From chemistry-request@server.ccl.net Thu Nov 4 04:07:03 1999 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12582 for ; Thu, 4 Nov 1999 04:07:02 -0500 Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3/8.9.3) with ESMTP id KAA05805; Thu, 4 Nov 1999 10:00:27 +0100 (MET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.40); 4 Nov 99 10:10:15 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.40); 4 Nov 99 10:10:11 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "G. Rechtsteiner" Date: Thu, 4 Nov 1999 10:10:00 +0100 Subject: CCL:ZINDO Parameters CC: CHEMISTRY@ccl.net, kristine.andersen@leo-pharma.com, wez@email.dk Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <30B64442E3@virgil.ruc.dk> Greg Rechtsteiner, Wed, 03 Nov 1999 10:30:04 -0600 > I have a colleague looking for the following: > >>What I need are the ZINDO/S parameters for chlorine. The >>values for the two-electron, one-center Coulomb integrals would be most >>handy, as it seems that those are the ones that Hyperchem 5 is lacking. >> >>I'm running these calculations on a mixed valence compound in an organic >>cyclic framework. It has a total of 70 atoms. The molecule has two >>ruthenium ions in it, each to which two chlorides are ligated. At the >>moment, I'm using fluorides instead. Try the ZINDO/S parameters for chlorine suggested by Kristine B. Andersen, Acta Chem. Scand. 53, 222-229 (1999): zeta = 2.03333 Is = 26.85 eV Ip = 13.86 eV beta = -19.00 eV F0 = 10.8662 eV F2 = 6.44670 eV G1 = 8.80224 eV See the original publication by Kristine for a demonstration of the performance of these parameters in calculations on a few organic compounds (naphthazarin and related species). Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Nov 4 04:09:44 1999 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12592 for ; Thu, 4 Nov 1999 04:09:43 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id JAA21349 for ; Thu, 4 Nov 1999 09:04:15 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Thu, 4 Nov 1999 09:04:15 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Small eigenvalues of overlap matrix Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am writing an LCAO-DFT code using numerical orbitals. For some basis sets the overlap matrix acquires very small eigenvalues, and this leads to ghost states with very low energy. I have heard of two ways to fix this: 1) Diagonalise the overlap matrix, shift the very small eigenvalues up, and then reconstruct the overlap matrix; 2) Diagonalise the overlap matrix, remove the eigenvectors with very small eigenvalues, and transform the overlap and Fock matrices accordingly. Are there any recommendations as to which is better? (The first approach would be a lot more convenient, but only if it works!) Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Thu Nov 4 09:50:01 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA14840 for ; Thu, 4 Nov 1999 09:50:01 -0500 Received: from tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.20.129]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id JAA24564 for ; Thu, 4 Nov 1999 09:44:21 -0500 Sender: richard@tc.cornell.edu Message-ID: <38219BC6.26A9E1A7@tc.cornell.edu> Date: Thu, 04 Nov 1999 09:44:22 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.2 IP22) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: ACS/NCS program? References: <381EBB43.339DEC20@chemcca10.ucsd.edu> <381F29B9.B4F30B51@ozone.umsl.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Does anyone know where I can obtain a current version of the ASC/NSC package for molecule surface area. The old link I have is out of date: > http://www.embl-heidelberg.de/Services/argos/ASC.21/asc2.html Thanks Richard Gillilan Cornell Theory Center From chemistry-request@server.ccl.net Thu Nov 4 07:07:38 1999 Received: from web305.mail.yahoo.com (web305.mail.yahoo.com [128.11.68.236]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA14238 for ; Thu, 4 Nov 1999 07:07:37 -0500 Message-ID: <19991104120201.10092.rocketmail@web305.mail.yahoo.com> Received: from [130.238.41.135] by web305.mail.yahoo.com; Thu, 04 Nov 1999 04:02:01 PST Date: Thu, 4 Nov 1999 04:02:01 -0800 (PST) From: Uno Maeorg Subject: MM3 parameters and options To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Sir, I'm traing to use the TINKER MM3 program for th calculations of IR frequencies. Unfortunately this program does not have all torsional parameeters needed. The parameters found in TINKER's mm3.prm are a direct translation of the values distributed by Allinger's group with "real" MM3. The "real" MM3 program does have an option to "guess" at missing parameters by using an interpolation from similar known parameters. TINKER does not have this as an option. Could you help me and tell a source for different torsional parameters for systems containing sp carbon atom (or atom type 4)or such inerpolating option which is working under TINKER. I'm not subscibed to this list, I'm just asking consultation. Dr. Uno Maeorg Institut of Organic Chemistry University of Tartu Estonia ===== __________________________________________________ Do You Yahoo!? Bid and sell for free at http://auctions.yahoo.com From chemistry-request@server.ccl.net Thu Nov 4 12:24:43 1999 Received: from hotmail.com (f174.law4.hotmail.com [216.33.149.174]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA15723 for ; Thu, 4 Nov 1999 12:24:43 -0500 Received: (qmail 85157 invoked by uid 0); 4 Nov 1999 17:17:03 -0000 Message-ID: <19991104171703.85156.qmail@hotmail.com> Received: from 128.205.115.10 by www.hotmail.com with HTTP; Thu, 04 Nov 1999 09:17:03 PST X-Originating-IP: [128.205.115.10] From: "Wen Qiu" To: chemistry@server.ccl.net Subject: aug-cc-pvtz basis set fro Li Date: Thu, 04 Nov 1999 17:17:03 GMT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Hi, in some recent publications (e.g., Glendening etal, J.Phys.Chem. 100, 17152(1996)) several authors used aug-cc-pvtz basis set for Li, which is not included in Dunning's original paper (J.Chem.Phys. 90, 1007 (1989)). Does anybody have this basis set? I will be happy to test this basis set for Li and thanks in advance. BTW, I have searched the Gaussian Basis Set forums and found nothing. Have a good day, Wen Qiu (qiuwen@hotmail.com) ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From chemistry-request@server.ccl.net Thu Nov 4 13:37:30 1999 Received: from wavefun.com (wave-fw.wavefun.com [209.125.133.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA16039 for ; Thu, 4 Nov 1999 13:37:29 -0500 From: liang@wavefun.com Date: Thu, 4 Nov 1999 10:31:05 -0800 Message-Id: <9911041031.ZM11069@wavefun.com > In-Reply-To: Andrew Horsfield "CCL:Small eigenvalues of overlap matrix" (Nov 4, 9:04am) References: Reply-To: liang@wavefun.com X-Mailer: Z-Mail-SGI (3.2S.3 08feb96 MediaMail) To: CHEMISTRY@ccl.net Subject: Re: CCL:Small eigenvalues of overlap matrix Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Nov 4, 9:04am, Andrew Horsfield wrote: > Subject: CCL:Small eigenvalues of overlap matrix > Hi, > > I am writing an LCAO-DFT code using numerical orbitals. For some basis > sets the overlap matrix acquires very small eigenvalues, and this leads to > ghost states with very low energy. > > I have heard of two ways to fix this: > > 1) Diagonalise the overlap matrix, shift the very small eigenvalues up, > and then reconstruct the overlap matrix; > > 2) Diagonalise the overlap matrix, remove the eigenvectors with very small > eigenvalues, and transform the overlap and Fock matrices accordingly. > > Are there any recommendations as to which is better? (The first approach > would be a lot more convenient, but only if it works!) > > Cheers, > > Andrew > Hi Andrew, It might not be as good either way: both try to alter the overlap matrix (and all the other things down the road). I suggest you to precondition the basis functions (only for atom-centered ones, of course) by schmidt orthogonalizing those attached to the same nuclei. This will eliminate much of the linear dependencies that could be seen in methods utilizing analytical integration with GTO basis functions, and can be done effortlessly on an atomic grid. Good luck, Liang From chemistry-request@server.ccl.net Thu Nov 4 13:43:13 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA16090 for ; Thu, 4 Nov 1999 13:43:12 -0500 Received: (from daemon@localhost) by bioc1.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id KAA14021 for ; Thu, 4 Nov 1999 10:39:02 -0800 (PST) Message-Id: <199911041839.KAA14021@bioc1.msi.com> Received: from osman-pc.msi.com(146.202.7.202) by bioc1.msi.com via smap (V2.0) id xma014018; Thu, 4 Nov 99 10:38:38 -0800 X-Sender: osman@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Thu, 04 Nov 1999 10:38:45 -0800 To: chemistry@ccl.net From: "Osman F. Guner" Subject: Fwd: ADME Tox symposium - call for papers We need one more paper to complete the open sessions (preferably in experimental, assays, etc.). The deadline has passed. Please submit your abstract on the ACS abstract form directly to me no later then November 11th. EXPERIMENTAL, COMPUTATIONAL, AND INFORMATICS CHALLENGES OF ADME/TOX IN EARLY STAGE DRUG DISCOVERY To be held at the 219th National American Chemical Society Meeting in San Francisco California, March 26-31, 2000 Sponsored by Division of Chemical Information (CINF) Co-sponsored by Divisions of Medicinal Chemistry (MEDI), Toxicology (TOXI), and Computers in Chemistry (COMP) Open symposia will be followed by a plenary session that will feature the following lectures: "Changes in the Profiles of Drug Properties: An Experimental, Computational, and Informatics Perspective" Christopher A. Lipinski, Ph.D. Senior Research Fellow, Pfizer Central Research "Bioavailability Considerations in Drug Design" John J. Baldwin, Ph.D. Chief Science and Technology Officer, Pharmacopeia "e-DDI: The Virtual Discovery-Development Interface" Dale E. Johnson, Pharm.D., Ph.D. Vice President Preclinical Development, Chiron "Changing the Paradigm to Reduce Compound Attrition: A Toxicology Perspective" Stephen K. Durham, Ph.D. Distinguished Research Fellow, Bristol Myers Squibb "Role of Informatics and Computational Tools in Optimizing ADME/Tox Properties" Mark A. Murcko, Ph.D. Vice President and Senior Research Fellow, Vertex This is an invitation for you to present your views and research results in the above topics. Papers will be organized with respect to experimental, computational, informatics aspects as well as others. If you have an opinion on this topic, or research results, or if you know of success stories or failures in this area, you may want to consider presenting your views in this symposium. The deadline for submission of abstracts has already passed. E-mail me an electronic copy of your abstract by filling out the word template that can be downloaded at http://www.acs.org/meetings/abstract/absdown.html. Cheers...Osman --- Osman F. G=FCner, Ph.D. Sr.Product Manager, Rational & Combinatorial Drug Design Molecular Simulations Inc. (858)799-5341 osman@msi.com http://www.msi.com --- Osman F. G=FCner, Ph.D. Sr.Product Manager, Rational & Combinatorial Drug Design Molecular Simulations Inc. (858)799-5341 osman@msi.com http://www.msi.com From chemistry-request@server.ccl.net Thu Nov 4 14:15:54 1999 Received: from mailhost.iitb.ac.in (mailhost.iitb.ac.in [202.54.44.115]) by server.ccl.net (8.8.7/8.8.7) with SMTP id OAA16305 for ; Thu, 4 Nov 1999 14:15:51 -0500 Received: (qmail 29952 invoked from network); 4 Nov 1999 19:34:32 -0000 Received: from ether.chem.iitb.ernet.in (144.16.103.129) by mailhost.iitb.ac.in with SMTP; 4 Nov 1999 19:34:32 -0000 Received: from localhost (arun@localhost) by ether.chem.iitb.ernet.in (8.8.8/8.8.8) with SMTP id AAA24505 for ; Fri, 5 Nov 1999 00:32:31 +0530 (IST) Date: Fri, 5 Nov 1999 00:32:31 +0530 (IST) From: Arun Venkathanathan To: chemistry@ccl.net Message-ID: Dear CCLers, Is there any FREEWARE 3-D plotting package (which runs on MS-Windows or DOS or Linux platforms) which reads x,y,z data in columns and gives a surface plot ? Can it compose more than one plot onto the same page and can it be converted to POSTSCRIPT FORMAT ? Thanks in advance. - Regards Arun Venkatnathan From chemistry-request@server.ccl.net Thu Nov 4 14:58:09 1999 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id OAA16674 for ; Thu, 4 Nov 1999 14:58:08 -0500 Received: (qmail 11031 invoked from network); 4 Nov 1999 19:52:25 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 4 Nov 1999 19:52:25 -0000 Received: from egppp1.physics.upatras.gr by pythagoras.physics.upatras.gr with SMTP (1.36.108.4/16.2) id AA24732; Thu, 4 Nov 1999 21:52:46 GMT Message-Id: <000d01bf223e$19da0ae0$5d9f8c96@stelios> From: "garoufal" To: Subject: g94w Date: Fri, 29 Oct 1999 21:47:49 +0300 I have installed g94w on a pentium III pc with 128mb ram. the operating system is win98. When the program changes link it gives me an error message sayng that win386 caused an error, and it prompts me to close or ignore. If I press ignore the program continues normally until the next link where it gives me the same error. (i.e the error appears every time the program changes link) Does anybody know how to resolve this problem? P.S The same problem apeared even with win95 operating system Thanks in advance ____________________________________ Christos S. Garoufalis Dept. of Physics, University of Patras, Greece ____________________________________ From chemistry-request@server.ccl.net Thu Nov 4 22:42:32 1999 Received: from chu1.chem.nthu.edu.tw (Chu1.Chem.nthu.edu.tw [140.114.45.236]) by server.ccl.net (8.8.7/8.8.7) with SMTP id WAA20049 for ; Thu, 4 Nov 1999 22:41:46 -0500 Received: by chu1.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA21130; Fri, 5 Nov 1999 11:30:09 +0800 From: hyl@chu1.chem.nthu.edu.tw (Hsin-Yi Liao) Message-Id: <9911050330.AA21130@chu1.chem.nthu.edu.tw> Subject: QCISD To: chemistry@server.ccl.net Date: Fri, 5 Nov 99 11:30:09 TAIST X-Mailer: ELM [version 2.4dev PL17] Dear Netters, When I doing the QCISD optimization in Gaussian package, I got an error message below. Iteration Nr. 49 ********************** DD1Dir will call FoFDir 1 times, MxPair= 184 NAB= 63 NAA= 36 NBB= 21 NumPrc= 1. DE(CORR)= -0.44110816D+00 E(CORR)= -0.22135422179D+04 NORM(A)= 0.11287004D+01 Iteration Nr. 50 ********************** DD1Dir will call FoFDir 1 times, MxPair= 184 NAB= 63 NAA= 36 NBB= 21 NumPrc= 1. DE(CORR)= -0.44110815D+00 E(CORR)= -0.22135422179D+04 NORM(A)= 0.11287005D+01 ************* *MAX. CYCLES* ************* Dominant configurations: *********************** Spin Case I J A B Value AA 25 26 -0.120377D+00 BB 23 24 0.116652D+00 Largest amplitude= 1.20D-01 Error termination via Lnk1e in /usr/local/package1//g98/l913.exe. What keywords should I add, or What can I do to let the calculation go on? Any reply will be appreciated. Thank you very much in advance! Han-Yen Lai hyl@chu1.chem.nthu.edu.tw