From owner-chemistry@ccl.net Wed Mar 1 01:34:00 2006 From: "joerg.wegner joerg.wegner]-[web.de" To: CCL Subject: CCL: AW: Feature request: Wiki Message-Id: <-31064-060228191213-28786-zFSMSXi5lueLT8kpUE89Cw^server.ccl.net> X-Original-From: "joerg.wegner" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Feb 2006 23:40:31 +0100 MIME-Version: 1.0 Sent to CCL by: "joerg.wegner" [joerg.wegner%%web.de] Thanks, for the fast answer, > While there is no CCL-Wiki running, there is a Computational Chemistry > Wiki running and does great things: http://en.wikipedia.org/wiki/Computational_chemistry So, I can really encourage people in the CCL field to contribute to Wikipedia. Just have a look at the brilliant CCL archive and you have more than enough material to contribute, e.g.: - Forward request, e.g. 'what is DFT?' also to Wikipedia, by citing the relevant articles. - Create docking program comparisons there, like e.g. http://en.wikipedia.org/wiki/Comparison_of_instant_messengers - Add chemical file formats http://en.wikipedia.org/wiki/Chemical_file_format - Cross/link Ullmann algorithm to Cheminformatics. Create cross-link to other subgraph isomorphism approaches. - and so on ... And I end with some comments with respect to the 'software patent' discussion ... I only agree partially with some of the previous mails ... but to save letters ... *!colleagues!* ... let's try to be constructive in that ... independently from which commercial or non-commercial site. We are to less people in that area to fight till the knock-out. Lets rather work on the commonalities than on the differences. >How can you expect to get state of the art public domain code, when many >are still using 1960s coding practices? That's not the fault of the students, but of the missing Chem/Modeling-Informatics education. And maybe the missing documentation for students (our future, they do not start as experts in software design, algorithm development or end users), which is available ... http://en.wikipedia.org How many people have ever heard about runtime complexity, combinatorial (not continuous) optimization problems, bias-variance (variance ... mmmh) and so on ... or more simply how many chemistry students had contact to a SDF or PDB file format and that it might be become important ...? BTW ... is that article not much too short ... http://en.wikipedia.org/wiki/Protein_Data_Bank Best, Joerg Kurt Wegner From owner-chemistry@ccl.net Wed Mar 1 02:09:01 2006 From: "Mgr. Lubos Vrbka lubos.vrbka/./uochb.cas.cz" To: CCL Subject: CCL: PBC software Message-Id: <-31065-060301014635-23267-BoVsgg13txNRVxSU8Bc2fQ#,#server.ccl.net> X-Original-From: "Mgr. Lubos Vrbka" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 01 Mar 2006 07:46:26 +0100 MIME-Version: 1.0 Sent to CCL by: "Mgr. Lubos Vrbka" [lubos.vrbka ~~ uochb.cas.cz] > pwSCF, CPMD, Siesta maybe CP2K as well? regards, lubos -- ..................................................... Mgr. Lubos Vrbka Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic http://www.molecular.cz/~vrbka ..................................................... From owner-chemistry@ccl.net Wed Mar 1 02:52:01 2006 From: "Konrad Hinsen konrad.hinsen+/-cea.fr" To: CCL Subject: CCL: software patents in chemistry? Message-Id: <-31066-060228154227-9247-EQkz2wadQgHxO+61RoyFmA^^^server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Tue, 28 Feb 2006 15:42:25 -0500 Sent to CCL by: "Konrad Hinsen" [konrad.hinsen{}cea.fr] On 28.02.2006, at 20:37, Dave Young dave.young^-^springmail.com wrote: >4) A limited time monopoly on the idea patented. Who would invest time and money into making >a nice commercial piece of software when someone could legally clone it and undercut your price >(because they didn't pay the high R&D costs). The users of the software benefit from having good >quality commercial software, just as much as the people who make money creating that software. That's the argument on which the whole idea of patents is based, and it has worked well enough in engineering in the past. I wouldn't mind carrying over these principles to software, but the specificities of the software world need to be taken into account, which at the moment is not done: 1) Development effort vs. patenting effort In engineering, a patent is granted for an invention whose development and description takes a serious amount of time and in most cases significant capital investment. Compared to that, the effort to search for existing patents and to prepare a patent application is small, so the patenting procedure is not an impediment to innovation. Moreover, the cost of physical production is often significant, further reducing the total economic impact of the patenting effort. Software patents, on the other hand, have routinely been granted for almost trivial innovations, for ideas that lots of competent programmers around the world could develop in a day or two. In that situation, the cost of the patent sytem vastly exceeds the development cost, with the net result of creating a development monopoly for big business that can pay for the patents. Conclusion: software patents should be granted only for significant development work. 2) Duration of a patent vs. speed of development in the computer world 20 years is equivalent to infinity in the fast-paced world of computers. Software patents should be granted for shorter periods. 3) Complexity of software products vs. complexity of a single invention In engineering, a product is usually concerned by a handful of patents, often just one. In the computing world, a real-life program makes use of lots of algorithms that could be patented, even if the criteria were stricter. Programmers might one day spend as much time figuring out which patents apply to their work than doing the actual programming. All this shows that the existing patent system doesn't work well for software, and I think the real- life experience with US software patents demonstrates this rather well. Hardly anyone ever uses a patent against the payment of licence fees. The big companies simply sign agreements not to attack each other for patent infringement. This is not how the patent system was supposed to work. However, I agree with Warren that copyright is equally badly adapted to the needs of the software business. What we need is something else entirely. In the meantime, my personal point of view of a computational scientist is that I can live very well with the current situation of Open Source software in Europe: no patents, and copyright used to encourage sharing. Until someone comes up with a better approach, this is what I will defend. >I have to admire the nobility of someone who gives away the fruits of their labor for free, while >risking starving their own children. However, I'm not that That is not the situation of academic researchers. They are paid mostly from public money to generate public wealth. If they publish their scientific findings for anyone to use freely, why shouldn't they do the same with their scientific software? My "ideal world" of scientific computing would have academic institutions pay for the developement of the infrastructure (algorithms, fundamental libraries, protocols, file formats) that would be freely available to anyone, and commercial companies develop end-user applications on top of that infrastructure that would be sold commercially. The way the Linux world works (Open Source code but commercial distributions) shows that this is feasible. >which are much more professional. Most of the public domain software I see has been written by >students, who haven't got a clue what Hungarian naming is, what design patterns are, or unit >testing, or many of the other tentants of good commercial software development. There are a >number of public That's a different problem, which has been discussed here before: the notorious lack of competence of most computational scientists in a key technique of their work, programming. But this is mostly a matter of education in my opinion. >But keep in mind that our society needs the commercial software, which fills needs that no public >domain software has ever come close to filling. I don't begrudge anyone their right to patent >codes and make what money they can from it. Me neither, as long as I can continue to develop Open Source software without having to become a patent lawyer or having to pay one. -- ------------------------------------------------------------------------------- Konrad Hinsen Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: konrad.hinsen+*+cea.fr ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Mar 1 03:27:01 2006 From: "Dr. Alexander Hofmann ah=-=chemie.hu-berlin.de" To: CCL Subject: CCL: PBC software Message-Id: <-31067-060228222036-30297-OoIpRCYDyQjqxEv0hjNetg .. server.ccl.net> X-Original-From: "Dr. Alexander Hofmann" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Tue, 28 Feb 2006 22:34:02 +0100 Mime-Version: 1.0 Sent to CCL by: "Dr. Alexander Hofmann" [ah[*]chemie.hu-berlin.de] Hi Pablo, check out the collection on the Psi_k webpage: http://psi-k.dl.ac.uk/index.html?codes Some of them are commercial, others not. License details are there, too. Cheers Alexander On Tue, Feb 28, 2006 at 03:45:19PM -0500, Pablo Andres Denis pablod^^^bilbo.edu.uy wrote: > Sent to CCL by: "Pablo Andres Denis" [pablod^bilbo.edu.uy] > Hi all, > > It is possible to work in ``molecular quantum chemistry with free programs like GAMESS, COLUMBUS, NWCHEM, DIRAC etc. but are there any free programs that work with periodic systems? (WIEN2k, CRYSTAL, VASP, CASTEP etc are all paid). > > > Thanks, > > Pablo> > > -- Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie Arbeitsgruppe Quantenchemie Post: Unter den Linden 6 10099 Berlin Visitors: Brook-Taylor-Strasse 2 12489 Berlin ah * chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35 From owner-chemistry@ccl.net Wed Mar 1 04:02:01 2006 From: "Gilles Frapper gilles.frapper**univ-poitiers.fr" To: CCL Subject: CCL: PBC software Message-Id: <-31068-060228171840-14071-c7QS/mImtPmBxmPzNWNOgg__server.ccl.net> X-Original-From: Gilles Frapper Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 28 Feb 2006 22:39:19 +0100 MIME-Version: 1.0 Sent to CCL by: Gilles Frapper [gilles.frapper|a|univ-poitiers.fr] Bonsoir ! Look at : *Abinit* : http://www.abinit.org/ ; DFT using pseudopotentials and a planewave basis. *CPMD *: http://www.cpmd.org/ The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. *The PINY_MD(c)* Simulation Package* : http://homepages.nyu.edu/~mt33/PINY_MD/PINY.html In our group, we use VASP, a robust DFT program for periodic systems. http://cms.mpi.univie.ac.at/vasp/ But it's not free of charge... Salutations du soir. Gilles Pablo Andres Denis pablod^^^bilbo.edu.uy a écrit : >Sent to CCL by: "Pablo Andres Denis" [pablod^bilbo.edu.uy] >Hi all, > > It is possible to work in ``molecular quantum chemistry with free programs like GAMESS, COLUMBUS, NWCHEM, DIRAC etc. but are there any free programs that work with periodic systems? (WIEN2k, CRYSTAL, VASP, CASTEP etc are all paid). > > >Thanks, > > Pablo > > -- Gilles Frapper, enseignant-chercheur. Groupe de chimie quantique appliquée LACCO UMR 6503 CNRS - Université de Poitiers Tel : 05 49 45 35 74 ; fax : mel : gilles.frapper_._univ-poitiers.fr site : http://labo.univ-poitiers.fr/yargla From owner-chemistry@ccl.net Wed Mar 1 04:36:00 2006 From: "German I. Sastre Navarro gsastre-x-itq.upv.es" To: CCL Subject: CCL: software patents in chemistry? Message-Id: <-31069-060301040742-24281-2UvDrg0i7aOu/RjGoAbwNw!=!server.ccl.net> X-Original-From: "German I. Sastre Navarro" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 1 Mar 2006 10:06:07 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "German I. Sastre Navarro" [gsastre(_)itq.upv.es] Dear Dave, You seem to imply that open source is a noble art made by those who can take the risk of earning a little less money, and therefore compromising their quality of life (whether with or without children is a secondary matter which I will not enter to discuss here). To my mind, the free software philosophy must be praised by all its achievements, one of them being the huge amount of generosity behind all the contributors that make possible this service to the society of software users. Sometimes free software does not mean unpaid programming, but, anyway, unpaid efforts should not imply irresponsible people regarding their family sustain. Try not to see everything in economic terms. Many public domain software is made by people who know very well Hungarian naming and many more things. Best regards German > I have to admire the nobility of someone who gives away the fruits of their labor for free, while risking starving their own children. However, I'm not that noble. I like working in commercial software development environments, which are much more pro fessional. Most of the public domain software I see has been written by students, who haven't got a clue what Hungarian naming is, what design patterns are, or unit testing, or many of the other tentants of good commercial software development. There ar e a number of public domain codes that I can't get to compile and run correctly, and I've been doing that over 20 years with some of the most complex codes in the world on a wide variety of operating systems. How can you expect to get state of the art pu blic domain code, when many are still using 1960s coding practices? > > There are places in the world for both public domain software and commercial software. > But keep in mind that our society needs the commercial software, which fills needs that no public domain software has ever come close to filling. I don't begrudge anyone their right to patent codes and make what money they can from it. > From owner-chemistry@ccl.net Wed Mar 1 05:52:00 2006 From: "Gilles Marcou gilles.marcou###pharma.u-strasbg.fr" To: CCL Subject: CCL: software patents in chemistry? Message-Id: <-31070-060301054558-15050-eswlZp+ibq/Bsw4umt0DaA^server.ccl.net> X-Original-From: Gilles Marcou Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Wed, 1 Mar 2006 11:55:20 +0100 MIME-Version: 1.0 Sent to CCL by: Gilles Marcou [gilles.marcou~~pharma.u-strasbg.fr] Hi, I did not wanted to take part to the discussion initially but I feel offended by what follows: > Commercial software packages are easier to install. > Commercial software packages have fewer bugs. > Bugs get fixed faster in commercial packages. > Commercial software incorporates more new features, more innovative > features, and does so much more quickly. Commercial software packages have > better documentation. > Commercial software has better tech support. > Commercial software has been more throughly tested on a wider variety > hardware platforms. First of all, this is a very subjective opinion. I have almost exactly the opposed one. > There are exceptions to all of these, but on average it is what I see. Of course. > I have to admire the nobility of someone who gives away the fruits of their > labor for free, while risking starving their own children. However, I'm > not that noble. I like working in commercial software development > environments, which are much more professional. First of all academics are not second rank professionals. Second, the author forgets that most of the commercial packages have their roots in -they are sometimes clusters of- programs and algorithms developped in academic environements. My personal feeling is that these environements have proved to be more innovative than any company ever was in our field. > Most of the public domain > software I see has been written by students, who haven't got a clue what > Hungarian naming is, what design patterns are, or unit testing, or many of > the other tentants of good commercial software development. This disdain for open source code is what hurts me the most. Besides, these griefs could be applied also to many of the commercial products I know: the commercial code I was enabled to see was not particularly clean, clear or even tested, not to speak about unit testing. > There are a > number of public domain codes that I can't get to compile and run > correctly, and I've been doing that over 20 years with some of the most > complex codes in the world on a wide variety of operating systems. Is it a confession? I'm not as old in the field but never experienced more difficulties with commercial programs than with open sources or academic ones. > How can > you expect to get state of the art public domain code, when many are still > using 1960s coding practices? C++ was created in 80's and normilized in 1998. Java was created in 1991. Python was created in the early 90's. Ruby was created in 1993. Even Fortran was modernized in 1995, Caml was first developped in 1987. Those langage are used in academic projects and even more in open source world. They all imply new paradigms. Yet many commercial code is written in Ada, Fortran77, Kobold or C. > There are places in the world for both public domain software and > commercial software. OK. > As for public domain code repositories. There are and have been quite a > few... Oak, Simtel20, CCL, QCPE, Sourceforge... All the authors have to do > is pick one, include their favorite public domain license, upload the > source, and let everyone else work on it. That's not as easy to do as it > sounds. It's a scary thing throwing your baby out into the street like > that. I invite anybody to read the requirements to submit contributions to a public library like boost: http://www.boost.org/more/lib_guide.htm#Requirements Releasing a source code or contributing to open source projects, in my opinion, is worth hundreds of publications. -- Gilles Marcou Université Louis Pasteur de Strasbourg Faculté de Pharmacie Laboratoire de Pharmacochimie de la Communication Cellulaire, UMR7081 74, Route du Rhin, BP24 67401 Illkirch tel.:(0033)(0)3.90.24.42.21 eMail: marcou%a%pharma.u-strasbg.fr From owner-chemistry@ccl.net Wed Mar 1 06:58:00 2006 From: "David F. Green dfgreen=ams.sunysb.edu" To: CCL Subject: CCL: software pattents in chemistry? Message-Id: <-31071-060301065526-16796-EsNfr6an51/cN72tvjlIVA(a)server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 01 Mar 2006 06:55:14 -0500 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen|ams.sunysb.edu] If you actually read these articles, they say precisely what I did: The experimental use exception does not allow for unrestricted non-commercial/non-profit use; it does, however, allow for testing, and it is very clear that validation of published results would fall under that umbrella. What was shot down in this case was the use of "experimental use" as a justification for academic, or other non-profit, labs to ignore patents altogether; if you are in the business of research (as universities, etc are) then use of a patented method to further that research is not a "purely philosophical" enterprise, and you must abibe by the patent protections. The question of whether there SHOULD be a non-profit exception to patent protection is another one altogether. ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Greg Landrum Landrum-#-RationalDiscovery.com wrote: > Sent to CCL by: Greg Landrum [Landrum[*]RationalDiscovery.com] > David F. Green dfgreen..ams.sunysb.edu wrote: > >>Sent to CCL by: "David F. Green" [dfgreen]-[ams.sunysb.edu] >>US patent law explicitly allows an exception for "experimental use." >>This includes testing, and would most certainly allow for validation of >>published results. It is true that the law does not make an exception >>for non-commercial or personal use -- you are not allowed to use a >>patented method for anything beyond testing unless you obtain permission >>from the patent holder -- but that is a separate issue. The arguments >>that patenting scientific work prevents it from being independently >>verified simply does not hold water. This is equally true for >>computational and non-computational methods. > > > Though things may have changed in the last couple of years, a court > decision in 2003 (Maday vs Duke U.) pretty much gutted the "experimental > use" exemption: > http://www.localtechwire.com/article.cfm?u=10135 > http://www.wiggin.com/db30/cgi-bin/pubs/Rev%20IP%20Advisory%20-%20Summer%2003%20this%20one.pdf > > -greg> > > From owner-chemistry@ccl.net Wed Mar 1 07:58:01 2006 From: "Michel Petitjean ptitjean]*[itodys.jussieu.fr" To: CCL Subject: CCL: software patents in chemistry? Message-Id: <-31072-060301075454-9082-OaJC3SQby+alT0+DmFFRqQ^_^server.ccl.net> X-Original-From: Michel Petitjean Date: Wed, 1 Mar 2006 13:54:34 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean_._itodys.jussieu.fr] To: chemistry^ccl.net Subject: CCL: Re: software patents in chemistry? Sent to CCL by: Dave Young [dave.young.^.springmail.com] > ... >1) You can't patent a law of nature, so you can't patent the exact solution to the Schrodinger equation, but you can patent a useful approximation method. > ... I disagree. You cannot patent the calculus of pi via some original serie, so you cannot patent any approximate calculation of some unknown value, set of values, function, etc.. So, you cannot patent any useful approximation method. Moreover, it could be much more difficult to prove that some original serie converges to pi rather than to do a minor change in an existing algorithm or method solving the Schrodinger equation for some system. As long as we deal with mathematics (numerical analysis, algorithmic, operation research, etc..), nothing should be patented, even if there are difficulties to award the discoverer, and discarding the difficulties to progress on the mathematical problem. If you would like to patent something, please do it for some physical device. You can copyright or sell a programme calculating pi, but please do not restrict the right to use algoritms and methods. Thanks. Michel Petitjean, Email: petitjean^itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean^ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From owner-chemistry@ccl.net Wed Mar 1 08:33:00 2006 From: "FyD fyd-*-u-picardie.fr" To: CCL Subject: CCL: software patents in chemistry? Message-Id: <-31073-060301082451-26133-Jfy4fiweqo+jfho+dqgbsw,+,server.ccl.net> X-Original-From: FyD Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 01 Mar 2006 13:25:46 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd^_^u-picardie.fr] > Sent to CCL by: Gilles Marcou [gilles.marcou~~pharma.u-strasbg.fr] > I did not wanted to take part to the discussion initially but I feel offended > by what follows: I totally agree with Gilles... > > Commercial software packages are easier to install. > > Commercial software packages have fewer bugs. This is totally wrong ! We write a communication about bugs: Please see http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12856194&dopt=Abstract > > Bugs get fixed faster in commercial packages. Wrong ! Totally wrong ! > > Commercial software incorporates more new features, more innovative > > features, and does so much more quickly. Commercial software packages have > > better documentation. > > Commercial software has better tech support. May be, although mailing lists such as the CCL or AMBER mailing lists are very active and help a lot... > > Commercial software has been more throughly tested on a wider variety > > hardware platforms. I totally disagree with what is written above! Please see http://www.gnu.org/software/reliability.html regards, Francois -- * F.-Y. Dupradeau * DMAG EA 3901 & Faculte de Pharmacie, Amiens, France **** http://www.u-picardie.fr/labo/lbpd/FyD/ From owner-chemistry@ccl.net Wed Mar 1 09:20:00 2006 From: "Alexandre Hocquet alexandre.hocquet:-:eeigm.inpl-nancy.fr" To: CCL Subject: CCL: software patents in europe Message-Id: <-31074-060301090110-13352-mpnnPQq8pbjI8iPlhYI9kA:-:server.ccl.net> X-Original-From: "Alexandre Hocquet" Date: Wed, 1 Mar 2006 09:01:06 -0500 Sent to CCL by: "Alexandre Hocquet" [alexandre.hocquet|a|eeigm.inpl-nancy.fr] The software patenting has been the subject of an intense debate at the european parliament last months : http://www.techworld.com/opsys/news/index.cfm?NewsID=5177 http://www.nosoftwarepatents.com/en/m/intro/index.html *********************************************** Alexandre Hocquet Ecole Europenne d'Ingnieurs en Gnie des Matriaux 6, rue Bastien Lepage 54010 Nancy Cedex http://www.eeigm.inpl-nancy.fr/~hocque23/hocquet.htm *********************************************** From owner-chemistry@ccl.net Wed Mar 1 09:54:00 2006 From: "Rene Thomsen rt-x-molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Virtual Docker 2006 Message-Id: <-31075-060301091914-22764-XvwQ2mQAD8Mtcp9Dhe9uww|server.ccl.net> X-Original-From: "Rene Thomsen" Date: Wed, 1 Mar 2006 09:19:10 -0500 Sent to CCL by: "Rene Thomsen" [rt~~molegro.com] Aarhus, Denmark, March 1st, 2006 - Molegro is pleased to announce the release of Molegro Virtual Docker 2006, an integrated platform for predicting protein-ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity. Highlights of Molegro Virtual Docker: * Automated preparation of molecular structures * Active site prediction * Constraints to reward/penalize docked solutions * Reranking score and estimation of binding energy * Visual inspection and clustering of docked solutions * Macro system to customize menus and program commands * GUI wizards and online help * Cross platform: Windows, Linux, and Mac OS X is supported For more information, or to download a trial version, please visit our company website at: http://www.molegro.com or contact: Rene Thomsen, CEO Molegro Hoegh-Guldbergs Gade 10, Bldg. 1090 DK-8000 Aarhus Denmark E-mail: rt.|.molegro.com Phone: (+45) 8942 3165 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process, and our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Wed Mar 1 10:30:00 2006 From: "Anselm H C Horn Anselm.Horn{:}chemie.uni-erlangen.de" To: CCL Subject: CCL: MD stability criterion Message-Id: <-31076-060301102045-10844-Q/x//ou3m1x3ye/A5+XEXQ|,|server.ccl.net> X-Original-From: "Anselm H C Horn" Date: Wed, 1 Mar 2006 10:20:44 -0500 Sent to CCL by: "Anselm H C Horn" [Anselm.Horn:+:chemie.uni-erlangen.de] Dear all, I have a (probably rather simple) question regarding a well-known stability criterion in molecular dynamics simulations: The decimal logarithm of the ratio between the average fluctuation of the total energy and the average total energy is calculated according to log_10 ( / ) = log_10 ( < E(t) - > / ) (cf Becker & Karplus, Springer 2006) When one calculates this value for a certain time t of a completed MD trajectory, is then the mean energy of the complete trajectory or just up to the snapshot of time frame t? Many thanks in advance. Best regards, Anselm Computer Chemie Centrum Friedrich-Alexander-Universitaet Erlangen-Nuernberg Germany From owner-chemistry@ccl.net Wed Mar 1 11:42:00 2006 From: "Jim Kress ccl_nospam]|[kressworks.com" To: CCL Subject: CCL: Feature request: Wiki Message-Id: <-31077-060301111541-9145-MnlCbBV028zsJo19gypwMA!=!server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 1 Mar 2006 11:15:29 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam!A!kressworks.com] There isn't much at: http://www.compchemwiki.org/index.php?title=Main_Page Jim > -----Original Message----- > From: Brian Salter-Duke b_duke(a)octa4.net.au > [mailto:owner-chemistry*_*ccl.net] > Sent: Tuesday, February 28, 2006 10:17 PM > To: Kress, Jim > Subject: CCL: Feature request: Wiki > > Sent to CCL by: Brian Salter-Duke [b_duke*|*octa4.net.au] On > Tue, Feb 28, 2006 at 04:34:14PM -0500, Jan Labanowski > janl---speakeasy.net wrote: > > Sent to CCL by: "Jan Labanowski" [janl{:}speakeasy.net] Joerg Kurt > > Wegner writes: > > > > > with respect to question redundancy and a facilitated design and > > > maintenance of the web pages I was wondering why we have > not already > > > an CCL-Wiki running? > > > > While there is no CCL-Wiki running, there is a > Computational Chemistry > > Wiki running and does great things: > > > > http://en.wikipedia.org/wiki/Computational_chemistry > > This is the Wikipedia article and not a Computational > Chemistry Wiki. Do you not mean:- > > http://www.compchemwiki.org/index.php?title=Main_Page > > Brian. > > > Why there is no CCL-Wiki running? > > 1) I do not think we need another one... The one above is > in great hands... > > 2) And beside, I have enough chores to take care of the > current CCL as is... > > and a few others... > > > > Jan > > CCL Admin...> > > > > > > -- > Brian Salter-Duke (Brian Duke) b_duke_-_octa4.net.au > Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia > Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ > Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. > > > > -= 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 look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Wed Mar 1 13:31:00 2006 From: "jle!^!theworld.com" To: CCL Subject: CCL: software patents in chemistry? Message-Id: <-31078-060301101201-29218-1czBJ5ogQFgt1YxB1h67fQ[-]server.ccl.net> X-Original-From: jle**theworld.com Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 1 Mar 2006 10:06:32 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: jle-*-theworld.com Having read the J Mol Model article cited below, I've got a few comments: 1) The reliability study cited (ref 10) compares unix utilities. I don't think this is a relevant comparison to large-scale scientific packages. The latter is (far) more complex, is used (far) less often and has (far) few users. Less testing of more complex code = less reliable code. 2) The article states "the whole community becomes involved in correcting problems...". This assumes said community has sufficient skill to comprehend what tends to be an insufficiently commented, monolithic/old design written in less desirable coding languages and/or styles. Once the code is understood, the community also has to have the patience to adaquately test and document their changes and rerun the (growing) test suite. Of course, many programs lack such a suite since the value of such things wasn't always recognized "back then". Oh, and then the revisers have to submit their changes to the code's maintainers for possible inclusion in the main tree. To do otherwise would be to introduce a fork which should be avoided at all reasonable cost. The maintainers have the option of rejecting the fix as they see fit. 3) Question for the readership - if you run a package for which you have made changes, how do you cite it? Do you say "Program XXX", or "A new program drawn from Program XXX, with changes YYY, ZZZ, ... which you can download". Unless there's a properly established test/validation suite, how can you do anything but admit you changed something - it's NOT the original program... 4) The article states "It is well known that this type of software" (i.e. commercial) " has one advantage over 'academic' software in that it is more functional because of elaborate molecular graphics and because it is better documented and supported". To me, this seems like 3, maybe 4 advantages, as there might be more functional computational as well as graphical methods. Keep the user base in mind, as some/many of them like black boxes... I have read many articles which points out that programmers like to develop things that "scratch an itch". Hence, we get a lot of tools and things that make tools. The number of people who want to create graphics, or write validation suites, or documentation, or tutorials must be really small, as those itches aren't being scratched very well. This suggests some means has to be created to pay for what's lacking in academic codes so as to broaden their use and appeal. Do granting agencies or academic departments view \such work as proper to receive funds? Are there or should there be efforts amongst the user base to organize and fund such activities? 5) My personal, somewhat jaded opinion is that chemists tend to be (far) worse programmers than they think they are. It wasn't taught "back then", and if that's changed of late, good! Codes being designed/developed today should be easier to work with and maintain, which is a great help. I would hope that those interested in chemistry codes take the time to read some of "their" literature as we've read ours over the years. Until we're blessed with a large group of well-trained developers, open-source chemistry software will remain a gift economy. I/we should/must be VERY grateful to those who take the time to create things like Pymol. It's just that they're not going to get a lot of help for the near term. Joe Leonard jle]_[theworld.com > Sent to CCL by: FyD [fyd^_^u-picardie.fr] >> Sent to CCL by: Gilles Marcou [gilles.marcou~~pharma.u-strasbg.fr] > >> I did not wanted to take part to the discussion initially but I feel >> offended >> by what follows: > > I totally agree with Gilles... > >> > Commercial software packages are easier to install. >> > Commercial software packages have fewer bugs. > > This is totally wrong ! > We write a communication about bugs: Please see > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12856194&dopt=Abstract > >> > Bugs get fixed faster in commercial packages. > > Wrong ! Totally wrong ! > >> > Commercial software incorporates more new features, more innovative >> > features, and does so much more quickly. Commercial software packages >> have >> > better documentation. >> > Commercial software has better tech support. > > May be, although mailing lists such as the CCL or AMBER mailing lists are > very > active and help a lot... > >> > Commercial software has been more throughly tested on a wider variety >> > hardware platforms. > > I totally disagree with what is written above! > > Please see http://www.gnu.org/software/reliability.html > > regards, Francois > > -- > * F.-Y. Dupradeau * > DMAG EA 3901 & Faculte de Pharmacie, Amiens, France > **** > http://www.u-picardie.fr/labo/lbpd/FyD/> > > From owner-chemistry@ccl.net Wed Mar 1 14:29:01 2006 From: "Egon Willighagen egonw###sci.kun.nl" To: CCL Subject: CCL: software patents in chemistry? Message-Id: <-31079-060301141845-10336-fP2ARbDalyuVwuscDc1M5Q[-]server.ccl.net> X-Original-From: Egon Willighagen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Wed, 1 Mar 2006 20:18:36 +0100 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egonw-$-sci.kun.nl] On Tuesday 28 February 2006 20:45, Dave Young dave.young^-^springmail.com wrote: > Commercial software packages are easier to install. Reasonable point, though I'm not sure commercial software can beat the 'apt-get install openbabel rasmol ghemical'. > Commercial software packages have fewer bugs. That's an interesting statement... where do you base this observation on? And how does this relate to software patents? > Bugs get fixed faster in commercial packages. Possibly. Chemoinformatics companies might very well be doing a better job than Microsoft. > Commercial software incorporates more new features, more innovative > features, and does so much more quickly. Mmm... as someone else mentioned, I thought a lot of source code leaked from academic environments. > Commercial software packages have better documentation. Please define better. Documentation I have seen often lacked any form of detail, in any sort. But at least it looked nice. > Commercial software has better tech support. Yes, there is always someone on the telephone. BTW, numerous open source projects *do* have commercial support. This might be lacking for open source projects. BTW, I hereby announce to be willing to talk about commercial support for open source chemoinformatics software :) > Commercial software has been more throughly tested on a wider variety > hardware platforms. I can't imagine this to be a general observation. There still is a lot of software which only runs on win98, comp chem likely a notable exception here. Dave, I am generally wondering wether you actually asked support with open source projects? Most open source developers I know are really very friendly to newcomers... at least I try to be... Egon -- e.willighagen#%#science.ru.nl PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen Blog: http://chem-bla-ics.blogspot.com/ http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 From owner-chemistry@ccl.net Wed Mar 1 18:33:00 2006 From: "joerg.wegner joerg.wegner*o*web.de" To: CCL Subject: CCL: AW: Feature request: Wiki Message-Id: <-31080-060301183119-28766-d+AWwi+JC4K7+KPGADzFbQ]|[server.ccl.net> X-Original-From: "joerg.wegner" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 2 Mar 2006 00:30:53 +0100 MIME-Version: 1.0 Sent to CCL by: "joerg.wegner" [joerg.wegner.|-|.web.de] No ranking, just a random picking. Impressed? I am! Some of the actual articles are not directly wrong or only insufficient ... but see yourself ... and even in areas were more than 600 publications exists (ComFA or ComSIA) there are articles missing. Highlight: http://en.wikipedia.org/wiki/Serendipity but too less connections to SBDD Partially o.k. ... but IMHO too less scientific link-outs: http://en.wikipedia.org/wiki/AMBER http://en.wikipedia.org/wiki/CHARMM http://en.wikipedia.org/wiki/Chemical_file_format http://en.wikipedia.org/wiki/Cheminformatics http://en.wikipedia.org/wiki/Computational_chemistry http://en.wikipedia.org/wiki/Corwin_Hansch http://en.wikipedia.org/wiki/Density_functional_theory http://en.wikipedia.org/wiki/Drug_discovery http://en.wikipedia.org/wiki/GROMACS http://en.wikipedia.org/wiki/Hartree-Fock_theory http://en.wikipedia.org/wiki/Homology_modelling http://en.wikipedia.org/wiki/Internal_Coordinate_Mechanics http://en.wikipedia.org/wiki/International_Chemical_Identifier http://en.wikipedia.org/wiki/Jeffrey_D._Ullman http://en.wikipedia.org/wiki/Molecular_docking http://en.wikipedia.org/wiki/Molecular_dynamics http://en.wikipedia.org/wiki/Molecular_modelling http://en.wikipedia.org/wiki/Pauli_principle http://en.wikipedia.org/wiki/Protein-protein_docking http://en.wikipedia.org/wiki/QSAR http://en.wikipedia.org/wiki/Quantum_mechanics http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specifica tion http://en.wikipedia.org/wiki/Slater_determinant http://en.wikipedia.org/wiki/Subgraph_isomorphism Non: ComFA, ComSIA, Autodock, Gold, Glide, FlexX, Fred, QXP, PSA, SMARTS, JCAMP, group contribution, SBDD, ESER (Essential Set of Rings), ... Strange: http://en.wikipedia.org/wiki/Induced_fit http://en.wikipedia.org/wiki/Substructure http://en.wikipedia.org/wiki/BCS http://en.wikipedia.org/wiki/SSSR (Smallest Set of Smallest Rings) Best, Joerg Kurt Wegner