From joubert@ext.jussieu.fr Sat May 30 16:09:19 1998 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA14688 Sat, 30 May 1998 16:09:18 -0400 (EDT) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.8.8/jtpda-5.3) with ESMTP id WAA14532 for ; Sat, 30 May 1998 22:09:19 +0200 (CEST) Received: from Starship.ext.jussieu.fr by idf.ext.jussieu.fr (8.8.8/jtpda-4.0) with SMTP; Sat, 30 May 1998 22:08:35 +0200 (METDST) Message-Id: <3.0.5.32.19980530220440.00842100@idf.ext.jussieu.fr> X-Sender: joubert@idf.ext.jussieu.fr X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Sat, 30 May 1998 22:04:40 +0200 To: chemistry@www.ccl.net From: Laurent Joubert Subject: Postdocs in computational chemistry : WWW sites or newsgroups ? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear netters, I'm looking for a postdoctoral position in computational chemistry. I already know the "job offered list" of the CCL, but I would like to know if there are other sites or newsgroups of interest concerning postdoctoral positions in this area of physical chemistry. Thanks in advance for your answers. Laurent Joubert ------------------------------------------------------------- Laurent Joubert PhD Student Laboratoire d'Electrochimie et de Chimie Analytique ENSCP 11, rue Pierre et Marie Curie 75231 Paris Cedex 05 e-mail : joubert@ext.jussieu.fr Tel : (33) 01-55-42-63-91 Fax : (33) 01-44-27-67-50 -------------------------------------------------------------- From prochem@biruni.erum.com.pk Fri Jun 5 02:25:15 1998 Received: from biruni.erum.com.pk ([196.3.72.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id CAA09038 Fri, 5 Jun 1998 02:25:10 -0400 (EDT) Received: from prochem by biruni.erum.com.pk (SMI-8.6/SMI-SVR4) id LAA14094; Fri, 5 Jun 1998 11:21:19 -0500 Message-ID: <357835FE.5BD3@biruni.erum.com.pk> Date: Fri, 05 Jun 1998 11:16:30 -0700 From: "Prof. Zafar H. Zaidi" Reply-To: prochem@biruni.erum.com.pk Organization: HEJ Res. Inst. Chemistry, University of Karachi X-Mailer: Mozilla 3.01Gold (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Ph.D. on homology modeling Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello All I am about to submit my Ph.D.thesis based on homology modelling studies of seven 3D models of different proteolytic enzymes, their complexes with inhibtors and polypeptide inhibitors. I have used MODELLER approach for the homology modeling of proteins, and also used other modeling software like WHATIF etc. I would appreciate if anyone can let me have a copy of Ph.D. thesis submitted under the above related theme or share his/her experience in this regard. With best regards. Kamran Azim HEJ Research Ins. of Chemistry University of Karachi Karachi, PAKISTAN. From goeller@pc04.chemie.uni-jena.de Fri Jun 5 03:38:36 1998 Received: from cnve.rz.uni-jena.de (root@cnve.rz.uni-jena.de [141.35.1.32]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA09540 Fri, 5 Jun 1998 03:38:33 -0400 (EDT) Received: from fsuj03.rz.uni-jena.de (root@fsuj03.rz.uni-jena.de [141.35.2.32]) by cnve.rz.uni-jena.de (8.8.7/8.8.7) with ESMTP id JAA03546 for ; Fri, 5 Jun 1998 09:38:28 +0200 (MESZ) Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj03.rz.uni-jena.de (8.7.1/8.6.10) with SMTP id JAA18135 for ; Fri, 5 Jun 1998 09:38:24 +0200 (MESZ) Received: from localhost by pc04.chemie.uni-jena.de (5.65v3.2/1.1.10.5/28Jan98-0152PM) id AA27053; Fri, 5 Jun 1998 09:38:27 +0200 Sender: goeller@pc04.chemie.uni-jena.de Message-Id: <3577A073.167E@pc04.chemie.uni-jena.de> Date: Fri, 05 Jun 1998 09:38:27 +0200 From: Andreas Goeller X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Sum: FF for polymers Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, here's the summary regarding the following question: could you please point me to force fields (public domain and commercial) parametrized for polymers? Or to those which could be easily reparametrized for this purpose? Possibility for MD would be favourable, but not necessary. I will post the results to the list. _____________________________________________________________________ shortly: - Dreiding and Dreiding II - Molecular Simulations offers the PCFF and the COMPASS forcefield developed from CFF - Suter, U. W.; Flory, P. J. Macromolecules 1975 8 765 - UFF - CFF - MMP, MMP2, MMP3 - YASP (Max-Planck-Ges. for Polymer-science in Mainz) AMBER, OPLS, MMx, CharMM seem not to be applicable except one considers DNA and proteins as polymers (biopolymers) as was suggested Thank you all very much for the information. ________________________________________________ Dreiding and Dreiding II are pretty popular as they have united atoms built in. I don't know if they are in public domain or not but they are definately implemented in Cerius2 by MSI Good Luck David Tilbrook ********************************************************** Dr. David A. Tilbrook Biomaterials in Relation to Dentistry IRC in Biomedical Materials, B.M.S 2.21.2 Queen Mary and Westfield College (East Gate), Mile End Road, London E1 4NS Tel. 0171 2957974, Fax. 0171 2957979 *********************************************************** Tel: 0171 2957974 Fax: 0171 2957979 e-mail D.A.Tilbrook@mds.qmw.ac.uk ********************************************************** _____________________________________________________ Dear Andreas, have a look to the force fields link at: http:/antas.agraria.uniss.it/software.html you may probably find something of your interest. bye Bruno Dr Bruno Manunza Molecular Modeling Lab DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it web: http://antas.agraria.uniss.it ____________________________________________________ Molecular Simulations offers the PCFF and the COMPASS forcefield which are intended for applications to polymers and organic materials. PCFF was developed based on CFF. See for parametrization, testing and validation : Sun et al. JACS, 116 (1994) 2978 Sun, J. Comp. Chem. 15 (1994) 752 Sun, Marcomolecules 28 (1995) 701 COMPASS (Condensed phase Optmized Molecular Potentials for Atomistic Simulation Studies) is the successor of PCFF. It is the first force field being parameterized using condensed-phased properties in addition to ab initio data and empirical data for gas phase molecules. It also accounts for temperature-dependent condensed phase properties. See: Rigby, Polymer International 44 (1997) 311. Best regards Klaus ------------------------------------------- Klaus Stark,PhD Application Scientist Molecular Simulations Ltd. 230/250 The Quorum, Barnwell Road Cambridge CB5 8RE England Phone : 0044-1223-507548 ********** NEW ******************* Mobile : 0044-411-886564 ********** NEW ******************* Fax : 0044-1223-413301 E-Mail : kstark@msicam.co.uk Web Page : http://skanda.msicam.co.uk/~kstark (only for internal use) Catalysis Examples : http://www.msi.com/info/applications _____________________________________________________ One of the earliest implementations of force field modeling to polymers (of which I am aware) is that of Suter and Flory. It doesn't have a common name, but is first reported in: Suter, U. W.; Flory, P. J. Macromolecules 1975 8 765. Much of Suter's more recent work involves variations on this, and he has successfully employed periodic boundary conditions in molecular dynamic simulations. The DREIDING force field has also been used to model polymers, see: Fan, C. F.; Gagin, T.; Chen, Z. M.; Smith, K. A. Macromolecules 1994 27 2383. Jones, M.-C. G.; Martin, D. C. Macromolecules 1995 28 6161. Kitano, Y.; Usami, I.; Obata, Y.; Okuyama, K.; Jinda, T. Polymer 1995 36 1123. The UFF formulation has also been used to model polymers, see: Grigoras, S.; Qian, C.; Crowder, C.; Harkness, B.; Mita, I. Macromolecules 1995 28 7370. The CFF formulation has also been used to model polymers, see: Sun, H.; Mumby, S. J.; Maple, J. R.; Hagler, A. T. J. Am. Chem. Soc. 1994 116 2978. Meier, R. J.; Maple, J. R.; Hwang, M.-J.; Hagler, A. T. J. Phys. Chem. 1995 99 5445. I hope this helps. --------------------------------- Matthew F. Schlecht DuPont Agricultural Products Newark, DE 19714-0030 USA tel 302-366-5760 fax 366-5738 Matthew.F.Schlecht@usa.dupont.com schlecmf@hotmail.com --------------------------------- __________________________________________________________ We have recently developed a new force field, COMPASS, specifically adapted to condensed phases with a focus on polymers. A couple of papers have appeared in print so far with others in preparation. The published papers focused on polysiloxanes, and alcohols, ethers and polyethers. The references are: H. Sun & D. Rigby, Spectrochimica Acta Part A 53, 1301-1323 (1997) D. Rigby, H. Sun & B.E. Eichinger Polymer International 44, 311-330 (1997) Parameters are given for the polymers covered in the papers, while the force field in its entirety is available as a commercial product from Molecular Simulations. Best Regards, David Rigby MSI Polymer Project ___________________________________________________________ Regarding forcefields for polymers; MMP MMP2 MMP3 are the only ones I know of specifically oriented towards polymers. Hope this helps. R. Valluzzi Tufts Biotechnology Center Dept. Chemical Engineering Medford, MA ___________________________________________________________ Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- From tihonen@univer.omsk.su Fri Jun 5 09:11:13 1998 Received: from univer.omsk.su (maks.omskreg.ru [194.226.28.250]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA11169 Fri, 5 Jun 1998 09:11:00 -0400 (EDT) Received: from CHF4 (corp1 [195.9.3.129]) by univer.omsk.su (8.8.5/8.7.3) with SMTP id UAA13527 for ; Fri, 5 Jun 1998 20:12:04 +0700 (OSS) Message-Id: <199806051312.UAA13527@univer.omsk.su> From: "Tikhonenko Vladimir" To: "chemistry@www.ccl.net" Date: Fri, 05 Jun 98 20:08:59 Reply-To: "Tikhonenko Vladimir" Priority: Normal X-Mailer: PMMail 1.92 For OS/2 MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit Subject: Program understanding organic nomenclature name Hi collegues, Did anybody see (or make) parser for organic compound names builded on IUPAC rules (better with Chemical Abstracts extensions) ? I know the only program that can do it - NamExpert, but it's commercial software, and sources are not available. I'll be glad to get all information about it. Summary is guarantied. Vladimir Tikhonenko, postgraduate, Omsk State University, Omsk, Russia. From kaupp@vsibm1.mpi-stuttgart.mpg.de Fri Jun 5 09:21:32 1998 Received: from mailer.mpi-stuttgart.mpg.de (mailer.mpi-stuttgart.mpg.de [134.105.17.221]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA11324 Fri, 5 Jun 1998 09:21:31 -0400 (EDT) Received: from vsibm1.mpi-stuttgart.mpg.de by MAILER.MPI-STUTTGART.MPG.DE (PMDF V5.1-9 #20789) with SMTP id <01IXVRGX1GM08WY9X1@MAILER.MPI-STUTTGART.MPG.DE> for chemistry@www.ccl.net; Fri, 5 Jun 1998 15:20:39 CET Received: by vsibm1.mpi-stuttgart.mpg.de (AIX 4.1/UCB 5.64/4.03) id AA38972; Fri, 05 Jun 1998 15:22:54 +0200 Date: Fri, 05 Jun 1998 15:22:53 +0200 (MES) From: kaupp@vsibm1.mpi-stuttgart.mpg.de (Martin Kaupp) Subject: NMR-EPR-98, call for abstracts/registration To: chemistry@www.ccl.net Cc: kaupp@vsibm1.mpi-stuttgart.mpg.de (Martin Kaupp), malkin@savba.sk (Vladimir Malkin), NMR98@savba.sk (NMR98 conference office) Message-id: <9806051322.AA38972@vsibm1.mpi-stuttgart.mpg.de> Content-type: text ############################################################################ Call for Abstracts - Registration Open ---------------------------------------------------------------------------- CONFERENCE ON "Quantum Chemical Calculations of NMR and EPR Parameters" Bratislava (castle Smolenice), Slovakia, on 14 - 18 September, 1998. ---------------------------------------------------------------------------- The conference is open for registration, and the second circular has been sent to those persons who had sent preliminary registration forms. The second circular, including registration forms and further information, is also available on the following conference web pages: http://www.theochem.uni-stuttgart.de/~mkaupp/smolen.html http://www.savba.sk/sav/inst/uach/smolen.html Deadlines for registration are June 15, 1998 (early registration) and August 1, 1998 (late registration). The deadline for Abstracts is also August 1, 1998. Please note that the number of participants has to be limited, and early registration is recommended. ---------------------------------------------------------------------------- If you need further information, please contact: NMR-EPR-98 Institute of Inorganic Chemistry Slovak Academy of Sciences Dubravska Cesta 9 SK-84236 Bratislava Slovak Republic e-mail: NMR98@savba.sk ---------------------------------------------------------------------------- Preliminary list of invited and plenary lecturers: ------------------------------------------------------ V. Barone (Napoli, Italy) R. J. Bartlett (Gainesville,USA) M. Buehl (Zuerich,Switzerland) D. M. Chipman (Notre Dame,USA) S. Colwell (Cambridge,UK) H. Ebert (Muenchen, Germany) B. Engels (Bonn,Germany) L. A. Eriksson (Stockholm, Sweden) R. R. Ernst (Zuerich,Switzerland) J. C. Facelli (Salt Lake City,USA) U. Fleischer (Bochum, Germany) J. Gauss (Mainz,Germany) C. J. Jameson (Chicago,USA) S. Karna (USAF,USA) P. Lazzeretti (Modena, Italy) G. H. Lushington (Columbus, USA) F. Mauri (Lausanne, Switzerland) A. Pines (Berkeley, USA) P. Pulay (Fayetteville,USA) W. T. Raynes (Sheffield, UK) K. Ruud (Oslo,Norway) E. Roduner (Stuttgart, Germany) D. R. Salahub (Montreal, Canada) K. Schwarz (Wien, Austria) N. M. Sergeyev (Moscow, Russia) O. Vahtras (Linkoeping, Sweden) E. van Lenthe (Amsterdam, The Netherlands) L. Visscher (Amsterdam, The Netherlands) P. von R. Schleyer (Erlangen,Germany) R. E. Wasylishen (Halifax,Canada) J. Weber (Geneva,Switzerland) T. Ziegler (Calgary,Canada) ------------------------------------------ ----------------------------------------------------------------------------