From chemistry-request@ccl.net Thu Apr 7 01:31:13 2005 Received: from mailhub05.readyhosting.com (mailhub05.readyhosting.com [63.99.213.16]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j375V8Ke012892 for ; Thu, 7 Apr 2005 01:31:09 -0400 Received: from VLifeSciences.com (mail018.readyhosting.com [63.99.224.14]) by mailhub05.readyhosting.com (Postfix) with ESMTP id C924B1D0D32; Wed, 6 Apr 2005 23:26:47 -0500 (CDT) Date: Wed, 6 Apr 2005 23:26:05 -0500 Message-Id: <200504062326.AA9240872 = = = VLifeSciences.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii From: "Sudhir Kulkarni" Reply-To: To: , "Lei Wang" Subject: Re: CCL:fingerprint generation software X-Mailer: X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net "Molecular Design Suite (MDS)" can generate fingerprints and search for similarity. Following database search options are provided in MDS - 2D substructure/template search - 3D substructure/template search - Descriptor based search - Fingerprint generation & search - Pharmacophore generation & search - Receptor based search Please look at http://www.vlifesciences.com/Products.htm and register for demo version. Sudhir Kulkarni ---------- Original Message ---------------------------------- From: "Lei Wang" Date: Wed, 06 Apr 2005 12:06:24 -0400 >I want to generate finger-prints for my chemical database. and want to use such info to do sub-structure or similarity search. What software could I use? > >Thanks! > >Lei > > > > >-= 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 = = = ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST = = = ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your is mail bouncing from ccl.net domain due to spam filters, please >use the Web based form from CCL Home Page >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > ________________________________________________________________ Sent via the WebMail system at VLifeSciences.com From chemistry-request@ccl.net Wed Apr 6 23:37:10 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j373b9VY008747 for ; Wed, 6 Apr 2005 23:37:09 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j373b9JG008746 for chemistry(at)ccl.net; Wed, 6 Apr 2005 23:37:09 -0400 Date: Wed, 6 Apr 2005 23:37:09 -0400 Message-Id: <200504070337.j373b9JG008746(at)server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request(at)ccl.net using -f From: "jian, , chen" To: chemistry(at)ccl.net X-Web-Message-Number: 050406233455-8710 Subject: W:CCL:format of a user-defined correlation function with TINKER X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear CCLer: Has anybody experience the correlate routine in Tinker package with a user-defined correlation function? Are there any guide or samples available of user-defined correlation function in correct format? The user guide says there are two samples available in its package. however,i couldn't find them. thanks in advance, Chen chenzhz(at)sohu.com From chemistry-request@ccl.net Wed Apr 6 21:19:37 2005 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j371JXQY003216 for ; Wed, 6 Apr 2005 21:19:34 -0400 Received: from eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id j3708OJ11160 for ; Wed, 6 Apr 2005 18:08:24 -0600 Message-ID: <425479F1.7030806-.at.-eyesopen.com> Date: Wed, 06 Apr 2005 18:08:17 -0600 From: George Vacek Organization: OpenEye Scientific Software User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry-.at.-ccl.net Subject: Szybki 1.0 released - fast structure optimization of ligands in gas-phase, solution, or within a protein active site Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net OpenEye announces the release of SZYBKI 1.0. SZYBKI (pronounced shib'kee) optimizes molecular structures with the Merck Molecular Force Field, either with or without solvent effect, to yield quality 3D molecular structures. SZYBKI will also refine portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs. Key features of SZYBKI include: - MMFF94 and MMFF94s energies or optimized geometries - solvent effects with Sheffield or Poisson-Boltzmann models for geometry optimization and binding energies - ligands optimization within the field of a protein active site - flexibility of protein active-site polar hydrogens or side-chains - gradient minimization in several coordinate frames (xyz, torsion only, etc.) SZYBKI's atom types, energies and gradients have been strictly validated for accuracy against Merck's published dataset. SZYBKI fully optimizes about 200 drug-sized molecules per minute on a modern processor. For large numbers of structures, SZYBKI also supports distributed processing via PVM. For further information, please visit www.eyesopen.com or contact business-.at.-eyesopen.com. Regards, George Vacek VP, Business OpenEye Scientific Software From chemistry-request@ccl.net Thu Apr 7 02:55:27 2005 Received: from postfix3-1.free.fr (postfix3-1.free.fr [213.228.0.44]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j376tNfZ018396 for ; Thu, 7 Apr 2005 02:55:23 -0400 Received: from [82.66.102.10] (michelet-4-82-66-102-10.fbx.proxad.net [82.66.102.10]) by postfix3-1.free.fr (Postfix) with ESMTP id 5F02A1734A2; Thu, 7 Apr 2005 08:55:22 +0200 (CEST) In-Reply-To: <200504061954.j36Jswoa022798 _(a)_ server.ccl.net> References: <200504061954.j36Jswoa022798 _(a)_ server.ccl.net> Mime-Version: 1.0 (Apple Message framework v619.2) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <3a4aa6b6cbc0d329e418faaea31f884c _(a)_ cea.fr> Content-Transfer-Encoding: 7bit Cc: chemistry _(a)_ ccl.net From: khinsen _(a)_ cea.fr Subject: Re: CCL:W:Free code for solvent accessible surface area Date: Thu, 7 Apr 2005 08:55:21 +0200 To: "Principal, , Component" X-Mailer: Apple Mail (2.619.2) X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net On 06.04.2005, at 21:54, Principal, , Component wrote: > Is there any free code available for calculating SASA, apart from > that suggested by M Petitjean. Fortran, C, C++, Java, Python, Perl > anything will do. Thanks in advance There's a SASA module in my Molecular Modelling Toolkit: http://dirac.cnrs-orleans.fr/MMTK/ Here is the relevant section of the manual: http://dirac.cnrs-orleans.fr/MMTK/Manual/MMTK_28.html -- ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen _(a)_ cea.fr ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Thu Apr 7 05:48:23 2005 Received: from smtp-out.rrz.uni-koeln.de (smtp-out.rrz.uni-koeln.de [134.95.19.53]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j379mDgn030218 for ; Thu, 7 Apr 2005 05:48:14 -0400 Received: from mail1.rrz.Uni-Koeln.DE (mail1.rrz.uni-koeln.de [134.95.100.208]) by smtp-out.rrz.uni-koeln.de (8.13.1/8.13.1) with ESMTP id j378AgPj020858 for ; Thu, 7 Apr 2005 10:10:42 +0200 Received: from [127.0.0.1] (relax.cubic.uni-koeln.de [134.95.200.21]) (authenticated as user acc91 bits=0) by mail1.rrz.Uni-Koeln.DE (8.13.1/8.13.1) with ESMTP id j378AaUQ001313 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Thu, 7 Apr 2005 10:10:40 +0200 (MEST) Message-ID: <4254EB01.7080701=at=uni-koeln.de> Date: Thu, 07 Apr 2005 10:10:41 +0200 From: Christoph Steinbeck User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Lei Wang CC: chemistry=at=ccl.net Subject: Re: CCL:fingerprint generation software References: In-Reply-To: Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new X-Scanned-By: MIMEDefang 2.48 on 134.95.19.104 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Lei Wang wrote: > I want to generate finger-prints for my chemical database. and want to use such info to do sub-structure or similarity search. What software could I use? Dear Lei, as Rajarshi has pointed out already, our Chemistry Development Kit (CDK), hosted at http://cdk.sf.net, can do what you are looking for [1]. I would like to add that the CDK is free software under LGPL license. There is already a public web database running completely based on CDK, which is NMRShiftDB, our open-access, open-submission, open-source database for organic structures and their NMR data [2,3]. There, substructure searching is done with a prefiltering using CDK fingerprints, followed by a CDK substructure search in the result set. NMRShiftDB is available to the public at http://www.nmrshiftdb.org. Further, the well known BRENDA database (http://www.brenda.uni-koeln.de/) does substructure searching based on the CDK. Cheers, Chris [1] Steinbeck, C.; Han, Y. Q.; Kuhn, S.; Horlacher, O.; Luttmann, E. et al. The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics. Journal of Chemical Information and Computer Sciences 2003, 43, 493-500. http://dx.doi.org/10.1021/ci025584y [2] Steinbeck, C.; Kuhn, S.; Krause, S. NMRShiftDB - Constructing a Chemical Information System with Open Source Components. Journal of Chemical Information & Computer Sciences 2003, 43, 1733 - 1739. http://dx.doi.org/10.1021/ci0341363 [3] Steinbeck, C.; Kuhn, S. NMRShiftDB compound identification and structure elucidation support through a free community-build web database. Phytochemistry 2004, 65, 2711-2717. http://dx.doi.org/10.1016/j.phytochem.2004.08.027 -- Priv. Doz. Dr. Christoph Steinbeck (c.steinbeck=at=uni-koeln.de) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z|lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@ccl.net Thu Apr 7 04:34:46 2005 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j378Yerc026095 for ; Thu, 7 Apr 2005 04:34:41 -0400 Received: from a84-0-130-82.adsl-pool.axelero.hu ([84.0.130.82] helo=[10.0.0.189]) by chemaxon.hu with esmtpsa (Exim 4.44 #1 (Debian)) id 1DJR9m-0007pg-Vc TLS Cipher TLSv1:AES256-SHA:256; Thu, 07 Apr 2005 09:10:27 +0200 Message-ID: <4254DC87.5070302|at|chemaxon.com> Date: Thu, 07 Apr 2005 09:08:55 +0200 From: Szabolcs Csepregi User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Lei Wang CC: chemistry|at|ccl.net Subject: CCL:Re: fingerprint generation software References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Lei, I suggest to have a look at JChem: http://www.jchem.com/ We offer free licenses for academia: http://www.chemaxon.hu/forum/ftopic193.html All the best, Szabolcs Lei Wang wrote: > I want to generate finger-prints for my chemical database. and want to use > such info to do sub-structure or similarity search. What software > could I use? > > Thanks! > > Lei > > > > > -= 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 is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Thu Apr 7 04:39:09 2005 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j378d447026316 for ; Thu, 7 Apr 2005 04:39:04 -0400 Received: by leitl.org (Postfix, from userid 500) id E04A63A8629; Thu, 7 Apr 2005 10:38:58 +0200 (CEST) Date: Thu, 7 Apr 2005 10:38:58 +0200 From: Eugen Leitl To: chemistry [] ccl.net Subject: Converting to CML [was Re: [cml/ccml-discuss] RE: [Zinc-fans] database formats? (fwd from jji [] cgl.ucsf.edu)] (fwd from pm286 [] cam.ac.uk) Message-ID: <20050407083858.GI24702 [] leitl.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net ----- Forwarded message from Peter Murray-Rust ----- From: Peter Murray-Rust Date: Thu, 07 Apr 2005 08:54:05 +0100 To: Geoff Hutchison , "John Irwin" Cc: cml-discuss [] lists.sourceforge.net, openbabel-discuss [] lists.sourceforge.net, simon Tyrrell , cdk-devel [] lists.sourceforge.net, Tom Oinn Subject: Converting to CML [was Re: [cml/ccml-discuss] RE: [Zinc-fans] database formats? (fwd from jji [] cgl.ucsf.edu)] X-Mailer: QUALCOMM Windows Eudora Version 6.0.1.1 [Crossposted to 3 lists, please be considerate] [John Irwin] >>... Can you recommend software for >>preparing and manipulating CML files? If OE offered CML, we could and might >>offer CML tomorrow. There are many good tools for converting files to CML. First, some words about strategy. CML is powerful enough to hold compound documents such as compound data cards, computational chemistry output and (when combined with XHTML) complete scientific documents. So "converting to CML" can involve components such as molecules, reactions, their properties, spectra, eigenproperties, etc. In general CML can hold any information composed of simple datatypes (numbers, strings, array, matrixes, etc.) and predefined schema elements (reactions, spectra...). We are devising a mechanism for building complex datatypes (e.g. critical point, phase diagrams). Most people currently want to manage molecular data and I'll stick with that. (JohnI and I have already corresponded usefully so I believe that a Zinc entry consists of at least: * a molecule * its provenance * published names * published properties * calculated properties * intellectual property rights CML can manage all of this except the IPR. To summarise John's mail, Zinc consists of molecular information supplied by compound suppliers under contract, for which properties are calculated using software made available under contract and then collected in a database which itself has restrictions on use (e.g. only limited subsets can be distributed, and for restricted use]). CML is not capable of managing the complexity of this IPR so the converter would have to add this, preferable in RDF. [Note that this problem does not occur for Open data since we can simply add a BOAI or Creative Commons license.] The provenance (without rights) is managed by the DublinCore dc:creator and dc:publisher in CML: CML can, in principle, hold everything else without loss. Since I don't know the range of properties I don't know which are complex, but assuming that most are scalar, then the simple approach is to render them as: === OK, most people weren't expecting that! BUT provenance and redistribution is increasingly important. That is why the default action of OpenBabel when outputting CML is to add metadata. We would hope that if users add metadata to the input (only possible in CML) it would be transported through === I suspect the question could be rephrased as "how do I convert a file containing small-molecule information and produce a CML file which contains the atoms, bonds and their properties without loss? Each molecule is separately identifiable and there is no contextual linkage between them (e.g. they aren't poses, supramolecules, etc. The file(s) may contain many independent molecules and batch conversion is required" I currently know of the current tools, and would approach them in this order: * Openbabel. This has the widest range of file types and can deal with lists of molecules. Billy Tyrrell, Chris Morley, Geoff Hutchison and I have variously developed this and Henry Rzepa has carried out roundtripping. We intend to maintain this a flagship for CML conversion - i.e. if there is a problem we will try to respond. * JUMBO. We have concentrated on complex formats and currently offer * MDL Molfile, SDF (and RXN). This attempts to follow the published spec for V2000 files. However since some of the spec appears to be specific to MDL programs it is necessarily a subset, albeit a fairly comprehensive one. * MOL2 format taken from the Tripos spec. This again is a subset and does not address recognition of atom type and fragments. Not validated. * CDX and CDXML. Most of the spec relating to molecules and reaction, but not graphic layout, has been implemented. Since CD is a very graphically oriented format it is extremely easy to create objects which do not formally represent the semantics of the molecule. Conversion of any CDX file is likely to be lossy and fuzzy. * CIF. This is a complete interpretation of DDL1 with manual coding of some of the core dictionary. Although CIF can contain chemical structure information this is virtually never used. Hence we have to use heuristics to calculate the chemistry and this is almost lossless for GOOD CIFs (as published by Acta Cryst.) * SMILES. I think this is fairly complete and should include stereochemistry. * CDK. This has a range of file readers and a CML writer. We haven't been directly involved in the coding but correspond daily with the group. If there are any problems then I am sure the CDK group would be keen to address them and we'll help in the discussions. * JOELib. This has a wide range of functionality, including the calculation of properties. Again we are in frequent touch, and although I haven't used it for CML I am sure the authors are responsive. * BlueObelisk, WebServices and Taverna. (http://wwmm.ch.cam.ac.uk/presentations/acs2005) This is a recent movement among a number of OpenSource and Open Data groups to ensure interoperability. "File conversions" will increasingly be packaged as WebServices (http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere) or workflows (such as http://taverna.sf.net). Scientists can then select the services they require and compose their own application. This will include conversion, validation, checks for uniqueness, submission to repository, etc. I suspect that Zinc actually requires a Taverrna-like workflow for its maintenance. Taverna can be used to warp closed source programs, but of course these cannot be distributed. We offer WebServices for OpenBabel and JUMBO as above so anyone can link their conversion requirements. Also our WS are Open so anyone can clone them to avoid connection problems. We do not currently offer WebServices that use close source programs because there are usually license restrictions by the suppliers and WS cannot yet deal with complex IPR negotiations. There is no reason why we might not create some in the future - if so the WebService wrapper would probably be OpenSource. There are some other Open Source programs (with whose authors we have had discussions) which read and/or emit CML including: * BKChem * Ghemical I don't know whether these can be used in batch but as they are open source then anyone can add this. I am also sure they'd be keen to help. I don't know the degree of conformance. There are an increasing number of computational chemistry programs which emit (and often read) CML but this is out of scope in this thread. We welcome implementations and use of CML by for-profit organisations. CML itself is an openly published, read-only specification and does not require implementations to be OpenSource. It does, however, require best efforts to conform and we shall write more of this later. Although, in principle, it is possible to write conformant software by reading the spec, in practice no spec is completely watertight and we encourage discussion. Obviously any posting to this list advertises the origin of the poster, so companies may wish to mail privately and will get a private reply. However we have limited resources and cannot generally give extended free private advice. There are some closed source tools which read/emit CML. Some of their authors have not approached us at all. Others have approached us but expected us to provide complete CML implementations at our own expense. Since, at present, this not an attractive business proposition, we haven't been able to accept these offers. We note that some of them (unidentified) have since added "CML". We do not know the degree of conformance or comprehensiveness. Note that some of them are only available through purchase and we may not have access to them. We do know that some of them do not conform to the published CML specification and shall be advising them that this is inconsistent with the use of the term and mark "CML". Other list readers might like to comment, but please make sure that statements are factually correct and avoid political discussions. * ACDLabs. No public information on conformance. * CambridgeSoft. No public information on conformance. * Chemaxon (Marvin). We have had no contact from them. This company lists the CML elements they supports and adds many others in the same namespace which are not CML. The "CML" is therefore not conformant to the published Schema. There are also semantics which are incompatible with CML (e.g. the order of atoms may be important). This is "semantic pollution". We shall write to them soon, advising them that this is unacceptable. There are technical fixes to some of this such as the use of proprietary namespaces for attributes, elements and datatypes. * Foo. private communication. * Bar. private communication * Xyzzy. private communication. I shall write separately on compchem and semantics. P. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 Fax: +44 1223 763076 ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click _______________________________________________ cml-discuss mailing list cml-discuss [] lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cml-discuss ----- End forwarded message ----- -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net From chemistry-request@ccl.net Thu Apr 7 15:07:25 2005 Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.200]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j37J7MZh026091 for ; Thu, 7 Apr 2005 15:07:22 -0400 Received: by wproxy.gmail.com with SMTP id 58so801658wri for ; Thu, 07 Apr 2005 12:07:21 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:in-reply-to:mime-version:content-type:content-transfer-encoding:references; b=SjXSb09PzF2K9FGjEdgQ1na6XKO7XpWmK81yU2II07VfnlHvoXkDAX4xkCXtKc5kKn7Ei7GZ3+RuGK7FJxfpBRl5k1KiZI6yOK02pQQ9082ofdwTeWuq0LwcCSTK0EKD0Tz5J1vnunWiXADLQKwYVsY7Ypc1hZ6VUGC90vqU6b0= Received: by 10.54.46.7 with SMTP id t7mr491145wrt; Thu, 07 Apr 2005 12:07:21 -0700 (PDT) Received: by 10.54.43.59 with HTTP; Thu, 7 Apr 2005 12:07:21 -0700 (PDT) Message-ID: Date: Thu, 7 Apr 2005 12:07:21 -0700 From: Eric Hu Reply-To: Eric Hu To: chemistry.-at-.ccl.net Subject: a bimolecular reaction In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit References: X-Spam-Status: No, score=0.6 required=5.0 tests=DNS_FROM_RFC_ABUSE,RCVD_BY_IP, UPPERCASE_25_50 autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi, I am experimenting a TI perturbation with Amber 8.0 on an enzyme-catalyzed bimolecular reaction (an alcohol reacts with a carboxylic acid to form an ester). The two species are away from each other in the enzyme pocket. First I run the simulation in vaccum without enzyme. I defined two new atom types for the carbonyl carbon (CX) and the hydroxyl oxygen (OX). They will become C and OS at the end (in the ester) and one OH and two HO atoms will disappear. Initially CX and OX distance is 6.0 angstrom. When I run minimization on the unperturbed system, the 1-4 EEL blows up quickly. I suspect that this has something to do with the restraints between two molecules. I tried to play around the force constants and so far has no luck. Any suggestions will be welcomed. Eric Initial minimisation of our complex &cntrl imin=1, maxcyc=2500, ncyc=1000, cut=1000,ntb=0, ntpr=50 / ... NSTEP ENERGY RMS GMAX NAME NUMBER 100 -8.6624E+01 6.0486E+00 3.0066E+01 C4 4 BOND = 2.9020 ANGLE = 40.9876 DIHED = 28.3713 VDWAALS = -3.3408 EEL = 58.0670 HBOND = 0.0000 1-4 VDW = 12.8320 1-4 EEL = -226.4433 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -5.6925E+03 6.0827E+04 4.8485E+05 H15 15 BOND = 6.7995 ANGLE = 78.2618 DIHED = 38.3658 VDWAALS = -2.9570 EEL = 54.6162 HBOND = 0.0000 1-4 VDW = 12.2254 1-4 EEL = -5879.7886 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.1864E+07 2.6376E+11 2.1022E+12 H15 15 BOND = 6.6603 ANGLE = 78.2334 DIHED = 38.3939 VDWAALS = -2.9575 EEL = 54.6011 HBOND = 0.0000 1-4 VDW = 12.2257 1-4 EEL = ************* RESTRAINT = 0.0000 emark goes here MASS CX 12.010 0.616 same as c OX 16.000 0.434 same as o BOND CX-OX 10.0 6.0 weak restraint ANGLE CX-OX-CT 10.0 117.18 CX-OX-HO 10.0 117.18 O -CX-OH 10.0 120.00 same as O -C -OH O -CX-OX 10.0 120.00 same as O -C -OH OH-CX-OX 10.0 117.18 CA-CX-OX 10.0 120.00 same as CA-C -OH DIHE X -CA-CX-X 4 14.50 180.0 2. same as X -C -C -X X -CT-OX-X 3 0.50 0.0 3. same as X -CT-OH-X X -CX-OH-X 2 4.60 180.0 2. same as X -C -OH-X X -CX-OX-X 2 4.60 180.0 2. same as X -C -OH-X IMPROPER NONBON CX 1.9080 0.0860 same as c OX 1.6612 0.2100 same as o From chemistry-request@ccl.net Thu Apr 7 11:50:57 2005 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j37FooOs015358 for ; Thu, 7 Apr 2005 11:50:51 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.11/jtpda-5.4) with ESMTP id j37Fold6091783 for ; Thu, 7 Apr 2005 17:50:47 +0200 (CEST) X-Ids: 166 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id j37Fofn7047297; Thu, 7 Apr 2005 17:50:41 +0200 (MEST) Date: Thu, 7 Apr 2005 17:50:41 +0200 (MEST) From: Michel Petitjean Message-Id: <200504071550.j37Fofn7047297.-at-.ds10.itodys.jussieu.fr> To: chemistry.-at-.ccl.net Subject: CCL: FIS2005 Conference Programme X-Greylist: Sender IP whitelisted, not delayed by milter-greylist-1.7.2 (shiva.jussieu.fr [134.157.0.166]); Thu, 07 Apr 2005 17:50:49 +0200 (CEST) X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Miltered: at shiva.jussieu.fr with ID 425556D7.001 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net To: Subj: FIS2005 Conference Programme /* We apologize for unwanted or multiple receipts */ The FIS2005 - Third Conference on the Foundations of Information Science, will be held in Paris the 4-7 July 2005. This pluridisciplinary Conference offers 4 sessions: Monday 4 July: Information in Physics and Chemistry. Data Banks and Data Mining. Tuesday 5 July: Neural Information, Bioinformation and Bioinformatics, Biosemiotics, Information and the Codes of Life, Genomics, Biomedical Applications, Ecology. Wednesday 6 July: Global Mathematical Aspects of Information: Information Theory and Its Applications, Networks, Symmetry, Agency, Semiotics. Thursday 7 July: Trends in Information and Communication Sciences. Open Access and the Information Society. Economic, Social and Philosophical Aspects. It includes a round table about: << Interdisciplinary Teaching and Information Science >> The detailed programme is on: http://www.mdpi.net/fis2005/programme.html *** Deadline to pay the reduced conference fee (200 Euros): 25 April 2005 *** Other useful informations are available from the FIS2005 welcome page: http://www.mdpi.net/fis2005 The FIS2005 Organizing Committee: Soren Brier (Denmark) Jerry Chandler (USA) John Collier (South Africa) Dail Doucette (USA) Ted Goranson (USA) Wolfgang Hofkirchner (Austria) Shu-Kun Lin (Switzerland) Pedro Marijuan (Spain) Koichiro Matsuno (Japan) Francis Muguet (France) Michel Petitjean (France, coordinator) Michel Petitjean Email: petitjean.-at-.itodys.jussieu.fr FIS2005 coordinator http://www.mdpi.org/fis2005 Editor-in-Chief of Entropy http://www.mdpi.org/entropy ITODYS (CNRS, UMR 7086) 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