From chemistry-request@ccl.net Mon Aug 23 18:06:29 2004 Received: from hotmail.com (bay15-f36.bay15.hotmail.com [65.54.185.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7NN6S99021909 for ; Mon, 23 Aug 2004 18:06:28 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 23 Aug 2004 16:15:04 -0700 Received: from 202.98.16.25 by by15fd.bay15.hotmail.msn.com with HTTP; Mon, 23 Aug 2004 23:15:04 GMT X-Originating-IP: [202.98.16.25] X-Originating-Email: [zhijw{at}hotmail.com] X-Sender: zhijw{at}hotmail.com From: "Zhijian Wu" To: jerome{at}scs.uiuc.edu Cc: chemistry{at}ccl.net Subject: RE: CCL:Gaussian: mixing basis sets ? Date: Mon, 23 Aug 2004 19:15:04 -0400 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 23 Aug 2004 23:15:04.0424 (UTC) FILETIME=[05BEBE80:01C48967] X-Spam-Status: No, hits=3.2 required=7.5 tests=HTML_50_60,HTML_MESSAGE, MIME_HTML_NO_CHARSET,MIME_HTML_ONLY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net

Hi,

Follow this example.

# b3lyp/gen pseudo=read opt

Title Card Required

0 2

Ca

La 1 R

 

R 0.9

 

Ca 0

6-311+g(d)

****

La 0

Lanl2dz

****

 

La 0

Lanl2dz

Regards,

Wu

>From: "Jerome Baudry" <jerome{at}scs.uiuc.edu>
>To: chemistry{at}ccl.net
>Subject: CCL:Gaussian: mixing basis sets ?
>Date: Mon, 23 Aug 2004 15:01:17 -0500
>
>Dear list
>Do you know how (is possible) to assign different basis sets to parts of the
>same calculation. For example I want to describe some Ag atoms by basis set
>A and a water molecule by basis set B.Couldn't find anything in the Gaussian
>technical help website.
>
>Thanks,
>Jerome
>
>----------------------------------------------------------
>Jerome Baudry, Ph.D.       Senior Research Scientist, VizLab Manager.
>School of Chemical Sciences    University of Illinois at Urbana-Champaign
>505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801
>  Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120;    e-mail:
>jerome{at}scs.uiuc.edu
>
>
>
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On the road to retirement? Check out MSN Life Events for advice on how to get there! From chemistry-request@ccl.net Mon Aug 23 17:38:18 2004 Received: from smtp812.mail.sc5.yahoo.com (smtp812.mail.sc5.yahoo.com [66.163.170.82]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i7NMcH99020606 for ; Mon, 23 Aug 2004 17:38:17 -0500 Message-Id: <200408232238.i7NMcH99020606:at:server.ccl.net> Received: from unknown (HELO bcnnt) (tapas.kar:at:sbcglobal.net@129.123.67.11 with login) by smtp812.mail.sc5.yahoo.com with SMTP; 23 Aug 2004 21:58:43 -0000 From: "Tapas Kar" To: "'Jerome Baudry'" , Subject: RE: Gaussian: mixing basis sets ? Date: Mon, 23 Aug 2004 17:58:43 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.5510 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 Thread-Index: AcSJWyWnK9gr6zqQT++lpYsa6LzoTQAAK6HQ In-Reply-To: <002401c4894b$f51c94a0$efe27e82@leonidas> X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, Use 'Gen' instead of any basis function in Route card. 'Gen' is general basis. At the end of your coordinates or z-matrix, after a blank line, add: Ag 0 Basis set A **** O H 0 Basis set B **** For more details see Gen in Gaussian manual Thanks Tapas Kar -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request:at:ccl.net] On Behalf Of Jerome Baudry Sent: Monday, August 23, 2004 4:01 PM To: chemistry:at:ccl.net Subject: CCL:Gaussian: mixing basis sets ? Dear list Do you know how (is possible) to assign different basis sets to parts of the same calculation. For example I want to describe some Ag atoms by basis set A and a water molecule by basis set B.Couldn't find anything in the Gaussian technical help website. Thanks, Jerome ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: jerome:at:scs.uiuc.edu -= 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, jlabanow:at:nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue Aug 24 09:58:16 2004 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7OEwGtE006491 for ; Tue, 24 Aug 2004 09:58:16 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 4.34) id 1Bzcsz-0006nM-TX for chemistry..at..ccl.net; Tue, 24 Aug 2004 17:06:58 +0200 Message-ID: <412B5991.8070206..at..mpi-bpc.mpg.de> Date: Tue, 24 Aug 2004 17:06:57 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL List Subject: converting g03 output to pdb Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: (clean) by exiscan+sophie X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, Do you know a software that converts gaussian 03 output to pdb trajectory in a similar way as babel can convert g94 output? Thank you very much vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru..at..mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@ccl.net Tue Aug 24 10:02:26 2004 Received: from simbiosys.ca ([65.18.214.160]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7OF2PtE006661 for ; Tue, 24 Aug 2004 10:02:25 -0500 Received: from phobos.simbiosys.ca (CPE0080c6f1fcb9-CM000f9f7b41ce.cpe.net.cable.rogers.com [69.195.104.248]) (authenticated (0 bits)) by simbiosys.ca (8.12.10/8.11.0) with ESMTP id i7OFAoP8011983 for ; Tue, 24 Aug 2004 11:10:57 -0400 X-Authentication-Warning: simbiosys.ca: simbiosys owned process doing -bs From: Aniko Simon Organization: SimBioSys Inc. To: chemistry(at)ccl.net Subject: CCL:Announcing eHiTS v4.3 flexible ligand docking Date: Tue, 24 Aug 2004 11:11:03 -0400 User-Agent: KMail/1.5.3 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200408241111.03919.aniko(at)simbiosys.ca> X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL members, SimBioSys Inc. is pleased to announce the release of eHiTS version 4.3. eHiTS 4.3 is a fast, flexible ligand docking package which is fully automated, making it suitable for high throughput screening applications. Version 4.3 boasts a new, highly efficient architecture, including improved multi-threading computations, decreasing overall wait times for dockings. eHiTS 4.3 is available for Linux and SGI platforms. eHiTS is based on an innovative systematic exhaustive algorithm, that does not have any random components. Furthermore, it is not limited to a predetermined discrete set of dihedral angles like other systematic methods. eHiTS guarantees to find the best solution according to the scoring function in the full continuous search space. For more information, or to obtain a demo version of eHiTS 4.3, please visit www.simbiosys.ca, or pick up a demo CD at the ACS meeting. Best regards, Ms Aniko Simon, Ph.D. -- VP Business Development SimBioSys Inc. Toronto, Canada From chemistry-request@ccl.net Tue Aug 24 10:04:06 2004 Received: from mail.scs.uiuc.edu (mail.scs.uiuc.edu [130.126.231.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7OF46tE006747 for ; Tue, 24 Aug 2004 10:04:06 -0500 Received: from leonidas (leonidas.scs.uiuc.edu [130.126.226.239]) by mail.scs.uiuc.edu with esmtp; Tue, 24 Aug 2004 10:12:47 -0500 Reply-To: jerome-.at.-scs.uiuc.edu From: "Jerome Baudry" To: chemistry-.at.-ccl.net Subject: SUMMARY :RE: Gaussian: mixing basis sets ? Date: Tue, 24 Aug 2004 10:08:49 -0500 Message-ID: <000601c489ec$42f3d620$efe27e82@leonidas> 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 CWS, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 Importance: Normal In-Reply-To: <002401c4894b$f51c94a0$efe27e82@leonidas> X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net THe answer to my original question is "Use the gen keyword." Thanks to all !!! Jerome ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: jerome-.at.-scs.uiuc.edu > -----Original Message----- > From: Computational Chemistry List > Dear list > Do you know how (is possible) to assign different basis sets > to parts of the > same calculation. For example I want to describe some Ag atoms by basis set > A and a water molecule by basis set B.Couldn't find anything > in the Gaussian technical help website. > > Thanks, > Jerome > > > From chemistry-request@ccl.net Tue Aug 24 11:14:53 2004 Received: from noralf.uib.no (noralf.uib.no [129.177.30.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7OGEptE012050 for ; Tue, 24 Aug 2004 11:14:51 -0500 Received: from alfred.uib.no (smtp.uib.no) [129.177.30.120] by noralf.uib.no with esmtp (Exim 4.34) id 1Bze51-0003Ik-PE; Tue, 24 Aug 2004 18:23:29 +0200 Received: from kamfer.ii.uib.no (ii.uib.no) [129.177.20.41] by smtp.uib.no for chemistry[at]ccl.net with esmtp (Exim 4.34) id 1Bze51-0001ER-Jc; Tue, 24 Aug 2004 18:23:27 +0200 Message-ID: <412B6B7F.2050304[at]ii.uib.no> Date: Tue, 24 Aug 2004 18:23:27 +0200 From: Nathalie Reuter User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030716 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry[at]ccl.net Subject: NMA for proteins: http://www.bioinfo.no/tools/normalmodes Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-checked-clean: by exiscan on noralf X-Scanner: 9114ddbf833fc5aef384ee6880b3e8fe http://tjinfo.uib.no/virus.html X-UiB-SpamFlag: NO UIB: -39.0 hits, 11.0 required X-UiB-SpamReport: spamassassin found; -30 -- From is listed in 'whitelist_from' -9.0 -- Message received from UIB X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net We are pleased to announce the release of a new version of our web server for normal analysis of proteins, WEBnm@, available at http://www.bioinfo.no/tools/normalmodes. Go and try it ! The server is meant to provide users with simple and automated computation and analysis of low-frequency normal modes for proteins. The computation performed through our server should help the user understand whether your protein of interest undergoes large amplitude movements, and thus decide if it is worthwile performing a complete study with more thorough analysis. Analysis tools provided here have been described and successfully applied /(Reuter et al., Biophys.J., 2003)/. Normal modes calculations are performed using the MMTK package /(K. Hinsen, J.Comput.Chem., 2000)/. Analysis tools available so far are: * deformation energies for low-frequency modes; * calculation of normalized squared atomic displacements: results are provided either as raw data or as plots (PDF format); * vector field representation: PNG image files or VMD state files; * animations of the vibrations associated with the low-frequency modes: animated gif or dcd trajectory files. We welcome comments and suggestions, and will surely take them into account in future versions. -- Nathalie Reuter Computational Biology Unit BCCS/Univ. of Bergen Thormohlensgt, 55 N-5008 Bergen Phone: +47 55 58 40 40 Fax: +47 55 58 42 95 From microelectronics-request Tue Aug 24 22:19:56 2004 From: Anatoli Korkin Received: from 68.230.113.194 (SquirrelMail authenticated user korkin) by asdn.net with HTTP; Tue, 24 Aug 2004 22:19:53 -0500 (EST) Message-ID: <56784.68.230.113.194.1093403993.squirrel{at}asdn.net> Date: Tue, 24 Aug 2004 22:19:53 -0500 (EST) Subject: International Journal of Nanotechnology: special issue on "Nanotechnology Toolkit" To: CCL List MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Colleagues, We invite you to submit a paper to the special issue of International Journal of Nanotechnology on Nanotechnology Toolkit". The Special issue of the International Journal of Nanotechnology will address the most advanced state of the art hardware and software tools currently available or under development for nanotechnology in manufacturing, characterization and computer simulations. The papers on experimental and computational (software) tools are invited and equally welcome. The deadline for the paper submission is 1 October 2004. This call for papers is affiliated with the Symposium and Summer School on "Nano and Giga Challenges in Microelectronics, September 13-17, 2004, Krakow, Poland, but not limited to the meeting participants. For further details and paper submission, please, visit the following web site: http://asdn.net/ngcm2004/publication-ijnt.shtml Guests Editors of IJNT special issue on "nanotechnology Toolkit", Anatoli Korkin, Nano & Giga Solutions, USA Jan Labanowski, University of Notre Dame, USA, Marek Szymonski, Jagiellonian University, Poland, Alex A. Volinsky, University of South Florida, USA From chemistry-request@ccl.net Tue Aug 24 16:21:12 2004 Received: from mhub-c4.tc.umn.edu (mhub-c4.tc.umn.edu [160.94.128.34]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7OLL99O032227 for ; Tue, 24 Aug 2004 16:21:09 -0500 Received: from [128.101.96.7] (chardonnay.chem.umn.edu [128.101.96.7]) by mhub-c4.tc.umn.edu with ESMTP for chemistry!at!ccl.net; Tue, 24 Aug 2004 16:29:52 -0500 (CDT) X-Umn-Remote-Mta: [N] chardonnay.chem.umn.edu [128.101.96.7] #+LO+TS+AU+HN Subject: One negative eigenvalue - No imaginary frequency!!?? From: csilval To: chemistry!at!ccl.net Content-Type: text/plain Message-Id: <1093382991.22041.783.camel!at!chardonnay.chem.umn.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.6 (1.4.6-2) Date: Tue, 24 Aug 2004 16:29:51 -0500 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.2 required=7.5 tests=PLING_QUERY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi CCLers! I have got a weird -well, to be honest, a couple of them- output files > from g03 where I try to locate the TS of a nucleophilic attack. After convergence a frequency job is performed. It results in one negative eigenvalue but no imaginary frequency associated to it. Actually it seems like there is one imaginary frequency, but gaussian is treating it as a traslation/rotation. The lowest (but positive) mode from the vibrational analysis is likely to be the nucleophilic attack but I cannot get it to be imaginary. I have tried several basis sets and several levels of calculation (HF, B3LYP, MP2) with the very same luck. Is there anything I can do to locate the "real" TS. Also I am enclosing here the very first modes of one of the structures in case it helps to understand what is going on: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Full mass-weighted force constant matrix: Low frequencies --- -31.0607 0.0014 0.0024 0.0025 22.5484 25.9445 Low frequencies --- 42.3766 64.9775 107.1348 Diagonal vibrational polarizability: 624.6067824 849.1987473 446.1087874 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), depolarization ratios for plane and unpolarized incident light, reduced masses (AMU), force constants (mDyne/A), and normal coordinates: 1 2 3 A A A Frequencies -- 18.6726 63.9044 105.9740 Red. masses -- 5.4210 4.4793 3.1978 Frc consts -- 0.0011 0.0108 0.0212 IR Inten -- 21.2490 13.5758 6.6021 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Thanks a lot! From chemistry-request@ccl.net Tue Aug 24 22:22:07 2004 Received: from web20924.mail.yahoo.com (web20924.mail.yahoo.com [216.136.224.139]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i7P3M1SD016488 for ; Tue, 24 Aug 2004 22:22:06 -0500 Message-ID: <20040825033036.14763.qmail!at!web20924.mail.yahoo.com> Received: from [68.230.113.194] by web20924.mail.yahoo.com via HTTP; Tue, 24 Aug 2004 20:30:36 PDT Date: Tue, 24 Aug 2004 20:30:36 -0700 (PDT) From: Anatoli Korkin Subject: International Journal of Nanotechnology: special issue on "Nanotechnology Toolkit" To: chemistry!at!ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Colleagues, We invite you to submit a paper to the special issue of International Journal of Nanotechnology on Nanotechnology Toolkit". The Special issue of the International Journal of Nanotechnology will address the most advanced state of the art hardware and software tools currently available or under development for nanotechnology in manufacturing, characterization and computer simulations. The papers on experimental and computational (software) tools are invited and equally welcome. The deadline for the paper submission is 1 October 2004. This call for papers is affiliated with the Symposium and Summer School on "Nano and Giga Challenges in Microelectronics, September 13-17, 2004, Krakow, Poland, but not limited to the meeting participants. For further details and paper submission, please, visit the following web site: http://asdn.net/ngcm2004/publication-ijnt.shtml Guests Editors of IJNT special issue on "nanotechnology Toolkit", Anatoli Korkin, Nano & Giga Solutions, USA Jan Labanowski, University of Notre Dame, USA, Marek Szymonski, Jagiellonian University, Poland, Alex A. Volinsky, University of South Florida, USA _______________________________ Do you Yahoo!? Win 1 of 4,000 free domain names from Yahoo! Enter now. http://promotions.yahoo.com/goldrush