From chemistry-request@ccl.net Mon May 10 17:24:18 2004 Received: from fidji.vianetworks.es (housing7136.vianetworks.es [213.236.7.136]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i4AMOFkh023474 for ; Mon, 10 May 2004 17:24:16 -0500 Received: (qmail 16048 invoked by uid 505); 10 May 2004 22:26:20 -0000 Received: from mromcue[at]alumni.unav.es by fidji by uid 505 with qmail-scanner-1.22 (clamdscan: 0.70. Clear:RC:1(83.34.67.168):. Processed in 12.973222 secs); 10 may 2004 22:26:20 -0000 Received: from unknown (HELO alumni.unav.es) (83.34.67.168) by correo with SMTP; 10 May 2004 22:26:07 -0000 Message-ID: <40A0017C.1040904[at]alumni.unav.es> Date: Tue, 11 May 2004 00:26:04 +0200 From: Miguel Romero Organization: =?ISO-8859-1?Q?Fundaci=F3n_Hospital_Carlos_Haya?= User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY[at]ccl.net Subject: CCL: FREE SOFTWARE SUMMARY Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=5.6 required=7.5 tests=FOR_FREE,FVGT_m_MULTI_ODD2, FVGT_m_MULTI_ODD3,LINES_OF_YELLING,MAILTO_TO_SPAM_ADDR,NO_COST, SUBJ_ALL_CAPS,SUBJ_FREE_CAP 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 all, Thanks to everyone who responded to my question on FREE MOLECULAR MODELING SOFTWARE. All asnwers will be useful for my pourposes of start the new project. Thank you very much!! If you need something else I will be pleased to help you. Best regards, I give a summary of the responses below. ------------------------------------------------------------------------------------------------------ FROM: jck61821[at]springmail.com Hola Miguel, No estoy seguro del tipo de cosas que quieres hacer cuando hablas de modelaje ni a que nivel de teoria. Hay algunos paquetes gratis que hacen muy buen trabajo; puedes chequear TINKER: http://dasher.wustl.edu/tinker/ y tambien los paquetes producidos por la Universidad de Illinois: http://www.ks.uiuc.edu/ estos ultimos son excelentes. Espero que esto ayude, Zac ----------------------------------------------------------------------------------------------------- FROM: chezbowlus[at]goldrush.com Perhaps this will get you started. Tis is aimed more at industrial/startup companies, but there is something for everyone. Academics have wider choices. sb (DOCUMENT ATTCHED: Preferably free.pdf ----------------------------------------------------------------------------------------------------- FROM: giulio.vistoli[at]unimi.it I can suggest our free program VEGA (www.ddl.unimi.it) Giulio ----------------------------------------------------------------------------------------------------- FROM: egonw[at]sci.kun.nl I'm not sure which programming language you plan to use (I guess C, C++ or even fortran...), but for visualization I do recommend Jmol (http://www.jmol.org) which is open source and has a very good 3D visualization of proteins which is even being improved every day by an international group of programmers and users. And since Java can easily bind to C/C++ code, it is quite straightforward to combine it with your code. I hope this helps, Egon ---------------------------------------------------------------------------------------------------- FROM: noel.oboyle2[at]mail.dcu.ie Hello Miguel, AUTODOCK for docking. GAMESS or PC-GAMESS for geometry optimisation. I am interested in the replies to your question - will you email the list with a summary of the answers? Noel --------------------------------------------------------------------------------------------------------------- FROM: dave.young[at]springmail.com Miguel, One that I would recommend is a reasonably priced commercial package called MOE from Chemical Computing Group. Good luck. Dave Young --------------------------------------------------------------------------------------------------------------- FROM: padrongj[at]fq.uh.cu Hola, Miguel: Como eres espaqol pues me quedo con nuestro idioma. Para manipulacion de estructuras (especialmente macromoleculas) te recomendaria el Deepview (o Swiss PDB viewer, en us.expasy.org), que tiene versiones lo mismo en Windows que en Linux. Mecanica molecular puedes conseguirla con el programa TINKER, con las mismas caracteristicas (Win/Lin, gratis) y puedes usarlo tambien para dinamica molecular. Docking es un poco mas complicado, pero busca Flexx o Autodock, creo que tienen un precio bastante razonable. Gramm es gratis tambien y creo que valdria la pena que le dieses un vistazo. Cualquier cosa en que te pueda ayudar estoy a tu disposicion. Saludos, Juan Alexander Padron Laboratorio de Quimica Computacional y Teorica Facultad de Quimica, Universidad de la Habana, Cuba ----------------------------------------------------------------------------------------------------------------- FROM: AMathieu[at]tranzyme.com Hello Miguel, In response to your question, I'm certain you'll find many free solutions for you needs probably spread over several packages. However, I'd like to point to you to the Molecular Operating Environment (MOE) by The Chemical Computing Group (CCG) based in Montreal(http://www.chemcomp.com). They offer interesting academic prices for the complete package. MOE will perform everything you need as stated below, although their docking algorithm may need a little help. If it does not meet your expectations, you can easily get academic version of free docking software elsewhere. MOE's scripting language is also easy to understand and it offers many tools to customize the scripts and/or environment. Plus, it works on all platforms!!! You can contact them for a demo (they also have an office in Europe) ... I hope this helps. APM ------------------------------------------------------------------------------------------------------------------- FROM: mark[at]arguslab.com Miguel, ArgusLab is free for academics. http://www.arguslab.com Runs on Windows (for now....) Mark -------------------------------------------------------------------------------------------------------------------- FROM: pgannett[at]hsc.wvu.edu Miguel: While not so good for manipulation and docking, the programs NAMD and VMD are very good for MM/MD and visualization with some post MD run processing. Versions are available for Unix/Linux/Win. Pete Gannett -------------------------------------------------------------------------------------------------------------------- FROM: warren[at]delanoscientific.com Well, I suppose I'd better "chime" in here too. PyMOL is another FREE option, and it has a complementary characteristics to Jmol, which is good solid stuff too. They're both worth a close look, as is VMD. As its name implies, PyMOL is heavily Python-oriented, in much the same way as Jmol is Java oriented. http://pymol.sf.net Unlike Jmol, PyMOL isn't so much developed internationally, but there is already a large international community (over 500 committed users, and thousands of casuals users) who work together every day to help each other make the most of the program. Though PyMOL is definitely a community-driven project, most PyMOL code development is still performed under my direction via my small private company. However, PyMOL absolutely remains available as Python-license open-source software, and our license is even less restrictive than Jmol's LGPL. The bottom line is that PyMOL can be used for FREE if you need a no cost tool today. We'd like you to pay for it, but the open-source license means that we can't in any way compel you to do so. The key difference with PyMOL is that if at some point you are willing to pay for it, then you will get additional value for your money: value such as the formal accountability that large pharmaceutical companies often need. Specifically, we'll work with your legal and IT departments to provide compiled versions of PyMOL that satisfy their requirements as well as your own. If you become a PyMOL sponsor, then it is our job to make sure that *your* specific needs for bug fixes, features, and support are met. Plus, DeLano Scientific will increasingly be offering a range of "incentive" products on top of PyMOL which should always go a little bit beyond what you can do with existing open-source code. In other words, our commercial approach doesn't involve directly competing with open-source, but rather going beyond it. Our vision is to ride the open-source wave, not to obstruct it! http://www.delanoscientific.com/about.html Cheers, Warren ---------------------------------------------------------------------------------------------------------------- FROM: wegnerj[at]informatik.uni-tuebingen.de Hi, Overview: http://zeus.polsl.gliwice.pl/~nikodem/linux4chemistry.html Docking (academics): Autodock (Linux only) http://www.scripps.edu/pub/olson-web/doc/autodock/ Ghemical (includes Mopac) (+ OELib,OpenBabel, conformer generation !): http://www.uku.fi/~thassine/ghemical/ QSAR: JOELib http://www-ra.informatik.uni-tuebingen.de/software/joelib/ Kind regards, Joerg ------------------------------------------------------------------------------------------------------------ FROM: hinsen[at]cnrs-orleans.fr Have a look at http://dirac.cnrs-orleans.fr/MMTK/ You probably have to write some code yourself (docking for example), but that should be easy given that a lot of support code is there. ------------------------------------------------------------------------------------------------------------- ******************************************* Miguel Romero, PhD. Fundacisn Hospital Carlos Haya Avda. Carlos Haya 82, Pabellsn A, 7*planta 29010 Malaga Spain Phone: +34 952307928 Fax: +34 951030447 web: http://www.fhch.net e-mail: mromero[at]imacyt.org *******************************************