From chemistry-request@server.ccl.net Tue Apr 29 22:18:40 2003 Received: from alkali.kaist.ac.kr ([143.248.37.171]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3U2IcV05613 for ; Tue, 29 Apr 2003 22:18:39 -0400 Received: from ilsun (ilsun.kaist.ac.kr [143.248.37.227]) by alkali.kaist.ac.kr (8.11.3/8.11.3) with SMTP id h3U2MtQ08920; Wed, 30 Apr 2003 11:22:55 +0900 Message-ID: <000c01c30ebe$c5687c00$e325f88f@ilsun> From: "Kwanyong Seo" To: "Roy Jensen" Cc: "CCL" References: <3EB137B9@webmail1> Subject: CCL: Re: G03W multiprocessor support? Date: Wed, 30 Apr 2003 11:18:20 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h3U2IeV05614 Yes, I have known that G03W can support multple processors. As I known, option is "nproc=n". Kwanyong Seo +++++++++++++++++++++++++++++++++++++++++++++++++++ Kwanyong Seo : (E-mail) blue_sky@webmail.kaist.ac.kr (first) cupid@alkali.kaist.ac.kr (MSN) chemist_sky@hotmail.com M.S. candidate Department of Chemistry Korea Advanced Institute of Science & Technology 373-1, Guseong-dong, Yuseong-gu, Taejon, Republic of Korea 305-701 +++++++++++++++++++++++++++++++++++++++++++++++++++ ----- Original Message ----- From: "Roy Jensen" To: Sent: Wednesday, April 30, 2003 1:57 AM Subject: CCL:G03W multiprocessor support? > > All > > There was hope that the next version of Gaussian, G03W, would support > multiple processors. I couldn't find anything on the Gaussian website, nor > has Gaussian answered my emails. Does anyone know if it can? > > Roy Jensen > > > -= 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 30 03:20:20 2003 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3U7KKV10791 for ; Wed, 30 Apr 2003 03:20:20 -0400 Received: (from ib@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) id JAA28936; Wed, 30 Apr 2003 09:32:53 +0200 (CEST) Date: Wed, 30 Apr 2003 09:32:53 +0200 (CEST) Message-Id: <200304300732.JAA28936@oc30.uni-paderborn.de> X-Authentication-Warning: oc30.uni-paderborn.de: ib set sender to ib@oc30.uni-paderborn.de using -f From: Ingo Brunberg To: tt-ccl@kky.ttu.ee CC: chemistry@ccl.net In-reply-to: <20030429154010.GA5651@kky.ttu.ee> (message from Toomas Tamm on Tue, 29 Apr 2003 18:40:10 +0300) Subject: Re: CCL:visualizing MOs from Turbomole References: <20030429154010.GA5651@kky.ttu.ee> I think Viewmol exactly meets your requirements. > Dear CCLers, > > Can anyone suggest a tool for visualizing MOs from Turbomole output? > The ability to plot a MO energy diagram would be a plus. The software > should preferentially be free and for Linux, but other options can be > considered. > > -- > Toomas Tamm e-mail: tt-ccl@kky.ttu.ee > Chair of Inorganic Chemistry voice: INT+372-620-2810 > Tallinn Technical University fax: INT+372-620-2796 > Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From chemistry-request@server.ccl.net Wed Apr 30 09:08:10 2003 Received: from Mentat.ucd.ie ([137.43.1.47]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3UD88V31721 for ; Wed, 30 Apr 2003 09:08:09 -0400 X-Confirm-reading-to: Laurence.Cuffe@ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON.Mentat.ucd.ie by Mentat.ucd.ie (PMDF V6.2 #30693) id <0HE504M01QLQM4@Mentat.ucd.ie> for chemistry@ccl.net; Wed, 30 Apr 2003 14:02:03 +0100 (IST) Received: from noelfitz6 (noelfitz6.ucd.ie [137.43.24.17]) by Mentat.ucd.ie (PMDF V6.2 #30693) with ESMTP id <0HE504MJSQMBKL@Mentat.ucd.ie> for chemistry@ccl.net; Wed, 30 Apr 2003 13:56:35 +0100 (IST) Date: Wed, 30 Apr 2003 13:56:35 +0100 From: Laurence Cuffe Subject: (Fwd) RE: CCL:updated scaling factors for calculated vibration To: chemistry@ccl.net Message-id: <3EAFD613.11609.5100E10@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal Sorry For sending this to the list, but when I sent it directly to Dr Balboa it got bounced. In addition to the Wong (1996) paper you might also want to look at Bytheway and Wong, Chem Phys Lett. 1998 vol 282 p 219 which also discuses the 6-31G* basis set. All the best Laurence Cuffe From chemistry-request@server.ccl.net Wed Apr 30 09:17:18 2003 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3UDHIV31961 for ; Wed, 30 Apr 2003 09:17:18 -0400 Received: by mailbox.engr.sc.edu with Internet Mail Service (5.5.2656.59) id ; Wed, 30 Apr 2003 09:17:17 -0400 Message-ID: From: "WANG, YIXUAN " To: "'chemistry@ccl.net'" Subject: mndo-d Date: Wed, 30 Apr 2003 09:17:08 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, Does anybody know if MNDO-d can be done by Gaussian A11? IF so, what is the key word? Thanks. Yixuan Wang Department Chem. Engineering University South Carolina From chemistry-request@server.ccl.net Wed Apr 30 05:50:15 2003 Received: from roche.bath.ac.uk ([138.38.32.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3U9oFV26841 for ; Wed, 30 Apr 2003 05:50:15 -0400 Received: from mary.bath.ac.uk ([138.38.32.14] ident=mmdf) by roche.bath.ac.uk with smtp id 19AoEB-0008Ql-6c; Wed, 30 Apr 2003 10:50:15 +0100 Received: from prpcn144 ( prpc-n144.bath.ac.uk [138.38.128.144] ) by bath.ac.uk id aa17059 ; 30 Apr 2003 10:50 +0100 From: James Robinson To: Kwanyong Seo , Roy Jensen Cc: CCL Subject: RE: G03W multiprocessor support? Date: Wed, 30 Apr 2003 10:50:17 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <000c01c30ebe$c5687c00$e325f88f@ilsun> X-Scanner: *19AoEB-0008Ql-6c*iM5A1Dla00A* Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3U9oFV26842 Kwanyong, Have you actually used a multiple processor windows machine (win98,2000,NT,XP or whatever, with MORE than one processor) to run G03W successfully? Attempting such a thing with G98w produces poor performance; one is better off using a single processor for G98w. If anyone has actually managed to run GO3w on a multiple processor machine, I would be interested! Mr James J Robinson MRSC Molecular Modeller Pharmacy and Pharmacology Dept. University of Bath Claverton Down Bath, Somerset, UK. BA2 7AY. J.J.Robinson@bath.ac.uk http://www.bath.ac.uk tel +44(0) 1225 384723 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Kwanyong Seo Sent: 30 April 2003 03:18 To: Roy Jensen Cc: CCL Subject: CCL:G03W multiprocessor support? Yes, I have known that G03W can support multple processors. As I known, option is "nproc=n". Kwanyong Seo +++++++++++++++++++++++++++++++++++++++++++++++++++ Kwanyong Seo : (E-mail) blue_sky@webmail.kaist.ac.kr (first) cupid@alkali.kaist.ac.kr (MSN) chemist_sky@hotmail.com M.S. candidate Department of Chemistry Korea Advanced Institute of Science & Technology 373-1, Guseong-dong, Yuseong-gu, Taejon, Republic of Korea 305-701 +++++++++++++++++++++++++++++++++++++++++++++++++++ ----- Original Message ----- From: "Roy Jensen" To: Sent: Wednesday, April 30, 2003 1:57 AM Subject: CCL:G03W multiprocessor support? > > All > > There was hope that the next version of Gaussian, G03W, would support > multiple processors. I couldn't find anything on the Gaussian website, nor > has Gaussian answered my emails. Does anyone know if it can? > > Roy Jensen > > > > > > > > > -= 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 30 06:49:05 2003 Received: from llar.net.uniovi.es ([156.35.11.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3UAmwV28673 for ; Wed, 30 Apr 2003 06:48:58 -0400 Received: from CONVERSION-DAEMON.llar.net.uniovi.es by llar.net.uniovi.es (PMDF V6.1 #39514) id <01KVC7SFYBWW003W4W@llar.net.uniovi.es> for chemistry@ccl.net; Wed, 30 Apr 2003 12:48:28 +0200 (MET) Received: from pinon.ccu.uniovi.es (pinon.ccu.uniovi.es [156.35.31.1]) by llar.net.uniovi.es (PMDF V6.1 #39514) with ESMTP id <01KVC7SDSMEA003WBA@llar.net.uniovi.es>; Wed, 30 Apr 2003 12:48:25 +0200 (MET) Received: from pinon.ccu.uniovi.es (localhost [127.0.0.1]) by pinon.ccu.uniovi.es (8.12.9/8.12.9) with ESMTP id h3UAmKn9003146; Wed, 30 Apr 2003 12:48:21 +0200 (METDST) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.12.9/8.12.8/Submit) id h3UAmJKC003145; Wed, 30 Apr 2003 12:48:19 +0200 (METDST) Date: Wed, 30 Apr 2003 12:48:19 +0200 (METDST) From: Victor Lua~na Subject: Re: CCL:Molden Laplacian Plot options. To: chemistry@ccl.net, owner-chemistry@server.ccl.net Cc: pueyo@pinon.ccu.uniovi.es Message-id: <200304301048.h3UAmJKC003145@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT > From: Stephen Cooke > Subject: CCL:Molden Laplacian Plot options. > > We have an interest in our laboratory in examining the bonding in rare gas > containing molecules through experiment. Accordingly we have begun > supplementing our experimental work with theoretical calculations and in > particular producing electron density plots of our molecules and also > examing the laplacian plots, all using Molden. > > Of increasing interest is the Laplacian. Molden has > 4 plot options for the laplacian, i'm sure many of you will know > these are: Euclid, 3D, 3D-X and Space. [.......] > > My question is how should one interpret the "Space plot" of the Laplacian? > I have examined the online documentation and have not been successful in > finding any help. Literal answer: molden "space plot" are isosurfaces of the 3D function. The program asks you for a value of the function and the plots as a collection of planes the aspect of the L(\vec{r}) = constant surface. Of particular interest is the L(\vec{r})=0 surface, called "reaction surface" after R. F. W. Bader. If you want to examine the isodensity or isolaplacian surfaces of a number of molecules you should consider leaving molden and using "molekel" or "gopenmol" instead. Both viewers provide you a quite improved interaction with the surface and they are faster by orders of magnitude. molekel: http://www.cscs.ch/molekel/ gopenmol: http://www.csc.fi/gopenmol/ On the other hand, you might be interested in the chemical information contained in the laplacian. In that case you could check a corpus of relevant literature related to the Quantum Theory of Atoms in Molecules. For instance, the critical points in the laplacian can be shown to provide a qualitative and quantitative support to Gillespie's VSEPR model. The negative and positive isosurfaces of the laplacian provide a map of the nucleophile and electrophile regions of the molecule. ... A collection of beatiful pictures of the laplacian can be found in the web pages by R.F.W. Bader and also on the web pages by Creon Levitt. Some relevant articles can be found by looking to the recent work (about five years to start with) by Bader, Gillespie or Bernard Silvi. Bader: http://www.chemistry.mcmaster.ca/faculty/bader/aim/ Levitt: http://people.nas.nasa.gov/~creon/home.html It appears to be unaccesible for me right now and google didn't provide an alternative site. Silvi: http://www.lct.jussieu.fr/silvi/ Gillespie: http://www.chemistry.mcmaster.ca/faculty/gillespie/ Finally, PLA. Popelier and E. Espinosa have been quite active in the analysis of intermolecular bonding through the characterization of the electron density, laplacian and related properties. You could check their work as it might provide you relevant ideas to your problem. Popelier: http://www2.umist.ac.uk/chemistry/contact/staff/popelier.htm Espinosa: http://www.u-bourgogne.fr/LIMSAG/publicat/espinosa.htm Hope this helps you. Best regards, Victor Lua~na From chemistry-request@server.ccl.net Wed Apr 30 11:40:12 2003 Received: from prserv.net ([32.97.166.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3UFeCV02793 for ; Wed, 30 Apr 2003 11:40:12 -0400 Received: from attglobal.net (dhcp065-029-075-111.indy.rr.com[65.29.75.111]) by prserv.net (asmtp1) with SMTP id <20030430154001251043kegne> (Authid: jmmckel); Wed, 30 Apr 2003 15:40:02 +0000 Message-ID: <3EAE58C0.7722C2EB@attglobal.net> Date: Tue, 29 Apr 2003 10:49:36 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.51 [en]C-CCK-MCD (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Intel Linux compiler 7.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings! I have successfully compiled a version of MOPAC using the unsupported Intel Linux fortran compiler Version7.0 [I need F90 for dynamic memory allocation.] Upon linking the code against the Intel libraries as well as libf77blas,libatlas, liblapack and lapack_linux libraries from netlib.org I get the following complaint: for dlamch.o s_wsfe, do_fio, and e_wsfe are not resolved. Comments and suggestions are most welcome... many thanks! John McKelvey From chemistry-request@server.ccl.net Wed Apr 30 06:00:53 2003 Received: from kdmail2.netcologne.de ([194.8.194.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3UA0rV27662 for ; Wed, 30 Apr 2003 06:00:53 -0400 Received: from cosmologic.de (xdsl-213-168-108-189.netcologne.de [213.168.108.189]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 2.9.3.5) with ESMTP id ABC87453 (AUTH klamt@cosmologic.de); Wed, 30 Apr 2003 12:00:13 +0200 (CEST) Message-ID: <3EAF9EAA.1020201@cosmologic.de> Date: Wed, 30 Apr 2003 12:00:10 +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: tt-ccl@kky.ttu.ee, "chemistry@ccl.net" Subject: CCL:visualizing MOs from Turbomole Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit With TURBOMOLE there comes a program tm2molden, which allows to convert TURBOMOLE output in a way that it can be visualized by MOLDEN. So that could be one way to do it. Andreas -- -------------------------------------------------------------------------------- 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 30 13:03:31 2003 Received: from sandmail01.sd.accelrys.com ([209.120.169.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3UH3VV03875 for ; Wed, 30 Apr 2003 13:03:31 -0400 To: CHEMISTRY@ccl.net Cc: "Elizabeth Crookenden" Subject: Accelrys Customer Training in July MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1 February 07, 2003 Reply-To: "Elizabeth Crookenden" Message-ID: From: "Jeff Nauss" Date: Wed, 30 Apr 2003 10:03:27 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 04/30/2003 10:03:31 AM, Serialize complete at 04/30/2003 10:03:31 AM Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h3UH3VV03876 Accelrys Inc. are holding the following training workshops at locations in the US and Europe during July 2003. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $450 per day for government and $330 per day for academic. Integrated Customer Training: Integrated Lead Identification using Discovery Studio: Pharmacophore Modeling and Database Searching 4th July 2003, Cambridge, UK Integrated Lead Identification using Discovery Studio: Pharmacophore Modeling and Database Searching 21st July 2003, Burlington, MA For course details and registration see: http://www.accelrys.com/training/integrated/schedule.html Macromolecular Modeling: Macromolecular X-ray Structure Determination 15th – 16th July 2003, San Diego, CA Introduction to DS Modeling 22nd - 23rd July 2003, Burlington, MA Desktop Visualization and Communication with DS ViewerPro 24th July 2003, Burlington, MA Structure Based Drug Design with InsightII 28th – 29th July 2003, Burlington, MA CHARMm 20th-31st July 2003, Burlington, MA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html Rational Drug Design: Introduction to Cerius2 for Life Sciences 22nd - 23rd July 2003, Cambridge, UK Pharmacophore Generation with Catalyst 24th – 25th July 2003, Cambridge, UK For course details and registration see: http://www.accelrys.com/training/rdd/schedule.html Elizabeth Crookenden Training Co-ordinator Accelrys Ltd 334 Cambridge Science Park Cambridge CB4 0WN UK Telephone number: +44 (0) 1223 228691 Fax number: +44 (0) 1223 228501 Web: http://www.accelrys.com -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Wed Apr 30 02:37:01 2003 Received: from mx3.datanet.hu ([194.149.13.160]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3U6b0V09765 for ; Wed, 30 Apr 2003 02:37:00 -0400 Received: from pagony (duna-76.dialin.datanet.hu [195.56.2.76]) by mx3.datanet.hu (DataNet) with SMTP id 53FCF1EA682 for ; Wed, 30 Apr 2003 08:36:58 +0200 (CEST) Message-ID: <06e101c30ee3$0a06f8e0$0100a8c0@pagony> Reply-To: =?iso-8859-1?Q?Janke_D=E1vid?= From: =?iso-8859-1?Q?Janke_D=E1vid?= To: References: <200304271707.14141.MChalla@LANL.Gov> Subject: Re:xyz->zmat->xyz Date: Wed, 30 Apr 2003 08:11:23 +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 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Try to look for some programs on www.openscience.org or on www.sourceforge.net. I remember finding some programs doing this, but i cannot remember the names. David ----- Original Message ----- From: "Matt Challacombe" To: Sent: Monday, April 28, 2003 1:07 de. Subject: CCL:xyz->zmat->xyz > Hi, > > Is there a simple program for converting from xyz to > z-matrix and back? I've spent quite a while examining > different versions of babel, but none of them seem to > work in this capacity... > > Thx, Matt > > -- > Matt Challacombe > Theoretical Division, Los Alamos > http://www.t12.lanl.gov/~mchalla/ > > > > -= 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 > > > > --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.476 / Virus Database: 273 - Release Date: 4/24/2003 From chemistry-request@server.ccl.net Wed Apr 30 20:05:35 2003 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4105YV12054 for ; Wed, 30 Apr 2003 20:05:35 -0400 Received: from LAQUICOM02 ([148.223.46.1]) by yakko.cimav.edu.mx (8.12.3/8.12.3/Debian-6.3) with SMTP id h4114TbQ003599 for ; Wed, 30 Apr 2003 18:04:35 -0700 Message-ID: <015401c30f75$5fca9c90$da00000a@LAQUICOM02> From: "Dr. Daniel Glossman-Mitnik" To: Subject: G03W keyword Date: Wed, 30 Apr 2003 18:05:24 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0151_01C30F43.12A2F200" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_0151_01C30F43.12A2F200 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear netters: I have a question about G03W. Is the keyword MPBE operating ? According to the Gaussian 03 Users' Reference it is working, but I have failed every time I tried. Thanks for your help. Daniel Glossman P.S.: MPBE is the modified version of the PBE functional according to Adamo and Barone (JCP 116 (2002) 5933-5940. *************************************************************************= *** Dr. Daniel Glossman-Mitnik Centro de Investigacion en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Quimica Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Phone: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com *************************************************************************= *** -------------------------------------------------------------------------= ------- ------=_NextPart_000_0151_01C30F43.12A2F200 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
 
Dear netters:
 
I have a question about G03W. Is the keyword MPBE
operating ?  According to the Gaussian 03 Users'
Reference it is working, but I have failed every time I
tried.
 
Thanks for your help.
 
           &n= bsp;           &nb= sp;           &nbs= p;=20 Daniel Glossman
 
P.S.: MPBE is the modified version of the PBE functional
according to Adamo and Barone (JCP 116 (2002) 5933-5940.
 
********************************************************************= ********
Dr.=20 Daniel Glossman-Mitnik
Centro de Investigacion en Materiales = Avanzados=20 (CIMAV)
LAQUICOM - Laboratorio de Quimica Computacional
Miguel de=20 Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. 31109 = -=20 Mexico
Phone: (52) 614 4391151      FAX: = (52) 614=20 4391112
E-mail: daniel.glossman@cimav.edu.mx=
           = ;=20 glossman@hotmail.com
 &n= bsp;         =20 dglossman@yahoo.com
**********= ******************************************************************
<= !--mail_content-->

------=_NextPart_000_0151_01C30F43.12A2F200-- From chemistry-request@server.ccl.net Wed Apr 30 16:47:22 2003 Received: from sentinel.ucr.edu ([138.23.226.228]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3UKlMV09133 for ; Wed, 30 Apr 2003 16:47:22 -0400 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentinel.ucr.edu (Mirapoint Messaging Server MOS 3.2.1-GA) with ESMTP id AKD02661 for ; Wed, 30 Apr 2003 13:47:21 -0700 (PDT) Reply-To: From: "Donald Keidel" To: Subject: test of sander in amber7 created errors Date: Wed, 30 Apr 2003 13:47:17 -0700 Organization: UCR Message-ID: <000c01c30f59$b02a8b30$529c178a@dopetec> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000D_01C30F1F.03CBB330" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_000D_01C30F1F.03CBB330 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello all, I ran the test.sander test on a Linux machine that I have and most of the molecules passed except for the circ_dna molecule. I got an error like this: cd circ_dna; ./Run.circdna Segmentation fault (core dumped) Program error Make: *** [test.sander] Error 1 This error was output to the shell. I do not know if there is an output file that might give me more information on why it failed. I am new to Amber and would greatly appreciate any help. Thanks and have a good day. Don ------------------------------------------------------------------------ --------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dopetec@dslextreme.com webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_000D_01C30F1F.03CBB330 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello all,

 

I ran the test.sander test on a Linux machine that I have and =

most of the molecules passed except for the circ_dna = molecule.  I got

an error like this:

 

cd circ_dna; ./Run.circdna

Segmentation fault (core dumped)

    Program error

Make: *** [test.sander] Error 1

 

 

This error was output to the shell.  I do not know if there = is an output file that might give me more information on why it failed.  = I am new to Amber and would greatly appreciate any help.  Thanks and = have a good day.

 

Don

 

 

------------------------------------------------------= ---------------------------------------------------------
Donald J. Keidel
University of California, Riverside
Department of Biochemistry and Molecular Biology
Riverside, CA = 92521
phone:  (909) 787-5493
fax:  (909) 787-4434
dopetec@dslextreme.com
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= /span>

 

 

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name="S_PdCNCH.gjf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="S_PdCNCH.gjf" %mem=128MB %chk=S_PdCNCH.chk #P mPW1PW91/GEN PSEUDO=Cards GEOM=Check GUESS=Read OPT SCF=(MaxCycle=1024) SCRF=(IEFPCM,Read) Pd(L)(H) (L=bis(l-imidazolyl)-pyridine dicarbene) 1 1 Pd 0 S 3 1.00 0.2787000000D+01 -0.1610239000D+01 0.1965000000D+01 0.1848984000D+01 0.6243000000D+00 0.6037492000D+00 S 4 1.00 0.2787000000D+01 0.1354078000D+01 0.1965000000D+01 -0.1678085000D+01 0.6243000000D+00 -0.8559381000D+00 0.1496000000D+00 0.1020030000D+01 S 1 1.00 0.4360000000D-01 0.1000000000D+01 P 3 1.00 0.5999000000D+01 -0.1034910000D+00 0.1443000000D+01 0.7456952000D+00 0.5264000000D+00 0.3656494000D+00 P 4 1.00 0.5999000000D+01 0.2670153000D-01 0.1443000000D+01 -0.2457828800D+00 0.5264000000D+00 -0.1426049000D-01 0.8990000000D-01 0.7898110300D+00 P 1 1.00 0.2620000000D-01 0.1000000000D+01 D 3 1.00 0.6091000000D+01 0.3761460000D-01 0.1719000000D+01 0.5200479000D+00 0.6056000000D+00 0.5706071000D+00 D 1 1.00 0.1883000000D+00 0.1000000000D+01 F 1 1.00 1.472000000 1.00000000 **** C N 0 6-31G(d') **** 18 19 20 21 22 23 24 25 26 6-31G(d') **** 27 6-31G(d',p') **** Pd 0 LANL2DZ rsolv=3.93 eps=38.93 nodis nocav dump ------=_NextPart_000_003E_01C30F3E.142D7BE0-- From chemistry-request@server.ccl.net Wed Apr 30 15:13:01 2003 Received: from mail.ccmsi.us ([143.132.103.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3UJD1V07091 for ; Wed, 30 Apr 2003 15:13:01 -0400 Received: from falcon [10.30.6.25] by mail.ccmsi.us (SMTPD32-7.14) id A03D700FC; Wed, 30 Apr 2003 14:13:01 -0500 Message-ID: <001001c30f4c$84788d50$19061e0a@ccmsi.us> From: "Yevgeniy Podolyan" To: Subject: 03.10.31 12th Conference on Current Trends in Computational Chemistry Date: Wed, 30 Apr 2003 14:13:00 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000D_01C30F22.9B945480" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_000D_01C30F22.9B945480 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable We are pleased to announce and to invite you to attend the 12th = Conference on Current Trends in Computational Chemistry (CCTCC). This = symposium, organized by Jackson State University, covers all areas of = computational chemistry as well as quantum chemistry. This year the 12th = CCTCC will be held at the Jackson Hilton Hotel, Jackson, Mississippi on = October 31 - November 1, 2003. A banquet is scheduled for the Saturday = evening and a dinner and reception for Friday. The format consists of a series of (invited) plenary lectures and poster = presentations on Friday and Saturday covering applications as well as = theory. As suggested by Professor Pople, last year we inaugurated a new = tradition for the second decade of our conferences. Starting with the = CCTCC-11 each meeting is featuring a talk named after eminent = computational chemists. This year the second presentation in this series = will be given by Ernest R. Davidson from the University of Washington. = The 12th Conference will also feature another talk given in the = ancillary Noble Lecture Series. The lectures in this series are = presented in a relaxed, after-dinner atmosphere by the noble speakers = and are devoted to noble scientific events and people. As such, it is an = exceptional lecture to the conference and, contrary to the regular = talks, might not necessarily report any Current findings. This year the = talk will be delivered by Isabella L. Karle from the Naval research = Laboratory, Washington, D.C. We are planning to publish extended abstracts (up to four pages each) of = all invited talks and poster presentations. Original scientific = contributions will be published in a special issue of the International = Journal of Quantum Chemistry. Manuscripts for inclusion in the special = issue should be submitted in triplicate upon arrival at the registration = desk. Submitted papers will be subject to the journal's standard referee = procedures. For more information, visit our conference web site at = http://cctcc.ccmsi.us=20 Jerzy = Leszczynski = Chairman of the Organizing Committee ------=_NextPart_000_000D_01C30F22.9B945480 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

We = are pleased=20 to announce and to invite you to attend the 12th Conference on Current = Trends in=20 Computational Chemistry (CCTCC). This symposium, organized by=20 Jackson=20 State=20 University, = covers all=20 areas of computational chemistry as well as quantum chemistry. This year = the=20 12th CCTCC will be held at the Jackson Hilton Hotel,=20 Jackson,=20 Mississippi on = October 31=20 =96 November 1,=20 2003. A = banquet is=20 scheduled for the Saturday evening and a dinner and reception for=20 Friday.

The = format=20 consists of a series of (invited) plenary lectures and poster = presentations on=20 Friday and Saturday covering applications as well as theory. As = suggested by=20 Professor Pople, last year we inaugurated a new tradition for the second = decade=20 of our conferences. Starting with the CCTCC-11 each meeting is featuring = a talk=20 named after eminent computational chemists. This year the second = presentation in=20 this series will be given by Ernest R. Davidson from the=20 University of=20 Washington. The = 12th=20 Conference will also feature another talk given in the ancillary Noble = Lecture=20 Series. The lectures in this series are presented in a relaxed, = after-dinner=20 atmosphere by the noble speakers and are devoted to noble scientific = events and=20 people. As such, it is an exceptional lecture to the conference and, = contrary to=20 the regular talks, might not necessarily report any Current findings. = This year=20 the talk will be delivered by Isabella L. Karle from the Naval research=20 Laboratory, Washington, D.C.

We = are planning=20 to publish extended abstracts (up to four pages each) of all invited = talks and=20 poster presentations. Original scientific contributions will be = published in a=20 special issue of the International Journal of Quantum Chemistry. = Manuscripts for=20 inclusion in the special issue should be submitted in triplicate upon = arrival at=20 the registration desk. Submitted papers will be subject to the journal's = standard referee procedures.

For = more=20 information, visit our conference web site at http://cctcc.ccmsi.us

          &nbs= p;            = ;            =             &= nbsp;           &n= bsp;      =20 Jerzy=20 Leszczynski
         =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;        =20 Chairman of the Organizing = Committee

------=_NextPart_000_000D_01C30F22.9B945480--