From jkl@ccl.net Thu Nov 20 05:02:17 2003 -0500 Message-ID: <004801c3af4d$5ae38a70$6c8506c1@Cthulhu> From: "Tamas E. Gunda" To: chemistry|at|ccl.net Subject: Sterimol parameters Date: Thu, 20 Nov 2003 11:02:06 +0100 Dear Jinsong, Mol2Mol can calculate Verloop's Sterimol parameters. See at: http://web.interware.hu/frenzy/mol2mol/ Best regards Tamas Gunda ..................................................... Dr. Tamas E. Gunda Dept. of Pharmaceutical Chemistry University of Debrecen POBox 36 H-4010 Debrecen, Hungary tgunda(AT)puma.unideb.hu ----- Original Message ----- From: "Jinsong Zhao" To: "CCL" Sent: Sunday, November 16, 2003 9:32 AM Subject: CCL:How to calculate the Verloop STERIMOL parameters? > Dear all, > > I wonder whether there is an free routine or program > that could be used to calculate the Verloop STERIMOL > parameters. > > Thanks in advance! > > Best wishes, > > Jinsong From chemistry-request@ccl.net Thu Nov 20 04:51:49 2003 Received: from mail.unl.edu.ar (mail.unl.edu.ar [168.96.132.10]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hAK9pFRW007181 for ; Thu, 20 Nov 2003 04:51:16 -0500 Received: (qmail 4246 invoked by uid 505); 20 Nov 2003 09:46:19 -0000 Received: from sgaray*at*fbcb.unl.edu.ar by mail by uid 502 with qmail-scanner-1.16 (sophie: 2.14/3.70. Clear:. Processed in 0.045324 secs); 20 Nov 2003 09:46:19 -0000 Received: from dfbioq.unl.edu.ar (HELO dfbio-2) (170.210.10.14) by fbcb.unl.edu.ar with SMTP; 20 Nov 2003 09:46:19 -0000 From: sgaray*at*fbcb.unl.edu.ar To: chemistry*at*ccl.net Date: Thu, 20 Nov 2003 06:49:47 -0300 MIME-Version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Subject: net charge in aimpac Message-ID: <3FBC640B.7539.2AF6EC3A@localhost> X-Confirm-Reading-To: sgaray*at*fbcb.unl.edu.ar X-pmrqc: 1 Priority: urgent X-mailer: Pegasus Mail for Win32 (v3.12c) X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by server.ccl.net id hAK9pnRW007190 Hi to all I4ve been working with aimpac program for calculate charge in a molecule with net charge 0 (I4m new working wiht aimpac). When I calculate the net charge atom by atom with aimpac I found that the net charge of the molecule was -0.66. I used gamess to introduce the wave function the molecule with 6311 basis set. Can someone give any idea? Thank you in advance. Sergio Garay Biochemist Faculty of Biochemistry and Biological Science Universidad Nacional del Litoral Santa Fe (3000)- Argentina Paraje "El Pozo" From chemistry-request@ccl.net Thu Nov 20 04:46:05 2003 Received: from dns.lpmc.univ-montp2.fr (dns.lpmc.univ-montp2.fr [162.38.149.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAK9jXRW006955 for ; Thu, 20 Nov 2003 04:45:33 -0500 Received: from localhost (pboulet@localhost) by dns.lpmc.univ-montp2.fr (8.11.6/8.11.6) with ESMTP id hAK9fOi22284; Thu, 20 Nov 2003 10:41:25 +0100 X-Authentication-Warning: dns.lpmc.univ-montp2.fr: pboulet owned process doing -bs Date: Thu, 20 Nov 2003 10:41:24 +0100 (CET) From: Pascal Boulet X-X-Sender: pboulet*at*dns.lpmc.univ-montp2.fr Reply-To: Pascal.boulet*at*lpmc.univ-montp2.fr To: Arvydas Tamulis cc: chemistry*at*ccl.net Subject: Re: CCL:H-bonds and Van-der-Waals intereactions In-Reply-To: <20031119203429.L65271-100000*at*mserv.itpa.lt> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,SIGNATURE_LONG_DENSE,USER_AGENT_PINE, X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello Arvydas, On Wed, 19 Nov 2003, Arvydas Tamulis wrote: > > I have done geometry optimization of DNA and Peptide Nucleic Acid (PNA) > fragments during last month using G98 B3LYP 6-311G but not received good > results. Seems DFT is not correct for finding geometry where exist H-bonds > and Van-der-Waals intereactions? B3LYP is known to give poor results for weak interactions. If you try the PW91 exchange and correlation functionals or the Barone's et al. modified PW91 functionals (MPW in Gaussian, see the manual), you should obtain better results. If I were you, I would also try PBE as it should work fine for weak interactions as well. I hope this help, Pascal -- Dr. Pascal Boulet Laboratoire de Physico-chimie de la Matihre Condensie UMR 5617 Universiti de Montpellier II Place Eughne Bataillon 34095 Montpellier Cedex 5 tel. 04 67 14 33 00 Fax 04 67 14 42 90 courriel: Pascal.Boulet*at*lpmc.univ-montp2.fr From chemistry-request@ccl.net Thu Nov 20 02:15:45 2003 Received: from ns.cwp.co.kr ([210.109.76.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAK7F7RW000853 for ; Thu, 20 Nov 2003 02:15:12 -0500 Received: from cri2p ([172.24.15.92]) by ns.cwp.co.kr (8.9.3 (PHNE_25184)/8.9.3) with ESMTP id QAA27512 for ; Thu, 20 Nov 2003 16:11:38 +0900 (KST) From: "Sei-Hwan Kim" To: Subject: Seminar on web. Date: Thu, 20 Nov 2003 16:13:39 +0900 Message-ID: <000001c3af35$d3b75200$5c0f18ac@cri2p> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C3AF81.43A20740" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.8 required=7.0 tests=HTML_FONT_FACE_BAD,HTML_FONT_FACE_ODD,HTML_MESSAGE version=2.55 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_0001_01C3AF81.43A20740 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear CCLer Seminar on web. Topic: SBD: "Fast Lead Identification Protocol (FLIP) for structure based data mining using 3D fingerprints" Date: Thursday, November 20, 2003 Time: 8:00 am, Pacific Standard Time (GMT -08:00, San Jose) Web site : www.accelrys.com sean ------=_NextPart_000_0001_01C3AF81.43A20740 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear CCLer =

 

Seminar on web.

 

Topic: SBD:  = “Fast Lead Identification Protocol (FLIP) for structure based data mining using 3D fingerprints”

Date: Thursday, November 20, = 2003

Time: 8:00 am, Pacific Standard Time = (GMT -08:00, = San = Jose)

 

Web site : = www.accelrys.com

 

sean

 

------=_NextPart_000_0001_01C3AF81.43A20740-- From chemistry-request@ccl.net Thu Nov 20 11:05:06 2003 Received: from web1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAKG4YRW020766 for >ccl.net>; Thu, 20 Nov 2003 11:04:35 -0500 Received: from wwwdev.ulb.ac.be (resu1 [164.15.59.200]) by web1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id RAA04632; Thu, 20 Nov 2003 17:04:33 +0100 (MET) for Date: Thu, 20 Nov 2003 17:04:33 +0100 (MET) Message-Id: <200311201604.RAA04632<>web1.ulb.ac.be> From: Giju Kalathingal >vub.ac.be> To: Pascal Boulet >lpmc.univ-montp2.fr> Cc: chemistry<>ccl.net Subject: re:CCL:H-bonds and Van-der-Waals intereactions X-Mailer: Webmail ULB v2.1 X-Spam-Status: No, hits=-0.5 required=7.0 tests=QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL-all, My suggestion is that all of those interested in DFT based applications should attend some DFT lessons. Many people tend to accuse a DFT method or the other because they do not know much about the practical applications possible within the approximations and shortcomings of DFT. There are some recent developments that treating the non-local correlation, which is important in weak complexes. Ideally, B3LYP, BP86, BLYP, etc. are not supposed to be used to treat weak complexes correctly. However, one may get reasonable results with these methods, which is "not a real success" of the method. So one needs to get a method that is resonable to treat problems involving non-local correlation, e.g, noble gas complexes, H-bonding, etc. Some progress in that direction is by PBE, revPBE, etc. > >Hello Arvydas, > >On Wed, 19 Nov 2003, Arvydas Tamulis wrote: > >> >> I have done geometry optimization of DNA and Peptide Nucleic Acid (PNA) >> fragments during last month using G98 B3LYP 6-311G but not received good >> results. Seems DFT is not correct for finding geometry where exist H-bonds >> and Van-der-Waals intereactions? > >B3LYP is known to give poor results for weak interactions. If you try the >PW91 exchange and correlation functionals or the Barone's et al. >modified PW91 functionals (MPW in Gaussian, see the manual), you should >obtain better results. > >If I were you, I would also try PBE as it should work fine for weak >interactions as well. > >I hope this help, > >Pascal > >-- >Dr. Pascal Boulet >Laboratoire de Physico-chimie de la Matihre Condensie >UMR 5617 >Universiti de Montpellier II >Place Eughne Bataillon >34095 Montpellier Cedex 5 >tel. 04 67 14 33 00 Fax 04 67 14 42 90 >courriel: Pascal.Boulet<>lpmc.univ-montp2.fr > > With best regards, Giju Kalathingal Present Address:- Dr. Kalathingal Thomas Giju Department of General Chemistry (ALGC) Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussels, Belgium. Tel.:++32-2-629-3315 Fax: ++32-2-629-3317 E-mail: Giju.Kalathingal<>vub.ac.be From chemistry-request@ccl.net Thu Nov 20 11:35:11 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 hAKGYdRW022136 for ; Thu, 20 Nov 2003 11:34:39 -0500 Received: from mserv.itpa.lt (localhost [127.0.0.1]) by mserv.itpa.lt (8.12.9p2/8.12.6) with ESMTP id hAKGYcVb088390; Thu, 20 Nov 2003 18:34:38 +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 hAKGYb9K088387; Thu, 20 Nov 2003 18:34:37 +0200 (EET) Date: Thu, 20 Nov 2003 18:34:37 +0200 (EET) From: Arvydas Tamulis To: Pascal Boulet cc: chemistry_at_ccl.net, , Jelena Tamuliene Subject: H-bonds and Van-der-Waals intereactions In-Reply-To: Message-ID: <20031120181919.N84376-100000_at_mserv.itpa.lt> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hAKGZBRW022161 Dear Netters, Thanks for almost ten contributors who answered me. I can do some summarising for quantum mechanical calculations of supramolecules possessing H-bonds and weak disspersion interactions: 1) needs to use MP2 and CC mehods but their are expensive - I will do this later. 2) using DFT better to use PW91 potential with inclusion difussion functions (I did not included these) and polarization functions - I will start from B3PW91 6-31+G** Regards, Arvydas Tamulis On Thu, 20 Nov 2003, Pascal Boulet wrote: > Hello Arvydas, > B3LYP is known to give poor results for weak interactions. If you try the > PW91 exchange and correlation functionals or the Barone's et al. > modified PW91 functionals (MPW in Gaussian, see the manual), you should > obtain better results. > If I were you, I would also try PBE as it should work fine for weak > interactions as well. > -- > Dr. Pascal Boulet > Laboratoire de Physico-chimie de la Matihre Condensie > UMR 5617 > Universiti de Montpellier II > Place Eughne Bataillon > 34095 Montpellier Cedex 5 > tel. 04 67 14 33 00 Fax 04 67 14 42 90 > courriel: Pascal.Boulet_at_lpmc.univ-montp2.fr From chemistry-request@ccl.net Thu Nov 20 11:13:58 2003 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAKGDPRW021222 for ; Thu, 20 Nov 2003 11:13:25 -0500 Expiry-Date: Sat, 31 Jan 2004 -1:-1:-1 +0000 Reply-To: training:at:accelrys.com To: CHEMISTRY:at:ccl.net Cc: Judith Madeley Subject: CCL: Accelrys Customer Training in January MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: From: Jeff Nauss Date: Thu, 20 Nov 2003 08:13:23 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 11/20/2003 08:13:25, Serialize complete at 11/20/2003 08:13:25 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) Accelrys Inc. are holding the following training workshops at locations in the US and Europe during January. 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. RATIONAL DRUG DESIGN Introduction to Cerius2 for Life Sciences 20-21 January in Burlington, MA Small Molecule and Drug Design with Cerius2 22 -23 January in Burlington, MA Library Design and Analysis 26-27 January in Burlington, MA Pharmacophore Generation with Catalyst 28-29 January in Burlington, MA For course details and registration see: http://www.accelrys.com/training/RDD/schedule.html CHEMINFORMATICS Accord Visual Objects 5 January in San Diego, CA Accord SDK 6-7 January in San Diego, CA Accord Chemistry Cartridge 8 January in San Diego, CA Accord CombiChem Add-on 9 January in San Diego, CA Accord Enterprise Client 12 January in Cambridge, UK DS Accord for Excel Enterprise 13 January in Cambridge, UK Accord Inventory 14 January in Cambridge, UK Accord HTS 15 January in Cambridge, UK DIVA 16 January in Cambridge, UK Accord Enterprise Database Administration 19-20 January in Cambridge, UK For course details and registration see: http://www.accelrys.com/training/cheminf/schedule.html MATERIALS SCIENCE Introduction to Materials Science 26 January in San Diego, CA Introduction to Polymer Modeling 27-28 January in San Diego, CA Introduction to Quantum Mechanics Modeling 29-30 January in San Diego, CA Workshop on Crystal Structure Determination 2 February in San Diego, CA For course details and registration see: http://www.accelrys.com/training/matsci/schedule.html -- 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:at:accelrys.com http://www.accelrys.com/training From chemistry-request@ccl.net Thu Nov 20 09:20:29 2003 Received: from morelia.be.devgen.com (212-123-24-6.iFiber.telenet-ops.be [212.123.24.6]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hAKEJvRW016685 for ; Thu, 20 Nov 2003 09:19:57 -0500 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Subject: CCL: compounds vs targets Date: Thu, 20 Nov 2003 15:19:52 +0100 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL: compounds vs targets Thread-Index: AcOvcVzdHjlaiLiHR7C5RLD/WLTT/g== From: "Jan De Kerpel" To: 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) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hAKEKURW016710 Dear CCL'-ers Does anyone know of a database that links chemical compounds to proteins based on activity (MOA)? Or are there any lists around with compounds (activator/inhibitor) and their targets? Ideally, since we would like to analyse these data in batch-mode bioinformatics, the compounds and targets are listed with a commonly used identifier (i.e. compound: generic name or CAS-number, target: EC number, Swiss-Prot ID(s), ...), rather than a name (e.g. protein kinase A). We are aware of database like MDDR or CMC or IDDB but these do not use a target-id number. Pharmaprojects comes in the neighborhood, but is not batch-mode queryable (as far as we know). I'll summerize the answers. cheers! jan Dr. Jan De Kerpel Head of CADD deVGen Technologiepark 9 9052 Zwijnaarde-Gent Belgium Tel : +32 9 3242464 Fax: +32 9 3242425 jan.dekerpel:at:devgen.com www.devgen.com From chemistry-request@ccl.net Thu Nov 20 16:25:56 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 hAKLPNRW000619 for ; Thu, 20 Nov 2003 16:25:24 -0500 Received: (from apache@localhost) by turmiel.ch.uj.edu.pl (8.11.6/8.11.6) id hAKLOmn22292; Thu, 20 Nov 2003 22:24:48 +0100 X-Authentication-Warning: turmiel.ch.uj.edu.pl: apache set sender to zborowsk^at^chemia.uj.edu.pl using -f Received: from 149.156.95.36 (SquirrelMail authenticated user zborowsk) by mail.ch.uj.edu.pl with HTTP; Thu, 20 Nov 2003 22:24:48 +0100 (CET) Message-ID: <1216.149.156.95.36.1069363488.squirrel^at^mail.ch.uj.edu.pl> Date: Thu, 20 Nov 2003 22:24:48 +0100 (CET) Subject: Re: CCL:Relativistic Corrections From: To: In-Reply-To: <1069265645.3fbbb2ed98eab^at^webmail.mta.ca> References: <1069265645.3fbbb2ed98eab^at^webmail.mta.ca> 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) Dear Jean-Marc A few years ago (2 or 3) I downloaded Molfdir package from the University of Groningen www page (http://theochem.chem.rug.nl/). It is a relativistic program based on Dirac-Fock equation. It was free of charge. Unfortunately I haven't used it so far so I cannot write you any other information about Molfdir but I think it can be useful for you. Best regards > Are there any programs that use methods based on the dirac equation > available? Mount Allison University > jmsmsn^at^mta.ca > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk^at^chemia.uj.edu.pl From chemistry-request@ccl.net Thu Nov 20 13:52:22 2003 Received: from puck.reed.edu (puck.reed.edu [134.10.2.8]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hAKIpoRW028238 for ; Thu, 20 Nov 2003 13:51:50 -0500 Received: (qmail 21142 invoked from network); 20 Nov 2003 18:51:48 -0000 Received: from rosencrantz.reed.edu (134.10.2.31) by puck.reed.edu with SMTP; 20 Nov 2003 18:51:48 -0000 Message-id: <17707700..at..rosencrantz.reed.edu> Date: 20 Nov 2003 10:51:50 PST From: Alan.Shusterman..at..directory.reed.edu (Alan Shusterman) Subject: CCL:AIM software To: chemistry..at..ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline 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) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hAKIqMRW028255 I am interested in obtaining software (free or commercial) to perform Atoms-in-Molecules analyses on electron density distributions and convert some of the results into graphical images. I'm using Spartan04(W2000) and Jaguar (Linux) to calculate wave functions, so I figure I'll probably have to do some file conversion to create the necessary input. Can anyone recommend Windows/Linux software that they *currently/recently* use that might be appropriate for this? By the same token, can anyone warn me about software that would be too difficult/out-of-date to use? I have just visited the Morphy98 and AIM2000 web pages, but I can't tell if these programs are still being maintained (the web pages haven't changed for a year or more!?). -Alan ==== Alan Shusterman Department of Chemistry Reed College 3203 S.E. Woodstock Blvd. Portland, OR 97202-8199 503-517-7699 From chemistry-request@ccl.net Thu Nov 20 18:39:59 2003 Received: from sag1.chem.pitt.edu (sag1.chem.pitt.edu [136.142.153.80]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAKNdSRW004673 for ; Thu, 20 Nov 2003 18:39:28 -0500 Received: from [136.142.60.48] (HELO IDO) by sag1.chem.pitt.edu (CommuniGate Pro SMTP 4.0.5) with SMTP id 740685 for chemistry!at!ccl.net; Thu, 20 Nov 2003 18:41:30 -0500 Message-ID: <012201c3afbf$8a0a6fe0$303c8e88@IDO> From: "Brad Tsai" To: Subject: Compile VASP & Siesta on Opteron Date: Thu, 20 Nov 2003 18:39:28 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_011F_01C3AF95.A12B4020" 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 X-Spam-Status: No, hits=4.7 required=7.0 tests=COMMUNIGATE,HTML_30_40,HTML_MESSAGE,RCVD_IN_NJABL, X_NJABL_OPEN_PROXY version=2.55 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) *This message was transferred with a trial version of CommuniGate(tm) Pro* This is a multi-part message in MIME format. ------=_NextPart_000_011F_01C3AF95.A12B4020 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CClers, I am trying to install VASP and SIsesta on our new Opteron machine. I = just wander if any one has done it before. What is the best compiler to = compile these two packages in 64 bit? Is any special library I need for = these 64 bit calculations? If one can share the makefiles, I would very = appreciated.=20 Best regards, -Brad =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Center for Molecular and Materials Simulations=20 University of Pittsburgh (412)-624-8694 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_011F_01C3AF95.A12B4020 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CClers,
 
I am trying to install VASP and SIsesta = on our new=20 Opteron machine. I just wander if any one has done it before. What is = the best=20 compiler to compile these two packages in 64 bit? Is any special library = I need=20 for these 64 bit calculations? If one can share the makefiles, I would = very=20 appreciated.
 
Best regards,
-Brad
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Center for Molecular and Materials Simulations
University of=20 Pittsburgh
(412)-624-8694
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
------=_NextPart_000_011F_01C3AF95.A12B4020-- From chemistry-request@ccl.net Thu Nov 20 17:27:21 2003 Received: from ms1.usu.edu (ms1.usu.edu [129.123.104.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAKMQoRW002891 for ; Thu, 20 Nov 2003 17:26:50 -0500 Received: from pc3 (pc3.chem.usu.edu [129.123.3.37]) by ms1.usu.edu (8.12.8/8.12.8) with SMTP id hAKMNTFr013840 for ; Thu, 20 Nov 2003 15:23:29 -0700 Reply-To: From: "Tapas Kar" To: "CCL" Subject: Nanotechnology course Date: Thu, 20 Nov 2003 15:19:19 -0700 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0049_01C3AF79.AB6962E0" 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 V6.00.2800.1165 X-USU-MailScanner-Information: Please contact the USU HelpDesk for more information (http://helpdesk.usu.edu) X-USU-MailScanner: Found to be clean X-USU-MailScanner-SpamCheck: not spam (whitelisted), SpamAssassin (score=0.475, required 5, HTML_40_50 0.47, HTML_MESSAGE 0.00) X-Spam-Status: No, hits=1.1 required=7.0 tests=HTML_40_50,HTML_FONT_FACE_ODD,HTML_MESSAGE, MSGID_GOOD_EXCHANGE 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_0049_01C3AF79.AB6962E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Hi, We are planning to introduce Nanotechnology Courses at undergraduate and graduate levels. Like to know how many universities offer such courses and some information on course materials. This will help us to develop such course. I appreciate your help to direct me related websites also. Thanks, Tapas *********************************************** "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - ---------------------------------------------------------------------------- ---- Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar..at..cc.usu.edu Web:http://www.chem.usu.edu/faculty/Tapas/index.html ------=_NextPart_000_0049_01C3AF79.AB6962E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,
We are=20 planning to introduce Nanotechnology Courses at undergraduate and = graduate=20 levels.
Like to=20 know how many universities offer such courses and some information on = course=20 materials.  This will help us to develop such course. =
I=20 appreciate your help to direct me related websites = also.
Thanks,
Tapas

***********************************************
"We owe a lot to the Indians, who taught = us how to=20 count, without
which no worthwhile scientific discovery could have = been=20 made."
         &n= bsp;           &nb= sp;           &nbs= p;        =20 - Albert Einstein=20 -
--------------------------------------------------------------------= ------------
Tapas=20 Kar, Ph. D
Department of Chemistry & Biochemistry
Utah State=20 University
Logan, UT 84322-0300

Tel: 435-797-7230
Fax:=20 435-797-3390
Email: tapaskar..at..cc.usu.edu
Web:http://www.chem.usu.edu/faculty/Tapas/index.html

 
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