270800.AA03472@cartan> Date: Thu, 27 Aug 1998 10:00:17 +0200 (MET DST) From: Matthias Rarey Reply-To: Matthias Rarey Subject: Feature Trees: new software for molecular similarity analysis To: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-Md5: zizdvVtexmPPUhcKL2+Ing== X-Mailer: dtmail 1.2.0 CDE Version 1.2 SunOS 5.6 sun4u sparc Dear CCLer, During the last year GMD-SCAI in cooperation with SmithKline Beecham R&D have developed a new molecular descriptor technology called 'Feature Trees'. The Feature Tree similarity value is based on molecular interaction profiles and a rough mapping computed between the molecules to compare. Due to efficient mapping algorithms (about 50ms per pair-comparison on an R10000 CPU) the method is applicable to large databases. A paper on Feature Trees will appear in J.Comput.-Aided Mol.Design in the next months. In order to get feedback about the usefulness and applicability of the method, GMD-SCAI offers now free-of-charge temporary licenses for evaluating the corresponding software tool called Ftrees. The license covers the full functionality of Ftrees and will be valid for about three months. More information can be found on: http://cartan.gmd.de/Ftrees Regards, Matthias Rarey (rarey@gmd.de) From chemistry-request@www.ccl.net Thu Aug 27 04:22:17 1998 Received: from ms10.hinet.net (root@ms10.hinet.net [168.95.4.100]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA20670 Thu, 27 Aug 1998 04:22:16 -0400 (EDT) From: a6173@ms10.hinet.net Received: from hinet (h189.s10.ts31.hinet.net [163.31.10.189]) by ms10.hinet.net (8.8.8/8.8.8) with SMTP id QAA13760 for ; Thu, 27 Aug 1998 16:22:02 +0800 (CST) Message-ID: <35E51721.7CEB@ms10.hinet.net> Date: Thu, 27 Aug 1998 16:21:53 +0800 X-Mailer: Mozilla 3.03 (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: molecular rendering software Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit dear netters: i am looking for shareware that can render molecules in ball and stick form, and allow us to specify lables for angles(e.g. arrow line) and bonds(e.g. r1, r2 ....). any sugguestion will be appreciated! e-mail: a6173@ms10.hinet.net albert 1998/8/27 From chemistry-request@www.ccl.net Thu Aug 27 06:26:08 1998 Received: from gatekeeper2.novartis.com (gatekeeper2.novartis.com [194.191.169.74]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA20996 Thu, 27 Aug 1998 06:26:04 -0400 (EDT) From: takanori.kanazawa@pharma.Novartis.com Received: from mta3.is.chbs (mail.novartis.com [192.37.10.59]) by gatekeeper2.novartis.com (8.9.0/8.9.0) with ESMTP id MAA29926 for ; Thu, 27 Aug 1998 12:25:32 +0200 (MET DST) Received: from nts1.novartis.com ([192.168.50.131]) by mta3.is.chbs (8.8.5/8.8.5) with SMTP id MAA01603 for ; Thu, 27 Aug 1998 12:27:15 +0200 (MET DST) Received: by nts1.novartis.com(Lotus SMTP MTA v1.2 (600.1 3-26-1998)) id 4125666D.0039D7C4 ; Thu, 27 Aug 1998 11:31:47 +0100 X-Lotus-FromDomain: PH@N1 To: CHEMISTRY@www.ccl.net Message-ID: <4925666D.00323CBC.00@nts1.novartis.com> Date: Thu, 27 Aug 1998 18:11:54 +0900 Subject: thanks : g94 problem Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Thanks everybody who responded to my question. The cause of the problem was just I made a simple mistake ; I forgot to put "Mem= ...." line in the input file. Thanks again for your kindess, Takanori Kanazawa > Dear CCLers, > > Could somebody help me with the following problem with G94 calculation? > > I did frequency calculation for a molecule(274 basis functions,6-31++G**) > with > B3LYP method. After about two hours of calc., g94 program dumped core ans > stopped. > The computer which I ran this calculation is an SGI machine,running under > IRIX6.4 > , with 256MB of memory and more than 8GB of disk space. > > Could you help me to find out what is the problem with this calc.? > > --------------------------------------------------------------------------- > > ........................................ > Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. > Requested convergence on MAX density matrix=1.00D-06. > Integral accuracy reduced to 1.0D-05 until final iterations. > Initial convergence to 1.0D-05 achieved. Increase integral accuracy. > SCF Done: E(RB+HF-LYP) = -497.107750514 A.U. after 16 cycles > Convg = 0.4171D-08 -V/T = 2.0097 > S**2 = 0.0000 > Range of M.O.s used for correlation: 1 274 > NBasis= 274 NAE= 40 NBE= 40 NFC= 0 NFV= 0 > NROrb= 274 NOA= 40 NOB= 40 NVA= 234 NVB= 234 > > **** Warning!!: The largest alpha MO coeffient is 0.39857755D+02 > > G2DrvN: can do 24 atoms at a time, so will make 1 passes doing > MaxLOS=2. > Not enough memory for a single radius per batch: > NAngPt= 302 MaxPt= 169. > Error termination via Lnk1e in /home/Gaussian/g94/l1110.exe. > Job cpu time: 0 days 1 hours 56 minutes 40.8 seconds. > File lengths (MBytes): RWF= 85 Int= 0 D2E= 0 Chk= 6 Scr= 1 > > --------------------------------------------------------------------------- From chemistry-request@www.ccl.net Thu Aug 27 09:38:59 1998 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA21791 Thu, 27 Aug 1998 09:38:58 -0400 (EDT) From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.1 (569.2 2-6-1998)) id 8625666D.0049508D ; Thu, 27 Aug 1998 08:20:47 -0500 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA To: CHEMISTRY@www.ccl.net Message-ID: <8625666C.005F2984.00@unomail.unomaha.edu> Date: Wed, 26 Aug 1998 12:21:43 -0500 Subject: Re: CCL:g94 problem Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Most likely a memory shortage. I had the same problem with a large freq. calculation where the freqmem utility did not predict the correct number of megawords for RAM allocation. Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3647 (fax) Douglas_Stack@unomaha.edu From chemistry-request@www.ccl.net Thu Aug 27 10:27:42 1998 Received: from hbcg.utmb.edu (hbcg.utmb.edu [129.109.73.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA22704 Thu, 27 Aug 1998 10:27:41 -0400 (EDT) Received: from [129.109.136.166] by hbcg.utmb.edu via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id JAA13446; Thu, 27 Aug 1998 09:38:42 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 27 Aug 1998 09:27:09 -0500 To: chemistry@www.ccl.net From: "Vincent J. Hilser" Subject: any suggestions? greetings folks, I am an asst. prof. of structural biology at UTMB, Galveston and I am researching my options as far as purchasing computers. My computational requirements involve at least four processors and I am currently borrowing time on a colleagues Origin 2000. I was investigating my own SGI options, and it seems to me that the bang for the buck is just not there. As my needs are purely number crunching, I am interested in finding out what LINUX based approach would best suit my needs. in addition to number and speed of processors, I need to consider start-up and upkeep time and expense, expandability, etc. Any help in this matter would be greatly appreciated. Regards, Vince =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-= Vincent J. Hilser, Ph.D. Assistant Professor Department of Human Biological Chemistry & Genetics, Sealy Center for Structural Biology, Sealy Center for Molecular Science University of Texas Medical Branch 5.166 Medical Research Bldg. Galveston, TX 77555-1055 (409) 747-6813 (office) (409) 747-6812 (lab) (409) 772-4298 (FAX) e-mail: vince@hbcg.utmb.edu http://www.hbcg.utmb.edu/faculty/hilser/hilser.html http://www.scsb.utmb.edu/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-= From chemistry-request@www.ccl.net Thu Aug 27 15:56:13 1998 Received: from dfw-ix5.ix.netcom.com (dfw-ix5.ix.netcom.com [206.214.98.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA27794 Thu, 27 Aug 1998 15:56:12 -0400 (EDT) Received: (from smap@localhost) by dfw-ix5.ix.netcom.com (8.8.4/8.8.4) id OAA27609; Thu, 27 Aug 1998 14:55:34 -0500 (CDT) Received: from bst-ma5-04.ix.netcom.com(205.186.73.164) by dfw-ix5.ix.netcom.com via smap (V1.3) id rma027577; Thu Aug 27 14:55:14 1998 Received: by localhost with Microsoft MAPI; Thu, 27 Aug 1998 15:56:45 -0400 Message-ID: <01BDD1D3.4AD1A5C0.kmtakita@knowledgefoundation.com> From: Kim Takita Subject: RFI on survey for new materials discovery/dvlpt. Date: Thu, 27 Aug 1998 15:56:33 -0400 X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 Encoding: 33 TEXT We are conducting an industry survey on general New Materials Discovery Technologies in conjunction with our conference on Combinatorial Approaches to New Materials Discovery being held January 25-26, 1999 in San Jose. We are compiling questions now (survey will be roughly 10 questions). The purpose is to identify leading methodologies, current usage of combi approaches, overall technological hurdles for rapid discovery and industry wish list. We are formulating the survey now (will be roughly 10 questions). Does anyone in the group have specific questions along these lines that you would like to see answered? -- if so, please email be prior to Sept. 1 and I can try to incorporate them. If you would like to participate in the survey, just send me your contact information and I'll mail a copy to you (you can also request it through our web site -- url below). Participants will receive free copy of the results when they are tabulated. Thank you for your time. Sincerely, Kim Takita ------------------------------------------------------------------------ ---------- Kim Takita Vice President The Knowledge Foundation, Inc. 101 Merrimac Street Boston, MA 02114 Phone: 617-367-7979 ext. 202 Fax: 617-367-7912 E-Mail: kmtakita@knowledgefoundation.com http://www.knowledgefoundation.com From chemistry-request@www.ccl.net Thu Aug 27 19:15:45 1998 Received: from cc.nifhi.ac.ru (router.nifhi.ac.ru [193.233.8.61]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA29124 Thu, 27 Aug 1998 19:12:07 -0400 (EDT) Received: from Tchougreeff.nifhi.ac.ru ([193.233.8.209]) by cc.nifhi.ac.ru (8.8.8/8.8.3) with SMTP id AAA20991; Fri, 28 Aug 1998 00:22:37 +0400 (MSD) Received: by Tchougreeff.nifhi.ac.ru with Microsoft Mail id <01BDD219.F63621C0@Tchougreeff.nifhi.ac.ru>; Fri, 28 Aug 1998 00:22:38 +0400 Message-ID: <01BDD219.F63621C0@Tchougreeff.nifhi.ac.ru> From: "Andrei L. Tchougreeff" To: "'chemistry@www.ccl.net'" , Subject: Fock meeting on Quantum and Computational Chemistry Date: Fri, 28 Aug 1998 00:20:55 +0400 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id TAA29147 Status: RO Content-Length: 4003 First V.A. Fock Meeting on Quantum and Computational Chemistry Yaroslav the Wise University of Novgorod 14-19 December 1998 Novgorod the Great RUSSIA Second Announcement and Call for Papers The information is also available from the meeting Web site: http://hcc.keldysh.ru/fock Dear colleagues! We are very pleased to invite you to join us in celebrating the 100-th anniversary of V.A. Fock - one of the founders of Quantum Chemistry by having a Meeting on Quantum and Computational Chemistry, which will be held on 14-19 December 1998 in the Yaroslav the Wise University in Novgorod the Great - Russia. The scientific specialization of the Meeting: The application of modern concepts and computational methods of quantum chemistry to studies of chemical, physical and biological problems. Organizing Commettee: O.M. Nefedov (HCC RAS - chairman); A.L. Buchachenko (ICP RAS); V.I. Minkin (IPOC RSU); V.V. Tartakovsky (IOC RAS); A.A. Berlin (ICP RAS); L.A. Gribov (GeoCI RAS); A.A. Ovchinnikov (IBCP RAS); R.A. Evarestov (SPbSU); A.A. Bagaturyants (ICP RAS); A.L. Gavrilov (NovSU); P.N. Dyachkov (IGNC RAS); D.V. Korolkov (SPbSU); B.I. Seleznev (NovSU); I.N. Senchenya (IOC RAS); V.I. Faustov (IOC RAS); D.A.Phillippov (NovSU); A.L. Tchougreeff (HCC RAS). Advisory Commettee: N.D. Sokolov (ICP RAS - chairman); M.V. Bazilevsky (NIFHI); I.B. Bersuker (Academy of Science of Moldova); R. Hoffmann (Cornell University); G.M. Zhidomirov (IC SB RAS - vice chairman); A.A. Levin (IGNC RAS - vice chairman); R.McWeeny (University of Pisa); R.M. Minyaev (IPOC RSU); I.A. Misurkin (NIFHI); Yu.E. Nikitin (NovSU); R.G. Parr (University of North Carolina) I.V. Stankevich (INEOS RAS); N.F. Stepanov (MSU); N.D. Chuvylkin (IOC RAS); V.I. Pupyshev (MSU); A.L. Tchougreeff (HCC RAS). The program of the Meeting includes invited lectures, oral presentations, poster session, subject discussions, round tables and software demonstrations. Some lectures will be delivered by leading experimentalists. Invited Speakers: V.I. Minkin; L.A. Gribov; A.A. Ovchinnikov; I.V. Abarenkov; M.V. Bazilevsky; I.B. Bersuker; Yu.N. Demkov; G.M. Zhidomirov; I.G. Kaplan; A.A. Levin; I.A. Misurkin; M.Ya. Ovchinnikova; O.M. Sarkisov; N.D. Sokolov; I.V. Stankevich; N.F. Stepanov; S.F. Timashev; A.V. Tulub; S.Ya. Umansky; V.I. Pupyshev. The list is open and the final program will be settled after receiving and analyzing the replies from the participants. A number of additional speakers will be selected to present plenary lectures and shorter oral presentations on the basis of submitted abstracts. The arrival and the registration of the participants will be on 13 December 1998. *Accomodation. Hotel room of about USD 120 per day. *Registration fee for academic participants: USD 200 paid upon arrival. Participants from industry will be asked to pay a registration fee of USD 500 or better to have their companies make a more substantial contribution to the school with appropriate recognition in the program, publications, and WWW site. (The participants from Russia and the CIS are welcome to check the russian version of this announcement on the meeting Web site: http://hcc.keldysh.ru/fock/fock_meeting.htm for amended information for the items marked with the asterisk *) The opening of the Meeting and all its sessions will take place in the Yaroslav the Wise University of Novgorod the Great. The address: B. Sankt-Peterburgskaya, 41. Working languages of the Meeting are English and Russian. The requests for participation in the Meeting (also as a lecturer) must be transmitted by filling out the electronic form located at the URL: http://qcc.ioc.ac.ru/registration.htm All the registered participants are welcome to submit their From chemistry-request@www.ccl.net Fri Aug 28 00:53:09 1998 Received: from theta1.ben2.ucla.edu (theta1.ben2.ucla.edu [164.67.131.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA00113 Fri, 28 Aug 1998 00:53:09 -0400 (EDT) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by theta1.ben2.ucla.edu (8.8.8/8.8.8) with SMTP id VAA37944; Thu, 27 Aug 1998 21:53:07 -0700 Received: from pc-ll.chem.ucla.edu by ewald.mbi.ucla.edu (5.65v4.0/1.1.10.5/18Aug98-0204AM) id AA24482; Thu, 27 Aug 1998 21:53:06 -0700 Message-Id: <9808280453.AA24482@ewald.mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Thu, 27 Aug 1998 21:58:43 -0700 To: chemistry@www.ccl.net From: Laurence Lavelle Subject: Amber 5 as back end with HyperChem 5 as front end Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Anyone tried using HyperChem 5 for data analysis of Amber 5 output? Any suggestions or good or bad reasons to do this. Laurence From chemistry-request@www.ccl.net Fri Aug 28 01:47:59 1998 Received: from karplus0.harvard.edu (tammy.harvard.edu [128.103.92.198]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA00302 Fri, 28 Aug 1998 01:47:58 -0400 (EDT) Received: from topanga.harvard.edu (topanga [128.103.92.179]) by karplus0.harvard.edu (8.8.2/8.8.2) with ESMTP id BAA26423 for ; Fri, 28 Aug 1998 01:58:23 -0400 (EDT) Received: from localhost (qiang@localhost) by topanga.harvard.edu (8.8.2/8.8.2) with SMTP id BAA29973 for ; Fri, 28 Aug 1998 01:35:17 -0400 (EDT) Date: Fri, 28 Aug 1998 01:35:17 -0400 (EDT) From: Qiang Cui Reply-To: Qiang Cui To: CHEMISTRY@www.ccl.net Subject: symmetry breaking? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I've encountered a weird problem with IRC calculations using G94. Even starting with a structure with Cs symmetry, the programm stopped as soon as it reaches the first IRC step and complains that the molecule is C1!!!! (Only one A' imaginary freq at the TS, and IRC should conserve symmetry after all). Any idea how to get around this problem? (except breaking the symmetry and run the calculation in C1:-) Thanks! Here is the simple input: %chk=pt_intra.chk #n am1 irc=(calcfc,maxpoints=15,stepsize=15) PT_TS -1 1 C 0.0000 0.0000 0.0000 C 1.3740 0.0000 0.0000 O 1.8497 1.2751 0.0000 C 2.3053 -1.1322 0.0000 O -0.4820 1.2657 0.0000 H -0.7000 -0.8297 0.0000 H 1.7506 -2.1032 0.0000 H 0.6754 1.8132 0.0000 H 2.9670 -1.1020 0.9028 H 2.9670 -1.1020 -0.9028 From chemistry-request@www.ccl.net Fri Aug 28 04:10:17 1998 Received: from anne.chemie.unibas.ch (anne.chemie.unibas.ch [131.152.112.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id EAA00890 Fri, 28 Aug 1998 04:10:16 -0400 (EDT) From: barbosa@anne.chemie.unibas.ch Received: by anne.chemie.unibas.ch (AIX 3.2/UCB 5.64/4.03) id AA15656; Fri, 28 Aug 1998 10:09:44 +0200 Message-Id: <9808280809.AA15656@anne.chemie.unibas.ch> Subject: uhf and biradicals: summary To: chemistry@www.ccl.net Date: Fri, 28 Aug 1998 10:09:44 +0200 (DFT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL, Some weeks ago I ask about references on UHF and biradicals. I did not receive a lot of answers. Below you could find my questions and the answers to it. Frederique ---------------------------------------------------------------------- Dear CCL, I am looking for some references on calculations with unrestricted hartree fock method on singlet biradicals in the ground state. Thanks in advance Frederique ---------------------------------------------------------------------- >From bernd@rs5.thch.uni-bonn.de (Bernd Engels) Dear Frederique You should not do uhf computations but you should use DFT theory. Actually, Dr. Werner Nau from the Physikal Chemistry in Basel can help you, doing such calculations. I am in contact with him, and we exchanged some literature. Nevertheless, if problems appear I can also help you. We are able to perform very accurate MR-CI calculations (e.g. Angew.Chem.Int.Ed. 1998, 37, page 1562; ibid. page 1960, JACS, 1998, 120, 6356) for quite large systems, so we would be able to check the DFT Results for model systems. bernd engels Inst. fuer Phys. und Theor. Chemie Universitaet Bonn Wegelerstr. 12 Germany ---------------------------------------------------------------------- >From karney@usfca.edu Fri Aug 14 23:00:43 1998 Dear Frederique, I don't think you can expect a UHF calculation on a singlet diradical to give you meaningful results. Any hartree-fock calculation on a singlet state will automatically calculate a single configuration for the closed-shell singlet. For a singlet diradical, either closed-shell or open-shell, you need to do at least a two-configuration calculation such as CASSCF(2,2). There are some exceptions to this general rule, but they usually involve the use of highly correlated computational methods like CCSD(T). You might take a look at the following reference: Wierschke, Nash, and Squires, J. Am. Chem. Soc., 1993, 115, 11958. A general reference on diradicals is the following book: "Diradicals"; Weston T. Borden, Ed.; Wiley: New York, 1982, Chapter 1. There is also a recent paper by Schreiner describing BLYP calculations on singlet 1,4-dehydrobenzene (p-benzyne): J. Am. Chem. Soc., 1998, 120, 4184. If you have any other questions about this, feel free to email me. Good luck! William ------------------------------------------------------------------------- William L. Karney phone: (415) 422-5842 Assistant Professor fax: (415) 422-2346 Department of Chemistry email: karney@usfca.edu University of San Francisco 2130 Fulton St. San Francisco, CA 94117-1080 ------------------------------------------------------------------------- ======================================================================= Frederique BARBOSA Institute for Organic Chemistry University of Basel E-mail: barbosa@anne.chemie.unibas.ch St. Johanns-Ring 19 phone : 061/267 11 57 4056 Basel fax : 061/267 11 05 Switzerland ======================================================================= From chemistry-request@www.ccl.net Fri Aug 28 08:37:37 1998 Received: from NPD1.NPD.UFPE.BR (npd1.npd.ufpe.br [150.161.6.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA01754 Fri, 28 Aug 1998 08:37:24 -0400 (EDT) Received: from danon ([150.161.5.125]) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with SMTP id <01J14RB38BFK000EC6@NPD.UFPE.BR> for chemistry@www.ccl.net; Fri, 28 Aug 1998 09:18:40 GMT-3 Date: Fri, 28 Aug 1998 09:40:34 -0300 From: Gustavo de Miranda Seabra Subject: Overlap Integrals on GAMESS US To: Computational Chemistry List Reply-to: Gustavo de Miranda Seabra Message-id: <005d01bdd282$0499ed60$7d05a196@danon.dqf.ufpe.br> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: multipart/alternative; boundary="----=_NextPart_000_004C_01BDD267.E74D9E10" X-Priority: 3 X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 This is a multi-part message in MIME format. ------=_NextPart_000_004C_01BDD267.E74D9E10 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, Sorry if this message is repeated, but we had some trouble with our = server, and I don't know if the first one has been delivered. So, my = question is: I would like Does anyone know how can I print the overlap integrals = on the GAMESS US? Thanks very much, -------------------------------------------------------------------------= ------------------ Gustavo de Miranda Seabra MSc Student in Chemistry seabra@npd.ufpe.br Federal University of Pernambuco Brazil -------------------------------------------------------------------------= ------------------ ------=_NextPart_000_004C_01BDD267.E74D9E10 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
 
    = Sorry if this=20 message is repeated, but we had some trouble with our server, and I = don't know=20 if the first one has been delivered. So, my question is:
 
    I = would like Does=20 anyone know how can I print the overlap integrals on the GAMESS = US?
 
    = Thanks very=20 much,
----------------------------------------------------------------= ---------------------------
       =             &= nbsp; =20 Gustavo de Miranda Seabra
MSc Student in=20 Chemistry          &nbs= p;      =20 seabra@npd.ufpe.br
Federal = University=20 of=20 Pernambuco          &nb= sp;           &nbs= p;     =20 Brazil
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------=_NextPart_000_004C_01BDD267.E74D9E10-- From chemistry-request@www.ccl.net Fri Aug 28 11:01:47 1998 Received: from dft.chem.cuhk.edu.hk (dft.chem.cuhk.edu.hk [137.189.38.216]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA02827 Fri, 28 Aug 1998 11:01:45 -0400 (EDT) Received: (from pang@localhost) by dft.chem.cuhk.edu.hk (8.9.0.Beta3/8.9.0.Beta3) id WAA07343; Fri, 28 Aug 1998 22:57:38 +0800 (HKT) Date: Fri, 28 Aug 1998 22:57:38 +0800 (HKT) From: patrick To: chemistry@www.ccl.net Subject: Frequency calculation of transition state In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! How are you? During computation of frequency of molecules at transition state, one of frequencies is negative. Why? Is it a rule for identification of transition state? Is it possible if two or more frequencies are negative when molecules are at transition state? Thank you for your attention. Patrick Pang From chemistry-request@www.ccl.net Fri Aug 28 11:46:08 1998 Received: from theory.chem.uottawa.ca (theory.chem.uottawa.ca [137.122.43.156]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA02960 Fri, 28 Aug 1998 11:46:05 -0400 (EDT) Received: by theory.chem.uottawa.ca (AIX 3.2/UCB 5.64/4.03) id AA26623; Fri, 28 Aug 1998 11:46:43 -0400 Date: Fri, 28 Aug 1998 11:46:43 -0400 From: st-amant@theory.chem.uottawa.ca (Alain St-Amant) Message-Id: <9808281546.AA26623@theory.chem.uottawa.ca> To: chemistry@www.ccl.net Subject: new version of DeFT available Hi Everyone, A new version of our DeFT gaussian density functional program can be downloaded from our website (http://www.chem.uottawa.ca/DeFT.html). Though this version does not contain our recent work on linear scaling methods, it is a significant improvement over the previously released version of DeFT as the SCF convergence is improved and redundant internal coordinates are used for the geometry optimizations. Once our linear scaling routines become less experimental, more robust, we will release them at the above web site. Please also note that DeFT does have gradient-corrected functionals, but hybrid (i.e., B3LYP) functionals are not included as the requisite four-center/two-electron integrals are not a part of DeFT. Basis sets for all elements up to Xe are included. DeFT is freely distributed to any researcher. This version runs on all platforms to which we have access: a Pentium running under RedHat Linux, an IBM RISC workstation, and a Cray T3E (it runs efficiently over a limited number of processors, depending on the problem). To run in parallel, MPI must be installed on your system. Take care, Alain St-Amant Department of Chemistry University of Ottawa From chemistry-request@www.ccl.net Fri Aug 28 13:25:21 1998 Received: from panix3.panix.com (JTt4EfTLzZ6Ct5ysq3TWT5/H7N2+2yQk@panix3.panix.com [166.84.1.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA05752 Fri, 28 Aug 1998 13:25:20 -0400 (EDT) Received: (from kynn@localhost) by panix3.panix.com (8.8.5/8.8.8/PanixU1.4) id NAA13198; Fri, 28 Aug 1998 13:25:19 -0400 (EDT) Date: Fri, 28 Aug 1998 13:25:19 -0400 (EDT) Message-Id: <199808281725.NAA13198@panix3.panix.com> From: "Kynn O. Jones" To: chemistry@www.ccl.net Subject: ISO non-alpha, non-beta proteins Dear CCL: I'm looking for non-alpha, non-beta proteins. I'll take whatever I can find, but I'm most interested in those that are disulphide-free, do not require metal ions to fold, and are longer than about 50 residues (a tall order indeed!). Through SCOP, I found two so far: Neurotoxin III (1ans) and echistatin (2ech), both of which are disulphide-rich; Neurotoxin III is also tiny (27 residues). Does anyone know of any others? Thanks, KJ From chemistry-request@www.ccl.net Sat Aug 29 05:27:41 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA19295 Sat, 29 Aug 1998 05:27:40 -0400 (EDT) Received: from nafas.fh.huji.ac.il (nafas.fh.huji.ac.il [132.64.96.13]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id FAA09999 for ; Sat, 29 Aug 1998 05:27:37 -0400 (EDT) Received: from poodle.fh.huji.ac.il by nafas.fh.huji.ac.il via ESMTP (951211.SGI.8.6.12.PATCH1502/951211.SGI.AUTO) for <@batata.fh.huji.ac.il:CHEMISTRY@ccl.net> id MAA06434; Sat, 29 Aug 1998 12:28:14 +0300 Received: (from viki@localhost) by poodle.fh.huji.ac.il (950413.SGI.8.6.12/950213.SGI.AUTOCF) id MAA06442 for CHEMISTRY@ccl.net; Sat, 29 Aug 1998 12:28:12 +0300 Date: Sat, 29 Aug 1998 12:28:12 +0300 From: viki@poodle.fh.huji.ac.il (Victoria Buch) Message-Id: <199808290928.MAA06442@poodle.fh.huji.ac.il> To: CHEMISTRY@ccl.net Subject: Linux on Alpha, math library >>>>>>>>>>>> >>>>>>>>> > Igor J. Barani writes: > > Dear CCL Readers, > > > > I have just recently installed Linux on a DEC Alpha and when I compile > > several programs in fortran on it, they seem to compile to twice the > > size and require 9 times as long to run than on DEC UNIX. Do you have > > any idea why this may be so and how I may be able to speed up the > > processes? Any suggestions would be greatly appreciated. Thank you. >>>>>>>>>>>>>> We have just been there. You have the latest Red Hat Linux, dont you? So: the latest math library libm version 2.0.7 from gnu is messed up. Our system menager installed old version 2.0.1 - works faster by a factor 2. More generally our sexperience suggests that Alpha / Linux for FP operations is good only for simple operations + - * / . My simulation programs are still 40% below the performance of Alpha-DEC, and only 10% faster than Petium II (400MHz) which is more than 2 times cheaper. Disappointing. Good luck. Victoria Prof. Victoria Buch The Hebrew University of Jerusalem The Fritz Haber Research Center for Molecular Dynamics and Department of Physical Chemistry Jerusalem 91904, Israel Tel. 972-2-6584223, Fax: 972-2-6513742 e-mail: viki@batata.fh.huji.ac.il http://www.fh.huji.ac.il/ From chemistry-request@www.ccl.net Sat Aug 29 12:17:24 1998 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA19780 Sat, 29 Aug 1998 12:17:04 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id MAA08476 for chemistry@www.ccl.net; Sat, 29 Aug 1998 12:16:53 -0400 (EDT) Date: Sat, 29 Aug 1998 12:16:53 -0400 (EDT) From: "E. Lewars" Message-Id: <199808291616.MAA08476@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: SPARTAN'S pBP DFT Sat,1998 Aug 29 Hello, Alan Shusterman asked about refs for Spartan's pBP method. I have a little info' on this from Wavefunction. >From: IN%"Alan.Shusterman@directory.Reed.EDU" 28 August 1998 >To: IN%"sparlist@wavefun.com" >Subj: SPARTAN: pBP86 reference >In early July I asked whether anyone has a reference to the "pBP" = >method. I still don't have an exact reference, but I may have come = >closer... > >Wavefunction recently sent me some papers concerning DFT methods, = >including one that describes the "use" (but not the implementation) = >of the pBP86 method. This reference is F. Liangyou and T. Ziegler, = >J Chem Phys, 94(9), 6057-6063 (1991). > >The most interesting paragraph is found on the first page of the = >article, which states: > >"Up to date, most nonlocal calculations have been based on a = >perturbative approach in which the gradient terms are evaluated = >from a density generated by local self-consistent (SCF) = >calculations." > >Unfortunately, no references are given. Later on, under the section = >"VI. Bond Lengths" It is stated that: > >"Becke has used the perturbative nonlocal (NL-P) approach (6b) to = >calculate bond distances for several homonuclear diatomics." > >Ref 6b is A.D. Becke, ACS Symposium Series 1989, Number 394 (ACS, = >Washington DC 1989) > >I don't have this monograph, however, so I can't verify whether the = >cited article describes the "pBP" approach or not. This is as close = >as I have come to tracking this issue down. If anyone does have = >this article, I'd be grateful for a copy. > >Alan > >----------------- >Alan Shusterman >Department of Chemistry >Reed College >Portland, OR >www.reed.edu/~alan =============== ============= From Wayne Huang of Wavefunction: 1998 Aug Spartans pBP method is closest to (of the Gaussian-type methods) B88-P86 (non-hybrid) functional combination. Use of post-SCF gradient corrections has been incorporated in several DFT programs (e.g. ADF, DGauss, DMol). Was typical before Gaussian implemented a hybrid method in 1992. See book on Spartan's DFT by Hehre and Lou. The DN* should be close to 6-311+G* and DN** to 6-311++G**. We do not have scaling factors [for freqs, ZPE]. However, pBP underestimates vib. freqs by a few percent (hardly beyond 5%). For heavier atoms, especially metals, with freqs < 500 cm-1, might underestimate by 5-10%. [I have some scaling factors huang@wavefun.com I worked out myself--EL] =========================== E. Lewars ========================== ==========================