From chemistry-request@server.ccl.net Thu Sep 30 02:19:33 1999 Received: from ns.apbiotech.com (ns.apbiotech.com [192.36.117.130]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA17551 for ; Thu, 30 Sep 1999 02:19:32 -0400 From: enrique.carredano@eu.apbiotech.com Received: from eunotes.apbiotech.com (unverified [193.180.20.124]) by ns.apbiotech.com (Rockliffe SMTPRA 3.3.1) with SMTP id for ; Thu, 30 Sep 1999 08:14:05 +0200 Received: by eunotes.apbiotech.com(Lotus SMTP MTA v4.6.3 (778.2 1-4-1999)) id 412567FC.00273103 ; Thu, 30 Sep 1999 08:08:04 +0100 X-Lotus-FromDomain: XYNET To: chemistry@ccl.net Message-ID: <412567FC.00272F37.00@eunotes.apbiotech.com> Date: Thu, 30 Sep 1999 08:09:49 +0100 Subject: CCL:protein data Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear CCLrs, Does anyone know where to find tables of data relevant to different proteins, namely diffusion coefficients, extinction coefficients and isoelectric points? More specifically, my questions are: What is the diffusion coefficient (in aquoeus solutions) for these proteins? What is their extinction coefficients (at 280 nm)? What is the isoelectric point for Catalase? |-----------------+------------------------| | | | | Proteins | Source | | | | |-----------------+------------------------| | | | | a-lactalbumin | bovine milk | | | | |-----------------+------------------------| | | | | myoglobulin | horse skeletal | | | | |-----------------+------------------------| | | | | trypsinogen | bovine pancreas | | | | |-----------------+------------------------| | | | | pepsin | porcine stomach mucosa | | | | |-----------------+------------------------| | | | | ovalbumin | chicken egg | | | | |-----------------+------------------------| | | | | BSA | bovine | | | | |-----------------+------------------------| | | | | lactoferrin | bovine | | | | |-----------------+------------------------| | | | | IgG | human | | (polyclonal) | | | | | |-----------------+------------------------| | | | | catalase | bovine liver | | | | |-----------------+------------------------| | | | | thyroglobulin | porcine | | | | |-----------------+------------------------| As usual, I will sumarize the answers if any. Thanks Enrique Enrique Carredano, MSc, PhD +46 (0)18 16 50 00 tel Polymer and Surface Chemistry +46 (0)18 16 50 42 direct Amersham Pharmacia Biotech +46 (0)18 16 63 96 fax Bjorkg 30, 751 84 Uppsala Sweden enrique.carredano@eu.apbiotech.com From chemistry-request@server.ccl.net Thu Sep 30 02:21:03 1999 Received: from ns.apbiotech.com (ns.apbiotech.com [192.36.117.130]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA17590 for ; Thu, 30 Sep 1999 02:21:03 -0400 From: enrique.carredano@eu.apbiotech.com Received: from eunotes.apbiotech.com (unverified [193.180.20.124]) by ns.apbiotech.com (Rockliffe SMTPRA 3.3.1) with SMTP id for ; Thu, 30 Sep 1999 08:15:36 +0200 Received: by eunotes.apbiotech.com(Lotus SMTP MTA v4.6.3 (778.2 1-4-1999)) id 412567FC.0027548C ; Thu, 30 Sep 1999 08:09:35 +0100 X-Lotus-FromDomain: XYNET To: chemistry@ccl.net Message-ID: <412567FC.002752F3.00@eunotes.apbiotech.com> Date: Thu, 30 Sep 1999 08:11:26 +0100 Subject: protein data Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear CCLrs, Does anyone know where to find tables of data relevant to different proteins, namely diffusion coefficients, extinction coefficients and isoelectric points? More specifically, my questions are: What is the diffusion coefficient (in aquoeus solutions) for these proteins? What is their extinction coefficients (at 280 nm)? What is the isoelectric point for Catalase? |-----------------+------------------------| | | | | Proteins | Source | | | | |-----------------+------------------------| | | | | a-lactalbumin | bovine milk | | | | |-----------------+------------------------| | | | | myoglobulin | horse skeletal | | | | |-----------------+------------------------| | | | | trypsinogen | bovine pancreas | | | | |-----------------+------------------------| | | | | pepsin | porcine stomach mucosa | | | | |-----------------+------------------------| | | | | ovalbumin | chicken egg | | | | |-----------------+------------------------| | | | | BSA | bovine | | | | |-----------------+------------------------| | | | | lactoferrin | bovine | | | | |-----------------+------------------------| | | | | IgG | human | | (polyclonal) | | | | | |-----------------+------------------------| | | | | catalase | bovine liver | | | | |-----------------+------------------------| | | | | thyroglobulin | porcine | | | | |-----------------+------------------------| As usual, I will sumarize the answers if any. Thanks Enrique Enrique Carredano, MSc, PhD +46 (0)18 16 50 00 tel Polymer and Surface Chemistry +46 (0)18 16 50 42 direct Amersham Pharmacia Biotech +46 (0)18 16 63 96 fax Bjorkg 30, 751 84 Uppsala Sweden enrique.carredano@eu.apbiotech.com From chemistry-request@server.ccl.net Wed Sep 29 18:59:06 1999 Received: from biosci.cbs.umn.edu (eyoung@biosci.cbs.umn.edu [134.84.144.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA15883 for ; Wed, 29 Sep 1999 18:59:06 -0400 Received: from localhost (eyoung@localhost) by biosci.cbs.umn.edu (8.9.1/8.9.1) with SMTP id RAA13748 for ; Wed, 29 Sep 1999 17:52:24 -0500 (CDT) Date: Wed, 29 Sep 1999 17:52:23 -0500 (CDT) From: Eva Young To: chemistry@ccl.net Subject: Online Course: Doing Biological Research on the Internet Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ADVANCED INTERNET TRAINING FOR BIOLOGISTS Online applications are invited immediately from qualified individuals for Internet Biologists' 2nd International Edition of Doing Biological Research on the Internet (DBRI). http://www.internetbiologists.org/dbri99/ The application deadline is October 8, 1999, and enrollment is limited. This advanced course promoting Internet literacy in the biological sciences runs for 3 weeks from October 11 to 29, 1999, with one additional week before and after the course for preparations and evaluations. The course relies heavily on skills taught in Internet Biologists' introductory course Bioscience Resources on the Internet http://www.internetbiologists.org/bri99/ BRI enrollment is now closed for 1999. DBRI thus assumes a working knowledge of mail lists, connecting to and participating in electronic conferencing on BioMOO, and finding basic biological information on the web. Applicants with equivalent web and electronic conferencing experience are welcome. Go to the following URL for FAQs on system/software requirements and BioMOO registration/connection information. http://www.internetbiologists.org/dbri99/faq.html This year's edition will explore three themes: Online Networking and Internet Communication, Building on BioMOO and Shared Resources on the Internet, and Internet Tools for Sequence Analysis and Molecular Visualization. The course is expected to benefit those doing doctoral/postdoctoral research or working on industrial/commercial applications in the biological sciences (particularly in biochemistry or molecular biology), or teachers and administrators integrating the Internet and biology into their curriculum. There is no fee for joining the course, but participants are expected to spend a minimum of 10 hours per week on course activities and a further 20 hours contribution to DBRI or Internet Biologists' projects over the next 2 months. From chemistry-request@server.ccl.net Thu Sep 30 06:25:47 1999 Received: from aditya.unigoa.ernet.in (rshirsat@[202.41.117.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA18735 for ; Thu, 30 Sep 1999 06:21:30 -0400 Received: from localhost (rshirsat@localhost) by aditya.unigoa.ernet.in (8.8.7/8.8.7) with ESMTP id PAA24211; Thu, 30 Sep 1999 15:43:32 +0530 Date: Thu, 30 Sep 1999 15:43:32 +0530 (IST) From: "Dr. Rajendra Shirsat" To: rajarshi@cts.iitkgp.ernet.in cc: Jochen , Computational Chemistry List Subject: C60 POINT GROUP In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all; Can any one tell me about the point group of C60 and related material. shirsat _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ |_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_| |_| |_| |_| |_| Dr. R.N. Shirsat |_| E-Mail: rshirsat@unigoa.ernet.in |_| |_| Department of Chemistry |_| Fax : 91-832-224184 |_| |_| Goa University |_| Ph : 221377 |_| |_| Taleigao Plateau |_| |_| |_| Goa - 403 206 INDIA |_| |_| |_|_ _ _ _ _ _ _ _ _ _ _ _ _ _ _|_|_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _|_| |_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_|_| From chemistry-request@server.ccl.net Thu Sep 30 06:42:59 1999 Received: from biol2.bio.nagoya-u.ac.jp ([133.6.127.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA18851 for ; Thu, 30 Sep 1999 06:42:58 -0400 Received: from [133.6.127.65] (jupiter [133.6.127.65]) by biol2.bio.nagoya-u.ac.jp (8.8.8/3.6Wbeta7) with SMTP id TAA00525 for ; Thu, 30 Sep 1999 19:40:48 +0900 (JST) Date: Thu, 30 Sep 1999 19:40:48 +0900 (JST) Message-Id: <199909301040.TAA00525@biol2.bio.nagoya-u.ac.jp> To: chemistry@ccl.net From: shinoda@biol2.bio.nagoya-u.ac.jp (Kazuki Shinoda) Subject: Parameter set for GTP MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear CCLers, I am using "discover" to perform MD simulation. Does anyone have any information about a parameter set for GTP ? Best regards ================================================ Kazuki Shinoda, M2 Division of Biological Science, Graduateschool of Science Nagoya University, Chikusa, Nagoya 464-01, Japan E-mail : shinoda@biol2.bio.nagoya-u.ac.jp URL: http://bio.nagoya-u.ac.jp:8001/~kazuki/kazuki.html ================================================ From chemistry-request@server.ccl.net Thu Sep 30 03:54:06 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA18075 for ; Thu, 30 Sep 1999 03:54:05 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id JAA17592; Thu, 30 Sep 1999 09:46:41 +0200 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: hinsen@dirac.cnrs-orleans.fr, taop@csb0.IPC.PKU.EDU.cn, CCL Subject: Re: CCL:How to call a C++ program from C? Date: Thu, 30 Sep 1999 09:34:04 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain Cc: chemistry@www.ccl.net References: <199909291453.QAA03165@chinon.cnrs-orleans.fr> In-Reply-To: <199909291453.QAA03165@chinon.cnrs-orleans.fr> MIME-Version: 1.0 Message-Id: <99093009464101.17539@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id DAA18076 On Mit, 29 Sep 1999 hinsen@dirac.cnrs-orleans.fr wrote: >> I have a big program which is written in C and Fortran, but mainly in C. >> The author compile each module by their own compiler ( cc and f77 on SGI) >> and link them by f77. >> >> Now I have another C++ program (still others) and want incorporate it >> into the previous big program. >The reason for this problem is that both C++ and Fortran program often >need specific initialization code that is added during linking. An >added complication with C++ is name mangling (the compiler must create >unique names for overloaded functions etc.), but there are ways around >that. Hi Konrad, you are right - as usual :-) Many times you can resolve the explained problems by incremental linkage (like ld -r), though. So you link all your FORTRAN code into one big object file using the FORTRAN compiler as linker driver, analogous the C++ code using the C++ linker driver. Then you link these into the final exectuable. The only remaining problem I ever encountered is some trouble about a duplicate or no main function. -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Thu Sep 30 04:06:33 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA18267 for ; Thu, 30 Sep 1999 04:06:31 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id JAA17612; Thu, 30 Sep 1999 09:59:01 +0200 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: rajarshi@cts.iitkgp.ernet.in Subject: Re: CCL:C++ vs Fortran performance Date: Thu, 30 Sep 1999 09:55:25 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain Cc: Computational Chemistry List References: In-Reply-To: MIME-Version: 1.0 Message-Id: <99093009590103.17539@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id EAA18268 On Don, 30 Sep 1999 rajarshi@cts.iitkgp.ernet.in wrote: >Hi, > could you explain a litle (or refer me to doc's that would) about f77 >optimizing NP and C++ not. I am sorry I don't have any reference handy. It just came to my mind that I read it some times before when Matt put it into game in his mail. You should find it in any book dealing with the _theoretical_ background of compiler theory. You might go to your CS library and look into theoretical computer science books to find one or a few that deal with compilers. You will also find it in books on compiler theory, some do have a FORTRAN vs C section. -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Thu Sep 30 08:50:09 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA20226 for ; Thu, 30 Sep 1999 08:50:07 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id OAA19321; Thu, 30 Sep 1999 14:34:59 +0200 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: "Dr. Rajendra Shirsat" , CCL Subject: Re: CCL:C60 POINT GROUP Date: Thu, 30 Sep 1999 14:33:47 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain Cc: Computational Chemistry List References: In-Reply-To: MIME-Version: 1.0 Message-Id: <99093014345909.17539@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id IAA20227 On Don, 30 Sep 1999 Dr. Rajendra Shirsat wrote: >Can any one tell me about the point group of C60 and related material. It's icosahedral, IIRC. You should find a charater table in any chemistry related group theory book. -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Thu Sep 30 11:57:51 1999 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA21847 for ; Thu, 30 Sep 1999 11:57:51 -0400 Received: from localhost (localhost [[UNIX: localhost]]) by ice.lanl.gov (8.9.3/8.9.3) id JAA16462; Thu, 30 Sep 1999 09:50:28 -0600 From: Matt Challacombe Reply-To: MChalla@T12.LANL.Gov Organization: Group T-12, Theoretical Chemistry and Molecular Physics To: rajarshi@cts.iitkgp.ernet.in, Jochen Subject: Re: CCL:C++ vs Fortran performance Date: Thu, 30 Sep 1999 09:49:39 -0600 X-Mailer: KMail [version 1.0.24] Content-Type: text/plain Cc: Computational Chemistry List References: MIME-Version: 1.0 Message-Id: <99093009502806.00776@ice.lanl.gov> Content-Transfer-Encoding: 8bit Hi CCLers, Rajarshi, To my knowedge optimization in F77, F90, F95 ... is not NP hard. For those interested, see: http://www.mailbase.ac.uk/lists/comp-fortran-90/1999-09/0000.html and http://www.mailbase.ac.uk/lists/comp-fortran-90/1999-09/0003.html Cheers, Matt On Wed, 29 Sep 1999, rajarshi@cts.iitkgp.ernet.in wrote: > Hi, > could you explain a litle (or refer me to doc's that would) about f77 > optimizing NP and C++ not. > > TIA > Rajarshi Guha > > > > > -= 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 -- +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + + Los Alamos National Laboratory email: mchalla@t12.lanl.gov + + Theoretical Division vmail: (505) 698-4112 + + Group T-12, Mail Stop B268 phone: (505) 665-5905 + + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + + + + "The secret to mountain biking is pretty simple. The slower you go + + the more likely it is you'll crash." -- Julie Furtado + +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@server.ccl.net Thu Sep 30 12:09:51 1999 Received: from aleph.net.uniovi.es (aleph.net.uniovi.es [156.35.11.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA21924 for ; Thu, 30 Sep 1999 12:09:50 -0400 Received: from pinon.ccu.uniovi.es (pinon.ccu.uniovi.es [156.35.31.1]) by aleph.net.uniovi.es (PMDF V5.2-32 #38866) with ESMTP id <01JGL9L4WDL8001CTD@aleph.net.uniovi.es> for chemistry@ccl.net; Thu, 30 Sep 1999 18:02:34 +0200 (MET) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.9.2/8.9.2) id SAA10102; Thu, 30 Sep 1999 18:02:33 +0200 (METDST) Date: Thu, 30 Sep 1999 18:02:33 +0200 (METDST) From: Victor Lua~na Subject: Re: CCL:C++ vs Fortran performance To: chemistry@ccl.net, owner-chemistry@server.ccl.net Message-id: <199909301602.SAA10102@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT > Date: Wed, 29 Sep 1999 10:31:54 +0200 > From: Jochen > Subject: CCL:C++ vs Fortran performance > > So - in principle FORTRAN is faster, but in C++ it is easier to code > fast programs (faster than usual FORTRAN code). > Do you agree ? Given the involvement that serious C++ projects like Blitz++ need to achieve small efficiency penalties with respect to any fortran code I would never say that is easier to produce faster code in C++ than in fortran. What C++ advocates proclaim is that the human effort to create and maintain a large computer program is reduced by using C++ AND sofisticated software engineering tools. Regards, Victor Lua~na -- HomePage %%http://www3.uniovi.es/~quimica.fisica/qcg/vlc/luana.html%% +----------------------------------------------+ +---^---/ / ! Victor Lua~na ! | ~ / Just in case ! Departamento de Quimica Fisica y Analitica ! | | you don't ! Universidad de Oviedo, 33006-Oviedo, Spain ! < / remember ! e-mail: %%victor@carbono.quimica.uniovi.es%% ! | / where Oviedo ! phone: +34-985-103491 fax: +34-985-103125 ! |____ ___/ is ;-) +----------------------------------------------+ \/ From chemistry-request@server.ccl.net Thu Sep 30 11:23:20 1999 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA21708 for ; Thu, 30 Sep 1999 11:23:16 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@ccl.net id AA20472; Thu, 30 Sep 99 23:15:40 -0700 Date: Thu, 30 Sep 1999 23:15:39 -0700 (PDT) From: Liu Zhijie To: CHEMISTRY@ccl.net Subject: Ask for help Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Can anyone do me a favor to offer the detail of how to find the transition state by mopac program. I don't know which keyword should be used in the situation. yours sincerely Bell lee From chemistry-request@server.ccl.net Thu Sep 30 15:00:58 1999 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA22776 for ; Thu, 30 Sep 1999 15:00:58 -0400 Message-ID: Date: 30 Sep 1999 14:03:03 -0500 From: "Boyd" Subject: Bioinformatics Short Course To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Dear CCLers, A 2-day ACS short course will be held on bioinformatics. The course is on December 16 - 17, 1999, at Indiana University-Purdue University at Indianapolis (IUPUI). The course instructor is Professor Shankar Subramaniam (University of California, San Diego), developer of the widely-used Biology Workbench, a web- based environment. Besides the classroom activities, participants will be able to get hands-on experience with modern workstations. For more information about attending the course, see http://chem.iupui.edu/acs/bioinformatics/ Or contact Professor Jack Breen at breen@chem.iupui.edu or tel. 317-274-0052. Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Research Professor of Chemistry Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Thu Sep 30 15:23:07 1999 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA22915 for ; Thu, 30 Sep 1999 15:23:07 -0400 Message-ID: Date: 30 Sep 1999 14:25:00 -0500 From: "Boyd" Subject: drug design conference next month To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 CCLers: --Announcement-- Innovative Computational Applications: The Interface of Library Design, Bioinformatics, Structure Based Drug Design, and Virtual Screening October 25-27, 1999, The Sir Francis Drake Hotel, San Francisco, California This international symposium will provide practical solutions to maximize value of chemical lead discovery protocols and enhance computational chemistry and computer-aided drug design programs. Featured Keynote Address: * DOCKING & SCORING Irwin "Tack" Kuntz, Ph.D. Director, Molecular Design Institute UNIVERSITY OF CALIFORNIA- SAN FRANCISCO Also featuring these presentations and industry leaders: * Flexible Docking in Lead Optimization: Comparison of Scoring Functions and Algorithms Michal Vieth, Ph.D., Senior Computational Chemist, ELI LILLY & CO. * Docking, Scoring and Virtual Screening with Free Energy Functions: Squeezing More from LogP Glen E. Kellogg, Ph.D., Professor, VIRGINIA COMMONWEALTH UNIV. * Exploring Computational Tools and Protocols for Structure-based Drug Design Charles L. Brooks, III, Ph.D. Professor, SCRIPPS RESEARCH INSTITUTE * Developing a Software and Data Infrastructure for Ligand Design Michael K. Gilson, Ph.D., M.D., Fellow, CENTER FOR ADVANCED RESEARCH IN BIOTECHNOLOGY (CARB) * De Novo Design of Synthetically Accessible Lead Compounds Peter Johnson, Ph.D. , Professor, UNIV. OF LEEDS * Facilitating Drug Discovery through an Integrated Chemoinformatics Environment Mic Lajiness, Computer-Aided Drug Design, PHARMACIA & UPJOHN * Quantifying Similarity and Diversity for Ligands, Proteins and Ligand-Protein Interactions Jonathan S. Mason, Ph.D., Director ,CADD, BRISTOL-MYERS SQUIBB * Applications of Flow NMR Spectroscopy to Monitor Binding of Small Molecules to Proteins Brian J. Stockman, Ph.D. Sr Research Scientist, PHARMACIA & UPJOHN * Using Crystallographic Databases for Practical Drug Design Robin Taylor, Ph.D., Director, CAMBRIDGE CRYSTALL. DATA CENTRE * Have We Made Progress Predicting Biological Activity? Yvonne C. Martin, Ph.D., Sr. Project Leader, ABBOTT LABORATORIES * Aligning 3D Structures Using Field-Based Similarity Searching (FBSS) Peter Willett, Ph.D., Professor, UNIVERSITY OF SHEFFIELD * A Computational Approach Towards Effective Lead Evolution Peter D.J. Grootenhuis, Ph.D., Director, Molecular Design, COMBICHEM * Novel Algorithms for the Design of Diverse and Focused Combinatorial Libraries Robert S. Pearlman, Ph.D, Director, UNIVERSITY OF TEXAS AT AUSTIN * The Indexing of Virtual Libraries by Shape and Electrostatics Anthony Nicholls, Ph.D., Founder, OPENEYE SCIENTIFIC SOFTWARE, INC. * Virtual Screening - An Integrated Approach for Advanced Library Evaluation W. Patrick Walters, Ph.D., Senior Staff Investigator, VERTEX PHARMA * Screening Large Structural Databases for Diverse Ligands to Flexible, Solvated Proteins Leslie Kuhn, Ph.D. Professor, Dept. of Biochemistry, MICHIGAN STATE * Discovery of a Small Molecule Motilin Antagonist through Electronic Database Screening Mary Pat Beavers, Ph.D., CADD, R.W. JOHNSON RESEARCH INSTITUTE * Enumeration and Canonicalization of Tautomers in Drug Design Roger Sayle, Ph.D., Vice President, Bioinformatics Group, METAPHORICS * Probability Modeling in High Throughput Drug Discovery Paul Labute, Ph.D., President and CEO, CHEMICAL COMPUTING GROUP * Sensitivity Analysis, 9-Point Pharmacophores, and Other Improved Tools for Combinatorial Library Design Eric Martin, Ph.D., Asst. Director, Computational Chemistry, CHIRON There will be a PRECONFERENCE SYMPOSIUM on Monday, October 25, 1999: Interfacing Bioinformatics, Chemoinformatics, and ADME Models for Accelerated Drug Discovery This is for individuals seeking to develop programs and protocols that integrate bioinformatics and chemoinformatics. Speakers: Andrew Lyall, Ph.D., IT Director & CIO, OXFORD GLYCOSCIENCES (UK) LTD. Michael N. Liebman, Ph.D., Director, Bioinformatics, WYETH-AYERST RESEARCH John Weinstein, M.D., Ph.D., Molecular Pharmacology, U.S. NATIONAL CANCER INST. Manfred J. Sippl, Ph.D.Professor, Applied Molecular Engineering, UNIV. OF SALZBURG Steven E. Brenner, Ph.D., Department of Structural Biology, STANFORD UNIVERSITY Michael S. Lawless, Ph.D., Applications Scientist, TRIPOS, INC. David Lewis, Reader in Molecular Toxicology , UNIVERSITY OF SURREY Vijay O. Bhargava, Ph.D., Sr. Director, Drug Metabolism, HOECHST MARION ROUSSEL For more information, see http://www.iir-ny.com/conference.cfm?EventID=p0459& and http://www.iir-ny.com/conference.cfm?EventID=p0459& Or contact Ellen Lubman, Director for this meeting, e-mail elubman@iirny.com. From chemistry-request@server.ccl.net Thu Sep 30 15:58:03 1999 Received: from nano.chem.nwu.edu (nano.chem.nwu.edu [129.105.14.190]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA23163 for ; Thu, 30 Sep 1999 15:58:03 -0400 Received: from nano.chem.nwu.edu ([129.105.14.190]) by nano.chem.nwu.edu (WESMTP 2.1 [Sep 22 1998]) with SMTP id 90517625; Thu, 30 Sep 1999 19:58:06 GMT Date: Thu, 30 Sep 1999 14:58:06 -0500 From: "G. Rechtsteiner" Subject: Free Energy Summary (Repost?) To: CHEMISTRY@ccl.net Message-Id: <4.2.0.58.19990930145415.00a289b0@nano.chem.nwu.edu> X-Sender: greg@nano.chem.nwu.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hello: Some time ago I asked a question concerning Gaussian 94/98 and Free Energy. I thought I had posted a summary, but maybe I did not. Regardless, here is the information. Question: > I have recently doen some calculations using Gaussian 98W > and I have come across the following question: > > What value reported from the Thermochemical Analysis > is the correct value to use for the Free Energy of the molecule. > > In Exploring Chemistry with Electronic Structure Methods, > they give the following labels: > > Zero-point correction= (Hartree/Particle) > Thermal correction to Energy= > Thermal correction to Enthalpy= > Thermal correction to Gibbs Free Energy= > Eo Sum of electronic and zero-point Energies= > E Sum of electronic and thermal Energies= > H=E+RT Sum of electronic and thermal Enthalpies= > G=H-TS Sum of electronic and thermal Free Energies= > > So, my question is, if I want to compare the Free Energies > of a set of molecules, do I compare the last value > shown (which includes the Electronic Energies) or do I > subtract out the Electronic Energies? Replies: 1. The free energy is G, so use the sum given. This is composed of the electronic energy, which is calculated at 0 K, plus a thermal correction to the desired temperature. By default this is 298 K, but it can be changed. Jaime Martell, Ph.D. Research Assistant Professor and Camille & Henry Dreyfus Fellow Department of Chemistry University of North Carolina at Asheville Asheville, NC 28805-8511 2. If you want to compare free energies at 298.15 K you should use the last number without substracting or adding anything. >Which is the standard method used, of if it is something >different, what is it? From what I know, people generally compare the enthalpies at 0 K, i.e., Sum of electronic and zero-point Energies. Cheers, Theis ** ** ** ** Mr. Theis Ivan Solling ** ** ** ** ** Department of Chemistry ****** ****** University of Copenhagen ** ** ** DK-2100 Copenhagen** ** ** Ph. 45-3532-0187/Fax. 45-3532-0212 3. The answer depends somewhat on what information you want. Gaussian returns total energies so to compare absolute stabilities you want the last line. If you want free energies of formation then you need to subtract out the free energy for the atoms in their standard states. The same holds true for enthalpies of formation. Does that clear it up? Douglas J. Fox Director of Technical Support help@gaussian.com