From chemistry-request@ccl.net Thu Apr 7 22:57:30 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j382vUVN019199 for ; Thu, 7 Apr 2005 22:57:30 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j382vUX7019198 for chemistry () ccl.net; Thu, 7 Apr 2005 22:57:30 -0400 Date: Thu, 7 Apr 2005 22:57:30 -0400 Message-Id: <200504080257.j382vUX7019198 () server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request () ccl.net using -f From: "Jinsong, , Zhao" To: chemistry () ccl.net X-Web-Message-Number: 050407225248-19041 Subject: W:CCL: How to calculate the energy of photoexicited molecule Dear all, Would any one here like to give me a example about how to calculate the energy of photoexicited molecule using MOPAC? I have used the keywords "1SCF AM1 GNORM=0.01 PRECISE MECI C.I.=2", but I don't know whether it's correct. Thanks for any suggestions! Best wishes, Jinsong From chemistry-request@ccl.net Fri Apr 8 07:27:43 2005 Received: from wasp.am.qub.ac.uk ([143.117.23.30]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j38BRgrq006142 for ; Fri, 8 Apr 2005 07:27:42 -0400 Received: (qmail 10707 invoked from network); 8 Apr 2005 10:27:40 -0000 Received: from onslaught.am.qub.ac.uk (mail@143.117.23.180) by wasp.am.qub.ac.uk with SMTP; 8 Apr 2005 10:27:40 -0000 Received: from ssen (helo=localhost) by onslaught.am.qub.ac.uk with local-esmtp (Exim 3.35 #1 (Debian)) id 1DJqiB-0008Fu-00 for ; Fri, 08 Apr 2005 11:27:39 +0100 Date: Fri, 8 Apr 2005 11:27:39 +0100 (BST) From: Sanjay Kumar Sen X-Wasp-Original-From: Sanjay Kumar Sen To: chemistry !! ccl.net Subject: CCP6 workshop: VECTOR CORRELATIONS AND ALIGNMENT IN CHEMISTRY Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id j38BRhrq006146 ----------------------------------------------------- CCP6 Workshop VECTOR CORRELATIONS AND ALIGNMENT IN CHEMISTRY Bristol, England, July 24-27, 2005 http://www.chm.bris.ac.uk/ccp6-workshop ----------------------------------------------------- Dear Molecular Dynamicists, We still have some places available for the above workshop. If you would like to attend, please register online using the workshop web site. As the initial registration deadline has already passed, we would urge you to do that immediately. The workshop will cover both theoretical and experimental aspects of vector correlation and alignment in chemical processes, with an approximately equal number of speakers from each area. The workshop will consist of oral presentations by 16 invited speakers, poster sessions and extended discussions. Poster contributions from all attendees will be accepted. The workshop will include talks by several of the leading scientists in the field, with an emphasis on discussion of new ideas and future prospects and applications. It shall therefore prove interesting not only for experts, but also for young scientists, for those new to the field and for those interested in suggesting or undertaking future projects. The venue will be Burwalls, a beautiful mansion situated on its own grounds adjacent to the historic Clifton suspension bridge. Workshop participants will gather on the evening of Sunday 24 July and the workshop will end at 2:00 p.m. on Wednesday 27 July. The invited speakers are: . Javier Aoiz (Universidad Complutense, Madrid) . Alberto Beswick (Universiti Paul Sabatier, Toulouse) . Alex Brown (University of Alberta) . Dave Chandler (Sandia National Laboratories, Livermore) . Richard Dixon (University of Oxford) . Gerrit Groenenboom (University of Nijmegen) . Ke-Li Han (Chinese Academy of Science, Dalian) . Paul Houston (Cornell University) . Marcelo Miranda (University of Leeds) . David Parker (University of Nijmegen) . Peter Rakitzis (University of Crete) . Rex Skodje (Academia Sinica, Taipei and University of Colorado) . Arthur Suits (Wayne State University, Detroit) . Claire Vallance (University of Oxford) . Oleg Vasyutinskii (Russian Academy of Sciences, St. Petersburg) . Richard Zare (Stanford University) Organisers: Gabriel Balint-Kurti (Gabriel.BalintKurti !! Bristol.ac.uk) Marcelo Miranda (M.Miranda !! leeds.ac.uk) From chemistry-request@ccl.net Fri Apr 8 05:58:36 2005 Received: from ppsw-8.csi.cam.ac.uk (ppsw-8.csi.cam.ac.uk [131.111.8.138]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j389wauJ002929 for ; Fri, 8 Apr 2005 05:58:36 -0400 Received: from arcturus.ch.cam.ac.uk ([131.111.121.52]:3241 helo=arcturus.cam.ac.uk) by ppsw-8.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.158]:25) with esmtpsa (LOGIN:pm286) (TLSv1:RC4-SHA:128) id 1DJqG1-0001qv-RJ (Exim 4.44) for chemistry +*+ ccl.net (return-path ); Fri, 08 Apr 2005 10:58:33 +0100 Message-Id: <6.0.1.1.0.20050408105245.01c060b8 +*+ pop.hermes.cam.ac.uk> X-Sender: pm286 +*+ pop.hermes.cam.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 6.0.1.1 Date: Fri, 08 Apr 2005 10:58:29 +0100 To: chemistry +*+ ccl.net From: Peter Murray-Rust Subject: Misrepresentation of forwarding [was Re: CCL:Converting to CML ...] In-Reply-To: <20050407083858.GI24702 +*+ leitl.org> References: <20050407083858.GI24702 +*+ leitl.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Sender: pm286 +*+ hermes.cam.ac.uk X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned X-Spam-Status: No, score=0.5 required=5.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net At 09:38 07/04/2005, Eugen Leitl wrote: >----- Forwarded message from Peter Murray-Rust ----- > >From: Peter Murray-Rust [long message snipped] I am sorry to take up more bandwidth, but have to point out that *I* did not forward this message to this list nor authorise its forwarding. It was inappropriate for this list in many ways and I have received mail from list members. I have written to Dr Leitl advising him that he may quote from any material of mine in the public domain (giving attribution and context) but must admit that he is the poster and not imply that I have sanctioned it. The content of the message is unclear without the context in which it was originally posted. Peter Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 Fax: +44 1223 763076 From chemistry-request@ccl.net Fri Apr 8 12:53:00 2005 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j38GqxZA024057 for ; Fri, 8 Apr 2005 12:52:59 -0400 Received: from gamow.scripps.edu (gamow [137.131.252.67]) by relay1.scripps.edu (8.12.11/TSRI-5.0.2rAV) with ESMTP id j38Gqw16012961; Fri, 8 Apr 2005 09:52:58 -0700 (PDT) Received: from quine.scripps.edu (dhcp-252-203 [137.131.252.203]) by gamow.scripps.edu (SGI-8.12.5/TSRI-5.0.1) with SMTP id j38Gr92o535985; Fri, 8 Apr 2005 09:53:10 -0700 (PDT) Received: by quine.scripps.edu (sSMTP sendmail emulation); Fri, 8 Apr 2005 09:52:54 -0700 Date: Fri, 8 Apr 2005 09:52:54 -0700 From: "David A. Case" To: chemistry +*+ ccl.net Cc: amber +*+ scripps.edu, "David A. Case" , Tom Macke , Russ.Brown +*+ sun.com, svrci +*+ tbi.univie.ac.at Subject: Announcment: Nucleic Acid Builder (NAB) version 5 is released Message-ID: <20050408165254.GA3528 +*+ scripps.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4.1i X-CanItPRO-Stream: admin redirected to 10_OptOut X-Spam-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . roaringpenguin . com) on 137.131.200.29 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net ANNOUNCEMENT: version 5 of the NAB (Nucleic Acid Builder) molecular manipulation language is now available Thomas J. Macke, W.A. Svrcek-Seiler, Russell A. Brown and David A. Case NAB was originally designed as a small modeling language (a "molecular awk"), with a principal focus on constructing models for non-helical nucleic acids. It has been used to construct models of helical and non-helical nucleic acids > from a few dozen to a few hundred nucleotides in size, and provides a combination of rigid body transformations and distance geometry to create candidate structures that match input criteria. As the code developed, an implementation of the AMBER force field was added, which includes a version of the generalized Born model for solvation effects. Version 5 adds analytical second derivatives, opening the way to new types of simulations. Force-field calculations can be carried out on proteins and small molecules, as well as nucleic acids, making NAB a useful platform for a variety of modeling tasks. For example, NAB code is incorporated into both AutoDock and Dock to perform force-field calculations on protein-ligand and nucleic-acid-ligand complexes. NAB consists of a language specification (constructed using lex and yacc) that has special support for macromolecules and their components, along with more general-purpose constructs such as strings, regular expressions and hashed arrays. This language has a C-like syntax, and is compiled to C code at an intermediate stage. There is also a support library (primarily coded in C) that implements rigid-body transformations, distance geometry, energy minimzation, molecular dynamics and normal mode analysis. Version 5 is a major update and consolidation. It makes better connections to the Amber suite of programs, and implements for the first time second derivatives of the generalized Born solvation model. Force field calculations can be carried out in parallel on machines that support OpenMP. NAB is distributed as source code under the GNU General Public License (GPL). It runs on Linux, Mac OSX, Windows (under cygwin), and on most flavors of UNIX. For more information, and to download the code, please visit our web site: http://www.scripps.edu/case and click on the "NAB" link in the left-hand menu. We encourage NAB users to contribute to the code, or to help us integrate it into other environments. Please contact Dave Case, if you wish to help out.