From chemistry-request@server.ccl.net Wed Apr 9 23:19:49 2003 Received: from marcy.nas.nasa.gov ([129.99.113.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3A3Jnb23912 for ; Wed, 9 Apr 2003 23:19:49 -0400 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.6+Sun/8.11.6/NAS 8.11.6-5n) with ESMTP id h3A3Jmj16875 for ; Wed, 9 Apr 2003 20:19:48 -0700 (PDT) Date: Wed, 9 Apr 2003 20:19:48 -0700 (PDT) From: Ioana Cozmuta To: Computational Chemistry List Subject: question about DNA Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCL users, I've run Molecular Dynamics for a single stranded nucleic acid homopolymer in water with the initial configuration being helical and the final sort of bulky. I was thinking that a way to characterize the "distortion" is to follow during the dynamics the values of the minor/major grooves and also the helicity. I have two questions: 1. Between which atoms exactly one should measure the minor/major grooves 2. What is the best way to calculate the helicity of a strand? Any advice on this matter would be appreciated. Thanks in advance, Ioana From chemistry-request@server.ccl.net Wed Apr 9 23:48:12 2003 Received: from smtp4.server.rpi.edu ([128.113.2.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3A3mCb25062 for ; Wed, 9 Apr 2003 23:48:12 -0400 Received: from rpi.edu (vpn-764.nss.rpi.edu [128.113.211.14]) by smtp4.server.rpi.edu (8.12.9/8.12.7) with ESMTP id h3A3mAtZ001258; Wed, 9 Apr 2003 23:48:10 -0400 Message-ID: <3E94E962.F693B971@rpi.edu> Date: Wed, 09 Apr 2003 23:47:47 -0400 From: "Curt M. Breneman" X-Mailer: Mozilla 4.8 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, qsar_society@accelrys.com Subject: CCG Excellence Award Application Deadline - April 14th, 2003 for New York ACS Meeting: (Second Notice) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.28 Dear Computational Chemistry graduate students and advisors: Applications for CCG Excellence Awards are due April 14th, 2003 for the New York ACS National Meeting! Application for these awards is a two-step process. First, an application for the Award must be submitted to the Treasurer of the COMP division for consideration. The application consists of an extended (2-page) abstract of the poster or presentation along with a letter of support from the research advisor, a two page CV, and a personal statement. Secondly, an abstract of a poster or oral presentation in the COMP program must be submitted through the ACS OASYS system for online submissions prior to the deadline for the meeting at which the awards will be presented (New York, in this case). Awardees are chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students are encouraged to submit applications for the Awards. Students from the same research group are encouraged to apply. Students from research groups that have won awards at previous ACS meetings are also encouraged to submit applications. Awards will be given only to those individuals making presentations, and not co-authors. For questions, contact: Prof. Curt M. Breneman; Treasurer, ACS COMP Division; RPI Department of Chemistry; 110 8th St.; Troy, NY 12180 To see photos and details of previous winners, see: http://membership.acs.org/C/COMP/CCG/ccg.html#winners From chemistry-request@server.ccl.net Wed Apr 9 23:47:16 2003 Received: from smtp4.server.rpi.edu ([128.113.2.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3A3lGb24993 for ; Wed, 9 Apr 2003 23:47:16 -0400 Received: from rpi.edu (vpn-764.nss.rpi.edu [128.113.211.14]) by smtp4.server.rpi.edu (8.12.9/8.12.7) with ESMTP id h3A3lEtZ001197; Wed, 9 Apr 2003 23:47:14 -0400 Message-ID: <3E94E92A.CB7C2AD1@rpi.edu> Date: Wed, 09 Apr 2003 23:46:51 -0400 From: "Curt M. Breneman" X-Mailer: Mozilla 4.8 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, qsar_society@accelrys.com Subject: Emerging Technology Symposium Competition - Deadline: April 14th. (Second Notice) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.28 Dear Computational Chemists and friends, This message is to remind everyone that the fourth annual Emerging Technology Symposium will take place at the New York ACS National Meeting this Fall. This COMP Division symposium is sponsored by Schrodinger, Inc who generously provides a $1,000 prize for the best presentation of the afternoon as determined by a panel of experts. Here's a copy of the announcement that's on the COMP Division website (http://membership.acs.org/C/COMP): ================= The Computers in Chemistry Division (COMP) of the ACS expects to hold the fourth annual Symposium on Emerging Technologies in ComputationalChemistry at the American Chemical Society National Meeting, New York City, USA, September 7-11, 2003. The objective of the symposium is to stimulate, reward, and publicize methodological advances in computational chemistry. The talks will be evaluated by a Panel of Experts based on the impact the research will have on the future of computational chemistry and allied sciences. The symposium will be ideal for presenting your latest and best research on new techniques and software development. Schrodinger, Inc., will again sponsor a $1000 prize for the best talk at the symposium. All are invited to participate. To participate, it is necessary to submit a regular short ACS abstract via http://oasys.acs.org/. It is also necessary to email a long (1000-word, text-only) abstract to the new organizer (Curt M. Breneman) by April 14, 2003. The talks must be original and not be repeats of talks at other ACS symposia. The long abstracts will be evaluated, and those individuals selected for an oral presentation at the symposium will be notified by the end of April. Applications for the Emerging Technologies Symposium that cannot be accepted will be rescheduled in one of the other COMP sessions at the meeting. Inquiries should sent to: Prof. Curt M. Breneman Department of Chemistry Rensselaer Polytechnic Institute Troy, NY 12180 E-mail: brenec@rpi.edu ====================================== See you in the Big Apple! Curt Breneman RPI Chemistry From chemistry-request@server.ccl.net Wed Apr 9 21:32:01 2003 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3A1W0b20625 for ; Wed, 9 Apr 2003 21:32:01 -0400 Received: from silicon.chem.ucla.edu (silicon.chem.ucla.edu [169.232.135.10]) by carbon.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id h3A1W0N5019487 for ; Wed, 9 Apr 2003 18:32:00 -0700 (PDT) Received: from uclaeric (houkdhcp236.chem.ucla.edu [169.232.140.236]) by silicon.chem.ucla.edu (8.11.1/8.11.1) with SMTP id h3A1W0424278 for ; Wed, 9 Apr 2003 18:32:00 -0700 (PDT) Reply-To: From: "Yunfeng Hu" To: Subject: experimental and computational solvation energy of acetate in acetonitrile Date: Wed, 9 Apr 2003 18:30:36 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal Hi, I wonder if anyone knows the published solvation energy for acetate in acetonitrile or similar solvent. Thanks. Regards, -Yunfeng Department of Chemistry & Biochemistry University of California Los Angeles, CA 90095 (310)206-0553 http://www.chem.ucla.edu/~yunfeng From chemistry-request@server.ccl.net Thu Apr 10 09:25:16 2003 Received: from laplace.quimica.ufpr.br ([200.17.215.88]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3ADPFb23586 for ; Thu, 10 Apr 2003 09:25:15 -0400 Received: from bohr.quimica.ufpr.br (localhost.quimica.ufpr.br [127.0.0.1]) by laplace.quimica.ufpr.br (Postfix) with ESMTP id CFC8B869 for ; Thu, 10 Apr 2003 10:25:12 -0300 (BRT) Message-ID: <3E9570B8.5060702@bohr.quimica.ufpr.br> Date: Thu, 10 Apr 2003 10:25:12 -0300 From: Eduardo User-Agent: Mozilla/5.0 (X11; U; FreeBSD i386; en-US; rv:1.0.1) Gecko/20021005 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: summary of my request about geometry optimization while an electrical field is applied Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Sirs I am sending to you a summary of my requested posted recently: >Sirs > > I would be very gratefull if someone pointed to me some softs > (preferible free and running under unix-pc plataforms) that can > performed organic molecules geometry optimization (AM1 and PM3 or PM5) > while an electrical field is being applied. > > I will sumarize the responses > > Thanks a lot in advance > > yours > > Eduardo > Special thanks to: *************************** Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Laboratorio de Modelagem Molecular Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo Av Bandeirantes, 3900 Ribeirao Preto, SP Brasil suggestions: - GAMESS: http://www.msg.ameslab.gov/GAMESS/ - NWChem: http://www.emsl.pnl.gov:2080/docs/nwchem/ ******************************* Dr. Vladimir Khavryutchenko (vkhavr@compchem.kiev.ua) I have got our software for the space structure optimization with external electric field: the old version 'CLUSTER-Z1' and new one 'QuChem'. They both run under Win32 or some UNIX platforms. You may read about some results in the our publications: E.Sheka, V.Khavryutchenko, E.A.Nikitina. - Quantum Technology on alpha-C:H Film. Modeling Aspect. - Phys. Low-Dim. Struct. 1996, No 11/12, p.65-80. E.Sheka, V.Khavryutchenko, P.Luskinovich, V.Nikishin, E.Nikitina, V.Ogenko, I.Ryzhikov, I.Gorelkin. - Computer modelling in an electric field: nanometric design with scanning tunnelling microscope.- Journal of the British Inter- planetary Society, 1994, v. 47, p.325-330. E.F.Sheka, V.Khavryutchenko, V.A.Zayetz. - Computer Modeling of Assembly of Atoms in an Electric Field. - Int. J. Quant. Chem. 1996, v.57, No 4, p. 741. **************************************** Mauricio Esguerra (mesguerra@cable.net.co) You can find MOPAC at: http://www.webmo.net/support/mopac_linux.html or the rpm in, http://rpmfind.net/linux/RPM/linuxPPC/contrib/software/Applications/Chemistry/mopac-7.01-4.ppc.html Comments Eduardo: I am not sure if this mopac version is straight *************************************** DC Kleb (kleb@chemie.uni-dortmund.de) kindly send to me an old summary that he got about this same issue: Christoph van Wuellen (Christoph.van.Wuellen@ruhr-uni-bochum.de) wrote: As far as I recall, Turbomole does the job. You have to specify the "Geo-Field" option ($geofld). Christoph van Wuellen. _________________________________ Tao Li (lit@engr.sc.edu) wrote: GAMESS allows you to optimize a geometry with an applied electric field. But, as far as I know, this kind of optimization can be done just for neutral molecules. To optimize charged molecules, you have to modify the original GAMESS code yourself. Tao _________________________________ Scheila Braga (scheila@ifi.unicamp.br) wrote: Try the new version of hyperchem 6, you can dowload a demo version in the hypercube site (http://www.hyper.com). Just one thing, the units of electrical field in this program is atomics units, I don't know this relation with V/m or N/C. Please , if you know this relation tell me. Scheila Braga _________________________________ Irena Efremenko (chrirena@techunix.technion.ac.il) wrote: I tried to solve a similar problem and found that for surfaces it may be reasonably modeled only by ASED MO method (by Alfred B. Anderson). Other programs suggest to include (point) charges instead of changing potentials. Sincerely, -- Dr. Irena Efremenko _________________________________ Theresa L. Windus (Theresa.Windus@pnl.gov) wrote: I believe that GAMESS US can do this calculation. Check out http://www.msg.ameslab.gov/GAMESS/GAMESS.html Theresa __________________________________ At last there were some answers in german language: Anselm Horn (Anselm.Horn@Organik.Uni-Erlangen.DE) advises the semiempirical package VAMP. _ _ _ _ _ _ _ _ _ Uwe Huniar (uwe@tchibm2.chemie.uni-karlsruhe.de)recommends Turbomole. He is pointing to pages 165/166 in the turbomole-docu available under http://www.chemie.uni-karlsruhe.de/PC/TheoChem/turbomole/index.html _______________________________________________________________________________ Gaussian can, in fact, do optimizations with an applied external field. In some cases, Opt=Z-matrix and/or NOSYMM may be needed, depending on what the perturbation does to the molecule. -- Joseph Ochterski, Ph.D Senior Customer Service Scientist help@gaussian.com Eduardo comments: DC Kleb point a mopac version modified by Douglas Galvão (galvao@ifi.unicamp.br) that performs geometry optimizations+electric field, but I have notices that this soft doesn't work very well. Even this, I am mentioning it. ************************************************************* An last note: I heard that Cache (a interface do mopac2002) can do the job, but it is commercial. Thanks a lot yours Eduardo -- Eduardo Lemos de Sa - edulsa@quimica.ufpr.br Dep. Quimica - Universidade Federal do Parana Curitiba - PR - Brazil Box: 19081 - Zip: 81531-990 - Phone: +55(41)361-3300 From chemistry-request@server.ccl.net Thu Apr 10 09:05:50 2003 Received: from as1200.organik.uni-erlangen.de ([131.188.128.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3AD5ob23093 for ; Thu, 10 Apr 2003 09:05:50 -0400 Received: from chemie.uni-erlangen.de (equinox.chemie.uni-erlangen.de [131.188.128.90]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id PAA01473; Thu, 10 Apr 2003 15:05:49 +0200 (MET DST) Sender: Harald.Lanig@chemie.uni-erlangen.de Message-ID: <3E956C4C.B6697656@chemie.uni-erlangen.de> Date: Thu, 10 Apr 2003 15:06:20 +0200 From: Harald Lanig Organization: Computer-Chemie-Centrum X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: 17th Darmstaedter Molecular Modelling Workshop in Erlangen, Germany: 2nd Circular Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit 17th Darmstaedter Molecular Modelling Workshop Computer-Chemie-Centrum, 91052 Erlangen, Germany Tuesday, May 27 - Wednesday, May 28, 2003 Second Circular Dear colleagues, as already mentioned in the first circular, the "Darmstaedter Molecular-Modelling-Workshop 2003" will take place the two days before Ascension Day. This is the first year in which the Workshop will be held at its new venue at the University of Erlangen. The goal of the Workshop is to give young scientists, especially PhD students and Post-Docs, the chance to present their current research, industrial colleagues are able to gain an overview about ongoing academic research. Contributions from all areas of molecular modelling, life sciences to materials, are highly welcome. We are pleased to announce that the following scientists have agreed to give plenary lectures Dr. H. Grubmueller (MPI Göttingen) Prof. R. Hubbard (Universität York) Prof. G. Schneider (Universität Frankfurt) The official conference language is German but talks can also be given in English. Slides and posters should be in English. Talks should take approximately 20 minutes including discussion. Posters should have portrait format (90x140 cm). Prior to the poster session each contribution should be presented briefly (2 minutes, using at most 2 overhead transparencies). Registration ends on April 30th. Only Posters and talks with abstracts received before April, 30th will be considered. Registration can be made online only Abstracts of posters and talks should be send by email as ASCII or RTF files to Dr. B. Beck (Bernd.Beck@bc.boehringer-ingelheim.com) or Dr. A. Teckentrup (Andreas.Teckentrup@bc.boehringer-ingelheim.com) before April 30th. As an opportunity, especially for beginners in the field of Molecular Modelling, we are pleased to announce a MGMS-DS One Day Mini-Workshop which will take place on Monday, May 26, 2003 at the Computer-Chemie-Centrum. The course gives an overview of the techniques and methods available to model small molecules and proteins on a classical and quantum-mechanical basis. Further information (in german) is available under . We also want to remind you about the Competition for Network Applications in the Field of Molecular Modelling announced by the MGMS-DS for the first time in 2003. It was decided to offer an award of 500 EUR for the best internet-based scientific application entered in the competition (look under for details). This prize will be presented for the first time during the 17th Darmstädter Molecular Modelling Workshop. Submissions should be made using the electronic input form available at the DGMS-DS website . The Deadline is May 1st, 2003. Hints for travelling/accommodation and also further information about the agenda will be available on the Workshop's website soon. Any additional questions about the Workshop can be sent to da.workshop@chemie.uni-erlangen.de. The annual general meeting of the MGMS-DS (german section) will be held during the Workshop. The conference fee, which depends on membership of the MGMS-DS, amounts to: Members: 35 EUR Student Members: 15 EUR Non-Members: 50 EUR Students: 25 EUR With regards, Bernd Beck Andreas Teckentrup Harald Lanig -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 Mailto:lanig@chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.ccc.uni-erlangen.de/lanig ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Apr 10 09:59:33 2003 Received: from alcor.rede.usc.es ([193.144.75.249]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3ADxXb24577 for ; Thu, 10 Apr 2003 09:59:33 -0400 Received: from localhost (localhost [127.0.0.1]) by alcor.rede.usc.es (Postfix) with ESMTP id 8D9464910C for ; Thu, 10 Apr 2003 15:59:32 +0200 (CEST) Received: from qfcronos.usc.es (qfcronos.usc.es [193.144.74.154]) by alcor.rede.usc.es (Postfix) with ESMTP id 7110D490FD for ; Thu, 10 Apr 2003 15:59:30 +0200 (CEST) Message-Id: <5.2.0.9.0.20030410155924.00a08410@pop.usc.es> X-Sender: qftjesus@pop.usc.es X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Thu, 10 Apr 2003 16:00:30 +0200 To: chemistry@ccl.net From: Jesus Rodriguez-Otero Subject: crash in MP2 frequencies with GAUSSIAN98 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Virus-Scanned: YES (by USC) Hi! I'm trying to calculate MP2 frequencies with GAUSSIAN98 and the program crash in the link 1112 (link that calculate the MP2 second derivatives). The calculated system has symmetry so I thought that it was due to some problem with the symmetry, but the problem still appears when I take away the symmetry. The system is a dimmer, so we have very small frequencies, most likely it also has one negative intermolecular frequency. Belong I show the last few lines of the Gaussian98 output. I will very grateful if some can give me and idea about what is going on and how to solve it. Thanks. Last lines of the output including symmetry: FoFDir used for L=0 through L=2. exception system: exiting due to multiple internal errors: handler returned invalid disposition exception dispatch or unwind stuck in infinite loop exception system: exiting due to multiple internal errors: handler returned invalid disposition handler returned invalid disposition -------------------------------------------------------- Las lines of the output taking off the symmetry: G2DrvN: will do 26 atoms at a time, making 1 passes doing MaxLOS=2. FoFDir used for L=0 through L=2. Last chance handler: pc = 0x3ff807e25b8, sp = 0x11fff88e0, ra = 0x3ff807e25b8 Last chance handler: internal exception: handler returned invalid disposition exception system: exiting due to multiple internal errors: handler returned invalid disposition handler returned invalid disposition P.S. The programs also produces a core file but i can't use the debugger because of compilation options. Jesus Rodriguez-Otero From chemistry-request@server.ccl.net Thu Apr 10 09:35:41 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3ADZdb23826 for ; Thu, 10 Apr 2003 09:35:40 -0400 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id VAA05679 for ; Thu, 10 Apr 2003 21:20:53 +0800 Message-Id: <200304101320.VAA05679@mx1.ustc.edu.cn> Date: Thu, 10 Apr 2003 21:22:48 +0800 From: ¶¡Ñ¸À× Reply-To: dxl@mail.ustc.edu.cn To: CCls Subject: RE: question: EA of O2 Organization: Öйú¿Æ´óÑ¡¼ü»¯Ñ§ÊµÑéÊÒ X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon401421255113_=====" This is a multi-part message in MIME format. --=====000_Dragon401421255113_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 RGVhciBBbGyjug0KICAgIA0KCVRoYW5rIERhdmlkIFNob2JlIGZvciB0aGUgcmVwbHkhDQoJDQoJ SSB1c2VkIHNvbWUgREZUIG1ldGhvZCAoQjNMWVAsIEJQVzkxLFBXOTFQVzkxLCBNUDIgKSB3aXRj aCB3ZXJlIHNhaWQgc3VpdGFibGUgDQoJZm9yIHRoZSBjYWxjdWxhdGlvbnMgd2l0aCBPMi4NCqGh oaENCiAgICBUaGFuayB5b3UgZm9yIHlvdXIgaGVscCGhoaGhoaGhoaGhoaGhoaGhDQogCQkJCQ0K oaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoURpbmcgWHVubGVpDQqhoaGhoaGhoaGhoaGhoaGh oaGhoaGhoaGhoaGhMjAwMy0wNC0xMA0KX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fXw0KRGluZyBYdW5sZWksIFBoLkQuIENhbmRpZGF0ZQ0KT3BlbiBMYWJvcmF0 b3J5IG9mIEJvbmQgU2VsZWN0aXZlIENoZW1pc3RyeQ0KVW5pdmVyc2l0eSBvZiBTY2llbmNlICYg VGVjaG5vbG9neSBvZiBDaGluYQ0KSGVmZWksIEFuaHVpIDIzMDAyNiwgUC5SLkNoaW5hDQpUZWwu OiAwMDg2LTU1MS0zNjAzNDE4DQpGYXguOiAwMDg2LTU1MS0zNjAyOTY5DQpFLW1haWw6IGR4bEBt YWlsLnVzdGMuZWR1LmNuDQpIdHRwOi8vd3d3LmJzYy51c3RjLmVkdS5jbi9+ZHhsDQoJDQpfX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fXw0KCQkJRXZlbiBtb3JlIGltcG9ydGFudCB0aGFuIHRoZSBiYXNpcyBzZXQgaXMgdGhl ICJtZXRob2QiIChIRiwgTVAyLCBRQ0lTRCwgZXRjLikgdXNlZCBmb3IgdGhlIGNhbGN1bGF0aW9u LiAgWW91IGRvIG5vdCBzcGVjaWZ5IHRoZSBtZXRob2QgaW4geW91ciBwb3N0LCBzbyBJIGRvbid0 IGtub3cgaWYgdGhpcyBpcyBhIHByb2JsZW0gb3Igbm90LiAgSSB3aWxsIHNheSB0aGF0IGlmIHlv dSBhcmUgdXNpbmcgSEYsIHlvdSB3aWxsIG9ubHkgZ2V0IGFncmVlbWVudCB3aXRoIGV4cGVyaW1l bnQgYnkgZHVtYiBsdWNrLiA6LSkgIEFsc28sIGlmIHlvdSBkb24ndCBzcGVjaWZ5IGEgbWV0aG9k LCBHOTggYXNzdW1lcyBIRiBiZWNhdXNlIGl0J3MgdGhlIHF1aWNrZXN0IGFiIGluaXRpbyBtZXRo b2QuICANCg0KLS1EYXZpZCBTaG9iZSANClP8ZC1DaGVtaWUgSW5jLiANCnBob25lICg1MDIpIDYz NC03NDA5IA0KZmF4ICAgICAoNTAyKSA2MzQtNzcyNCANCmVtYWlsICBkc2hvYmVAc3VkLWNoZW1p ZWluYy5jb20gDQoNCkRvbid0IGJvdGhlciBmbGFtaW5nIG1lOiBJJ20gYmVoaW5kIGEgZmlyZXdh bGwuIA0KDQo= --=====000_Dragon401421255113_===== Content-Type: image/gif; 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Thu, 10 Apr 2003 10:45:45 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.9/8.12.9/Guy-01-04-2003) with ESMTP id h3AEjgc1021262 for ; Thu, 10 Apr 2003 16:45:43 +0200 (METDST) Received: from lctn.uhp-nancy.fr (pt-xav.lctn.uhp-nancy.fr [193.50.239.125]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id QAA24100 for ; Thu, 10 Apr 2003 16:35:37 +0200 Message-ID: <3E9582F7.FB19C3A1@lctn.uhp-nancy.fr> Date: Thu, 10 Apr 2003 16:43:03 +0200 From: Xavier Assfeld X-Mailer: Mozilla 4.75 [fr] (Win98; U) X-Accept-Language: fr MIME-Version: 1.0 To: CCL Chemistry Subject: Reminder Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Scanned-By: arcturus.ciril.fr Modelling chemical reactivity: from gas-phase to solution and enzymes. An international conference in honor of Professor Jean-Louis Rivail 16-18 July 2003, Nancy, France http://www.lctn.uhp-nancy.fr/JLR/ Dear Colleague, we remind you the deadlines for Registration and Abstract submission: Early registration: April 15th, 2003 Registration at extra fee: After April 15th, 2003 Abstracts for posters: April 15th, 2003 Accommodation: June 15th, 2003 (early booking is strongly recommended) We also remind you that this is a satellite meeting of the XIth ICQC congress to be held at Bonn (July 20-26). Registration and accommodation forms, program of lectures and further information are available at the conference web site above. Please bring this announcement to the attention of your colleagues. We apologize to those who receive multiple copies of this email. -- ...Xav Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie théorique (T) 33 3 83 68 43 74 Université Henri Poincaré (F) 33 3 83 68 43 71 F-54506 Nancy B.P. 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Thu Apr 10 11:38:12 2003 Received: from mail.cybermesa.com ([198.59.109.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3AFcB328531 for ; Thu, 10 Apr 2003 11:38:12 -0400 Received: from dave (qwest253-dsl3.cybermesa.com [216.84.163.253]) by mail.cybermesa.com (8.11.6/8.11.6) with SMTP id h3AFd9v25285 for ; Thu, 10 Apr 2003 09:39:15 -0600 (MDT) From: "David Miller" To: Subject: ChemTK software on ccl.net Date: Thu, 10 Apr 2003 09:39:41 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 ChemTK evaluation software is now available for download from the CCL Software Archive: http://server.ccl.net/cca/software/MS-WIN98/chemtk/index.shtml ChemTK is a Windows based cheminformatics toolkit providing chemists the ability to visualize, organize, query, and analyze chemical screening data. It functions both as a simple and convenient SD file browser and as a powerful decision-support platform, offering intuitive clustering and property-calculation capabilities, QSAR model generation and virtual screening, rapid similarity analyses, and many additional features. Visit www.chemtk.com to download the ChemTK product sheet, release notes, and full documentation. Comments and feedback are welcome. Please feel free to send me an email at the address below. Best regards, David W. Miller, Ph.D. Sage Informatics LLC dmiller@sageinformatics.com From chemistry-request@server.ccl.net Thu Apr 10 14:30:21 2003 Received: from adenine.cgl.ucsf.edu ([169.230.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3AIUK302833 for ; Thu, 10 Apr 2003 14:30:20 -0400 Received: from localhost (socrates.cgl.ucsf.edu [169.230.27.3]) by adenine.cgl.ucsf.edu (8.12.9/8.12.9/GSC1.16) with ESMTP id h3AIUKbN929799 for ; Thu, 10 Apr 2003 11:30:20 -0700 (PDT) Date: Thu, 10 Apr 2003 11:30:20 -0700 (PDT) From: Pradipta Bandyopadhyay To: chemistry@ccl.net Subject: Matlab!! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Has anyone used MATLAB for volume visualization - I want to visualize electrostatic potential V(x,y,z). I am having trouble in generating data as 3-D arrays as Matlab requires. It is thinking the data as 2D. What should be the format of an external file which has 3D array data (e.g. X coordinates for all grid points)? Any kind of help would be appreciated. Pradipta From chemistry-request@server.ccl.net Thu Apr 10 15:26:45 2003 Received: from pacific-carrier-annex.mit.edu ([18.7.21.83]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3AJQj303924 for ; Thu, 10 Apr 2003 15:26:45 -0400 Received: from central-city-carrier-station.mit.edu (CENTRAL-CITY-CARRIER-STATION.MIT.EDU [18.7.7.72]) by pacific-carrier-annex.mit.edu (8.12.4/8.9.2) with ESMTP id h3AJQhlP015833 for ; Thu, 10 Apr 2003 15:26:45 -0400 (EDT) Received: from melbourne-city-street.mit.edu (MELBOURNE-CITY-STREET.MIT.EDU [18.7.21.86]) by central-city-carrier-station.mit.edu (8.12.4/8.9.2) with ESMTP id h3AJQgQq028336 for ; Thu, 10 Apr 2003 15:26:43 -0400 (EDT) Received: from magic-pi-ball.mit.edu (MAGIC-PI-BALL.MIT.EDU [18.7.16.80]) ) by melbourne-city-street.mit.edu (8.12.4/8.12.4) with ESMTP id h3AJQgU8027484 for ; Thu, 10 Apr 2003 15:26:42 -0400 (EDT) Received: from localhost (damians@localhost) by magic-pi-ball.mit.edu (8.9.3p2) with ESMTP id PAA08962; Thu, 10 Apr 2003 15:26:42 -0400 (EDT) Date: Thu, 10 Apr 2003 15:26:42 -0400 (EDT) From: Damian A Scherlis Perel To: Subject: spin contamination Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I have performed UHF calculations on pi dimers which are known to be singlet states, to eventually compute the MP2 energies. I got the singlet UHF wave function, which turned out to be unstable. The stable state, though, about 0.1 hartree lower in E, exhibits a large extent of spin contamination: S**2 before annihilation: 3.7642, after: 14.6554 Moreover, if MP2 is applied to both HF wave functions, the UMP2 energy that results from the pure state, initially higher, is lower than the corresponding to the contaminated state. I wonder what state is more reliable, if any, to get the total energies. All comments will be appreciated. Thanks! ------------------------ Damian Scherlis Department of Materials Science & Engineering Massachusetts Institute of Technology damians@mit.edu 617 253 6026 From chemistry-request@server.ccl.net Thu Apr 10 14:24:46 2003 Received: from krypton.hosting4u.net ([209.15.2.78]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3AIOk302714 for ; Thu, 10 Apr 2003 14:24:46 -0400 Received: from proinformatix.com (zeus.hosting4u.net [209.35.191.131]) by krypton.hosting4u.net (Postfix) with ESMTP id A2885B343C for ; Thu, 10 Apr 2003 12:49:21 -0500 (CDT) Received: from bio89162 ([129.240.89.162]) by proinformatix.com ; Thu, 10 Apr 2003 12:49:20 -0500 Message-ID: <00f801c2ff89$58bb5670$a259f081@uio.no> From: "Sergio Manzetti" To: Subject: MOPAC format from mol file Date: Thu, 10 Apr 2003 19:46:58 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00F5_01C2FF99.F2AC6A20" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 X-Rcpt-To: This is a multi-part message in MIME format. ------=_NextPart_000_00F5_01C2FF99.F2AC6A20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I try to generate a MOPAC calculation of NADP, but when I try with = the input file it says unrecognized keyword, or atom ill defined...below = is the MOPAC input for NADP, can anyone see something missing? Thanks. Sergio KEYWORDS GO HERE C 0.0000000 0 0.000000 0 0.000000 0 0 0 0 0.0000 C 1.4909987 1 0.000000 0 0.000000 0 1 0 0 0.0000 C 1.4589154 1 120.833751 1 0.000000 0 1 2 0 0.0000 C 1.5952887 1 104.179711 1 -123.629997 1 1 2 3 0.0000 C 1.4327690 1 118.649162 1 -177.109970 1 4 1 2 0.0000 C 1.4961080 1 107.216845 1 -161.441326 1 5 4 1 0.0000 C 1.4141955 1 113.692259 1 -69.678566 1 6 5 4 0.0000 C 1.4861497 1 114.497941 1 51.716667 1 6 5 4 0.0000 C 1.4452941 1 111.437239 1 74.248685 1 8 6 5 0.0000 C 1.5054733 1 103.365827 1 -166.496868 1 8 6 5 0.0000 C 1.4574546 1 111.809306 1 -86.763311 1 10 8 6 0.0000 C 1.4501824 1 106.004635 1 161.480085 1 7 6 5 0.0000 C 1.4742222 1 107.653685 1 -139.809374 1 12 7 6 0.0000 C 1.3833969 1 128.944472 1 66.940975 1 13 12 7 0.0000 C 1.2992633 1 112.520808 1 178.715024 1 14 13 12 0.0000 C 1.3880497 1 104.385214 1 -0.091869 1 15 14 13 0.0000 C 1.4212055 1 132.803663 1 -178.929926 1 16 15 14 0.0000 C 1.3238100 1 121.797140 1 0.190214 1 17 16 15 0.0000 C 1.3672524 1 118.021273 1 -179.725459 1 17 16 15 0.0000 C 1.3491634 1 120.848602 1 -0.066268 1 19 17 16 0.0000 C 1.3502274 1 125.054262 1 -0.679602 1 20 19 17 0.0000 C 1.3539457 1 111.183849 1 0.730735 1 16 15 14 0.0000 O 1.5778419 1 110.549256 1 126.272978 1 1 2 3 0.0000 N 1.5977684 1 134.654605 1 -121.941769 1 23 1 2 0.0000 N 1.4758096 1 110.162467 1 -56.814322 1 24 23 1 0.0000 N 1.5009081 1 105.285562 1 72.156186 1 24 23 1 0.0000 N 1.5660166 1 104.006219 1 -178.870480 1 24 23 1 0.0000 N 1.4258156 1 118.281226 1 69.379294 1 27 24 23 0.0000 N 1.5245626 1 111.272573 1 175.371156 1 28 27 24 0.0000 N 1.4342420 1 110.854111 1 -60.335961 1 29 28 27 0.0000 N 1.5326307 1 114.247710 1 57.889983 1 29 28 27 0.0000 N 1.4234219 1 112.607565 1 144.895209 1 31 29 28 0.0000 N 1.5163852 1 105.507122 1 -95.103814 1 31 29 28 0.0000 N 1.4066321 1 113.843089 1 -150.480848 1 33 31 29 0.0000 N 1.4146388 1 111.185567 1 114.063306 1 30 29 28 0.0000 N 1.4537538 1 111.078782 1 -139.680558 1 35 30 29 0.0000 N 1.4161479 1 118.169858 1 79.144271 1 36 35 30 0.0000 N 1.4306551 1 116.150232 1 -179.373873 1 37 36 35 0.0000 N 1.4574762 1 121.740928 1 -178.042998 1 38 37 36 0.0000 N 1.2482388 1 120.855729 1 167.276205 1 39 38 37 0.0000 N 1.3598312 1 121.250981 1 -10.757352 1 39 38 37 0.0000 N 1.4154049 1 118.632746 1 0.854415 1 38 37 36 0.0000 N 1.3635670 1 123.585731 1 -1.005756 1 42 38 37 0.0000 N 1.3617566 1 118.413749 1 0.448534 1 43 42 38 0.0000 C 1.6104652 1 123.853336 1 -145.123171 1 11 10 8 0.0000 C 1.5048751 1 109.327762 1 -91.096377 1 45 11 10 0.0000 C 1.5109020 1 102.991438 1 29.325753 1 45 11 10 0.0000 C 1.4871210 1 100.481918 1 147.314143 1 45 11 10 0.0000 ------=_NextPart_000_00F5_01C2FF99.F2AC6A20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi, I try to generate a MOPAC = calculation of NADP,=20 but when I try with the input file it says unrecognized keyword, or atom = ill=20 defined...below is the MOPAC input for NADP, can anyone see something = missing?=20 Thanks.
 
Sergio
 
KEYWORDS GO HERE
C 0.0000000 0 0.000000 =
0 0.000000 0 0 0 0 0.0000
C 1.4909987 1 0.000000 0 0.000000 0 =
1 0 0 0.0000
C 1.4589154 1 120.833751 1 0.000000 0 1 2 0 =
0.0000
C 1.5952887 1 104.179711 1 -123.629997 1 1 2 3 =
0.0000
C 1.4327690 1 118.649162 1 -177.109970 1 4 1 2 =
0.0000
C 1.4961080 1 107.216845 1 -161.441326 1 5 4 1 =
0.0000
C 1.4141955 1 113.692259 1 -69.678566 1 6 5 4 =
0.0000
C 1.4861497 1 114.497941 1 51.716667 1 6 5 4 =
0.0000
C 1.4452941 1 111.437239 1 74.248685 1 8 6 5 =
0.0000
C 1.5054733 1 103.365827 1 -166.496868 1 8 6 5 =
0.0000
C 1.4574546 1 111.809306 1 -86.763311 1 10 8 6 =
0.0000
C 1.4501824 1 106.004635 1 161.480085 1 7 6 5 =
0.0000
C 1.4742222 1 107.653685 1 -139.809374 1 12 7 6 =
0.0000
C 1.3833969 1 128.944472 1 66.940975 1 13 12 7 =
0.0000
C 1.2992633 1 112.520808 1 178.715024 1 14 13 12 =
0.0000
C 1.3880497 1 104.385214 1 -0.091869 1 15 14 13 =
0.0000
C 1.4212055 1 132.803663 1 -178.929926 1 16 15 14 =
0.0000
C 1.3238100 1 121.797140 1 0.190214 1 17 16 15 =
0.0000
C 1.3672524 1 118.021273 1 -179.725459 1 17 16 15 =
0.0000
C 1.3491634 1 120.848602 1 -0.066268 1 19 17 16 =
0.0000
C 1.3502274 1 125.054262 1 -0.679602 1 20 19 17 =
0.0000
C 1.3539457 1 111.183849 1 0.730735 1 16 15 14 =
0.0000
O 1.5778419 1 110.549256 1 126.272978 1 1 2 3 =
0.0000
N 1.5977684 1 134.654605 1 -121.941769 1 23 1 2 =
0.0000
N 1.4758096 1 110.162467 1 -56.814322 1 24 23 1 =
0.0000
N 1.5009081 1 105.285562 1 72.156186 1 24 23 1 =
0.0000
N 1.5660166 1 104.006219 1 -178.870480 1 24 23 1 =
0.0000
N 1.4258156 1 118.281226 1 69.379294 1 27 24 23 =
0.0000
N 1.5245626 1 111.272573 1 175.371156 1 28 27 24 =
0.0000
N 1.4342420 1 110.854111 1 -60.335961 1 29 28 27 =
0.0000
N 1.5326307 1 114.247710 1 57.889983 1 29 28 27 =
0.0000
N 1.4234219 1 112.607565 1 144.895209 1 31 29 28 =
0.0000
N 1.5163852 1 105.507122 1 -95.103814 1 31 29 28 =
0.0000
N 1.4066321 1 113.843089 1 -150.480848 1 33 31 29 =
0.0000
N 1.4146388 1 111.185567 1 114.063306 1 30 29 28 =
0.0000
N 1.4537538 1 111.078782 1 -139.680558 1 35 30 29 =
0.0000
N 1.4161479 1 118.169858 1 79.144271 1 36 35 30 =
0.0000
N 1.4306551 1 116.150232 1 -179.373873 1 37 36 35 =
0.0000
N 1.4574762 1 121.740928 1 -178.042998 1 38 37 36 =
0.0000
N 1.2482388 1 120.855729 1 167.276205 1 39 38 37 =
0.0000
N 1.3598312 1 121.250981 1 -10.757352 1 39 38 37 =
0.0000
N 1.4154049 1 118.632746 1 0.854415 1 38 37 36 =
0.0000
N 1.3635670 1 123.585731 1 -1.005756 1 42 38 37 =
0.0000
N 1.3617566 1 118.413749 1 0.448534 1 43 42 38 =
0.0000
C 1.6104652 1 123.853336 1 -145.123171 1 11 10 8 =
0.0000
C 1.5048751 1 109.327762 1 -91.096377 1 45 11 10 =
0.0000
C 1.5109020 1 102.991438 1 29.325753 1 45 11 10 =
0.0000
C 1.4871210 1 100.481918 1 147.314143 1 45 11 10 =
0.0000
------=_NextPart_000_00F5_01C2FF99.F2AC6A20-- From chemistry-request@server.ccl.net Thu Apr 10 14:03:20 2003 Received: from websnail.mit.edu ([18.7.21.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3AI3K302092 for ; Thu, 10 Apr 2003 14:03:20 -0400 Received: (from www@localhost) by websnail.mit.edu (8.9.3) id OAA18307; Thu, 10 Apr 2003 14:03:20 -0400 (EDT) From: jhliao@mit.edu Received: from langm.lms.mit.edu ( [langm.lms.mit.edu]) as user jhliao@MIT.EDU by webmail.mit.edu with HTTPS; Thu, 10 Apr 2003 14:03:19 -0400 Message-ID: <1049997799.3e95b1e7f189b@webmail.mit.edu> Date: Thu, 10 Apr 2003 14:03:19 -0400 To: chemistry@ccl.net Subject: help with MD simulation of polyelectrolyte micelles MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.1-cvs X-Originating-IP: 18.60.1.84 X-Originating-Host: langm.lms.mit.edu X-MIT-WebMail-Sender: X-MIT-WebMail-User-Browser: Mozilla/4.78C-CCK-MCD (Macintosh; U; PPC) Hello to all, I am inquiring any pertinent advice for approaching this type of simulation, regarding how to take into account the charges of the molecules (I will be constructing polymer chains out of conjugated polymer PPEs). Any help would greatly be appreciated for this -- I am a novice to simulation. Thanks, Jessica Liao Swager Group Ph.D.candidate in Materials Science/Program in Polymer Science and Technology Massachusetts Institute of Technology Cambridge, MA 02139 jhliao@mit.edu From chemistry-request@server.ccl.net Thu Apr 10 15:31:51 2003 Received: from mx3.trentu.ca ([206.248.118.2]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3AJVo304022 for ; Thu, 10 Apr 2003 15:31:50 -0400 Received: (qmail 11551 invoked by uid 504); 10 Apr 2003 19:31:08 -0000 Received: from elewars@trentu.ca by mx3.trentu.ca by uid 501 with qmail-scanner-1.14 (fsecure: 4.15/4370/2003-04-07/2003-04-07. 2003-04-07/ Clear:. Processed in 0.723946 secs); 10 Apr 2003 19:31:08 -0000 X-Qmail-Scanner-Mail-From: elewars@trentu.ca via mx3.trentu.ca X-Qmail-Scanner: 1.14 (Clear:. Processed in 0.723946 secs) Received: from unknown (HELO trentu.ca) (206.248.117.30) by mx3.trentu.ca with SMTP; 10 Apr 2003 19:31:07 -0000 Message-ID: <3E95C75B.4E10D347@trentu.ca> Date: Thu, 10 Apr 2003 15:34:54 -0400 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Refs, H bond calcs 100 atoms Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 2003 April 10 re the question about H bonds in a "supramolecular system...100 atoms". These refs may be helpful: Comparison of semiempirical and ab initio calculations on H bonds: J. J. Dannenberg, THEOCHEM, 1997, 401, 279. H bonding and DFT: M. Lozynski, D. Rusinska-Roszak, H.-G. Mack, J Phys Chem A, 1998, 102, 2899. A DFT study of a hydrogen bond: J. Spangett-Larson, Chem. Phys., 1999, 240, 51. "Understanding the hydrogen bond with Quantum Chemistry": M. S. Gordon, J. H. Jensen, Acc. Chem. Res., 1996, 29, 536. E. Lewars ==== From chemistry-request@server.ccl.net Thu Apr 10 15:22:20 2003 Received: from pscuxc.psc.edu ([128.182.66.177]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3AJMK303844 for ; Thu, 10 Apr 2003 15:22:20 -0400 Received: from pscuxc.psc.edu (localhost.psc.edu [127.0.0.1]) by pscuxc.psc.edu (8.12.9/8.12.5) with ESMTP id h3AJMKmu023286 for ; Thu, 10 Apr 2003 15:22:20 -0400 (EDT) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.12.9/8.12.8/Submit) with ESMTP id h3AJMKf9016317 for ; Thu, 10 Apr 2003 15:22:20 -0400 (EDT) Date: Thu, 10 Apr 2003 15:22:19 -0400 (EDT) From: Troy Wymore To: Subject: PSC Summer Workshop: Modeling from Protein Sequence to Structure Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII *************************************************** PSC BIOMEDICAL INITIATIVE WORKSHOP 2003 MODELING FROM PROTEIN SEQUENCE TO STRUCTURE: COMPUTATIONAL TOOLS FOR STRUCTURE PREDICTION June 2-5 Application Deadline: April 30 This workshop will introduce researchers to computational tools (the MMTSB Tool Set available at http://mmtsb.scripps.edu) aimed at predicting structure based on sequence alone, from identification of suitable homology templates, or through application of secondary-structure templated de novo folding, as well as refinement and energy calculations on "ensembles" of molecular structures. This freely available tool set comprises a perl-based library of applications that interface to the molecular modeling packages CHARMM and Amber, and the MONSSTER package for protein structure prediction. Participants in the workshop will be presented lectures on molecular modeling theory and practice, protein structure prediction, loop modeling and energy-based structure refinement. Advanced sampling methods such as replica-exchange molecular dynamics, as utilized in structure prediction algorithms, will be discussed. Practical tutorials exploring the use and application of the MMTSB tool set will focus on conventional molecular mechanics calculations of energy, minimization and dynamics as well as loop modeling and refinement using replica-exchange molecular dynamics and hierarchical protein structure prediction using de novo (or secondary structure templated) folding algorithms in the MONSSTER and CHARMM packages. Web-based servers for protein sequence alignment, secondary structure prediction and homology template identification will be discussed in the context of their utility to the overall structure prediction pipeline utilizing the MMTSB Tool Set. For specific details, including an electronic application form, see: http://www.psc.edu/biomed/training/workshops/2003/proteomics/index.html If you have any questions, please contact Nancy Blankenstein at blankens@psc.edu From chemistry-request@server.ccl.net Thu Apr 10 17:02:04 2003 Received: from prserv.net ([32.97.166.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3AL24305840 for ; Thu, 10 Apr 2003 17:02:04 -0400 Received: from attglobal.net (dhcp065-029-075-111.indy.rr.com[65.29.75.111]) by prserv.net (asmtp1) with SMTP id <20030410210156251009vgpae> (Authid: jmmckel); Thu, 10 Apr 2003 21:01:56 +0000 Message-ID: <3E95978B.3C7281C@attglobal.net> Date: Thu, 10 Apr 2003 16:10:51 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Damian A Scherlis Perel CC: chemistry@ccl.net Subject: Re: CCL:spin contamination References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Damian and others, I showed an example quite a while ago where triplet instability decreased as the basis set was improved. Someone else showed that it is also reduced with geometry optimization. I'm not sure this helps here, except to say that improving the basis set might decrease the triplet component; if this does in fact happen I would play look at geometry changes. John McKelvey Damian A Scherlis Perel wrote: > Dear all, > > I have performed UHF calculations on pi dimers which are > known to be singlet states, to eventually compute the MP2 > energies. I got the singlet UHF wave function, which > turned out to be unstable. The stable state, though, > about 0.1 hartree lower in E, exhibits a large extent > of spin contamination: > > S**2 before annihilation: 3.7642, after: 14.6554 > > Moreover, if MP2 is applied to both HF wave functions, the > UMP2 energy that results from the pure state, initially higher, > is lower than the corresponding to the contaminated state. > > I wonder what state is more reliable, if any, to get the > total energies. All comments will be appreciated. > > Thanks! > > ------------------------ > Damian Scherlis > Department of Materials Science & Engineering > Massachusetts Institute of Technology > damians@mit.edu > 617 253 6026 > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Apr 10 18:13:57 2003 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3AMDv307338 for ; Thu, 10 Apr 2003 18:13:57 -0400 Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id 8E0BA50361; Thu, 10 Apr 2003 15:13:55 -0700 (PDT) Received: from ultra.chem.ucsb.edu ([127.0.0.1]) by localhost (ultra [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 02212-08; Thu, 10 Apr 2003 15:13:55 -0700 (PDT) Received: by ultra.chem.ucsb.edu (Postfix, from userid 3016) id 00C2E50360; Thu, 10 Apr 2003 15:13:54 -0700 (PDT) Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id E7B161707D2; Thu, 10 Apr 2003 15:13:54 -0700 (PDT) Date: Thu, 10 Apr 2003 15:13:54 -0700 (PDT) From: John Bushnell To: Damian A Scherlis Perel Cc: chemistry@ccl.net Subject: Re: CCL:spin contamination In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new Your S**2 values look like garbage. You have a "singlet" with an S**2 value of about a "quartet"? And the S**2 after annihilation gives S approx. 3.4? I can't imagine this result is meaningful. - John On Thu, 10 Apr 2003, Damian A Scherlis Perel wrote: > > Dear all, > > I have performed UHF calculations on pi dimers which are > known to be singlet states, to eventually compute the MP2 > energies. I got the singlet UHF wave function, which > turned out to be unstable. The stable state, though, > about 0.1 hartree lower in E, exhibits a large extent > of spin contamination: > > S**2 before annihilation: 3.7642, after: 14.6554 > > Moreover, if MP2 is applied to both HF wave functions, the > UMP2 energy that results from the pure state, initially higher, > is lower than the corresponding to the contaminated state. > > I wonder what state is more reliable, if any, to get the > total energies. All comments will be appreciated. > > Thanks! > > ------------------------ > Damian Scherlis > Department of Materials Science & Engineering > Massachusetts Institute of Technology > damians@mit.edu > 617 253 6026