From chemistry-request@server.ccl.net Thu May 11 04:32:06 2000 Received: from gpo.cam.msi-eu.com (cam.msi-eu.com [192.190.183.254]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA18354 for ; Thu, 11 May 2000 04:32:05 -0400 Received: from msi-eu.com (dhcp105.cam.msi-eu.com [172.27.65.105]) by gpo.cam.msi-eu.com (8.9.3/8.9.3/Debian/GNU) with ESMTP id JAA11705 for ; Thu, 11 May 2000 09:29:54 +0100 Message-ID: <391A6F81.A6F95DAE@msi-eu.com> Date: Thu, 11 May 2000 09:29:53 +0100 From: Stephen Todd X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: MSI Presents: Polymer and Quantum Workshops in York Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Molecular Simulations Inc. will be holding a pair of 2 day workshops on Cerius2 between June 27th-30th, 2000 at the University of York, UK. The first 2 day workshop, entitled “Polymer Modeling in Cerius2”, is relevant to any of our customers who are interested in the use of Cerius2 in the area of polymer modeling. During the workshop, we will be covering an introduction to Cerius2 and the basics of molecular modeling, building polymers, using the amorphous cell builder and mesoscale modeling. The second 2 day workshop, entitled “Quantum and Solid State Modeling” is relevant to any customers that are interested in the use of Cerius2 in quantum and solid state modeling. During the workshop, we will be covering a brief introduction to Cerius2 and the basics of molecular modeling followed by training in the use of applications such as CASTEP and DMol3. Fees for the 2 day course are £650 commercial and £260 academic. Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's web site (http://www.msi.com/about/events/training). Please do not hesitate to contact me should you have any questions. Thank you very much. - Stephen Todd MSI Training Programs (+44) 1223 507568 -- For information regarding training sessions: http://www.msi.com/about/events/training/training_schedule.html Dr Stephen Todd Materials Science - Training tel: +44 1223 507568 Molecular Simulations Ltd fax: +44 1223 413301 240/250 The Quorum email: stodd@msi-eu.com Barnwell Road Cambridge CB5 8RE England From chemistry-request@server.ccl.net Thu May 11 12:30:42 2000 Received: from breaker.dakotacom.net (breaker.dakotacom.net [208.235.160.21]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA21125 for ; Thu, 11 May 2000 12:30:41 -0400 Received: (qmail 17119 invoked from network); 11 May 2000 16:19:37 -0000 Received: from tuc-dsl-7.dakotacom.net (HELO bear.dakotacom.net) (208.211.27.7) by breaker.dakotacom.net with SMTP; 11 May 2000 16:19:37 -0000 Message-ID: <02bf01bfbb65$b01943c0$0200000a@dakotacom.net> From: "Soaring Bear" To: References: Subject: CCL:Re:Herb Databases Date: Thu, 11 May 2000 09:25:03 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hello: > Does anyone know any structure and biological acitivities databases > of medicinal herbs, or where I may get more information? > Sue Kong > University of Miami HerbMed at http://www.amfoundation.org/herbmed.htm is an evidence-based resource for over a hundred plants now. Each herb has a standardized layout with clinical studies at top, going down through case reports, toxicity, preparation and biochemical mechanisms and chemical structures. There is a capsule of each abstract in accessible language and extensive linking to the Medline database and other sources on the internet to facilitate further study. Soaring Bear Ph.D. Research Pharmacologist, Informatics, Chemistry & Biochemistry, Herbalist & Healthy Lifestyles Herbal Science: http://www.amfoundation.org/herbmed.htm My web tools: http://www.dakotacom.net/~bear email: bear@dakotacom.net, sbear@uswestmail.net fax: 559-663-5833, 520-795-9350 From chemistry-request@server.ccl.net Thu May 11 12:49:11 2000 Received: from wodc7-2.relay.mail.uu.net (wodc7-2.relay.mail.uu.net [199.171.54.115]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA21322 for ; Thu, 11 May 2000 12:49:11 -0400 Received: from wodc7-1.uucp-gw.mail.uu.net by wodc7mr0.ffx.ops.us.uu.net with ESMTP (peer crosschecked as: wodc7-1.uucp-gw.mail.uu.net [199.171.54.178]) id QQiosx00468 for ; Thu, 11 May 2000 16:48:57 GMT Received: from wodc7uc0.ffx.ops.us.uu.net by wodc7ug0.ffx.ops.us.uu.net with SMTP (peer crosschecked as: wodc7-2.uucp.uu.net [199.171.54.180]) id QQiosx06349 for ; Thu, 11 May 2000 16:48:57 GMT Message-Id: Received: from m10.UUCP by wodc7uc0.ffx.ops.us.uu.net with UUCP/RMAIL ; Thu, 11 May 2000 16:48:57 +0000 Received: by m10.gaussian.com; Thu, 11 May 2000 12:43:20 -0400 Received: by mousse.gaussian.com; Thu, 11 May 2000 10:20:10 -0400 From: gaussian.com!moses@gaussian.com (David Moses) Subject: Announcing GaussViewW To: chemistry@ccl.net Date: Thu, 11 May 2000 10:20:09 -0400 (EDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Colleague: Gaussian, Inc. is pleased to announce the availability of GaussViewW (GVW), the latest development of the graphical interface, customized for use with Gaussian 98W. GVW is supported under Windows 95/98, Windows 2000 and Windows NT. Like G98W, GVW is a complete implementation, offering all the features and functionality contained in the Unix Workstation version. If you would like to obtain a license for GaussViewW, or if you desire additional information, please contact us at the e-mail address, telephone or fax numbers given below, or visit our WebSite at www.gaussian.com. We also remind users that we maintain a mailing list (both electronic and hardcopy) for those interested in receiving Gaussian announcements. Those on the mailing list will be updated about new implementations, revisions, and future developments of the Gaussian system of programs. You will also be informed about upcoming user meetings and workshops. To subscribe to our mailing list, please e-mail your full postal address to info@gaussian.com. *------------------------*------------------------*-----------------------* | David J. Moses, Ph.D. | Carnegie Office Park | info@gaussian.com | | Vice President, C.O.O. | Building Six | 412-279-6700 (Voice) | | Gaussian, Inc. | Pittsburgh, PA 15106 | 412-279-2118 (FAX) | *------------------------*------------------------*-----------------------* This notice is sent without warranty of any kind, expressed or implied. Gaussian and GaussView are registered trademarks of Gaussian, Inc. All other trademarks are the property of their respective holders. From chemistry-request@server.ccl.net Thu May 11 16:04:54 2000 Received: from lambda.inrs.uquebec.ca (lambda.inrs.uquebec.ca [207.162.3.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22360 for ; Thu, 11 May 2000 16:04:54 -0400 Received: from iaf.uquebec.ca ([198.168.44.40]) by lambda.inrs.uquebec.ca (Netscape Messaging Server 3.62) with ESMTP id 344 for ; Thu, 11 May 2000 16:01:45 -0400 Message-ID: <391B1481.EC29E282@iaf.uquebec.ca> Date: Thu, 11 May 2000 16:13:53 -0400 From: "Jianhui Wu" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CombiChem + Synthesizer Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, I am seeking for advice from people which apply computional chemistry in combinatorial chemistry and have experience in organic synthesizer. (1) What software do you use? We are looking for a software that can generate combinatorial library according to the binding site of recepter (vdw, electrostatic, solvation). A designed compound will be useful only when it can be made in the lab. The construction of each compound should therefore comply with known organic reaction rules. The library will perhaps be screened by docking study (virtual screen) to obtain top 100-200 candiates for organic synthesizer. Do you cluster the library and virtually screen each sublibrary? What property people usually use to cluster a library? (2) Which model of synthesizer do you use? We are looking for a small organic synthesizer that have 20-40 vessels, capable of doing Solid phase/solution phase reaction and temperature can be adjusted. In other words, it should be cheap and still can do the job although it is small. If you have experience on this kind of parallel organic synthesizer, please give me some advice (what model, from which company, is it really doing the job?). Thanks a lot, Jian Hui Wu Institute Armand-Frappier 531 Boul des prairies Laval, Quebec H7N 4Z3 Phone: 1-450-687-5010 ext 4329 Fax: 1-450-686-5501, 1-450-9780198 email: JianHui_Wu@IAF.Uquebec.ca From chemistry-request@server.ccl.net Thu May 11 21:08:27 2000 Received: from linux2.ipc.pku.edu.cn (mao@linux2.ipc.pku.edu.cn [162.105.177.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA23831 for ; Thu, 11 May 2000 21:08:24 -0400 Received: from localhost (mao@localhost) by linux2.ipc.pku.edu.cn (8.9.3/8.9.3) with ESMTP id JAA27320 for ; Fri, 12 May 2000 09:13:23 +0800 Date: Fri, 12 May 2000 09:13:23 +0800 (CST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: summary: Superpose algorithm Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII >From Nick Jewell, If I've got this right, some superposition algorithms (for small molecules) include: Flex-S : http://www.tripos.com by Gerhard Klebe ASP: http://www.oxmol.co.uk by Kate Burt and Graham Richards FBSS: http://cisrg.shef.ac.uk by Dave Wild and Peter Willett -------------------------------------------------------------------------- >From Anselm Horn, try the quatfit program in the CCL archives (references are given within). -------------------------------------------------------------------------- >From Jarrod Smith, Kearsley, Simon K; "An Algorithm for the Simultaneous Superposition of a Structural Series"; J. Comp. Chem., 11, 1187-1192 (1990). -------------------------------------------------------------------------- Found by myself, Ferro D R and J Hermans 1977, A Different Best Rigid-body Molecular Fit Routine, Acta Crystallography A33:345-347 Kabsch W 1978. A Disscussion of the Solution for the Best Rotation to Relate Two Sets of Vectors. Acta Crystallography A34:827-828. Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Institute of Physical Chemistry Peking University BeiJing P.R.China Tel:86-10-62756833 Fax:86-10-62751725 From chemistry-request@server.ccl.net Fri May 12 06:42:58 2000 Received: from lilac.csi.cam.ac.uk (exim@lilac.csi.cam.ac.uk [131.111.8.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA26602 for ; Fri, 12 May 2000 06:42:57 -0400 Received: from su4.phar.cam.ac.uk ([131.111.156.196]) by lilac.csi.cam.ac.uk with smtp (Exim 3.13 #1) id 12qCu1-0003fp-00; Fri, 12 May 2000 11:42:41 +0100 Received: from sg4.phar.cam.ac.uk by su4.phar.cam.ac.uk (SMI-8.6/CS-SUB) id LAA27562; Fri, 12 May 2000 11:42:10 +0100 Received: from localhost by sg4.phar.cam.ac.uk; Fri, 12 May 2000 11:42:09 +0100 (BST) Date: Fri, 12 May 2000 11:42:09 +0100 (BST) From: James Smith X-Sender: js252@sg4.phar.cam.ac.uk To: Fenglou Mao cc: "CHEMISTRY@www.ccl.net" Subject: More Superposition algorithms In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We use: Gerber & Muller (1987) Superimposing Several Sets of Atomic Coordinates, Acta Cryst, A43, 426-428 Perkins & Dean (1993) An exploration of a novel strategy for superposing several flexible molecules, J. Computer-Aided Molecular Design, 7, 155-172 Also McLaughlin's algorithm for superposing two molecules. Which also allows the use of null correspondances Could have a look at: Masek, Merchant and Matthew's method also uses Molecular Skins: A New Concept for Quantitative Shape Matching of a Protein with it Small Molecule Mimics _________________________________________________________________________ James Smith Drug Design Group 01223 338 600 (College) St John's College Department of Pharmacology 01223 331 985 (Office) Cambridge University of Cambridge 01223 331 740 (Fax) CB2 1TP CB2 1QJ 07625 395 084 (Pager) United Kingdom United Kingdom js252@cam.ac.uk http://www.cus.cam.ac.uk/~js252 _________________________________________________________________________ From chemistry-request@server.ccl.net Fri May 12 11:10:42 2000 Received: from mail.mpi-sb.mpg.de (mail.mpi-sb.mpg.de [139.19.1.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA28459 for ; Fri, 12 May 2000 11:10:41 -0400 Received: from mpii03905.ag1.mpi-sb.mpg.de (mpii03905.ag1.mpi-sb.mpg.de [139.19.10.224]) by mail.mpi-sb.mpg.de (8.8.7/8.8.8) with ESMTP id RAA17524 for ; Fri, 12 May 2000 17:10:31 +0200 Received: from mpii03905 (localhost.mpi-sb.mpg.de [127.0.0.1]) by mpii03905.ag1.mpi-sb.mpg.de (8.9.3/8.9.3) with ESMTP id RAA18318 for ; Fri, 12 May 2000 17:10:54 +0200 (MET DST) Message-Id: <200005121510.RAA18318@mpii03905.ag1.mpi-sb.mpg.de> X-Mailer: exmh version 2.0.3 2/24/98 To: CHEMISTRY@ccl.net Subject: IGLO III basis sets Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Fri, 12 May 2000 17:10:53 +0200 From: Oliver Kohlbacher Dear CCLers, has anybody the IGLO III basis sets by Kutzelnigg et al. available in a digital format (preferably for Gaussian 98)? Many thanks in advance, Oliver ---- Oliver Kohlbacher (oliver@mpi-sb.mpg.de) Max-Planck-Institut fuer Informatik, Im Stadtwald, 66123 Saarbruecken/GERMANY Tel.: 0681-9325-140 Fax: 0681-9325-199 From chemistry-request@server.ccl.net Fri May 12 11:58:21 2000 Received: from mail.science.siu.edu (mail.science.siu.edu [131.230.107.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA28714 for ; Fri, 12 May 2000 11:58:21 -0400 Received: from tapas (131.230.99.83) by mail.science.siu.edu with SMTP (Eudora Internet Mail Server 2.2.2); Fri, 12 May 2000 10:58:10 -0500 Message-ID: <003f01bfbc2a$aae75980$5363e683@thchem.siu.edu> From: "Tapas Kar" To: "CCL" Subject: GAMESS problem Date: Fri, 12 May 2000 10:56:43 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi GAMESS experts/users, I got the following error while doing a MOROKUMA analysis. What's make a change to Normal termination of the job. PWRT: NODE 0 ENCOUNTERED I/O ERROR WRITING UNIT 8 EXECUTION OF GAMESS TERMINATED ABNORMALLY Input file: $CONTRL SCFTYP=RHF RUNTYP=MOROKUMA ICHARG= 0 MULT=1 UNITS=BOHR $END $basis gbasis=n311 ngauss=6 ndfunc=3 npfunc=3 DIFFSP=.TRUE. DIFFS=.TRUE. $end $MOROKM iatm(1)=7 $END $DATA hoc(o)ooh-h2o geometry C1 1 Second question: How to include H's d function in the basis set? Tapas ---------------------------------------------------- Tapas Kar Department of Chemistry 1245 Lincoln Dr. # 146F Southern Illinois University Carbondale, IL 62901-4409 Tel: 618-453-6485(Off)/6433(Lab) Fax: 618-453-6408 email: tapaskar@siu.edu tapas@risky3.thchem.siu.edu