From chemistry-request@server.ccl.net Thu Apr 18 04:23:52 2002 Received: from radon.pc.helsinki.fi (postfix@[128.214.14.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3I8Npj04535 for ; Thu, 18 Apr 2002 04:23:51 -0400 Received: from fermium.pc.helsinki.fi (fermium.pc.helsinki.fi [128.214.14.205]) by radon.pc.helsinki.fi (Postfix) with ESMTP id 2CF221E689 for ; Thu, 18 Apr 2002 11:23:45 +0300 (EEST) Received: by fermium.pc.helsinki.fi (Postfix, from userid 522) id 2380B1233A; Thu, 18 Apr 2002 11:23:39 +0300 (EEST) Date: Thu, 18 Apr 2002 11:23:39 +0300 To: chemistry@ccl.net Subject: VIEWMOL PROBLEM Message-ID: <20020418082339.GA950@chem.helsinki.fi> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.25i From: straka@chem.helsinki.fi (Michal Straka) Dear CCLers, I tried to setup viewmol to show distances in pm instead of Angstroms, in a way as is written on http://viewmol.sourceforge.net/documentation/node29.html, editing the .Xdefaults file in $HOME. It doesn't work. Even if I change Ang to pm in Xdefaults in viewmol default directory it doesn't help. Does someone know where could be the problem? (viewmol was installed from Debian package on Debian machine) Michal -- I----------------------------------------------------------------------------I I Michal Straka Telephone: 358-9-191 50173 I Department of Chemistry Secretary: 358-9-191 50170 I P.O.B. 55 (A.I. Virtasen aukio 1) FAX: 358-9-191 50169 I FIN-00014 Helsinki E-mail: straka@chem.helsinki.fi I Finland http://www.chem.helsinki.fi/~straka I I----------------------------------------------------------------------------I From chemistry-request@server.ccl.net Thu Apr 18 05:49:30 2002 Received: from thor.chem.sdu.dk ([130.225.142.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3I9nTj06377 for ; Thu, 18 Apr 2002 05:49:29 -0400 Received: from localhost (tetz@localhost) by thor.chem.sdu.dk (SGI-8.9.3/8.9.3) with ESMTP id LAA17843 for ; Thu, 18 Apr 2002 11:52:12 +0200 (MDT) Date: Thu, 18 Apr 2002 11:52:11 +0200 From: Per Tetzschner Olsen To: chemistry@ccl.net Subject: Tinker: atom type format for OPLSAA or AMBER Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCL I am working with the TINKER package (ver. 3.9), because I am interested in the analytical Gradient and the 'not diagonalized' Hessian for different kinds of molecular systems. TINKER has the advantage that you can use several FF. Because of no Graphical interface, where you can draw your molecules I am using Macromodel ver. 7.0 (which is not capable of calculate the 'not diagonalized' Hessian). My problem is when converting from Macromodel format (.dat or PDB) to TINKER (.xyz) with Babel or pdbxyz.x I received atomtypes for the molecule saying 0 (with PDBXYZ.x) or the atomtype belonging to MM3. What about a program which is capable of converting into OPLSAA, AMBER etc. ???? I think of a program of my own, which is capable of reading: 1. The atom type (C,H,N.....) 2. The connectivity 3. If the atom belongs to a substructure (i.e. DNA-part) and convert the atom type into the approriate atom number for a chosen FF in TINKER. I would appreciate if anyone have written or know to the existence of such program, because manually converting of 500 atoms molecules takes for ever (or just really long time) regards Per Tetzschner University of Southern Denmark tetz@thor.chem.sdu.dk +45-65502570 From chemistry-request@server.ccl.net Thu Apr 18 02:45:16 2002 Received: from web11108.mail.yahoo.com ([216.136.131.155]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g3I6jGj02365 for ; Thu, 18 Apr 2002 02:45:16 -0400 Message-ID: <20020418064502.17605.qmail@web11108.mail.yahoo.com> Received: from [137.158.128.17] by web11108.mail.yahoo.com via HTTP; Thu, 18 Apr 2002 07:45:02 BST Date: Thu, 18 Apr 2002 07:45:02 +0100 (BST) From: =?iso-8859-1?q?Jeff=20C?= Subject: Intra-molecular hydrogen bonds To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi CCLers, Can anyone please help me out here. Using g98, what is the more reliable method when one tries to evaluate the distribution, as well as the strength, of each intra-molecular hydrogen bonds formed between three or more functional groups found within the same molecule. All responses appreciated. Many thanks. Jeff __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page > from News and Sport to Email and Music Charts http://uk.my.yahoo.com From chemistry-request@server.ccl.net Thu Apr 18 05:55:14 2002 Received: from webnii.nii.res.in ([202.54.102.178]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3I9tCj06504 for ; Thu, 18 Apr 2002 05:55:13 -0400 Received: from localhost by webnii.nii.res.in (8.8.8/1.1.22.3/28Dec99-1231PM) id PAA0000005130; Thu, 18 Apr 2002 15:25:27 +0500 (GMT+0500) Date: Thu, 18 Apr 2002 15:25:26 +0500 (GMT+0500) From: Gitanjali Yadav To: amor san juan cc: chemistry@ccl.net Subject: Re: CCL:mol2topdbq.awk missing: AutoDock3 In-Reply-To: <20020416113923.95398.qmail@web12801.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII dear juan the size of the Autodock3.0 dist_3.0.tar.gz file i got is 12726377 bytes and it is the same as yours. the mol2topdbq.awk script is missing in my case also(on sgiIRIX6.5) my version is infact missing scripts 'prepare' and 'chckqs' and another .awk script! I worked around these and managed to get the software functioning by using two other softwares *For pdbq,Try downloading the GUI for autodock, called Autodocktools it is freely available at http://www.scripps.edu/pub/olson-web/doc/autodock/tools.html (on the pdbq file, use 'addsol' to add solvation parameters) *A better option for charges would be to use MSI InsightII The rest of the scripts are alright but may not work in some csh shells. They too start working after changing them to suit your environment or splitting them into smaller scripts. i hope this helps you. **************************************************************************** \ / | \ / \ / | | GITANJALI YADAV JUNIOR RESEARCH FELLOW BIOINFORMATICS UNIT NATIONAL INSTITUTE OF IMMUNOLOGY ARUNA ASAF ALI MARG NEW DELHI-110067 INDIA. PHONE:9111- 6162281/6103008/6183004/6163009-ext 424 ***************************************************************************** From chemistry-request@server.ccl.net Thu Apr 18 08:25:22 2002 Received: from aspirine.u-strasbg.fr ([130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3ICPLj08677 for ; Thu, 18 Apr 2002 08:25:21 -0400 Received: from hit8.pharma.u-strasbg.fr (lead2.u-strasbg.fr [130.79.85.21]) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id g3ICM0g05610 for ; Thu, 18 Apr 2002 14:22:00 +0200 Message-Id: <5.1.0.14.0.20020418142018.01744ba8@aspirine.u-strasbg.fr> X-Sender: rognan@aspirine.u-strasbg.fr X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 18 Apr 2002 14:25:01 +0200 To: chemistry@ccl.net From: Didier Rognan Subject: Docking dataset & ConsDock Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed To all of you who could not open the compressed archive file: The file was effectively corrupted (I am deeply sorry). A new one can be now downloaded at http://med-chem.u-strasbg.fr/~didier/db/dock_base.html Sorry for this disagreement, Best regards ----------------------------------------------------------------------------------------------- Dr. Didier ROGNAN Directeur de Recherches - CNRS Laboratoire de Pharmacochimie de la Communication Cellulaire UMR 7081 74, route du Rhin, B.P.24 F-67401 Illkirch phone: +33 (0)3 90 24 42 35 fax: +33 (0)3 90 24 43 10 mobile: +33 (0)6 89 56 24 46 email: didier.rognan@pharma.u-strasbg.fr From chemistry-request@server.ccl.net Thu Apr 18 09:24:06 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3IDO5j09685 for ; Thu, 18 Apr 2002 09:24:05 -0400 Received: from unisi.it (ccmaol3.chim.unisi.it [192.167.123.208]) by unisi.it (PMDF V6.0-24 #43309) with ESMTPA id <01KGPJLZFUF6000YX3@unisi.it> for chemistry@ccl.net; Thu, 18 Apr 2002 12:39:23 +0100 (MET) Date: Thu, 18 Apr 2002 12:39:58 +0200 From: "Nicolas Ferre'" Subject: Re: CCL:Tinker: atom type format for OPLSAA or AMBER Sender: ferre@unisi.it To: Per Tetzschner Olsen Cc: chemistry@ccl.net Message-id: <3CBEA27E.6F5C4983@unisi.it> Organization: Universita` di Siena MIME-version: 1.0 X-Mailer: Mozilla 4.61i [en_US] (X11; I; AIX 4.3) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: fr, en References: Hi, In principle, Molden should be used for your purpose (i.e. Tinker's Amber, MM3 and Charmm forcefields), but unfortunatly the actual conversion (pdb -> FF) does not match the last version of Tinker parameters (version 3.9). Let's hope it will be corrected soon (this is a request to G. Schaftenaar, Molden's author), or you can correct the Molden source yourself ... Nicolas Per Tetzschner Olsen wrote: > > Hi CCL > > I am working with the TINKER package (ver. 3.9), because I am > interested in the analytical Gradient and the 'not diagonalized' > Hessian for different kinds of molecular systems. TINKER has > the advantage that you can use several FF. > > Because of no Graphical interface, where you can draw your > molecules I am using Macromodel ver. 7.0 (which is not capable > of calculate the 'not diagonalized' Hessian). > > My problem is when converting from Macromodel format (.dat or PDB) > to TINKER (.xyz) with Babel or pdbxyz.x I received atomtypes > for the molecule saying 0 (with PDBXYZ.x) or the atomtype belonging > to MM3. What about a program which is capable of converting into > OPLSAA, AMBER etc. ???? > > I think of a program of my own, which is capable of reading: > > 1. The atom type (C,H,N.....) > 2. The connectivity > 3. If the atom belongs to a substructure (i.e. DNA-part) > > and convert the atom type into the approriate atom number for > a chosen FF in TINKER. > > I would appreciate if anyone have written or know to the existence > of such program, because manually converting of 500 atoms molecules > takes for ever (or just really long time) > > regards > > Per Tetzschner > > University of Southern Denmark > tetz@thor.chem.sdu.dk > +45-65502570 > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE' (PhD) phone/fax : +39-0577-234278 Dipartimento di Chimica Universita` di Siena mailto:ferre@unisi.it via Aldo Moro 53100 SIENA (Italia) http://ccmaol1.chim.unisi.it/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Thu Apr 18 10:50:27 2002 Received: from mr3.cc.ic.ac.uk ([155.198.5.113]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3IEoQj12308 for ; Thu, 18 Apr 2002 10:50:26 -0400 Received: from icex9.cc.ic.ac.uk ([155.198.3.9]) by mr3.cc.ic.ac.uk with esmtp (Exim 3.35 #1) id 16yDEr-0006uZ-03 for CHEMISTRY@ccl.net; Thu, 18 Apr 2002 15:50:21 +0100 Received: from [155.198.234.86] (rzepa-mac.ch.ic.ac.uk [155.198.234.86]) by icex9.cc.ic.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id G4N7HTSW; Thu, 18 Apr 2002 15:50:18 +0100 Mime-Version: 1.0 X-Sender: rzepa@argon.ch.ic.ac.uk Message-Id: Date: Thu, 18 Apr 2002 15:50:13 +0100 To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: Sourceforge, Chemistry, XML and CML Content-Type: text/plain; charset="us-ascii" This is sort of a general purpose post with several observations and some information to post 1. Many of you know about http://www.sourceforge.net (but if you don't, you should). It supports around 37,000 OpenSource projects. 2. It was a small surprise to me to find relatively few references on the CCS pages to it (about 30, going back two years). 3. Given this, it was perhaps no surprise to find they have no subject category such as "chemistry" or "molecular science" at sourceforege. Bio-informatics certainly has! Remember, we are the community that started this with the QCPE archive in the early 1960s! Whatever happened? 4. Well, it will hardly come as a surprise to see me posting: http://cml.sourceforge.net/ Its still early days , but this site will contain much to do with XML, such as XML libraries, including XSD (schemas), XSLT (filters and transformations) and various Java-based tools, mostly relating to CML (Chemical markup language) Its software, "but not as you may know it". If you wish to learn, ask FAQs, or make contributions, do please consider joining the mailing list linked to the site. 5. An of course we join a select community of other chemistry projects homed there. A short list of these exists on our site, but no doubt it will grow (and apologies to anyone who is not there yet, let me know and you will be!) -- Henry Rzepa. +44 (0870) 132 3747 (eFax) +44 0778 6268 220 (Mobile) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College, London, SW7 2AY, UK. From chemistry-request@server.ccl.net Thu Apr 18 12:23:26 2002 Received: from juliet.schrodinger.com ([192.156.98.102]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3IGNPj14801 for ; Thu, 18 Apr 2002 12:23:25 -0400 Received: from localhost (jshelley@localhost) by juliet.schrodinger.com (8.9.3/8.9.3) with ESMTP id JAA23057; Thu, 18 Apr 2002 09:22:30 -0700 X-Authentication-Warning: juliet.schrodinger.com: jshelley owned process doing -bs Date: Thu, 18 Apr 2002 09:22:30 -0700 (PDT) From: John Shelley To: Per Tetzschner Olsen cc: chemistry@ccl.net Subject: Re: CCL:Tinker: atom type format for OPLSAA or AMBER In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Per, Sorry if I misunderstand your query. On Thu, 18 Apr 2002, Per Tetzschner Olsen wrote: > > Hi CCL > > I am working with the TINKER package (ver. 3.9), because I am > interested in the analytical Gradient and the 'not diagonalized' > Hessian for different kinds of molecular systems. TINKER has > the advantage that you can use several FF. > > Because of no Graphical interface, where you can draw your > molecules I am using Macromodel ver. 7.0 (which is not capable > of calculate the 'not diagonalized' Hessian). MacroModel should be able to calculate the analytical gradient (from the command line). If you take the .com file from an energy listing run and include the command: DLST 1 Then run the job from the command line (not via the interface). The numerical and analytical first derivatives of the potential energy should be listed in the .log file. > > My problem is when converting from Macromodel format (.dat or PDB) > to TINKER (.xyz) with Babel or pdbxyz.x I received atomtypes > for the molecule saying 0 (with PDBXYZ.x) or the atomtype belonging > to MM3. What about a program which is capable of converting into > OPLSAA, AMBER etc. ???? > > I think of a program of my own, which is capable of reading: > > 1. The atom type (C,H,N.....) > 2. The connectivity > 3. If the atom belongs to a substructure (i.e. DNA-part) > > and convert the atom type into the approriate atom number for > a chosen FF in TINKER. > > I would appreciate if anyone have written or know to the existence > of such program, because manually converting of 500 atoms molecules > takes for ever (or just really long time) > > regards > > Per Tetzschner > > University of Southern Denmark > tetz@thor.chem.sdu.dk > +45-65502570 Hope this helps. If not you might try writing to help@schrodinger.com. John Shelley Senior Scientist Schrodinger, Inc. > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Apr 18 12:36:45 2002 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3IGajj15160 for ; Thu, 18 Apr 2002 12:36:45 -0400 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KGPJI624JM0036LZ@trentu.ca> for chemistry@ccl.net; Thu, 18 Apr 2002 12:36:18 EDT Date: Thu, 18 Apr 2002 12:38:31 -0400 From: elewars Subject: Comp Chem courses, Summary To: chemistry@ccl.net Message-id: <3CBEF686.37B7D813@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (WinNT; U) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT X-Accept-Language: en 2002 April 18 Here is the summary of replies; I apologize if I have omitted someone. ========= The question 2002 April 8 Hello, If anyone knows approximately, or even has just a rough idea, how many universities in North America (or anywhere else, if you know) offer a course in computational chemistry, I would very much appreciate this information. Even an educated guess could be useful. Thank you. E. Lewars ================= The replies, #1--#11 #1 Mon, 08 Apr 2002 16:43:47 -0700 (PDT) From: "J. Zheng" To: elewars http://pollux.chem.umn.edu/~kormos/8021/ use google to search Computational chemistry course, you will find a lot websites related to this course. ----------------------------------------------- | JIE ZHENG | | Department of Chemical Engineering | | University of Washington | | Seattle, WA 98105, USA | ----------------------------------------------- | Tel: (206) 616-6510 (o) | | Email: jzheng73@u.washington.edu | | Webpg: students.washington.edu/jzheng73 | ----------------------------------------------- ---------- #2 For several years the Northern Territory University, Swinburne University of Technology and Monash University with the help of one person at the University of Tasmania have offered a M Sc in Computational Chemistry which is 2/3 taught over the internet followed by a residential period of research project. The same people teach a Graduate Diploma in Computational Chemistry, but awarded only by the Northern Territory University, comprising just the 2/3 internet units. This has been quite amazingly unsuccessful as we have had few students. For this reason and also because I formally retired on Dec 31st last year and one other member of the team is approaching retirement, we have discontinued both programs, but are still teaching continuing students. Our students are based in the US, Malaysia, Taiwan, England, Singapore, India and one from Australia. Have a look at:- http://lacebark.ntu.edu.au/msc/ Regards, Brian. Brian Salter-Duke (Brian Duke) b_duke@octa4.net.au Honorary Fellow in Chemistry, NT University, Darwin, NT 0909, Australia. Post: Box 1028, Humpty Doo, NT 0836, Australia. Phone 08-89881600. Fax 08-89881302. http://www.octa4.net.au/linden/brian/ ---------------- #3 The University of Nottingham, UK, has three and four year courses in Chemistry with Computational Chemistry. http://www.nottingham.ac.uk/chemistry/student-opportunities/undergraduate/co mpchem.html http://www.nottingham.ac.uk/chemistry/teaching/undergraduate/handbooks/compu tational_chemistry/index.html Best wishes, Richard Wheatley. Richard Wheatley, School of Chemistry, University of Nottingham "Exploring Modern Computational Chemistry" University of Nottingham, July 31 - Aug 2, 2002 http://www.nottingham.ac.uk/chemistry/emc2 --------------------- #4 Hello, I know that there are courses in computational chemistry at the University of Geneva, both for undergraduate and graduate students. Pascal Dr. Pascal Boulet Queen Mary, University of London Centre for Computational Science Department of Chemistry Mile End Road London, E1 4NS UK Phone: (+44) (0)20 7882 7759 fax: (+44) (0)20 7882 7794 -------------- #5 Hi, I can only speak from my own perspective... In Ireland Trinity College Dublin (www.tcd.ie) offers a BSc. in computational chemistry (and physics); in University College Dublin (www.ucd.ie) and at Dublin City University (www.dcu.ie) it is possible to do computational chemistry in the third and fourth years. hope this helps regards michael ******************************************************* Michael Nolan Computational Modelling, NMRC Lee Maltings, Prospect Row, Cork, IRELAND michael.nolan@nmrc.ie; http://www.nmrc.ie/research/computational-modelling-group/index.html http://www.asdn.net Tel: + 353 21 4904113; Fax: +353 21 4270271 ******************************************************** ------------- #6 We offer a dual-level course in Chemical Engineering at the University of Cincinnati each year that receives very high enrollment (typically 30-40). Joel R. Fried Professor and Head Department of Chemical Engineering University of Cincinnati Cincinnati, Ohio 45221-0171 Director, Ohio Molecular Computation and Simulation Network and Center for Computer-Aided Molecular Design (513) 556-2761 Fax: 556-3473 Email: Joel.Fried@UC.Edu Home page: http://www.chemical.uc.edu/fried.html ******************************************************************** -------------- #7 9.04.02 Dear Prof. Lewars, In a collaborative effort, seventeen spanish universities offer together a PhD course on Theoretical and Computational Chemistry. The Universities involved are Euskal Herriko Unibersitatea, Universitat Autònoma de Barcelona, Universidad Autónoma de Madrid, Universitat de Barcelona, Universidad de Cantabria, Universidad Complutense de Madrid, Universidad de Extremadura, Universitat de Girona, Universidad de Granada, Universitat de les Illes Balears, Universitat Jaume I, Universidad de Oviedo, Universidad de Salamanca, Universidad de Sevilla, Universitat Rovira i Virgili, Universitat de València, and Universidad de Valladolid. See for instance: http://www.udg.edu/publicacions/doctorat/2001-2002/spa/quimica.pdf and http://www.udg.edu/publicacions/doctorat/2000-2001/pdf/17Qumica.pdf Best regards, Miquel -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* Dr. Miquel Solà Departament de Química i Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona, CATALONIA (Spain) Phone: +(34).972.41.89.12 Cellular-Phone: +(34).626.16.35.80 FAX: +(34).972.41.83.56 World Wide Web: http://iqc.udg.es/~miquel/mike.html e-mail: miquel.sola@udg.es -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* --------------- #8 From: Gemma Kinsella Hi, Theres a 4 year comp chem/physics course in Trinity College Dublin as well, students can specialise in the 3rd year and chose either physics or chemistry as their major then. Hope that helps a little, Gemma ------------------- #9 I have no idea how many universities offer such a course, but Brock has one on the graduate level titled: Computational Chemisty: Applications in Biotechnology. This course is CHEM 5P14 crosslisted as BTEC 5P14. We don't have such a course on the undergraduate level, ignoring the third year course in quantum chemistry which has nothing on force fields and the like. Yours sincerely Stuart M. Rothstein, Professor of Chemistry and Physics, Director, Brock "Institute" for Scientific Computation (B"I"SC), Brock University, St. Catharines, Ontario, L2S 3A1 CANADA srothste@abacus.ac.brocku.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/rothstein/ ------------------ #10 From: Johannes Weber Hi, some time ago I searched in the WWW for universities with a theoretical chemistry department. There was a webpage of the german academic exchange service (DAAD) where you had to fill in a form and got the universities back out of a database. I suppose this must be available in other languages/countries, too. Alas, I don´t remember the URL but probably google and friends will give you this information. After filtering out the universities teaching theoretical chemistry you may have a look at the department´s webpage for the courses in computational chemistry. (I guess, nearly every Theor. Chem. Dept. offers a course.) Hope it helps, :-)ohannes PS: This information would also be of interest for me. If you find a complete list, would you be so kind and summarize it ? ----------------------- #11 From: ysabnis@yahoo.com Hello Elewars, Our university offers 2 courses in molecular modeling. One is QSAR and the other is basics in molecular modeling. I am a graduate student at the University of Mississippi. Let me know if you need any other help. cheeers! Yogi ======================================== ============================ ================= From chemistry-request@server.ccl.net Thu Apr 18 12:40:20 2002 Received: from thing2.dev.netgenics.com ([63.69.121.199]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3IGeKj15221 for ; Thu, 18 Apr 2002 12:40:20 -0400 Received: from netgenics.com (coronado-15.dev.netgenics.com [192.168.150.215]) by thing2.dev.netgenics.com (8.10.2+Sun/8.10.2) with ESMTP id g3IGdxg26550; Thu, 18 Apr 2002 12:40:07 -0400 (EDT) Message-ID: <3CBEF6DA.82A4E270@netgenics.com> Date: Thu, 18 Apr 2002 09:39:54 -0700 From: Scott Markel Organization: LION bioscience Inc. X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net CC: "Rzepa, Henry" Subject: Re: CCL:Sourceforge, Chemistry, XML and CML References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit CCL readers may also be interested in the OpenScience Project, which lists 89 efforts in chemistry. The next most populated category is mathematics with 56. Life sciences has 35. For more information see http://www.openscience.org. Scott "Rzepa, Henry" wrote: > > This is sort of a general purpose post with several observations and some > information to post > > 1. Many of you know about http://www.sourceforge.net (but if you don't, you > should). It supports around 37,000 OpenSource projects. > > 2. It was a small surprise to me to find relatively few references on the > CCS pages to it (about 30, going back two years). > > 3. Given this, it was perhaps no surprise to find they have no subject category > such as "chemistry" or "molecular science" at sourceforege. > Bio-informatics certainly has! > Remember, we are the community that started this with the QCPE archive > in the early 1960s! Whatever happened? > > 4. Well, it will hardly come as a surprise to see me posting: > http://cml.sourceforge.net/ > > Its still early days , but this site will contain much to do with > XML, such as XML libraries, including XSD (schemas), > XSLT (filters and transformations) > and various Java-based tools, mostly relating to CML (Chemical markup language) > Its software, "but not as you may know it". > > If you wish to learn, ask FAQs, or make contributions, do please consider > joining the mailing list linked to the site. > > 5. An of course we join a select community of other chemistry projects > homed there. A short list of these exists on our site, but no doubt it > will grow (and apologies to anyone who is not there yet, let me know and > you will be!) > -- > > Henry Rzepa. > +44 (0870) 132 3747 (eFax) +44 0778 6268 220 (Mobile) > http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College, London, SW7 2AY, UK. -- Scott Markel, Ph.D. LION bioscience Inc. scott.markel@lionbioscience.com 4350 Executive Drive Tel: 858 455 5223 Suite 260 FAX: 858 455 1388 San Diego, CA 92121 From chemistry-request@server.ccl.net Thu Apr 18 14:05:11 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3II5Bj16727 for ; Thu, 18 Apr 2002 14:05:11 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id OAA24863; Thu, 18 Apr 2002 14:05:00 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3CBF001E.F3F0B2A1@cornell.edu> Date: Thu, 18 Apr 2002 13:19:26 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: SOLANA Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all Does anybody know if there is any documentation for the CHARMM solvent analysis facility called SOLANA anywhere? Thanks, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu Apr 18 17:16:10 2002 Received: from pollux.chem.umn.edu ([128.101.156.56]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3ILGAj20741 for ; Thu, 18 Apr 2002 17:16:10 -0400 Received: (from cramer@localhost) by pollux.chem.umn.edu (8.9.3/8.9.3) id QAA12580; Thu, 18 Apr 2002 16:15:59 -0500 (CDT) From: Christopher Cramer Message-Id: <200204182115.QAA12580@pollux.chem.umn.edu> Subject: Re: CCL:Comp Chem courses, Summary To: elewars@trentu.ca (elewars) Date: Thu, 18 Apr 2002 16:15:59 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <3CBEF686.37B7D813@trentu.ca> from "elewars" at Apr 18, 2002 12:38:31 PM X-Mailer: ELM [version 2.5 PL2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Note that the most modern "version" of the site listed below is actually http://vesta.chem.umn.edu/classes/ch8021/2002/ch8021s02.htm while the pollux site is more of an archive of past course materials (which may, of course, be very useful). CJC elewars > > > 2002 April 18 > > Here is the summary of replies; I apologize if I have omitted someone. > ========= > The question > > 2002 April 8 > > Hello, > > If anyone knows approximately, or even has just a rough idea, how many > universities in North America (or anywhere else, if you know) offer a > course in computational chemistry, I would very much appreciate this > information. Even an educated guess could be useful. > > Thank you. > > E. Lewars > ================= > The replies, #1--#11 > > #1 > Mon, 08 Apr 2002 16:43:47 -0700 (PDT) > From: > "J. Zheng" > To: > elewars > > http://pollux.chem.umn.edu/~kormos/8021/ > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 cramer@pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about new textbook "Essentials of Computational Chemistry: Theories and Models")