From chemistry-request@ccl.net Wed Dec 8 20:18:29 2004 Received: from TheWorld.com (pcls2.std.com [192.74.137.142]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB91IQ8Y028011 for ; Wed, 8 Dec 2004 20:18:27 -0500 Received: from [206.15.140.88] (206-15-140-88.dialup.ziplink.net [206.15.140.88]) by TheWorld.com (8.12.8p1/8.12.8) with ESMTP id iB91QGYR003517 for ; Wed, 8 Dec 2004 20:26:17 -0500 Mime-Version: 1.0 (Apple Message framework v619) In-Reply-To: <20041208105152.GR9221.-at-.leitl.org> References: <20041208105152.GR9221.-at-.leitl.org> Content-Type: text/plain; charset=US-ASCII; format=flowed Message-Id: Content-Transfer-Encoding: 7bit From: Joe Leonard Subject: Re: CCL:[QSAR-devel] Chemical Semantic Web and Thanks (fwd from pm286.-at-.cam.ac.uk) Date: Wed, 8 Dec 2004 20:28:49 -0500 To: chemistry.-at-.ccl.net X-Mailer: Apple Mail (2.619) X-Spam-Status: No, hits=5.5 required=7.5 tests=FVGT_m_MULTI_ODD2, FVGT_s_OBFU_Q1,MAILTO_TO_SPAM_ADDR,RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Dec 8, 2004, at 5:51 AM, Eugen Leitl wrote: > ----- Forwarded message from Peter Murray-Rust ----- > [Crossposted to several OpenSource lists - please reply thoughtfully. I > will collate significant replies] > > I presented an invited lecture at the Royal Soc Chem yesterday on "The > Chemical Semantic Web" and highlighted the impressive contribution of > the > Open Source movement in chemistry. I hope I managed to acknowledge most > people's contributions. It generated a lively discussion in which, I > think, > the Open Source approach came out very positively. Open source tools, in terms of O/S and languages are big wins - Linux has made cheap hardware possible. The GCC language suite, Perl/Python, etc., have been huge benefits as well. I think we'll see work in the scripting languages become the basis for inter-group collaborations, given that developer time's back to being a critical resource. > > Two common negative questions were presented: > > "Who pays for it" > the implication was that if there was no commercial development the > software was second-class and there was no future for it. Not true for those areas which have a broad/deep interest amongst the general development community. However, as one gets more and more specialized, the number of people capable of and interested in working on something gets small - particularly those in a position to do in a la Open Source. Outside of Academia, we've got to work for a living, and it's usually not on Open Source projects. > My response was > that the code would be eagerly adopted by the bioinformatics community > (strongly confirmed by Mike Ashburner) and we are starting to set up > strong > links with the Bioinformatics community on small molecules. This > question > came from the pharma industry and so I challenged them to put something > back into the communal process. How many pharma/biotech's are actively developing more than "glue routines"? Places like Merck and Vertex have published a bit of what they've developed over the years, but aside from Vertex feeding OpenEye, I'm unfamiliar with any contributed code that is generally available. There's real sensitivity towards IP in this industry, which might extend to the "competitive advantage" of in-house code. It's probably difficult to justify development people on the payroll, and "they'll give it away" isn't want management wants to hear. Chemists, on the whole, aren't all that good when it comes to professional development. They've got OLD tools, which (unfortunately) tend to be in old languages. They also tend to be monolithic solutions, which isn't the easiest to use in other applications. > It's noticeable that the pharma industry is > a consumer of our efforts but has not contributed anything in return > and > continues to pay for overpriced software products that do not use > modern > methodology. (I spent 15 years in Glaxo so I feel I have a right to > criticise the industry). Yeah, but paying 2-20 FTE's worth of money for software rental probably fits their management/budget structure. It seems easier to get cash than headcount, and "having somebody to call for support" satisfies a lot of people. From what I've seen over the years, modelers are paid to know medicinal chemistry, some organic synthesis and then their own tools. Real development skills, on the whole, just aren't as available or as valuable - it doesn't directly help projects. There's also no effort on the part of the customer base to realize where things are and maybe where they should be. Probably too difficult to work with those of competitor companies - better to use the software companies as neutral agencies? > I know that pharma industry reads this list and I > would be delighted if there were some who wished to support communal > activity. [I would suggest they mail me directly and I will summarise > replies. All replies will be assumed to be Open unless specifically > indicated]. One approach would be to support a physical workshop on > chemical open source. Particular topics could be: > - markup languages > - communal chemical ontologies (e.g. descriptors) > - Open datasets This is going to be difficult - people like John Dearden and others have been asking for this for years and years. Who's going to get this data in a form which is consistent across labs (assuming such can be done)? > - use of InChI (we are very excited about this) > - graphical components This, aside from things like PyMol, seems to be the hardest. One can get QM codes, and even some classical codes on the web, but graphics is rare. Maybe it's because Chemists can't or won't write this (and CS people aren't interested enough to try - "chemistry, yuck!")? > - common code libraries Hell, our community can't even agree on common data formats...! This would be a HUGE win, coupled with common data representations in languages such as Python. There are several efforts which have shown scripting languages to be a real win as they are easily extended for discipline-specific knowledge and they're pretty much platform independent. This kind of work allows for both serious development and user scripting - thus only one environment must be maintained/documented, etc. > - web services (I'll mail later) > The only contribution that I know of from the pharma industry to > chemoinformatics is the JME editor which is free, but despite repeated > requests is not Open and not likely to be. It could be withdrawn at > any time. Programming is hard. Groups with 1-2 people, unless they're willing to "go in the hole" for several years, just can't create all that's necessary to use modern environments well. It's hard for some sites to justify applications modelers - asking for some of them who'll only develop code (and probably cost more due to rarity) isn't a game group leaders want to play unless there's LOTS of money and head count available? > > "Open source is unfair to commercial developers" > I think this attitude is particularly strong in the US and perhaps > Germany. > The idea is that public funding should not be used to compete against > commercial organisations. As Mike Ashburner replied, most Open > software in > bioinformatics is written by people on short term contracts often with > no > possibility of extension. I know that made contributors to these lists > do > not have jobs. I developed much of CML when I was unemployed after > being > made redundant from Glaxo. Commercial developers should be able to compete on IP and implementation quality. Modelers seem to be a community who really do seek out the better mousetrap. Therefore, for commercial vendors to keep their customers, they'll need to offer what can't easily be created otherwise, or offer tools which are really new/state of art. Given that the major vendors are public companies and the modeler community is a mature market, I'm not entirely optimistic when I think of where new stuff's going to come from. It's tough for them to compete with people like Microsoft or other software companies... Perhaps some kind of industry/non-profit consortium might be created to do this work, which would semi-commercialize it? Can't see it being truly Open Source until there's more of a desire to share and fund... > I would be more (slightly) more sympathetic to this view if the > chemical > software industry provided anything substantial to the community. I > know of > no support for Open efforts from the chemical software industry other > than > a very undersupported effort to get an Open Management Group spec for > chemistry. I was invited to contribute CML as the core of this spec, > but > even then it was made clear that I would not even have my (foreign) > travel > expenses paid - even though I had no job. Again, Linux and things like Perl/Python are critical to modern development. The collapse of hardware prices has made it a little more difficult for the commercial vendors, but it's a WONDERFUL time to be a user right now! I'm less interested in web development as methods and server development, but that's me - there's work on GUI tools in Python, for example, although it's nowhere near as advanced as Java. Is our academic brethren training people who actually know how to develop code, or are they concentrating on science and what can be published? If they're Chemistry faculty, I think the science is the better choice, at least for the student's employability. Would industry hire developers, or do they want those with applications experience? Are we all just a little too conservative, or merely being careful in what we back with lots of money? > Note that "free" is not good enough and may even by counterproductive. > Closed software often stifles development as there is no API and the > software can be withdrawn at any time. That is why we are so keen to > see a > JChempaint component as a universal Open chemical editor for the web. To me, for things to be really open, they should be done in a scripting language. Compiled languages aren't accessible by 50-75% of our community - having the source is meaningless as they'll never look at it. We've all got supercomputers for $500, so lets make better use of developer time than CPU time. > > In fact I think the tide is turning. The components that you are all > developing are ideal for Web Services, which will have the potential to > rapidly become a major player in the chemoinformatics market. Between > the > members of this community we have standards, data, transformers, > algorithms, repositories, query languages, graphics and much more. > I'll put > forward a strategy in the next mail(s). Common data structures. Common file formats. Perhaps if each commercial, semi-commercial and Open Source vendor could contribute a reader and a writer for their "personal" file formats towards something like OpenBabel? Maybe we could agree on some commonality which would (hopefully) reduce the number of wheels which get reinvented each year? > > Meanwhile - when you are hacking the latest set of bugs at 0200 in the > morning, take heart - it really is appreciated - and yes - the day of > Open > Source for "chemistry" is dawning. In fact I think the centre of > gravity of > chemical software development is starting to shift towards bioscience > [and > materials] so that people will simply refer to the informatics of small > molecules as "bioinformatics" Will pharma pay the cash needed to give the (putative) Open Source developers a lifestyle like their modeler cousins? Is this something Academia can/should jump on (what with their extra bodies and lower costs)? Is this a role for Government labs? Multi-Government efforts? Joe From chemistry-request@ccl.net Thu Dec 9 06:05:48 2004 Received: from aspirine.u-strasbg.fr (aspirine.u-strasbg.fr [130.79.84.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB9B5lKK004046 for ; Thu, 9 Dec 2004 06:05:47 -0500 Received: from hit8.pharma.u-strasbg.fr (pcf-b315a-hit3.u-strasbg.fr [130.79.85.33]) (authenticated) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id iB9BD2r10521 for ; Thu, 9 Dec 2004 12:13:02 +0100 Message-Id: <6.0.3.0.0.20041209121752.01d63280[at]aspirine.u-strasbg.fr> X-Sender: rognan[at]aspirine.u-strasbg.fr X-Mailer: QUALCOMM Windows Eudora Version 6.0.3.0 Date: Thu, 09 Dec 2004 12:21:16 +0100 To: CHEMISTRY[at]ccl.net From: Didier Rognan Subject: filtering sd files Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed 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 We are using Filter from OpenEyes to process sd files and remove non drug-like compounds. We have just noticed that two flags (atom stereo parity, bond stero) are modified within the process. Has anyone some workaround ? Kind regards Didier ----------------------------------------------------------------------------------------------- Dr. Didier ROGNAN Directeur de Recherche CNRS UMR 7081 74, route du Rhin, B.P.24 F-67401 Illkirch direct line: +33 (0)3 90 24 42 35 secretary: +33(0)3 90 24 42 20 fax: +33 (0)3 90 24 43 10 email: didier.rognan[at]pharma.u-strasbg.fr www:http://bioinfo-pharma.u-strasbg.fr From chemistry-request@ccl.net Thu Dec 9 06:15:35 2004 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB9BFYKK004657 for ; Thu, 9 Dec 2004 06:15:35 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 2 (built Jul 14 2004)) with ESMTP id <0I8G00AGYDBG83~at~mailserver.unimi.it> for chemistry~at~ccl.net; Thu, 09 Dec 2004 12:30:52 +0100 (MET) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0I8G000F1DBD8P~at~smtp.unimi.it> for chemistry~at~ccl.net; Thu, 09 Dec 2004 12:30:50 +0100 (MET) Date: Thu, 09 Dec 2004 12:34:48 +0100 From: Alessandro Contini Subject: IRC with G03 To: chemistry~at~ccl.net Reply-to: alessandro.contini~at~unimi.it Message-id: <200412091234.48904.alessandro.contini~at~unimi.it> Organization: =?iso-8859-1?q?Universit=E0=20di?= Milano MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.4 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iB9BFZKK004661 Dear CCL Community, I'm trying to perform an IRC calculation with G03. At a certain point the calculation fails in achieving convergence. I tried to use the maxcyc keyword in order to increase the number of optimization cycles, however I obtained the following error message: IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC Berny reaction coordinate optimization. Restoring state from the checkpoint file "ts2_b3lyp.chk". Title: ts2 B3LYP/6-31++G** irc Route: # IRC=(MAXPOINTS=8,CALCFC,STEPSIZE=20,MAXCYC=150) B3LYP/6-31++ G(D,P) GEOM=CONNECTIVITY NOSYMM Restart Attempt # 2 Number of steps in this run= 200 maximum allowed number of steps= 108. Error termination via Lnk1e in /home/mcae/gaussian03/g03/l115.exe at Thu Dec 9 10:04:58 2004. Job cpu time: 0 days 0 hours 0 minutes 0.8 seconds. It seems that I can't go over the 108 steps. Does anybody knows how to override this? Thanks a lot Alessandro -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini~at~unimi.it From chemistry-request@ccl.net Wed Dec 8 17:47:55 2004 Received: from mailbox.syr.edu (mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB8Mls1L019875 for ; Wed, 8 Dec 2004 17:47:54 -0500 Received: from [127.0.0.1] (esf020066.esf.edu [149.119.20.66]) by mailbox.syr.edu (8.12.10/8.12.10) with ESMTP id iB8N36gH023803; Wed, 8 Dec 2004 18:03:07 -0500 (EST) Message-ID: <41B78824.8030902.-at-.syr.edu> Date: Wed, 08 Dec 2004 18:03:00 -0500 From: "William T. Winter" Organization: Cellulose Reseach Foundation@SUNY-ESF User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040804 Netscape/7.2 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Arvydas Tamulis , CHEMISTRY.-at-.ccl.net Subject: CCL:nanomathematics References: <9DD56492790889439F731F5BD6DACA0007D78A14.-at-.srvkyem1.americas.sc-world.com> <20041208135536.E57829.-at-.mserv.itpa.lt> In-Reply-To: <20041208135536.E57829.-at-.mserv.itpa.lt> Content-Type: multipart/alternative; boundary="------------030808030601060709050206" X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_30_40,HTML_MESSAGE, HTML_TITLE_EMPTY,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 This is a multi-part message in MIME format. --------------030808030601060709050206 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Arvydas Tamulis: A "Google" search for nanomathematics only turned up sites that have registered domain names containing the word, but the purpose is to sell those sites to the highest bidder and they are currently devoid of real content. Similarly, a search of Chemical Abstracts using "Sci Finder Scholar" failed to find a single occurrence of the term. So, I guess the term is yours to run up a flagpole and see if someone salutes. William T. Winter Arvydas Tamulis wrote: > I think nanomathematics should describe processes in quantum > nanophysics: quantum statistics, quantum noises. Very important is > that quantum logics possesses more logic functions (gates) in > comparison with classical Boolean logics. > > Regards, > Arvydas Tamulis > www.itpa.lt/~tamulis/ > > On Tue, 7 Dec 2004, Shobe, David wrote: > >> I've never seen the term before, but logically it should refer to >> arithmetic in which all numbers are rounded off to the nearest >> billionth. :-) >> >> --David Shobe, Ph.D., M.L.S. >> S|d-Chemie, Inc. >> phone (502) 634-7409 >> fax (502) 634-7724 >> >> Don't bother flaming me: I'm behind a firewall. >> >> >> -----Original Message----- >> From: Computational Chemistry List [mailto:chemistry-request.-at-.ccl.net]On >> Behalf Of Chungen Liu >> Sent: Monday, December 06, 2004 7:44 PM >> To: chemistry.-at-.ccl.net >> Subject: CCL:nanomathematics >> >> Hi, all, >> Would anyone give a description about the concept "nanomathematics"? >> Thanks in advance. >> Chungen > > -- ============================================================== Prof. W.T.Winter Tel: 315-470-6876 SUNY-ESF FAX: 315-470-6856 Cellulose Research Institute E-Mail: wtwinter.-at-.syr.edu 121 E.C. Jahn Laboratory http://www.esf.edu/cellulose Syracuse, NY 13210 --------------030808030601060709050206 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Arvydas Tamulis:
A "Google" search for nanomathematics only turned up sites that have registered domain names containing the word, but the purpose is to sell those sites to the highest bidder and they are currently devoid of real content.  Similarly, a search of Chemical Abstracts using "Sci Finder Scholar" failed to find a single occurrence of the   term.  So, I guess the term is yours to run up a flagpole and see if someone salutes.
William T. Winter

Arvydas Tamulis wrote:
I think nanomathematics should describe processes in quantum nanophysics: quantum statistics, quantum noises. Very important is that quantum logics possesses more logic functions (gates) in comparison with classical Boolean logics.

Regards,
Arvydas Tamulis
www.itpa.lt/~tamulis/

On Tue, 7 Dec 2004, Shobe, David wrote:

I've never seen the term before, but logically it should refer to arithmetic in which all numbers are rounded off to the nearest billionth.  :-)

--David Shobe, Ph.D., M.L.S.
S|d-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a firewall.


-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request.-at-.ccl.net]On
Behalf Of Chungen Liu
Sent: Monday, December 06, 2004 7:44 PM
To: chemistry.-at-.ccl.net
Subject: CCL:nanomathematics

Hi, all,
Would anyone give a description about the concept "nanomathematics"?
Thanks in advance.
Chungen

--
signature ==============================================================
Prof. W.T.Winter                                                                      Tel: 315-470-6876
SUNY-ESF                                                                              FAX: 315-470-6856
Cellulose Research Institute                                                       E-Mail:  wtwinter.-at-.syr.edu
121 E.C. Jahn Laboratory                                                         http://www.esf.edu/cellulose
Syracuse, NY 13210
--------------030808030601060709050206-- From chemistry-request@ccl.net Thu Dec 9 14:14:30 2004 Received: from electra.cc.umanitoba.ca (electra.cc.umanitoba.ca [130.179.16.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB9JESCb003456 for ; Thu, 9 Dec 2004 14:14:29 -0500 Received: from Fledermaus (net165.chem.umanitoba.ca [130.179.49.85]) by electra.cc.umanitoba.ca (8.13.0/8.13.0) with ESMTP id iB9JTlqY014568 for ; Thu, 9 Dec 2004 13:29:48 -0600 (CST) Message-Id: <200412091929.iB9JTlqY014568/at/electra.cc.umanitoba.ca> Reply-To: From: "Philip Hultin" To: "Computational Chemistry List" Subject: RE: IRC on G03 Date: Thu, 9 Dec 2004 13:29:41 -0600 Organization: Chemistry, U of Manitoba MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002D_01C4DDF3.272BF480" X-Mailer: Microsoft Office Outlook, Build 11.0.6353 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Thread-Index: AcTeJW4xk+a5sWN2TtO0Te10FoBtvQ== X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_40_50,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_002D_01C4DDF3.272BF480 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Alessandro: We did a fair bit of IRC a while ago (look for upcoming papers in J Phys Chem A) and we found that sometimes a calculation would begin to have convergence failures as it moved further from the initial structure (i.e. the TS). This was because the force constants became less reliable the further one got along the IRC. In such cases, if we wanted to move further along the IRC, we needed to specify CALCALL to get fresh force constants at each point. This is a bit time-consuming but not nearly as slow as a failed calculation. Using small step sizes in the IRC also helped a bit. My understanding of the documentation is that CALCFC only does the force constant calculation at the initial structure, NOT at the beginning of each point along the IRC - that is what CALCALL does in this case. After doing this a few times, we concluded that what Gaussian should consider building into the IRC was an option to specify when new force constants should be calculated. It would be nice, for example, to be able to calculate force constants at every Nth point along the IRC - it would keep the calculation on track but take much less time than calculating them at each new point. Another useful variation would be to move N points along the IRC using extrapolated force constants and only then start doing calculated force constants. After all, in most cases one would expect force constants to be drastically different near the "starting material" and "product" states than they are near the TS, but that the differences would initially be small. Any thoughts about this suggestion would be welcome. P. Hultin Associate Professor of Chemistry University of Manitoba ------=_NextPart_000_002D_01C4DDF3.272BF480 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Alessandro:

 

We did a fair bit of IRC a while ago (look for = upcoming papers in J Phys Chem A) and we found that sometimes a calculation would = begin to have convergence failures as it moved further from the initial = structure (i.e. the TS).  This was because the force constants became less = reliable the further one got along the IRC.

 

In such cases, if we wanted to move further along the = IRC, we needed to specify CALCALL to get fresh force constants at each = point.  This is a bit time-consuming but not nearly as slow as a failed = calculation.  Using small step sizes in the IRC also helped a = bit.

 

My understanding of the documentation is that CALCFC = only does the force constant calculation at the initial structure, NOT at the beginning of each point along the IRC – that is what CALCALL does = in this case.

 

After doing this a few times, we concluded that what Gaussian should consider building into the IRC was an option to specify = when new force constants should be calculated.  It would be nice, for = example, to be able to calculate force constants at every Nth point along the IRC = – it would keep the calculation on track but take much less time than calculating = them at each new point.  Another useful variation would be to move N points = along the IRC using extrapolated force constants and only then start doing = calculated force constants.  After all, in most cases one would expect force = constants to be drastically different near the “starting material” and = “product” states than they are near the TS, but that the differences would = initially be small.  Any thoughts about this suggestion would be = welcome.

 

P. Hultin

Associate Professor of = Chemistry

University of Manitoba

------=_NextPart_000_002D_01C4DDF3.272BF480-- From chemistry-request@ccl.net Thu Dec 9 11:12:18 2004 Received: from f04n07.cac.psu.edu (f04s07.cac.psu.edu [128.118.141.35]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB9GCHCb024530 for ; Thu, 9 Dec 2004 11:12:18 -0500 Received: from blue.chem.psu.edu ([128.118.56.38]) by f04n07.cac.psu.edu (8.12.11/8.12.11) with ESMTP id iB9GRX9C078436; Thu, 9 Dec 2004 11:27:34 -0500 Subject: Re: CCL:[QSAR-devel] Chemical Semantic Web and Thanks (fwd from pm286)at(cam.ac.uk) From: Rajarshi Guha Reply-To: rxg218)at(psu.edu To: Joe Leonard Cc: chemistry)at(ccl.net In-Reply-To: References: <20041208105152.GR9221)at(leitl.org> Content-Type: text/plain Date: Thu, 09 Dec 2004 11:27:35 -0500 Message-Id: <1102609655.27984.2.camel)at(blue.chem.psu.edu> Mime-Version: 1.0 X-Mailer: Evolution 2.0.2 (2.0.2-3) Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=7.4 required=7.5 tests=FROM_ENDS_IN_NUMS, FVGT_m_MULTI_ODD2,FVGT_s_OBFU_Q1,MAILTO_TO_SPAM_ADDR,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Wed, 2004-12-08 at 20:28 -0500, Joe Leonard wrote: > To me, for things to be really open, they should be done in a scripting > language. > Compiled languages aren't accessible by 50-75% of our community - having > the source is meaningless as they'll never look at it. We've all got > supercomputers > for $500, so lets make better use of developer time than CPU time. Jython would allow you to reuse existsing Java frameworks in Python This does not apply if you want to have method development in pure Python - but it does allow for code sharing/reuse ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Science kind of takes the fun out of the portent business. -Hobbes From chemistry-request@ccl.net Thu Dec 9 12:31:07 2004 Received: from web50410.mail.yahoo.com (web50410.mail.yahoo.com [206.190.38.245]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iB9HV6Cb029681 for ; Thu, 9 Dec 2004 12:31:06 -0500 Received: (qmail 55627 invoked by uid 60001); 9 Dec 2004 17:46:25 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=h184UOQaZLsGzIWkaXtl1pGr8r/8YHN2SJRPrEw7aIZ6VWQexb6Rh+vF4rJbKeoaJozt1kGzBup7lfORbacv9VHMWVHqQKmQses/5YVEblODprrVF/srWFjpNM4UGc4IDGLNnqz2DLImKgcwwM3i1A8y8S43mW8GCW99wMR2Pk0= ; Message-ID: <20041209174625.55625.qmail)at(web50410.mail.yahoo.com> Received: from [143.183.121.3] by web50410.mail.yahoo.com via HTTP; Thu, 09 Dec 2004 09:46:25 PST Date: Thu, 9 Dec 2004 09:46:25 -0800 (PST) From: Joseph Han Reply-To: jhh3851)at(yahoo.com Subject: Re: CCL:IRC with G03 To: Alessandro Contini , chemistry)at(ccl.net In-Reply-To: <200412091234.48904.alessandro.contini)at(unimi.it> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS 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've seen similar error messages. I get then when I try to restart an IRC calculation with the following option: opt=(restart,maxcycle=xxx) instead, try this: opt=(restart) Joseph --- Alessandro Contini wrote: > Dear CCL Community, > I'm trying to perform an IRC calculation with G03. At a certain point > the > calculation fails in achieving convergence. I tried to use the maxcyc > keyword > in order to increase the number of optimization cycles, however I > obtained > the following error message: > > > IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC > Berny reaction coordinate optimization. > Restoring state from the checkpoint file "ts2_b3lyp.chk". > Title: ts2 B3LYP/6-31++G** irc > Route: # IRC=(MAXPOINTS=8,CALCFC,STEPSIZE=20,MAXCYC=150) > B3LYP/6-31++ > G(D,P) GEOM=CONNECTIVITY NOSYMM > Restart Attempt # 2 > Number of steps in this run= 200 maximum allowed number of steps= > 108. > Error termination via Lnk1e in /home/mcae/gaussian03/g03/l115.exe at > Thu Dec > 9 10:04:58 2004. > Job cpu time: 0 days 0 hours 0 minutes 0.8 seconds. > > > It seems that I can't go over the 108 steps. Does anybody knows how > to > override this? > > Thanks a lot > > Alessandro > -- > Alessandro Contini, Ph.D. > Istituto di Chimica Organica "Alessandro Marchesini" > Universit` degli Studi di Milano, Facolt` di Farmacia > Via Venezian, 21 20133 Milano > Tel. +390250314480 Fax. +390250314476 > e-mail alessandro.contini)at(unimi.it > > > > > > -= 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)at(ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST)at(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)at(nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Dec 9 15:21:16 2004 Received: from mta3.appstate.edu (mta3.appstate.edu [152.10.1.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB9KLFV9008119 for ; Thu, 9 Dec 2004 15:21:15 -0500 Received: from ws1.appstate.edu (ws1.appstate.edu [152.10.1.40]) by mta3.appstate.edu (8.12.11/8.12.10) with ESMTP id iB9KANww004186 for ; Thu, 9 Dec 2004 15:10:23 -0500 Received: from kohn.appstate.edu (cohn.chem.appstate.edu [152.10.114.100]) by appstate.edu (PMDF V6.2-X26 #30685) with ESMTP id <01LI76RZ42H6A11C98/at/appstate.edu> for chemistry/at/ccl.net; Thu, 09 Dec 2004 15:21:00 -0500 (EST) Date: Thu, 09 Dec 2004 15:23:04 -0500 From: Steve Williams Subject: Re: CCL:IRC on G03 In-reply-to: <200412091929.iB9JTlqY014568/at/electra.cc.umanitoba.ca> X-Sender: willsd/at/imap.appstate.edu To: Philip Hultin , Computational Chemistry List Message-id: <5.1.0.14.0.20041209151525.01d5f970/at/imap.appstate.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; format=flowed; charset=us-ascii X-MailScanner-Information: Please contact the Helpdesk @ 6266 for more information X-MailScanner-ASU-mta3: Found to be clean X-MailScanner-SpamCheck: X-MailScanner-From: willsd/at/appstate.edu 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 At 01:29 PM 12/9/2004 -0600, Philip Hultin wrote: >Alessandro: > > > >We did a fair bit of IRC a while ago (look for upcoming papers in J Phys >Chem A) and we found that sometimes a calculation would begin to have >convergence failures as it moved further from the initial structure (i.e. >the TS). This was because the force constants became less reliable the >further one got along the IRC. > > > >In such cases, if we wanted to move further along the IRC, we needed to >specify CALCALL to get fresh force constants at each point. This is a bit >time-consuming but not nearly as slow as a failed calculation. Using >small step sizes in the IRC also helped a bit. > > > >My understanding of the documentation is that CALCFC only does the force >constant calculation at the initial structure, NOT at the beginning of >each point along the IRC that is what CALCALL does in this case. > > > >After doing this a few times, we concluded that what Gaussian should >consider building into the IRC was an option to specify when new force >constants should be calculated. It would be nice, for example, to be able >to calculate force constants at every Nth point along the IRC it would >keep the calculation on track but take much less time than calculating >them at each new point. Another useful variation would be to move N >points along the IRC using extrapolated force constants and only then >start doing calculated force constants. After all, in most cases one >would expect force constants to be drastically different near the starting >material and product states than they are near the TS, but that the >differences would initially be small. Any thoughts about this suggestion >would be welcome. I've long thought that a calcsometimes option would be useful for optimizations as well, particularly for transition state optimizations. I've done this manually for some tricky transition state optimizations by limiting the number of steps, computing new force constants, doing several more steps, etc. Automatically computing the Hessian every 5 or 10 steps could be useful in several types of calculations. Count me on supporting this as a future Gaussian option. (Mike, Doug, did you hear this?) Steve Williams Department of Chemistry Appalachian State University Boone, NC 28608 > > >P. Hultin > >Associate Professor of Chemistry > >University of Manitoba From chemistry-request@ccl.net Thu Dec 9 17:05:42 2004 Received: from imail4.gazeta.pl (imail4.gazeta.pl [193.42.231.135]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB9M5ebF014748 for ; Thu, 9 Dec 2004 17:05:41 -0500 Received: from poczta.gazeta.pl (unverified [172.20.25.75]) by (imail4.gazeta.pl) with ESMTP id 10046283 for ; Thu, 09 Dec 2004 23:20:59 +0200 Received: from ew2 (unverified [172.20.26.232]) by av.gazeta.pl (av.gazeta.pl) with ESMTP id 74115 for ; Thu, 09 Dec 2004 23:20:59 +0100 Message-ID: <1102630859503.ew2.sterzel-.at.-gazeta.pl> Date: Thu, 9 Dec 2004 23:20:59 +0100 (CET) From: Mariusz Sterzel Reply-To: msterzel-.at.-buffalo.edu To: chemistry-.at.-ccl.net Subject: A question about software Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: 8bit X-mailer: (c)Agora mailer (v3.00) Organization: Portal Agory S.A. X-IP: ja08.chem.buffalo.edu X-Complaints-To: abuse-.at.-gazeta.pl X-URL: http://www.gazeta.pl X-Spam-Status: No, hits=-0.8 required=7.5 tests=BAD_X_HEADERS,X_URL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLs, Do you happend to know a program, which for a given molecule (organometalic{M=Pt,Pb etc.}) generates a number of conformers automaticaly. Then locates a number of solvent molecules (which could it read or have in library) randomly around conformers and minimize the energy (by program itself or by external software {mm? level})? Prefered platform is unix/linux. What would you suggest? Best regards, Mariusz PS. I'll sumarise results -- Mariusz Sterzel Email: sterzel/^at^\gazeta.pl From chemistry-request@ccl.net Thu Dec 9 18:47:52 2004 Received: from postoffice10.mail.cornell.edu (postoffice10.mail.cornell.edu [132.236.56.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB9NlpbF020930 for ; Thu, 9 Dec 2004 18:47:51 -0500 Received: from [192.168.0.139] (ip.253.34.140-dhcp.chem.cornell.edu [128.253.34.140]) by postoffice10.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id iBA03BDJ016411 for ; Thu, 9 Dec 2004 19:03:11 -0500 (EST) Mime-Version: 1.0 (Apple Message framework v619) In-Reply-To: <1102546555.41b7867b9ce28[at]webmail.mail.rice.edu> References: <1102546555.41b7867b9ce28[at]webmail.mail.rice.edu> Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: From: Geoff Hutchison Subject: Re: CCL:Gaussian PBC input files? Date: Thu, 9 Dec 2004 19:03:08 -0500 To: chemistry[at]ccl.net X-Mailer: Apple Mail (2.619) X-Spam-Status: No, hits=3.0 required=7.5 tests=FROM_ENDS_IN_NUMS, MAILTO_TO_SPAM_ADDR autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iB9NlqbF020934 Of course I forgot the blank line at the end of the input file. D'oh! Sorry for the silly mistake. -Geoff -- -Dr. Geoffrey Hutchison Abruqa Group, Molelectronics (607) 255-7568 Cornell Chemistry http://abruna.chem.cornell.edu/ On Dec 8, 2004, at 5:55 PM, enb[at]rice.edu wrote: > Geoff: > > Put a blank line or several at the end of the file and see if that > works. > Almost everything in Gaussian is blank line terminated. If the file > is just > coordinates to the end of the file, gaussian reads til the end of the > coords > and then tries to read another line, gets an end of file error, and > quits. > With the blank line, it reads to the end of the coordinates, reads a > blank line > which tells it coords are finished, and then precedes to either do the > calculation or read in other things it has been directed to do. > > Ed Brothers. > > > Quoting Geoff Hutchison : > >> I've been trying to run PBC calculations with g03 unsuccessfully. (I'm >> currently trying g03 C.02, but have tried older versions too.) This is >> running on a Linux box, and runs other Gaussian jobs just fine. >> >> Here's my test file -- it's for graphite, and was quite literally >> copied out of the G03 manual. (I figured I was having problems with >> input in *my* files first, so I decided to try theirs...) >> >> ---- graphite.com >> #n HF/6-31+G* SCF=Tight PBC(NKPoint=48,CellRange=20) >> >> graphite >> >> 0 1 >> C 0.000000 0.000000 0.000000 >> C 0.000000 1.429118 0.000000 >> TV 2.475315 0.000000 0.000000 >> TV -1.219952 2.133447 0.000000 >> ---- >> >> In return, I get: (lots of stuff, and carbon coordinates) ... >> TV 2.47532 0. 0. >> TV -1.21995 2.13345 0. >> End of file in ZSymb. >> Error termination via Lnk1e in /usr/local/g03/l101.exe at Wed Dec 8 >> 15:22:53 >> 2004. >> >> Any help or suggestions would be greatly appreciated. Thanks in >> advance! >> -Geoff >> >> -- >> -Dr. Geoffrey Hutchison >> Abruqa Group, Molelectronics (607) 255-7568 >> Cornell Chemistry http://abruna.chem.cornell.edu/ >> >> >> >> -= 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[at]ccl.net >> >> Send your subscription/unsubscription requests to: >> CHEMISTRY-REQUEST[at]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[at]nd.edu (read about it on CCL Home Page) >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >> +-+ >> >> >> >> >> >> > >