From chemistry-request@server.ccl.net Tue Jun 27 16:37:09 2000 Received: from bastion.tbc.com (bastion.tbc.com [207.243.182.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA21550 for ; Tue, 27 Jun 2000 16:37:09 -0400 Received: from domino.tbc.com (mickey.tbc.com [207.243.182.149]) by bastion.tbc.com (8.8.5/8.8.5) with ESMTP id OAA00195 for ; Tue, 27 Jun 2000 14:58:34 -0500 (CDT) Received: from tbc.com ([192.168.1.164]) by domino.tbc.com (Lotus Domino Release 5.0.3) with ESMTP id 2000062715395398:872 ; Tue, 27 Jun 2000 15:39:53 -0500 Sender: jli@bastion.tbc.com Message-ID: <39591064.B5254C83@tbc.com> Date: Tue, 27 Jun 2000 15:36:52 -0500 From: jli X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: pharmacokinetic database X-MIMETrack: Itemize by SMTP Server on tbcnotes/TBC(Release 5.0.3 |March 21, 2000) at 06/27/2000 03:39:54 PM, Serialize by Router on tbcnotes/TBC(Release 5.0.3 |March 21, 2000) at 06/27/2000 03:39:58 PM, Serialize complete at 06/27/2000 03:39:58 PM Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=gb2312 Hi All, Does anyone know any database for pharmacokinetic data like half-life, bioavailibility etc. ? Regards, Jian From chemistry-request@server.ccl.net Wed Jun 28 10:56:25 2000 Received: from Carbon.udea.edu.co (root@carbon.udea.edu.co [200.24.17.76]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA26465 for ; Wed, 28 Jun 2000 10:53:56 -0400 Received: from localhost (alemoe@localhost) by Carbon.udea.edu.co (8.9.3/8.9.3) with ESMTP id OAA01297 for ; Wed, 28 Jun 2000 14:52:12 -0500 Date: Wed, 28 Jun 2000 14:52:12 -0500 (COT) From: Alejandro Montoya To: chemistry@ccl.net Subject: AIM code Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello CCLers, I would apreciate if someone can point me on what is the best procedure to obtained the Bond order using the AIM theory when the AIM code fails in G98 and an error message is obtained at the end of the file. NO CONVERGENCE IN SVDSOL FOR SURFACE SHEET 14 Error termination thanks in advance, Regards, From chemistry-request@server.ccl.net Wed Jun 28 05:03:39 2000 Received: from nenuphar.saclay.cea.fr (nenuphar.saclay.cea.fr [132.166.192.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA24352 for ; Wed, 28 Jun 2000 05:03:38 -0400 Received: from drfmc.ceng.cea.fr (drfmc.ceng.cea.fr [132.168.10.1]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.D20+Y2K) with ESMTP id LAA11720 for ; Wed, 28 Jun 2000 11:03:30 +0200 (MET DST) Received: from drfmc.ceng.cea.fr (localhost [127.0.0.1]) by drfmc.ceng.cea.fr (8.9.3/8.8.8) with ESMTP id LAA04560 for ; Wed, 28 Jun 2000 11:03:27 +0200 Message-ID: X-Mailer: XFMail 1.4.4 on Solaris X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit MIME-Version: 1.0 Resent-Date: Wed, 21 Jun 2000 10:42:52 +0200 (MET DST) Resent-Message-Id: Resent-From: Valentina Vetere Resent-To: chemistry@ccl.net Date: Wed, 28 Jun 2000 11:03:27 +0200 (MET DST) From: Valentina Vetere To: chemistry@ccl.net Subject: Summary: CCL:a second question:BSSE/pseudo Content-Transfer-Encoding: 8bit I received one answer, probably my question was not so clear... I'm calculating BSSE correction on systems containing heavy elements. To describe heavy elements I'm using ECP basis sets and core potentials. Now, I have strange results because, on similar systems, BSSE can change from 2Kcal to 100Kcal.. So I'm not sure that the BSSE procedure (I mean using ghost atoms) is theoretically right if ECP core potential are used. If, as Doug Fox proposed, the procedure of removing core in the BSSE calculation is theoretically right...what could be the problem? I'm sure about the initial guess, every SP calculation is with conver=8.. So ..other suggestion? thank you valentina -----FW: ----- ------------------------------------------------------------ The only answer: Doug Fox ------------------------------------------------------------ Vetere, I don't see other discussion but you may have direct responses. I agree that you need to remove the ECP when setting the ghosts. I don't see a problem with absence of the core since the point for the core potential is to keep the valence electrons from collapsing into the region about that nucleus. Since you are removing both electrons on that atom and the nucleus you will get the interaction between the remaining atoms and those valence basis sets but no energy contributions. When you reverse and compute the ECP portion you will get the corepotential contributions to the energy. I don't see where this is dramatically different than the other potential errors in the CP process. If someone else sees a bigger flaw let me know. ---------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Jun 28 09:32:08 2000 Received: from hotmail.com (f15.law3.hotmail.com [209.185.241.15]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA26156 for ; Wed, 28 Jun 2000 09:32:07 -0400 Received: (qmail 75252 invoked by uid 0); 28 Jun 2000 13:29:56 -0000 Message-ID: <20000628132956.75251.qmail@hotmail.com> Received: from 138.231.68.39 by www.hotmail.com with HTTP; Wed, 28 Jun 2000 06:29:56 PDT X-Originating-IP: [138.231.68.39] From: "David Touboul" To: chemistry@ccl.net Subject: GAUSSIAN98 ONIOM AMBER and parameters Date: Wed, 28 Jun 2000 13:29:56 GMT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Dear CCLer's, I'm a french student who studies, in the LBPA (Laboratory of Biotechnology and Applicated Pharmacology) at the ENS of Cachan, a protein with Gaussian 98 and the option ONIOM. We have some difficulties to find a good description of water. The parameters of AMBER are not efficient: G98 doesn't find the molecular parameters HW and OW. Moreover we have to study an ion Mg2+ and we don't know how to define its parameters. If someone has some information about this problem, I appreciate very much, thanks a lot Touboul David ENS Cchan LBPA UMR 8532 Av Camille Desmoulins 94230 CACHAN FRANCE email:toubouldavid@hotmail.com ________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com From chemistry-request@server.ccl.net Wed Jun 28 11:08:44 2000 Received: from smtp.mail.yahoo.com (smtp.mail.yahoo.com [128.11.68.32]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA26556 for ; Wed, 28 Jun 2000 11:08:43 -0400 Received: from s10062.pc.nus.edu.sg (HELO scip8239) (137.132.24.189) by smtp.mail.yahoo.com with SMTP; 28 Jun 2000 07:32:22 -0700 X-Apparently-From: Message-ID: <003f01bfe10d$a4626700$bd188489@nus.edu.sg> From: "Li Zhenhua" To: "Yubo Fan" , "CCL" References: <3958C0D7.85A9D423@guomai.sh.cn> Subject: Re: CCL:Oh Symmetry Date: Wed, 28 Jun 2000 22:32:00 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4029.2901 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4029.2901 You can use a loose tolerance to determine the symmetry in G98. Add Iop(2/17=N), the default N is 7, you can try numbers smaller than 7 untill the program say"OK, it is Oh symmetry". Or you can try to write the Z-Matrix with the help of dummy atoms. But seems a little complex following this way. Zhenhua ----- Original Message ----- From: "Yubo Fan" To: Sent: Tuesday, June 27, 2000 10:57 PM Subject: CCL:Oh Symmetry > Hi, everyone, > > I have a Keggin structure metal cluster anion, which has a Oh symmetry > >from its Monocrystal XRD. The problem is G98 couldn't get its Oh > symmetry when I do geometry optimization. Could anyone help me to write > the right Z-Matrix orientation, which can indicate the symmetry. I > attach the PDB file below. > > Thanks in advance > > Y. Fan > > COMPND Mo6O19.pdb > HETATM 1 O 0.000 0.000 0.000 > HETATM 2 Mo 0.000 2.393 0.000 > HETATM 3 Mo -2.393 0.000 0.000 > HETATM 4 Mo 0.000 0.000 2.393 > HETATM 5 Mo 0.000 -2.393 0.000 > HETATM 6 Mo 2.393 0.000 0.000 > HETATM 7 Mo 0.000 0.000 -2.393 > HETATM 8 O 0.000 4.123 0.000 > HETATM 9 O -4.123 0.000 0.000 > HETATM 10 O 0.000 0.000 4.123 > HETATM 11 O 0.000 -4.123 0.000 > HETATM 12 O 4.123 0.000 0.000 > HETATM 13 O 0.000 0.000 -4.123 > HETATM 14 O -1.887 1.887 0.000 > HETATM 15 O -1.887 0.000 1.887 > HETATM 16 O 0.000 1.887 1.887 > HETATM 17 O 1.887 -1.887 0.000 > HETATM 18 O 1.887 0.000 -1.887 > HETATM 19 O 0.000 -1.887 -1.887 > HETATM 20 O 1.887 1.887 0.000 > HETATM 21 O 0.000 1.887 -1.887 > HETATM 22 O -1.887 0.000 -1.887 > HETATM 23 O -1.887 -1.887 0.000 > HETATM 24 O 0.000 -1.887 1.887 > HETATM 25 O 1.887 0.000 1.887 > CONECT 2 8 14 16 20 > CONECT 2 21 > CONECT 3 9 14 15 22 > CONECT 3 23 > CONECT 4 10 15 16 24 > CONECT 4 25 > CONECT 5 11 17 19 23 > CONECT 5 24 > CONECT 6 12 17 18 20 > CONECT 6 25 > CONECT 7 13 18 19 21 > CONECT 7 22 > CONECT 8 2 > CONECT 9 3 > CONECT 10 4 > CONECT 11 5 > CONECT 12 6 > CONECT 13 7 > CONECT 14 2 3 > CONECT 15 3 4 > CONECT 16 2 4 > CONECT 17 5 6 > CONECT 18 6 7 > CONECT 19 5 7 > CONECT 20 2 6 > CONECT 21 2 7 > CONECT 22 3 7 > CONECT 23 3 5 > CONECT 24 4 5 > CONECT 25 4 6 > END > > > -- > ============================================================= > Yubo Fan Email: yubofan@guomai.sh.cn > Organic Synthesis Lab > The Department of Chemistry > Fudan University Phone: 8621-65648139 > No. 220 Handan Road Fax: 8621-65641740 > Shanghai, 200433 > P. R. China > ============================================================= > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > __________________________________________________ Do You Yahoo!? Talk to your friends online with Yahoo! Messenger. http://im.yahoo.com From chemistry-request@server.ccl.net Wed Jun 28 12:51:09 2000 Received: from tiger.jsums.edu (tiger.jsums.edu [143.132.85.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA26924 for ; Wed, 28 Jun 2000 12:51:08 -0400 Received: from localhost (jerzy@localhost) by tiger.jsums.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA41774; Wed, 28 Jun 2000 11:37:49 -0500 (CDT) Date: Wed, 28 Jun 2000 11:37:49 -0500 From: Jerzy Leszczynski To: CHEMISTRY@ccl.net cc: jerzy@tiger.jsums.edu Subject: 9th Conference on Current Trends in Computational Chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 9th CCTCC - First Announcement 9th Conference on Current Trends in Computational Chemistry US Army Corps of Engineers Waterways Experiment Station Vicksburg, Mississippi November 3rd and 4th, 2000. Dear Colleague: We are pleased to announce the 9th Conference on Current Trends in Computational Chemistry. This symposium, organized by Jackson State University, will cover all areas of computational chemistry as well as quantum chemistry. The local host of the conference is the US Army Corps of Engineers Waterways Experiment Station (WES) in Vicksburg, Mississippi. (40 miles west of Jackson) on November 3rd and 4th, 2000. The format consists of a series of plenary lectures and poster presentations on Friday and Saturday covering applications as well as theory. In addition, a banquet is scheduled for Friday evening and a dinner and reception for Saturday evening. The 9th Conference will also feature another talk given in the ancillary Noble Lecture Series. This series was initiated during the 6th CCTCC by a remarkable presentation by Istvan Hargittai entitled The Molecules Among Us: Conversations with Famous Chemists and followed by a lecture Past and Future of the Fullerene Story delivered by Eiji Osawa during the 7th CCTCC. The lectures in this series are presented in a relaxed, after-dinner atmosphere by the noble speakers and are devoted to noble scientific events and people. As such, it is an exceptional lecture to the conference and, contrary to the regular talks, might not necessarily report any Current findings. This year the talk will be delivered by Henry F. Schaefer, III from the University of Georgia. We are planning to publish extended abstracts (up to four pages each) of all invited talks and poster presentations. Original scientific contributions will be published in a special issue of the Journal of Molecular Structure (THEOCHEM). Manuscripts for inclusion in the special issue should be submitted in triplicate upon arrival at the registration desk. Submitted papers will be subject to the journals standard referee procedures. Sincerely, Jerzy Leszczynski Chairman of the Organizing Committee Enclosure 9th Conference on Current Trends in Computational Chemistry November 3 & 4, 2000 Vicksburg, MS Name ________________________________________________________________________ Mailing Address ______________________________________________________________________ Telephone: __________________FAX ________________ E-mail ______________________ If you wish to present a poster, please indicate the title below. All abstracts are due by September 1, 2000 (up to 4 pages in length), presenting author underlined, photo ready quality, in duplicate) to ensure publication in the Conference materials. TITLE: _______________________________________________________________________ ______________________________________________________________________________ AUTHORS: __________________________________________________________________ Conference materials, banquet and reception fee, all meals from breakfast Friday through dinner Saturday, coffee, and refreshments are included per paid participant. Make Checks payable to: Current Trends in Computational Chemistry. Registration fee before September 1, 2000 US$ $150.00 - - $______________ Registration fee thereafter $200.00 - - $______________ Registration fee at student discount $ 75.00 $_____________ Housing: the organizers will not make housing reservations. To reserve a room at the special conference rate of $50.00 - $60.00 per room, contact the Holiday Inn of Vicksburg, 3330 Clay Street, Vicksburg, MS 39180, Tel. (601) 636-4552, Reservations should be arranged with the Holiday Inn prior to October 10, 2000. I do ____ do not ____ plan to stay at the conference hotel I do ____ do not ____ plan to submit a paper to the special issue of THEOCHEM http://tiger.jsums.edu/~cctcc/conf homepage.html Department of Chemistry, Jackson State University, Jackson, MS 39217, USA Conference Chairman: Jerzy Leszczynski, Tel: 601-979-3482, email jerzy2.iris5.jsums.edu; Conference Secretary: Ms. Shonda R. Allen, Tel: (601)979-3723, email: srallen@stallion.jsums.edu List of Invited Speakers Benoit Champagne University Notre-Dame de la Paix Jurgen Gauss Mainz University Ilya Kaplan University of Mexico Jerome Karle Naval Research Laboratory Iwao Ohmine Nagoya University Mark Olson Biomedical Supercomputer Center Roman Osman Mt. Sinai School of Medicine Michele Parrinello Max-Planck Institute Andrzej Sadlej Nicolaus Copernicus University at Torun Henry F. Schaefer III* University of Georgia Vladimir Spirko Hejrovsky Institute of Physical Chemistry Robert E. Wyatt University of Texas at Austin Tom Ziegler University of Calgary * After dinner Noble Lecture Series From chemistry-request@server.ccl.net Wed Jun 28 13:25:30 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA27040 for ; Wed, 28 Jun 2000 13:25:29 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id NAA16998; Wed, 28 Jun 2000 13:29:30 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Wed, 28 Jun 2000 13:21:33 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V5.2-32 #33820) with ESMTP id <0FWV00812KGY2X@lvlmail.unitedcatalysts.com>; Wed, 28 Jun 2000 13:26:58 -0400 (EDT) Received: by LVLXCH01 with Internet Mail Service (5.5.2650.21) id ; Wed, 28 Jun 2000 13:21:43 -0400 Content-return: allowed Date: Wed, 28 Jun 2000 13:21:42 -0400 From: "Shobe, Dave" Subject: RE: AIM code To: "'Alejandro Montoya'" , chemistry@ccl.net, "'help@gaussian.com'" Message-id: <157A51F55AAAD3119CD70008C7B1629D6383C0@LVLXCH01> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id NAA27041 I'd like to ask a more general question. The G98 manual lists errors that can occur, but says nothing about ways to correct them, giving me the impression that if the AIM code fails for any reason, you're out of luck. Is there anything one can do when the AIM calculations fail? --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Any opinions herein are not necessarily representative of Süd-Chemie. -----Original Message----- From: Alejandro Montoya [mailto:alemoe@Carbon.udea.edu.co] Sent: Wednesday, June 28, 2000 3:52 PM To: chemistry@ccl.net Subject: CCL:AIM code Hello CCLers, I would apreciate if someone can point me on what is the best procedure to obtained the Bond order using the AIM theory when the AIM code fails in G98 and an error message is obtained at the end of the file. NO CONVERGENCE IN SVDSOL FOR SURFACE SHEET 14 Error termination thanks in advance, Regards, From chemistry-request@server.ccl.net Wed Jun 28 17:11:39 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA28315 for ; Wed, 28 Jun 2000 17:11:39 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id QAA13697; Wed, 28 Jun 2000 16:54:13 -0400 (EDT) Message-ID: <098501bfe143$3d870320$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Alejandro Montoya" Cc: "CCL - all" References: Subject: Re: CCL:AIM code Date: Wed, 28 Jun 2000 16:55:48 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Alejandro, the AIM code was developed by Richard Bader's group in Canada (I think at McMaster University). They have a download possibility for the code on their web page. The suite of programs is much more flexible when you encounter problems, since you run each program for itself. Each program requires a little input file where you specify thresholds according to your needs. The required wavefunction file can be created by e.g. G9x with output=wfn. Be prepared to do a little file editing before the compilation (e.g. removing an e-mail header from one file). There also was a construct that xlf interpreted as a jump into a loop at one place. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435