From chemistry-request@ccl.net Wed Mar 24 20:23:06 2004 Received: from ns3.twi.com.br (ns3.twi.com.br.60.192.200.in-addr.arpa [200.192.60.5] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with SMTP id i2P1N2js019267 for ; Wed, 24 Mar 2004 20:23:03 -0500 Message-Id: <200403250123.i2P1N2js019267^at^server.ccl.net> Received: (qmail 66876 invoked by uid 1002); 24 Mar 2004 22:25:35 -0300 Received: from info^at^colacro.com by ns3.twi.com.br by uid 82 with qmail-scanner-1.20 (uvscan: v4.3.20/v4341. spamassassin: 2.63. Clear:RC:1(200.158.222.123):. Processed in 1.324515 secs); 25 Mar 2004 01:25:35 -0000 Received: from unknown (HELO info^at^colacro.com) (200.158.222.123) by twi-mail.freebsdbrasil.com.br with SMTP; 24 Mar 2004 22:25:33 -0300 Reply-To: "COLACRO X" From: "COLACRO X" To: Subject: COLACRO X - Congresso Latino Americano de Cromatografia e Ticnicas Afins Date: Wed, 24 Mar 2004 20:15:22 -0300 MIME-Version: 1.0 Content-Type: text/html; charset="us-ascii" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Qmail-Scanner-Message-ID: <108017793365266833^at^ns3.twi.com.br> X-Spam-Status: No, hits=5.6 required=7.0 tests=FORGED_MUA_OUTLOOK,HTML_70_80, HTML_COMMENT_RATIO,HTML_MESSAGE,MIME_HTML_ONLY,RCVD_IN_DYNABLOCK, RCVD_IN_NJABL,RCVD_IN_NJABL_PROXY,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Level: ***** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net 10o

10o. Congresso Latino-Americano de Cromatografia e Ticnicas Afins

(COLACRO X)

 

 

Arts & Convention Center, Campos do Jordco (SP) Brasil

20-22 de Outubro de 2004 (Cursos: 18 e 19)

 

O 10o. Congresso Latino-Americano de Cromatografia e Ticnicas Afins (COLACRO X) sera realizado de 20 a 22 de Outubro de 2004. Antecedendo o evento, e seguindo a tradigco estabelecida desde o COLACRO I, nos dias 18 e 19 de Outubro serco oferecidos varios Cursos de Atualizagco (Pri-Congresso) em diversas areas da cromatografia e ticnicas correlatas, ministrados por convidados do exterior e pesquisadores nacionais.

Pesquisadores de renome internacional estarco apresentando as zltimas novidades e projetando as tendjncias futuras em seu campo de especializagco, na forma de Conferjncias Plenarias. Os Expositores, em nzmero expressivo de stands ja confirmados, irco mostrar as zltimas novidades em instrumentagco, acesssrios e literatura na area. Os Patrocinadores estarco apresentando, atravis de seus especialistas, Seminarios Ticnicos visando informar os usuarios sobre os mais recentes avangos na area. Tspicos de grande interesse na atualidade serco discutidos por especialistas atravis de Tutoriais especmficos. A Sessco de Painiis (Ptsteres), sempre muito concorrida, permitira aos interessados apresentarem e discutirem os resultados de seus trabalhos (envio de resumos ati 01 de Setembro de 2004).

Contamos com sua presenga no maior e mais importante fsrum para discussco dos zltimos desenvolvimentos na area de Cromatografia e correlatas da Amirica Latina. Para maiores informagues envie uma mensagem para info^at^colacro.com ou consulte nosso website www.colacro.com.

 

Prof. Dr. Fernando M. Langas,

COLACRO X, Chairman

From chemistry-request@ccl.net Thu Mar 25 12:25:24 2004 Received: from osgood.cc.nd.edu (osgood.cc.nd.edu [129.74.250.227]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2PHPNjs016740 for ; Thu, 25 Mar 2004 12:25:23 -0500 Received: from localhost (localhost [127.0.0.1]) by osgood.cc.nd.edu (Switch-3.1.4/Switch-3.1.0) with ESMTP id i2PHSHrN016724; Thu, 25 Mar 2004 12:28:17 -0500 (EST) Received: from laptop.ccl.net (laptop.ccl.net [129.74.52.62]) by webmail.nd.edu (IMP) with HTTP for ; Thu, 25 Mar 2004 12:28:17 -0500 Message-ID: <1080235697.406316b194fc5$at$webmail.nd.edu> Date: Thu, 25 Mar 2004 12:28:17 -0500 From: Jan K Labanowski To: chemistry$at$ccl.net Cc: jlabanow$at$nd.edu Subject: Which Linux to use in a research/educational envioronment? MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 129.74.52.62 X-ND-MTA-Date: Thu, 25 Mar 2004 12:28:19 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4343 X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL, With Linux getting more popular and becoming a commercial entity one, has to make a decision what to install on his/her desktop. The situation is even more complicated, if you need to install Linux on hundreds of desktops. The critical points from my perspective are: 1) Which flavor/vendor of Linux will be supported by the vendors of application software. As much, as I may like Debian, many commercial packages will not work with it (e.g., due to file system differences). 2) What is the deployment cost (in a broad sense, "the real cost of ownership"): a) how much you need to pay for the license (for example some "Enterprise" Linux distributions)? b) how solid is a linux distribution and how much time you need to install it and make it work? c) How much maintainance is required? i) The "Enterprise" (and pricy) Linuces promise stability, easy upgrade and patching paths, and Administration tools, which make maintainance easier for large installed base. They also promise continuity and backward compatibility for older packages installed on your computer. ii) The "development" (and free) Linuces will require frequent patches, release upgrades, etc. You will most likely face glibc compatibility problems for many packages when you upgrade, have constant problems with kernel versions (e.g., for device drivers, which require recompilation for specific kernel), etc., etc... 3) Portability... Related to the above. If you compile your software on one Linux, can you expect it to run on many other Linux boxes, or only on a specific flavor of Linux. There are obviously more issues. I will summarize the answers and will make sure that I protect the sources (for corporate respondees, this may be important). Thanks in advance Jan -- Jan K. Labanowski, Ph.D. Tel. (574) 631-4565 Science Computing Facility FAX (574) 631-9293 University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556-5670 From chemistry-request@ccl.net Thu Mar 25 11:12:59 2004 Received: from linus.ornl.gov (linus.ornl.gov [160.91.244.219]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2PGCwjs013858 for ; Thu, 25 Mar 2004 11:12:58 -0500 Received: by linus.ornl.gov (Postfix, from userid 600) id E0B7C3B7C8; Thu, 25 Mar 2004 10:58:29 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by linus.ornl.gov (Postfix) with ESMTP id DEC003B25C for ; Thu, 25 Mar 2004 10:58:29 -0500 (EST) Date: Thu, 25 Mar 2004 10:58:29 -0500 (EST) From: "Pratul K. Agarwal" To: chemistry^at^ccl.net Subject: Announcing live CD for bio/chemical modeling Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net http://www.vigyaancd.org/ Vigyaan is an electronic workbench for computational biology and computational chemistry. It has been designed to meet the needs of both beginners and experts. VigyaanCD is a Linux-live CD containing all the required software to boot the computer with ready to use modeling software. From chemistry-request@ccl.net Thu Mar 25 14:31:49 2004 Received: from smtp3.Stanford.EDU (smtp3.Stanford.EDU [171.67.16.117]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2PJVmjs021318 for ; Thu, 25 Mar 2004 14:31:49 -0500 Received: from cardinal4.Stanford.EDU (cardinal4.Stanford.EDU [171.64.15.252]) by smtp3.Stanford.EDU (8.12.11/8.12.11) with ESMTP id i2PJYiwc019420 for ; Thu, 25 Mar 2004 11:34:44 -0800 Received: from cardinal4.Stanford.EDU (localhost.localdomain [127.0.0.1]) by cardinal4.Stanford.EDU (8.12.10/8.12.10) with ESMTP id i2PJYePS006675 for ; Thu, 25 Mar 2004 11:34:44 -0800 Received: (from gorelsky@localhost) by cardinal4.Stanford.EDU (8.12.10/8.12.8/Submit) id i2PJYWcx006632; Thu, 25 Mar 2004 11:34:32 -0800 Date: Thu, 25 Mar 2004 11:34:32 -0800 (PST) From: "S.I.Gorelsky" To: CHEMISTRY:at:ccl.net Subject: SWizard and AOMix updates Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, I would like to let SWizard and AOMix users know that the updated versions of the programs are available for downloading. The updated version of AOMix can perform Lowdin population analysis. With best regards, S. Gorelsky ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0553. ---------------------------------------------------------------- From chemistry-request@ccl.net Thu Mar 25 15:22:45 2004 Received: from btr0x1.rz.uni-bayreuth.de (btr0x1.rz.uni-bayreuth.de [132.180.8.29]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2PKMhjs023388 for ; Thu, 25 Mar 2004 15:22:44 -0500 Received: from uni-bayreuth.de (btbsx2.bio.uni-bayreuth.de [132.180.52.129]) by btr0x1.rz.uni-bayreuth.de (8.12.10/8.12.1) with ESMTP id i2PKPRpZ011255; Thu, 25 Mar 2004 21:25:27 +0100 (MET) Message-ID: <40634042.3080009*at*uni-bayreuth.de> Date: Thu, 25 Mar 2004 21:25:38 +0100 From: Timm Essigke User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6a) Gecko/20031029 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry*at*ccl.net, jlabanow*at*nd.edu Subject: Re: CCL:Which Linux to use in a research/educational envioronment? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Jan, > Dear CCL, > > With Linux getting more popular and becoming a commercial entity > one, has to make a decision what to install on his/her desktop. > The situation is even more complicated, if you need to install Linux > on hundreds of desktops. I think it depends on experience and personal taste. It is a great question to start a flame war, since the points below are hard to analyse in an objective way. Who knows what future will bring us? The choice for installing something on the personal desktop and for hundreds of desktops is (maybe) different. For a single desktop, maybe having little experience with Linux a comercial insert-CD-and-press-button installation might be preferable. For hundreds of PCs one should think a bit more carefull: - How different will the desktops be? Best: To have only a few (one) groups of computers (maybe even with similar hardware), but this depends how similar the work of the users is. - What is more important: - stable system - long update cycles (not to install a new distro ever 3 months on all computers, as it is the case for some comercial) Or: - cutting edge features - newest software versions installed Probably you have to make a trade-off. Maybe you have some developers which depend on having the newest glibc or lots of feature loving kiddies which complain all the time if they have not the coolest newest features in their desktop environment. For me personally stability and security counts most and I want to have as little work as possible (sysadmin is not my main job, but I want to do my PhD at some point...). A desktop environment is good for placing lots of console windows, but I do not need any features except that it does not consume much space on my screen. But people comming from M$ are probably less puristic... > The critical points from my perspective are: > > 1) Which flavor/vendor of Linux will be supported by the vendors > of application software. As much, as I may like Debian, many > commercial packages will not work with it (e.g., due to file > system differences). In the moment there is no Linux distro with which you are free of such problems. Suse RPMs do not work for Redhat and vice versa. If you have to deal a lot with commercial packages from the US, Redhat is probably preferred. In Europe (esp. Germany) it will be Suse. For some open-source projects you may only find DEBs and tar, but no RPMs... So if you require some commercial package on all computers (and (re-)building a package or installing as tar (e.g. on a central fileserver) is not possible) you might take what the company forces you to use. (I would think twice if there is no alternative for the software...) I use Debian for our lab. If possible (and desired) I try to get DEBs and install them on all computers, but for special (scientific software, software with frequently new versions, e.g. browsers) I think it is better to have a central server and mount it to all desktops via NFS. So far it works fine for me. > > 2) What is the deployment cost (in a broad sense, "the real cost > of ownership"): > a) how much you need to pay for the license (for example > some "Enterprise" Linux distributions)? And how often you have to pay it. If you do not follow the upgrade path of the commercial distro and skip some updates it is quite likely that you will have to reinstall everything. > > b) how solid is a linux distribution and how much time you need > to install it and make it work? Solid: As stated above, is most important for me. Debian stable is therefore my preference - with some rebuild packages from testing for things I use often and the stable version is lacking function. It is an advantage from Debian that you can mix packages by using apt pinning. (Unfortunatly the official packages have different glibc versions, that recompiling is neccessary, but this is also widely automated in Debian) Installation time: On a single computer it might take longer because hardware autodetection is not that advanced as in some commercial distros, but I like it because I never trust plug-and-play... If you want to install hundreds of computers you can not do it individually anyway. You need a automated solution. Suse started relatively late with something like that and it was not very useable, when I looked at it (but this may have changed - it was over a year ago). Redhat has its kickstart, which seems to be useable. I have not used it myself, but know others who use it. For Debian there is FAI, which works fine. It takes a while to define what you actually want, but then you can install your 100 computers in 15 min (dependend on hardware, packageselection etc.). Make it work: I am not sure what you mean exactly. I guess you mean the postinstallation, after the installation program finished. This depends on your network infrastructure, e.g. how user management is organized, if you use DHCP or not, if you have centralized servers e.g. for printing etc. If you are very standard with everything, the installation program might be able to do everything right. If you are less standard, than it is more handwork, but this is automated by the network installation software. FAI is very flexible on that. Another point is to provide all the infrastructure (server for all services) needed in your network. This is more work than the 100 desktops if they are all the same. There are all-in-one solutions from some companies, but I personally don't like it when I don't know what is going on. If you installed everything by hand, you get a system suited for your needs and if there are errors you can debug them. With the commercial solutions you depend on the support - do you want that? For me security is as important as stability (an insecure system is not a reliable system). Therefore I don't trust any company solution. If I do it myself I know where the weaknesses are. Company solutions have usually the aim to replace a sysadmin by a GUI. Easy usage is more important than security. I think this is a missconception. > > c) How much maintainance is required? > i) The "Enterprise" (and pricy) Linuces promise stability, > easy upgrade and patching paths, and Administration tools, > which make maintainance easier for large installed base. > They also promise continuity and backward compatibility > for older packages installed on your computer. But mainly they want to sell new versions and support contracts. > ii) The "development" (and free) Linuces will require frequent > patches, release upgrades, etc. Debian Woody is there now since Jul 2002. Ofcause you have to do some security updates, but this can be nearly automated by some scripts. Patches etc. are only neccessary if you want to be cutting edge. > You will most likely face > glibc compatibility problems for many packages when > you upgrade, If you go to a newer glibc you have to upgrade many packages at the same time, but such dependencies are resolved automatically by apt. For most programs you can still get packages for older versions. I had more problems with Suse being ahead of certain package developments (not yet ready for the new version). > have constant problems with kernel versions > (e.g., for device drivers, which require recompilation > for specific kernel), etc., etc... If you need lots of exotic hardware... A conservative approach (what is really needed and provide only this) saves a lot of time. > > 3) Portability... Related to the above. If you compile your software on > one Linux, can you expect it to run on many other Linux boxes, > or only on a specific flavor of Linux. Depends, but it is not unlikely that you get problems with different libraries. But if you keep all computers the same, than there are no problems. If you have too many differences you will never get a running network because you have to care about each computer individually. Put time in automating things instead of redoing things on different computers. This scales much better. An advantage of Unix is that you CAN compile your software for your OS and architecture. This is what I understand by real portability... > > There are obviously more issues. I will summarize the answers and > will make sure that I protect the sources (for corporate respondees, > this may be important). > > Thanks in advance > > Jan In the end you have to try different distros yourself. Again, it depends on experience, time (full time admin or is something else your real job), how many computers and how similar there are, what the users do with them, if you prefer GUI or command line, if you want to know what is going on or if the software should be 'smart' etc. I started with Suse, but I failed with it. It was too much work to do upgrades between versions (3 months cycle) and after leaving one out I had to reinstall everyting. Suse follows its own concept of config files and if you start editing configs by hand instead of using Yast it will overwrite your changes the next time you use it (I know there are also configs for that...). There is no automated installation (or was at this time). Debian takes maybe a bit longer to get it running initially, but than saves you a lot of time on the long run. Stability improved a lot when going from Suse to Debian. I don't think it was completely Suses fault (early 2.4 kernels were not that stable, there were problems with ReiserFS, early NVidia drivers were unstable...), it was just my observation. With Redhat I have not much experience. I didn't like the company politics aiming for a monopoly on Linux (esp. in the US). We have something like that allready and we see where it leads... Hope all that helps, Timm From chemistry-request@ccl.net Thu Mar 25 15:55:19 2004 Received: from smtp1.server.rpi.edu (smtp1.server.rpi.edu [128.113.2.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2PKtIjs024615 for ; Thu, 25 Mar 2004 15:55:18 -0500 Received: from rpi.edu (omniocular-46.dynamic.rpi.edu [128.113.135.55]) by smtp1.server.rpi.edu (8.12.8/8.12.8) with ESMTP id i2PKw8HA002665; Thu, 25 Mar 2004 15:58:08 -0500 Message-ID: <406347B1.786CC12E.-at-.rpi.edu> Date: Thu, 25 Mar 2004 15:57:21 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry.-at-.ccl.net, qsar_society.-at-.accelrys.com, crames.-at-.rpi.edu, gardes.-at-.rpi.edu Subject: Annoucement: CCG Excellence Award Application Deadling for Philadelphia ACS Meeting (Fall 2004) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Computational Chemistry graduate students and advisors: Applications for CCG Excellence Awards are due April 9th, 2004 for the Philadelphia National ACS Meeting in the Fall of 2004. The abstract deadlines for OAsys submission to the COMP Division is April 16th, so we plan to announce winners by this date. 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 by a panel of experts. 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. Electronic submission via E-mail attachment is preferred. 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 (Philadelphia, 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 to 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@ccl.net Thu Mar 25 15:58:37 2004 Received: from smtp3.server.rpi.edu (smtp3.server.rpi.edu [128.113.2.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2PKwbjs024700 for ; Thu, 25 Mar 2004 15:58:37 -0500 Received: from rpi.edu (omniocular-46.dynamic.rpi.edu [128.113.135.55]) by smtp3.server.rpi.edu (8.12.8/8.12.8) with ESMTP id i2PL1XLO010029 for ; Thu, 25 Mar 2004 16:01:33 -0500 Message-ID: <4063487E.B56A77FC.-at-.rpi.edu> Date: Thu, 25 Mar 2004 16:00:46 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry.-at-.ccl.net Subject: Application Deadline: Emerging Technologies in Computational Chemistry Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Computational Chemists and friends, This message is to remind everyone that the FIFTH annual Emerging Technologies in Computational Chemistry Symposium will take place at the Philadelphia 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 Computational Chemistry at the American Chemical Society National Meeting, Philadelphia, USA, August 22-26, 2004. 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/ by April 16th, 2004. It is also necessary to email a long (~1000-word) abstract to the organizer (Curt M. Breneman, RPI Chemistry) by the same date (April 16, 2004). 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 and application materials should sent electronically to: Prof. Curt M. Breneman Department of Chemistry Rensselaer Polytechnic Institute Troy, NY 12180 E-mail: brenec.-at-.rpi.edu ====================================== See you in Philadelphia! Curt Breneman RPI Chemistry From chemistry-request@ccl.net Thu Mar 25 15:32:27 2004 Received: from smtpout.mac.com (smtpout.mac.com [17.250.248.86]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2PKWRjs023783 for ; Thu, 25 Mar 2004 15:32:27 -0500 Received: from mac.com (smtpin08-en2 [10.13.10.153]) by smtpout.mac.com (Xserve/MantshX 2.0) with ESMTP id i2PKZLBi000736 for ; Thu, 25 Mar 2004 12:35:23 -0800 (PST) Received: from [192.168.169.238] (momentum.chem.duke.edu [152.3.169.5]) (authenticated bits=0) by mac.com (Xserve/smtpin08/MantshX 3.0) with ESMTP id i2PKZK1m021595 for ; Thu, 25 Mar 2004 12:35:20 -0800 (PST) Mime-Version: 1.0 (Apple Message framework v613) Content-Transfer-Encoding: 7bit Message-Id: Content-Type: text/plain; charset=US-ASCII; format=flowed To: chemistry.-at-.ccl.net From: Takumi Hori Subject: parameters for AMBER95 or CHARMM22 Date: Thu, 25 Mar 2004 15:35:19 -0500 X-Mailer: Apple Mail (2.613) X-Spam-Status: No, hits=0.3 required=7.0 tests=UPPERCASE_25_50 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL, Does anyone know the parameters of ALPHA-AMINO-N-BUTYRIC ACID ( ABA in PDB ) and protonated Aspartic Acid for the AMBER95 or CHARMM22 force fields? Thanks in advance. Takumi Hori -- Takumi Hori Duke University Department of Chemistry Paul M. Gross Chemical Laboratory Box 90349 Durham, NC 27708, U.S.A. TEL: 1-919-660-1658 E-mail: thori3jp.-at-.mac.com From chemistry-request@ccl.net Thu Mar 25 15:58:51 2004 Received: from neptune.tranzymepharma.com (neptune.med.usherbrooke.ca [132.210.158.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2PKwojs024723 for ; Thu, 25 Mar 2004 15:58:51 -0500 Received: from mercure.neokimia.com (exchange.tranzymepharma.com [192.168.1.3]) by neptune.tranzymepharma.com (8.12.10/8.12.10) with ESMTP id i2PL1hQi016204 for ; Thu, 25 Mar 2004 16:01:44 -0500 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C412AC.603DED04" Subject: CCL: Phamacophore mapping -> semi-quantitative? X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Date: Thu, 25 Mar 2004 16:01:43 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL: Phamacophore mapping -> semi-quantitative? thread-index: AcQSrF+UdznwFUxhQlSF0lJUgPs2XA== From: "Axel Mathieu" To: X-NK-Spam-Status: Ce message n'est pas du SPAM, (Score: 2.66, Requis: 5, FVGT_u_HAS_2LETTERFLDR,HTML_60_70,HTML_MESSAGE,J_CHICKENPOX_33,RM_rb_FONT) X-NK-Spam-Version: SpamAssassin version 2.63 X-Scanned-By: MIMEDefang 2.39 X-Spam-Status: No, hits=0.1 required=7.0 tests=HTML_60_70,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C412AC.603DED04 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL'ers, =20 I'm relatively new to pharmacophore mapping but have been successful at = mapping pharmacophores for our projects. I was recently pondering on the = limitations of pharmacophore mapping. As our projects are well into lead = optimization, I'm wondering if by experience any of you have encountered = a limit for a successful 3D-pharmacophore map in terms of binding = affinity. I understand that much literature uses pharmacophore mapping = for scaffold hopping (search for micro molar hits?) but is there a = practical/technical limit to using a pharmacphore map to search for high = affinity molecules, i.e. low nM hits? I guess this is in the direction = of making pharmacophore mapping semi-quantitative without going into = full fledged 3D-QSAR models ... =20 Any comments, suggestions, or observations are welcome. Many thanks, =20 APM =20 ------_=_NextPart_001_01C412AC.603DED04 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CCL’ers,

 

I’m relatively new to pharmacophore mapping but have been successful at mapping pharmacophores for our projects. I was recently pondering on the limitations of pharmacophore mapping. As our projects are well = into lead optimization, I’m wondering if by experience any of you have = encountered a limit for a successful 3D-pharmacophore map in terms of binding = affinity. I understand that much literature uses pharmacophore mapping for scaffold hopping (search for micro molar hits?) but is there = a practical/technical limit to using a pharmacphore map to search for high affinity molecules, i.e. low nM hits? I guess this is in the direction of making pharmacophore mapping semi-quantitative without going into full fledged 3D-QSAR models = …

 

Any comments, suggestions, or observations are = welcome.

Many thanks,

 

APM

 

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