From chemistry-request@ccl.net Thu Jul 22 03:47:51 2004 Received: from sungod.ccs.yorku.ca (mailrelay.yorku.ca [130.63.236.104]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6M8ln9k014349 for ; Thu, 22 Jul 2004 03:47:49 -0500 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.12.10/8.12.8) with ESMTP id i6M8sPEB023875 for ; Thu, 22 Jul 2004 04:54:25 -0400 (EDT) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id i6M8pxg19400 for chemistry:at:ccl.net; Thu, 22 Jul 2004 04:51:59 -0400 (EDT) From: Wai-To Chan Message-Id: <200407220851.i6M8pxg19400:at:curl.gkcl.yorku.ca> Subject: Re: QUESTION STABILITY_KEYWORD? To: chemistry:at:ccl.net Date: Thu, 22 Jul 2004 04:51:58 -0400 (EDT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net From: Paul Momoh <<<<<<<<<<<<<<<<<,, Good morning, I initially performed a stability job (STABLE) on a DFT (B3LYP) job. I got the message RHF-> UHF instability. I then performed another stabilty test (using Stable=repopt). The instability was subsequently corrected (I got a lower abs energy). Where/how can I get the corrected coordinates and/or multiplicity and/or method used for the corrected structure? >>>>>>>>>>>>>>>>>>>>>> By 'corrected' structure you probably mean the structure obtained from geometry optimization with the stable wavefunction. If you have the reoptimized wavefunction saved in your checkpoint file you can easily start a geometry optimization job with unrestricted B3LYP this way # ub3lyp/(basis set) guess=read opt Provided that the ub3lyp solution does not converge back to rb3lyp during the course of geometry optimization your job may pick up a different structure. In some cases if the structure has spatial symmetry it may be necessary to specify scf=nosymm to prevent the collapse of the unrestricted solution back to the unstable restricted solution. Whether the obtained structure is correct or not may or may not be contingent on the stability of the wavefunction. Wai-To Chan From chemistry-request@ccl.net Thu Jul 22 08:51:43 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6MDpfH1026165 for ; Thu, 22 Jul 2004 08:51:41 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 3586247FA7 for ; Thu, 22 Jul 2004 09:57:03 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 25883-08 for ; Thu, 22 Jul 2004 09:56:57 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 7210247FA5 for ; Thu, 22 Jul 2004 09:56:57 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Thu, 22 Jul 2004 09:56:57 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: force constants of diatomics in GAUSSIAN-03 Date: Thu, 22 Jul 2004 09:56:56 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0007D78938$at$srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: force constants of diatomics in GAUSSIAN-03 Thread-Index: AcRvaVVsU+PdW7fHTqGi7RMSTOBkewAhRVqA From: "Shobe, David" To: X-OriginalArrivalTime: 22 Jul 2004 13:56:57.0377 (UTC) FILETIME=[C0B0E110:01C46FF3] X-Spam-Status: No, hits=4.0 required=7.5 tests=LINES_OF_YELLING,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6MDpiH1026169 A few loose ends here (now that my interest has been kindled). To aid the discussion, let's call R the ratio of [the force constant with respect to Gaussian's mass-weighted definition of a unit step] to [the force constant with respect to interatomic distance]. fc Gaus fc dist R HF 10.66 9.70 1.10 HCl 5.22 4.80 1.09 HBr 4.19 4.10 1.02 HI 3.23 3.20 1.01 CO 41.34 18.60 2.22 NO 39.29 15.30 2.57 1. One thing that puzzled me was the difference between the H-X molecules for which Gaussian and the web site http://hyperphysics.phy-astr.gsu.edu/hbase/molecule/vibspe.html R is close to 1, and on the other hand NO and CO where R is much larger. Given your explanation [first attached message], it seems that the mass ratio of the two atoms is the important thing here, and that the ratio R between the mass-weighted comes between two limits. The upper limit is the homonuclear case with R=2. The lower limit occurs with an infinite mass ratio, in which case R=1 because the normal-mode step is purely the movement of the light atom. 2. But if that's true, why is R>2 for CO and NO? 3. What definition does GAMESS(US) use for the unit step [second attached message]? It doesn't agree with either Gaussian or the web site! --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request$at$ccl.net]On Behalf Of Michael Frisch Sent: Wednesday, July 21, 2004 10:24 AM To: chemistry$at$ccl.net Subject: CCL:force constants of diatomics in GAUSSIAN-03 On Wed, Jul 21, 2004 at 03:15:48PM +0400, Dmitry Rozmanov wrote: Dmitry Rozmanov wrote > If this is the case, then I guess this is just a wrong way of doing things > and the force constants got by Gaussian are not correct at all. There is a > definition of the thing and there is no two way of calculation. > > ---Dmitry. > This is nonsense. The details are in a white paper on our web site, but the key point is that the force constant is the second derivative with respect to a normal mode displacement and the units for the normal mode, or equivalently the convention for what consititues a unit step, are arbitrary. For polyatomic molecules, one typically diagonalizes the force constant matrix in mass-weighted coordinates, so the natural unit step is a normalized displacement in these coordinates. This approach is general and applicable to any polyatomic molecule. In the particular case of H2 with the molecule along the x-axis, this normalized step would be (1/sqrt(2),0,0,1/sqrt(2),0,0) in the 6 cartesian coordinates. This unit step changes the H-H distance by sqrt(2). For the particular case of diatomic molecules when people calculate by hand, they use the distance between atoms as the coordinate, which simpler for diatomics but doesn't apply to polyatomics. In that coordinate system, a unit displacement changes the distance by 1 rather than sqrt(2), so the force constants (second derivatives of the energy) differ by a factor of 2. The corresponding reduced masses for the mode also differ by a factor of two and the frequency is the same. For the diatomic, the "by hand" coordinates give a reduced mass for the mode which is the same as the overall reduced mass for the molecule. For a general polyatomic molecule, the reduced mass corresponding to a particular mode is not an observable quantity and is not defined until one adopts a convention for the (arbitrary) size of a unit normal mode displacement. Mike Frisch -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow$at$nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Earlier, Dmitry Rozmanov wrote: This is what Gaussian says: Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), depolarization ratios for plane and unpolarized incident light, reduced masses (AMU), force constants (mDyne/A), and normal coordinates: 1 SG Frequencies -- 2117.8243 Red. masses -- 14.8673 Frc consts -- 39.2882 IR Inten -- 86.4086 Atom AN X Y Z 1 7 0.00 0.00 0.75 2 8 0.00 0.00 -0.66 This is what GAMESS (US) says: ------------------------------------------------------------------------------- INTRINSIC VIBRATIONAL FREQUENCIES AND FORCE CONSTANTS FREQUENCIES AND FORCE CONSTANTS IN PARENTHESES SCALED BY 1.000 AND 1.000, RESP. ------------------------------------------------------------------------------- INTERNAL COORDINATE INTRINSIC FREQUENCIES (CM**-1) -------------------------------------------------- STR. 2 1 2117.8 (2117.8 ) -------------------------------------------------------------------- INTERNAL COORDINATE INTRINSIC FORCE CONSTANTS (HARTREES/BOHR**2) (MDYN/ANG) -------------------------------------------------------------------- STR. 2 1 1.2673 ( 1.2673) 19.731 ( 19.731) You see, the frequencies are perfectly the same and the units are the same. However, I was pointed to a document which describes some pecularities of how Gaussian treats the reduced masses. I saw it before and I cannot still get how the same value with definite units can be different with two ways of calculation anyway. Here is the link: http://www.gaussian.com/g_whitepap/vib.htm#SECTION00036000000000000000 If this is the case, then I guess this is just a wrong way of doing things and the force constants got by Gaussian are not correct at all. There is a definition of the thing and there is no two way of calculation. ---Dmitry. Per-Ola Norrby wrote: > Hi Dmitry > >> I do no agree here. In fact I can do the same calculation with GAMESS >> (US) easily and get the meaningful result with the same method >> (ROHF/6-31G): > > > OK, I think you have two problems. First, if GAMESS and G98 differ > that much, it's probably because you located two different states. Have > you compared the total energies of the molecules, and the orbital > output? I had a look in Jaguar, using C2v symmetry (I have to stay with > Abelian subgroups). In that notation, the 2a1 state is high in energy, > whereas the 2b1 and 2b2 states are degenerate. Watch out for this type > of situation! The final wavefunction is completely dependent on the > first guess, it's very possible that Gaussian and GAMESS locate > different states (you can modify it in Gaussian using the GUESS > keyword). And you can be quite sure that the 2b1 and 2b2 states will > not be correctly represented by a simple ROHF. > > I get my output as frequencies. For the 2a1 state (the wrong one, > since it's high in energy), I get 943 cm-1, whereas 2b1 gives 2278 > cm-1. My guess is that GAMESS actually is the culprit here, locating > the high-energy state and thus giving a reasonable frequency for the > completely wrong reason. You'd expect that an ROHF solution for a > problem that is inherently multideterminant would be expected to give a > too high force constant, like Gaussian is doing. > > And I know the problems of applying MCSCF to "real" situations, I'm > currently working with CASPT2 on some metal complexes. Sometimes you > have to, when you run into problems that not even B3LYP or CCSD(T) can > handle... > > Regards, > > Per-Ola -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow^at^nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Jul 22 00:48:33 2004 Received: from smtp4.dti.ne.jp (smtp4.dti.ne.jp [202.216.228.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6M5mVZf005280 for ; Thu, 22 Jul 2004 00:48:32 -0500 Received: from oemcomputer (PPP76.fukuoka-ip.dti.ne.jp [211.132.92.76]) by smtp4.dti.ne.jp (3.08s) with SMTP id i6M5t2Xg005072 for ; Thu, 22 Jul 2004 14:55:03 +0900 (JST) Message-ID: <001801c46fb0$42b67ec0$4c5c84d3@oemcomputer> From: "Telkuni Tsuru" To: Subject: CCL:Fluorescence from Intercalated Dye Date: Thu, 22 Jul 2004 14:53:48 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, CCLers. I like to ask my interpretation for the fluorescence from the intercalated dye. All responses, I will appreciate and summarize them. I'm studying the fluorescence intensity magnification of the intercalated dye > from the viewpoint of molecular orbital theory. My question is about the mechanism of this magnification, and I need your comment for my interpretation. For example, when a dye EtBr(Ethidium Bromide) intercalated into the stacked DNA(*) or RNA bases (it is just like a sandwich !), the fluorescence intensity is magnified. (*) Bases are paired and stacked I've read books, papers, and web documents, but I'm yet to understand the correct theoretical and molecular orbital effect from stacked bases. Now, I guess the scheme between the stacked bases and dye as follows: The dye had intercalated. --> MOs of dye are changed by each base. --> Degree-of-freedom of dye electron is increased, so the charge separation become easier. --> Quantum yield for fluorescence is increased, then the fluorescence intensity is magnified. ... Is this scheme true? Comment please. Thanks in advance, -------------------------------------------------------- Telkuni Tsuru telkuni..at..venus.dti.ne.jp Tekcel corp. -------------------------------------------------------- From chemistry-request@ccl.net Thu Jul 22 15:25:27 2004 Received: from mxout4.cac.washington.edu (mxout4.cac.washington.edu [140.142.33.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6MKPPVl009420 for >ccl.net>; Thu, 22 Jul 2004 15:25:26 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.32.139]) by mxout4.cac.washington.edu (8.13.0+UW04.06/8.13.0+UW04.06) with ESMTP id i6MKVrQv021274 for >ccl.net>; Thu, 22 Jul 2004 13:32:00 -0700 Received: from u.washington.edu (D-128-95-235-187.dhcp4.washington.edu [128.95.235.187]) (authenticated bits=0) by smtp.washington.edu (8.13.0+UW04.06/8.13.0+UW04.06) with ESMTP id i6MKVrx5024925 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for >ccl.net>; Thu, 22 Jul 2004 13:31:53 -0700 Message-ID: <4100243A.3070006<>u.washington.edu> Date: Thu, 22 Jul 2004 13:31:54 -0700 From: Oliver Hucke >u.washington.edu> Reply-To: ohucke<>u.washington.edu User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL >ccl.net> Subject: CCL:binding energy of Zn2+ ligands - SUMMARY References: <40C8AAC8.4090008<>u.washington.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL'ers, some time ago I sent the request shown below concerning the influence of ligand basicity on the binding affinity to a zinc ion. I received two replies pointing me to interesting papers. Many thanks to Ida Ma and Miquel Sola! Oliver -----------------------my request------------------------------------- > I am looking for literature describing the influence of the basicity of > metal ion ligands (ideally Zn2+ ligands) on the binding energy. > > For example, I would expect the binding energy for an imidazole to be > more favorable than for an imidazole with an electron withdrawing > substituent, let's say an -SO2-group. > > Can somebody point me to articles on this matter? > ----------------------the replies------------------------------------- Our group has been working on the gas phase cation-ligand affinities (both expt and theory), in particular for K+ and Ag+, and recently published a paper for potassium cation affinities in Chem. Eur. J. 2003, 9, 3383 - 3396, which maybe of interest to you. For Zn2+, Ohanessian and Hoppillard been working on the it but I think the focus is more on amino acids currently, rather than small model organic ligands. For general cation-ligand interaction, pls consult work from Peter Armentrout and Mary Rodger's group. Their work, and some other key references in the area, can be found in the reference section in the our paper above. --- You may find interesting the following papers: M. Sol`, A. Lledss, M. Duran and J. Bertran, Inorg. Chem. 30 (1991) 2523-2527. M. Sol`, J. L. Andris, M. Duran, A. Lledss and J. Bertran, Theor. Chim. Acta 91 (1995) 333-351 ----------------------------------------------------------------------- -- _______________________________________________________________ Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: ohucke<>u.washington.edu _______________________________________________________________ From chemistry-request@ccl.net Thu Jul 22 23:03:33 2004 Received: from mx3.ust.hk (mx3.ust.hk [143.89.13.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6N43UVl025790 for ; Thu, 22 Jul 2004 23:03:31 -0500 Received: from ust.hk (sqmail2.ust.hk [143.89.13.12]) by mx3.ust.hk (8.12.11/8.12.11) with SMTP id i6N4A4u2052292 for ; Fri, 23 Jul 2004 12:10:09 +0800 (HKT) Received: from 143.89.53.94 (SquirrelMail authenticated user chgy) by sqmail.ust.hk with HTTP; Fri, 23 Jul 2004 12:10:09 +0800 (HKT) Message-ID: <4149.143.89.53.94.1090555809.squirrel=at=sqmail.ust.hk> Date: Fri, 23 Jul 2004 12:10:09 +0800 (HKT) Subject: Evaluate the electrostatic interaction of intramolecules From: "GAO Yi" To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.8) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I want to evaluate the electrostatic interaction contributions of the intramolecule, such as an alanine residue. My method is to divided the intramolecular N-C(alpha) and O=C-C(alpha) bonds, and use hydrogen atoms instead of the alpha-carbon atoms. But these artificial H-atoms are too close to represent the real situation. Could you give me any suggestions to evaluate the electrostatic interactions of such intramolecular hydrogen bonding? Best, Yi Gao Department of Chemistry, The HongKong University of Science and Technology, HK From chemistry-request@ccl.net Fri Jul 23 07:47:41 2004 Received: from mserv7.dl.ac.uk (mserv7.dl.ac.uk [148.79.80.138]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6NCldKJ019164 for ; Fri, 23 Jul 2004 07:47:40 -0500 X-DL-MFrom: X-DL-Connect: Received: from exchange06.dl.ac.uk (exchange06.dl.ac.uk [148.79.162.91]) by mserv7.dl.ac.uk (8.12.10/8.12.8/[ref postmaster(at)dl.ac.uk]) with ESMTP id i6NCrHpn008526; Fri, 23 Jul 2004 13:53:17 +0100 Received: by exchange06.dl.ac.uk with Internet Mail Service (5.5.2653.19) id ; Fri, 23 Jul 2004 13:54:38 +0100 Message-ID: From: "Couch, PA (Philip)" To: Andrew Fisher , Arnuad Marmier , Ben Slater , Bjorn Roos , "Blanshard, LJ (Lisa)" , CCP1BB , CCP4BB , Clovis Chapman , CompChemList , CPMD Consortium , David Moss , Edward Armour , "Emerson, DR (David)" , Ernest Laue , e-Science Centre All Staff , Fritz Schaefer , FSAtom Managing Committee , Fumio Hirata , Georg Kresse , "Hans.Lischka" , James Annett , Jeremy Cockcroft , Jeremy Hutson , John Harding , John Squire , John Stanton , Juergen Gauss , Kimihiko Hirao , Mark Gordon , Michael Frisch , Mike Colvin , NeSC , "Noble, CJ (Cliff)" , Open Babel , Peter Gill , Peter Taylor , Reinhart Ahlrichs , Richard Friesner , Robert Harrison , Roland Lindh , Sam French , Stefano Evangelisti , Stuart Cant , "Temmerman, WM (Walter)" , "Tyer, RP (Rick)" , Walter Thiel , "Wander, A (Adrian)" Subject: Towards a Common Data and Command Representation for Quantum Chem istry Date: Fri, 23 Jul 2004 13:54:33 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-CCLRC-SPAM-report: -4.9 : BAYES_00 X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Towards a Common Data and Command Representation for Quantum Chemistry - the eCCP1 Project. The eCCP1 project is a collaboration between CCP1 (Quantum Chemistry) of the UK CCPs (http://www.ccp.ac.uk/) and the CLRC Daresbury Laboratory's e-Science Centre (http://www.e-science.clrc.ac.uk). The project aims to develop, with broad consensus, mechanisms to facilitate the interoperation of quantum chemistry and other codes, allowing, for example, a plug-and-play approach to techniques such as QM/MM, or tools such as graphical user interfaces. The eCCP1 project also builds on developments in Grid technology and other e-science activities to enable effective use of Grid resources by the quantum chemistry community. A specific first object for the eCCP1 project is to track and develop, where necessary, emerging standards in computational chemistry data and command representation, with the aim of producing a common widely-accepted format for quantum chemistry data. The project is beginning to gather the requirements for the data and meta-data models and associated tools from the international quantum chemistry community. If you have an interest in this area, I would encourage you to participate at this early stage, as any comments/suggestions that you may have could impact on our decisions and would be very gratefully received. Some information has already been collected via meetings such as those at NeSC 'Toward a Common Data and Command Representation for Quantum Chemistry' (http://www.nesc.ac.uk/esi/events/394/) and 'CCP/e-Science Workshop' (http://www.nesc.ac.uk/esi/events/298/). It is also planned to start discussions on the eCCP TWiki site (http://grids.ac.uk/eccp) and email list (eccp-data(at)forge.nesc.ac.uk). Reference implementation tools will be available at NeSCForge (http://forge.nesc.ac.uk/projects/eccp) and data and meta-data models will available at the eCCP TWiki site. The models will be made available as UML and XML schema. Detailed discussions will take place on the mail list and overview documents will be maintained at the TWiki site. These overviews will include details of the components of the models and software tools and issues associated with each. An initial document, based on the data-type discussions at the NeSC meeting, can now be found at the site. The TWiki documents will be editable by anyone who has registered at the site and been given edit access permissions (please see the site main page for guidance). This project is about producing something which is practically useful for quantum chemistry and based on the desires of the quantum chemistry community, so if you have an interest, please get involved. For more information on the eCCP1 project, please refer to the eCCP TWiki site (http://grids.ac.uk/eccp). Very best wishes, Philip Couch. -- Dr Philip Couch, A46, CCLRC Daresbury Laboratory, Daresbury, Warrington, Cheshire, WA4 4AD, UK. E-mail: p.a.couch(at)dl.ac.uk From chemistry-request@ccl.net Thu Jul 22 12:03:37 2004 Received: from dasher.wustl.edu (dasher.wustl.edu [128.252.208.48]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6MH3ZH1002621 for ; Thu, 22 Jul 2004 12:03:35 -0500 Received: from dasher.wustl.edu (comet.wustl.edu [128.252.208.50]) by dasher.wustl.edu (8.12.8/) with ESMTP id i6MHA2cA400331; Thu, 22 Jul 2004 12:10:02 -0500 (CDT) Message-ID: <40FFF4EA.7050507/at/dasher.wustl.edu> Date: Thu, 22 Jul 2004 12:10:02 -0500 From: Jay Ponder Organization: Biochemistry, Washington University Medical School User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry/at/ccl.net Subject: TINKER and Force Field Explorer 4.2 are Available Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Computational Chemistry List, A new release of the TINKER Molecular Modeling Package, version 4.2, is available from the Ponder Lab web site at http://dasher.wustl.edu/ or via anonymous ftp from dasher.wustl.edu in the /pub/tinker area. We encourage all current TINKER users to upgrade to the new version. TINKER 4.2 is a modular, general package for molecular mechanics and dynamics with some special features, facilities and parameter sets for biopolymers. It currently supports several force fields, including Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials and our own AMOEBA polarizable atomic multipole force field. The software contains many advanced algorithms for energy minimization, molecular dynamics, distance geometry and global search, including some methods that are not readily available elsewhere. Included with TINKER 4.2 are new and updated force field parameter sets. In particular, this version contains the first public release of the full AMOEBA polarizable atomic multipole protein force field (AMOEBAPRO). Several additional AMOEBA parameters for small molecules are also available, and others will be added shortly. In addition, release of TINKER version 4.2 coincides with an updated version of the Force Field Explorer (FFE) visualization program and GUI for the TINKER package. This new FFE contains major improvements over previous releases in stability, speed, features, and integration with TINKER. FFE is currently supported on the Linux, Windows and Mac OSX 10.3 platforms. Also new with TINKER 4.2 are downloadable self-extracting installation packages that install ready-to-use TINKER and FFE versions on Linux, Windows or Mac OSX 10.3 systems. As before, TINKER and Force Field Explorer are available with full source code, a User's Guide, and several examples and molecule files. Directions are supplied for building the package on most commonly used CPU/OS combinations. Prebuilt command line executables limited to a maximum of 10000 atoms are also provided. Please see the web site above for further information. We ask those who make significant use of TINKER to complete, sign, and return by regular mail the license form available on our web site. We keep all the returned forms and use them to help justify further development of the package. Comments, questions and suggestions for improvements should be sent to ponder/at/dasher.wustl.edu. We are particularly eager to get feedback > from people who are considering using TINKER and Force Field Explorer in an instructional setting. Best wishes, Jay Ponder -- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Campus Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder/at/dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ From chemistry-request@ccl.net Thu Jul 22 09:06:05 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6ME64H1026842 for ; Thu, 22 Jul 2004 09:06:04 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 431E747FAA; Thu, 22 Jul 2004 10:11:27 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 28764-10; Thu, 22 Jul 2004 10:11:21 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id D624047FA9; Thu, 22 Jul 2004 10:11:21 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Thu, 22 Jul 2004 10:11:21 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: 2 questions Date: Thu, 22 Jul 2004 10:11:21 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0007D78939=at=srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: 2 questions Thread-Index: AcRvac1i6dUfq9EXT7+p2UK1pjTDRwAilTmw From: "Shobe, David" To: , "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 22 Jul 2004 14:11:21.0752 (UTC) FILETIME=[C3E60980:01C46FF5] X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6ME65H1026846 1. You can continue a TS calculation with "opt=(ts,readfc) geom=check"; if you think the force constants are inaccurate you can use "opt=(ts,calcfc) geom=check" instead. 2. I don't know this myself, but the question of how to add explicit hydrogens to a heavy-atom-only structure comes up a lot on this list, so I'm sure you'll get a useful asnwer from someone. --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request=at=ccl.net]On Behalf Of Stanislav.Ivan=at=unibas.ch Sent: Wednesday, July 21, 2004 5:56 AM To: chemistry=at=ccl.net Subject: CCL:2 questions Dear ccl'ers, I have 2 questions regarding g03: 1. is it possible to restart previous TS calculation ? 2. how to define explicit (hydrogen) atoms in g03 ? Thank you. -- Stanislav Ivan Universitdt Basel Departement Chemie St.Johanns-Ring 19 4056 Basel Switzerland Tel.: (+41) (61) 267 11 44 Email: stanislav.ivan=at=unibas.ch ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow=at=nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Jul 22 01:41:34 2004 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6M6fXZf007562 for ; Thu, 22 Jul 2004 01:41:33 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0I1800L68QWBC3=at=mailserver.unimi.it> for chemistry=at=ccl.net; Thu, 22 Jul 2004 08:48:11 +0200 (MEST) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0I1800BQSQW9ZJ=at=smtp.unimi.it> for chemistry=at=ccl.net; Thu, 22 Jul 2004 08:48:10 +0200 (MEST) Date: Thu, 22 Jul 2004 09:00:53 +0200 From: Alessandro Contini Subject: Re: CCL:2 questions In-reply-to: <1090403743.40fe3d9fd4cf3=at=webmail.unibas.ch> To: Stanislav.Ivan=at=unibas.ch Cc: chemistry=at=ccl.net Reply-to: alessandro.contini=at=unimi.it Message-id: <200407220900.53593.alessandro.contini=at=unimi.it> Organization: =?iso-8859-1?q?Universit=E0=20di?= Milano MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.4 References: <1090403743.40fe3d9fd4cf3=at=webmail.unibas.ch> X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6M6fYZf007568 Dear Ivan, yes, TS calculations can be restarted with the opt=(ts,restart) keyword. It could be a good idea using opt=(ts,restart,noeigentest,rcfc) set of keywords in order to avoid the interruption of the calculation whenever more than one negative eigenvalue are found. For the point 2 do you mean expliciting H in SCRF calculations? if yes you could use scrf=(pcm,read) and put radii=model (wher model could be uff, bondi, pauling, etc.) at the end of molecule specifications. Hope this help, reguards Alessandro Alle 11:55, mercoledl 21 luglio 2004, Stanislav.Ivan=at=unibas.ch ha scritto: > Dear ccl'ers, > I have 2 questions regarding g03: > 1. is it possible to restart previous TS calculation ? > 2. how to define explicit (hydrogen) atoms in g03 ? > > Thank you. > > > -- > Stanislav Ivan > Universitdt Basel > Departement Chemie > St.Johanns-Ring 19 > 4056 Basel > Switzerland > > Tel.: (+41) (61) 267 11 44 > Email: stanislav.ivan=at=unibas.ch > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow=at=nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini=at=unimi.it From chemistry-request@ccl.net Thu Jul 22 14:13:30 2004 Received: from atlas.pnl.gov (atlas.pnl.gov [130.20.248.194]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6MJDMVl006905 for ; Thu, 22 Jul 2004 14:13:22 -0500 Received: from emailfilter2.pnl.gov (emailfilter2.pnl.gov [130.20.248.24]) by pnl.gov (PMDF V6.2-X17 #30796) with ESMTP id <0I1900B5FPPE9I/at/pnl.gov> for chemistry/at/ccl.net; Thu, 22 Jul 2004 12:20:02 -0700 (PDT) Received: from pnlmse22.pnl.gov (Not Verified[130.20.128.58]) by emailfilter2.pnl.gov with NetIQ MailMarshal (v5.5.6.6) id ; Thu, 22 Jul 2004 12:20:02 -0700 Received: from pnlmse24.pnl.gov ([130.20.128.29]) by pnlmse22.pnl.gov with Microsoft SMTPSVC(5.0.2195.6713); Thu, 22 Jul 2004 12:20:01 -0700 Date: Thu, 22 Jul 2004 12:20:01 -0700 From: "Black, Gary D" Subject: CCL:Extensible Computational Chemistry Environment To: chemistry/at/ccl.net Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.5.6944.0 Content-type: multipart/alternative; boundary="----_=_NextPart_001_01C47020.E2B349C1" Thread-Topic: CCL:Extensible Computational Chemistry Environment Thread-Index: AcRwIOKiLRJ3mZ99TpeQHVdMEOPo0w== Content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 22 Jul 2004 19:20:01.0796 (UTC) FILETIME=[E2B47C40:01C47020] X-Spam-Status: No, hits=5.1 required=7.5 tests=HTML_20_30,HTML_FONTCOLOR_BLUE, HTML_MESSAGE,IMPRONONCABLE_1,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C47020.E2B349C1 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Colleagues, The Extensible Computational Chemistry Environment, ECCE (pronounced etch-ay), is a freely available suite of graphical user interface applications with underlying data management support. Many features for setup, submission, monitoring, and visualization of output from NWChem (http://www.emsl.pnl.gov/docs/nwchem), Gaussian 03, Gaussian 98, and Amica (http://gdanitz.hec.utah.edu/amica) electronic structure calculations are available. ECCE was first released in 1997 as a core component of the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory. The ECCE project team of computer scientists and computational chemists continue to provide new functionality and operational support. Version 3.2.1 of ECCE has recently been released and runs on Linux platforms with Intel Pentium and Itanium compatible processors, SGI workstations, and Sun workstations. Distributions of both the full ECCE software suite and just the three-dimensional direct manipulation Molecule Builder are available. New computational codes and features of existing codes not currently supported can be integrated into Ecce by users through a code registration capability. This is the first time ECCE has been widely announced to the computational chemistry community beyond NWChem users and EMSL collaborators. More information about ECCE is available at our website, http://ecce.emsl.pnl.gov. Instructions for registering to download the free software are found at http://ecce.emsl.pnl.gov/using/download.shtml. You may subscribe to an email list for new ECCE release announcements at http://ecce.emsl.pnl.gov/support/mailing_list.shtml. Please send any questions to our support address, ecce-support/at/emsl.pnl.gov. Gary Black ECCE project lead, on behalf of the ECCE team ------_=_NextPart_001_01C47020.E2B349C1 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable CCL:Extensible Computational Chemistry Environment

Dear Colleagues,

The Extensible Computational Chemistry = Environment, ECCE (pronounced etch-ay), is a freely available suite of = graphical user interface applications with underlying data management = support. Many features for setup, submission, monitoring, and = visualization of output from NWChem (http://www.emsl.pnl.gov/docs/nwchem), Gaussian 03, Gaussian 98, and Amica = (http://gdanitz.hec.utah.edu/amica) electronic structure calculations are = available.  ECCE was first released in 1997 as a core component of = the Environmental Molecular Sciences Laboratory (EMSL) at Pacific = Northwest National Laboratory.  The ECCE project team of computer = scientists and computational chemists continue to provide new = functionality and operational support.  Version 3.2.1 of ECCE has = recently been released and runs on Linux platforms with Intel Pentium = and Itanium compatible processors, SGI workstations, and Sun = workstations.  Distributions of both the full ECCE software suite = and just the three-dimensional direct manipulation Molecule Builder are = available.  New computational codes and features of existing codes = not currently supported can be integrated into Ecce by users through a = code registration capability.

This is the first time ECCE has been = widely announced to the computational chemistry community beyond NWChem = users and EMSL collaborators.  More information about ECCE is = available at our website, http://ecce.emsl.pnl.gov.  Instructions for registering to = download the free software are found at http://ecce.emsl.pnl.gov/using/download.shtml.  You may subscribe to an email list for = new ECCE release announcements at http://ecce.emsl.pnl.gov/support/mailing_list.shtml= .  Please send any questions to our = support address, ecce-support/at/emsl.pnl.gov.

Gary Black
ECCE project lead, on behalf of the = ECCE team

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