From chemistry-request@server.ccl.net Mon Mar 20 18:57:00 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA05461 for ; Mon, 20 Mar 2000 18:56:59 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id PAA20787; Mon, 20 Mar 2000 15:57:12 -0800 From: Eugene Leitl Message-ID: <14550.47831.920036.685622@lrz.uni-muenchen.de> Date: Mon, 20 Mar 2000 15:57:11 -0800 (PST) To: Subject: CENSA Open House March 28th (((slightly edited and reformatted for better readability))) From: Andy Berks Sender: CHEMICAL INFORMATION SOURCES DISCUSSION LIST To: CHMINF-L@LISTSERV.INDIANA.EDU Subject: Re: CENSA Open House March 28th Date: Mon, 20 Mar 2000 11:40:42 -0800 Forwarded on behalf of Mike Flannery of CENSA. --- flannery@censa.org wrote: You are invited to an Open House given by CENSA The Collaborative Electronic Notebook Systems Association Tuesday, March 28th 9:00 a.m. ? 12:00 p.m. Breakfast provided The Argent Hotel 50 Third Street San Francisco, California (Just one block from the Moscone Convention Center, location of the ACS National Meeting and Expo) Please R.S.V.P. by March 24, 2000 Telephone 781.935.9600 Info@censa.org CENSA is hosting an Open House to discuss the practical applications for electronic laboratory notebooks and electronic recordkeeping systems. We will review the legal, strategic and business processes needed to implement these systems within your organization. Through discussions on the current and future state of this growing market, CENSA will address Regulatory compliance, R&D automation and the benefits and misconceptions of implementing these systems. Learn how your organization can participate with industry leaders and partner with government agencies to influence the future of R&D automation About Who We Are CENSA is a global market development association of leading Fortune 500 companies and innovative suppliers. Focused on the challenges of today's R&D enterprises, CENSA is responding to the need for better information, technology, and systems for electronic laboratory notebooks and electronic recordkeeping systems. Through our partnership with regulatory agencies worldwide CENSA is addressing regulatory compliance and developing legally acceptable guidelines for electronic records management. Who Should Attend this Open House R&D Managers, Records Managers, Information and Knowledge Management Directors, Patent Attorneys, Chemists, Researchers, IT Directors, Archivists, Regulatory Affairs and Compliance Managers, Library and Information Center Managers. ---------------------< >--------------------- Michael J. Flannery CENSA 800 West Cummings Park, Suite 5400 Woburn, MA 01801 Telephone: 781-935-9600 Fax: 781-935-3113 e-mail: flannery@censa.org www.censa.org ===== Andy Berks andyberks@yahoo.com From chemistry-request@server.ccl.net Tue Mar 21 11:41:02 2000 Received: from bartman.ic.sunysb.edu (bartman.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA10331 for ; Tue, 21 Mar 2000 11:41:02 -0500 Received: from sparky.ic.sunysb.edu (jwebb@sparky.ic.sunysb.edu [129.49.1.3]) by bartman.ic.sunysb.edu (8.9.3/8.9.3) with ESMTP id LAA19681 for ; Tue, 21 Mar 2000 11:40:48 -0500 (EST) Received: from localhost (jwebb@localhost) by sparky.ic.sunysb.edu (8.9.3/8.9.1) with ESMTP id LAA16977 for ; Tue, 21 Mar 2000 11:40:47 -0500 (EST) X-Authentication-Warning: sparky.ic.sunysb.edu: jwebb owned process doing -bs Date: Tue, 21 Mar 2000 11:40:47 -0500 (EST) From: Jeffrey Webb To: chemistry@ccl.net Subject: Quasi-Realtivistic ECP Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCl'ers, What are quasi-realtivistic potentials and how do they differ from normal ECP's??? Are they any quasi realtivistic ECP's for iodine which can be used in DFT calculations?? Thank you in advance. jwebb@ic.sunysb.edu Jeff Webb From chemistry-request@server.ccl.net Tue Mar 21 10:32:56 2000 Received: from mcdc-us-smtp4.cdc.gov (mcdc-us-smtp4.cdc.gov [198.246.96.75]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA10103 for ; Tue, 21 Mar 2000 10:32:56 -0500 Received: from mcdc-us-bis.cdc.gov (mcdc-us-bisgate.cdc.gov [198.246.96.18]) by mcdc-us-smtp4.cdc.gov with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.10) id HLVG7NRY; Tue, 21 Mar 2000 10:30:38 -0500 Received: by mcdc-us-bis.cdc.gov with Internet Mail Service (5.5.2650.10) id ; Tue, 21 Mar 2000 10:30:52 -0500 Message-ID: From: "Poda, Gennady" To: "'chemistry@ccl.net'" Subject: CCL: QSAR software Date: Tue, 21 Mar 2000 10:30:22 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.10) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, I am trying to collect information about QSAR software alternative to well-known suites of Tripos and Oxford Molecular (mainly chemometrics, freeware or for a reasonable price). So I would appreciate if you could site any competitive program (web site?) which can do good QSAR work (NNs, GAs, PLS, GOLPE, etc.) with a good descriptor set, variable selection/pruning/data preprocessing and model validation (LOO, cross-validation, etc.). Any hints will be highly appreciated. I will post a summary. Thanks a lot for your participation. Gennady Poda NIOSH/CDC E-mail: gep4@cdc.gov From chemistry-request@server.ccl.net Tue Mar 21 11:53:03 2000 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 LAA10426 for ; Tue, 21 Mar 2000 11:53:00 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id QAA07509 for ; Tue, 21 Mar 2000 16:55:39 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Tue, 21 Mar 2000 16:55:39 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: GGA - Perdew, Burke and Ernzerhof Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am trying to implement the GGA functional of Perdew, Burke and Ernzerhof (Phys. Rev. Lett. 77, 3865 (1996)). It would appear that the functional derivative of the gradient correction for the correlation energy (i.e. the gradient correction to the correlation potential) diverges for a fully spin polarized system (zeta = +/-1). The paper cites atomization energies for hydrogen, so there must be some way around this. Has anyone implemented this functional and solved this problem? 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 Tue Mar 21 13:51:07 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 NAA11183 for ; Tue, 21 Mar 2000 13:51:07 -0500 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id NAA21761; Tue, 21 Mar 2000 13:50:44 -0500 (EST) Message-ID: <031301bf9366$7fe8e560$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Jeffrey Webb" Cc: References: Subject: Re: CCL:Quasi-Realtivistic ECP Date: Tue, 21 Mar 2000 13:51:42 -0500 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 Jeffrey, quasi-relativistic ECPs include some of the relativistic effects (the scalar ones) and ignore other effects like e.g. spin-orbit coupling. Experience shows that quasi- relativistic ECPs are necessary for elements of the 5th and higher periods. Apart >from reducing calculational time, they improve the results notably. An alternative is the inclusion of scalar relativistic operators into the Hamiltonian (or to apply them perturbatively to the reference wavefunction; I don't remember too exactly) like it is possible in e.g. ADF. In the case of transition metals it is a good idea to use small core ECPs which treat the electrons of the sub-valence shell explicitly. A good choice for ECPs (quasi-relativistic and other) are the Stuttgart-ECPs by Stoll, Preuss et al.. They are available at: http://www.theochem.uni-stuttgart.de/ Another good source for ECPs and basis sets is http://www.emsl.pnl.gov:2080/forms/basisform.html or it's european mirror site: http://wserv1.dl.ac.uk:800/emsl_pnl/basisform.html Stefan ______________________________________________________________________ Dr. Stefan Fau fau@qtp.ufl.edu Quantum Theory Project (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Tue Mar 21 14:43:09 2000 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA11572 for ; Tue, 21 Mar 2000 14:43:09 -0500 Received: from mail.chem.tamu.edu ([165.91.176.197]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu; Tue, 21 Mar 2000 13:51:38 -0600 Sender: fan@mail.chem.tamu.edu (Huajun Fan) Message-ID: <38D7D047.DBF5445D@mail.chem.tamu.edu> Date: Tue, 21 Mar 2000 13:40:55 -0600 From: Huajun Fan X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: Stefan Fau CC: Jeffrey Webb , chemistry@ccl.net Subject: Re: CCL:Quasi-Realtivistic ECP References: <031301bf9366$7fe8e560$bbc0e380@qtp.ufl.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Stefan Fau wrote: > Hi Jeffrey, > > quasi-relativistic ECPs include some of the relativistic effects (the > scalar ones) and > ignore other effects like e.g. spin-orbit coupling. Experience shows > that quasi- > relativistic ECPs are necessary for elements of the 5th and higher > periods. Apart > >from reducing calculational time, they improve the results notably. > Dear Stafan, How would I know if the basis set I used includes quasi-relativistic ECPs? Say I am using LANL2DZ basis set for Ir atom, is that the one? Is there a good reference I can read about it? Many thanks. huajun > > An alternative is the inclusion of scalar relativistic operators into > the Hamiltonian > (or to apply them perturbatively to the reference wavefunction; I > don't remember > too exactly) like it is possible in e.g. ADF. > > In the case of transition metals it is a good idea to use small core > ECPs which treat > the electrons of the sub-valence shell explicitly. > > A good choice for ECPs (quasi-relativistic and other) are the > Stuttgart-ECPs by > Stoll, Preuss et al.. They are available at: > http://www.theochem.uni-stuttgart.de/ > Another good source for ECPs and basis sets is > http://www.emsl.pnl.gov:2080/forms/basisform.html > or it's european mirror site: > http://wserv1.dl.ac.uk:800/emsl_pnl/basisform.html > > Stefan > ______________________________________________________________________ > Dr. Stefan Fau > fau@qtp.ufl.edu > Quantum Theory Project > (352) 392-6714 > University of Florida > Gainesville, FL 32611-8435 > > -= 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 From chemistry-request@server.ccl.net Tue Mar 21 21:25:40 2000 Received: from mailjay.creighton.edu (mailjay.creighton.edu [147.134.2.126]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA14001 for ; Tue, 21 Mar 2000 21:25:39 -0500 From: crwatts@creighton.edu Received: from bluejay.creighton.edu (bluejay.creighton.edu [147.134.2.20]) by mailjay.creighton.edu (8.8.6 (PHNE_17190)/8.8.6) with ESMTP id UAA26030; Tue, 21 Mar 2000 20:25:18 -0600 (CST) Date: Tue, 21 Mar 2000 20:25:17 -0600 (CST) To: AMBER Mailing List , Computational Chemistry List Subject: CARNAL Code Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues: The CARNAL module of AMBER has an option where you can compare the pairwise RMSD's for two streams of conformations generating a triangluar matrix containging all of the pairwise measurements. Currently this can only be done with two streams containg equal numbers of conformers. Does anybody know how to modify the C code or where in the C code a modification can be made to generate a square matrix for comparing two streams containing different numbers of conformers? Regards, Charles R. Watts, Ph.D. ************************************ Research Assistant * * Department of Biomedical Sciences * An appeaser is one who feeds * Creighton University * a crocodile, hoping it will eat * School of Medicine * him last. * 2500 California Plaza * * Omaha, NE 68178 * -Winston Churchill * phone: (402) 280-2210 * * Fax: (402) 553-8841 * * E-Mail: crwatts@bluejay.creighton.edu ************************************ From chemistry-request@server.ccl.net Tue Mar 21 18:18:51 2000 Received: from bobino.chemcomp.com (bobino.sefmedia.com [207.164.6.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA12547 for ; Tue, 21 Mar 2000 18:18:51 -0500 Received: from mfs-pci-bqn-vty39.as.wcom.net (mfs-pci-bqn-vty39.as.wcom.net [212.211.18.39]) by bobino.sefmedia.com (NTMail 5.05.0002/NT6102.00.ff403942) with ESMTP id zwjfaaaa for chemistry@ccl.net; Tue, 21 Mar 2000 18:20:45 -0500 Message-ID: <005c01bf941a$628f9220$2712d3d4@pan> From: "bill email" To: "Poda, Gennady" , References: Subject: Re: CCL:QSAR software Date: Wed, 22 Mar 2000 08:10:19 -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 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Hi. Try Chemical Computing Group at; http://www.chemcomp.com Thanks, Bill Hayden ----- Original Message ----- From: Poda, Gennady To: Sent: Tuesday, March 21, 2000 7:30 AM Subject: CCL:QSAR software > > Dear CCLers, > > I am trying to collect information about QSAR software alternative to > well-known suites of Tripos and Oxford Molecular (mainly chemometrics, > freeware or for a reasonable price). > > So I would appreciate if you could site any competitive program (web site?) > which can do good QSAR work (NNs, GAs, PLS, GOLPE, etc.) with a good > descriptor set, variable selection/pruning/data preprocessing and model > validation (LOO, cross-validation, etc.). Any hints will be highly > appreciated. > > I will post a summary. > > Thanks a lot for your participation. > > Gennady Poda > > NIOSH/CDC > E-mail: gep4@cdc.gov > > > -= 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 > > > > >