From chemistry-request@ccl.net Tue Feb 15 16:23:46 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1FLNgGi005664 for ; Tue, 15 Feb 2005 16:23:43 -0500 Received: from [130.126.120.204] (wellington.ks.uiuc.edu [130.126.120.204]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j1FK334X009053 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 15 Feb 2005 14:03:04 -0600 (CST) Message-ID: <42125566.5030809 +*+ ks.uiuc.edu> Date: Tue, 15 Feb 2005 14:02:46 -0600 From: David Brandon Reply-To: brandon +*+ ks.uiuc.edu User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry +*+ ccl.net Subject: "Hands-On" Workshop on Computational Biophysics - San Francisco Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.5 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 "Hands-On" Workshop on Computational Biophysics http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco/ Application Deadline: April 14, 2005 The Theoretical and Computational Biophysics Group, an NIH Resource for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu ) at the University of Illinois at Urbana-Champaign (www.uiuc.edu ), will organize a "'Hands-On' Workshop on Computational Biophysics" to be held June 26 to June 30, 2005 at The Club Quarters Hotel San Francisco, San Francisco, California. The workshop will explore a wide range of physical models and computational approaches for the simulation of biological systems. The workshop will be based on case studies including the properties of membranes and membrane proteins, mechanism of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Physical concepts, mathematical techniques, and computational methods required will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, steered molecular dynamics simulations, and combined quantum mechanical - molecular mechanical calculations The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which participants will be able to set up and run simulations. Applications to the workshop are due by April 14, 2005. Selection and notification of participants from the application pool will be completed by April 21. Those selected to attend must register and pay a workshop fee by April 29, 2005. The base registration fee is $150 for students, $210 for non-student academics, and $285 for all other applicants. Housing and course materials are included in the fee. Due to space and equipment constraints, the workshop is limited to 20 participants. For further information, and online application, go to http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco/ . Additional workshops are planned for May 23-27, 2005 in Tahoe City, California (http://www.ks.uiuc.edu/Training/Workshop/Granlibakken/) and June 9-13, 2005 in Chicago, Illinois (http://www.ks.uiuc.edu/Training/Workshop/Chicago/). We look forward to receiving your application. Please note that we cannot help with travel expenses or arrangements. Workshop Organizers E-mail: workshop+sanfrancisco +*+ ks.uiuc.edu From chemistry-request@ccl.net Tue Feb 15 18:38:42 2005 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1FNcbGg013234 for ; Tue, 15 Feb 2005 18:38:38 -0500 Received: from eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id j1FMPtJ12125 for ; Tue, 15 Feb 2005 15:25:56 -0700 Message-ID: <421276EA.8030603 (a) eyesopen.com> Date: Tue, 15 Feb 2005 15:25:46 -0700 From: George Vacek Organization: OpenEye Scientific Software User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry (a) ccl.net Subject: ROCS 2.1 and EON 1.1 released - shape and electrostatics in ligand-based drug design Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net OpenEye announces the release of ROCS 2.1 and EON 1.1, which screen databases of molecules for shape and electrostatic similarity, respectively, and thereby facilitate lead generation in drug discovery. In a typical workflow, with a known active as the query molecule, ROCS is used to screen multi-conformer corporate databases, while EON is used as a secondary screen on the best ROCS results. This process can be run on million-compound libraries in a day on a single processor. Recently, researchers at Wyeth wrote, "The ROCS-identified molecules provided us with ideal, lead-like scaffolds for further development." [T.S. Rush, et al., J. Med. Chem., 2005] Key new features in ROCS 2.1 and EON 1.1 include: 7 support for CCP4 and XPLOR map files as grid queries 7 new chemically aware color force-fields 7 more efficient scaling to large numbers of processors 7 improved workflow between ROCS and EON Shape and electrostatics are whole molecule properties and fundamental metrics with significant advantages over 2D descriptors or simple pharmacophore models. ROCS and EON screens of corporate collections have successfully rescued hits missed by HTS, generated alignments for QSAR models, and driven SAR analyses. The Wyeth publication credits the software with "allowing us to 'scaffold hop' to molecules without the same toxicity and potential intellectual property issues as the query." For further information, please visit www.eyesopen.com or contact business (a) eyesopen.com. Regards, George Vacek VP, Business Development OpenEye Scientific Software From chemistry-request@ccl.net Tue Feb 15 14:43:02 2005 Received: from anchor-post-33.mail.demon.net (anchor-post-33.mail.demon.net [194.217.242.91]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1FJh0Gg032525 for ; Tue, 15 Feb 2005 14:43:01 -0500 Received: from ccrsolutions.demon.co.uk ([83.104.158.99] helo=tile.optimanumerics.com) by anchor-post-33.mail.demon.net with smtp (Exim 4.42) id 1D17Xq-000BRJ-By for chemistry ~~ ccl.net; Tue, 15 Feb 2005 18:35:35 +0000 Received: (qmail 11208 invoked by uid 1015); 15 Feb 2005 18:35:55 -0000 Received: from 192.168.3.93 by tile.internal.optimanumerics.com (envelope-from , uid 1002) with qmail-scanner-1.25 (f-prot: 4.5.3/3.16.1. Clear:RC:1(192.168.3.93):. Processed in 31.269804 secs); 15 Feb 2005 18:35:55 -0000 X-Qmail-Scanner-Mail-From: cjtan ~~ OptimaNumerics.com via tile.internal.optimanumerics.com X-Qmail-Scanner: 1.25 (Clear:RC:1(192.168.3.93):. Processed in 31.269804 secs) Received: from kontrovich.internal.optimanumerics.com (192.168.3.93) by 0 with QMTP; 15 Feb 2005 18:35:18 -0000 Received: (qmail 27758 invoked from network); 15 Feb 2005 18:35:16 -0000 Received: from unknown (HELO localhost) (127.0.0.1) by 0 with SMTP; 15 Feb 2005 18:35:16 -0000 Date: Tue, 15 Feb 2005 18:35:16 +0000 (UTC) From: C J Kenneth Tan -- OptimaNumerics To: "Noel O'Boyle" cc: polumrak , chemistry ~~ ccl.net Subject: CCL:end-of-line and Gaussian for Linux In-Reply-To: <1108460705.3517.296.camel ~~ drugs.ucd.ie> Message-ID: References: <7530258805021410051441c3c ~~ mail.gmail.com> <1108460705.3517.296.camel ~~ drugs.ucd.ie> Organization: "OptimaNumerics" URL: http://www.OptimaNumerics.com MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.7 required=7.5 tests=FVGT_m_MULTI_ODD2, IMPRONONCABLE_1,RM_fw_FromIsPhras2,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Another solution: 'addcr' and 'delcr' from UCSPI-TCP package (http://cr.yp.to/ucspi-tcp/addcr.html). Kenneth Tan ----------------------------------------------------------------------- News: OptimaNumerics Libraries 3.0: 200% Faster! ----------------------------------------------------------------------- C. J. Kenneth Tan, Ph.D. OptimaNumerics Ltd. E-mail: cjtan ~~ OptimaNumerics.com Telephone: +44 798 941 7838 Web: http://www.OptimaNumerics.com Facsimile: +44 289 066 3015 ----------------------------------------------------------------------- On 2005-02-15 09:45 -0000 Noel O'Boyle (noel.oboyle2 ~~ mail.dcu.ie) wrote: > Date: Tue, 15 Feb 2005 09:45:05 +0000 > From: Noel O'Boyle > To: polumrak > Cc: chemistry ~~ ccl.net > Subject: CCL:end-of-line and Gaussian for Linux > > Nice program, but this is a well-known problem and the solution is > available for both Windows and Linux: > > dos2unix and unix2dos > > Noel > > On Mon, 2005-02-14 at 18:05, polumrak wrote: > > Hello guys! > > > > We've start using Gaussian only 6 month ago and... > > Well, that's a common problem - input files, created with GaussView > > for Windows comes in windows end-of-line format, which is not > > acceptable for UNIX Gaussian. > > Yes, you can convert them with something like Openoffice.org, Kate... > > or any another X editor... But who need that? > > So Mr. Svetlichny wrote the tiny utility, which we call Converter. > > It simply deletes wrong EOLs from files which you gives them. > > I know that people can easily do that with one line Perl or Python > > script, but... who cares? :))) > > > > That's ANSI C source code. If you want to use converter, save it to > > file, (name it "converter.c" for example), then just compile it with > > your favorite compiler. > > On Linux you can make so: > > gcc -o converter converter.c > > then run binary converter: ./converter > > You will see its output. Of course you need gcc installed. > > You can do that under Windows with your favorite C compiler. > > > > So now just type in something like that: > > >./converter lalala.gjf lalala.com > > under Linux, or > > converter.exe lalala.gjf lalala.com > > And you will get your desired input for UNIX Gaussian :) > > > > Okay, that's it: > > > > /* delete 0d from string */ > > > > > > #include "stdio.h" > > #include "string.h" > > #include > > > > int main(int argc, char * argv[]) > > { > > > > char szBin[50], szHex[50]; > > char iData; > > FILE *fpBin, *fpHex; > > > > if (argc<2) > > { > > printf("\Deletes 0x0d at the end of every string \n"); > > printf("Usage: convert inputfile.ext outputfile.ext \n"); > > printf("14 feb 2005 by V.Svetlychny\n"); > > printf("\n"); > > exit(0); > > }; > > > > > > /* make filenames */ > > strcpy(szBin, argv[1]); > > strcpy(szHex, argv[2]); > > fpBin = fopen(szBin,"rb"); > > if (fpBin==NULL) > > { > > printf("Cannot open %s\n",szBin); > > exit(1); > > } > > > > fpHex = fopen(szHex,"wb"); > > if (fpHex==NULL) > > { > > printf("Cannot open %s\n",szHex); > > exit(1); > > } > > > > /* read and write */ > > putchar('\n'); > > printf("Writing to %s:\n",szHex); > > putchar('\n'); > > putchar('\n'); > > > > while (1) { > > iData=fgetc(fpBin); > > if(iData==EOF) break; > > putchar(iData); > > if(iData != 0x0d) fputc(iData, fpHex); > > }; > > fclose(fpBin); > > fclose(fpHex); > > putchar('\n'); > > putchar('\n'); > > putchar('\n'); > > printf("End of file\n"); > > > > return 0; > > > > } > > > > > > > > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > > > > > > > > > > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY ~~ ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST ~~ ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow ~~ nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Tue Feb 15 16:23:43 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1FLNgGg005664 for ; Tue, 15 Feb 2005 16:23:42 -0500 Received: from [130.126.120.204] (wellington.ks.uiuc.edu [130.126.120.204]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j1FK3J4X009088 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 15 Feb 2005 14:03:20 -0600 (CST) Message-ID: <42125576.6050104 %a% ks.uiuc.edu> Date: Tue, 15 Feb 2005 14:03:02 -0600 From: David Brandon Reply-To: brandon %a% ks.uiuc.edu User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry %a% ccl.net Subject: "Hands-On" Workshop on Computational Biophysics - Chicago Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.5 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 "Hands-On" Workshop on Computational Biophysics http://www.ks.uiuc.edu/Training/Workshop/Chicago/ Application Deadline: April 14, 2005 The Theoretical and Computational Biophysics Group, an NIH Resource for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu ) at the University of Illinois at Urbana-Champaign (www.uiuc.edu ), will organize a "'Hands-On' Workshop on Computational Biophysics" to be held June 9 to June 13, 2005 at The Club Quarters Hotel Central Loop, Chicago, Illinois. The workshop will explore a wide range of physical models and computational approaches for the simulation of biological systems. The workshop will be based on case studies including the properties of membranes and membrane proteins, mechanism of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Physical concepts, mathematical techniques, and computational methods required will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, steered molecular dynamics simulations, and combined quantum mechanical - molecular mechanical calculations The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which participants will be able to set up and run simulations. Applications to the workshop are due by April 14, 2005. Selection and notification of participants from the application pool will be completed by April 21. Those selected to attend must register and pay a workshop fee by April 29, 2005. The base registration fFrom chemistry-request@ccl.net Tue Feb 15 16:23:49 2005 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1FLNgGk005664 for ; Tue, 15 Feb 2005 16:23:46 -0500 Received: from [130.126.120.204] (wellington.ks.uiuc.edu [130.126.120.204]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id j1FK3b4X009099 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 15 Feb 2005 14:03:37 -0600 (CST) Message-ID: <42125587.4070302 %a% ks.uiuc.edu> Date: Tue, 15 Feb 2005 14:03:19 -0600 From: David Brandon Reply-To: brandon %a% ks.uiuc.edu User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry %a% ccl.net Subject: "Hands-On" Workshop on Computational Biophysics - Granlibakken Conference Center, Tahoe City, CA Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 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 "Hands-On" Workshop on Computational Biophysics http://www.ks.uiuc.edu/Training/Workshop/Granlibakken/ Application Deadline: April 14, 2005 The Theoretical and Computational Biophysics Group, an NIH Resource for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu ) at the University of Illinois at Urbana-Champaign (www.uiuc.edu ), will organize a "'Hands-On' Workshop on Computational Biophysics" to be held May 23 to May 27 at the Granlibakken Conference Center, Tahoe City, California. The workshop will explore a wide range of physical models and computational approaches for the simulation of biological systems. The workshop will be based on case studies including the properties of membranes and membrane proteins, mechanism of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Physical concepts, mathematical techniques, and computational methods required will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, steered molecular dynamics simulations, and combined quantum mechanical - molecular mechanical calculations The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which participants will be able to set up and run simulations. Applications to the workshop are due by April 14, 2005. Selection and notification of participants from the application pool will be completed by April 21, 2005. Those selected to attend must register and pay a workshopee is $150 for students, $210 for non-student academics, and $285 for all other applicants. Housing and course materials are included in the fee. Due to space and equipment constraints, the workshop is limited to 20 participants. For further information, and online application, go to http://www.ks.uiuc.edu/Training/Workshop/Chicago/ . Additional workshops are planned for May 23-27, 2005 in Tahoe City, California (http://www.ks.uiuc.edu/Training/Workshop/Granlibakken/) and June 26-30, 2005 in San Francisco, California (http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco/). We look forward to receiving your application. Please note that we cannot help with travel expenses or arrangements. Workshop Organizers E-mail: workshop+chicago %a% ks.uiuc.edu fee by April 29, 2005. The registration fee is $150 for students, $210 for non-student academics, and $285 for all other applicants. Housing and course materials are included in the fee. Due to space and equipment constraints, the workshop is limited to 20 participants. For further information, and online application, go to http://www.ks.uiuc.edu/Training/Workshop/Granlibakken/ . Additional workshops are planned for June 9-13, 2005 in Chicago, Illinois (http://www.ks.uiuc.edu/Training/Workshop/Chicago/) and June 26-30, 2005 in San Francisco, California (http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco/). We look forward to receiving your application. Please note that we cannot help with travel expenses or arrangements. Workshop Organizers E-mail: workshop+granlibakken %a% ks.uiuc.edu From chemistry-request@ccl.net Tue Feb 15 15:33:58 2005 Received: from server.ccl.net (t157 [127.0.0.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1FKXwGg002645 for ccl.net>; Tue, 15 Feb 2005 15:33:58 -0500 Received: (from apache@localhost) by server.ccl.net (8.12.8/8.12.8/Submit) id j1FKXwem002643 for chemistry <> ccl.net; Tue, 15 Feb 2005 15:33:58 -0500 Date: Tue, 15 Feb 2005 15:33:58 -0500 Message-Id: <200502152033.j1FKXwem002643 <> server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request <> ccl.net using -f From: "Marek, , Danilczuk" orange.ichtj.waw.pl> To: chemistry <> ccl.net X-Web-Message-Number: 050215152940-2499 Subject: W:hyperfine couplings X-Spam-Status: No, hits=2.0 required=7.5 tests=DNS_FROM_RFCI_DSN autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I am wonder if somebody knows how to extract anisotropic hfc from the gaussian output?