From chemistry-request@ccl.net Fri Mar 18 16:04:56 2005 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2IL4pgV007616 for < ccl.net>; Fri, 18 Mar 2005 16:04:51 -0500 Received: by leitl.org (Postfix, from userid 500) id 4D9873A84DB; Fri, 18 Mar 2005 21:06:12 +0100 (CET) Date: Fri, 18 Mar 2005 21:06:12 +0100 From: Eugen Leitl < leitl.org> To: chemistry >< ccl.net Subject: [Open Babel] Open Babel and CML in the news (fwd from geoff >< geoffhutchison.net) Message-ID: <20050318200611.GK17303 >< leitl.org> ----- Forwarded message from Geoff Hutchison < geoffhutchison.net> --- From: Geoff Hutchison < geoffhutchison.net> Date: Fri, 18 Mar 2005 14:43:55 -0500 To: openbabel-discuss >< lists.sourceforge.net, cml-discuss >< lists.sourceforge.net Subject: [Open Babel] Open Babel and CML in the news X-Mailer: Apple Mail (2.619.2) CML and Open Babel have been in the news recently, and not just with talks at the ACS meeting. For one, I was just told that a recent issue of Drug Discovery Today had a pro/con debate about open-source software. Both sides made reference to Babel -- Matt Stahl of the "con" position referred to it as OELib. (Freudian slip, perhaps? Open Babel is not OELib any longer -- there have been many changes.) DeLano, Warren L.; Drug Discovery Today (2005) 10(3) p. 213-217. "The case for open-source software in drug discovery" http://dx.doi.org/10.1016/S1359-6446(04)03363-X Stahl, Matthew T.; Drug Discovery Today (2005) 10(3) p. 219-222. "Open-source software: not quite endsville" http://dx.doi.org/10.1016/S1359-6446(04)03364-1 By far the more interesting news, I think, is the report from the Chemistry division of the NSF on "Cyber Enabled Chemistry." A recent NSF-sponsored workshop on facilitating chemistry research using "cyberinfrastructure" had the following in the final report: http://bioeng.berkeley.edu/faculty/cyber_workshop/report_cyber_solu.html > Finally, models, algorithms and software must be carefully >integrated. Common component architectures, common interfaces, and >inter-language ?translators,? for example, will facilitate software >integration and interoperability; while better methods of integrating >I/O, standardized formats for input (such as babel and CML), and >error/accuracy assessments within a framework will facilitate >integration. We encourage the support, development, and integration of >public-domain community codes and, in particular, the solving of >associated problems such as long-term maintenance, intellectual >property, and tutorial development (with recognition of the varying >expertise of likely users). Cheers, -Geoff ----- End forwarded message ----- From chemistry-request@ccl.net Sat Mar 19 00:21:30 2005 Received: from mrbusi1.netcologne.de (mrbusi1.netcologne.de [194.8.194.213]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2J5LNib024657 for ccl.net>; Sat, 19 Mar 2005 00:21:24 -0500 Received: from cosmologic.de (xdsl-213-168-105-152.netcologne.de [213.168.105.152]) by mrbusi1.netcologne.de (Postfix) with ESMTP id 5F3AD1A0020; Sat, 19 Mar 2005 06:21:22 +0100 (CET) Message-ID: <423BB6C6.80405 <> cosmologic.de> Date: Sat, 19 Mar 2005 06:21:10 +0100 From: Andreas Klamt cosmologic.de> User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4 X-Accept-Language: en-us, en MIME-Version: 1.0 To: amvaldez <> uach.mx Cc: chemistry <> ccl.net Subject: Re: CCL:problems with Gaussian 03, model CPCM References: <9c4fc49c6a2b.9c6a2b9c4fc4 <> uach.mx> In-Reply-To: <9c4fc49c6a2b.9c6a2b9c4fc4 <> uach.mx> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Amelia, we have done several hundreds of amiacids and oligopeptides in water with DFT/COSMO in TURBOMOLE. Apart from the big conformational flexibility, there were no problems in the optimization at all. Unfortunately we do not have efficient COSMO frequency calculations in TURBOMOLE yet, but let me ask what you need them for. In some way continuum solvation models appear to include the change in vibrational free energy by solvation implicitly. So when you calculate the vibrational contributions in the gas phase for the corresponding conformations, you will have all you need for thermochemistry. If you should really want to go into frequencies in solutions, be aware that 2nd derivatives of the total energy are not the same as frequencies in solution, due to the non-equilibrium solvation problem, which will hinder the rotational degrees of polarization to follow the highe frequency vibrations of the solute instantaneously. So you enter a very complicated area if you decide to do so. Regards Andreas (father of COSMO) -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt <> cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- amvaldez <> uach.mx wrote: >To whom it may concern: >I am working in Centro de Investigacion en Materiales Avanzados de >Chihuahua, Mexico. >I am working with Gaussian 03, and I have tried to calculate >optimization, frequency and energy, in water solution, using CPCM >model, DFT, basis set 3-21 G, for some aminoacids and tripeptides, but >all procesing have aborted, because some bonds disapear and they form >hidrogen bonds. In all cases, a legend appears, saying that a hidrogen >has two bonds. > I think I could try another model, but I'd like you to sugest me the >best for water solution, for DFT. >I'll thank you for your kindly attention. > Sincerely: > Amelia Valdez Aguirre > > > > > >-= 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 mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow <> nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > > From chemistry-request@ccl.net Sat Mar 19 12:44:28 2005 Received: from mtaout-m.tc.umn.edu (mtaout-m.tc.umn.edu [160.94.23.21]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2JHiOYU021324 for >server.ccl.net>; Sat, 19 Mar 2005 12:44:25 -0500 Received: from pobox.com (abacavir.pharmacy.umn.edu [160.94.172.208]) by mtaout-m.tc.umn.edu with ESMTP for chemistry<>server.ccl.net; Sat, 19 Mar 2005 10:44:14 -0600 (CST) X-Umn-Remote-Mta: [N] abacavir.pharmacy.umn.edu [160.94.172.208] #+HF+LO+TS+AU Message-ID: <423C56CA.9000505<>pobox.com> Date: Sat, 19 Mar 2005 10:43:54 -0600 From: Eric Bennett >POBOX.COM> User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP30; en-US; rv:1.4.1) Gecko/20040326 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry<>server.ccl.net Subject: CCL: Re: need literature help on MD simulation of AdoMet References: >godzilla.acpub.duke.edu> In-Reply-To: >godzilla.acpub.duke.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net jz7<>duke.edu wrote: >Dear all, > >I want to run a MD on a protein which has AdoMet as a cofactor. But >currenctly there is no parameter for the cofactor AdoMet in Amber or >Charmm. > > > Another paper which might get you started is: George D. Markham, Per-Ola Norrby, and Charles W. Bock S-Adenosylmethionine Conformations in Solution and in Protein Complexes: Conformational Influences of the Sulfonium Group Biochemistry 2002, 41, 7636-7646 However, these parameters were determined for the old Amber 3 force field and they were used only for conformational energy comparisons, not for dynamics. -- Eric Bennett, Center for Drug Design, U of Minnesota Drawing on my fine command of the language, I said nothing. -Robert Benchley From chemistry-request@ccl.net Sat Mar 19 08:32:34 2005 Received: from osgood.cc.nd.edu (osgood.cc.nd.edu [129.74.250.227]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2JDWU4x010282 for ; Sat, 19 Mar 2005 08:32:30 -0500 Received: from localhost (localhost [127.0.0.1]) by osgood.cc.nd.edu (Switch-3.1.7/Switch-3.1.7) with ESMTP id j2JDWTLM012338 for ; Sat, 19 Mar 2005 08:32:29 -0500 (EST) Received: from ns.piwnica.com (ns.piwnica.com [66.93.212.3]) by webmail.nd.edu (IMP) with HTTP for ; Sat, 19 Mar 2005 08:32:29 -0500 Message-ID: <1111239149.423c29ed13913=at=webmail.nd.edu> Date: Sat, 19 Mar 2005 08:32:29 -0500 From: Jan K Labanowski To: chemistry=at=ccl.net Subject: 05.09.11 Biomolecular Simulations - from Prediction to Practice MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.6 X-Originating-IP: 66.93.212.3 X-ND-MTA-Date: Sat, 19 Mar 2005 08:32:30 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4450 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 ----- Forwarded message from David Lloyd ----- Date: Fri, 18 Mar 2005 11:13:49 -0000 From: David Lloyd Reply-To: David Lloyd Subject: meeting notification for ccl posting To: jlabanow=at=nd.edu Dear Jan, could you possibly post the following to CCL? Biomolecular Simulations - from Prediction to Practice - a Molecular Graphics and Modelling Society International meeting, will be held from September 11th-14th in Trinity College Dublin, Ireland. The meeting is focusing on two main themes - Drug Discovery : including docking / rational design / molecular recognition & Protein Simulations : including folding / systems biology / homology modelling / mechanistic studies - with special emphasis on linking computational work to experimental validation. Confirmed speakers include : Sir Tom Blundell, University of Cambridge / Astex Pharmaceuticals, UK Curt Breneman, Rensselaer Polytechnic Institute, USA Martyn Ford, University of Portsmouth, UK Bobby Glen, University of Cambridge, UK Ian Gould, Imperial College London, UK Osman Guner, Accelrys, USA Mike Hahn, Glaxo-SmithKline, UK Rod Hubbard, Vernalis, UK Diane Joseph-McCarthy, Wyeth, USA Paul Lyne, Astra Zeneca, USA Yvonne Martin, Abbott, USA Stefano Moro, Padova University, Italy Julia Rice, IBM Research, USA Roger Sayle, OpenEye Scientific, USA Gisbert Schneider, Johann Wolfgang Goethe-Universitdt Frankfurt, Germany Brian Shoichet, UCSF, USA Vladimir Sobolev, Weismann Institute, Israel Mike Thorpe, Arizona State University, USA Gert Vriend, CMBI, The Netherlands Rebecca Wade, MBL research, Germany Tony Watts, Oxford, UK Early Registration for this event is now open at :http://www.tchpc.tcd.ie/mgms Thanks! David ---------------------------------------------------------------------------- -------- Dr David G. Lloyd Hitachi Lecturer Molecular Design Group Department of Biochemistry Trinity College Dublin, Dublin 2, Ireland Tel: +353-1-6082904 Fax: +353-1-6772400 Mobile: +353-87-2112732 e-mail: lloyddg=at=tcd.ie ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ---------- Group Web : http://www.tcd.ie/biochemistry/DLloyd.html Centre for Structural Biology and Molecular Design : http://www.tcd.ie/Biochemistry/csbmd/index.php MGMS International Meeting, Dublin, September 2005 : http://www.tchpc.tcd.ie/mgms ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ---------- ----- End forwarded message ----- From chemistry-request@ccl.net Sat Mar 19 19:38:22 2005 Received: from prserv.net (asmtp1.prserv.net [32.97.166.51]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2K0cEvI012888 for ; Sat, 19 Mar 2005 19:38:14 -0500 Received: from [127.0.0.1] (cpe-65-29-66-160.indy.res.rr.com[65.29.66.160]) by prserv.net (asmtp1) with ESMTP id <20050319233733251058u47he> (Authid: jmmckel); Sat, 19 Mar 2005 23:37:33 +0000 Message-ID: <423CC415.2050107_at_attglobal.net> Date: Sat, 19 Mar 2005 18:30:13 -0600 From: John McKelvey User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Dr. Daniel Glossman-Mitnik" CC: chemistry_at_ccl.net Subject: Re: CCL:a question about Koopmans' theorem References: In-Reply-To: Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit 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 Hello... Thought I'd throw in my $0.02 just in case the horse is not yet dead... If we consider the process E(products) - E(reactants), and use a simple Huckel theory model one gets delta-E (ionization) = -eps(Homo) delta-E (electron affinity) = + eps(LUMO).. I like this because it make sense to me in the thermodynamic sense, assuming that occupied energy levels are usually < 0. If occupied MO's have negative eigenvalyes then KT says one has to expend energy to remove an electron, but also if the HOMO is > 0 then removal of an electron is "facilitated", so to speak. For the electron affinity a negative LUMO eigenvalue means "favorable" while a positive one would mean "unfavorable" Cheers, john McKelvey Dr. Daniel Glossman-Mitnik wrote: > Dear netters: > > I am a bit confused about Koopmans theorem. In Essentials of > Computational > > Chemistry, C.J. Cramer, Wiley, 2002, we can read on page 181: Koopmans > > theorem equates the energy of the HOMO with the IP . On page 182, we > > can read Koopmans4 theorem can be formally applied to electron > affinities > > (EAs) as well. i.e., the EA can be taken to be the orbital energy of > the lowest > > unoccupied (virtual) orbital > > That is IP = -E(HOMO) and EA = E(LUMO) > > But many articles, quote the opposite for the EA. > > As an example, in Reactivity Descriptors, PK Chattaraj et al, in the book > > Computational Medicinal Chemistry for Drug Discovery, we can read on > > page 302: In ab initio MO theory, I and A can be approximated as the > > negative of energies of HOMO and LUMO, respectivelu, using Koopmans > > theorem > > That is IP = -E(HOMO) and EA = -E(LUMO) > > Beyond the validity of this approximation, specially for anions, which one > > is correct : EA = E(LUMO) or EA = -E(LUMO) ?? > > Thanks for your help > > Daniel > > ************************************************************ > > Dr. Daniel Glossman-Mitnik > > Grupo NANOCOSMO - CIMAV > > Nanociencia y Nanotecnologma Computacional > > Simulacisn y Modelado Molecular > > Miguel de Cervantes 120 - Comp. Ind. Chihuahua > > Chihuahua, Chih. 31109 - MEXICO > > Tel.: (52) 614 4391151 FAX: (52) 614 4391130 > > Part.: (52) 614 4987113 Cel.: (52) 614 1635322 > > E-mail: daniel.glossman_at_cimav.edu.mx > > dglossman_at_prodigy.net.mx > > ************************************************************* > From chemistry-request@ccl.net Sat Mar 19 20:53:38 2005 Received: from server.ccl.net (server.ccl.net [66.93.212.15]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2K1rVIC019957 for ; Sat, 19 Mar 2005 20:53:31 -0500 Date: Sat, 19 Mar 2005 20:53:26 -0500 (EST) From: Computational Chemistry List To: chemistry/at/ccl.net Subject: 05.11.28 Combinatorial Methods and Informatics in Materials Science Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net CALL FOR PAPERS MRS Symposium LL: Combinatorial Methods and Informatics in Materials Science 2005 MRS Fall Meeting, Nov. 28-Dec.2, 2005 Boston http://www.mrs.org/meetings/fall2005/program/f05_cfp_ll.html ABSTRACT DEADLINE: JUNE 21, 2005 REMINDER: In fairness to all potential authors, late abstracts will not be accepted. In the past 10 years, combinatorial, and/or high-throughput, and artificial intelligence methods have permitted scientists to rapidly explore new and complex systems in materials and device research and development. As a consequence to this aim, numerous novel research programs and products have emerged from a variety of universities, national laboratories, and industry research groups. This symposium will bring together scientists from disciplines such as materials sciences, chemistry, physics, electrical engineering, chemical and mechanical engineering, informatics, and systems engineering to share the successful studies and illuminate current challenges in four major technical areas: combinatorial fabrication of new materials and novel devices; high-throughput methods for materials and device characterization; artificial intelligence methods and software development; and combinatorial approach in undergraduate and graduate research. Papers are solicited in the following principal topical areas: - Combinatorial fabrication of new materials and novel devices - Functional materials, electronic materials, nanomaterials, and biomaterials - Homogeneous and heterogeneous catalysts - Polymer composites - Millireactors and millifluidics - Combinatorial compounding and formulation - Ink-jet dispensing and continuous gradient methods - High-throughput characterizations of materials and devices - Microinstrumentation - Rapid characterization of composition and microstructure - Mechanical, thermal, and optoelectronic properties - Fluid properties such as rheology, stability, and structure - Algorithms for high-throughput optimization of materials and process parameters - Artificial intelligence methods and software development - New screening principles and ideas - Library fabrication and experimental design - Computational combinatorial chemistry and high-throughput screening techniques - Informatics, efficient user interfaces, and statistical and data mining techniques - QSPR and QSAR techniques - Traditional ab-initio and semi-empirical quantum methods - Quantum Monte Carlo, density-functional approaches, and tight binding techniques - Force-field-based molecular mechanics, dynamics, and Monte Carlo simulations - Mesoscale and multiscale modeling, molecular modeling, and graphics approaches - Combinatorial approach in undergraduate and graduate research Invited speakers (partial list) include: Arik Aleksanyan (National Academy Armenia), Eric J. Amis, Kathryn Beers, and Albert Davydov (National Inst. of Standards & Technology), Alex Demkov (Univ. of Texas-Austin), Mats Eriksson (Linkoping Univ., Sweden), J.A. Goschnick (Forschungszentrum Karlsruhe, Germany), Jim Greer (NMRC, Ireland), Jaime Grunlan (Texas A&M Univ.), Damian Hajduk (Symyx), Andrew Hillier (Iowa State Univ.), Ghassan Jabbour (Univ. of Arizona), Yuji Matsumoto (Tokyo Inst. Of Technology, Japan), Carson Meredith (Georgia Inst. of Technology), Tsuyoshi Ohnishi (Univ. of Tokyo, Japan), Akira Ohtomo (Tohoku Univ., Japan), Noriaki Okazaki (National Inst. for Material Science), John Perkins (National Renewable Energy Lab), Krishna Rajan (Rensselaer Polytechnic Inst.), Joe Shinar (Ames Lab), Paul Stradins (National Renewable Energy Lab), Andrei Touzik (IFW), Dean Webster (North Dakota State Univ.), Douglas Wicks (Univ. of S. Mississippi), Xiao-Dong Xiang (Intematix), Yusuke Yamada (AIST, Japan), Michiko Yoshitake (National Inst. for Material Science), and Andrei K. Yudin (Univ. of Toronto, Canada). Symposium Organizers Qi Wang National Renewable Energy Laboratory, MS 3212, 1617 Cole Blvd. Golden, CO 80401 Tel 303-384-6681, Fax 303-384-6430, qi_wang/at/nrel.gov Radislav A. Potyrailo G.E. Global Research Center, Combinatorial Chemistry Laboratory P.O. Box 8, Schenectady, NY 12301 Tel 518-387-7370 or -5257, Fax 518-387-5604, potyrailo/at/crd.ge.com Michael Fasolka National Institute of Standards and Technology, Polymers Division MS 8542, 100 Bureau Dr., Gaithersburg, MD 20899 Tel 301-975-6588, Fax 301-975-4924, michael.fasolka/at/nist.gov Toyohiro Chikyow National Institute for Material Science, Nanomaterial Research Laboratories 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan Tel 81-298-59-2746, Fax 81-298-59-2701, chikyo.toyohiro/at/nims.go.jp Ulrich S. Schubert Eindhoven University of Technology, Laboratory of Macromolecular Chemistry & Nanoscience (SMN), Dutch Polymer Institute, P.O. Box 513, NL-5600 MB Eindhoven, The Netherlands Tel 31-40-247-4083, Fax 31-40-247-4186, u.s.schubert/at/tue.nl Anatoli Korkin Nano & Giga Solutions, 1683 E. Spur St., Mesa, AZ 85296 Tel/Fax 480-539-4754, korkin/at/nanoandgiga.com