From chemistry-request@ccl.net Mon May 10 02:30:13 2004 Received: from fgwmail5.fujitsu.co.jp (fgwmail5.fujitsu.co.jp [192.51.44.35]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4A7UBkh007633 for ; Mon, 10 May 2004 02:30:11 -0500 Received: from m6.gw.fujitsu.co.jp ([10.0.50.76]) by fgwmail5.fujitsu.co.jp (8.12.10/Fujitsu Gateway) id i4A7WFvH006950 for ; Mon, 10 May 2004 16:32:15 +0900 (envelope-from m-ito_at_jp.fujitsu.com) Received: from s2.gw.fujitsu.co.jp by m6.gw.fujitsu.co.jp (8.12.10/Fujitsu Domain Master) id i4A7WEFv002659 for ; Mon, 10 May 2004 16:32:14 +0900 (envelope-from m-ito_at_jp.fujitsu.com) Received: from dm.atsugi.flab.fujitsu.co.jp (dm.atsugi.flab.fujitsu.co.jp [10.36.64.1]) by s2.gw.fujitsu.co.jp (8.12.10) id i4A7WDrX013316 for ; Mon, 10 May 2004 16:32:13 +0900 (envelope-from m-ito_at_jp.fujitsu.com) Received: from dm.atsugi.flab.fujitsu.co.jp by dm.atsugi.flab.fujitsu.co.jp (8.9.3p2/3.7W-030708-Fujitsu Labs. Atsugi Domain Mail Master (NAVGW)) id QAA01377; Mon, 10 May 2004 16:32:13 +0900 (JST) Received: from ccg-main.ccg.flab.fujitsu.co.jp ([10.36.64.126]) by dm.atsugi.flab.fujitsu.co.jp (NAVGW 2.5.2.9) with SMTP id M2004051016320926544 ; Mon, 10 May 2004 16:32:09 +0900 Received: by ccg-main.ccg.flab.fujitsu.co.jp (8.8.8+2.7Wbeta7/3.6W) id QAA08263; Mon, 10 May 2004 16:43:53 +0900 (JST) Date: Mon, 10 May 2004 16:28:08 +0900 (JST) Message-Id: <20040510.162808.846936230.Masakatsu Ito_at_ccg.flab.fujitsu.co.jp> To: chemistry_at_ccl.net Cc: markus_at_ks.uiuc.edu, senn_at_mpi-muelheim.mpg.de, knapp_at_chemie.fu-berlin.de, er-chan_at_scn.org, m-ito_at_jp.fujitsu.com Subject: Summary Re: CCL:Jarzynski's equality for free energy From: Masakatsu Ito In-Reply-To: <"20040422.141916.468716365.Masakatsu Ito"@ccg.flab.fujitsu.co.jp> References: <"20040422.141916.468716365.Masakatsu Ito"@ccg.flab.fujitsu.co.jp> X-Mailer: Mew version 2.3 on XEmacs 21.1.14 (Cuyahoga Valley) Mime-Version: 1.0 Content-Type: Text/Plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.0 required=7.5 tests=FVGT_m_MULTI_ODD2, INVALID_MSGID,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 Dear CCLers, I posted the query about the free energy calculation with Jarzynski's equality last month. Thank you all for an interest in my query and in particular I thank people who responded to my query, Dr. Dittrich, Dr. Senn, Dr. Knapp, and Dr. Er-chan. My original question is : > I am looking for reviews and articles about the free energy > calculation of biomolecules. I have been impressed by Jarzynski's > equality (Phys.Rev.Lett. 78, 2690 (1997)) which enables one to > estimate free energy difference from an ensemble of short MD > simulations. This implies that the estimation can be drastically > accelerated by distributed computing. But those MD simulations should > start from equilibrium, and I am wondering how such initial conditions > can be prepared for biomolecules. Because it is notoriously difficult > to get an equilibrium ensemble of biomolecular structures. > > Thus I am very interested in the application of Jarzynski's equality > to biomolecular processes. Could someone please give me some advice or > point me to articles? The following is a summary of articles and reviews. Jarzynski eqauility and path-ensemble (1) C. Jarzynski, "Nonequilibrium Equality for Free Energy Differences", 224, Phys. Rev. Lett. 1997, 78, 2690-2693. (2) C. Jarzynski, "Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach", Phys. Rev. E, 56, 5018-5035 (1997). (3) G. E. Crooks, "Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems", J. Stat. Phys. 1998, 90, 1481-1487 . (4) G. E. Crooks, "Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences", Phys. Rev. E, 1999, 60, 2721- 2726. (5) G. E. Crooks, "Path-ensemble averages in systems driven far from equilibrium", Phys. Rev. E , 2000, 61, 2361-2366. (6) C. Jarzynski, "Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach", Phys. Rev. E 1997, 56, 5018-5035. (7) C. Jarzynski, "Equilibrium free energies from nonequilibrium processes", Acta Physica Polonica B 1998, 29, 1609-1622. (8) H. Hu, R.H. Yun, and J. Hermans, "Reversibility of free energy simulations: slow growth may have a unique advantage. (with a note on use of ewald summation)", Mol. Simul. 2002, 28, 67. Fast growth thermodynamic integration (9) D. A. Hendrix, C. Jarzynski, "A fast-growth method of computing free energy differences", J. Chem. Phys 2001, 114, 5974-5981. (10) G. Hummer, "Fast-growth thermodynamic integration : results for sodium ion hydration", Mol. Simul. 2002, 28, 81-90. (11) C. Jarzynski, and D. K. Wojcik, "Classical and Quantum Fluctuation Theorems for Heat Exchange", arXiv:cond-mat/0404475 . Statistical error in free energy estimations (12) G. Hummer, "Fast-growth thermodynamic integration: Error and efficiency analysis", J. Chem. Phys 2001, 114, 7330-7337. (13) D. M. Zuckerman, and T. B. Woolf, "Overcoming finite-sampling errors in fast-switching free-energy estimates: extrapolative analysis of a molecular system", Chem. Phys. Lett. 2002, 351, 445-453. (14) D.M. Zuckerman, and T.B. Woolf, PRL 2002, 89, 180602-1. (15) J.Gore, F. Ritort, and C. Bustamante, "Bias and errors in estimates of equilibrium free-energy differences from nonequilibrium measurements", PNAS 2003, 100, 12564. Nonequilibrium measurements (experiments) (16) G. Hummer, A. Szabo, "Free energy reconstruction from nonequilibrium single-molecule pulling experiments", Proc. Natl. Acad. Sci. USA 2001, 98, 3658-3661. (17) R. F. Fox, "Using nonequilibrium measurements to determine macromolecule free-energy differences", Proc. Natl. Acad. Sci. USA 2003, 100, 12537-12538. Minimization of the statistical error by optimal midpoints of lambda (18) I. Muegge, U. Ermler, G. Fritzsh, and W. Knapp, "Free Energy of Cofactors at the Quinone Qa Site of the Photosynthetic Reaction Center of Rhodobacter sphaeroides Calculated by Minimizing the Statistical Error", J. Phys. Chem. 1995, 99, 17917-17925. Steered molecular dynamics (19) Sanghyun Park and Klaus Schulten. "Calculating potentials of mean force from steered molecular dynamics simulations.", J. Chem. Phys. 120, 5946-5961 (2004). (20) Sanghyun Park, Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten. "Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality." J. Chem. Phys. 119, 3559-3566 (2003). (21) Morten ?. Jensen, Sanghyun Park, Emad Tajkhorshid, and Klaus Schulten. "Energetics of glycerol conduction through aquaglyceroporin GlpF." PNAS, 99, 6731-6736 (2002). ps. I am still not sure if the free energy difference of a biomolecular process can be calculated from an large set of short MD simulations in a way like the fast growth thermodynamic integration (FGTI) method. Although the method works very well for small molecules, I have heard from some people that it might be worse for biomolecules than a way using a small set of long MD simulations like free energy perturbation. On the other hand, it seems to me that several papers of Schulten group (19-21) show that FGTI can work well if it is argumented with a guiding potential (in steered molecular dynamics). Masakatsu Ito , Ph.D Nanotechnology Research Center FUJITSU LABORATORIES LTD. 10-1 Morinosato-Wakamiya, Atsugi 243-0197 Japan Phone : +81-46-250-8234 Fax : +81-46-250-8844 E-mail m-ito_at_jp.fujitsu.com URL http://sourceforge.net/projects/remdtk From chemistry-request@ccl.net Mon May 10 07:42:52 2004 Received: from prserv.net (asmtp2.prserv.net [32.97.166.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4ACgpkh019832 for ; Mon, 10 May 2004 07:42:51 -0500 Received: from goofy (dhcp065-029-074-207.indy.rr.com[65.29.74.207]) by prserv.net (asmtp2) with SMTP id <2004051012445025204eg2j8e> (Authid: jmmckel); Mon, 10 May 2004 12:44:50 +0000 Message-ID: <004601c4368c$8ed1c510$6401a8c0@goofy> From: "John McKelvey" To: Subject: Computing absorbtion and emission spectral band shapes Date: Mon, 10 May 2004 07:44:37 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0043_01C43662.A4F570A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=3.5 required=7.5 tests=HTML_40_50,HTML_MESSAGE, 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 This is a multi-part message in MIME format. ------=_NextPart_000_0043_01C43662.A4F570A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello.. I am interested in computing UV-VIS absorbtion and emission band shapes. = I can optimize geometries in the ground and excited states and can = compute the respective vibrational frequencies and normal modes. I = would like to locate a paper or two, or even some code, that provides = enough detailed information so that the remaining steps can be coded. Any assistance would most appreciated. Best regards, John McKelvey ------=_NextPart_000_0043_01C43662.A4F570A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello..
 
I am interested in computing UV-VIS = absorbtion and=20 emission band shapes.  I can optimize geometries in the ground and = excited=20 states and can compute the respective vibrational frequencies and normal = modes.  I would like to locate a paper or two, or even some = code, that=20 provides enough detailed information so that the remaining steps can be=20 coded.
 
Any assistance would most = appreciated.
 
Best regards,
 
John McKelvey
 
 
------=_NextPart_000_0043_01C43662.A4F570A0-- From chemistry-request@ccl.net Mon May 10 09:18:54 2004 Received: from heisenberg.zen.co.uk (heisenberg.zen.co.uk [212.23.3.141]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4AEIqkh025449 for ; Mon, 10 May 2004 09:18:52 -0500 Received: from [82.68.46.238] (helo=cresset23) by heisenberg.zen.co.uk with esmtp (Exim 4.30) id 1BNBeJ-0005Eq-Kl for chemistry*at*ccl.net; Mon, 10 May 2004 14:20:55 +0000 From: "Mark Mackey" To: Subject: Enumeration / SMILES handling software Date: Mon, 10 May 2004 15:20:24 +0100 Message-ID: <000601c43699$ef9d5be0$0207a8c0@cresset23> MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Originating-Heisenberg-IP: [82.68.46.238] X-Spam-Status: No, hits=-0.5 required=7.5 tests=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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4AEIskh025457 Hi all. Ib re looking at quickb nb dirty ways to enumerate some libraries for a database. There seem to be hundreds of commercial library enumeration tools out there, most of which are horribly overpriced for what they do :). All we want is to enumerate a couple of libraries reasonably quickly and get the resulting molecules either as OKish 3D structures or as reasonable 2D structures. Enumerating libraries in SMILES space is trivial, but thereb s a lack of tools available to do the coordinate generation. So, does anyone know of a free/cheap tool that will either (a) enumerate simple libraries into, say, SDF files, or (b) generate 2D or 3D coordinates for SMILES strings. I know that Corina et al. do (b), but we don't really need very good 3D coordinates (the molecules are going to be subjected to conformational searches and minimisation) so it's overkill and overexpensive for what we want. Mark. From chemistry-request@ccl.net Mon May 10 11:57:23 2004 Received: from smtp4.es.uci.edu (smtp4.es.uci.edu [128.200.80.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4AGvGkh006491 for ; Mon, 10 May 2004 11:57:21 -0500 Received: from frenkel.ps.uci.edu (frenkel.ps.uci.edu [128.200.11.119]) by smtp4.es.uci.edu (8.12.8/8.12.8) with ESMTP id i4AGx3I4027411 for ; Mon, 10 May 2004 09:59:06 -0700 Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz.-at-.mail.rochester.edu Organization: university of california at Irvine To: chemistry.-at-.ccl.net Subject: NMA parameters in charmm Date: Mon, 10 May 2004 09:59:41 -0400 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200405100959.41374.wzhuang.-at-.uci.edu> X-NACS_ES-MailScanner: No viruses found 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 i4AGvNkh006501 Dear All: I want to do a simulation of NMA in charmm,but the parameters (especially the partial charges) of the amino acids can't be used directly. can anyone give me some help about this wei From chemistry-request@ccl.net Mon May 10 11:27:54 2004 Received: from electre.pasteur.fr (electre.pasteur.fr [157.99.64.120]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4AGRrkh003335 for ; Mon, 10 May 2004 11:27:54 -0500 Received: from pasteur.fr (zorg.bis.pasteur.fr [157.99.90.87]) by electre.pasteur.fr (8.12.11/8.12.11) with ESMTP id i4AGTxV8068111 for ; Mon, 10 May 2004 18:30:01 +0200 (CEST) Date: Mon, 10 May 2004 18:31:04 +0200 Mime-Version: 1.0 (Apple Message framework v553) Content-Type: text/plain; charset=ISO-8859-1; format=flowed Subject: EMBO course on biomolecular simulation (Paris) deadline 15th of May From: Michael Nilges To: chemistry~at~ccl.net Message-Id: <6E761104-A29F-11D8-B84B-000A959E2530~at~pasteur.fr> X-Mailer: Apple Mail (2.553) 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 i4AGRskh003344 Please note that it is still possible to apply to the EMBO practical course on biomolecular simulation July 18-25 2004, Pasteur Institute, Paris, France organized by Rebecca Wade and Michael Nilges More information about the course: http://www.pasteur.fr/recherche/unites/Binfs/EMBO2004/ ... about the Pasteur Institute: http://www.pasteur.fr ... ... and about Paris: http://www.paris.fr/EN/ Application deadline is the 15th of May (end of this week). Michael Nilges, Bioinformatique Structurale, Institut Pasteur 25-28 rue du docteur Roux, F-75015 Paris, France. Tel: +33 1 45 68 82 30; Fax: +33 1 45 68 87 19 secritariat: +33 1 44 38 91 09 From chemistry-request@ccl.net Mon May 10 13:35:18 2004 Received: from atc.atccu.chula.ac.th (atc.atccu.chula.ac.th [192.207.64.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4AIZGkh014708 for ; Mon, 10 May 2004 13:35:17 -0500 Received: (from nobody@localhost) by atc.atccu.chula.ac.th (8.9.3/8.9.3) id BAA24125; Tue, 11 May 2004 01:51:35 +0700 Date: Tue, 11 May 2004 01:51:35 +0700 Message-Id: <200405101851.BAA24125(at)atc.atccu.chula.ac.th> From: "Nadtanet Nunthaboot" To: chemistry(at)ccl.net Subject: field fit in SYBYL X-Mailer: NeoMail 1.25 X-IPAddress: 131.130.44.211 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 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 -- NeoMail - Webmail that doesn't suck... as much. http://neomail.sourceforge.net Dear Cclers, I try to use CoMFA in SYBYL6.8. I got the poor q2 (0.3)value . I want to know the alignment method especiallly " Field Fit " alignment. I try to use field fit in SYBYL follow the manual but not success. I can not align my compounds by field fit method. Any body known about these procedure or method to use field fit alignment in SYBYL? Pleaes tell me about informations or datails about how to align compounds by field fit method. I will appreciate for your help. Thank you very much. Best Wishes, Nadtanet From chemistry-request@ccl.net Mon May 10 14:15:42 2004 Received: from mercury.chem.pitt.edu (mercury.chem.pitt.edu [136.142.60.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4AJFfkh016608 for ; Mon, 10 May 2004 14:15:41 -0500 Received: from ringo.chem.pitt.edu (localhost.localdomain [127.0.0.1]) by mercury.chem.pitt.edu (Postfix) with SMTP id 27D53483E for ; Mon, 10 May 2004 15:12:30 -0400 (EDT) Received: from 136.142.60.133 (SquirrelMail authenticated user sebnem) by mercury.chem.pitt.edu with HTTP; Mon, 10 May 2004 15:12:30 -0400 (EDT) Message-ID: <1384.136.142.60.133.1084216350.squirrel-.at.-mercury.chem.pitt.edu> Date: Mon, 10 May 2004 15:12:30 -0400 (EDT) Subject: vibrational analysis in Gaussian From: "sebnem" To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit 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 Hi, does anybody know how to take rotational and translational vectors as an output from gaussian 03? thanks in advance Sebnem Essiz 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 *******************************************