From jkl@ccl.net Wed Aug 16 03:18:13 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id DAA15076; Wed, 16 Aug 1995 03:06:23 -0400 Received: from mail0.iij.ad.jp for murakami@lab.takeda.co.jp by bedrock.ccl.net (8.6.10/930601.1506) id DAA26336; Wed, 16 Aug 1995 03:06:21 -0400 Received: from uucp0.iij.ad.jp (uucp0.iij.ad.jp [192.244.176.51]) by mail0.iij.ad.jp (8.6.12+2.4W/3.3W9-MAIL) with ESMTP id QAA04181 for ; Wed, 16 Aug 1995 16:06:19 +0900 Received: (from uucp@localhost) by uucp0.iij.ad.jp (8.6.12+2.4W/3.3W9-UUCP) with UUCP id QAA06044 for chemistry@ccl.net; Wed, 16 Aug 1995 16:06:19 +0900 Received: from C83009 by lab.takeda.co.jp (AIX 4.1/UCB 5.64/IIJ-U1.1) id AA23752; Wed, 16 Aug 1995 15:02:17 +0900 Date: Wed, 16 Aug 1995 15:02:17 +0900 Message-Id: <9508160602.AA23752@lab.takeda.co.jp> To: chemistry@ccl.net From: murakami@lab.takeda.co.jp (Morio Murakami) Subject: Ab initio MO calculation on spin density of aminyl radical Cc: murakami@lab.takeda.co.jp (Morio Murakami) Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8-J13) Dear CCLers: I have measured the ESR (electron spin resonance) spectrum of the aminyl radical, that was generated by the oxidation of the aromatic amine compound (PhNH2 type molecule). In order to interpret the hyperfine structure of this ESR signal, I need to calculate the spin density of this radical. In our laboratory, MOPAC and Gaussian (ab initio MO method) are available to us. I have calculated the aminyl radical, using Gaussian, but SCF calculation is unsuccessful. I recieved the following message from Gaussian. MESSAGE FROM GAUSSIAN >>>>>>>>>> Convergence criterion not met. SCF DONE: E(UHF) = -623.173164435 A.U. AFTER 65 CYCLES CONVG = .6507D-04 -V/T = 2.0042 S**2 = .7558 KE= 6.205858607182D+02 PE=-3.496078104843D+03 EE= 1.233735076388D+03 Annihilation of the first spin contaminant: S**2 BEFORE ANNIHILATION .7558, AFTER .7500 Convergence failure -- run terminated. Error termination in Lnk1e. Please inform me about this error message and tell me how to succeed in this ab initio calculation. Does anyone know any recent works and references about the calculation of spin density using ab initio MO method such as Gaussian program? Sincerely, Morio Murakami (E-mail murakami@lab.takeda.co.jp) From jkl@ccl.net Wed Aug 16 06:03:15 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id FAA16777; Wed, 16 Aug 1995 05:59:57 -0400 Received: from hermes.fundp.ac.be for pirard@couperin.scf.fundp.ac.be by bedrock.ccl.net (8.6.10/930601.1506) id FAA28078; Wed, 16 Aug 1995 05:59:54 -0400 Received: by hermes.fundp.ac.be; id AA11697; Wed, 16 Aug 1995 12:08:45 +0200 Received: from couperin.scf.fundp.ac.be by hermes.fundp.ac.be; id AA11697; Wed, 16 Aug 1995 12:08:45 +0200 Received: by couperin.scf.fundp.ac.be (AIX 3.2/UCB 5.64/4.03) id AA14003; Wed, 16 Aug 1995 11:35:37 +0200 From: Bernard Pirard Message-Id: <9508160935.AA14003@couperin.scf.fundp.ac.be> To: chemistry@ccl.net Subject: heparin Date: Wed, 16 Aug 95 11:35:37 +0100 Dear colleagues, Last year, David D R Devan from the Department of Biochemistry of the University of Virginia asked the followin question : "We are studying the ability of polyanions to act as enzymes inhibitors. The polyanions that we are using include heparin, dermatan sulfate, chondroitian sulfate, polygalacturonic acid, polyaspartic acid and polyglutamic acid. As part of these studies, we would like to generate computer models of the interaction of the polyanions with enzymes. I can find structures of short segments chondroitan sulfate in the Brookhaven PDB and some structural information for polyaminoacids (though at low pH). Can anyone provide information (reference for better coordinates for the models themselves) about models that have developed for these or other polyanions. We are especially interested in structural models of heparin". I would like to get a summary of the answers to this question. In addition, have additional papers been published in this field since last year. I will mail a summary of the answers. Many thanks in advance, Best regards, Bernard Pirard Research Assistant Laboratoire de Chimie Moleculaire Structurale rue de Bruxelles, 61 B-5000 Namur Belgium E-mail Pirard@SCF.FUNDP.AC.BE Fax 32 81 72 45 30 Tel 32 81 72 45 69 From thomas_w@btm2xg.mat.uni-bayreuth.de Wed Aug 16 06:33:16 1995 Received: from btr0x1.hrz.uni-bayreuth.de for thomas_w@btm2xg.mat.uni-bayreuth.de by www.ccl.net (8.6.10/950810.1506) id GAA16911; Wed, 16 Aug 1995 06:20:28 -0400 From: Received: from btm2xg.mat.uni-bayreuth.de by btr0x1.hrz.uni-bayreuth.de (4.1/btr0x1 (UBTGW/btr0x1-2.4.7)) id AA02767; Wed, 16 Aug 95 12:20:15 +0200 Received: from localhost by btm2xg.mat.uni-bayreuth.de; (5.65/1.1.8.2/21Nov94-0539PM) id AA07489; Wed, 16 Aug 1995 12:19:59 +0200 Message-Id: <9508161019.AA07489@btm2xg.mat.uni-bayreuth.de> To: FS300627@Sol.YorkU.CA, chemistry@www.ccl.net Subject: Re: CCL:New chemistry related WWW sites In-Reply-To: Your message of "Tue, 15 Aug 95 09:05:46 CDT." <01HU3HNGV5C2018ZFA@Sol.YorkU.CA> Date: Wed, 16 Aug 95 12:19:59 +0200 X-Mts: smtp In the announcement cited above, a program MOLGEN was advertised. We have, however, been developing a molecular structure generator called MOLGEN at least since 1992. So we were a little astonished about this announcement. To use this name, we would have preferred to be informed first before presenting it to the public. There is another modelling (or probably the same?) program with that name, usually distributed by J.E. Slone from George Mellon University, VA. In negotiations with Dr. Slone we came to the agreement that he will change the name of his program in its upcoming next release. We don't want to get into judical trials, but we insist on the name of our product MOLGEN: http://btm2xd.mat.uni-bayreuth.de/molgen Besides that, I announced our MOLGEN only a few months ago in this list and would have appreciated if Dr. van der Valk had looked up there first. Best regards, in the name of the MOLGEN crew Thomas Wieland +---------------+ Dipl. Math. |+---- +----+| Lehrstuhl II f. Mathematik |\ \ | || Universitaet Bayreuth | \ \ | || | \ \ | || 95440 Bayreuth | \ \\ || Germany | \ \\ || Tel. +49 (921) 553386 | \ \\ || Fax +49 (921) 553385 | \-------|| +---------------+ From jkl@ccl.net Wed Aug 16 08:33:17 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id IAA17973; Wed, 16 Aug 1995 08:32:43 -0400 Received: from xr1.atlas.fr for Olivier.O.GIGONZAC@RPR/RD/CRVA/INF.RP-RORER.rp.fr by bedrock.ccl.net (8.6.10/930601.1506) id IAA29807; Wed, 16 Aug 1995 08:32:38 -0400 From: X400-Received: by /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 14:32:22 +0200 X400-Received: by mta xr1.atlas.fr in /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 14:32:22 +0200 X400-Received: by /ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 14:32:32 +0200 X400-Received: by /PRMD=RP/ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 16:23:46 +0200 Date: Wed, 16 Aug 1995 16:23:46 +0200 X400-Originator: Olivier.O.GIGONZAC@RPR/RD/CRVA/INF.RP-RORER.rp.fr X400-Recipients: chemistry@ccl.net X400-MTS-Identifier: [/PRMD=RP/ADMD=ATLAS/C=FR/;SSWA 950816142343422351] X400-Content-Type: P2-1984 (2) Content-Identifier: converting 3D to Alternate-Recipient: Allowed Message-ID: <"SSWA 950816142343422351*/I=O/G=Olivier/S=GIGONZAC/OU=RPR$/RD$/CRVA$/INF/O=RP-RORER/PRMD=RP/ADMD=ATLAS/C=FR/"@MHS> To: "X400 -CHEMIOSC *?:CHEMISTRY" Subject: converting 3D to 2D Dear Netters, Do you know if someone has done a database containing all the ligands extracted from the PDB and where such a database is available ? Thanks in advance Sincerely, Dr. Anne Morgat CADD-MM Department Rhone-Poulenc Rorer Vitry/Seine France E-mail : morgat@rp.fr From jkl@ccl.net Wed Aug 16 08:48:18 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id IAA18010; Wed, 16 Aug 1995 08:38:36 -0400 Received: from xr1.atlas.fr for Olivier.O.GIGONZAC@RPR/RD/CRVA/INF.RP-RORER.rp.fr by bedrock.ccl.net (8.6.10/930601.1506) id IAA29923; Wed, 16 Aug 1995 08:38:31 -0400 From: X400-Received: by /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 14:37:30 +0200 X400-Received: by mta xr1.atlas.fr in /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 14:37:30 +0200 X400-Received: by /ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 14:37:40 +0200 X400-Received: by /PRMD=RP/ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 16:29:31 +0200 Date: Wed, 16 Aug 1995 16:29:31 +0200 X400-Originator: Olivier.O.GIGONZAC@RPR/RD/CRVA/INF.RP-RORER.rp.fr X400-Recipients: chemistry@ccl.net X400-MTS-Identifier: [/PRMD=RP/ADMD=ATLAS/C=FR/;SSWA 950816142923422391] X400-Content-Type: P2-1984 (2) Content-Identifier: Ligands extracte Alternate-Recipient: Allowed Message-ID: <"SSWA 950816142923422391*/I=O/G=Olivier/S=GIGONZAC/OU=RPR$/RD$/CRVA$/INF/O=RP-RORER/PRMD=RP/ADMD=ATLAS/C=FR/"@MHS> To: "X400 -CHEMIOSC *?:CHEMISTRY" Subject: Ligands extracted from the PDB Dear Netters, Do you know if someone has done a database containing all the ligands extracted from the PDB and where such a database is available ? Thanks in advance Sincerely, Dr. Anne Morgat CADD-MM Department Rhone-Poulenc Rorer Vitry/Seine France e-mail : morgat@rp.fr From jkl@ccl.net Wed Aug 16 08:59:35 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id IAA18015; Wed, 16 Aug 1995 08:38:39 -0400 Received: from xr1.atlas.fr for Olivier.O.GIGONZAC@RPR/RD/CRVA/INF.RP-RORER.rp.fr by bedrock.ccl.net (8.6.10/930601.1506) id IAA29926; Wed, 16 Aug 1995 08:38:34 -0400 From: X400-Received: by /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 14:37:33 +0200 X400-Received: by mta xr1.atlas.fr in /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 14:37:33 +0200 X400-Received: by /ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 14:37:43 +0200 X400-Received: by /PRMD=RP/ADMD=ATLAS/C=FR/; Relayed; Wed, 16 Aug 1995 16:29:34 +0200 Date: Wed, 16 Aug 1995 16:29:34 +0200 X400-Originator: Olivier.O.GIGONZAC@RPR/RD/CRVA/INF.RP-RORER.rp.fr X400-Recipients: chemistry@ccl.net X400-MTS-Identifier: [/PRMD=RP/ADMD=ATLAS/C=FR/;SSWA 950816142930422401] X400-Content-Type: P2-1984 (2) Content-Identifier: 3D to 2D Alternate-Recipient: Allowed Message-ID: <"SSWA 950816142930422401*/I=O/G=Olivier/S=GIGONZAC/OU=RPR$/RD$/CRVA$/INF/O=RP-RORER/PRMD=RP/ADMD=ATLAS/C=FR/"@MHS> To: "X400 -CHEMIOSC *?:CHEMISTRY" Subject: 3D to 2D Dear Netters, I am looking for softwares which are able to convert a 3D structure into a 2D representation for molecule as big as polypeptides or oligonucleotides. Do you know if such softwares exist and where they are available ? Thanks in advance Sincerely Anne Morgat CADD-MM Department Rhone-Poulenc Rorer Vitry/Seine France e-mail : morgat@rp.fr From jkl@ccl.net Wed Aug 16 09:48:18 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id JAA18966; Wed, 16 Aug 1995 09:35:41 -0400 Received: from rugch4.chem.rug.nl for tieleman@chem.rug.nl by bedrock.ccl.net (8.6.10/930601.1506) id JAA00955; Wed, 16 Aug 1995 09:35:32 -0400 From: Received: from rugmd10.chem.rug.nl by rugch4.chem.rug.nl with SMTP (1.38.193.4/16.2) id AA22574; Wed, 16 Aug 1995 15:35:11 +0200 Received: by rugmd10 (940816.SGI.8.6.9/930416.SGI) id PAA07403; Wed, 16 Aug 1995 15:35:08 +0200 Date: Wed, 16 Aug 1995 15:35:08 +0200 Message-Id: <199508161335.PAA07403@rugmd10> To: chemistry@ccl.net Subject: makefile for Gaussian 94, Cray J-16 We would like to install Gaussian 94 on a Cray J-16. Has anybody done this before? Does anybody have a makefile for building G94 on such a machine? I'd be most grateful for any help. Peter Tieleman -- email: tieleman@chem.rug.nl home: Louise Henriettestraat 11 telephone: 31-50-634338 9717 LH Groningen fax: 31-50-634800 The Netherlands address: Dept. of Biophysical Chemistry tel: 31-50-183714 Nijenborgh 4 9747 AG Groningen The Netherlands From smb@smb.chem.niu.edu Wed Aug 16 10:18:19 1995 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.10/950810.1506) id KAA19471; Wed, 16 Aug 1995 10:05:52 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA06945 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net>); Wed, 16 Aug 1995 09:06:02 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA17733; Wed, 16 Aug 95 07:56:52 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA03937; Wed, 16 Aug 95 07:56:51 -0500 Date: Wed, 16 Aug 95 07:56:51 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9508161256.AA03937@smb.chem.niu.edu> To: CHEMISTRY@www.ccl.net Subject: Academic Chemistry Employment Clearighouse With the acadmeic year just about opun us once again, I would like to remind everyone about the Academic Chemistry Employment Clearighouse that we run on the Northern Illinois University Chemistry WWW Site. This site lists job ads for chemists in the academic community. Jobs may be submitted at no cost, and are listed for 45 days. Please feel free to visit the site. You can access the NIU Chemistry WWW site at URL http://hackberry.chem.niu.edu Below are the instructions for submitting an ad to the service. Finally, we do have plans to open the service up to commercial employment opportunities as well in the near future. Stay tuned... Thanks, Steve ***************************************************** On-Line Academic Chemistry Employment Clearinghouse Sponsored by the Northern Illinois University Chemistry Web Site With the increasing difficulty in locating employment in the chemistry community, we wish to announce a new facility to aid in the search for jobs in the academic chemical community. The Northern Illinois University Chemistry Gopher and Web sites, sponsored by a pilot grant from the Camille and Henry Dreyfus Foundation, is now operating an academic employment clearinghouse on the Internet. Access to this clearinghouse is open to all, without charge, using the gopher or world-wide web navigation systems. This service will list employment opportunities in the chemical academic community, including jobs at the professor, instructor, post- doctoral, and graduate research assistant levels. Employment opportunities will be broken down into five categories (disciplines): analytical, inorganic, organic and physical chemistry and biochemistry. How to access the Clearinghouse To access the clearinghouse, you must have Internet access and either a gopher or web client. Access via gopher can be obtained by pointing your gopher client at hackberry.chem.niu.edu port 70. Access via the web is through URL: http://hackberry.chem.niu.edu/ How to Submit an Entry to the Clearinghouse Submission of a job listing is accomplished by electronic mail. The ad must be sent to chemjob@hackberry.chem.niu.edu and the Subject: line must have the following format Subject: discipline institution name where discipline is ANALYTICAL, BIOCHEM, INORGANIC, ORGANIC, or PHYSICAL (note that these terms do not have to been in caps) and the institution name is whatever name you wish to use as the heading of your listing. An example subject line is: Subject: organic StarFleet Academy - Assistant Professor The listings will be ordered alphabetically by institution name. The body of the message is format free and you may include as much detailed information you wish.Keep in mind that while this service is offered at NO CHARGE, very long files can lead to problems with maintenance of the service. An institution may submit more than one ad. Institutions are encouraged to place separate entries for every position offered. Listings will be maintained for 45 days and then automatically deleted. Once the file is deleted, feel free to resubmit the ad if the position is not yet filled. Once a listing is received, a return message will be sent to confirm the transmission. Entries will be added to the directories at midnight (CST) every day. ***************************************** Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From zauhar@rigel.tripos.com Wed Aug 16 10:48:19 1995 Received: from gatekeeper.tripos.com for zauhar@rigel.tripos.com by www.ccl.net (8.6.10/950810.1506) id KAA19939; Wed, 16 Aug 1995 10:37:20 -0400 Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id JAA13219; Wed, 16 Aug 1995 09:36:19 -0500 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma013217; Wed Aug 16 09:35:59 1995 Received: from rigel.tripos (rigel.tripos.com [192.160.145.150]) by tripos.tripos.com (8.6.12/8.6.12) with ESMTP id JAA17170; Wed, 16 Aug 1995 09:33:43 -0500 Received: by rigel.tripos (940816.SGI.8.6.9/5.6) id JAA07388; Wed, 16 Aug 1995 09:31:57 -0500 Date: Wed, 16 Aug 1995 09:31:57 -0500 From: zauhar@rigel.tripos.com (Randy Zauhar) Message-Id: <199508161431.JAA07388@rigel.tripos> To: chemistry@www.ccl.net, FS300627@Sol.YorkU.CA, Subject: Acronyms for programs Thomas Wieland wrote: > > In the announcement cited above, a program MOLGEN was advertised. > We have, however, been developing a molecular structure generator > called MOLGEN at least since 1992. So we were a little astonished > about this announcement. To use this name, we would have preferred > to be informed first before presenting it to the public. snip > We don't want to get into judical trials, but we insist on the name > of our product MOLGEN: > http://btm2xd.mat.uni-bayreuth.de/molgen > Speaking as someone who has come up with acronyms for my own programs, it has never occurred to me to do an extensive search to check for "collisions" when naming a program that is not intended to be a commercial product. Such names should be thought of as "shorthand", and I have seen several cases where unrelated programs had very similar names. The case is of course different if you are accidentally infringing on somone's trademark - but is that the case here? Thomas is writing from a university, but is already threatening to send lawyers!! Randy All opinions expressed here are mine, not my employer's ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // \\ Tripos, Inc. | : zauhar@crl.com // \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // \\ St. Louis, MO 63144 | // ///////////////////////////////////////////////////////////////////////// ** ** ** "If you have conceptions of things that you can have no conception ** ** of, then the conception and the thing appear to co-incide." ** ** --- C.G. Jung ** ************************************************************************* From jkl@ccl.net Wed Aug 16 11:33:21 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id LAA21192; Wed, 16 Aug 1995 11:28:49 -0400 Received: from faui45.informatik.uni-erlangen.de for jmolmod@organik.uni-erlangen.de by bedrock.ccl.net (8.6.10/930601.1506) id LAA03354; Wed, 16 Aug 1995 11:28:41 -0400 Received: from derioc1.organik.uni-erlangen.de by uni-erlangen.de with SMTP; id AA20266 (5.65c-7/7.3w-FAU); Wed, 16 Aug 1995 17:28:25 +0200 Received: by organik.uni-erlangen.de; id AA10086 (5.64/7.4b-FAU); Wed, 16 Aug 95 17:28:16 +0200 From: Journal of Molecular Modeling Message-Id: <9508161528.AA10086@derioc1.organik.uni-erlangen.de> Subject: J.Mol.Model. at the ACS Meeting To: chemistry@ccl.net Date: Wed, 16 Aug 95 17:28:08 METDST X-Mailer: ELM [version 2.3 PL11] .................................. : : : Are you one of the : : 10000 chemists : : who will see the : : : : Journal of Molecular Modeling : : : : live at the ACS Meeting : : : : or one of the million : : who can't ? : : : .................................. If you can not meet us personally come to know us through our WWW-homepage. Don't miss to have a look at our list of abstracts of published papers and feel free to get your personal copy of selected papers. The Journal of Molecular Modeling is the first journal in chemistry to offer network, print based and CD-ROM editions. Don't hesitate: here is your opportunity to compare three different presentation technologies and to get insight into the impact the WWW is going to have upon your daily scientific work. If you want to keep up pace with leading edge research in the field of molecular modeling and experience the rapid development of scientific publishing the Journal of Molecular Modeling is a must for you. Subscribe NOW to the first fully electronic journal in chemistry by getting your electronic order form from our WWW-homepage OR publish your next paper in the Journal of Molecular Modeling and become one of the authors pioneering the use of the Web in chemistry, thus shaping the future of scientific publishing. Journal of Molecular Modeling URL: http://www.organik.uni-erlangen.de/info/JMOLMOD/jmolinfo.html ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ Journal of Molecular Modeling ^ Tel: [+49](0)9131 / 85-2948 ^ ^ Computer-Chemie-Centrum ^ [+49](0)9131 / 85-6567 ^ ^ Universitaet Erlangen-Nuernberg ^ ^ ^ Naegelsbachstrasse 25 ^ Fax: [+49](0)9131 / 85-6565 ^ ^ D-91052 Erlangen ^ ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ email: jmolmod@organik.uni-erlangen.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ URL: http://www.organik.uni-erlangen.de/info/JMOLMOD/jmolinfo.html ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From jle@world.std.com Wed Aug 16 12:03:20 1995 Received: from europe.std.com for jle@world.std.com by www.ccl.net (8.6.10/950810.1506) id LAA21763; Wed, 16 Aug 1995 11:56:38 -0400 Received: from world.std.com by europe.std.com (8.6.12/Spike-8-1.0) id LAA13415; Wed, 16 Aug 1995 11:56:29 -0400 Received: by world.std.com (5.65c/Spike-2.0) id AA17032; Wed, 16 Aug 1995 11:55:58 -0400 Date: Wed, 16 Aug 1995 11:55:58 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199508161555.AA17032@world.std.com> To: chemistry@www.ccl.net Subject: Seeking LogP estimators/Lipophilic plotting Folks, I am interested in finding pointers to Log P estimation models (whole-molecule and particularly fragment-based) as well as lipophilicity plotting/surfaces. I am also interested in any survey articles which discuss the good/bad points of the commonly-used models. I will summarize if there is a good response... Thanks in advance, Joe Leonard jle@world.std.com From acp37@rs1.rrz.Uni-Koeln.DE Wed Aug 16 12:18:20 1995 Received: from rs1.rrz.Uni-Koeln.DE for acp37@rs1.rrz.Uni-Koeln.DE by www.ccl.net (8.6.10/950810.1506) id LAA21461; Wed, 16 Aug 1995 11:42:57 -0400 From: Received: by rs1.rrz.Uni-Koeln.DE id AA113024 (5.67b/IDA-1.5 for CCL ); Wed, 16 Aug 1995 17:42:30 +0200 Date: Wed, 16 Aug 1995 17:42:28 +0200 (MST) To: CCL Subject: Calculation on biradical Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, At the moment I am doing ab initio calculations on 1,5-Dehydronaphthalin, so it is supposed to be a biradical. It is an isomer to a ordinary closed-shell molecule which I am interested in. So to compare the energies of the molecules, I am interested in the singlet-groundstate of the biradical. But this doesn't seem to be a trivial problem. It was no problem at all to get the wavefunction for the triplet state. So I optimized the geometry for the triplet state and tried to get some singlet wavefunctions for this geometry. Here is what I got: 1. UHF, 6-31G*, mult=3 : E=-382.059168, =2.2470 (2.0346 after annihilation of first spin contaminant) 2. UHF, 6-31G*, mult=1 : E=-381.906022, =0.0000 This result was the same as the result with RHF. Especially the spin desity was zero everywhere. So I thought that this wouldn't be a proper description of a biradical. 3. UHF, 6-31G*, mult=1, GUESS=mix This calculation didn't converge at all. 4. In fact I was able to get another singlet state wavefunction. The only way to get it was from a stability analysis and optimization from the wavefunction obtained with 2. The result was: E=-382.086893, =2.2807 (8.1431 after annihilation of the first spin contaminant) At least the spin density gave two unpaired electrons with different spin at the right carbons. Because dft is known to give lower spin contaminations, I tried it this way: 5. UHF, 6-31G*/B3LYP, mult=3 : E=-384.510256, =2.0136 (1.9996) 6. UHF, 6-31G*/B3LYP, mult=1 : E=-384.484437, =0.000 Again the same result as with RHF, spin density zero everywhere. 7. UHF, 6-31G*/B3LYP, mult=1, GUESS=mix : E=-384.518499, =0.9392 (0.1510 after annihilation) This calculation had no difficulties to converge. ROHF calculations for the singlet states always gave the same wavefunction as for RHF calculations. So there are a couple of questions: a) Why is it so difficult to get a UHF singlet wavefunktion for a normal biradical? b) Can I rely on the energies obtained when the spin contamination is about 1.0 (Point 7.)? This is especially problematic because I want to compare it to the energiy of a closed-shell isomer. Since I got this results with 6-31G*/B3LYP it seems to be the best I can get... Is a geometry optimization sensible in this case? c) What can I say about the wavefunction of point 4.? The spin contamination is about 2.3 before annihilation (not a very small value for a singlet ;-) and about 8.1 AFTER annihilation of the first spin contaminant. I have no idea what this should mean! d) Am I right when I think that the spin density of a system with to unpaired electrons in the sigma frame separated far enough from another should exhibit these two electrons at the carbons they are attached to? e) Having all these problems in mind: Which way should I go to determine the energiy of the singlet ground state? Sorry for this somewhat lengthy question, but I'll summarize the responses, when there is interest :-) Bye, Thorsten /-----------------------------------------------------------------\ | Thorsten Koch | | Institut fuer physikalische Chemie II der Universitaet zu Koeln | | acp37@rrz.uni-koeln.de | | Tel. +49 [0]221 470 4816 | \-----------------------------------------------------------------/ From 94970459@vax1.dcu.ie Wed Aug 16 14:48:22 1995 Received: from VAX1.DCU.IE for 94970459@vax1.dcu.ie by www.ccl.net (8.6.10/950810.1506) id OAA23968; Wed, 16 Aug 1995 14:42:16 -0400 Received: from vax1.dcu.ie by vax1.dcu.ie (PMDF V4.2-12 #4433) id <01HU5HSI97KW9VVI3W@vax1.dcu.ie>; Wed, 16 Aug 1995 19:40:56 GMT Date: Wed, 16 Aug 1995 19:40:56 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: RUTHENIUM To: HYPERCHEM@HYPER.COM, CHEMISTRY@www.ccl.net Message-id: <01HU5HSIAA5U9VVI3W@vax1.dcu.ie> X-Envelope-to: CHEMISTRY@www.ccl.net X-VMS-To: IN%"HYPERCHEM@HYPER.COM" X-VMS-Cc: IN"CHEMISTRY@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi HyperChemers CCL'ers A colleague of mine needs parameters for Ruthenium so that she can molecular mechanics calculations in HyperChem with the MM+ force field. If you can supply such information for any oxidation state, we would be much obliged. Paddy. Paddy Kane Dublin City University Ireland 94970459@vax1.dcu.ie From eslone@osf1.gmu.edu Wed Aug 16 15:18:22 1995 Received: from osf1.gmu.edu for eslone@osf1.gmu.edu by www.ccl.net (8.6.10/950810.1506) id PAA24403; Wed, 16 Aug 1995 15:04:26 -0400 Received: by osf1.gmu.edu; (5.65v3.0/1.1.8.2/07Sep94-1001AM/GMUv3) id AA15760; Wed, 16 Aug 1995 15:03:35 -0400 Date: Wed, 16 Aug 1995 15:03:35 -0400 (EDT) From: Eric Slone To: Randy Zauhar Cc: chemistry@www.ccl.net, FS300627@Sol.YorkU.CA, thomas_w@btm2xg.mat.uni-bayreuth.de Subject: Re: CCL:Acronyms for programs In-Reply-To: <199508161431.JAA07388@rigel.tripos> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 16 Aug 1995, Randy Zauhar wrote: > > In the announcement cited above, a program MOLGEN was advertised. > > We have, however, been developing a molecular structure generator > > called MOLGEN at least since 1992. So we were a little astonished > > about this announcement. To use this name, we would have preferred > > to be informed first before presenting it to the public. > snip > > We don't want to get into judical trials, but we insist on the name > > of our product MOLGEN: > > http://btm2xd.mat.uni-bayreuth.de/molgen As co-author of the Molgen program cited as "offending", I can assure members of the list that the name is appropriately being used. This issue was resolved with one of Mr. Zauhar's co-authors. Eric ________________________________________________________________________________ J. Eric Slone George Mason University Department of Chemistry Fairfax, Virginia 22030-4444 Internet: eslone@gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Pager: (202) 597-2373 Miguel de Unamuno Voice: (703) 461-7078 ________________________________________________________________________________ From jlye@tx.ncsu.edu Wed Aug 16 16:18:22 1995 Received: from sparc4.tx.ncsu.edu for jlye@tx.ncsu.edu by www.ccl.net (8.6.10/950810.1506) id QAA25738; Wed, 16 Aug 1995 16:07:55 -0400 Received: from hamby.tx.ncsu.edu by sparc4.tx.ncsu.edu (8.6.9/ES17aug94) id QAA15520; Wed, 16 Aug 1995 16:07:52 -0400 Received: by hamby.tx.ncsu.edu (5.65b/SAM 12-13-90 16:56:22) id AA02978; Wed, 16 Aug 95 16:07:50 -0400 Date: Wed, 16 Aug 95 16:07:50 -0400 Posted-Date: Wed, 16 Aug 95 16:07:50 -0400 Message-Id: <9508162007.AA02978@hamby.tx.ncsu.edu> To: chemistry@www.ccl.net Cc: jlye@tx.ncsu.edu, dhinks@tx.ncsu.edu, Harold_Freeman@ncsu.edu From: jlye@tx.ncsu.edu (Jason Lye) Subject: MOPAC: Comments found in output files. X-Mailer: Cem X11/Mailer Version 9.2mgm (Wed Jan 5 12:38:09 EST 1994) Content-Type: text Content-Length: 1462 Dear Net-Surfers, Our group has recently started to use the CAChe Scientific implementation of MOPAC 6.0 to undertake some modeling work on dyestuffs. We have a few queries concerning comments found in the output files of MOPAC after geometry optimizations, which we have not been able to answer by looking in the MOPAC manual. 1st Comment: `GRADIENT TEST NOT PASSED, BUT FURTHER WORK NOT JUSTIFIED' `SCF FIELD WAS ACHEIVED' What does `gradient test not passed' mean, and should we worry about it? Why is `further work not justified'? 2nd Comment: `HERBERTS TEST WAS SATISFIED IN BFGS' What is Herbert's test? What does BFGS stand for? Finally, can anyone recomend a good book which covers molecular modeling with MOPAC, or other semi-empirical packages/methods. Thank you all for your time and effort; I will sumarise responses to the questions raised and post them to the list. Yours Faithfully, Jason _____________________________________________________________________________ Jason Lye, | "Light travels very fast indeed. Dye Synthesis Research Group, | So fast, in fact, that it takes College Of Textiles, Box 8301, | most civilizations many thousands of North Carolina State University, | years to work out that it travels Raleigh, N.C. 27695 - 8301 | at all." | Douglas Adams. jlye@tx.ncsu.edu | _____________________________________________________________________________ From zauhar@rigel.tripos.com Wed Aug 16 16:48:23 1995 Received: from gatekeeper.tripos.com for zauhar@rigel.tripos.com by www.ccl.net (8.6.10/950810.1506) id QAA26090; Wed, 16 Aug 1995 16:34:32 -0400 Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id PAA14502; Wed, 16 Aug 1995 15:33:38 -0500 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma014498; Wed Aug 16 15:33:22 1995 Received: from rigel.tripos (rigel.tripos.com [192.160.145.150]) by tripos.tripos.com (8.6.12/8.6.12) with ESMTP id PAA03420; Wed, 16 Aug 1995 15:31:05 -0500 Received: by rigel.tripos (940816.SGI.8.6.9/5.6) id PAA15829; Wed, 16 Aug 1995 15:29:20 -0500 Date: Wed, 16 Aug 1995 15:29:20 -0500 From: zauhar@rigel.tripos.com (Randy Zauhar) Message-Id: <199508162029.PAA15829@rigel.tripos> To: Randy Zauhar , Eric Slone Subject: Re: CCL:Acronyms for programs Cc: chemistry@www.ccl.net Dear CCLers, Although I THOUGHT my original post was clearly worded, it has already been misinterpreted by several people. Here are the facts: 1) I have nothing to do with EITHER of the MOLGEN programs! 2) I was simply commenting on what I perceived to be the overreaction of a MOLGEN author to the fact that someone else used the same name for their program. 3) I wrote this communication ONLY because I have been in the similar position of having invented an acronym for a program, only to discover that someone else also used it. 4) My employer, Tripos, Inc., knows NOTHING about a program called MOLGEN. 5) I have NO lawyers in my employ! I usually respond only to the authors of communications, not to the whole list, and should have followed that policy here!!! Sorry for the confusion, Randy All opinions expressed here are mine, not my employer's ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // \\ Tripos, Inc. | : zauhar@crl.com // \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // \\ St. Louis, MO 63144 | // ///////////////////////////////////////////////////////////////////////// ** ** ** "If you have conceptions of things that you can have no conception ** ** of, then the conception and the thing appear to co-incide." ** ** --- C.G. Jung ** ************************************************************************* From mark_hanning-lee@qmail2.aero.org Wed Aug 16 18:33:24 1995 Received: from aero.org for mark_hanning-lee@qmail2.aero.org by www.ccl.net (8.6.10/950810.1506) id SAA26990; Wed, 16 Aug 1995 18:32:16 -0400 Received: from qmail2.aero.org ([130.221.132.47]) by aero.org with SMTP id <111106-3>; Wed, 16 Aug 1995 15:31:44 -0700 Message-ID: Date: Wed, 16 Aug 1995 16:33:43 -0700 From: "Mark Hanning-Lee" Subject: Kinetics programs: summary To: "Compchem List" X-Mailer: Mail*Link SMTP-QM 3.0.2 Some time ago I posted this question to CCL: > We would like to get some new software to run simulations of chemical > kinetics. Our simulations would include gas-gas and gas-solid reactions, > and they might consider isothermal or adiabatic conditions. However, we do > not expect to model the kinetics of more than about 20 species. > > We have CHEMKIN from Sandia Labs (but we spend a lot of time editing > source code). We are also considering purchasing FACSIMILE from AEA Technology > (but the price seems a bit high). > > I like both pieces of software, but I would welcome any comments about > them. I would also be glad to hear about other software on the market. > Can anyone point me to users' groups, Usenet, etc.? > > I will summarise & post the responses. Thanks in advance, Mark. Unfortunately I forgot to mention that we were using Surface CHEMKIN not just CHEMKIN. Here are the responses: From: gotwals@mcnc.org (Bob Gotwals) ( 8/1/95 ) Check out STELLA, from High Performance Systems...this software models systems of first-order ODEs using Euler's or Runge-Kutta methods, and is cheap and easy to use.....take a look at the web page: http://tfnet.ils.unc.edu/~gotwals/stella/stella.html I have no financial or other interest, just a satisfied customer... _______________________________________________________________________ From: mecoltr@somnet.sandia.gov (Mike Coltrin) ( 8/1/95 ) Hello Mark, I saw your posting on the CCL about kinetics software and was just curious about a couple of things. I am not familiar with FACSIMILE, and wondered what it does. I also wanted to make sure that you had Sandia's Surface Chemkin package. It is supposed to make descriptions of gas-solid reactions easier (than mapping them onto gas-phase Chemkin). I also wondered if you were using any of the Sandia application codes, and if so which ones. (You mentioned that you spent a lot of time editing source code, and wondered what sort of modifications that you had to do. We are always interested in ideas for making our software better or more general or easier to use.) I don't know of user's groups or Usenet groups about Chemkin, but we have recently been wondering about the benefits of both. If I can be of any help, please let me know. ==================================================================== Mike Coltrin Phone: 505-844-7843 Sandia National Laboratories, MS 0601 Fax: 505-844-3211 Chemical Processing Sciences Dept. 1126 Albuquerque, NM 87185 coltrin@sandia.gov _______________________________________________________________________ Kinetics runs under Windows 3+: From: ars@ari.net (ARSoftware Corporation) ( 8/1/95 ) We have a kinetics program which will fit your needs. Our Kinetics program uses the GEAR method for the numerical integration of multistep rate equations. Systems contain up to 100 reversible reactions and 50 chemical compounds can easily be examined. Ea. individual reaction can contain as many as 5 reactants and 5 products.... We can also get the Fax machine for you at a reasonable price. You can contact us at 1-800-257-0073. Thank you. John ===================================================== ARSoftware Corporation 8201 Corporate Drive Landover, MD 20785 Phone: (301) 459-3773 FAX: (301) 459-3776 e-mail: ars@ari.net _______________________________________________________________________ Alexey kindly sent me this freeware DOS program by e-mail: From: abc@polytech.yaroslavl.su (A.V.Sokolov) ( 8/8/95 ) Dear Sir ! In reply to your question in CCL. Beg your pardon, I'd like to offer you something more. Several years ago when I worked in kinetic chemistry I'd written a programm for the purpose. Any simulation and optimization. Simultanious calculation of several variants. Math. expressions in Rate Constants (e.g. you can use Arrhenius form of them) etc. Never used since then and it's a pity. May be you'll like it. If you give me your incoming ftp directory I can send a program and a demo. The only problem with it was that optimization block (to calculate rate constants from experimental data) was not too much accomplished. But that are details. Respectfully yours, Alexey Sokolov, abc@polytech.yaroslavl.su And that's advertising sheet of those years. Kinetics Integrated Product for Simulation v2 of Chemical Technology Processes and Solution of Chemical Kinetics Problems. In simulation of chemical processes you may meet some calculation difficulties, i.e. composition of differential equation systems, adequate choice of numerical integration method, creation of efficient program for your PC, etc. Kinetics v2 will make it possible for you to deal only with chemical problems; it will turn any difficult work into a pleasant dialogue with your computer! Kinetics is: - an elaborated menu system for the input of data and kinetic scheme parameters; - a built-in calculator and text editor for the input chemical process schemes; - process layout in form that is customary among chemists; - flexibility and high speed during change of a kinetic scheme and its parameters; - a convenient way of viewing of calculation results; - a possibility to simultaneously process/view several variants of a process which differ in their initial conditions. The calculation is based upon the solution of the differential equation system with the Gear method. All calculations are automated, though you may change the calculation method parameters (step, accuracy). The simulated process is set by a number of chemical reactions. The rate constants and the initial concentrations may be input as mathematical expressions. That allows to study non-formal kinetics processes (catalytic, thermochemical, diffusive). There is a possibility to enter the experimental data for their optimization and for solution of a reverse kinetic problem. When viewing you may choose the following modes: chart\plot, smoothing, rate\concentration, anamorphosis. You may use intermediate concentration values of a calculation as the initial data for another variant. The kinetic scheme, its features and calculation results are stored on the disk for their repeated use. The results may be stored as a ASCII file and used in other programs. If you are not a chemist, you may use kinetics for the study of any process that is described by a system of the first order differential equations. E-Mail Address: abc@polytech.yaroslavl.su Post Address: Sokolov A.V. Computer Center, Technical University, Moskovsky Av. 88, Yaroslavl, 150053, Russia From jkl@ccl.net Wed Aug 16 19:18:25 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id TAA27208; Wed, 16 Aug 1995 19:13:04 -0400 Received: from portal.vpharm.com for markm@portal.vpharm.com by bedrock.ccl.net (8.6.10/930601.1506) id TAA10866; Wed, 16 Aug 1995 19:13:02 -0400 Received: by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA15102; Wed, 16 Aug 1995 19:00:13 -0400 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9508162300.AA15102@portal.vpharm.com> Subject: pKa of metal-bound water in protein active site To: chemistry@ccl.net Date: Wed, 16 Aug 1995 19:00:12 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 488 Hello all. I am looking for references to experimental data for the pKa's of water molecules bound to metals in protein active sites. In general, it is well known that the pKa comes down a great deal -- but what I want to know is any specific examples that people are aware of. Also, if there is a good review of the experimental data for metal - water pKa's in general (not just in the active site of proteins) that would be helpful too. Thanks in advance! / Mark (markm@vpharm.com) From boyd@chem.iupui.edu Wed Aug 16 19:28:53 1995 Received: from indyvax.iupui.edu for boyd@chem.iupui.edu by www.ccl.net (8.6.10/950810.1506) id TAA27222; Wed, 16 Aug 1995 19:16:52 -0400 Return-receipt-to: Boyd Received: from macgw.chem.iupui.edu by INDYVAX.IUPUI.EDU (PMDF V5.0-3 #5862) id <01HU5F7MTBR400O3PA@INDYVAX.IUPUI.EDU> for chemistry@www.ccl.net; Wed, 16 Aug 1995 18:16:48 -0500 Date: Wed, 16 Aug 1995 18:14:15 -0500 From: Boyd Subject: Chicago ACS To: OSC CCL Message-id: <01HU5F7MWT4Y00O3PA@INDYVAX.IUPUI.EDU> Content-transfer-encoding: 7BIT Hello, A preview copy of Volume 7 of "Reviews in Compuptational Chemistry" will be available at the VCH booth (#301,303) at the ACS National Meeting in Chicago next week. The contents of this volume are: Geoffrey M. Downs and Peter Willett, Similarity Searching in Databases of Chemical Structures Andrew C. Good and Jonathan S. Mason, Three-Dimensional Structure Database Searches Jiali Gao, Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials Libero J. Bartolotti and Ken Flurchick, An Introduction to Density Functional Theory Alain St-Amant, Density Functional Methods in Biomolecular Modeling Danya Yang and Arvi Rauk, The A Priori Calculation of Vibrational Circular Dichroism Intensities Donald B. Boyd, Compendium of Software for Molecular Modeling Volume 6, which was published earlier this summer, can also be inspected. Don Boyd URL http://chem.iupui.edu/