From chemistry-request@ccl.net Sun Jun 6 21:11:17 2004 Received: from qcmm9 ([202.103.38.171]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i572B5o7000707 for ; Sun, 6 Jun 2004 21:11:12 -0500 Received: from 163.com (qcmm9 [10.10.1.9]) by qcmm9 (8.12.8/8.12.8) with ESMTP id i572CaG5031647 for ; Mon, 7 Jun 2004 10:12:46 +0800 Message-ID: <40C3CF14.9040409(at)163.com> Date: Mon, 07 Jun 2004 10:12:36 +0800 From: scopio User-Agent: Mozilla/5.0 (X11; U; Linux i686; zh-CN; rv:1.2.1) Gecko/20030225 X-Accept-Language: zh-cn,zh MIME-Version: 1.0 To: chemistry(at)ccl.net Subject: how to get mulliken charges of Fe by G03? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=5.0 required=7.5 tests=DNS_FROM_RFCI_DSN,NO_RDNS2, WORKSTATION_NAME 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 all: I got GetVDW error when I tried to do 'pop=mk' calculation by g03. I don't know how to resovle this problem and hope anyone who knows it can help me. Thanks in advance! Here is the input file. -------------- # HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt Title Card Required 2 1 Fe 0.0 0.0 0.0 ============== The error msg are as below: -------------- Atom Element Radius 1 26 0.00 GetVDW: no radius for atom 1 atomic number 26. Error termination via Lnk1e in /usr/local/g03/l602.exe at Mon Jun 7 09:39:17 2004. ============== Any help would be very appreciated! Regards! Liu From chemistry-request@ccl.net Mon Jun 7 03:14:24 2004 Received: from sainfoin.extra.cea.fr (sainfoin.extra.cea.fr [132.166.172.103]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i578EMt3020857 for ; Mon, 7 Jun 2004 03:14:23 -0500 Received: from araneus.saclay.cea.fr (araneus.saclay.cea.fr [132.166.192.110]) by sainfoin.extra.cea.fr (8.12.10/CEAnet-Internet.3.0) with ESMTP id i578I7be007214 for ; Mon, 7 Jun 2004 10:18:07 +0200 (MEST) Received: from nenuphar.saclay.cea.fr (unverified) by araneus.saclay.cea.fr (Content Technologies SMTPRS 4.3.12) with ESMTP id ; Mon, 7 Jun 2004 10:18:07 +0200 Received: from llb.saclay.cea.fr (llb.saclay.cea.fr [132.166.17.100]) by nenuphar.saclay.cea.fr (8.12.10/CEAnet-Internes.3.0) with ESMTP id i578I7f2004474; Mon, 7 Jun 2004 10:18:07 +0200 (MEST) Received: from [132.166.18.212] (mac212 [132.166.18.212]) by llb.saclay.cea.fr (8.12.10/jtpda-5.3.2) with ESMTP id i578HdvQ009480 ; Mon, 7 Jun 2004 10:18:05 +0200 (MEST) In-Reply-To: <43165.130.36.62.126.1086349577.squirrel$at$www.TheWorld.com> References: <43165.130.36.62.126.1086349577.squirrel$at$www.TheWorld.com> Mime-Version: 1.0 (Apple Message framework v618) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: 7bit Cc: chemistry$at$ccl.net From: hinsen$at$cnrs-orleans.fr Subject: Re: CCL:Why program in Java? Date: Sat, 5 Jun 2004 14:20:07 +0200 To: jle$at$theworld.com X-Mailer: Apple Mail (2.618) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 04.06.2004, at 13:46, jle$at$theworld.com wrote: > Folks, I would appreciate pointers to any article/book discussing > the pros and cons of programming in Java. Either with regards to > other interpreted languages such as Python/Perl, or with regards > to compiled languages such as C/C++. Truly comparative articles > I'd put Java into the "compiled languages" category, as native code compilers are available, and JIT byte code compilation is getting close to native in speed as well, though not necessarily for numeric applications (probable just because the JIT compilers are not made for that). Perhaps the best summary description of Java is "C++ cleaned up". The only aspect in which Java is quiet different from C and C++ is memory management, which is fully automatic (with garbage collection) in Java. The Python Web site (www.python.org) has pointers to articles that compare Python to other languages, including Java and Perl. Beyond all the more or less objective comparisons, there is one aspect that is rarely mentioned: you should pick a language that suits your way of working and thinking. Just like some people prefer geometry and others algebra for attacking the same problem, some programmers get better results with one langugae and others with another one. I am still waiting for the first personality tests that include programming preferences. -- ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen$at$llb.saclay.cea.fr ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Mon Jun 7 09:39:29 2004 Received: from hermes1.cf.ac.uk (hermes1.cf.ac.uk [131.251.0.112]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i57Ed8t3013066 for >ccl.net>; Mon, 7 Jun 2004 09:39:18 -0500 Received: from thor.cf.ac.uk ([131.251.0.1]) by hermes1.cf.ac.uk with esmtp (Exim 4.34) id 1BXLKq-0001Ce-20; Mon, 07 Jun 2004 15:42:48 +0100 Received: from localhost (sacjap@localhost) by thor.cf.ac.uk (8.8.8/8.6.12) with ESMTP id PAA18432; Mon, 7 Jun 2004 15:42:43 +0100 (BST) Date: Mon, 7 Jun 2004 15:42:42 +0100 (BST) From: Jamie Platts >Cardiff.ac.uk> X-X-Sender: sacjap@thor To: "Zottola, Mark (Cont,ARL/CISD)" >arl.army.mil> cc: CHEMISTRY<>ccl.net Subject: Re: CCL:Use of AIM in Examining Transition States In-Reply-To: <3DEB727CED850444BC67A65ECB26796AE8AFB1<>ARLABML01.DS.ARL.ARMY.MIL> Message-ID: References: <3DEB727CED850444BC67A65ECB26796AE8AFB1<>ARLABML01.DS.ARL.ARMY.MIL> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 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 Hi Mark - Good question, to which my answer would be yes, but only up to a point. Most of Bader et al's ideas can be applied to any electron distribution, whether at a stationary point or not. Thus, it is possible to define a basin which obeys the zero-flux condition, and associated interatomic surfaces at any point on the PES. Having done this, one can generate the usual atomic charges, multipoles etc. Critical points are similar, and are generally conserved at small changes away from equilbrium. There are two main caveats to this statement. Firstly, calculation of an atomic energy in Bader's scheme is only valid at a stationary point on the PES, since it assumes there are no (Hellman-Feynman) forces on nuclei. Clearly, this is fine for a true TS or other saddle point. Second, the identification of an atomic interaction line with associated (3,-1) critical point with a bond is only strictly valid at equilibrium. So at a TS, the presence of a (3,-1) cp is not enough to state that two atoms are bonded, but only that they're interacting. An example of applying AIM to transition states is our old paper: J. Phys. Chem., 1996, 100, 13455. Please note that I'm not claiming this to be the first or the best, just the one for which I have the reference to hand . Hope this helps, Jamie ---------------------------------------------------------- Jamie Platts Dept. of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts<>cf.ac.uk P.O. Box 912 FAX: +44 (0) 2920 874030 Cardiff CF10 3TB www.cf.ac.uk/chemy > Can AIM be used to evaluate bonding in a transition state structure? > After reading Bader's web site, he often refers to equilibrium > structures. Yet it seems that there is no apparent prohibition against > employing AIM to studying transition states. Since AIM is based on a > physical observable and a TS is not a physical observable is it still > valid to apply AIM analysis to a transition state? > > Thanks! > > Mark > ************************************************ > Dr. Mark A. Zottola > Army Research Laboratory > Aberdeen Proving Grounds > PB #134 939-I Beards Hill Road > Aberdeen, MD 21001 > Voice: 410 278 7250 FAX: 410 297 9521 > Email: mzottola<>arl.army.mil > > > From chemistry-request@ccl.net Mon Jun 7 02:03:04 2004 Received: from ozone.cs.vu.nl (ozone-student1.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i57733t3015965 for ; Mon, 7 Jun 2004 02:03:03 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #91) id m1BXEDc-00001YC; Mon, 7 Jun 2004 09:06 +0200 Message-ID: <40C0A102.6020207*at*chem.vu.nl> Date: Fri, 04 Jun 2004 18:19:14 +0200 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Karin Gutkowski CC: chemistry*at*ccl.net Subject: Re: CCL:universal L-J parameters" References: <40B5B4FB.18277.241F22@localhost> In-Reply-To: <40B5B4FB.18277.241F22@localhost> 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 Karin Gutkowski wrote: > I would like to ask you for help for the following issue: > > I need to use Lenanrd jones molecular parameters (sigma and e/k) in > order to adjust my program to the Henry constant, for systems with > the following molecules: > methane > carbon dioxide > CO > N2 > O2 > CH3OH > C2H5OH > > I found already some values for the LJ parameters, but they vary a > lot depending on the reference. So I would like to have the whole > information from only one source. Unfortunately, LJ params are always a property of the atom *pair* under consideration, which in turn is influenced by the molecules in your system. In practice, however, you may get away with fewer parameters, and/or use combination rules. Try any of the biomolecular forcefields (Gromos, OPLS, Charmm, Amber), they will have at least many molecules and building blocks similar to those you list. The Gromos and OPLS ff's are implemented in Gromacs, which I use a lot so I know the website: www.gromacs.org (and it's free). Beware that some ff's will list parameters in c6/c12 in stead of sigma/epsilon. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra*at*chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Mon Jun 7 08:13:02 2004 Received: from up.univ-mrs.fr (mailup.univ-mrs.fr [147.94.113.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i57DD0t3007544 for ; Mon, 7 Jun 2004 08:13:01 -0500 Received: from localhost (localhost [127.0.0.1]) by up.univ-mrs.fr (Postfix) with ESMTP id 84AAC2083B5 for ; Mon, 7 Jun 2004 15:13:53 +0200 (CEST) Received: from up.univ-mrs.fr ([127.0.0.1]) by localhost (mailup.univ-mrs.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 183012-08 for ; Mon, 7 Jun 2004 15:13:48 +0200 (CEST) Received: from up.univ-mrs.fr (unknown [147.94.185.160]) by up.univ-mrs.fr (Postfix) with ESMTP id 992BF1E0842 for ; Mon, 7 Jun 2004 15:13:26 +0200 (CEST) Message-ID: <40C46A49.5090003^at^up.univ-mrs.fr> Date: Mon, 07 Jun 2004 15:14:49 +0200 From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Organization: LCTMM User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr-FR; rv:1.6) Gecko/20040113 X-Accept-Language: fr-fr, en-us, en MIME-Version: 1.0 To: CCL posting Subject: Spin corrected single-determinant wave functions, energies and gradients Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new at up.univ-mrs.fr X-Spam-Status: No, hits=4.0 required=7.5 tests=NO_RDNS,NO_RDNS2,RM_ft_Iso8859 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, I am looking for a program able to compute a reaction path, or at least geometry optimizations, using spin corrected single-determinant wavefunction (HF, MP, CC ...), energies and gradients when large spin contamination occurs. I am aware of the spin projection techniques, a priori or a posteriori, the later being implemented e.g. in gaussian but I don't believe gradients are coded in (I think a population analysis can be done using a spin projected wfn). Because the systems I want to study are of medium size to large size, I cannot really consider multi-reference methods (unfortunately). By the way, Chen and Schlegel published in 96 that projected dft is even worse than unrestricted dft. Is there any alternative technique for using dft when large spin contamination occurs (yes, even at the dft level) ? Or should I, in any case, use a non hybrid functional ? Best regards, -- Dr. Nicolas Ferre' Laboratoire de Chimie Theorique et de Modelisation Moleculaire UMR 6517 - CNRS Universite' de Provence Case 521 - Faculte' de Saint-Jerome Av. Esc. Normandie Niemen 13397 MARSEILLE Cedex 20 (FRANCE) Tel : (+33)4.91.28.27.33 Fax : (+33)4.91.28.87.58 From chemistry-request@ccl.net Mon Jun 7 08:45:16 2004 Received: from mail.MATERIANOVA.BE (mn-vpn.materianova.be [193.190.132.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i57DjEt3009626 for ; Mon, 7 Jun 2004 08:45:15 -0500 Received: from mn-europe.MATERIANOVA.BE ([10.108.200.13]) by mail.MATERIANOVA.BE with Microsoft SMTPSVC(5.0.2195.6713); Mon, 7 Jun 2004 15:48:12 +0200 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: Hammett constants X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 Date: Mon, 7 Jun 2004 15:48:12 +0200 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Hammett constants Thread-Index: AcRMlhI4WESkzGLvSkeIt/4AOX94vA== From: "Igor Avilov" To: X-OriginalArrivalTime: 07 Jun 2004 13:48:12.0431 (UTC) FILETIME=[1335B9F0:01C44C96] X-Spam-Status: No, hits=3.9 required=7.5 tests=MY_BAD_DOT,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 i57DjGt3009637 Dear colleagues, Recently I started to analyze the effect of different electron-withdrawing/electro-donating groups on the triplet energy of the phosphorescent metal-organic compounds. I'm doing this at the DFT level (there is quite good correlation with the available experimental data). Now I'm trying to rationalize my results. As far as I noticed, experimental chemists often utilize the concept of Hammett constant to explain the effect of the substituents on the spectral properties of the compounds of interest. Could you suggest the good literature (review?) on the subject? The cases where the values of Hammett constants do not correlate well with the experimental spectral data would be of particular interest. Best regards, Igor Avilov. From chemistry-request@ccl.net Mon Jun 7 05:43:41 2004 Received: from smtp.gamma.ocn.ne.jp (gamma.ocn.ne.jp [222.146.40.135]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i57Ahet3030713 for ; Mon, 7 Jun 2004 05:43:40 -0500 Received: from tomoko (p6217-ipad03kyoto.kyoto.ocn.ne.jp [61.214.56.217]) by smtp.gamma.ocn.ne.jp (Postfix) with ESMTP id 6025F1389 for ; Mon, 7 Jun 2004 19:47:29 +0900 (JST) From: "tomoko niwa" To: Subject: The hydrophocities for 20 amino acids Date: Mon, 7 Jun 2004 19:47:14 +0900 Message-ID: <000001c44c7c$cef8e410$030ba8c0@tomoko> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 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 We have defined hydrophobic parameters for 20 amino acids by using experimentally determined octanol/water partition coefficients of peptides by Dr. Akamatsu and co-workers. Our parameters have been shown to work well in analyzing biological activities of peptides and protein stabilities and characterizing ligand binding sites of proteins. Reprints are available on request. Sotomatsu-Niwa, Tomoko; Ogino, Akio, Evaluation of the hydrophobic parameters of the amino acid side chains of peptides and their application in QSAR and conformational studies, THEOCHEM (1997), 392, 43-54. Niwa, Sotomatsu Tomoko; Ogino, Akio, Multiple regression analysis of the beta-sheet propensity of amino acids, THEOCHEM (1997), 419, 155-160. Regards, Tomoko At 11:46 AM 5/19/2004 -0400, Baoqiang Cao wrote: >Dear CCL members, > >I need the experimental results of the hydrophobicities for 20 amino >acids, could you please show me how I can get them? Any tips will be >welcome! > >Best, > Cao > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Tomoko Niwa, Ph.D. Discovery Research Lab. Nippon Shinyaku Co., Ltd. 14, Nishinosho-Monguchi-cho, Kisshoin, Minami-ku Kyoto, 601-8550 Japan tel +81-75-321-9171, fax +81-75-321-9038 t.niwa!at!po.nippon-shinyaku.co.jp =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Mon Jun 7 02:44:57 2004 Received: from qcmm9 ([202.103.38.171]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i577htt3018527 for ; Mon, 7 Jun 2004 02:44:37 -0500 Received: from 163.com (qcmm9 [10.10.1.9]) by qcmm9 (8.12.8/8.12.8) with ESMTP id i577jPG5001119; Mon, 7 Jun 2004 15:45:25 +0800 Message-ID: <40C41D15.4010302..at..163.com> Date: Mon, 07 Jun 2004 15:45:25 +0800 From: scopio User-Agent: Mozilla/5.0 (X11; U; Linux i686; zh-CN; rv:1.2.1) Gecko/20030225 X-Accept-Language: zh-cn,zh MIME-Version: 1.0 To: Angelo Favia , chemistry..at..ccl.net Subject: Re: CCL:how to get mulliken charges of Fe by G03? References: <40C3CF14.9040409..at..163.com> <002e01c44c61$7c1b7750$c6b3ccc1..at..farmacia.uniba.it> In-Reply-To: <002e01c44c61$7c1b7750$c6b3ccc1..at..farmacia.uniba.it> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=5.0 required=7.5 tests=DNS_FROM_RFCI_DSN,NO_RDNS2, WORKSTATION_NAME 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 Favia: Thank you very much for your response! I completely agree with that. But I don't know how to assign vdw radius to Fe. Could you please give me an example or a reference explaining it? Thanks a lot! Best! Liu Angelo Favia wrote: >I believe that you must specify the Fe radius at the end of the input file >in gaussian.... >that's it. > >bye > >angy > > > >>Dear all: >> >>I got GetVDW error when I tried to do 'pop=mk' calculation by g03. I >>don't know how to resovle this problem and hope anyone who knows it can >>help me. Thanks in advance! >> >>Here is the input file. >>-------------- >># HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt >> >> >>Title Card Required >> >> >>2 1 >>Fe 0.0 0.0 0.0 >>============== >> >>The error msg are as below: >>-------------- >>Atom Element Radius >> 1 26 0.00 >> GetVDW: no radius for atom 1 atomic number 26. >> Error termination via Lnk1e in /usr/local/g03/l602.exe at Mon Jun 7 >>09:39:17 2004. >>============== >> >>Any help would be very appreciated! >> >>Regards! >> >>Liu >> >> >> >>-= 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 Mon Jun 7 04:19:38 2004 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i579Jat3024836 for >ccl.net>; Mon, 7 Jun 2004 04:19:37 -0500 Received: from ac12.sci.kun.nl [131.174.179.19] (helo=ac12.sci.kun.nl) by wn1.sci.kun.nl (8.12.10/3.67) with ESMTP id i579NN1O014081; Mon, 7 Jun 2004 11:23:23 +0200 (MEST) From: "E.L. Willighagen" >sci.kun.nl> Reply-To: egonw<>sci.kun.nl To: hinsen<>cnrs-orleans.fr, jle<>theworld.com Subject: Re: CCL:Why program in Java? Date: Mon, 7 Jun 2004 11:23:21 +0200 User-Agent: KMail/1.5.4 Cc: chemistry<>ccl.net References: <43165.130.36.62.126.1086349577.squirrel<>www.TheWorld.com> >cnrs-orleans.fr> In-Reply-To: >cnrs-orleans.fr> MIME-Version: 1.0 Content-Type: Text/Plain; charset="iso-8859-1" Content-Description: clearsigned data Content-Disposition: inline Message-Id: <200406071123.22950.egonw<>sci.kun.nl> 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 i579Jct3024840 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Saturday 05 June 2004 14:20, hinsen<>cnrs-orleans.fr wrote: > On 04.06.2004, at 13:46, jle<>theworld.com wrote: > Beyond all the more or less objective comparisons, there is one aspect > that is rarely mentioned: you should pick a language that suits your > way of working and thinking. Just like some people prefer geometry and > others algebra for attacking the same problem, some programmers get > better results with one langugae and others with another one. That's indeed an important point... I've spent too many hours finding bugs in C/C++ code dealing with memory issues, which sometimes where even caused by compiler differences... While this is likely no problem when working a lot in C++, in Java I never had such problems... Egon - -- egonw<>sci.kun.nl PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAxDQJd9R8I9Yza6YRAoJoAJ9zZFlSPP1DyqE+rEF1T/jTeJJdWQCgoDjs 62bSFWSh6V0YJa7kSx657wc= =0vec -----END PGP SIGNATURE----- From chemistry-request@ccl.net Mon Jun 7 07:00:28 2004 Received: from marilyn.uochb.cas.cz (marilyn.uochb.cas.cz [147.231.120.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i57C0Qt3002427 for ; Mon, 7 Jun 2004 07:00:26 -0500 Received: from localhost (iveta.uochb.cas.cz [147.231.129.170]) by marilyn.uochb.cas.cz (8.11.6/8.11.6) with ESMTP id i57C4EJ26663 for ; Mon, 7 Jun 2004 14:04:15 +0200 Received: from svozil by localhost with local (Exim 3.35 #1 (Debian)) id 1BXIrH-0003R3-00 for ; Mon, 07 Jun 2004 14:04:07 +0200 Date: Mon, 7 Jun 2004 14:04:07 +0200 To: chemistry=at=ccl.net Subject: G03 frequency calculation error Message-ID: <20040607120407.GA13182=at=iveta.uochb.cas.cz> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.28i From: Daniel Svozil 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 all, when I try to calculate MP2/aug-cc-pvdz frequencies of thymine (15 atoms, 9 heavy atoms, 6 hydrogens, 281 basis functions) at 32-bit machine the job finishes soon after the beginnig of the frequency calculation with this error message: Error termination in NtrErr: NtrErr Called from FileIO. and a few lines above is the following message: End of Minotr Frequency-dependent properties file 721 does not exist. MDV= 104857600. Form MO integral derivatives with frozen-active canonical formalism. Discarding MO integrals. Reordered first order wavefunction length = 133955712 Warning! MaxDisk= 1572864000 but minimum for overlay 11= 1693729261.. WUsed= 115192717 WInt= 1512480 WEnd= 1093267456 Dk804= 503348736. Dk1111= 0. Dk1112= 1577024064. MaxDsk= 1572864000 LAFull= 133955712 DskLim= 1572864000. NUsed= -620931003. 2511644491. 1757983297. 1602696451. 1332289343. 1152017937. In DefCFB: NBatch= 1, ICI= 33, ICA=248, LFMax= 23 Large arrays: LIAPS= 0, LIARS= 496744248 words. Illegal file or unit passed to FileIO. FileIO: IOper=1 IFilNo(1)=0 Len=899300 IPos=0 Q=1347875000 I am using rwf directive to use more large scratch files: %rwf=s1/a,2000MB,s1/b,2000MB,s1/c,2000MB,s1/d,2000MB,s1/e,2000MB,s1/f,2000MB,s1/g,- I played with MaxDisk directive, but without success. I am sure it has something to do with the disk limits, I managed to run the same job on 64-bit machine (which is unfortunately not available to me anymore) without any problems. Did somebody encounter this problem on 32-bit architecture as well? Is it possible to run such a frequency calculation without crashing and how to do that? Thanks in advance Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry and Center for Complex Molecular Systems and Biomolecules http://www.molecular.cz/ Czech Republic phone: +420-220 410 313 From chemistry-request@ccl.net Mon Jun 7 10:16:33 2004 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i57FGWt3015978 for ; Mon, 7 Jun 2004 10:16:32 -0500 Importance: Normal X-Priority: 3 (Normal) Expiry-Date: Tue, 31 Aug 2004 -1:-1:-1 +0000 Reply-To: training.-at-.accelrys.com To: CHEMISTRY.-at-.ccl.net Cc: Judith Madeley Subject: CCL: Accelrys Customer Training in August MIME-Version: 1.0 Sensitivity: X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 Message-ID: From: Jeff Nauss Date: Mon, 7 Jun 2004 08:20:22 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.3|September 18, 2003) at 06/07/2004 08:20:23, Serialize complete at 06/07/2004 08:20:23 Content-Type: text/plain; charset="US-ASCII" 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 Accelrys will be holding the following training workshops during AUGUST 2004. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $520 per day for government and $380 per day for academic. MOLECULAR MODELING Introduction to InsightII for Life Sciences 17-18 August in San Diego, CA Homology-Based Protein Design 19-20 August in San Diego, CA Structure-Based Drug Design with InsightII 23-24 August in San Diego, CA CHARMm 25-26 August in San Diego, CA Modeling of GPCR Proteins with InsightII 27 August in San Diego, CA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html and http://www.accelrys.com/training/rdd/schedule.html Rational Drug Design Introduction to Cerius2 for Life Sciences 3-4 August in San Diego, CA Small Molecular and Drug Design with Cerius2 5-6 August in San Diego, CA Library Design and Analysis 9-10 August in San Diego, CA Pharmacophore Generation with Catalyst 11-12 August in San Diego, CA For course details and registration see: http://www.accelrys.com/training/rdd/schedule.html -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 9685 Scranton Road San Diego, CA 92121-1761 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss.-at-.accelrys.com http://www.accelrys.com/training From chemistry-request@ccl.net Mon Jun 7 18:04:58 2004 Received: from web50401.mail.yahoo.com (web50401.mail.yahoo.com [206.190.38.66]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i57N4uSB013919 for ; Mon, 7 Jun 2004 18:04:56 -0500 Message-ID: <20040607230838.13804.qmail~at~web50401.mail.yahoo.com> Received: from [200.55.139.213] by web50401.mail.yahoo.com via HTTP; Mon, 07 Jun 2004 18:08:38 CDT Date: Mon, 7 Jun 2004 18:08:38 -0500 (CDT) From: =?iso-8859-1?q?Reynier=20Suardiaz=20del=20Rio?= Subject: CCL: looking for a software to calculate angles of lateral chain in proteins To: chemistry~at~ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-528057574-1086649718=:12301" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.4 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, RM_ft_Iso8859,RM_fw_FromIsPhras2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-528057574-1086649718=:12301 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers' I need a program that calculate automatically the angles of the lateral chain of a protein, given an especific aminoacid or something like that, i know a lot of softwares in which those angles can be obtained clicking on the four atoms that form the torsion angle but i don't know any that automatically do that. I will apreciate any help Best RSR --------------------------------- Do You Yahoo!? Yahoo! Net: La mejor conexisn a internet y 25MB extra a tu correo por $100 al mes. --0-528057574-1086649718=:12301 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear CCLers'
 I need a program that calculate automatically the angles of the lateral chain of a protein, given an especific
aminoacid or something like that, i know a lot of softwares in which those angles can be obtained clicking on the four atoms
that form the torsion angle but i don't know any that automatically do that.
I will apreciate any help
 Best
 
 RSR


Do You Yahoo!?
Yahoo! Net: La mejor conexisn a internet y 25MB extra a tu correo por $100 al mes.
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