From chemistry-request@ccl.net Tue Jul 5 04:19:01 2005 Received: from pecan.UGent.be (pecan.ugent.be [157.193.49.18]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j658IwWp018999 for ; Tue, 5 Jul 2005 04:18:59 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by pecan.UGent.be (Postfix) with ESMTP id 6ECEF35277E for ; Tue, 5 Jul 2005 10:18:57 +0200 (CEST) Received: from pecan.UGent.be ([127.0.0.1]) by localhost (gorilla.UGent.be [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 09314-05 for ; Tue, 5 Jul 2005 10:18:53 +0200 (CEST) Received: from tarzan.ugent.be (tarzan.ugent.be [157.193.40.45]) by pecan.UGent.be (Postfix) with ESMTP id EC4ED352759 for ; Tue, 5 Jul 2005 10:18:53 +0200 (CEST) Received: from [157.193.99.41] (molmod05.ugent.be [157.193.99.41]) by tarzan.ugent.be (Postfix) with ESMTP id CC33531D67 for ; Tue, 5 Jul 2005 10:18:53 +0200 (CEST) Received: from 127.0.0.1 (AVG SMTP 7.0.323 [267.8.9]); Tue, 05 Jul 2005 10:18:40 +0200 Message-ID: <42CA4260.8060107 #%# UGent.be> Date: Tue, 05 Jul 2005 10:18:40 +0200 From: Ewald Pauwels User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040804 Netscape/7.2 (ax) X-Accept-Language: en-us, en To: chemistry #%# ccl.net Subject: SUMMARY: BOMD calculations in gaussian Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed X-Virus-Scanned: by UGent DICT X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear all, Recently I enquired whether it is possible to use constraints in the BOMD routine of Gaussian03. I got one swift reply from Gaussian (represented below) that it is not (yet) possible to do this. Yours sincerely, Ewald Pauwels. My original question: > Hello all, > > I am currently trying out the BOMD routine in Gaussian03 on some radical > structures. Presumably (i hope), this routine allows an insight in the > dynamics of a radical at different temperatures. > However, I would like to introduce some constraints (e.g. fixed bond > angles). I've already tried the Geom=Modredundant option or adding a -1 > parameter in the molecule specification, but both methods seem to be > ignored. > > Does someone has any idea of how to constrain a molecular system in > these calculations? > > Any help is more than welcome and I will summarize my responses. > > Sincerely, > Ewald Pauwels. The message I received from Gaussian: > Dr. Pauwels, > > The BOMD code in G03 is still pretty young. It evolved out of the > Traj capability in G98 but it still is not complete and will mature as > time goes by. > > Currently it is implemented for study of reactions on small molecules > and does not include constraints. I doubt this will be added as a new > feature in G03. -- Ewald Pauwels Centre for Molecular Modelling Laboratory of Theoretical Physics Ghent University Proeftuinstraat 86 B-9000 Gent Belgium ewald.pauwels #%# UGent.be +32 9 264 65 76 -- No virus found in this outgoing message. Checked by AVG Anti-Virus. Version: 7.0.323 / Virus Database: 267.8.9/39 - Release Date: 4/07/2005 From chemistry-request@ccl.net Tue Jul 5 03:12:09 2005 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j657C5tw013117 for ; Tue, 5 Jul 2005 03:12:07 -0400 Received: from Pauli (IDENT:U2FsdGVkX18Zk2sA1Jj2kc+AsVehLaVe2mMUaGKlq9w = pauli.fen.bilkent.edu.tr [139.179.97.176]) by century.fen.bilkent.edu.tr (8.12.8/8.12.8) with ESMTP id j65718jS027622 for ; Tue, 5 Jul 2005 10:01:09 +0300 (EET DST) Subject: Re: CCL:How to define HOMO-LUMO gap in open shell system ? From: Ulrike Salzner Reply-To: salzner = bilkent.edu.tr To: chemistry In-Reply-To: <20050704124537.20044.qmail = web33203.mail.mud.yahoo.com> References: <20050704124537.20044.qmail = web33203.mail.mud.yahoo.com> Content-Type: text/plain Date: Tue, 05 Jul 2005 10:11:55 +0300 Message-Id: <1120547515.16312.21.camel@Pauli> Mime-Version: 1.0 X-Mailer: Evolution 2.0.2 (2.0.2-3) Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear Ricardo, I have a partial answer to your question. I have done calculations on polyenes in the neutral ground states and on cations, which are open- shell systems. I give you the results for C12H14 and C12H14+ as examples. The experimental excitation energy of the neutral in the gas phase is 3.65 eV (d'Amico, JACS, 1980, 102, 1777).I do not know of experimental values for the cation. The only information I have is that doped conducting polymers have "midgap gap states" with about half the excitation energies of the neutral forms. But this involves counter ions. The HOMO-LUMO gap of neutral C12H14 with the B3P86 functional with 30% HF exchange and a polarized split valence basis set is 3.49 eV. TDDFT (same functional) gives 3.26 eV and TDHF 3.78 eV. The HOMO-LUMO transition is the dominant transition in the excited state wavefunction. With a CASSCF calculation including 12 electrons and all 12 pi-orbitals the first excited states lies at 3.89 eV. The cation has the following orbital energies (DFT same functional as above). alpha: HOMO 10.06 eV, LUMO 6.94 eV, beta: HOMO 10.83 eV, LUMO 7.80 eV. Thus there are three possible gaps: alpha HOMO-LUMO: 3.12 eV, beta HOMO-LUMO 3.30 eV, alpha-beta HOMO-LUMO 2.27 eV. The lowest TDDFT excitation energy with large oscillator strength is 2.42 eV. This is close to the alpha HOMO beta LUMO gap but in the TDDFT wave function there is no such transition. The excited state arises from several excitations with HOMO-LUMO transistions within alpha and beta space being dominant. I am working on CASSCF calculations but these are not finished. My conclusion at the moment: be careful, it seems to work for the wrong reason. Regards, Ulrike On Mon, 2005-07-04 at 05:45 -0700, Ricardo Oliveira wrote: > Dear all, > > I have noticed that some excitation energies , in > closed shell systems, have energies similar to the > HOMO-LUMO gap. > > Considering that the term 'HOMO-LUMO gap' is not very > appropriate for open shell systems, how can we do a > rough estimate of the excitation energies in this > case? > Shall they be somewhat similar to the homo-somo(singly > occupied orbital) gap? > Can the gaps mentioned by Ding Xunlei,on his CCL > communication, have any meaning at all? > > Thanks > > Ricardo O Esplugas > Dept of Chemistry > Sussex University > UK > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY = ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST = ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > -- Ulrike Salzner Associate Professor Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkey From chemistry-request@ccl.net Tue Jul 5 12:35:12 2005 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j65GZ8SF021827 for ; Tue, 5 Jul 2005 12:35:08 -0400 Received: from shrek.eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id j65FkdJ08937; Tue, 5 Jul 2005 09:46:40 -0600 Date: Tue, 5 Jul 2005 09:46:34 -0600 (MDT) From: Jeremy J Yang To: JunJun Liu cc: chemistry|at|ccl.net Subject: Re: CCL:SUMARRY --- 3D->2D softwares? In-Reply-To: Message-ID: References: <20050618225857.40395.qmail|at|web41201.mail.yahoo.com> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear Liu, May I explain, for your benefit and others', that you obtained an evaluation license from OpenEye, not an academic license, as you stated. Our normal evaluation license term is two months. Our normal academic license term is one year or more. As you would expect, each license is governed by a specific agreement. The evaluation agreement, to which you agreed when submitting the online form, allows for evaluation use only. Output files must be destroyed at the end of the evaluation period. Academic licensing, also available via online application, allows for full academic use as defined in the agreement. Note that the OE logo can be hidden using the toolkit and appropriate function call. And finally, thank you for the nice comments! Best Wishes, Jeremy. Jeremy J. Yang VP, Support Openeye Scientific Software On Sat, 2 Jul 2005, JunJun Liu wrote: > Deal All: > > After receiving Ogham academic licenses now, I can evaluate all the > recommended programs. Thanks all that gave me advices! I have a lot of > molecules to be converted to 2D images, so a command line program is more > of interest. Among the below recommended softwares, I like MolConverter > and Ogham most, although these two programs still have some shortcomes. > Molconverter: > 1. works well only when remove all hydrogens. > 2. it has some problem in recognizing some aromatic rings. > > Ogham: > 1. works a slightly better and smarter, but the program could be used for > only two months with an academic license. > 2. the produced images will be stamped with an OpenEye logo. > > > ----- Recommended Softwares ------- > MolConverter (in the package of Marvin) > http://www.chemaxon.hu/marvin/ > > JChemPaint > http://jchempaint.sf.net/ > > Ogham > one product of OpenEye Scientific Softwares. > http://www.eyesopen.com/products/toolkits/ogham.html > > xdrawchem > http://xdrawchem.sourceforge.net/ > > CACTVS > http://www.xemistry.com > ------------------------------ > > Best Regards! > > Liu > > On Mon, 27 Jun 2005 15:56:15 +0800, JunJun Liu wrote: > > > Dear All: > > > > Is there a software in linux can convert 3D small organic structures to > > 2D > > sketch structures? It will be more preferable if the software has a > > function of exporting 2D structures to picutures. Thanks in advance! > > > > Liu > > > > > > > -- > JunJun Liu > > College of Chemistry > Central China Normal University > WuHan 430079 > P.R. China > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY|at|ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Tue Jul 5 06:52:18 2005 Received: from noralf.uib.no (noralf.uib.no [129.177.30.12]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j65AqFoI030388 for ; Tue, 5 Jul 2005 06:52:15 -0400 Received: from alfred.uib.no (smtp.uib.no) [129.177.30.120] by noralf.uib.no with esmtp (Exim 4.34) id 1DpkSC-00042j-Nz; Tue, 05 Jul 2005 12:15:02 +0200 Received: from hornved.ii.uib.no (cbu.uib.no) [129.177.123.4] by smtp.uib.no with esmtp (Exim 4.34) id 1DpkSC-0004VA-8k; Tue, 05 Jul 2005 12:15:00 +0200 Message-ID: <42CA5CF1.3090308|at|cbu.uib.no> Date: Tue, 05 Jul 2005 12:12:01 +0200 From: Nathalie Reuter Reply-To: contact|at|bioinfo.no To: users|at|bioinfo.no, socbin|at|socbin.org, cbo-all|at|usit.uio.no, chemistry|at|ccl.net CC: contact|at|bioinfo.no Subject: Structure prediction course, Bergen, Norway - Sept. 19-22 COURSE ANNOUNCEMENT: Beginners course in Protein Structure Prediction Computational Biology Unit - Bergen, Norway September 19-22, 2005 www.bioinfo.no/training The Computational Biology Unit and the Norwegian Bioinformatics platform are pleased to announce a beginners-course in structure prediction of proteins in September 2005 (19-22). The course will consist of lectures and exercises, including a tutorial on the Modeller program. ***Lecturers*** /Darrell Conklin/ Department of Computing, City University, London /William R. Taylor/ & /Jose Saldanha/ National Institute for Medical Research, London /M.S. Madhusudhan/ & /Eswar Narayanan/ Dpt of Biopharmaceutical Sciences, Andrej Sali Lab, Univ. of California, San Francisco The course is aimed towards PhD students and researchers who have little or no experience in protein structure prediction. Basic knowledge of protein structure and ability to use windows and linux operating systems (participants must be able to edit files and run programs) are pre-requisite to be able to follow the course. Experience in sequence analysis will be helpful. Please contact us (contact|at|bioinfo.no) if you have questions regarding that aspect. The course is free of charge (cancellation fees 1000 NOK). Registration deadline: August 20th, 2005 (http://www.bioinfo.no/training/courses/registration). Program and practical information can be found on http://www.bioinfo.no/training Best regards, Nathalie Reuter --- Computational Biology Unit Bergen Center for Computational Science Univ. of Bergen N-5008 Bergen Norway http: //www.cbu.uib.no http://www.bioinfo.no **** From chemistry-request@ccl.net Tue Jul 5 10:18:26 2005 Received: from web30309.mail.mud.yahoo.com (web30309.mail.mud.yahoo.com [68.142.200.102]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j65EIOxv012673 for ; Tue, 5 Jul 2005 10:18:24 -0400 Received: (qmail 18021 invoked by uid 60001); 5 Jul 2005 13:18:22 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=a0cORy3TMaQ6IKyAi7i9S1oD9UqaG2kBgOoqRC6kpc7scQ4e2zfqoikfbfEvg6pETqd8HSTnTf+YwzBwIkWtII8vsmD/rtffHkdCC7/tWrlZwFdF3UWNAVrA2iyUo1xHeDf3ZamWsiZPUVyIabLD3CM0tVDUCGSMi4WRC8fmraY= ; Message-ID: <20050705131822.18019.qmail|at|web30309.mail.mud.yahoo.com> Received: from [130.238.38.182] by web30309.mail.mud.yahoo.com via HTTP; Tue, 05 Jul 2005 06:18:22 PDT Date: Tue, 5 Jul 2005 06:18:22 -0700 (PDT) From: Yogesh Sabnis Subject: CCL: Amber8 workshop To: CHEMISTRY|at|ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear All, I would like to know if there are any Amber8 workshops being held in Europe at this time or in the near future. Thank you. Kind regards, Yogesh ######################## Yogesh Sabnis, PhD BMC, Box 574, Avd Org. Farm. Kemi, Husargatan 3, Uppsala - 751 23 Sweden __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Tue Jul 5 08:21:53 2005 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j65CLl7U004406 for ; Tue, 5 Jul 2005 08:21:49 -0400 Received: from Pauli (IDENT:U2FsdGVkX19j9WIcnmkhg84IPhAyFPZqOSMnysWuA48|at|pauli.fen.bilkent.edu.tr [139.179.97.176]) by century.fen.bilkent.edu.tr (8.12.8/8.12.8) with ESMTP id j65CAtjS008607 for ; Tue, 5 Jul 2005 15:10:57 +0300 (EET DST) Subject: CCL: computer (hardware?) problem From: Ulrike Salzner Reply-To: salzner|at|bilkent.edu.tr To: chemistry|at|ccl.net Content-Type: text/plain Date: Tue, 05 Jul 2005 15:21:39 +0300 Message-Id: <1120566100.16312.39.camel@Pauli> Mime-Version: 1.0 X-Mailer: Evolution 2.0.2 (2.0.2-3) Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear all, I have a very strange problem with a computer. It is a P4 2.8 GHz, 1GB of RAM, 120 GB SATA HD, purchased in February 2004. For about 11 month the machine was doing fine. Then jobs all of a sudden started to exit randomly. At first I had Windows on it and used G98. Since I wanted to upgrade anyways, I installed Fedora Core 3 and G03. The problem, remained. Small jobs finish, bigger ones exit or remain in the queue, collecting time and doing nothing. Since there is warranty and I suspect it is a hardware problem, I contacted the company. They took the computer kept it for 2 months!!! for testing but claim there is nothing wrong. They exchanged the memory anyways. The problem persists. I reinstalled the system, the problem remains. Right now there is a job stuck in link 103 for 3 1/2 hours. The CPU usage (top command) changes between 0 and 99% but there seems to be no more progress. Is there any trick to test what the machine is actually doing and to check what causes the jobs to get kicked out? The same jobs run just fine on all my other computers, which are installed and configured in exactly the same way. One thing I noticed is a message upon booting: "overclocking failure, press F2 to load default values". I did this. Could this be a hint the BIOS is configured wrong? Could the problem have to do with the power management? I am at a loss. Any hints would be greatly appreciated. Thanks, Ulrike -- Ulrike Salzner Associate Professor Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkey From chemistry-request@ccl.net Tue Jul 5 17:20:57 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 j65LKqNr009180 for >ccl.net>; Tue, 5 Jul 2005 17:20:52 -0400 Received: from dns1.scripps.edu (dns1 [137.131.200.9]) by relay1.scripps.edu (8.12.11/TSRI-5.0.2rAV) with ESMTP id j65KVEkL011794; Tue, 5 Jul 2005 13:31:14 -0700 (PDT) Received: from Coffee (coffee.scripps.edu [137.131.252.43]) by dns1.scripps.edu (8.11.7/TSRI-4.3rBAV) with ESMTP id j65KVE011809; Tue, 5 Jul 2005 13:31:14 -0700 (PDT) Message-Id: <200507052031.j65KVE011809<>dns1.scripps.edu> From: "Ross Walker" >rosswalker.co.uk> To: >ccl.net> Cc: >yahoo.com> Subject: RE: Amber8 workshop Date: Tue, 5 Jul 2005 13:31:10 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.6353 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2527 In-Reply-To: <20050705131822.18019.qmail<>web30309.mail.mud.yahoo.com> Thread-Index: AcWBnuleDso8MQkYTDqtGJWeRjBSxAAAFV5g X-Virus-Scanned: ClamAV 0.86.1/967/Mon Jul 4 14:36:05 2005 on dns1 X-Virus-Status: Clean 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=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear Yogesh, > I would like to know if there are any Amber8 workshops > being held in Europe at this time or in the near > future. We held a workshop at Imperial College, London (UK) in September 2004 that covered simulations with Amber 8. This was sponsored by the EPSRC (http://www.nsccs.ac.uk/index.php). We hope to run another workshop sometime in 2006 to coincide with the release of Amber 9. There are no firm plans for this at the moment however. I also do not know what the restrictions on the EPSRC's funding will be with regards to non-UK nationals. There are no workshops planned in europe at the moment but if there was enough demand and we could get funding for it then we would be interested in hosting a workshop. Can you please post a message to the amber mailing list (see http://amber.scripps.edu for signup info). Here you may get a more definative answer. All the best Ross /\ \/ |\oss Walker | Department of Molecular Biology TPC15 | | The Scripps Research Institute | | Tel: +1 858 784 8889 | EMail:- ross<>rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be ready every day, and should not be used for urgent or sensitive issues.