From owner-chemistry@ccl.net Tue Sep 2 02:31:01 2008 From: "Andrew Dalke dalke(!)dalkescientific.com" To: CCL Subject: CCL: Python training for cheminformatics Message-Id: <-37694-080902022303-7947-gMbwaR/kkwxAvQSw39PSgw . server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Tue, 2 Sep 2008 08:22:16 +0200 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Andrew Dalke [dalke!^!dalkescientific.com] Hello all, About a month ago I wrote: I will be teaching a two-day training course in Python programming in Leipzig, Germany on 6-7 October. This course is designed for cheminformatics researchers who want to be more effective at the software side of their work. For more details see http://dalkescientific.com/training/ . If you're interested in attending, space is still available. Apply before 10 September to get the early bird rates. Andrew dalke|*|dalkescientific.com From owner-chemistry@ccl.net Tue Sep 2 09:46:01 2008 From: "Lucy Cooney lucy_play_go.:.yahoo.com" To: CCL Subject: CCL: AIM Analysis in Gauss 03 Message-Id: <-37695-080902052135-16454-c/bQH1w0iisW/OAe3pgUlQ . server.ccl.net> X-Original-From: "Lucy Cooney" Date: Tue, 2 Sep 2008 05:21:31 -0400 Sent to CCL by: "Lucy Cooney" [lucy_play_go : yahoo.com] Hello all, I have a few questions; 1. Is it possible to perform AIM analysis in Gauss 03? 2. Can you suggest me a route if possible 3. I want to perform aim analysis on a copper complex. Thank you... From owner-chemistry@ccl.net Tue Sep 2 12:32:01 2008 From: "Elaine Meng meng---cgl.ucsf.edu" To: CCL Subject: CCL: DNA base pair step parameters from DCD trajectory Message-Id: <-37696-080902123105-30103-Zbt/rYkIoXpbperNZJy7bQ]|[server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 2 Sep 2008 12:31:01 -0400 Sent to CCL by: "Elaine Meng" [meng ~ cgl.ucsf.edu] Hi Cesar, Take a look at the 3DNA program. I have not used it myself, but from the papers and documentation it apparently calculates many nucleotide geometric descriptors. It is available for download for several platforms including Linux. I suspect you would need to write out your trajectory frames in PDB format to analyze them, however - I didn't see anything about analyzing trajectories directly. web site: http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html paper: 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. X-J Lu and WK Olson Nature Protocols 3(7):1213 (2008) Best, Elaine ----- Elaine C. Meng, Ph.D. meng]*[cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Tue Sep 2 14:14:00 2008 From: "Jeff Woodford jwoodfor|,|eou.edu" To: CCL Subject: CCL:G: AIM Analysis in Gauss 03 Message-Id: <-37697-080902141249-29581-JsBV07sKy4sL399BMSYRuA|server.ccl.net> X-Original-From: "Jeff Woodford" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 2 Sep 2008 13:12:28 -0500 MIME-Version: 1.0 Sent to CCL by: "Jeff Woodford" [jwoodfor~!~eou.edu] Hi, Yes it is possible although it doesn't appear to be in the G03 manual, but it is in the G98 manual. All you do is specify the AIM keyword in the route section. Although, I confess, I've never tried it with metals. Here is the route I used: # B3LYP/6-311++G** SCF=Tight AIM -Jeff Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 -----Original Message----- > From: owner-chemistry _ ccl.net [mailto:owner-chemistry _ ccl.net] Sent: Tuesday, September 02, 2008 4:22 AM To: Woodford, Jeffrey N Subject: CCL: AIM Analysis in Gauss 03 Sent to CCL by: "Lucy Cooney" [lucy_play_go : yahoo.com] Hello all, I have a few questions; 1. Is it possible to perform AIM analysis in Gauss 03? 2. Can you suggest me a route if possible 3. I want to perform aim analysis on a copper complex. Thank you...http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Sep 2 16:30:01 2008 From: "David Hose Anthrax_brothers*hotmail.com" To: CCL Subject: CCL:G: AIM Analysis in Gauss 03 Message-Id: <-37698-080902162924-1784-KPyxRTV0WtmWQ3tOyovltw,,server.ccl.net> X-Original-From: "David Hose" Date: Tue, 2 Sep 2008 16:29:20 -0400 Sent to CCL by: "David Hose" [Anthrax_brothers-.-hotmail.com] Lucy, This was discussed back in January of this year. See this message for the first reply to the thread. http://www.ccl.net/cgi-bin/ccl/message-new?2008+01+28+007 If I recall correctly, G03 Rev. D and higher doesn't support the AIM calculation. What was recommended was the wavefunction is saved (output=wfn), and that is then inputted into Morphy, AIM2000 or AIMPAC. If you type "AIM inurl:2008" into the forum search box, you should be able to follow the thread. http://www.ccl.net/chemistry/resources/messages/index.shtml More info on Morphy98, AIMPAC and AIM2000 can be found at the following: http://morphy.mib.man.ac.uk/ http://www.chemistry.mcmaster.ca/aimpac/imagemap/imagemap.htm http://www.aim2000.de/ Hope that helps. -- Regards, Dave. ----- Sent to CCL by: "Jeff Woodford" [jwoodfor~!~eou.edu] Hi, Yes it is possible although it doesn't appear to be in the G03 manual, but it is in the G98 manual. All you do is specify the AIM keyword in the route section. Although, I confess, I've never tried it with metals. Here is the route I used: # B3LYP/6-311++G** SCF=Tight AIM -Jeff Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 -----Original Message----- > From: owner-chemistry]![ccl.net [mailto:owner-chemistry]![ccl.net] Sent: Tuesday, September 02, 2008 4:22 AM To: Woodford, Jeffrey N Subject: CCL: AIM Analysis in Gauss 03 Sent to CCL by: "Lucy Cooney" [lucy_play_go : yahoo.com] Hello all, I have a few questions; 1. Is it possible to perform AIM analysis in Gauss 03? 2. Can you suggest me a route if possible 3. I want to perform aim analysis on a copper complex. Thank you... From owner-chemistry@ccl.net Tue Sep 2 20:44:00 2008 From: "Guenter Grethe ggrethe*o*comcast.net" To: CCL Subject: CCL: 2009 Herman Skolnik Award Recipient Message-Id: <-37699-080902192144-26245-8qW4va+Oe/qbU1MzDUodJw_-_server.ccl.net> X-Original-From: "Guenter Grethe" Date: Tue, 2 Sep 2008 19:21:40 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe%comcast.net] 2009 Herman Skolnik Award Winner Announced Yvonne Connolly Martin, retired Senior Volwiler Research Fellow at Abbott Laboratories, is the recipient of the 2009 Herman Skolnik Award presented by the ACS Division of Chemical Information (CINF). The award recognizes outstanding contributions to and achievements in the theory and practice of chemical information science and related disciplines. The prize consists of a $3,000 honorarium and a plaque. Yvonne Martin has been at the forefront of cheminformatics throughout her professional career which was spent entirely at Abbott Laboratories. She has been a founder and constant driving force in the development and use of computational chemistry and its application to computer aided drug discovery. Her studies in QSAR, molecular diversity, molecular graphics, pharmacophore analysis, molecular similarity and combinatorial chemistry greatly impacted the work of theoretical and experimental medicinal chemists. Her overall contributions have helped shape the modern definition of drug discovery. While she developed many methods and supervised their implementation, she never limited herself to a single method or application to solve real-world problems. She finds great pleasure in sharing her work with any interested researchers. Yvonne has authored or co-authored more then 60 peer-reviewed papers, about 40 book chapters, and more than 20 reviews. Additionally, she edited 6 books and 7 patents were issued in her name. These publications and her numerous presentations at national and international meetings provided important insights into computational drug discovery. She has served on many journal editorial boards and NIH study sections. For her many contributions to the field of molecular modeling, Yvonne has received several awards and honors including the Accomplishment Award from the Society for Biomolecular Sciences. Yvonne Martin received a BA in Chemistry (1958) from Carleton College and a Ph.D. in Chemistry (1964) from Northwestern University. She started her career in 1958 as Research Assistant at Abbott Laboratories and moving through the ranks retired in 2006 as Senior Volwiler Research Fellow. In 1967 1968, she spent a sabbatical year at Pomona College with Professor Corwin Hansch which made her an early proponent of QSAR. Yvonne was one of the founders of the International QSAR Society (now called Cheminformatics and QSAR Society) in 1989 and served as its Chair in 2001 2005. Yvonne is highly respected by all of her colleagues worldwide and this Award is a well-deserved recognition of an outstanding research careee. Guenter Grethe Chair, CINF Awards Committee From owner-chemistry@ccl.net Tue Sep 2 22:44:01 2008 From: "Guenter Grethe ggrethe .. comcast.net" To: CCL Subject: CCL: 2008 CINF-FIZ Chemie Scholarship Recipients Message-Id: <-37700-080902214545-3277-v6lGafrV6RatJ+nivftnTA/a\server.ccl.net> X-Original-From: "Guenter Grethe" Date: Tue, 2 Sep 2008 21:45:41 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe * comcast.net] 2008 CINF- FIZ CHEMIE Berlin Scholarship for Scientific Excellence The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by FIZ CHEMIE Berlin is designed to reward graduate and post-graduate students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Applicants showed their posters at the CINF Welcoming Reception and the Sci-Mix session of the 2008 Fall ACS National Meeting in Philadelphia. Three scholarships valued at $1,000 were given out at the divisional luncheon at the same meeting. The winners were presented with cash awards and plaques by Dr. Rene Deplanque, Executive Director of FIZ CHEMIE Berlin, and Dr. Wolfram Koch, Executive Director of the Gesellschaft Deutscher Chemiker (GDCh). The names of the recipients and the titles of their poster are: Gene M. Ko, Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1245, Cheminformatics analysis of HIV-1 protease mutations; Sara E. Nichols, Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, Hierarchical screening with multiple receptor structures to target the nonnucleoside binding site of HIV-1 reverse transcriptase; Jonathan H. Chen, Institute for Genomics and Bioinformatics School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, Reaction mechanism prediction by transformation rules and general principles. Guenter Grethe Chair, CINF Awards Committee From owner-chemistry@ccl.net Tue Sep 2 23:19:01 2008 From: "Guenter Grethe ggrethe*_*comcast.net" To: CCL Subject: CCL: Call for Nominations - 2010 Herman Skolnik Award Message-Id: <-37701-080902213841-2106-gZJoBjGIGD4icAwnUznqHQ=server.ccl.net> X-Original-From: "Guenter Grethe" Date: Tue, 2 Sep 2008 21:38:37 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe__comcast.net] 2010 Herman Skolnik Award Call for Nominations The ACS Division of Chemical Information established this Award to recognize outstanding contributions to and achievements in the theory and practice of chemical information science. The Award is named in honor of the first recipient, Herman Skolnik. By this Award, the Division of Chemical Information is committed to encouraging the continuing preparation, dissemination and advancement of chemical information science and related disciplines through individual and team efforts. Examples of such advancement include, but are not limited to, the following: Design of new and unique computerized information systems; Preparation and dissemination of chemical information; Editorial innovations; Design of new indexing, classification, and notation systems; Chemical nomenclature; Structure-activity relationships; and Numerical data correlation and evaluation. Advancement of knowledge in the field The Award consists of a $3000 honorarium and a plaque. The recipient is expected to give an address at the time of the Award presentation. In recent years, the Award Symposium has been organized by the recipient. Nominations for the Herman Skolnik Award should describe the nominee's contributions to the field of chemical information and should include supportive materials such as a biographical sketch and a list of publications and presentations. Three seconding letters are also required. Nominations and supporting material should be sent by email to Guenter Grethe at ggrethe_-_comcast.net. Paper submissions are no longer acceptable. The deadline for nominations for the 2010 Herman Skolnik Award is June 1, 2009. Guenter Grethe, CINF Awards Chair From owner-chemistry@ccl.net Tue Sep 2 23:59:00 2008 From: "Guenter Grethe ggrethe__comcast.net" To: CCL Subject: CCL: Call for Applications Message-Id: <-37702-080902222523-8087-rgdtRW78hppdn7FkVAd1QQ- -server.ccl.net> X-Original-From: "Guenter Grethe" Date: Tue, 2 Sep 2008 22:25:18 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe]*[comcast.net] CINF Scholarship for Scientific Excellence Sponsored by Symyx The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by Symyx is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to five scholarships valued at $1,000 each will be presented at the 237th ACS National Meeting in Salt Lake City, March 22 26, 2009. Applicants must be enrolled at a certified college or university, and they will present a poster during the Welcoming Reception of the division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through OASYS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe%%comcast.net, that you are applying for a scholarship. Submit your abstract at http://oasys.acs.org/acs/237nm/cinf/papers/index.cgi by clicking on Scholarship Award Posters. To enter your abstract, just follow the instructions. The deadline for submitting an abstract to OASYS is October 20, 2008. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by January 15, 2008. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked Winner of Symyx-CINF Scholarship for Scientific Excellence at the poster session. Guenter Grethe About Symyx Symyx Technologies, Inc. is the scientific R&D integration partner to companies in the life sciences, chemicals, energy, electronics and consumer products industries. With scientific R&D under tremendous economic and technical pressure, we help companies reduce R&D risk and enhance R&D productivity to help them bring more and better products to market quickly and cost-effectively. Our integrated technology platform combines Symyx Software (electronic laboratory notebooks, content, laboratory logistics and analysis), Symyx Tools (software-driven integrated workflows) and Symyx Research (collaborative research and directed services) to support the entire R&D process. In October 2007, Symyx acquired MDL Information Systems, Inc., a leading provider of innovative informatics software, databases and services that accelerate successful scientific R&D by improving the speed and quality of scientists decision making. Information about Symyx, including reports and other information filed by Symyx with the Securities and Exchange Commission, is available at www.symyx.com.