From chemistry-request@server.ccl.net Mon Jun 4 01:51:28 2001 Received: from melia.qut.edu.au ([131.181.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f545pQ527800 for ; Mon, 4 Jun 2001 01:51:26 -0400 Received: from tu02m2.qut.edu.au ([131.181.127.148]) by melia.qut.edu.au (PMDF V5.2-33 #40788) with ESMTP id <0GEE02ILG5J665@melia.qut.edu.au> for chemistry@ccl.net; Mon, 4 Jun 2001 15:49:54 +1000 (EST) Received: by tu02m2.qut.edu.au id PAA1078096; Mon, 04 Jun 2001 15:49:39 +1000 (EST) Date: Mon, 04 Jun 2001 15:49:38 +1000 (EST) From: Sergio Manzetti Subject: LIPLOT To: chemistry@ccl.net Message-id: <991633778.3b1b217280322@email.qut.edu.au> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.3 X-IMP-User: n2618117 X-Originating-IP: 131.181.120.220 Hey every1, I am trying to install LIGPLOT, but it's really a pain in the bum. Does anyone here with access to LIGPLOT have time to make me to plots? This is not for a publication, but for presentation name and proper reference will be assigned. Best Regards Sergio Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 Tlf2:+61 7 3864 1185 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Mon Jun 4 04:18:53 2001 Received: from c0mailgw03.prontomail.com ([216.163.180.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f548Iq526349 for ; Mon, 4 Jun 2001 04:18:53 -0400 Received: from mail18.prontomail.com (209.185.149.118) by c0mailgw03.prontomail.com (NPlex 5.1.050) id 3B182169000924FC for chemistry@ccl.net; Mon, 4 Jun 2001 01:15:27 -0700 Received: from c0web109 (216.163.180.10) by mail18.prontomail.com (NPlex 2.0.123) for chemistry@ccl.net; Mon, 4 Jun 2001 01:15:27 -0700 From: "markus mayer" Message-Id: <17CA1D2B99855D115A1600807CFBD63A@markus.nandomail.com> Date: Mon, 04 Jun 2001 01:15:27 -0800 X-Priority: Normal Content-Type: text/plain; charset=ISO-8859-1 To: chemistry@ccl.net Subject: MD melting simulation X-Mailer: Web Based Pronto Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Dear netters, sometimes ago I have asked for the program to study the melting of some inorganic hydrides. And thanks for the persons who answered my questions. It was suggested that DL_Poly can do the job. On the other hand I found out that we have cerius2 installed in some of our computers. My goal is the study of the melting of hydrides like NaH, MgH2 and AlH3, studying the diffusion behavior of different species at high pressure. Can somebody please suggest me on what force field best suited to study this system? I notice that NaH is more ionic than AlH3 so a force field which can describe both ionic and covalent interaction of H with these elements seems to be essential. THank you in advance for your help. markus ________________________________________________________________ To get your free Web-based E-mail go to http://www.nandomail.com From chemistry-request@server.ccl.net Mon Jun 4 09:24:46 2001 Received: from alfmail.cii.fc.ul.pt ([194.117.6.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f54DOg511877 for ; Mon, 4 Jun 2001 09:24:45 -0400 Received: from alf1.cii.fc.ul.pt (alf1 [194.117.6.1]) by alfmail.cii.fc.ul.pt (8.11.2/8.11.2) with ESMTP id f54DQrj18107 for ; Mon, 4 Jun 2001 14:26:53 +0100 (WEST) Received: from localhost (rguedes@localhost) by alf1.cii.fc.ul.pt (8.11.2/8.11.0) with ESMTP id f54DKsZ39832 for ; Mon, 4 Jun 2001 14:20:54 +0100 (WEST) Date: Mon, 4 Jun 2001 14:20:54 +0100 (WEST) From: Rita Cardoso Guedes To: Subject: visualization software .... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I am having a problem that perhaps same of you already solve... I am plotting, with molekel, the electrostatic potential of a molecule on top of an surface of isoelectronic density, then I get on top of that surface an array of colours that express the electrostatic potential. The problem is that this colours are relative to the molecule and not absolut therefore you cannot compare 2 molecules. Any ideia which software can I use to do this? Thank you all very much, R. Guedes From chemistry-request@server.ccl.net Mon Jun 4 11:20:32 2001 Received: from pxq76.iq.ufrj.br (root@[146.164.6.76]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f54FKV513427 for ; Mon, 4 Jun 2001 11:20:31 -0400 Received: from localhost (localhost [[UNIX: localhost]]) by pxq76.iq.ufrj.br (8.9.3/8.9.3/SuSE Linux 8.9.3-0.1) id CAA03792; Tue, 8 Aug 2000 02:11:12 -0300 From: Daniel Lopes Bhering Reply-To: bhering@iq.ufrj.br Organization: LARHCO-IQ-UFRJ To: chemistry@ccl.net Subject: Summary:Trasition Metals NMR shifts Date: Tue, 8 Aug 2000 01:56:52 -0300 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <4.3.0.20010102121419.00b70530@service2.area.fi.cnr.it> <00080902024200.01945@pxq76> In-Reply-To: <00080902024200.01945@pxq76> Cc: sgodinho@itqb.unl.pt MIME-Version: 1.0 Message-Id: <00080802111100.03788@pxq76> Content-Transfer-Encoding: 8bit Dear CCLs: I would to thanks to the answers of my question in CCL > I would like to get some references of ab initio NMR calculations in > organometals compounds. Does anyone can help me? Thanks for Dr. Georg Schreckenbach (CLRC Daresbury Laboratory) and Dr. Arvydas Tamulis (ITPA, Lithuania) Dr. Georg Schreckenbach wrote: > >In case you include DFT into 'ab initio', there are a number of >NMR calculations available. Perhaps your best choice is to start >from the (DFT-NMR) reviews: >Schreckenbach, G.; Ziegler, T. Theor. Chem. Acc. 1998, 99, 71 >(I'd be happy to send you a copy, either paper or pdf ...) >Buhl, M. et al., J. Comp. Chem. 1999, 20, 91 >Kaupp et al. in: Encyclopedia of Computational Chemistry, >Vol. 3, p. 1857 >I could send you a couple of references to the original literature >as well but if you search for M. Buhl (or Buehl, it is an Umlaut-U), >M. Kaupp, T. Ziegler, and E. Oldfield, you'll get a pretty good >start. >If your 'ab initio' excludes DFT, then what you'll find will be few >and far between - and not very accurate, see also the article by >Kaupp et al. ******************************************************************************* Dr. Arvydas Tamulis wrote: > We are doing now not good proton NMR calculations of biliverdine > derivatives using Gaussian 98. > Not good, because G98 in principle does not account most relativistic > terms in open shell systems. > Currently our collegue Zilvinas RINKEVICIUS wrote formulae for exact > evaluation of all relativistic terms and starting to make program > suplementing DALTON package which calculating little better NMR in > comparison with G98. > > Please send us summary of your received responses from other authors > because we are interesting in developing of NMR calculations and wish to > know the real state in this field. > ****************************************************************************************** Thanks again Daniel L. Bhering From chemistry-request@server.ccl.net Mon Jun 4 12:48:13 2001 Received: from mserv3.dl.ac.uk ([148.79.80.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f54GmD514989 for ; Mon, 4 Jun 2001 12:48:13 -0400 Received: from tca7.dl.ac.uk (tca7.dl.ac.uk [193.62.112.105]) by mserv3.dl.ac.uk (8.11.3/8.11.3/[ref postmaster@dl.ac.uk]) with ESMTP id f54GmBS30322 for ; Mon, 4 Jun 2001 17:48:12 +0100 Received: from dl.ac.uk by tca7.dl.ac.uk (8.9.3/1.1.27.5/13Jul00-0147PM) id RAA0000005778; Mon, 4 Jun 2001 17:40:13 +0100 (BST) Message-Id: <200106041640.RAA0000005778@tca7.dl.ac.uk> Sender: H.G.Schreckenbach@dl.ac.uk Date: Mon, 04 Jun 2001 17:40:13 +0100 From: Georg Schreckenbach <"h.g.schreckenbach"@dl.ac.uk (Georg Schreckenbach)> Reply-To: Georg Schreckenbach Organization: CLRC Daresbury Lab X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V5.0 alpha) X-Accept-Language: en MIME-Version: 1.0 CC: CCL Subject: Re: CCL:Summary:Trasition Metals NMR shifts References: <4.3.0.20010102121419.00b70530@service2.area.fi.cnr.it> <00080902024200.01945@pxq76> <00080802111100.03788@pxq76> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Dr. Tamulis, (and sorry for posting this to the list - the E-mail was not given in the summary) > Dr. Arvydas Tamulis wrote: > > > We are doing now not good proton NMR calculations of biliverdine > > derivatives using Gaussian 98. > > Not good, because G98 in principle does not account most relativistic > > terms in open shell systems. You can do relativistic DFT-NMR calculation with the current version of the ADF code (http://www.scm.com/) - in case you don't mind using DFT .... I can send you some of our references in case you are interested. Best regards, Georg From chemistry-request@server.ccl.net Mon Jun 4 15:53:34 2001 Received: from galaxy.pnl.gov ([130.20.64.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f54JrY517927 for ; Mon, 4 Jun 2001 15:53:34 -0400 Received: from odyssey.emsl.pnl.gov ([198.128.85.53]) by pnl.gov (PMDF V5.2-33 #42505) with ESMTP id <01K4DBFKO3N09N5EWC@pnl.gov> for chemistry@ccl.net; Mon, 4 Jun 2001 12:53:26 PDT Received: from odyssey.emsl.pnl.gov (wv04533.emsl.pnl.gov [198.128.82.100]) by odyssey.emsl.pnl.gov (8.8.8+Sun/8.8.5) with SMTP id MAA03559 for chemistry@ccl.net; Mon, 04 Jun 2001 12:53:25 -0700 (PDT) Date: Mon, 04 Jun 2001 12:43:52 -0700 (PDT) From: ESHQ - mscf-consulting Subject: MSCF Call For Proposals To: chemistry@ccl.net Message-id: <200106041953.MAA03559@odyssey.emsl.pnl.gov> The Molecular Science Computing Facility (MSCF) is soliciting proposals, for allocations of computer time, for Computational Grand Challenge Projects of 3-year duration in environmental molecular science basic and applied research areas that address the environmental problems and research needs facing the U.S. Department of Energy and the Nation. Computational resources at the MSCF include 512-, 104-, and 64-processor IBM SP computer systems, with plans to upgrade to at least 2 to 3 Teraflops in early 2002. Other resources include a 20-Terabyte storage management system and molecular science software. Award allocations are typically 250,000-500,000 processor wall-hours per year. For details about the MSCF and the Call for Proposals, including the proposal form and instructions, see http://www.emsl.pnl.gov:2080/docs/tms/mscf/proposals/. Important Dates: - August 1, 2001: Receipt of Abstract, Team List, and Allocation Requested - August 15, 2001: Receipt of Completed Proposal Form - October 1, 2001: Announcement of Awards Donald R. Jones, Technical Group Leader William R. Wiley Environmental Molecular Sciences Laboratory Pacific Northwest Laboratory P.O. Box 999, MS K1-96 Richland, WA 99352 telephone: 509-375-2279 facsimile: 509-375-6631 email: mscf@emsl.pnl.gov ----------------------------------------------- The MSCF is part of the William R. Wiley Environmental Molecular Sciences Laboratory located at Pacific Northwest National Laboratory (PNNL), one of nine U.S. Department of Energy multiprogram national laboratories. From chemistry-request@server.ccl.net Mon Jun 4 23:35:49 2001 Received: from mail.shcnc.ac.cn ([202.127.16.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f553Zm522317 for ; Mon, 4 Jun 2001 23:35:48 -0400 Received: from PC18 ([202.127.19.225]) by mail.shcnc.ac.cn (8.9.3/8.9.3) with SMTP id LAA12555 for ; Tue, 5 Jun 2001 11:34:39 +0800 (CDT) Message-Id: <200106050334.LAA12555@mail.shcnc.ac.cn> Date: Tue, 5 Jun 2001 11:30:29 +0800 From: bxiong To: "chemistry@ccl.net" Subject: what's means?(AMBER message) X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear members: I used the AMBER program to minimization the protein. when I saveAmberParm ,the xleap tell me the following message: Checking Unit. WARNING: There is a bond of 4.080112 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: 10.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 789 improper torsions applied Building H-Bond parameters. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CGLU 1 CHIP 1 NHIP 1 NSER 1 ) (no restraints) then I used the sander to minimize the protein,I get the message : namelist read: cannot position within current file apparent state: unit 5 named min.in last format: namelist io Unit 5 is a sequential formatted external file *** Execution Terminated (170) *** I do not know what's means about these messages, can someone tell me this means and how to tackle this problem? thanks a lot!!! Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office)