From chemistry-request@server.ccl.net Wed Apr 2 01:09:56 2003 Received: from pu.ac.in ([203.200.97.230]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3269kf15627 for ; Wed, 2 Apr 2003 01:09:55 -0500 Received: from pu.ac.in ([192.168.4.201]) by pu.ac.in (8.11.0/8.11.0) with ESMTP id h3277rb06453; Wed, 2 Apr 2003 12:37:58 +0530 Message-ID: <3E8A7E17.6020209@pu.ac.in> Date: Wed, 02 Apr 2003 11:37:19 +0530 From: parveen Organization: P.U User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20021003 X-Accept-Language: en-us, en MIME-Version: 1.0 To: gamess-l@gl.ciw.edu, chemistry@ccl.net Subject: Problems with nbo Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear All, After a lot of effort we compiled NBO with the latest GAMESS version. After running a sample file, we are getting an error: STOP Unknown WFNTYP statement executed ******************************************************************************* N A T U R A L A T O M I C O R B I T A L A N D N A T U R A L B O N D O R B I T A L A N A L Y S I S ******************************************************************************* Filename: Changed to FILE1 Broken pipe unknown WAVEFNTYP used The INPUT file was the following: $CONTRL SCFTYP=RHF RUNTYP=ENERGY COORD=ZMT $END $SYSTEM TIMLIM=2 MEMORY=100000 $END $BASIS GBASIS=n21 NGAUSS=3 $END $GUESS GUESS=HUCKEL $END $NBO $END $DATA Methylamine Cs C N 1 1.47 H 1 1.09 2 109.4712 H 1 1.09 2 109.4712 3 120.0 H 1 1.09 2 109.4712 3 240.0 H 2 1.01 1 109.4712 3 60.0 H 2 1.01 1 109.4712 3 300.0 $END Any clues? Thanks.............. Parveen From jkl@ccl.net Tue Apr 1 08:00:56 2003 -0500 Return-Path: Message-ID: From: Emma Roberts To: "'jkl@ccl.net'" Cc: "'elewars '" Subject: New Book on Computational Chemistry Date: Tue, 1 Apr 2003 07:53:37 -0500 Emma Roberts, PhD Senior Publishing Editor (Chemistry) Kluwer Academic Publishers 241 Borough High Street London SE1 1GB UK Email: emma.roberts@wkap.com Tel: +44 (0) 20 7940 8482 Fax: +44 (0) 20 7940 7496 ______________________________ ==================================================================== Computational Chemistry: Introduction to the Theory and Applications of Molecular Quantum Mechanics by Errol Lewars. Dear Colleagues, We are pleased to announce this recently published book title, available as both a hardback and paperback. Please find below some brief details as well as an abbreviated Table of Contents. If you require further information, please contact me or see: http://www.wkap.nl/prod/b/1-4020-7285-6 Best wishes, Emma Roberts Senior Publishing Editor (Chemistry) Kluwer Academic Publishers E-mail: emma.roberts@wkap.com -------------------------------------------------------------------- Computational chemistry has become extremely important in the last decade, being widely used in academic and industrial research. Yet there have been few books designed to teach the subject to nonspecialists. Computational Chemistry: Introduction to the Theory and Applications of Molecular and Quantum Mechanics is an invaluable tool for teaching and researchers alike. The book provides an overview of the field, explains the basic underlying theory at a meaningful level that is not beyond beginners, and it gives numerous comparisons of different methods with one another and with experiment. The following concepts are illustrated and their possibilities and limitations are given: * potential energy surfaces * simple and extended Hückel methods * ab initio, AM1 and related semiempirical methods * density functional theory (DFT) Topics are placed in a historical context, adding interest to them and removing much of their apparently arbitrary aspect. The large number of references, to all significant topics mentioned, should make this book useful not only to undergraduates but also to graduate students and academic and industrial researchers. Table of Contents Chapter 1: An outline of what computational chemistry is all about Chapter 2: The concept of the potential energy surface Chapter 3: Molecular mechanics Chapter 4: Introduction to quantum mechanics in computational chemistry Chapter 5: Ab initio calculations Chapter 6: Semiempirical calculations Chapter 7: Density functional calculations Chapter 8: Literature, software, books and websites Approximately 470 pages -------------------------------------------------------------------- ==================================================================== From chemistry-request@server.ccl.net Tue Apr 1 16:16:48 2003 Received: from aguila.dti.udec.cl ([152.74.16.63]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h31LGcC08031 for ; Tue, 1 Apr 2003 16:16:42 -0500 Received: (qmail 11694 invoked from network); 1 Apr 2003 21:16:32 -0000 Received: from andes.dpi.udec.cl (HELO pccarola) ([127.0.0.1]) (envelope-sender ) by 0 (qmail-ldap-1.03) with SMTP for ; 1 Apr 2003 21:16:32 -0000 Message-ID: <003001c2f894$169f92c0$0e0f4a98@pccarola> From: =?iso-8859-1?Q?Carola_Bruna_Jofr=E9?= To: Subject: help chemistry Date: Tue, 1 Apr 2003 17:17:23 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002D_01C2F872.8F692CB0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_002D_01C2F872.8F692CB0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Where can I obtain Zinc-related parameters? I use HyperChem, which has = until Amber 96.=20 I have been asked to model a mutation in a protein which has Zinc = fingers. It is a phosphorilation, so the charge of the Zn ion is = important and to maintain the finger structure I need to establish that = it is coordinated by 4 cysteines. Unfortunately Zn iones are not = recognized. Please, if anybody can give me some guidelines, I would be very = grateful. Best regards, Carola Bruna Jofr=E9 Universidad de Concepci=F3n Chile ------=_NextPart_000_002D_01C2F872.8F692CB0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Where can=20 I obtain Zinc-related parameters? I use HyperChem, which has until Amber = 96.=20

I have=20 been asked to model a mutation in a protein which has Zinc fingers. It = is a=20 phosphorilation, so the charge of the Zn ion is important and to = maintain the=20 finger structure I need to establish that it is coordinated by = 4=20 cysteines. Unfortunately Zn iones are not recognized.

Please, if=20 anybody can give me some guidelines, I would be very = grateful.

 
Best regards,
 
Carola Bruna Jofr=E9
Universidad de = Concepci=F3n
Chile
------=_NextPart_000_002D_01C2F872.8F692CB0-- From chemistry-request@server.ccl.net Tue Apr 1 16:57:53 2003 Received: from web21210.mail.yahoo.com ([216.136.175.253]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h31Lvr708994 for ; Tue, 1 Apr 2003 16:57:53 -0500 Message-ID: <20030401215753.38424.qmail@web21210.mail.yahoo.com> Received: from [4.20.197.6] by web21210.mail.yahoo.com via HTTP; Tue, 01 Apr 2003 13:57:53 PST Date: Tue, 1 Apr 2003 13:57:53 -0800 (PST) From: Konstantin Kudin Subject: Re: CCL:Report from the ACS in New Orleans To: h.rzepa@ic.ac.uk, chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear colleagues I'd like to find out what was the company that presented the 3D technology described below. I stopped by at the same booth, and was quite impressed by the demo they had. They showed a clip converted into a pseudo-3D from flat images and it looked not as good as true 3D but better than 2D. The modelling part was good too. I talked to the presenter briefly, and he mentioned that he actually was from a different company (not Fujitsu). Unfortunately, I did not write down the name, and can't remember what the company was. Anybody remembers/knows what was the company with that 3D technology? Thanks! Konstantin > ---------- Forwarded message ---------- > Date: Fri, 28 Mar 2003 13:02:57 +0000 > From: "Rzepa, Henry" > To: chemweb@ic.ac.uk > Subject: Report from the ACS in New Orleans > > Its been a few years since I did one of these > reports from an ACS > meeting, but one item in particular caught my (and > a lot of other ) eyes. > > CAChe were displaying LCD panel monitors which > display true 3D images > WITHOUT any need for glasses. The technology > apparently comes in four > flavours, each vying for market, which is a good > omen for costs, which are > expected to come spiraling down over the next 12 > months. > > The largest display is a 40" (@$17,000), a 20" (@ > around $8000) and most > interestingly, a laptop to be released later this > year. The effects were remarkable, > although the depth of stereo vision is probably not > (yet) as impressive as dedicated > Crystaleyes systems > > Currently, it does need software drivers (openGL) > and so specific software > must be enabled. The CAChe software is so, and I > gather a Powerpoint > enabled 3D display is on the cards; I argued for > enabling the Weh browser, > perhaps Mozilla/Netscape will do it? > > >From what we saw, and with the predictions, it does > seem that any serious > molecular modeller or anyone interested in the 3D > properties of molecules > will be buying themselves these 3D LCD panels > routinely in a years time > or so! > > Apparently, a demonstration might be on the cards > at Heathrow Airport on April > 24. Anyone who is seriously interested in attending > should contact > Magda Karabon for free registration at + 48 12 429 > 43 45 or ccs@fqspl.com.pl > -- > > Henry Rzepa. > +44 (0870) 132 3747 (eFax) > http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, > Imperial College London, SW7 2AZ, UK. > > > chemweb: A list for Chemical Applications of the > Internet. > To post to list: mailto:chemweb@ic.ac.uk > Archived as: > http://www.lists.ic.ac.uk/hypermail/chemweb/ > To (un)subscribe, mailto:majordomo@ic.ac.uk the > following message; > (un)subscribe chemweb > List coordinator, Henry Rzepa > (mailto:rzepa@ic.ac.uk) > > > > -= This is automatically added to each message by > mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > __________________________________________________ Do you Yahoo!? Yahoo! Tax Center - File online, calculators, forms, and more http://platinum.yahoo.com From chemistry-request@server.ccl.net Wed Apr 2 02:37:58 2003 Received: from mail.fqspl.com.pl ([212.244.147.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h327bwf17196 for ; Wed, 2 Apr 2003 02:37:58 -0500 Received: (qmail 27629 invoked by uid 505); 2 Apr 2003 07:28:57 -0000 Received: from magda@fqspl.com.pl by mail by uid 502 with qmail-scanner-1.13 ( Clear:. Processed in 0.044018 secs); 02 Apr 2003 07:28:57 -0000 Received: from unknown (HELO magda) (212.244.147.4) by mail.fqspl.com.pl with SMTP; 2 Apr 2003 07:28:56 -0000 Message-ID: <004801c2f8ea$58f7b660$200a0a0a@fqspl.com.pl> Reply-To: "Karabon Magdalena" From: "Karabon Magdalena" To: Subject: Seminar: Active-Site Identification, Ligand Design and QSAR; New Windows-based SW Tools Date: Wed, 2 Apr 2003 09:34:24 +0200 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 5.50.4920.2300 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 Seminar: "Active-Site Identification, Ligand Design and QSAR; New Windows-based SW Tools" date: 24th of April, 2003 (10.30 am - noon) place: Crowne Plaza Hotel, Heathrow, London, UK A presentation and demonstration of the latest Windows-based tools for analysing proteins, locating active sites and designing ligands will be offered, including examples of homology modelling, rational drug design, pharmocaphore modelling, 3D sequence alignment and superposition, and novel quantum methods for calculating electronic properties of whole proteins. Quantitative Structure-activity Relationships (QSAR) and fast screening methods for predicting properties such as pKa, water solubility, HIA, Rule-of-5, carcinogenicity, antibacterial activity, etc. will also be reviewed. (presentation - 55mins; demonstration - 25 mins) Sponsored by Fujitsu. For details and free registration please contact Ms. Magda Karabon at magda@fqspl.com.pl or call: + 48 12 429 43 45 From chemistry-request@server.ccl.net Tue Apr 1 22:45:51 2003 Received: from bioboss.bio.ucalgary.ca ([136.159.234.204]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h323jpf13972 for ; Tue, 1 Apr 2003 22:45:51 -0500 Received: (from craig@localhost) by bioboss.bio.ucalgary.ca (SGI-8.9.3/8.9.3) id UAA27225 for chemistry@ccl.net; Tue, 1 Apr 2003 20:45:35 -0700 (MST) Date: Tue, 1 Apr 2003 20:45:35 -0700 (MST) From: Craig Shepherd Message-Id: <200304020345.UAA27225@bioboss.bio.ucalgary.ca> To: chemistry@ccl.net Subject: 1D secondary structure plot Hi all, Does anyone know of a tool or viewer which can take a PDB file and, based on the secondary structure, make a one-dimensional secondary structure plot? What I'm envisioning is the type of figures where helices are drawn as rectangles or cylinders and sheet elements are drawn as arrows. Some database websites might do this, but ideally I'd like to have a scalable PostScript plot rather than a rasterized image. Also, since I'd like to place pictures like this above or below graphs displaying quantities calculated on a per-residue (or per-atom) basis from an MD simulation (so as to make clearer which secondary structure elements are involved), I'd like a standalone tool that could work on an intermediate structure from the simulation, not just a structure from a database. Sorry about the length of the message - just wanted to be specific about what I would ideally like. Many thanks, Craig Shepherd From chemistry-request@server.ccl.net Tue Apr 1 18:06:25 2003 Received: from sciences.sdsu.edu ([130.191.226.112]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h31N6O709876 for ; Tue, 1 Apr 2003 18:06:25 -0500 Received: from localhost (jcuervo@localhost) by sciences.sdsu.edu (8.11.6+Sun/8.8.8/SCEC-8.8.8-AS.AR.S5) with ESMTP id h31N6Oh27407 for ; Tue, 1 Apr 2003 15:06:24 -0800 (PST) Date: Tue, 1 Apr 2003 15:06:24 -0800 (PST) From: Javier Cuervo To: chemistry@ccl.net Subject: Installing AMBER7 on alpha Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, I'm triying to build amber7 on an alpha machine, I set the following: ln -s -f Machines/Machine.axp MACHINE or ln -s -f Machines/Machine.axp_f90 MACHINE and I got the following error: mkdir ../exe mkdir: cannot create directory `../exe': File exists make: [install] Error 1 (ignored) cd lib; make install make[1]: Entering directory `/home/jcuervo/amber/amber7/src/lib' ../Compile L2 -P new2oldparm.f cat new2oldparm.f | /lib/cpp -C -P -DAXP_OSF -DNO_SIGN -DHAS_FTN_ERFC > _new2oldparm_.f :360:25: missing terminating ' character :361:52: missing terminating ' character :362:6: missing terminating ' character make[1]: *** [new2oldparm.o] Error 1 make[1]: Leaving directory `/home/jcuervo/amber/amber7/src/lib' make: *** [install] Error 2 If I check the file new2oldparm.f, I can't find anything wrong, actually lines 360-362 are comments... I would really apreciate any help Regards Javier Cuervo Graduate Student Computational Sciences Program San Diego State University From chemistry-request@server.ccl.net Tue Apr 1 17:30:05 2003 Received: from sandmail01.sd.accelrys.com ([209.120.169.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h31MU4709458 for ; Tue, 1 Apr 2003 17:30:04 -0500 To: chminf-l@listserv.indiana.edu, chemistry@server.ccl.net, qsar_society@accelrys.com Subject: CINF Program at the 226th ACS National Meeting in New York MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: "Osman F Guner" Date: Tue, 1 Apr 2003 14:29:58 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 04/01/2003 02:30:05 PM, Serialize complete at 04/01/2003 02:30:05 PM Content-Type: multipart/alternative; boundary="=_alternative 007B608C88256CFB_=" This is a multipart message in MIME format. --=_alternative 007B608C88256CFB_= Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable You are invited to participate with the Chemical Information Division=20 program at the upcoming ACS National Meeting in New York, September 7-11,=20 2003. Please use the OASYS to submit your abstracts (click on CINF at http= ://oasys.acs.org/oasys.htm). The deadline for submitting abstracts is May = 12th, 2003. For any=20 further questions, contact individual session organizers directly. New York, Sept. 7-11, 2003 Division of Chemical Information Program Chair: O. F. G=FCner, Accelrys Inc, 9685 Scranton Road, San Diego, = CA 92121-3752, 858-799-5341, fax 858-7995100, e-mail: osman@accelrys.com=20 Please note that 35mm slide projector are no longer considered standard=20 equipment. If you need to use a slide projector, you need to indicate=20 this. Advances in reaction searching T. Wright, MDL Information Systems, Inc, 146= 00 Catalina Street, San=20 Leandro, CA 94577, 510-357-2222, fax 510-614-3652, e-mail: terryw@mdli.com At your Fingertips: Use of PDAs in Chemical Information E. Kajosalo, Librar= ies, Massachusetts Institute of Technology, 77=20 Masschusetts Avenue, Room 14S-134, Cambridge, MA 02155, 617-253-9795, fax=20 617-253-6365, e-mail: kajosalo@mit.edu Building the virtual chemistry library: e-books and e-journals A. B. Twiss-= Brooks, John Crerar Library, University of Chicago, 5730 S.=20 Ellis, Chicago, IL 60637, 773-702-8777, fax 773-702-7429, e-mail:=20 atbrooks@midway.uchicago.edu; S. E. Lee, Symyx Technologies, Inc, 3100=20 Central Expressway, Santa Clara, CA 95051, 408-330-3974, fax 408-492-9178, = e-mail: slee@symyx.com Business information for chemists (Cosponsored with bmgt). T. Hoctor, MDL I= nformation Systems, Inc, 14600=20 Catalina Street, San Leandro, CA 94577, 510-895-1313, fax 510-614-3651,=20 e-mail: timh@mdli.com Careers in Chemical Information (Cosponsored with ycc). P. Barnett, Science= /Engineering Library, City=20 College of New York, Convent Avenue at 138th Street, New York, NY 10031,=20 212-650-8243, fax 212-650-7626, e-mail: phibarn@sci.ccny.cuny.edu Emerging Trends in Discovery Data Integration M. A. Miller, LION Bioscience= , 955 Ridge Hill Lane, Suite 30, Midvale, UT=20 84047, 801 569 1390, e-mail: mitchell.miller@lionbioscience.com Fishing for the right scientific information in the information sea E. M. S= hanbrom, Manager, CAS and Web Content, Chemical Abstracts Service,=20 2540 Olentangy River Road, Columbus, OH 43202, (614) 447-3710, fax (614)=20 461-7149, e-mail: eshanbrom@cas.org General Papers O. F. G=FCner Novel database and knowledge mining techniques (Cosponsored with medi). S. = B. Singh, Department of Pharmaceutical=20 Chemistry, Merck Research Laboratories, RY50SW 100, 126 E. Lincoln Avenue, = Rahway, NJ 07065, 732-594-4954, fax 732-594-4224, e-mail:=20 suresh=5FSingh@merck.com Sci-Mix Posters O. F. G=FCner Skolnik Award Symposium: Crystallographic Databases and their Applications = in Structural Chemistry, Drug Design and Materials Development F. H. Allen,= CCDC, 12 Union Road, Cambridge, CB2 1EZ, United Kingdom,=20 +44-(0)1223-336425, fax +44-(0)1223-336033, e-mail: allen@ccdc.cam.ac.uk Standards for Chemistry Informatics J. Rumble Jr., Standard Reference Data,= NIST, 100 Bureau Drive MS 2310,=20 Gaithersburg, MD 20899-2310, 301 975 2203, fax 301-926-0416, e-mail:=20 john.rumble@nist.gov Technical Intelligence A. Trippe, Vertex Pharmaceuticals Inc, 130 Waverly S= t, Cambridge, MA=20 02139, 617-444-6459, fax 617-444-6680, e-mail: tony=5Ftrippe@vrtx.com Osman F. G=FCner, Ph.D. Executive Director Cheminformatics and Rational Drug Design Accelrys Inc., 858-799-5341 osman@accelrys.com, http://www.accelrys.com --=_alternative 007B608C88256CFB_= Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
You are invited to participate with = the Chemical Information Division program at the upcoming ACS National Meet= ing in New York, September 7-11, 2003.  Please use the OASYS to submit= your abstracts (click on CINF at )= .  The deadline for submitting abstracts is May 12th, 2003.  For = any further questions, contact individual session organizers directly.

New York,
Sept. 7-11, 2003

Division of Chemical Informat= ion
Program Chair: O. F. G=FCner, Accelrys Inc, 9685 Scranton Road, San Diego, = CA 92121-3752, 858-799-5341, fax 858-7995100, e-mail: osman@accelrys.com

Please note that 35mm slide proj= ector are no longer considered standard equipment. If you need to use a sli= de projector, you need to indicate this.
Advances in reaction searching T. Wright, MDL Information Systems, Inc,= 14600 Catalina Street, San Leandro, CA 94577, 510-357-2222, fax 510-614-36= 52, e-mail: terryw@mdli.com
At your Fingertips: Use of PDAs in Chemical Information E. Kajosalo, Li= braries, Massachusetts Institute of Technology, 77 Masschusetts Avenue, Roo= m 14S-134, Cambridge, MA 02155, 617-253-9795, fax 617-253-6365, e-mail: kaj= osalo@mit.edu
Building the virtual chemistry library: e-books and e-journals A. B. Tw= iss-Brooks, John Crerar Library, University of Chicago, 5730 S. Ellis, Chic= ago, IL 60637, 773-702-8777, fax 773-702-7429, e-mail: atbrooks@midway.uchi= cago.edu; S. E. Lee, Symyx Technologies, Inc, 3100 Central Expressway, Sant= a Clara, CA 95051, 408-330-3974, fax 408-492-9178, e-mail: slee@symyx.com
Business information for chemists (Cosponsored with bmgt). T. Hoctor, M= DL Information Systems, Inc, 14600 Catalina Street, San Leandro, CA 94577, = 510-895-1313, fax 510-614-3651, e-mail: timh@mdli.com
Careers in Chemical Information (Cosponsored with ycc). P. Barnett, Sci= ence/Engineering Library, City College of New York, Convent Avenue at 138th= Street, New York, NY 10031, 212-650-8243, fax 212-650-7626, e-mail: phibar= n@sci.ccny.cuny.edu
Emerging Trends in Discovery Data Integration M. A. Miller, LION Biosci= ence, 955 Ridge Hill Lane, Suite 30, Midvale, UT 84047, 801 569 1390, e-mai= l: mitchell.miller@lionbioscience.com
Fishing for the right scientific information in the information sea E. = M. Shanbrom, Manager, CAS and Web Content, Chemical Abstracts Service, 2540= Olentangy River Road, Columbus, OH 43202, (614) 447-3710, fax (614) 461-71= 49, e-mail: eshanbrom@cas.org
General Papers O. F. G=FCner
Novel database and knowledge mining techniques (Cosponsored with medi).= S. B. Singh, Department of Pharmaceutical Chemistry, Merck Research Labora= tories, RY50SW 100, 126 E. Lincoln Avenue, Rahway, NJ 07065, 732-594-4954, = fax 732-594-4224, e-mail: suresh=5FSingh@merck.com
Sci-Mix Posters O. F. G=FCner
Skolnik Award Symposium: Crystallographic Databases and their Applications = in Structural Chemistry, Drug Design and Materials Development F. H. Al= len, CCDC, 12 Union Road, Cambridge, CB2 1EZ, United Kingdom, +44-(0)1223-3= 36425, fax +44-(0)1223-336033, e-mail: allen@ccdc.cam.ac.uk
Standards for Chemistry Informatics J. Rumble Jr., Standard Reference D= ata, NIST, 100 Bureau Drive MS 2310, Gaithersburg, MD 20899-2310, 301 975 2= 203, fax 301-926-0416, e-mail: john.rumble@nist.gov
Technical Intelligence A. Trippe, Vertex Pharmaceuticals Inc, 130 Waver= ly St, Cambridge, MA 02139, 617-444-6459, fax 617-444-6680, e-mail: tony=5F= trippe@vrtx.com



Osman F. G=FCner, Ph.D.
Executive Director
Cheminformatics and Rational Drug Design
Accelrys Inc.,  858-799-5341
osman@accelrys.com, http://www.accelrys.com --=_alternative 007B608C88256CFB_=-- From chemistry-request@server.ccl.net Wed Apr 2 03:31:41 2003 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h328Vef19044 for ; Wed, 2 Apr 2003 03:31:41 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id C543DA4E2F6; Wed, 2 Apr 2003 10:31:39 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id B4161A4E2F2 for ; Wed, 2 Apr 2003 10:31:38 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 2 Apr 03 10:31:38 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 2 Apr 03 10:31:36 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@ccl.net Date: Wed, 2 Apr 2003 10:31:35 +0100 Subject: CCL: Temperature dependence of electronic transitions Reply-To: spanget@ruc.dk X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <104288751C1@virgil.ruc.dk> X-Spam-Status: No, hits=0.0 required=5.0 tests=none version=2.50 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.50 (1.173-2003-02-20-exp) Dear CCL: In Nurrell's classical book from 1963, "The Theory of the Electronic Spectra of Organic Molecules", Erich Clar is quoted for the following observations concerning the characteristic transitions in benzenoid hydrocarbons (pp 92-94): "Clar designates the three types of bands 1, 2 and 3 by the symbols alpha, p (for para) and beta respectively, distinguishing different bands of the same type by primed subscripts. Apart from their intensity and structural characteristics he distinguishes the alpha bands by the fact that they move to shorter wavelengths on lowering the temperature whereas the p and beta bands move to longer wavelengths." I am presently trying to get hold of the original work of Erich Clar. However, I wonder if someone could give me a key to more recent literature dealing with experimental and theoretical aspects of the temperature dependence of electronic transitions? - Thanks. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Wed Apr 2 05:44:06 2003 Received: from igor.urz.unibas.ch ([131.152.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h32Ai5f02630 for ; Wed, 2 Apr 2003 05:44:06 -0500 Received: from unibas.ch (filou.chemie.unibas.ch [131.152.112.19]) by igor.urz.unibas.ch (PMDF V6.1-1 #40761) with ESMTP id <0HCP00AATPTH4I@igor.urz.unibas.ch> for chemistry@ccl.net; Wed, 02 Apr 2003 12:44:05 +0200 (MET DST) Date: Wed, 02 Apr 2003 12:45:19 +0200 From: Stanislav Ivan Subject: g3mp2 TS To: chemistry@ccl.net Message-id: <3E8ABF3F.5020503@unibas.ch> MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en-us, en User-Agent: Mozilla/5.0 (Windows; U; WinNT4.0; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 Dear CCL'ers, I would like to ask you for a help. Is it possible to do G3mp2 calculation on the transition state in G98a7? If yes can someone advice me how to do that? Any help is appriciated. The problem is how to bypass first minimisation steps. regards, -- Stanislav Ivan Departement Chemie St. Johanns Ring 19 4056 Basel Switzerland Tel.: (+41) (61) 267 11 44 E-mail: stanislav.ivan@unibas.ch From chemistry-request@server.ccl.net Wed Apr 2 05:50:48 2003 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h32Aolf02825 for ; Wed, 2 Apr 2003 05:50:47 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 812A4A5030F; Wed, 2 Apr 2003 12:50:46 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 89F6CA5030C; Wed, 2 Apr 2003 12:50:45 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 2 Apr 03 12:50:45 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 2 Apr 03 12:50:42 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Stefan Grimme , grimmes@uni-muenster.de Date: Wed, 2 Apr 2003 12:50:29 +0100 Subject: CCL:Temperature dependence of electronic transitions Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <1067A1E5D01@virgil.ruc.dk> X-Spam-Status: No, hits=0.0 required=5.0 tests=none version=2.50 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.50 (1.173-2003-02-20-exp) Stefan Grimme > Hot bands of small aromatics are discussed in > JPC A, 102 (1998) 7157. Dear Stefan, thanks for the information. Maybe I should be more specific: I am primarily interested in the temperature dependence of 'normal' electronic transitions, like the alpha and p bands of benzenoid hydrocarbons: "[Clar] distinguishes the alpha bands by the fact that they move to shorter wavelengths on lowering the temperature whereas the p and beta bands move to longer wavelengths." (Murrell, 1963) Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Wed Apr 2 06:51:55 2003 Received: from celebris04.cetem.gov.br ([200.20.105.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h32Bpsf04279 for ; Wed, 2 Apr 2003 06:51:54 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Wed, 2 Apr 2003 08:58:22 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56AF1@correio.cetem.gov.br> From: Ian Hovell To: "'chemistry@ccl.net'" Subject: vibrational analysis using hyperchem Date: Wed, 2 Apr 2003 08:58:13 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h32Bptf04280 Dear CCLers, I have recently come across a problem. I have a molecule which is fairly large which I have carried out an single point abinitio analysis using direct SCF calculation Hyperchem states that it is using 787 basis functions (I'm using 3-21g basis set) and 1296 primative gausians in the calculations. This seems to run without any problems and took a little over 4 days. Afterwards I ran a vibrational analysis which seems to have come to a halt after 10 days computing, although stated to the contary by the computer, and for two days now has remained on its final (50) iteration. Will it finish? The log file does not give me any help. Is there anything which I can do? I have written to the support people at Hyperchem but they have not replied. I am using a Pentium IV with 768 MB ram and 80 GB of hard disk space. Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Ciência e da Tecnologia- MCT Avenida Ipê, No 900 - Cidade Universitaria Ilha do Fundão Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell@cetem.gov.br From chemistry-request@server.ccl.net Wed Apr 2 03:11:23 2003 Received: from mail.fqspl.com.pl ([212.244.147.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h328BMf18461 for ; Wed, 2 Apr 2003 03:11:22 -0500 Received: (qmail 28207 invoked by uid 505); 2 Apr 2003 08:02:21 -0000 Received: from magda@fqspl.com.pl by mail by uid 502 with qmail-scanner-1.13 ( Clear:. Processed in 0.043887 secs); 02 Apr 2003 08:02:21 -0000 Received: from unknown (HELO magda) (212.244.147.4) by mail.fqspl.com.pl with SMTP; 2 Apr 2003 08:02:21 -0000 Message-ID: <008e01c2f8ef$03c639f0$200a0a0a@fqspl.com.pl> Reply-To: "Karabon Magdalena" From: "Karabon Magdalena" To: Subject: Seminar: "Property Prediction and Reaction Modelling with Computer Aided Chemistry" Date: Wed, 2 Apr 2003 10:08:09 +0200 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 5.50.4920.2300 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 Seminar: "Property Prediction and Reaction Modelling with Computer Aided Chemistry" date: 24th of April, 2003 (13:30 - 15:00) place: Crowne Plaza Hotel, Heathrow, London, UK The prediction of biological, chemical and physical properties such as reaction rates, UV-Visible & IR spectra, water solubility, vapour pressure, polymer properties, environmental fate, etc., will be illustrated with CAChe, a computer aided chemistry package for the experimental chemist that runs on a desktop PC. Prediction of reaction pathways, thermodynamics and kinetics will also be discussed. Computer aided chemistry can be used to improve success rate in the laboratory and speed up research by pre-screening candidates and testing ideas, before investing valuable laboratory time. This presentation reviews the expanding scope of computer-aided chemistry. (presentation - 55 mins; demonstration - 25 mins) Sponsored by Fujitsu. For details and free registration please contact Ms. Magda Karabon at magda@fqspl.com.pl or call: + 48 12 429 43 45 From chemistry-request@server.ccl.net Wed Apr 2 02:46:20 2003 Received: from kdmail2.netcologne.de ([194.8.194.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h327kKf17654 for ; Wed, 2 Apr 2003 02:46:20 -0500 Received: from cosmologic.de (xdsl-195-14-221-209.netcologne.de [195.14.221.209]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 2.9.3.5) with ESMTP id AAW12890 (AUTH klamt@cosmologic.de); Wed, 2 Apr 2003 09:45:43 +0200 (CEST) Message-ID: <3E8A9522.8090507@cosmologic.de> Date: Wed, 02 Apr 2003 09:45:38 +0200 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en,pdf MIME-Version: 1.0 To: Emma Roberts CC: "'jkl@ccl.net'" , "'elewars '" , CHEMISTRY Subject: Re: CCL:New Book on Computational Chemistry References: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit I got a bit confused by the title of the book Computational Chemistry: Introduction to the Theory and Applications of Molecular Quantum Mechanics because I thought that Lewars wanted to tell us that comp. chem. is just Molecular Quantum Mechanics. But indeed, going to the web site I saw that that the correct title is: Computational Chemistry: Introduction to the Theory and Applications of Molecular and Quantum Mechanics This makes much more sense, because comp. chem. in my understanding is the art of using the entire suite of methods from Molecular Mechanics up to high level Quantum Mechanics, and of finding the right method for each problem. Anyway, it is a bit of a pity that the book appears to lack a chapter on solvation methods. Comp. Chem. is an applied science, and the vast majority of applications are in the liquid systems. Regards Andreas Emma Roberts wrote: > Emma Roberts, PhD > Senior Publishing Editor (Chemistry) > Kluwer Academic Publishers > 241 Borough High Street > London > SE1 1GB > UK > Email: emma.roberts@wkap.com > Tel: +44 (0) 20 7940 8482 > Fax: +44 (0) 20 7940 7496 > ______________________________ > > > > ==================================================================== > Computational Chemistry: > Introduction to the Theory and Applications of Molecular Quantum > Mechanics > by Errol Lewars. > > Dear Colleagues, > > We are pleased to announce this recently published book title, available as > both a hardback and paperback. Please find below some brief details as > well as an abbreviated Table of Contents. > > If you require further information, please contact me or see: > http://www.wkap.nl/prod/b/1-4020-7285-6 > > Best wishes, > > Emma Roberts > Senior Publishing Editor (Chemistry) > Kluwer Academic Publishers > > E-mail: emma.roberts@wkap.com > > -------------------------------------------------------------------- > Computational chemistry has become extremely important in the last > decade, being widely used in academic and industrial research. Yet there > have been few books designed to teach the subject to nonspecialists. > > Computational Chemistry: Introduction to the Theory and Applications of > Molecular and Quantum Mechanics is an invaluable tool for teaching and > researchers alike. The book provides an overview of the field, explains > the basic underlying theory at a meaningful level that is not beyond > beginners, and it gives numerous comparisons of different methods with > one another and with experiment. > > The following concepts are illustrated and their possibilities and > limitations are given: > * potential energy surfaces > * simple and extended Hückel methods > * ab initio, AM1 and related semiempirical methods > * density functional theory (DFT) > > Topics are placed in a historical context, adding interest to them and > removing much of their apparently arbitrary aspect. The large number of > references, to all significant topics mentioned, should make this book > useful not only to undergraduates but also to graduate students and > academic and industrial researchers. > > > Table of Contents > Chapter 1: An outline of what computational chemistry is all about > Chapter 2: The concept of the potential energy surface > Chapter 3: Molecular mechanics > Chapter 4: Introduction to quantum mechanics in computational chemistry > Chapter 5: Ab initio calculations > Chapter 6: Semiempirical calculations > Chapter 7: Density functional calculations > Chapter 8: Literature, software, books and websites > > Approximately 470 pages > -------------------------------------------------------------------- > ==================================================================== > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Apr 2 06:23:12 2003 Received: from pat.ccc.nottingham.ac.uk ([128.243.40.194]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h32BNBf03632 for ; Wed, 2 Apr 2003 06:23:11 -0500 Received: from ccw0m1.ccc.nottingham.ac.uk ([128.243.220.65] helo=ccw0m1.nottingham.ac.uk) by pat.ccc.nottingham.ac.uk with esmtp (Exim 3.34 #1) id 190fWz-0002AH-00 for chemistry@ccl.net; Wed, 02 Apr 2003 11:31:45 +0100 Received: from Gwweb1-MTA by ccw0m1.nottingham.ac.uk with Novell_GroupWise; Wed, 02 Apr 2003 11:31:31 +0100 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.3 Beta Date: Wed, 02 Apr 2003 11:31:25 +0100 From: "Mark Goddard" To: Subject: The best methods for describing excited states? Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h32BNCf03633 I am an undergraduate taking part in a research project entitled "Quantum chemical methods for describing electronic excited states". I was wondering if anybody would be able to provide me with a list of the best and most widely used methods for describing electronic excited states and/or any literature suggestions on this topic. For the project I am taking in to account accuracy and computational costs (and any other parameter I am unaware of at present) on all sizes of molecules. kind regards Mark Goddard From chemistry-request@server.ccl.net Wed Apr 2 13:43:40 2003 Received: from york.smtp.ru ([62.118.249.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h32IhdG15567 for ; Wed, 2 Apr 2003 13:43:40 -0500 Received: from [193.233.4.29] (account ) by york.smtp.ru (CommuniGate Pro WebUser 3.5.9) with HTTP id 13488846 for ; Wed, 02 Apr 2003 22:43:39 +0400 From: "Ivan Fedyanin" Subject: Memory problem running Gamess To: chemistry@ccl.net X-Mailer: CommuniGate Pro Web Mailer v.3.5.9 Date: Wed, 02 Apr 2003 22:43:39 +0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="KOI8-R" Content-Transfer-Encoding: 8bit Hello, I've got a problem running GAMESS MP2 calculation. The system is FreeBSD with 512MB RAM, and swap size set to 2000GB. But every time I run MP2 calculation (C16H16, 3-21G, symmetry is C1, RUNTYP=OPTIMIZE) I get "Increase memory size" message. Swap using is less than 100Mb. Has anybody met this problem (or even know how to solve it?) Thanks. Ivan Fedyanin, e-mail: octy@smtp.ru From chemistry-request@server.ccl.net Wed Apr 2 17:43:34 2003 Received: from bast.u.arizona.edu ([128.196.133.225]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h32MhYG21776 for ; Wed, 2 Apr 2003 17:43:34 -0500 Received: from localhost (okwon@localhost) by bast.u.arizona.edu (8.11.6+Sun/8.10.2) with ESMTP id h32MhZD03117 for ; Wed, 2 Apr 2003 15:43:35 -0700 (MST) X-Authentication-Warning: bast.u.arizona.edu: okwon owned process doing -bs Date: Wed, 2 Apr 2003 15:43:34 -0700 (MST) From: Ohyun Kwon To: chemistry@ccl.net Subject: CCL:New Book on Computational Chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h32MhYG21777 Dear CCLers; Is any review of the new book titled "Computational Chemistry: Introduction to the Theory and Applications of Molecular Quantum Mechanics" by Errol Lewars? Thanks in advance. Yours, Tommy Kwon ---------- Forwarded message ---------- Date: Tue, 1 Apr 2003 07:53:37 -0500 From: Emma Roberts To: "'jkl@ccl.net'" Cc: 'elewars ' Subject: CCL:New Book on Computational Chemistry Emma Roberts, PhD Senior Publishing Editor (Chemistry) Kluwer Academic Publishers 241 Borough High Street London SE1 1GB UK Email: emma.roberts@wkap.com Tel: +44 (0) 20 7940 8482 Fax: +44 (0) 20 7940 7496 ______________________________ ==================================================================== Computational Chemistry: Introduction to the Theory and Applications of Molecular Quantum Mechanics by Errol Lewars. Dear Colleagues, We are pleased to announce this recently published book title, available as both a hardback and paperback. Please find below some brief details as well as an abbreviated Table of Contents. If you require further information, please contact me or see: http://www.wkap.nl/prod/b/1-4020-7285-6 Best wishes, Emma Roberts Senior Publishing Editor (Chemistry) Kluwer Academic Publishers E-mail: emma.roberts@wkap.com -------------------------------------------------------------------- Computational chemistry has become extremely important in the last decade, being widely used in academic and industrial research. Yet there have been few books designed to teach the subject to nonspecialists. Computational Chemistry: Introduction to the Theory and Applications of Molecular and Quantum Mechanics is an invaluable tool for teaching and researchers alike. The book provides an overview of the field, explains the basic underlying theory at a meaningful level that is not beyond beginners, and it gives numerous comparisons of different methods with one another and with experiment. The following concepts are illustrated and their possibilities and limitations are given: * potential energy surfaces * simple and extended Hückel methods * ab initio, AM1 and related semiempirical methods * density functional theory (DFT) Topics are placed in a historical context, adding interest to them and removing much of their apparently arbitrary aspect. The large number of references, to all significant topics mentioned, should make this book useful not only to undergraduates but also to graduate students and academic and industrial researchers. Table of Contents Chapter 1: An outline of what computational chemistry is all about Chapter 2: The concept of the potential energy surface Chapter 3: Molecular mechanics Chapter 4: Introduction to quantum mechanics in computational chemistry Chapter 5: Ab initio calculations Chapter 6: Semiempirical calculations Chapter 7: Density functional calculations Chapter 8: Literature, software, books and websites Approximately 470 pages -------------------------------------------------------------------- ==================================================================== -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Apr 2 18:03:25 2003 Received: from dasher.wustl.edu ([128.252.208.48]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h32N3OG22214 for ; Wed, 2 Apr 2003 18:03:25 -0500 Received: from dasher.wustl.edu (comet.wustl.edu [128.252.208.50]) by dasher.wustl.edu (8.11.0/8.11.0) with ESMTP id h32N245327616; Wed, 2 Apr 2003 17:02:04 -0600 (CST) Message-ID: <3E8B6CDF.9020309@dasher.wustl.edu> Date: Wed, 02 Apr 2003 17:06:07 -0600 From: Jay Ponder Organization: Biochemistry, Washington University Medical School User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: TINKER 4.0 and Force Field Explorer are Available Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Computational Chemistry List, A major, new release of the TINKER Molecular Modeling Package, version 4.0 dated February 2003, is available from the Ponder Lab web site at http://dasher.wustl.edu/ or via anonymous ftp download from dasher.wustl.edu in the /pub/tinker area. TINKER is a modular, general package for molecular mechanics and dynamics with some special facilities and parameter sets for biopolymers. It currently supports several force fields, including AMBER94, AMBER96, CHARMM19, CHARMM27, MM2, MM3, OPLS-UA, OPLS-AA and our own AMOEBA polarizable atomic multipole force field. The software contains many advanced algorithms for energy minimization, molecular dynamics, distance geometry and global search, including some methods that are not readily available elsewhere. In addition, TINKER version 4.0 comes with a new Java GUI which is named Force Field Explorer. This initial public release of the GUI requires Java 1.4 or later and the Java3D extensions. It has been tested on Linux and Windows, and should run correctly on any platform that supports recent Java versions and Java3D. Mac OS X does not currently support Java3D, and hence will not run the GUI. Force Field Explorer is tightly integrated with the TINKER code via a socket mechanism, and can be used to setup, launch, control and visualize TINKER calculations and results. TINKER and Force Field Explorer are distributed with full source code, a User's Guide, and several examples and test molecule files. Directions are supplied for building the package on most commonly used CPU/OS combinations. Prebuilt executables limited to a maximum of 10000 atoms are also provided for Linux, Windows and Mac OS X. Please see the web site above for further information. We ask those who make significant use of TINKER to complete, sign, and return by regular mail the license form available on our web site. We keep all the returned forms and use them to help justify further development of the package. Comments, questions and suggestions for future improvements should be sent to tinker@dasher.wustl.edu. Best wishes, Jay Ponder -- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ From chemistry-request@server.ccl.net Wed Apr 2 08:17:50 2003 Received: from sccrmhc02.attbi.com ([204.127.202.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h32DHof06184 for ; Wed, 2 Apr 2003 08:17:50 -0500 Received: from c1353359a (12-207-200-38.client.attbi.com[12.207.200.38]) by sccrmhc02.attbi.com (sccrmhc02) with SMTP id <2003040213174800200744t7e>; Wed, 2 Apr 2003 13:17:49 +0000 Reply-To: From: "Mark Thompson" To: "Konstantin Kudin" , , Subject: RE: Report from the ACS in New Orleans Date: Wed, 2 Apr 2003 05:16:26 -0800 Message-ID: <000601c2f91a$109596a0$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: <20030401215753.38424.qmail@web21210.mail.yahoo.com> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal Konstantin, The company was Dynamic Digital Depth Inc (www.ddd.com) The DDD VP that was at the booth was Robert Mannino (rmannino@ddd.com) Mark ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 http://www.arguslab.com FAX: 206-440-3305 ================================= > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Konstantin Kudin > Sent: Tuesday, April 01, 2003 1:58 PM > To: h.rzepa@ic.ac.uk; chemistry@ccl.net > Subject: CCL:Report from the ACS in New Orleans > > > Dear colleagues > > I'd like to find out what was the company that > presented the 3D technology described below. > > I stopped by at the same booth, and was quite > impressed by the demo they had. They showed a clip > converted into a pseudo-3D from flat images and it > looked not as good as true 3D but better than 2D. > The modelling part was good too. > > I talked to the presenter briefly, and he mentioned > that he actually was from a different company (not > Fujitsu). Unfortunately, I did not write down the > name, and can't remember what the company was. > > Anybody remembers/knows what was the company with > that 3D technology? > > Thanks! > > Konstantin > > > ---------- Forwarded message ---------- > > Date: Fri, 28 Mar 2003 13:02:57 +0000 > > From: "Rzepa, Henry" > > To: chemweb@ic.ac.uk > > Subject: Report from the ACS in New Orleans > > > > Its been a few years since I did one of these > > reports from an ACS > > meeting, but one item in particular caught my (and > > a lot of other ) eyes. > > > > CAChe were displaying LCD panel monitors which > > display true 3D images > > WITHOUT any need for glasses. The technology > > apparently comes in four > > flavours, each vying for market, which is a good > > omen for costs, which are > > expected to come spiraling down over the next 12 > > months. > > > > The largest display is a 40" (@$17,000), a 20" (@ > > around $8000) and most > > interestingly, a laptop to be released later this > > year. The effects were remarkable, > > although the depth of stereo vision is probably not > > (yet) as impressive as dedicated > > Crystaleyes systems > > > > Currently, it does need software drivers (openGL) > > and so specific software > > must be enabled. The CAChe software is so, and I > > gather a Powerpoint > > enabled 3D display is on the cards; I argued for > > enabling the Weh browser, > > perhaps Mozilla/Netscape will do it? > > > > >From what we saw, and with the predictions, it does > > seem that any serious > > molecular modeller or anyone interested in the 3D > > properties of molecules > > will be buying themselves these 3D LCD panels > > routinely in a years time > > or so! > > > > Apparently, a demonstration might be on the cards > > at Heathrow Airport on April > > 24. Anyone who is seriously interested in attending > > should contact > > Magda Karabon for free registration at + 48 12 429 > > 43 45 or ccs@fqspl.com.pl > > -- > > > > Henry Rzepa. > > +44 (0870) 132 3747 (eFax) > > http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, > > Imperial College London, SW7 2AZ, UK. > > > > > > chemweb: A list for Chemical Applications of the > > Internet. > > To post to list: mailto:chemweb@ic.ac.uk > > Archived as: > > http://www.lists.ic.ac.uk/hypermail/chemweb/ > > To (un)subscribe, mailto:majordomo@ic.ac.uk the > > following message; > > (un)subscribe chemweb > > List coordinator, Henry Rzepa > > (mailto:rzepa@ic.ac.uk) > > > > > > > > -= This is automatically added to each message by > > mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | > > CHEMISTRY-REQUEST@ccl.net -- To Admins > > Ftp: ftp.ccl.net | WWW: > > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > > > > > > > __________________________________________________ > Do you Yahoo!? > Yahoo! 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