From chemistry-request@server.ccl.net Mon Jun 12 04:22:16 2000 Received: from linux2.ipc.pku.edu.cn (lzj@linux2.ipc.pku.edu.cn [162.105.177.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA07521 for ; Mon, 12 Jun 2000 04:22:13 -0400 Received: from localhost (lzj@localhost) by linux2.ipc.pku.edu.cn (8.9.3/8.9.3) with ESMTP id QAA06288 for ; Mon, 12 Jun 2000 16:28:57 +0800 Date: Mon, 12 Jun 2000 16:28:57 +0800 (CST) From: Liu Zhijie To: chemistry@ccl.net Subject: Ask for references on structural fitting Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I have a simple question that can anyone offer me some references on how to fit two structures (such as two protein structures) to calculate the RMSD values? (mainly principles of mathematics) Thanks in advance. elmer ---------------------------------------------------------------------- My Name : Liu Zhijie English Name : Elmer Work lab : Molecular Design Laboratory Institute of Physical Chemistry Peking University Beijing 100871 , P.R.China Telephone : 8610-62756833 (lab) 8610-62763501 (dorm) Fax : 8610-62751725 Email : lzj@linux2.ipc.pku.edu.cn Address : Building 39 Room 324 , Peking University ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Jun 12 07:49:24 2000 Received: from quim.iq.usp.br (quim.iq.usp.br [143.107.46.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA09233 for ; Mon, 12 Jun 2000 07:49:06 -0400 Received: (from sjardino@localhost) by quim.iq.usp.br (8.9.3/8.9.3) id IAA08766; Mon, 12 Jun 2000 08:33:36 -0300 (EST) Date: Mon, 12 Jun 2000 08:33:34 -0300 (EST) From: Sergio Augusto Jardino Filho To: chemistry@ccl.net cc: info@gaussian.com Subject: Error in G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Does anyone know what is the problem that cause the followig message of error in Gaussian98? thanks in advance Sergio A. Jardino Filho Universidade de Sao Paulo Brazil *************************************************** Gaussian 98: Cray-J90-Unicos-G98RevA.7 11-Apr-1999 11-Jun-2000 *************************************************** %Chk=s11b.chk ---------------------- #N RHF 6-31G** SP FREQ ---------------------- Illegal IType generated by parse. Error termination via Lnk1e in /usr/local/g98/l1.exe. Beginning of Traceback: Called from line 42 (address 755513a) in routine 'TRBK'. Called from line 11 (address 360570d) in routine 'TBACK'. Called from line 29 (address 325764c) in routine 'LNK1E'. Called from line 12 (address 316724c) in routine 'GAUERR'. Called from line 851 (address 5561b) in routine 'DECOTP'. Called from line 1142 (address 41352d) in routine 'GPARSE'. Called from line 1002 (address 22655a) in routine 'EROUTE'. Called from line 5275 (address 63050c) in routine 'LINK1'. Called from line 12 (address 427a) in routine 'ML1'. Called from line 334 (address 413617c) in routine '$START$'. End of Traceback. Job cpu time: 0 days 0 hours 0 minutes 2.9 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1 Received signal:11 Error termination via Lnk1e. Received signal:6 Error termination via Lnk1e. logout From chemistry-request@server.ccl.net Mon Jun 12 08:48:11 2000 Received: from relay.uni-heidelberg.de (relay.uni-heidelberg.de [129.206.100.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA09501 for ; Mon, 12 Jun 2000 08:48:10 -0400 Received: from ix.urz.uni-heidelberg.de (mail.urz.uni-heidelberg.de [129.206.119.234]) by relay.uni-heidelberg.de (8.9.3+Sun/8.9.3) with ESMTP id OAA07033 for ; Mon, 12 Jun 2000 14:47:59 +0200 (MET DST) Received: from urz.uni-heidelberg.de (cpu18-akcomba.oci.uni-heidelberg.de [129.206.40.118]) by ix.urz.uni-heidelberg.de (8.8.8/8.8.8) with ESMTP id OAA18170 for ; Mon, 12 Jun 2000 14:47:57 +0200 Message-ID: <3944DCEC.3D9C9FDD@urz.uni-heidelberg.de> Date: Mon, 12 Jun 2000 14:51:57 +0200 From: Achim Lienke Organization: =?iso-8859-1?Q?Universit=E4t?= heidelberg X-Mailer: Mozilla 4.72 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Energy of donor-acceptor bond Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi there, calculating the strength of a M-chloro bond - how important is commonly a counterpoise correction and corrections for ZPE? Achim -- Achim Lienke Anorganisch Chemisches Institut Heidelberg Im Neuenheimer Feld 270 D 69120 Heidelberg Phone: ++ 49 - 62 21 - 54 86 53 Fax: ++ 69 - 62 21 - 54 66 17 Email: achim.lienke@urz.uni-heidelberg.de From chemistry-request@server.ccl.net Mon Jun 12 10:13:15 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA09931 for ; Mon, 12 Jun 2000 10:13:10 -0400 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id KAA04812 for ; Mon, 12 Jun 2000 10:12:56 -0400 (EDT) Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.9.3/8.9.3) with ESMTP id KAA28117; Mon, 12 Jun 2000 10:12:39 -0400 (EDT) Received: from localhost (chem@localhost) by feldmann.nist.gov (8.8.8+Sun/8.8.8) with SMTP id JAA01076; Mon, 12 Jun 2000 09:53:18 -0400 (EDT) Date: Mon, 12 Jun 2000 09:53:18 -0400 (EDT) From: Steve Heller Reply-To: Steve Heller To: lists , amber@cgl.ucsf.edu, APPLSPEC@listserv.uga.edu, cache@pacificu.edu, CHEMCHAT@UAFSYSB.UARK.EDU, CHEME-L@ULKYVM.LOUISVILLE.EDU, CHEMED-L@atlantis.UWF.EDU, CHEMIG@LIST.NIH.GOV, CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, ICS-L@UMDD.UMD.EDU, isisforum-l@mdli.com, ISOGEOCHEM@LIST.UVM.EDU, listproc@msi.com, listserver@ic.ac.uk, mailbase@mailbase.ac.uk, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, molecular-dynamics-news@mailbase.ac.uk, NATODATA@CC1.KULEUVEN.AC.BE, pdb-l@rcsb.org, PHILCHEM@VM.SC.EDU, PLASMACHEM-L@LISTSERV.SYR.EDU, POLYMER@TECHUNIX.TECHNION.AC.IL, SAFETY@LIST.UVM.EDU, spectroscopy-group@mailbase.ac.uk, ToxList@esc.syrres.com, ucair-lib@twu.edu Subject: ChemInt2000 - July 1 Early Registration Deadine Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This note is to also announce that the deadline for early registration for Chemistry & the Internet - ChemInt2000 early registration is July 1, 2000. Poster abstract are still being accepted. To date 19 have been accepted. September 1, 2000 is the final deadline for poster abstract submssions. The Chemistry and the Internet (ChemInt2000) meeting being held in at Georgetown University in Washington DC on September 23-26, 2000. The program of invited speakers and panel members of the panel sessions is available on the meeting web site - www.chemint.org You are urged to look at the program and to consider submitting a poster paper to the meeting. The main lecturers for the meeting will be: Rene DePlanque, FIZ - Berlin Jim Myers, Pacific Northwest Labs Glen Hopkinson, Synopsys Scientific Systems Wolf-Dietrich Ihlenfeldt, University of Erlangen-Nurenberg Miloslav Nic, IDOOX, Prague Jim Ostell, NIH/NLM/NCBI Engelbert Zass, ETH Henry Rzepa, Imperial College, London Peter Murray-Rust, Nottingham University Technical Sponsors are: ACS CINF Division ACS COMP Division The Chemical Structure Association (CSA) Georgetown University - Department of Chemistry Special Libraries Association (SLA) Chemistry Division Royal Society of Chemistry (RSC) Steve Heller Steve Heller, Guest Researcher NIST/SRD, Mail Stop: 820/113 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899-2310 USA E-mail: srheller@nist.gov From chemistry-request@server.ccl.net Mon Jun 12 09:54:33 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 JAA09850 for ; Mon, 12 Jun 2000 09:54:32 -0400 Received: from s10062.pc.nus.edu.sg (HELO scip8239) (137.132.24.189) by smtp.mail.yahoo.com with SMTP; 12 Jun 2000 06:29:58 -0700 X-Apparently-From: Message-ID: <008d01bfd472$4b05e120$bd188489@nus.edu.sg> From: "Li Zhenhua" To: "Achim Lienke" , References: <3944DCEC.3D9C9FDD@urz.uni-heidelberg.de> Subject: Re: CCL:Energy of donor-acceptor bond Date: Mon, 12 Jun 2000 21:29:52 +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 The relative importance of the BSSE is depended on how strong is the bonding. For strong bond, BSSE correction is not so important since it doesn't affect the convergency of the bond energy vs basis set. However for hydrogen bond, maybe the donor-acceptor bond of M-Cl, it is important. ZPE correction is always important, but the value is depended on the bonding. And also depended on what you are calculating. For example, if you calc bond energy, surely it is very important. But seems no good codes available for calculating BSSE correction to ZPE yet. ----- Original Message ----- From: "Achim Lienke" To: Sent: Monday, June 12, 2000 8:51 PM Subject: CCL:Energy of donor-acceptor bond > Hi there, > > calculating the strength of a M-chloro bond - how important is commonly > a counterpoise correction and corrections for ZPE? > > Achim > > -- > > Achim Lienke > Anorganisch Chemisches Institut Heidelberg > Im Neuenheimer Feld 270 > D 69120 Heidelberg > > Phone: ++ 49 - 62 21 - 54 86 53 > Fax: ++ 69 - 62 21 - 54 66 17 > > Email: achim.lienke@urz.uni-heidelberg.de __________________________________________________ Do You Yahoo!? Talk to your friends online with Yahoo! Messenger. http://im.yahoo.com From chemistry-request@server.ccl.net Mon Jun 12 09:17:13 2000 Received: from hosts ([202.194.10.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA09709 for ; Mon, 12 Jun 2000 09:17:06 -0400 Received: from zhaoxian by hosts (SMI-8.6/SMI-SVR4) id WAA09166; Mon, 12 Jun 2000 22:14:49 +0900 Message-ID: <000801bfd46f$6fa66f20$290ac2ca@icm.sdu.edu.cn> From: "zhaoxian" To: Subject: about MRD-CI Date: Mon, 12 Jun 2000 21:09:17 +0800 Hi, I am a new comer of computational chemistry, How can I actualize the MRD-CI (multireference double-configuration interaction) calculation using the ZINDO program which is included in BIOSYM package.If it cannot, which kind of program can actualize such calculation. Zhaoxian Zhaoxian@icm.sdu.edu.cn From chemistry-request@server.ccl.net Mon Jun 12 10:33:36 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 KAA10187 for ; Mon, 12 Jun 2000 10:33:36 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id KAA17263; Mon, 12 Jun 2000 10:32:34 -0400 (EDT) Message-ID: <049a01bfd47b$5f0963a0$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Sergio Augusto Jardino Filho" Cc: "CCL - all" References: Subject: Re: CCL:Error in G98 Date: Mon, 12 Jun 2000 10:34:51 -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 Sergio, although an analytical frequency calc. is a single point calc. in the sense that the geometry is not altered, you can not combine the SP and FREQ keywords in a Gaussian input. In Gaussian, SP means a single energy calculation without any derivative calculations. 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 Mon Jun 12 11:24:31 2000 Received: from B.PSC.EDU (b.psc.edu [128.182.66.102]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA10557 for ; Mon, 12 Jun 2000 11:24:31 -0400 Received: from armada by CPWSCA.PSC.EDU with SMTP for chemistry@ccl.net; Mon, 12 Jun 2000 11:24:14 -0400 From: "Nick Nystrom" To: Subject: Workshop: Structure Determination Using NMR, July 26-29, 2000 Date: Mon, 12 Jun 2000 11:24:11 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 ********************************************************************** PSC Biomedical Initiative Workshops 2000 Structure Determination Using NMR Pittsburgh Supercomputing Center July 26-29, 2000 Application Deadline: June 14, 2000 The objective of this workshop is to introduce participants to the different techniques for the elucidation of solution structures of biological macromolecules from nuclear magnetic resonance data. The programs AMBER and MORASS will be discussed. In addition to lectures, there will be extensive hands-on sessions. Participants are encouraged to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. For specific details, including an electronic application form, see: http://www.psc.edu/biomed/workshops/workshops.htm#NMR If you have any questions, please contact Nancy Blankenstein at blankens@psc.edu or 412/268-4960 (FAX). Many thanks for your interest and help. ********************************************************************** From chemistry-request@server.ccl.net Mon Jun 12 12:42:00 2000 Received: from gpo.cam.msi-eu.com (cam.msi-eu.com [192.190.183.254]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA11073 for ; Mon, 12 Jun 2000 12:41:59 -0400 Received: from lekha (lekha.cam.msi-eu.com [172.27.64.201]) by gpo.cam.msi-eu.com (8.9.3/8.9.3/Debian/GNU) with ESMTP id RAA17722; Mon, 12 Jun 2000 17:39:23 +0100 Message-Id: <4.2.0.58.20000612173712.00a7d450@mailhost> X-Sender: katriona_knapman@mailhost X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Mon, 12 Jun 2000 17:39:23 +0100 To: chemistry@ccl.net From: Katriona Knapman Subject: Materials Science Software Award Cc: kluckman@msi-eu.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed The MSI Materials Science Academic Award 2000 has just been launched. Two awards of MSI software worth up to $20,000 are available, and every entrant will receive a free 60-day trial of Materials Studio, MSI's new PC modeling environment for materials science. Pre-applications are requested for innovative projects that apply computational materials science in the areas of Reaction Mechanisms, Crystallization, Surface Science, Polymers, Mesoscale, and Catalysis. Shortlisted pre-applications will be asked for full proposals. The deadline for submitting pre-applications is July 15th 2000. More information is available in the new Materials Science Academic web pages on MSI's website: http://www.msi.com/materials/academic/award/index.html Regards, Katriona ------------ Katriona Knapman Senior Marketing Specialist Molecular Simulations Inc. 230/250 The Quorum Barnwell Road Cambridge CB5 8RE UK Tel: 44 1223 413300 Fax: 44 1223 413301 kknapman@msi-eu.com http://www.msi.com/ From chemistry-request@server.ccl.net Mon Jun 12 13:57:37 2000 Received: from bellatrix.pcl.ox.ac.uk (bellatrix.pcl.ox.ac.uk [163.1.35.134]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA11596 for ; Mon, 12 Jun 2000 13:57:37 -0400 Received: from localhost (plyne@localhost) by bellatrix.pcl.ox.ac.uk (8.9.3/8.8.7) with ESMTP id SAA26137 for ; Mon, 12 Jun 2000 18:57:21 +0100 Date: Mon, 12 Jun 2000 18:57:21 +0100 (BST) From: Paul Lyne To: CHEMISTRY@ccl.net Subject: hammet coefficients Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Does anyone know of methods to calculate meta and para Hammet coefficients, sigma_m and sigma_p? Thanks in advance. Paul From chemistry-request@server.ccl.net Mon Jun 12 17:35:42 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA12661 for ; Mon, 12 Jun 2000 17:35:42 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JQIV96VGDY004L8H@trentu.ca> for chemistry@ccl.net; Mon, 12 Jun 2000 17:35:40 EDT Date: Mon, 12 Jun 2000 17:39:56 -0400 From: elewars Subject: (1) Xalpha method (2)current DFT To: chemistry@ccl.net Message-id: <394558AC.3B87F920@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Monday 2000 June 12 Hello, the Xalpha method, developed by John slater (1951) mainly for solids and atoms, and used till at least the early 1970's , was perhaps the first really useful DFT method. For molecules it has now been replaced by Kohn-Sham-based approaches to DFT. (1) Is the Xalpha method still used for solids/crystals (e.g. by solid-state physicists?). If not, what replaced it? (2) In modern molecular DFT, probably the most popular method is B3LYP/6-31G*. What seems to be the second most widely-used? Thanks E. Lewars =====