From chemistry-request@ccl.net Wed Oct 29 00:49:53 2003 Received: from bureau6.utcc.utoronto.ca (bureau6.utcc.utoronto.ca [128.100.132.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9T5nMLj012387 for ; Wed, 29 Oct 2003 00:49:22 -0500 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1166]) by bureau6.utcc.utoronto.ca with SMTP id <468196-26953>; Tue, 28 Oct 2003 10:34:01 -0500 From: "William Wei" To: "CCLers" Subject: DMS molecular surface generation proplem used in DOCK Date: Tue, 28 Oct 2003 10:37:24 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-Spam-Status: No, hits=-0.4 required=7.0 tests=MSGID_GOOD_EXCHANGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi all, After I tried to get molecular surface using dms from ucsf, it can not be used for "sphgen". After I checked the .ms format, it looks like: THR 1 N -0.313 18.726 33.523 A THR 1 N -1.640 18.005 34.002 SR0 0.185 ..... THR 1 N -2.044 17.790 33.619 SS0 0.177 THR 1 N -2.143 18.042 33.275 SS0 0.177 THR 1 N -0.313 18.726 35.023 SC0 0.195 THR 1 N 0.110 18.726 34.962 SC0 0.195 .... It looks like I did not use dms properly. Did anybody meet this problems before? I used SGI IRIX6.5.16. Could anyone give me hint for this? Or if somebody could provide me the SGI version dms, that would be great. Thank you and have a good day! William ------------------------- William Wei Molecular Design and Information Technology (MDIT) center Faculty of Pharmacy, University of Toronto 19 Russell Street, Toronto, ON. M5S 2S2 Tel: 1-416-946-8469 Fax: 1-416-978-8511 Email: william.wei^at^utoronto.ca william^at^phm.utoronto.ca From chemistry-request@ccl.net Wed Oct 29 04:26:55 2003 Received: from smtp2.ruc.dk (smtp2.ruc.dk [130.225.220.70] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9T9QOLj021156 for ; Wed, 29 Oct 2003 04:26:24 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id ED23314EB369; Wed, 29 Oct 2003 10:26:23 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 9D7A414EB364; Wed, 29 Oct 2003 10:26:20 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 29 Oct 03 10:26:18 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 29 Oct 03 10:26:17 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: zhijian WU , chemistry)at(ccl.net Date: Wed, 29 Oct 2003 10:26:01 +0100 Subject: Re: CCL:TDDFT problem Reply-To: spanget)at(ruc.dk Message-ID: <3F9F95BD.28639.56FF406@localhost> Priority: normal In-reply-to: <200310290136.JAA02359)at(ns.ciac.jl.cn> X-mailer: Pegasus Mail for Windows (v4.01) X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) X-Spam-Status: No, hits=-1.0 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Level: zhijian WU : > I am trying to calculate the vertical excited states of AuCl2 cluster, > but my calculation fails with the error message "Cannot mix post-SCF > and DFT". > #b3lyp/lanl2dz td=(nstates=5) scf=(direct,maxcycle=1024) density > geom=check guess=read Dear zhijian WU! With Gaussian, you cannot perform a DFT calculation (B3LYP) and include the keyword 'density'; the density analysis is a post-SCF procedure. > My second question is: is it now > possible to optimize the structure using TDDFT? No, it is not possible to optimize the geometries of molecules in their excited states with TDDFT. You may optimize the geometry of the lowest triplet state with DFT (f.inst. UB3LYP). 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)at(ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Wed Oct 29 04:01:14 2003 Received: from ns9.mmaweb.net (ns9.mmaweb.net [64.71.143.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9T90gLj019552 for ; Wed, 29 Oct 2003 04:00:43 -0500 Received: from chemaxon.com (221.124-182-adsl-pool.axelero.hu [81.182.124.221]) by ns9.mmaweb.net (8.12.10/8.11.0) with ESMTP id h9T8xCCb004996; Wed, 29 Oct 2003 03:59:13 -0500 (EST) Message-ID: <3F9F81AE.4080007{at}chemaxon.com> Date: Wed, 29 Oct 2003 10:00:30 +0100 From: Ferenc Csizmadia User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en, hu, zh-cn MIME-Version: 1.0 To: Donald Keidel CC: chemistry{at}ccl.net Subject: Re: CCL:Program to search SD/MDL formatted files from chemical companies References: <000101c39cf7$81cc2240$529c178a@dopetec> In-Reply-To: <000101c39cf7$81cc2240$529c178a@dopetec> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.3 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,REFERENCES,REPLY_WITH_QUOTES, SIGNATURE_LONG_DENSE,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Don, If you need a chemically intelligent database solution that can also be used to build an intra- or internet application, please check out JChem Base. http://www.chemaxon.com/products.html#JChemBase You can try it here: http://www.jchem.com/examples.html JChem can be downloaded from the site. An example application that can be easily customized is included in the package. The software is in Java so it is portable. It can be connected to several databases, like MySQL, PosgreSQL, Oracle, etc. Best regards, Ferenc -- Dr. Ferenc Csizmadia http://www.chemaxon.com Donald Keidel wrote: >Hello, > >I am looking for a program to search SD/MDL formatted files (chemical >company libraries of compounds). I have found ISIS/Base and 3DFS, but I >was wondering if anyone knows of others that might be cheaper than >ISIS/Base (hopefully free), but commercial examples would be of great >help also. Thank you in advance to anyone who reads and responds to >this request. Have a great 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{at}dslextreme.com >webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm > > > > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY{at}ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST{at}ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl{at}ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > -- Dr. Ferenc Csizmadia CEO ChemAxon Ltd. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Cell: +3620 9570988 Tel: +361 4532660 Fax: +361 4532659 mailto:fcsiz{at}chemaxon.com From chemistry-request@ccl.net Wed Oct 29 05:19:40 2003 Received: from puga.vdu.lt (puga.vdu.lt [193.219.38.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9TAJ8Lj023579 for ; Wed, 29 Oct 2003 05:19:09 -0500 Received: from amavis by puga.vdu.lt with scanned-ok for chemistry{at}ccl.net id 1AEnPt-0001go-00; Wed, 29 Oct 2003 12:19:05 +0200 Received: from vaidila.vdu.lt ([193.219.38.52]) by puga.vdu.lt with esmtp for chemistry{at}ccl.net id 1AEnPs-0001gf-00; Wed, 29 Oct 2003 12:19:04 +0200 Received: from af804-1.vdu.lt ([193.219.38.83] helo=localhost) by vaidila.vdu.lt with esmtp for chemistry{at}ccl.net id 1AEnQ3-0005lG-00; Wed, 29 Oct 2003 12:19:15 +0200 Date: Wed, 29 Oct 2003 12:19:12 +0200 From: Arturas X-Mailer: The Bat! (v2.00) CD5BF9353B3B7091 Reply-To: Arturas Organization: SemteX X-Priority: 3 (Normal) Message-ID: <95202078.20031029121912{at}vaidila.vdu.lt> To: chemistry{at}ccl.net Subject: Atom transfer model In-Reply-To: <3E7F86CC.6060305{at}u.washington.edu> References: <3E7F86CC.6060305{at}u.washington.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS snapshot-20020300 X-Spam-Status: No, hits=-0.1 required=7.0 tests=IN_REP_TO,RCVD_IN_NJABL,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, Despite low conference traffic I'd like ask a question anyway :) What a model I should use to estimate the ratio of transfer probability, or transfer times, of some light atom (say it N or O) over ranges, e.g. 1.6 and 2.0 Angstroms ? I tryed harmonic oscillator, Morse function. Obviously, that should be exponential behavior. But I am nor quite sure I go right way. Best Arturas From chemistry-request@ccl.net Wed Oct 29 01:33:45 2003 Received: from smtp.hotbox.ru (smtp.hotbox.ru [80.68.244.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9T6XCLj013591 for ; Wed, 29 Oct 2003 01:33:13 -0500 Received: from verena.ineos.ac.ru (verena.ineos.ac.ru [193.233.4.18]) (authenticated bits=0) by smtp.hotbox.ru (8.12.9/8.12.9) with ESMTP id h9T6Wc95095745 for ; Wed, 29 Oct 2003 09:32:38 +0300 (MSK) (envelope-from dengolovanov:at:pisem.net) Date: Wed, 29 Oct 2003 09:29:30 +0300 From: dengolovanov X-Mailer: The Bat! (v1.61) Reply-To: dengolovanov X-Priority: 3 (Normal) Message-ID: <191224233610.20031029092930:at:pisem.net> To: chemistry:at:ccl.net Subject: Orbital symmetry? MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Is there any way to get the symmetry characteristics of the orbitals calculated in Gaussian? (in form of irreducible representation group) Thanx in advance every one -- Best regards, Denis G. Golovanov mailto:dengolovanov:at:pisem.net From chemistry-request@ccl.net Wed Oct 29 06:53:19 2003 Received: from turmiel.ch.uj.edu.pl (turmiel.ch.uj.edu.pl [149.156.71.252]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9TBqlLj027861 for ; Wed, 29 Oct 2003 06:52:47 -0500 Received: (from apache@localhost) by turmiel.ch.uj.edu.pl (8.11.6/8.11.6) id h9TBqJo16814; Wed, 29 Oct 2003 12:52:19 +0100 X-Authentication-Warning: turmiel.ch.uj.edu.pl: apache set sender to makowskm/at/chemia.uj.edu.pl using -f Received: from 149.156.71.133 (SquirrelMail authenticated user makowskm) by mail.ch.uj.edu.pl with HTTP; Wed, 29 Oct 2003 12:52:19 +0100 (CET) Message-ID: <4955.149.156.71.133.1067428339.squirrel/at/mail.ch.uj.edu.pl> Date: Wed, 29 Oct 2003 12:52:19 +0100 (CET) Subject: Re: CCL:TDDFT problem From: To: In-Reply-To: <200310290136.JAA02359/at/ns.ciac.jl.cn> References: <200310290136.JAA02359/at/ns.ciac.jl.cn> X-Priority: 3 Importance: Normal Cc: X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=-1.6 required=7.0 tests=IN_REP_TO,NO_REAL_NAME,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > Hi, CCLers, > > I am trying to calculate the vertical excited states of AuCl2 cluster, > but my calculation fails with the error message "Cannot mix post-SCF and > DFT". Does anybody tell me how to solve the problem? My second question > is: is it now possible to optimize the structure using TDDFT? You may try numerical optimization: either using simplex-like methods or using opt(EnOnly,RCFC) - in the latter case you will need some starting hessian. Yours, -- Marcin Makowski Ph.D. student in Theoretical Chemistry, Jagellonian University From chemistry-request@ccl.net Wed Oct 29 03:03:51 2003 Received: from websmtp03.sohu.com ([61.135.145.13]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9T83GLj016789 for ; Wed, 29 Oct 2003 03:03:18 -0500 Received: from mx23.mail.sohu.com (unknown [192.168.41.141]) by websmtp03.sohu.com (Postfix) with ESMTP id 5068366BB2 for ; Wed, 29 Oct 2003 16:03:16 +0800 (CST) Message-ID: <113939.1067414596847.JavaMail.postfix$at$mx23.mail.sohu.com> Date: Wed, 29 Oct 2003 16:03:10 +0800 (CST) From: To: Subject: software for self-interaction correction(SIC) of DFT Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 8bit X-Mailer: Sohu Web Mail 2.0.13 X-SHIP: 202.119.32.27 X-Priority: 3 X-SHMOBILE: 0 X-SHBIND: 0 X-Spam-Status: No, hits=2.2 required=7.0 tests=NO_REAL_NAME,RCVD_IN_RFCI version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, I am studying a reaction involving odd-electron problems using UDFT method. Three electrons participate in the reaction. The self-interaction correction (SIE) is expected to be serious. I have to calculate the self-interaction correction (SIC) of DFT. But I don't know which program package can be used to calculate SIC. Someone has suggested me to use the package NWChem. Three keyword in NWchem can be to used to calculate the SIC (SIC perturbative, SIC OEP and SIC OEP-loc). But in manual of NWchem, "SIC perturbative" cannot be applied to open-shell system. For SIC OEP and SIC OEP-loc, SIC is failed to calculate for bad convergence. Does anyone have any suggestions or experiences with this problem? Are there other program packages that can be used to calculate the SIE of DFT? Thank you. Best Wishes! Xin Wang Department of Chemistry Nanjing University P.R. China From chemistry-request@ccl.net Wed Oct 29 13:34:36 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9TIY3Lj011005 for ; Wed, 29 Oct 2003 13:34:04 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.10/jtpda-5.4) with ESMTP id h9TIY24B054288 for ; Wed, 29 Oct 2003 19:34:02 +0100 (CET) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h9TIY2rM018872; Wed, 29 Oct 2003 19:34:02 +0100 (MET) Date: Wed, 29 Oct 2003 19:34:02 +0100 (MET) From: Michel Petitjean Message-Id: <200310291834.h9TIY2rM018872[at]ds10.itodys.jussieu.fr> To: chemistry[at]ccl.net Subject: CCL: Monte-Carlo surfaces and volumes X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) CCL: Monte-Carlo surfaces and volumes Some colleagues having required them, the Monte-Carlo f77 subroutines computing the surface and volume of the union and intersection of N d-dimensional spheres, are now downloadable (free) from: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV The binaries of the analytical calculation for d=3 are of course still available (and free) from this page. Michel Petitjean, Email: petitjean[at]itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean[at]ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From chemistry-request@ccl.net Wed Oct 29 17:34:29 2003 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9TMXuLj030024 for ; Wed, 29 Oct 2003 17:33:56 -0500 Received: from cornell.edu (cs6711168-41.satx.rr.com [67.11.168.41]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id h9TMXqeG005805; Wed, 29 Oct 2003 17:33:56 -0500 (EST) Message-ID: <3FA04047.8010002$at$cornell.edu> Date: Wed, 29 Oct 2003 16:33:43 -0600 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry$at$ccl.net" Subject: ArgusLab 4 question Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.6 required=7.0 tests=FROM_ENDS_IN_NUMS,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi all I have a molecule that I've built in ArgusLab4. It's a small peptide that has a Zinc in it. I have optimized it using the Universal Force Field (UFF). Is there a way that I can "convert" my file so that I can do an optimization using a higher level of theory? For example, if I try to do an AMI calculation, I get an error message saying, "Unrecognized exception caught in runCalcThread". Thanks in advance, Richard From chemistry-request@ccl.net Wed Oct 29 10:00:22 2003 Received: from samuel.unet.maine.edu (samuel.unet.maine.edu [130.111.39.86]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9TExoLj003633 for ; Wed, 29 Oct 2003 09:59:50 -0500 Received: from osgood.unet.maine.edu (osgood.unet.maine.edu [130.111.39.64]) by samuel.unet.maine.edu (8.12.8/8.12.8) with ESMTP id h9TEvROt009616 for ; Wed, 29 Oct 2003 09:57:27 -0500 Received: from adamantane.maine.edu (Adamantane.umecit.maine.edu [130.111.234.157]) by osgood.unet.maine.edu (8.11.6/8.11.6) with ESMTP id h9TEvvS04128 for ; Wed, 29 Oct 2003 09:57:57 -0500 Message-Id: <5.1.1.6.0.20031029095508.00a1d9e0$at$mail.maine.edu> X-Sender: rcfort$at$mail.maine.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Wed, 29 Oct 2003 09:58:16 -0500 To: chemistry$at$ccl.net From: "Raymond C. Fort Jr." Subject: Symmetry and Gaussian Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-MailScanner: Found to be clean, Found to be clean X-MailScanner-Information: Please contact the ISP for more information X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I'm sure this has been asked before, but the list archives currently are not very searchable. I've been running some optimizations of small molecules with G98 (ethylene, formaldehyde; Cartesian input) to illustrate use of the program to a class. The calculations fail rapidly with the message that there has been a change in point group or standard orientation. So far, the only way I can get a calculation to finish is to turn off symmetry. I'd appreciate suggestions of alternatives. Ray Professor Ray Fort Jr. Voice: (207)-581-1180 Department of Chemistry FAX: (207)-581-1191 University of Maine EMail: rcfort$at$maine.edu Orono, ME 04469 Web: chemistry.umeche.maine.edu/fort.html Molecular modeling of organic and biological molecules; chemistry of lignin and cellulose From chemistry-request@ccl.net Wed Oct 29 12:10:09 2003 Received: from ned.sims.nrc.ca (ned.SIMS.nrc.ca [132.246.109.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9TH9cLj008456 for ; Wed, 29 Oct 2003 12:09:38 -0500 Received: from ned.sims.nrc.ca (localhost [127.0.0.1]) by ned.sims.nrc.ca (8.12.6/8.12.6/SuSE Linux 0.6) with ESMTP id h9TH9ZW1004940; Wed, 29 Oct 2003 12:09:35 -0500 Received: from localhost (ps@localhost) by ned.sims.nrc.ca (8.12.6/8.12.6/Submit) with ESMTP id h9TH9Zmb004937; Wed, 29 Oct 2003 12:09:35 -0500 Date: Wed, 29 Oct 2003 12:09:35 -0500 (EST) From: Serguei Patchkovskii Reply-To: Serguei.Patchkovskii!at!nrc.ca To: wxinmail!at!sohu.com cc: chemistry!at!ccl.net Subject: Re: CCL:software for self-interaction correction(SIC) of DFT In-Reply-To: <113939.1067414596847.JavaMail.postfix!at!mx23.mail.sohu.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS - amavis-milter (http://www.amavis.org/) X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Wed, 29 Oct 2003 wxinmail!at!sohu.com wrote: > Does anyone have any suggestions or experiences with this problem? Are > there other program packages that can be used to calculate the SIE of DFT? ADF can do SIC-DFT. See www.scm.com Serguei --- Dr. Serguei Patchkovskii Tel: +1-(613)-990-0945 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii!at!nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2011, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From chemistry-request@ccl.net Wed Oct 29 11:06:09 2003 Received: from aleph.net.uniovi.es (aleph.net.uniovi.es [156.35.11.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9TG5bLj005808 for ; Wed, 29 Oct 2003 11:05:37 -0500 Received: from CONVERSION-DAEMON.aleph.net.uniovi.es by aleph.net.uniovi.es (PMDF V6.1 #39514) id <01L2EPSVYCDC00KQSR!at!aleph.net.uniovi.es> for chemistry!at!ccl.net; Wed, 29 Oct 2003 17:05:25 +0100 (MET) Received: from webuniovi.innova.uniovi.es (webuniovi.innova.uniovi.es [156.35.33.99]) by aleph.net.uniovi.es (PMDF V6.1 #39514) with ESMTP id <01L2EPSUNSWI00K5F6!at!aleph.net.uniovi.es> for chemistry!at!ccl.net; Wed, 29 Oct 2003 17:05:23 +0100 (MET) Received: from localhost ([127.0.0.1] helo=gijon.quimica.uniovi.es) by webuniovi.innova.uniovi.es with esmtp (Exim 3.35 #1 (Debian)) id 1AEsq1-0000a3-00 for ; Wed, 29 Oct 2003 17:06:25 +0100 Date: Tue, 29 Oct 2013 17:27:59 +0100 From: =?UNKNOWN?Q?Rub=E9n?= Meana =?UNKNOWN?Q?Pa=F1eda?= Subject: Linux Cluster X-Sender: rubenmp!at!correo.uniovi.es To: chemistry!at!ccl.net Reply-to: rubenmp!at!correo.uniovi.es Message-id: MIME-version: 1.0 X-Mailer: Mailreader.com v2.3.29 (2001-07-20) Content-type: text/plain; charset=iso8859-1 Content-transfer-encoding: 8BIT X-Originating-Host: gijon.quimica.uniovi.es [156.35.55.153]; Wed, 29 Oct 2003 16:06:25 GMT X-Browser: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020830, JavaScript: On X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello CCLers, We want to obtain information about building cluster of Linux. Where can we obtain it? Thank in advanced Rubin Meana Paqeda Ph.D. Student Laboratorio de Qummica Computacional. Dpto de Qummica Fmsica y Analmtica. Facultad de Qummica. Universidad de Oviedo. C/Julian Claverma 8, 332006 Oviedo, Principado de Asturias, Spain e-mail: rubenmp!at!correo.uniovi.es Tel. +34-985105016 Fax From chemistry-request@ccl.net Wed Oct 29 09:55:20 2003 Received: from mserv.itpa.lt (mserv.itpa.lt [193.219.53.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9TEslLj003423 for ; Wed, 29 Oct 2003 09:54:47 -0500 Received: from mserv.itpa.lt (localhost [127.0.0.1]) by mserv.itpa.lt (8.12.9p2/8.12.6) with ESMTP id h9TEsjVb075955; Wed, 29 Oct 2003 16:54:45 +0200 (EET) (envelope-from tamulis!at!mserv.itpa.lt) Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.12.9p2/8.12.6/Submit) with ESMTP id h9TEsj8M075952; Wed, 29 Oct 2003 16:54:45 +0200 (EET) Date: Wed, 29 Oct 2003 16:54:44 +0200 (EET) From: Arvydas Tamulis To: CHEMISTRY!at!ccl.net cc: Jelena Tamuliene , Subject: bug in the G98 RHF ? Message-ID: <20031029162814.D72943-100000!at!mserv.itpa.lt> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Netters, I am optimizing Peptide Nucleic Acids (PNA) fragments with G98 and compare with optimization results obtained with GAMESS-US. During optimization with G98 RHF 6-31G in the CytosinePNA fragment was formed not expected H-bond with Cytosine and peptide group. Total energy lowered down to -977.916 a.u. While GAMESS-US RHF 6-31G optimization of CytosinePNA fragment gives total energy equal to -938.906 a.u. and not appeared wrong H-bond between Cytosine and peptide group. By the way G98 B3LYP 6-31G optimization of CytosinePNA fragment does not gives wrong H-bond between Cytosine and peptide group. Interesting that AdeninePNA fragment optimization with G98 RHF 6-31G does not gives wrong H-bond between Adenine and peptide group, while GAMESS-US AdeninePNA RHF 6-31G optimized total energy is slightly lower. So, it seems that sometimes during G98 RHF optimization might occur something like wrong H-bond with very lowered total energy: difference arround 40 a.u. Do it is bug in G98 or something else? Best regards, Arvydas Tamulis ******************************************************************* Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Vilnius University, Theoretical Molecular Electronics and Spintronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mails: tamulis!at!itpa.lt or arvydas_tamulis!at!yahoo.com WEBsite: http://www.itpa.lt/~tamulis/ fax: +370-5-2125361 Phones: +370-5-2625036 or +370-5-2620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Mobile phone: +370-69919397 ******************************************************************* From chemistry-request@ccl.net Wed Oct 29 21:46:43 2003 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9U2kBLj006674 for ; Wed, 29 Oct 2003 21:46:11 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id h9U2jfjm016043; Wed, 29 Oct 2003 21:45:41 -0500 Date: Wed, 29 Oct 2003 21:45:41 -0500 (EST) From: Jan Labanowski To: chemistry{at}ccl.net cc: jkl{at}ccl.net Subject: ACS 04.03.28 Anaheim -- Grid computing, research collaboratories, virtual labs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This notice has been published on several listservers, I apologize for any inconvenience. You are invited to present a paper at the symposium "Research collaboratories, virtual laboratories, and Grid computing" organized jointly by the Division of Chemical Information (CINF) and the CSA Trust during the 227th National Meeting of the American Chemical Society (ACS) in Anaheim, March 28 - April 1, 2004. We specifically solicit papers discussing research, design, and development of Grid technologies that help in solving large-scale compute and data intensive applications in the broader area of drug design, including software tools and resource brokers that facilitate large-scale molecular studies on geographically distributed computational and data resources. Abstracts should be submitted online using OASYS ( http://oasys.acs.org). The deadline for submission is November 25, 2003. Any changes to an abstract can be made until December 1st. If you have any questions regarding the symposium or problems with submitting your abstract please call or e-mail me (see below). Co-organizer of the symposium is Dr. Wendy Warr of Wendy Warr & Associates. The targeted length of a presentation is 30 minutes including 5 minutes for Q&A. When planning your presentation, consider a back-up person from your organization who could deliver your talk if for any reason you are prevented > from attending the meeting. Speakers are responsible for their own travel and registration costs. One-day registration fees will be paid by the Division after approval by the organizers for speakers who are non-US scientists or non-ACS members Dr. Guenter Grethe 352 Channing Way Alameda, CA 94502-7409 Tel/Fax: 510-865-5152 Mobile: 510-333-7526 e-mail: ggrethe{at}comcast.net From chemistry-request@ccl.net Wed Oct 29 22:19:53 2003 Received: from ns.cwp.co.kr ([210.109.76.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9U3JGLj015119 for ; Wed, 29 Oct 2003 22:19:22 -0500 Received: from cri2p ([172.24.15.92]) by ns.cwp.co.kr (8.9.3 (PHNE_25184)/8.9.3) with ESMTP id MAA26725 for ; Thu, 30 Oct 2003 12:15:52 +0900 (KST) From: "Sei-Hwan Kim" To: Subject: [CCL] Request the information of 15th European Symposium Date: Thu, 30 Oct 2003 12:18:17 +0900 Message-ID: <000c01c39e94$77df57e0$5c0f18ac@cri2p> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000D_01C39EDF.E7C6FFE0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4925.2800 X-Spam-Status: No, hits=4.2 required=7.0 tests=HTML_80_90,HTML_COMMENT_8BITS,HTML_FONT_FACE_BAD, HTML_FONT_FACE_ODD,HTML_MESSAGE version=2.55 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_000D_01C39EDF.E7C6FFE0 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable Dear CCL=20 Anyone inform information about =A1=B015th European Symposium on QSAR(Quantitative Structure-Activity Relationship) and Molecular Modeling=A1=B1 Included registration fee.=20 =20 Thank you.=20 =20 Sei-Hwan Kim Senior Research Scientist Central Research Instituts Choongwae Pharma Co. 146-141, Annyiung-ri, Taean-eup Hwasung-city, Kyounggi-do 445-976 Republic of Korea=20 E-mail : Seihkim_at_cwp.co.kr Tel : 82-31-230-6322 Fax : 82-31-234-0210 =20 ------=_NextPart_000_000D_01C39EDF.E7C6FFE0 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable

Dear CCL

Anyone inform information about = =A1=B015th = European Symposium on QSAR(Quantitative Structure-Activity Relationship) and Molecular = Modeling=A1=B1 Included registration fee.

 

Thank you. =

 

Sei-Hwan Kim

Senior Research Scientist

Central Research Instituts

Choongwae Pharma Co.

146-141, Annyiung-ri, Taean-eup

Hwasung-city, Kyounggi-do 445-976

Republic of = Korea

E-mail : Seihkim_at_cwp.co.kr

Tel : 82-31-230-6322

Fax : 82-31-234-0210

 

------=_NextPart_000_000D_01C39EDF.E7C6FFE0-- From chemistry-request@ccl.net Wed Oct 29 22:47:33 2003 Received: from ccl.net (pagergate.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9U3l1Lj015621 for ; Wed, 29 Oct 2003 22:47:01 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id h9U3k0jm019932; Wed, 29 Oct 2003 22:46:00 -0500 Date: Wed, 29 Oct 2003 22:46:00 -0500 (EST) From: Jan Labanowski To: chemistry{at}ccl.net, mel{at}asdn.net cc: Jan Labanowski Subject: Nov. 15 Deadline: Abstracts for ECS Symp. on ADVANCED SHORT-TIME THERMAL PROCESSING FOR Si-BASED CMOS DEVICES II Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Please find attached the CALL FOR PAPERS for our annual symposium on "ADVANCED SHORT-TIME THERMAL PROCESSING FOR Si-BASED CMOS DEVICES, II", at the 205th Electrochemical Society Meeting in San Antonio, Texas (USA), May 9-14, 2004. DEADLINE for abstract submission: NOVEMBER 15, 2003. This symposium will cover the latest developments in Rapid Thermal Processing and other short-time processing technologies with emphasis on mainstream CMOS engineering (or integration), in particular on gate stack, source/drain and channel engineering. As such in addition to conventional RTP technologies such as RTA, RTO and RTCVD, and related equipment and modelling issues, we welcome applications of techniques such as UV or laser-assisted processing in annealing, doping, etc., and advanced thin-film deposition techniques such as Atomic Layer Deposition (ALD), MOCVD and UHV-CVD, remote plasma and, sputtering, MBE, etc. Researchers and technologists are encouraged to submit their abstracts on applications in the areas of: formation and/or deposition of ultra-thin gate dielectrics (including novel higher dielectric constant materials) and their gate electrodes (including metal gates); doping technologies to form ultra-shallow junctions; formation of low-resistivity contacts to such junctions; advanced channel engineering approaches including Si-Ge channels and ultrathin SOI technologies; modelling and equipment issues. Finally, new developments in RTP and other short-time processing and inspection equipment to improve throughput, uniformity, in-situ monitoring, non-intrusive wafer inspection, process control and modelling are of special interest to this symposium. Publication of a Proceedings Volume is planned to be available at the meeting. All authors accepted for presentation are obligated to submit a camera-ready Proceedings Volume manuscript. For review purposes the electronic version of this manuscript should be sent by Email to the symposium organizers before December 15, 2003. Instructions for preparing the manuscript will be sent out by the symposium organizers after the official notification of acceptance is distributed by the ECS Headquarters Office. A tentative list of invited speakers includes J. Woo / UCLA ; R. Lindsay / IMEC; K. Suguro / Toshiba, Japan; W. Lerch / Mattson, Germany ; M. Ieong / IBM; K. Saraswat / Stanford; A. Ritenour / MIT: C.W. Liu / National Taiwan Univ.; T.J King /UC Berkeley; S. Thompson / Intel; E. Gerritsen / Philips-STM, France; W. Tsai / Intel; G. Higashi / Applied Materials; E. Garfunkel / Rutgers Univ.; T. Horikawa / MIRAI, Japan W. Maszara / AMD ; J.P. Lu / Texas Instruments ; C. Hobbs / Motorola, France ; Z. Zhang / Georgia Tech Symposium Organizers: M.C. Vzt|rk, North Carolina State University, Dept. of Electrical and Computer Engineering, Centennial Campus, 1010 Main Campus Drive, EGRC Building, Rm 339, Campus Box 7920, Raleigh, NC 27695-7920, USA, Phone: (919) 481 4057, Fax (919) 515-5055, E-mail: mco{at}eos.ncsu.edu; E. Gusev, IBM T.J. Watson Research Center, P.O. Box 218, Yorktown Heights, NY 10598, USA, Phone (914)-945-1168, Fax (914)-945-2141, E-mail: gusev{at}us.ibm.com ; L.J. Chen, National Tsing Hua University, Dept. of Materials Science and Engineering 101, Sec. 2, Kuang-Fu Road, Hsinchu, Taiwan 300, Republic of China, Phone + 886-3-5731166, Fax +886-3-5718328, E-mail: ljchen{at}mse.nthu.edu.tw ; D.-L. Kwong, University of Texas at Austin, MER 2.60A, Mailcode R9950, Austin, TX 78712-1100, USA, Phone: (512) 471-5922, Fax (512) 471-4345, E-mail: dlkwong{at}mail.utexas.edu ; P.J. Timans, Mattson Technology Inc., 47131 Bayside Parkway, Fremont, CA 94538, USA, Phone (510)-492-6114, Fax: (510)-226-8241, E-mail: Paul.Timans{at}mattson.com ; G. Miner, Applied Materials, 2727 Augustine Dr., M/S 0768, Santa Clara, CA 95054, USA, Phone: (408)235-4518, Fax: (408)563-8468, E-mail: gary_miner{at}amat.com; F. Roozeboom, Philips Research Labs (WA 14), Prof. Holstlaan 4, 5656 AA Eindhoven, The Netherlands, Phone: + 31-40-2742767, Fax: + 31-40-2743352, E-mail: Fred.Roozeboom{at}philips.com . For more information: http://www.electrochem.org/meetings/future/205/meeting.htm and ecs{at}electrochem.org The Electrochemical Society Inc., 65 South Main Street, Pennington, NJ 08534-2896, USA Phone 609-737-1902 , fax 609-737-2743 From chemistry-request@ccl.net Wed Oct 29 23:00:41 2003 Received: from moroka.molsci.csiro.au (moroka.molsci.CSIRO.AU [138.194.51.53]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9U409Lj015954 for ; Wed, 29 Oct 2003 23:00:09 -0500 Received: from [138.194.51.27] (gold-fa.chem.csiro.au [138.194.51.27]) by moroka.molsci.csiro.au (8.12.10/8.12.10) with ESMTP id h9U3VOHr020215 for ; Thu, 30 Oct 2003 14:31:24 +1100 (EST) Mime-Version: 1.0 X-Sender: win097!at!clex4.vic.csiro.au Message-Id: In-Reply-To: <000c01c39e94$77df57e0$5c0f18ac@cri2p> References: <000c01c39e94$77df57e0$5c0f18ac@cri2p> Date: Thu, 30 Oct 2003 15:00:05 +1100 To: chemistry!at!ccl.net From: "Prof. Dave Winkler" Subject: Re: [spam] CCL:[CCL] Request the information of 15th European Symposium Content-Type: multipart/alternative; boundary="============_-1144636089==_ma============" X-Spam-Status: No, hits=0.2 required=7.0 tests=HTML_40_50,HTML_MESSAGE,IN_REP_TO,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --============_-1144636089==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Dear CCL > >Anyone inform information about "15th European Symposium on >QSAR(Quantitative Structure-Activity Relationship) and Molecular >Modeling" Included registration fee. > > Here is the web site. It looks a great meeting. http://www.euro-qsar2004.org/ -- Cheers, Dave Prof. David A. Winkler FRACI CChem CPChem Email: dave.winkler!at!csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au --============_-1144636089==_ma============ Content-Type: text/html; charset="us-ascii" Re: [spam] CCL:[CCL] Request the information of 15th E
Dear CCL
Anyone inform information about "15th European Symposium on QSAR(Quantitative Structure-Activity Relationship) and Molecular Modeling" Included registration fee.
 
Here is the web site.  It looks a great meeting.

http://www.euro-qsar2004.org/

--
Cheers,
Dave

Prof. David A. Winkler FRACI CChem CPChem    Email: dave.winkler!at!csiro.au  
Senior Principal Research Scientist               Voice: 61-3-9545-2477     
CSIRO Molecular Science                       Fax:   61-3-9545-2446
Private Bag 10,Clayton South MDC 3169              http://www.csiro.au
Australia                                    http://www.molsci.csiro.au
--============_-1144636089==_ma============--