From chemistry-request@ccl.net Wed May 5 08:34:13 2004 Received: from bonito.ulb.ac.be (mailhost.ulb.ac.be [164.15.59.220]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i45DYBkh024538 for ; Wed, 5 May 2004 08:34:12 -0500 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.8]) by bonito.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id PAA11896; Wed, 5 May 2004 15:34:38 +0200 (MEST) for Received: from ulb.ac.be (chimorg-pc5.ulb.ac.be [164.15.61.104]) by mach.vub.ac.be (Postfix) with ESMTP id D50A42304 for ; Wed, 5 May 2004 15:35:59 +0200 (CEST) Message-ID: <409968A6.6080705_at_ulb.ac.be> Date: Thu, 06 May 2004 00:20:22 +0200 From: Christophe Biot Organization: ULB User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: fr, en-us MIME-Version: 1.0 To: Liste CCL Subject: solvent temperature epsilon Content-Type: text/plain; charset=ISO-8859-1; format=flowed X-Spam-Status: No, hits=3.7 required=7.5 tests=DATE_IN_FUTURE_06_12, LINES_OF_YELLING,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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i45DYDkh024548 Dear All, I have a question regarding a Gaussian03 frequency job in a solvent at different temperatures. Could someone tell me if the dielectric constant should be specify in the input file for each solvent and at the considered temperature, or if the value is automatically known? Do you have any bibliographic references to obtain these values ? Best regards -- ******************************************************** BIOT Christophe Bioinformatique Ginomique et Structurale, CP 165/61 Universiti Libre de Bruxelles 50 Av. F.D. Roosevelt 1050 Bruxelles, BELGIQUE Phone: 32-2-650 3001 Fax: 32-2-650 3575 E-mail:cbiot_at_ulb.ac.be ******************************************************** THE ... SCIENTISTS WERE WRONG ... THE MOST PERSISTENT PRINCIPLES OF THE UNIVERSE WERE ACCIDENT AND ERROR. -- FRANK HERBERT IN DUNE From chemistry-request@ccl.net Wed May 5 09:12:35 2004 Received: from bilbo.fq.edu.uy (bilbo.fq.edu.uy [164.73.160.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i45ECHkh026030 for ; Wed, 5 May 2004 09:12:28 -0500 Received: from bilbo.fq.edu.uy (localhost [127.0.0.1]) by bilbo.fq.edu.uy (8.12.1/8.12.1) with ESMTP id i45EE3Cs019018 for ; Wed, 5 May 2004 11:14:04 -0300 Received: from localhost (marc@localhost) by bilbo.fq.edu.uy (8.12.1/8.12.1/Submit) with SMTP id i45EDr0T019014 for ; Wed, 5 May 2004 11:14:02 -0300 X-Authentication-Warning: bilbo.fq.edu.uy: marc owned process doing -bs Date: Wed, 5 May 2004 11:13:52 -0300 (GRNLNDST) From: Marc Segovia X-Sender: marc:at:bilbo.fq.edu.uy To: chemistry:at:ccl.net Subject: IRC phase option In-Reply-To: <000301c43209$a2d52a70$df01000a@laquicom05> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 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 Hi Trying to use the phase option in gaussian 98 IRC, I cannot find out any difference with the normal IRC without it. Has somebody experience on it or where to look for ? many thanks .marc ================================================================= Marc Eduardo Segovia Becker Catedra de Quimica Cuantica MTC-Lab Facultad de Quimica email: marc:at:bilbo.edu.uy CC 1157 http://bilbo.edu.uy/MTC-Lab.html Montevideo 11800 URUGUAY ' A scientist is someone whose curiosity survives education's assault on it' Herman Bondi " Mambu Baddu" kiswahili "The best is coming" " We are different, in essence from other men. If you want to will something run 100m. If you want to experience something run a marathon" Emil Zatopek ============================================================== From chemistry-request@ccl.net Wed May 5 12:00:39 2004 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i45H0bkh032203 for ; Wed, 5 May 2004 12:00:38 -0500 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1BLPm6-0004ia-T3 for chemistry..at..ccl.net; Wed, 05 May 2004 14:01:38 -0300 Received: from 138.73.24.157 ( [138.73.24.157]) as user khunter..at..mailserv.mta.ca by webmail.mta.ca with HTTP; Wed, 5 May 2004 14:01:38 -0300 Message-ID: <1083776498.40991df2d5f50..at..webmail.mta.ca> Date: Wed, 5 May 2004 14:01:38 -0300 From: khunter..at..mta.ca To: chemistry..at..ccl.net Subject: solvation question regarding PCM techniques in G98 and G03 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.157 X-Spam-Status: No, hits=0.5 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Upon doing a solvation calculation using the following command prompt, #b3lyp/6-31g(d,p) opt SCRF=(IEFPCM, solvent=water), with the Gaussian 98 suite the calculation would run to completion but would list an Error message such as shown below. (With emphasis on Error on NUCLEAR pol.charges) Two-electron integral symmetry is turned on. 215 basis functions 385 primitive gaussians 43 alpha electrons 43 beta electrons nuclear repulsion energy 693.2194006859 Hartrees. One-electron integrals computed using PRISM. NBasis= 215 RedAO= T NBF= 215 NBsUse= 215 1.00D-04 NBFU= 215 Projected INDO Guess. Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. ---------------------------------------------------------------------- Solvent: WATER Model : IEF/UAHF, Icomp = 0 Version: MATRIX INVERSION Cavity : PENTAKISDODECAHEDRA with 60 initial tesserae ---------------------------------------------------------------------- Nord Group Hybr Charge Alpha Radius Bonded to 1 N sp2 0.00 1.20 1.590 C2 [s] C5 [s] C12 [s] 2 C sp3 0.00 1.20 1.500 N1 [s] C3 [s] N9 [s] 3 C sp3 0.00 1.20 1.500 C2 [s] N4 [s] C6 [s] 4 N sp2 0.00 1.20 1.590 C3 [s] C5 [d] 5 CH sp2 0.00 1.20 1.860 N1 [s] N4 [d] 6 C sp2 0.00 1.20 1.635 C3 [s] N7 [s] O11 [d] 7 NH sp2 0.00 1.20 1.680 C6 [s] C8 [s] 8 C sp2 0.00 1.20 1.680 N7 [s] N9 [d] N10 [s] 9 N sp2 0.00 1.20 1.590 C2 [s] C8 [d] 10 NH2 sp3 0.00 1.20 1.680 C8 [s] 11 O sp2 0.00 1.20 1.590 C6 [d] 12 CH3 sp3 0.00 1.20 1.860 N1 [s] ---------------------------------------------------------------------- Warning: nuclear charge 211 neglected Warning: electronic charge 211 neglected FIRST ITERATION Error on NUCLEAR pol.charges = 0.02091 Error on ELECTR. pol.charges =-0.03449 Upon doing a similar calculation using the Gaussian 03 suite but with #b3lyp/6-31g(d,p) opt SCRF=(PCM, solvent=water) as the command prompt, due to the alteration in the solvation methods, the calculation would end up going into a loop of optimization cycles and fail due to exceeding the number of optimization steps. Besides the error of exceeding the number of optimization steps, an Error comment would appear before the SCF stating : Error on total polarization charges = 0.01117 My questions are does the error produced in the Gaussian 98 significant and how to correct the error in the Gaussian 03 suite and why the different errors? Ken Hunter From chemistry-request@ccl.net Wed May 5 12:39:40 2004 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 i45Hdckh001105 for >ccl.net>; Wed, 5 May 2004 12:39:39 -0500 Expiry-Date: Sat, 31 Jul 2004 -1:-1:-1 +0000 Reply-To: training<>accelrys.com To: CHEMISTRY<>ccl.net Subject: CCL: Accelrys Customer training Events for July MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 Message-ID: >accelrys.com> From: Jeff Nauss >accelrys.com> Date: Wed, 5 May 2004 10:41:27 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 05/05/2004 10:41:28, Serialize complete at 05/05/2004 10:41:28 Content-Type: text/plain; charset="US-ASCII" 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 Accelrys Inc. are holding the following training workshops during July. 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, $520 per day for government and $380 per day for academic. MOLECULAR MODELING Introduction to DS Modeling 1.1 27-28 July in San Diego, CA Structure-Based Design with DS Modeling 1.2 29 July in San Diego, CA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html and http://www.accelrys.com/training/rdd/schedule.html MATERIALS MODELING Introduction to Materials Studio 12 July in San Diego, CA Introduction to Polymer Modeling 13-14 July in San Diego, CA Introduction to Quantum Mechanics Modeling 15-16 July in San Diego, CA For course details and registration see: http://www.accelrys.com/training/matsci/schedule.html BIOINFORMATICS Wisconsin Package and SeqLab 20-21 July in San Diego, CA Introduction to SeqWeb 22 July in San Diego, CA Introduction to DS Gene 23 July in San Diego, CA For course details and registration see: http://www.accelrys.com/training/bioinf/schedule.html CHEMINFORMATICS Accord Enterprise Clients 12 July in Cambridge, UK Accord Enterprise Database Administration 13-14 July in Cambridge, UK Accord HTS 15 July in Cambridge, UK Accord Inventory 16 July in Cambridge, UK For course details and registration see: http://www.accelrys.com/training/cheminf/schedule.html -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-1761 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss<>accelrys.com http://www.accelrys.com/training From chemistry-request@ccl.net Wed May 5 12:04:25 2004 Received: from gip2.u-picardie.fr (gip2.u-picardie.fr [193.49.184.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i45H4Okh032396 for >ccl.net>; Wed, 5 May 2004 12:04:25 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 7A87193A6; Wed, 5 May 2004 19:06:10 +0200 (CEST) To: chemistry<>ccl.net Subject: Running InsightII under Linux Message-ID: <1083776770.40991f026e2a8<>webmail.u-picardie.fr> Date: Wed, 05 May 2004 19:06:10 +0200 (CEST) From: FyD >u-picardie.fr> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 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 All, I am trying to use the LINUX version of InsightII under RedHat 9.0. To run it, I execute before the following sequence of commands: source /tsri/msi/cshrc setenv BIOSYM_PLATFORM Linux_2_Intel_3 set_context I2000.3L setenv LD_ASSUME_KERNEL 2.4.1 setenv LD_LIBRARY_PATH /usr/X11R6/lib:$LD_LIBRARY_PATH Then when I run "insightII -axxess", insightII works with the following problem: the buttons on the LEFT side of the graphic interface are BLACK (the buttons cannot be recognized...). I try to install different versions of 'openmotif' or 'lesstif' without success... Did someone had this problem and solved it ? Best regards, Francois F.-Y. Dupradeau -- The Scripps Research Institute, San Diego, CA Faculte de Pharmacie, UPJV, Amiens, France -- http://www.u-picardie.fr/labo/lbpd/fyd.htm From chemistry-request@ccl.net Wed May 5 10:33:09 2004 Received: from oceanite.ens-lyon.fr (oceanite.ens-lyon.fr [140.77.1.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i45FX8kh029098 for >ccl.net>; Wed, 5 May 2004 10:33:08 -0500 Received: from localhost (oceanite.ens-lyon.fr [127.0.0.1]) by oceanite.ens-lyon.fr (Postfix) with ESMTP id E252932029D for >ccl.net>; Wed, 5 May 2004 17:34:32 +0200 (CEST) Received: from oceanite.ens-lyon.fr ([127.0.0.1]) by localhost (oceanite [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 01076-01 for >ccl.net>; Wed, 5 May 2004 17:34:32 +0200 (CEST) Received: from ens-lyon.fr (unknown [140.77.2.15]) by oceanite.ens-lyon.fr (Postfix) with ESMTP id B4C57320274 for >ccl.net>; Wed, 5 May 2004 17:34:32 +0200 (CEST) Message-ID: <40992759.3000209<>ens-lyon.fr> Date: Wed, 05 May 2004 17:41:45 +0000 From: Paul Fleurat-Lessard >ens-lyon.fr> Reply-To: Paul.Fleurat-Lessard<>ens-lyon.fr User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr; rv:1.3.1) Gecko/20030428 X-Accept-Language: fr-fr, en-us, en MIME-Version: 1.0 To: CHEMISTRY<>ccl.net Subject: [Summary] Compiling g03 with ifort Content-Type: text/plain; charset=ISO-8859-1; format=flowed X-Virus-Scanned: by amavisd-new-20030616-p7 (Debian) at ens-lyon.fr X-Spam-Status: No, hits=2.0 required=7.5 tests=NO_RDNS,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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i45FX9kh029102 Dear CClers, Some times ago, I asked if somone has already compiled G03 with Intel Fortran. I received many hints and I thank here everybody. With your help, I could manage compiling g03 ... BUT: - ifort 8.0.034 does not deal with files greater than 2GB, so that you have to be careful (back to the old time where you had to put %rwf option !) - I could not compile newzmat (at least, it did not compile easily and I did not bother taking care of this.) - Some tests did not suceed. One important point is that ifort is not (yet?) supported by Gaussian Inc. As such, I am not allowed to make my changes publicly available. I have to say that I understand this limitations: as they told me, if someone use such changes and has trouble, that means more work for the Gaussian support. As some tests did not succeed, that means that my changes are not yet 100% usable. So, I will not publish here my changes, but just tell you that I needed to modify the following files: - bldg03 - i386.make (one 'public hint': you have to use the -Vaxlib option) - mdutil.c (I added some 'interfaces') With best regards, Paul. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard<>ens-lyon.fr Laboratoire de Chimie Ecole Normale Supirieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allie d'Italie Fax: + 33 (0)4 72 72 88 60 69364 Lyon Cedex 07 Si vous ne pouvez expliquer un concept ` un enfant de six ans, c'est que vous ne le comprenez pas complhtement. Albert Einstein