From owner-chemistry@ccl.net Fri Jul 17 00:40:00 2009 From: "Guenter Grethe ggrethe++comcast.net" To: CCL Subject: CCL: Call for Applications - CINF-Symyx Scholarships Message-Id: <-39798-090717003749-28017-K4obge8o3tcACbMWpQQCSw,+,server.ccl.net> X-Original-From: "Guenter Grethe" Date: Fri, 17 Jul 2009 00:37:45 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe*o*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 two scholarships valued at $1,000 each will be presented at the 239th ACS National Meeting in San Francisco,, CA, March 21 25, 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/239nm/cinf/papers/index.cgi by clicking on CINF Scholarship for Scientific Excellence. To enter your abstract, just follow the instructions. The deadline for submitting an abstract to OASYS is October 19th, 2009. 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, 2010. 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 ggrethe__comcast.net 510-865-5152 About Symyx Symyx Technologies, Inc. (NASDAQ: SMMX) enables companies in life sciences, chemicals and energy, and consumer and industrial products to transform scientific R&D and achieve extraordinary breakthroughs in productivity and return on investment. Symyx scientific information management enables scientists to design, execute, analyze, and report experimental results faster, easier, and less expensively. Symyx microscale, parallel experimentation enables a single scientist to rapidly explore a broad experimental space and develop comprehensive data sets in days not weeks or months. Symyx contract research delivers these advantages on a project basis and enables companies to increase R&D productivity, agility, and flexibility. Information about Symyx, including reports and other information filed by Symyx with the Securities and Exchange Commission, is available at www.symyx.com. From owner-chemistry@ccl.net Fri Jul 17 02:20:01 2009 From: "Uttama Mukherjee uttamachemistry .. gmail.com" To: CCL Subject: CCL:G: IOp command on G03 Message-Id: <-39799-090717021602-29251-v0ZqeUJ8NCpUtujr8TwsUQ : server.ccl.net> X-Original-From: "Uttama Mukherjee" Date: Fri, 17 Jul 2009 02:15:58 -0400 Sent to CCL by: "Uttama Mukherjee" [uttamachemistry-#-gmail.com] My problem is, as I'm giving the IOp command for DZVP2 basis set as additional keyword in the suggested format(in IOp overlay 3 in G03), the job gets terminated via link 301 and in the output it says "Unrecognized DG basis in PutBas." The additional keyword was given as; IOp(3/5)=27 (DZVP2). I'm doing it on B3LYP/DZVP2 level in Gaussian03. Please suggest. Uttama Mukherjee. uttamachemistry^^^gmail.com From owner-chemistry@ccl.net Fri Jul 17 04:25:01 2009 From: "xunlei ding dingxunlei+/-gmail.com" To: CCL Subject: CCL:G: IOp command on G03 Message-Id: <-39800-090717033122-27901-QO7nW/TN2E2pZaIukKysoQ+/-server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Date: Fri, 17 Jul 2009 15:31:08 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei!A!gmail.com] Hi, Try " IOp(3/5=3D27)", with 27 in the (). Hope it work. Ding 2009/7/17 Uttama Mukherjee uttamachemistry .. gmail.com : > > Sent to CCL by: "Uttama Mukherjee" [uttamachemistry-#-gmail.com] > My problem is, as I'm giving the IOp command for DZVP2 basis set as addit= ional keyword in the suggested format(in IOp overlay 3 in G03), the job get= s terminated via link 301 and in the output it says "Unrecognized DG basis = in PutBas." > The additional keyword was given as; IOp(3/5)=3D27 (DZVP2). > I'm doing it on B3LYP/DZVP2 level in Gaussian03. Please suggest. > Uttama Mukherjee. > uttamachemistry|,|gmail.= com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 ------------------------------------------------------ Xun-Lei Ding (=B6=A1=D1=B8=C0=D7) Associate Research Professor of Physical Chemistry, Ph.D State Key Lab for Struct. Chem. of Unstable and Stable Species Institute of Chemistry, The Chinese Academy of Sciences Zhongguancun North First Street 2=A3=AC Beijing 100190, P. R. China Phone 86-10-62568330 Fax 86-10-62559373 From owner-chemistry@ccl.net Fri Jul 17 06:17:02 2009 From: "Anastasios Papadopoulos anastp(0)chem.auth.gr" To: CCL Subject: CCL: Error 502 in G03 Message-Id: <-39801-090716102957-19772-/CNABjWP+3T+vqJhpMnUOQ() server.ccl.net> X-Original-From: Anastasios Papadopoulos Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-7; DelSp="Yes"; format="flowed" Date: Thu, 16 Jul 2009 16:51:27 +0300 MIME-Version: 1.0 Sent to CCL by: Anastasios Papadopoulos [anastp~!~chem.auth.gr] You could try to use the readwrite files files. Because you might have problems in disk space. You could type: %rwf=2gb,rwf1,2gb,rwf2,2gb,rwf3,2gb,rwf4,2gb,rwf5,2gb,rwf6 I hope that you solve your problem. From owner-chemistry@ccl.net Fri Jul 17 07:34:01 2009 From: "Shunichi OZAWA s.ozawa(0)infocom.co.jp" To: CCL Subject: CCL: Marvin Family Nodes Campaign Message-Id: <-39802-090717070925-30789-kdOibE7B+4aZZ2b5t0su8w : server.ccl.net> X-Original-From: "Shunichi OZAWA" Date: Fri, 17 Jul 2009 07:09:21 -0400 Sent to CCL by: "Shunichi OZAWA" [s.ozawa#%#infocom.co.jp] Marvin Family Nodes Campaign: Infocom provides some nodes of JChemExtensions for KNIME free of charge INFOCOM Corporation (Tokyo, Japan), a ChemAxon Integration Partner and a KNIME partner, today is pleased to release new version of JChem Extensions version 2 for KNIME2.0.2 or later, which allows researchers to deal with chemical structure data using ChemAxons software tools such as Marvin, JChem, Standardizer, on the KNIME open source workflow platform. In time for releasing new version, some nodes of JChemExtensions are distributed free of charge. These nodes are called "Marvin Family Nodes" which include "Marvin Sketch", "Marvin View", "Marvin Space" and some Converter nodes. Marvin Family Nodes allow researchers to achieve a high quality drawing and visualization of chemical structure on the KNIME workflow platform. Infocom estimates that the use of "KNIME" and the "JChemExtensions" product is promoted by this campaign. Please see our page for getting Marvin Family Nodes; http://www.infocom.co.jp/bio/develop/jchemextension_en.html [Marvin Family Nodes] Marvin Sketch node Chemical editor for drawing chemical structures, queries and reactions. Marvin View node Load multiple molecules from a data and displays them in a scrollable viewer. Marvin Space node Visualize small molecules, proteins, nucleic acids, crystals, various molecular surfaces, molecular orbitals as well as volumetric data such as electrostatic potential, hydrophobicity. Converter nodes Convert Molecular Type between JChemExtensions and other nodes. [Contact Us] ------------------------------------------------------------- Shunichi OZAWA s.ozawa=-=infocom.co.jp or info-science=-=infocom.co.jp Chem & Bio Informatics Department Infocom Corporation From owner-chemistry@ccl.net Fri Jul 17 10:18:00 2009 From: "Andreas Klamt klamt]![cosmologic.de" To: CCL Subject: CCL: Dipolar interactions in polar medium Message-Id: <-39803-090717101254-14073-UI6tqm9BNCzcdESD3ZqyzQ]~[server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 17 Jul 2009 16:12:37 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt .. cosmologic.de] Our view of the conformational energy change by solvation is somewat different. - In solution in general the net dipole moment is not of that importance. It is much more the arrangement of local dipole moments. Please note that the electrostatic component of the solvation energy of 1,4-dihydroxybenzene is almost twice that of phenol, and rather similar for both conformers, although one of them has zero dipole moment. - Differences in vdW energy may be of great importance as well. In your case we do find with COSMO-RS based on BP86-TZVP DFT/COSMO calculations for the syn-anti difference (in kcal/mol) water 0.06736 cyclohexane 0.85088 acetonitrile 0.11836 gasphase -1.641 This means we find that in the gasphase the more polar syn-conformer is by far the best, while in the non-polar cyclohexane the anti-conformer is lower by about 1 kcal/mol. Tigs appear to be a bit more complicated than just tbeing driven by the net dipole moment. Andreas Kalju Kahn kalju*|*chem.ucsb.edu schrieb: > Sent to CCL by: "Kalju Kahn" [kalju\a/chem.ucsb.edu] > Mark, > > The way I usually think about solvent effects is in terms on net dipole > moments, not in terms of "bad dipolar interactions". In your case, > antiperiplanar conformation has zero dipole moment due to symmetry; > synclinal conformer has a dipole moment. Thus, polar solvent stabilizes > the synclinal conformation more than it stabilizes the antiperiplanar one, > and the energy difference betweeen the two is lowered in polar solvents. > > A classic example, studied by too many to be named here, is > 1,2-dichloroethane (anti and gauche minima, syn rotational saddle point). > > Best regards, > > Kalju > > >> For simplicity, assume the compound XCH2CH2Y has two conformers. The >> first >> conformer has X and Y arranged antiperiplanar. The second conformer has X >> and Y synclinal. The relative population of the two conformers in the gas >> phase would depend on the dipolar interaction of X and Y. Now assume that >> X >> and Y were both electronegative and the compound was dissolved in a polar >> medium. Would the polar medium stabilize the bad dipolar interaction and >> lessen the energy difference between conformers? Or would the polar >> medium >> exacerbate the situation and increase the energy difference between >> conformers? I tend to think the former is true. Is this correct? >> >> Thanks, >> >> >> Mark >> >> HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Fri Jul 17 10:52:01 2009 From: "Mar Forster xyzmjf_._gmail.com" To: CCL Subject: CCL: 2009 Oracle Life Science User Group Meeting - 8 Sept 2009 Message-Id: <-39804-090717034656-30432-rj5zPdTk2MIxX34XXBHuwg]_[server.ccl.net> X-Original-From: "Mar Forster" Date: Fri, 17 Jul 2009 03:46:52 -0400 Sent to CCL by: "Mar Forster" [xyzmjf~!~gmail.com] 2009 Oracle Life Science user group Meeting. Venue: Wellcome Trust Conference Centre , Hinxton, UK Date: 8 September 2009 Cost: 99 GB pounds (or your currency equivalent) Registration : http://www.olsug.org/wiki/index.php?title=Registration_information Confirmed presentations: Richard Durbin (Sanger Centre) - Processing terabases of DNA data to sequence 1000 human genomes Eric Neumann (Clinical semantics group) - The Impact of Semantic Aggregation and Analysis on Scientific R&D Ian Buchan (Accelrys) - Faster chemical searching using a Novel Approach Jan Jensen (Biochemfusion) - Building a BioChemformatics database. Mark Rijnbeek (EBI) - OrChem an open source chemistry extension for Oracle Martin Widlake (Ora600) - Managing the data mountain. From owner-chemistry@ccl.net Fri Jul 17 13:47:00 2009 From: "Sten Nilsson Lill stenil::chem.gu.se" To: CCL Subject: CCL:G: predicting NMR shiftings Message-Id: <-39805-090717134429-14151-kC3jADUAzy4UQ8MwUVg/HA++server.ccl.net> X-Original-From: "Sten Nilsson Lill" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 17 Jul 2009 19:44:15 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Sten Nilsson Lill" [stenil!=!chem.gu.se] Serdar, make sure your optimized TMS is a minimum structure for your method and basis set by performing a frequency calculation. Although you have Td symmetry, different methods and different basis sets can give different answers to how the methyl groups are oriented to each other and this will affect the calculated chemical shielding. Hope that helps, Sten > > Sent to CCL by: "Serdar Badoglu" [sbadoglu{:}gazi.edu.tr] > Hi, all. I'm trying to learn how to predict NMR shiftings using Gaussian > 03. As a start I worked on the example from Foresman & Frisch's book pg > 21. My calculated isotropic value for methane is OK, but I have some > trouble on obtaining an acceptable value for TMS. I'm suspicious about my > own optimization of TMS (gives an NMR shielding tensor between 199-200, > which means there are no reasonable shiftings at all, but the book refers > to a shifting of -3.9 ppm and the experimental value was -7.0 ppm), and I > don't have the example files indicated in the book. So, if anyone can send > me a properly optimized TMS (and any other common reference substances) > output I'd be grateful. Thank you.> > > Ph. D. Sten Nilsson Lill Dep. of Chemistry University of Gothenburg Kemigården 4 S-412 96 Göteborg, Sweden Phone: +46-31-772 2873 Fax: +46-31-772 3840 E-mail: stenil^^chem.gu.se Alternative e-mail: stenil^^physto.se From owner-chemistry@ccl.net Fri Jul 17 20:28:00 2009 From: "Heather Carlson carlsonh=-=umich.edu" To: CCL Subject: CCL: CSAR 2010 Workshop and Benchmark Exercise Message-Id: <-39806-090717193104-16862-wOqHRelrpQaR0etPX1ZVlg%x%server.ccl.net> X-Original-From: Heather Carlson Content-Type: multipart/alternative; boundary="------------060804040506030500090504" Date: Fri, 17 Jul 2009 18:51:53 -0400 MIME-Version: 1.0 Sent to CCL by: Heather Carlson [carlsonh*o*umich.edu] This is a multi-part message in MIME format. --------------060804040506030500090504 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit CSAR logo *2010 Workshop: When Do Scoring Functions Fail and How Can They Be Improved?* The Community Structure-Activity Resource (CSAR ) aims to improve docking and scoring by engaging the entire community. To initiate participation and begin a dialogue, we will hold a workshop in March 2010 at the 239th ACS National Meeting (COMP) in San Francisco. The focus of this first workshop is scoring functions, and *we need your help!* We have designed a Benchmark Exercise based on crystal structures of ~550 protein-ligand complexes. We are asking participants to score the crystal poses using their current approach and then rescore after some retraining or improvement. Data for the Exercise will be released Aug 1st, 2009. Some participants in the Exercise will be invited to speak at the workshop.* If you wish to be considered for giving a talk, please submit your scores by Oct 5th, 2009* to allow us to make selections and contact potential speakers well before the ACS abstract deadline. (Please note: All contributed data will remain anonymous to the community unless the participant wishes to be identified!) Most evaluations of docking and scoring are based on a small collection of targets, and the limited scope prevents us from properly identifying which targets are most difficult. Furthermore, using a few targets does not point toward how to improve our methods. No single code is best for all systems, so we each seem to have a different piece of the puzzle. Participants must be willing to submit failures (/don't worry -- you will be in excellent company!/). Only by examining across many approaches can we provide the appropriate insights. *Goals for the workshop:* * Foster community participation in CSAR * Provide a baseline assessment of current scoring functions using diverse proteins and ligands * Gauge the impact of high-quality data for retraining scoring functions, particularly emphasizing what changes are most universal and/or have greatest impact * Document which targets are most difficult and require new approaches * Help direct target priorities and data generation at Michigan * Spur data deposition Thank you, Heather Carlson for CSAR (www.CSARdock.org) -- Heather A. Carlson, Ph.D. Associate Professor of Medicinal Chemistry, College of Pharmacy Associate Professor of Chemistry, College of LSA University of Michigan, Ann Arbor --------------060804040506030500090504 Content-Type: multipart/related; boundary="------------020309030504040400090700" --------------020309030504040400090700 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit CSAR logo

2010 Workshop: When Do Scoring Functions Fail and How Can They Be Improved?

The Community Structure-Activity Resource (CSAR) aims to improve docking and scoring by engaging the entire community. To initiate participation and begin a dialogue, we will hold a workshop in March 2010 at the 239th ACS National Meeting (COMP) in San Francisco. The focus of this first workshop is scoring functions, and we need your help!

We have designed a Benchmark Exercise based on crystal structures of ~550 protein-ligand complexes. We are asking participants to score the crystal poses using their current approach and then rescore after some retraining or improvement. Data for the Exercise will be released Aug 1st, 2009. Some participants in the Exercise will be invited to speak at the workshop. If you wish to be considered for giving a talk, please submit your scores by Oct 5th, 2009 to allow us to make selections and contact potential speakers well before the ACS abstract deadline. (Please note: All contributed data will remain anonymous to the community unless the participant wishes to be identified!)

Most evaluations of docking and scoring are based on a small collection of targets, and the limited scope prevents us from properly identifying which targets are most difficult. Furthermore, using a few targets does not point toward how to improve our methods. No single code is best for all systems, so we each seem to have a different piece of the puzzle. Participants must be willing to submit failures (don’t worry -- you will be in excellent company!). Only by examining across many approaches can we provide the appropriate insights.

Goals for the workshop:
  • Foster community participation in CSAR
  • Provide a baseline assessment of current scoring functions using diverse proteins and ligands
  • Gauge the impact of high-quality data for retraining scoring functions, particularly emphasizing what changes are most universal and/or have greatest impact
  • Document which targets are most difficult and require new approaches
  • Help direct target priorities and data generation at Michigan
  • Spur data deposition
Thank you,
Heather Carlson for CSAR (www.CSARdock.org)
-- 
Heather A. Carlson, Ph.D.
Associate Professor of Medicinal Chemistry, College of Pharmacy
Associate Professor of Chemistry, College of LSA
University of Michigan, Ann Arbor
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