From owner-chemistry@ccl.net Wed Dec 14 10:02:00 2005 From: "=?ISO-8859-9?Q?Alimet_Sema_=D6zen?= semaozen ~ sabanciuniv.edu" To: CCL Subject: CCL:G: TDDFT for conjugated systems Message-Id: <-30317-051214052250-29239-Qj1WzHyQlW1gy+pdwTTiRg*server.ccl.net> X-Original-From: =?ISO-8859-9?Q?Alimet_Sema_=D6zen?= Content-Type: multipart/alternative; boundary="------------020401000901000401000509" Date: Wed, 14 Dec 2005 11:50:10 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-9?Q?Alimet_Sema_=D6zen?= [semaozen^^^sabanciuniv.edu] This is a multi-part message in MIME format. --------------020401000901000401000509 Content-Type: text/plain; charset=ISO-8859-9; format=flowed Content-Transfer-Encoding: 8bit Dear Members of CCL, I have been trying to run some TDDFT calculations at the B3LYP/6-31G* level for two conjugated oligomers using Gaussian 03. For the first one, everything worked perfectly. For the second oligomer, however, I faced some difficulties with the trimer and tetramer cases.. The iterations were going almost forever after the message Davidson failed to converge within maximum sub-space dimensions. I also tried to change the initial guess to IVOguess and obtained the same results.. When I increased the level of theory to B3LYP/6-31+G**, there was an SCF convergence error... I know TDDFT might fail with the conjugated oligomers but what could you recommend to do? I would appreciate any comments on this... Thanks in advance... Best Regards Alimet -- "SCIENCE SANS CONSCIENCE N'EST QUE RUINE DE L'AME" RABELAIS Alimet Sema Özen, PhD Sabancı University, 34956 Tuzla, İstanbul +90 216 4839566 http://people.sabanciuniv.edu/~semaozen/ --------------020401000901000401000509 Content-Type: text/html; charset=ISO-8859-9 Content-Transfer-Encoding: 8bit Dear Members of CCL,

I have been trying to run some TDDFT calculations at the B3LYP/6-31G* level for two conjugated oligomers using Gaussian 03.
For the first one, everything worked perfectly. For the second oligomer, however,  I faced some difficulties with the trimer and tetramer cases..
The iterations were going almost forever after the message

Davidson failed to converge within maximum sub-space dimensions.

I also tried to change the initial guess to IVOguess and obtained the same results..

When I increased the level of theory to B3LYP/6-31+G**, there was an SCF convergence error...

I know TDDFT might fail with the conjugated oligomers but what could you recommend to do? I would appreciate any comments on this...

Thanks in advance...

Best Regards
Alimet





-- 
"SCIENCE SANS CONSCIENCE N'EST QUE RUINE DE L'AME" RABELAIS

Alimet Sema Özen, PhD
Sabancı University, 
34956 Tuzla, İstanbul
+90 216 4839566
http://people.sabanciuniv.edu/~semaozen/
--------------020401000901000401000509-- From owner-chemistry@ccl.net Wed Dec 14 12:17:01 2005 From: "Andreas Bender (CompLife 06) andreas.bender() complife.org" To: CCL Subject: CCL: CompLife'06 Cambridge, UK, 27-29 September 2006 Message-Id: <-30318-051214114901-31995-BGxFt+IbCj+CslJRnOeliQ%x%server.ccl.net> X-Original-From: "Andreas Bender (CompLife'06)" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=WINDOWS-1252 Date: Wed, 14 Dec 2005 15:46:21 +0000 MIME-Version: 1.0 Sent to CCL by: "Andreas Bender (CompLife'06)" [andreas.bender+*+complife.org] Dear CCL'ers, I am pleased to announce the 2nd International Symposium on Computational Life Sciences in Cambridge, UK, in September 2006! You are cordially invited to contribute to this symposium. A 'Call for Papers' with more detailed instructions will follow early next year. Best wishes and have a good Christmas time! Andreas -------------------------------------------------------------- -- Announcing CompLife '06 (http://www.complife.org) -- -------------------------------------------------------------- Following the success of the 1st International Symposium on Computational Life Science in Konstanz in September 2005 The 2nd International Symposium on Computational Life Science is to be held in Cambridge, United Kingdom, on September 27 - 29, 2006 -------------------------------------------------------------- Topics of Interest The focus of the symposium are computational methods for the modelling, analysis and exploration of all aspects of life sciences, ranging from effects on the molecular level to complex interactions networks. Of prime importance for this truly interdisciplinary event will be the integration of the three disciplines Computer Science, Biology, and Chemistry. The program will consist of contributed presentations regarding application aspects as well as new theoretical developments. In addition, due to the interdisciplinary nature of the symposium the program will feature not only plenary speakers but also a series of short tutorials introducing relevant areas of the specific research fields to the audience from the respective other fields such as drug discovery, chemical similarity searching, receptor site docking, protein structure prediction, data mining, machine learning, to name a few. Submissions will be reviewed by representatives of all fields to make sure that not only the algorithmic aspects are suited for publication but the application to life science is promising as well. Submissions are sought in (but not limited to) the following areas: # Molecular data analysis # Systems biology # Analysis of heterogeneous information sources # Human Computer Interaction in Information Mining # Computational proteomics # Integrative data analysis # Statistical data analysis # Data mining # Molecular simulation # Biological networks / Metabolism # Molecular informatics # Data pipelining # Data visualization # Large scale chemical computation # Data integration/semantics # Grid/web services # Computer architectures in life sciences A limited number of Student Grants are available for CompLife 2006: Thanks to our sponsors we can offer a limited number of student grants to enable full-time students to attend the Second International Symposium on Computational Life Science, CompLife 2006. First priority will be given to full-time students who are first authors of papers and present their paper at the conference. Grants are handed out at the conference and will be in the amount of a maximum of €500, covering registration, travel, and accommodation. When submitting a paper, students should indicate that they plan to apply for a student grant. -------------------------------------------------------------- Important Dates May 15 Papers due June 26 Notification of acceptance July 10 final papers and sources due Sept 27-29 CompLife '06 Final versions of accepted papers will appear in Springer's Lecture Notes in Bioinformatics (LNBI) Series: http://www.springer.com/sgw/cda/frontpage/0,11855,4-164-2-73658-0,00.html For further information and submission instructions, please refer to the symposium website: http://www.complife.org -------------------------------------------------------------- -- Andreas Kieron Patrick Bender - http://www.andreasbender.de ICQ#: 166 835 816 - Yahoo Messenger: andreasbender From owner-chemistry@ccl.net Wed Dec 14 15:32:00 2005 From: "errol lewars elewars!=!trentu.ca" To: CCL Subject: CCL:G: Freq cal error Message-Id: <-30319-051214151615-31256-MtpLkQSk73zumCxN/tG2zw,+,server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 14 Dec 2005 15:14:04 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars.:.trentu.ca] 2005 Dec 14 I have not seen your input file, but you could try changing the name of the checkpoint file then deleting all the scratch files for this job. E. Lewars === Hongbing Fu hongbing.f=gmail.com wrote: >Sent to CCL by: "Hongbing Fu" [hongbing.f*gmail.com] >Hi, > I have a problem completing a gaussian98 frequency job. I have a system > with ~600 basis functions and the freq job quits with the following > message: > "Compute integral second derivatives. > ... and contract with generalized density number 0. > FileIO operation on non-existent file. > FileIO: IOper= 2 IFilNo(1)= -690 Len= 1 IPos= 1 Q= > 1089289192 > dumping /fiocom/, unit = 1 NFiles = 78 SizExt = 524288 WInBlk = 512 > defal = T LstWrd = 667585536 FType=2 FMxFil=10000 > .... (similar lists as below)... > Number 989 993 997 998 > Base 788700 791200 791300 23677 > End 791200 791300 911304 23727 > End1 791200 791300 911304 23727 > Wr Pntr 788700 791200 791300 23677 > Rd Pntr 788700 791200 791300 23677 > dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = > 512 > defal = T LstWrd = 65536 FType=2 FMxFil=10000 > Number 0 > Base 20480 > End 65536 > End1 65536 > Wr Pntr 20480 > Rd Pntr 20480 > Error termination in NtrErr: > NtrErr Called from FileIO." > Anyone has any idea about this? > Any help will be appreciated. > Thank you,> > > > > > > From owner-chemistry@ccl.net Wed Dec 14 16:39:01 2005 From: "Spencer Snyder Ericksen spencer_ericksen++hotmail.com" To: CCL Subject: CCL: Analysis of docking output Message-Id: <-30320-051214163423-28447-iOp7WLDunAWG1bU8y4Dvig[-]server.ccl.net> X-Original-From: "Spencer Snyder Ericksen" Sent to CCL by: "Spencer Snyder Ericksen" [spencer_ericksen:-:hotmail.com] Howdy CCLers! My docking job from QXP/FLO++/LazyMouse yields, as most do, a variety of solutions (three dimensional atomic structures of enzyme-substrate complexes) in .pdb format. As is done in versions of AutoDock, I'd like to perform a structure binning or clustering analysis to examine the relative populations of various binding modes and compare this to their energy rankings. Does anyone know of a free resource that will perform this analysis automatically? Or alternatively, could someone point me toward (1) a better way of looking at docking output or (2) a nice free program that would statistically separate the output structures into their respective binding modes so that I may perform my own analysis? Thanks Spence Spencer S. Ericksen, Ph.D. Postdoctoral Research Associate University of Wisconsin - Madison 601 Science Dr. Madison, WI 53711 ericksen[#]physiology.wisc.edu From owner-chemistry@ccl.net Wed Dec 14 17:15:01 2005 From: "Eugen Leitl eugen###leitl.org" To: CCL Subject: CCL: Britannica and Wikipedia about as accurate Message-Id: <-30321-051214171004-20415-+4ZjaptIjBvKQ6Z7i0CcvQ,,server.ccl.net> X-Original-From: Eugen Leitl Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=unknown-8bit Date: Wed, 14 Dec 2005 23:09:52 +0100 Mime-Version: 1.0 Sent to CCL by: Eugen Leitl [eugen^_^leitl.org] (And if they're not, you can always fix the wrong entry). http://www.nature.com/nature/journal/v438/n7070/full/438900a.html Nature 438, 900-901 (15 December 2005) | doi:10.1038/438900a Special Report Internet encyclopaedias go head to head Jim Giles Abstract Jimmy Wales' Wikipedia comes close to Britannica in terms of the accuracy of its science entries, a Nature investigation finds. One of the extraordinary stories of the Internet age is that of Wikipedia, a free online encyclopaedia that anyone can edit. This radical and rapidly growing publication, which includes close to 4 million entries, is now a much-used resource. But it is also controversial: if anyone can edit entries, how do users know if Wikipedia is as accurate as established sources such as Encyclopaedia Britannica? Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg::nature.com AP PHOTO/M. PROBST Several recent cases have highlighted the potential problems. One article was revealed as falsely suggesting that a former assistant to US Senator Robert Kennedy may have been involved in his assassination. And podcasting pioneer Adam Curry has been accused of editing the entry on podcasting to remove references to competitors' work. Curry says he merely thought he was making the entry more accurate. However, an expert-led investigation carried out by Nature — the first to use peer review to compare Wikipedia and Britannica's coverage of science — suggests that such high-profile examples are the exception rather than the rule. The exercise revealed numerous errors in both encyclopaedias, but among 42 entries tested, the difference in accuracy was not particularly great: the average science entry in Wikipedia contained around four inaccuracies; Britannica, about three. Considering how Wikipedia articles are written, that result might seem surprising. A solar physicist could, for example, work on the entry on the Sun, but would have the same status as a contributor without an academic background. Disputes about content are usually resolved by discussion among users. But Jimmy Wales, co-founder of Wikipedia and president of the encyclopaedia's parent organization, the Wikimedia Foundation of St Petersburg, Florida, says the finding shows the potential of Wikipedia. "I'm pleased," he says. "Our goal is to get to Britannica quality, or better." Wikipedia is growing fast. The encyclopaedia has added 3.7 million articles in 200 languages since it was founded in 2001. The English version has more than 45,000 registered users, and added about 1,500 new articles every day of October 2005. Wikipedia has become the 37th most visited website, according to Alexa, a web ranking service. But critics have raised concerns about the site's increasing influence, questioning whether multiple, unpaid editors can match paid professionals for accuracy. Writing in the online magazine TCS last year, former Britannica editor Robert McHenry declared one Wikipedia entry — on US founding father Alexander Hamilton — as "what might be expected of a high-school student". Opening up the editing process to all, regardless of expertise, means that reliability can never be ensured, he concluded. Yet Nature's investigation suggests that Britannica's advantage may not be great, at least when it comes to science entries. In the study, entries were chosen from the websites of Wikipedia and Encyclopaedia Britannica on a broad range of scientific disciplines and sent to a relevant expert for peer review. Each reviewer examined the entry on a single subject from the two encyclopaedias; they were not told which article came from which encyclopaedia. A total of 42 usable reviews were returned out of 50 sent out, and were then examined by Nature's news team. Only eight serious errors, such as misinterpretations of important concepts, were detected in the pairs of articles reviewed, four from each encyclopaedia. But reviewers also found many factual errors, omissions or misleading statements: 162 and 123 in Wikipedia and Britannica, respectively. Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg::nature.com D. I. FRANKE/WIKIMEDIA FDN Kurt Jansson (left), president of Wikimedia Deutschland, displays a list of 10,000 Wikipedia authors; Wikipedia's entry on global warming has been a source of contention for its contributors. Editors at Britannica would not discuss the findings, but say their own studies of Wikipedia have uncovered numerous flaws. "We have nothing against Wikipedia," says Tom Panelas, director of corporate communications at the company's headquarters in Chicago. "But it is not the case that errors creep in on an occasional basis or that a couple of articles are poorly written. There are lots of articles in that condition. They need a good editor." Several Nature reviewers agreed with Panelas' point on readability, commenting that the Wikipedia article they reviewed was poorly structured and confusing. This criticism is common among information scientists, who also point to other problems with article quality, such as undue prominence given to controversial scientific theories. But Michael Twidale, an information scientist at the University of Illinois at Urbana-Champaign, says that Wikipedia's strongest suit is the speed at which it can updated, a factor not considered by Nature's reviewers. "People will find it shocking to see how many errors there are in Britannica," Twidale adds. "Print encyclopaedias are often set up as the gold standards of information quality against which the failings of faster or cheaper resources can be compared. These findings remind us that we have an 18-carat standard, not a 24-carat one." The most error-strewn article, that on Dmitry Mendeleev, co-creator of the periodic table, illustrates this. Michael Gordin, a science historian at Princeton University who wrote a 2004 book on Mendeleev, identified 19 errors in Wikipedia and 8 in Britannica. These range from minor mistakes, such as describing Mendeleev as the 14th child in his family when he was the 13th, to more significant inaccuracies. Wikipedia, for example, incorrectly describes how Mendeleev's work relates to that of British chemist John Dalton. "Who wrote this stuff?" asked another reviewer. "Do they bother to check with experts?" But to improve Wikipedia, Wales is not so much interested in checking articles with experts as getting them to write the articles in the first place. As well as comparing the two encyclopaedias, Nature surveyed more than 1,000 Nature authors and found that although more than 70% had heard of Wikipedia and 17% of those consulted it on a weekly basis, less than 10% help to update it. The steady trickle of scientists who have contributed to articles describe the experience as rewarding, if occasionally frustrating (see 'Challenges of being a Wikipedian'). Greater involvement by scientists would lead to a "multiplier effect", says Wales. Most entries are edited by enthusiasts, and the addition of a researcher can boost article quality hugely. "Experts can help write specifics in a nuanced way," he says. Wales also plans to introduce a 'stable' version of each entry. Once an article reaches a specific quality threshold it will be tagged as stable. Further edits will be made to a separate 'live' version that would replace the stable version when deemed to be a significant improvement. One method for determining that threshold, where users rate article quality, will be trialled early next year. -- Eugen* Leitl leitl http://leitl.org ______________________________________________________________ ICBM: 48.07100, 11.36820 http://www.ativel.com 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE From owner-chemistry@ccl.net Wed Dec 14 20:47:00 2005 From: "zhendong zhao zzhao++olemiss.edu" To: CCL Subject: CCL:G: [CCL]Re: Freq cal error Message-Id: <-30322-051214183402-32127-J+nfq/vOWC9qpbSXXB8DZA _ server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Wed, 14 Dec 2005 16:55:27 -0600 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao#,#olemiss.edu] Hi, I think this job can not be handled by G98, there will be IO/FS problem. But you can try Freq=Numer, also you need use seperated scratch file, %rwf=w1,240000000,w2,240000000,w3,240000000,w4,240000000,w5,-1. it will take more time. ZZ On Tue, 13 Dec 2005 15:24:22 -0500 "Hongbing Fu hongbing.f=gmail.com" wrote: > Sent to CCL by: "Hongbing Fu" [hongbing.f*gmail.com] > Hi, > I have a problem completing a gaussian98 frequency job. I have a > system with ~600 basis functions and the freq job quits with the > following message: > "Compute integral second derivatives. > ... and contract with generalized density number 0. > FileIO operation on non-existent file. > FileIO: IOper= 2 IFilNo(1)= -690 Len= 1 IPos= 1 > Q= 1089289192 > dumping /fiocom/, unit = 1 NFiles = 78 SizExt = 524288 WInBlk > = 512 defal = T LstWrd = 667585536 FType=2 FMxFil=10000 > .... (similar lists as below)... > Number 989 993 997 998 > Base 788700 791200 791300 23677 > End 791200 791300 911304 23727 > End1 791200 791300 911304 23727 > Wr Pntr 788700 791200 791300 23677 > Rd Pntr 788700 791200 791300 23677 > dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk > = 512 > defal = T LstWrd = 65536 FType=2 > FMxFil=10000 Number 0 > Base 20480 > End 65536 > End1 65536 > Wr Pntr 20480 > Rd Pntr 20480 > Error termination in NtrErr: > NtrErr Called from FileIO." > Anyone has any idea about this? > Any help will be appreciated. > Thank you, > > > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the #,# sign. You can > also> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > > From owner-chemistry@ccl.net Wed Dec 14 23:08:00 2005 From: "Faisal Rahman s101alif-#-mail.chem.itb.ac.id" To: CCL Subject: CCL: Protonated structure of nucloebase to calculate proton affinities Message-Id: <-30323-051214225845-27588-u+DqcwOS+SoGaX3nI4Lilg%server.ccl.net> X-Original-From: "Faisal Rahman" Sent to CCL by: "Faisal Rahman" [s101alif^^mail.chem.itb.ac.id] Hi every one I'am Faisal I still have question about calculating proton affinities of nucleobase > from the answered of my previous question. In order To calculate proton afinities I must have a frequencies calculation of the optimised structure((the protonated nucleobase and the non-protonated one). What make me confuse is that as we know nucleobase such as adenine or guanine have many side/points that can be protonated. For example adenine have three points of nitrogen in it molecule (N1, N3, N7) that can be protonated. then guanine have one point of Oxigen and one point of nitrogen.. so what sructure I have to use for calculating proton affinities of adenine and guanine. Your help will be very usefull for me ... Thank's before -Faisal Rahman-