From chemistry-request@server.ccl.net Wed Jan 8 01:42:57 2003 Received: from mx3.ust.hk ([143.89.13.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h086gtD12656 for ; Wed, 8 Jan 2003 01:42:56 -0500 Received: from ust.hk (sqmail3.ust.hk [143.89.15.19]) by mx3.ust.hk (8.12.5/8.12.5) with SMTP id h086ge8W079420 for ; Wed, 8 Jan 2003 14:42:41 +0800 (HKT) X-Authentication-Warning: mx3.ust.hk: Host sqmail3.ust.hk [143.89.15.19] claimed to be ust.hk Received: from 143.89.53.94 (SquirrelMail authenticated user chgy) by sqmail.ust.hk with HTTP; Wed, 8 Jan 2003 14:42:41 +0800 (HKT) Message-ID: <4367.143.89.53.94.1042008161.squirrel@sqmail.ust.hk> Date: Wed, 8 Jan 2003 14:42:41 +0800 (HKT) Subject: Dalton's basis function limit From: "GAO Yi" To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.8) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear cclers, When I'm doing the calculations with Dalton program, I encounter the limitation of the basis function of 255, while the manual said it can deal with the 1200 basis functions. Would you tell me how to overcome it? Thanks. Best regards, Gao Yi The output is: NUMBER OF BASIS FUNCTIONS IS 289 WHICH EXCEEDS THE LIMITATION OF 255 --- SEVERE ERROR, PROGRAM WILL BE ABORTED --- Date and time (Linux) : Wed Jan 8 14:29:26 2003 Host name : CHZ282 Reason: SUPSRT ERROR: max. # basis funcions exceeded >>>> Total CPU time used in DALTON: 6 minutes 26 seconds >>>> Total wall time used in DALTON: 6 minutes 30 seconds QTRACE dump of internal trace stack ==================== level module ==================== 6 HERINT 5 HERMIT 4 GTNRGY 3 GTGRAD 2 OPTMIN 1 DALTON ==================== Linux has no obvious system traceback facility. From chemistry-request@server.ccl.net Wed Jan 8 03:33:18 2003 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h088XID16922 for ; Wed, 8 Jan 2003 03:33:18 -0500 Received: from as2100.itodys.jussieu.fr (as2100.itodys.jussieu.fr [134.157.24.23]) by shiva.jussieu.fr (8.12.5/jtpda-5.4) with SMTP id h088XHb4017757 for ; Wed, 8 Jan 2003 09:33:17 +0100 (CET) Date: Wed, 8 Jan 2003 09:33:17 +0100 Message-Id: <03010809331728@itodys.jussieu.fr> From: petitjean@itodys.jussieu.fr To: chemistry@ccl.net Subject: Re: CCL:Superimpose program X-VMS-To: SMTP%"chemistry@ccl.net" X-Antivirus: scanned by sophie at shiva.jussieu.fr To: chemistry@ccl.net Subject: Re: CCL:Superimpose program The freeware CSR do that, even for non linear structures. The documentation is append below. Just tell me which for which platform(s) you need it, and I shall email to you the uuencoded CSR. Note that no Windows version is available. 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 Atchara Wijitkosoom wrote: >To whom it may concern, > >Does anybody know about the superimpose program that can deal with the >structures that have different length? > >Thank you very much in advance. > >Yours, >Atchara ................ SHORT DOC ............................................. CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. Reference: M. Petitjean, Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm, Comput. Chem. 1998,22[6],463-465). Author email: petitjean@itodys.jussieu.fr CSR reads the cartesian coordinates of two molecules, then optimally rotates and translates the molecule 2 onto the molecule 1 to find the maximal common 3D motif. The two input molecules should be concatenated into a single file prior execution. Input data and parameters: ------------------------- INPUT FORMAT: CAS : Reserved for internal purposes HIN : Hyperchem-type files MDL : Cambridge Crystallographic Model files ML2 : SYBYL Mol2 files PDB : Protein Data Bank or Nucleic Acid Data Bank files (only HEADER, ATOM, ENDMDL and END records are recognized) BIO : Biosym (MSI) files ISU : Reserved for internal purposes INPUT MOLEC FILE NAME: name of the input file containing both molecules OUTPUT MOLEC FILE NAME: name of the output file containing the optimally rotated and translated molecule 2 IMOL1: sequential position number of molecule 1 in the input molecules file IMOL2: sequential position number of molecule 2 in the input molecules file ITERMX: maximum number of iterations; recommended value: about 200 for small molecules (<100at.), about 2000 for a hundred to a thousand atoms, and 20000 for larger molecules CUT-OFF DIST: This parameter does NOT affect the results. It saves space and time. As a rule of thumb, this value should be roughly near a bondlength. E.g. about 1.5 to 2 for small inorganic molecules, 0.9 to 1.2 for full proteins, 4 to 5 for C-alpha protein backbones). Output results: -------------- The size N of the common 3D motif, and the r.m.s. between the N pairs of atoms, followed by the one-to-one correspondence between the N atoms of molecule 1 and the N atoms of molecule 2. The new coordinates of the optimally rotated and translated molecule 2. Remarks: ------- The number of atoms is currently limited to 15000 for each molecule. The source has to be recompiled to read larger molecules. To operate on C-alpha protein backbones, the other atoms should be removed prior execution. The computing time is roughly proportional to the product n1*n2 of the number of atoms of the two molecules, and proportional to the number of iterations (reading and writing files not included). The generated file containing the output moved molecule 2 is empty for CAS, MDL and BIO formats, and the message "EERCO2 = 1" is displayed. ................ END SHORT DOC ......................................... From chemistry-request@server.ccl.net Wed Jan 8 04:33:33 2003 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h089XWD31012 for ; Wed, 8 Jan 2003 04:33:32 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18WCVt-0003iI-00; Wed, 08 Jan 2003 09:28:41 +0000 Date: Wed, 8 Jan 2003 09:28:41 +0000 (GMT) From: Szilveszter Juhos To: Atchara Wijitkosoom cc: chemistry@ccl.net Subject: Re: CCL:Superimpose program In-Reply-To: <3E1B0B99.3DF839A0@mercury.hec.utah.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 7 Jan 2003, Atchara Wijitkosoom wrote: > Does anybody know about the superimpose program that can deal with the > structures that have different length? MOE also can superimpose structures, you can select some atoms/substructures that are common. Szilva From chemistry-request@server.ccl.net Tue Jan 7 20:50:30 2003 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h081oTD07397 for ; Tue, 7 Jan 2003 20:50:30 -0500 Received: from penguin.sunesis.com ([192.168.1.63]) by mercury.sunesis.com with Microsoft SMTPSVC(5.0.2195.2966); Tue, 7 Jan 2003 17:50:19 -0800 Date: Tue, 7 Jan 2003 17:51:05 -0800 (PST) From: "Warren L. DeLano" To: Subject: New PyMOL Release: 0.86 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-OriginalArrivalTime: 08 Jan 2003 01:50:19.0443 (UTC) FILETIME=[4C8E5830:01C2B6B8] PyMOL 0.86 has been released. Session saves and Amber trajectory file reads are the main new features. Usability is slightly improved over previous versions. With session saves, PyMOL is now more useful to computational chemists who need to share models and 3D structures with other collaborating scientists. PyMOL session files can be sent as email attachments or shared via local intranets. A "naive" user can simply double-click on the session file and then manipulate exactly what you would like to show them > from within PyMOL. Likewise, PyMOL can now become much more useful for educators in creating "live" examples for their students, without the server infrastructure required to support something like Chime. Unlike the commercial alternatives, PyMOL can be freely redistributed to all of your students and collaborators. Binaries are currently available for Windows, Linux, and SGI. http://pymol.sf.net Never heard of PyMOL? PyMOL is a powerful free and open-source molecular visualization system created by Warren L. DeLano. Although the user interface is still somewhat primitive, it has impressive graphics, a rich command language, and powerful scripting support, including a native Python API. We now have several hundred subscribers on the PyMOL mailing list -- encouraging evidence that PyMOL is really helping some people to get their research done. Please do give it a try sometime! Cheers, Warren L. DeLano Ph.D. DeLano Scientific LLC PS. An OSX mac version supporting session files will be released soon. From chemistry-request@server.ccl.net Wed Jan 8 04:18:46 2003 Received: from ims01.stf.nus.edu.sg ([137.132.14.208]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h089IjD29702 for ; Wed, 8 Jan 2003 04:18:45 -0500 Received: from mbxsrv05.stf.nus.edu.sg ([137.132.14.215]) by ims01.stf.nus.edu.sg with Microsoft SMTPSVC(5.0.2195.4905); Wed, 8 Jan 2003 17:17:17 +0800 X-MimeOLE: Produced By Microsoft Exchange V6.0.6334.0 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Subject: ask for help about parameters for PEOE method for P atoms Date: Wed, 8 Jan 2003 17:17:17 +0800 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: ask for help about parameters for PEOE method for P atoms Thread-Index: AcK29r12cqdeBO7AQeahASK0Z5C1ng== From: "Li Zerong" To: X-OriginalArrivalTime: 08 Jan 2003 09:17:17.0836 (UTC) FILETIME=[BD905CC0:01C2B6F6] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h089IkD29777 Dear CCLers, Recently, I am writing a program to calculate atomic charges with PEOE (Partial equalization of orbital elecronegativity) method. I can find only the a,b c parameters for H,C,N,O,F,Cl,Br,I,S atoms from : Gastriger,J. and Marsili, M., tetrhedron, 36,3219-3288(1980). But I can not find parameters for P, Si atoms, which are very important to me. can anybody give me any information ? Li,ZR smalizr@nus.edu.sg From chemistry-request@server.ccl.net Tue Jan 7 09:13:04 2003 Received: from api_lab_bdc.achillion.com ([64.51.60.221]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h07ED4D19031 for ; Tue, 7 Jan 2003 09:13:04 -0500 Received: by api_lab_bdc.achillion.com with Internet Mail Service (5.5.2653.19) id ; Tue, 7 Jan 2003 09:11:19 -0500 Message-ID: From: Ken Torikoshi To: "'chemistry@ccl.net'" Subject: catalogs of compounds in SDF format Date: Tue, 7 Jan 2003 09:11:16 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi All: I am looking for catalogs of compounds for drug discovery in SDF format. I am not interested in catalogs that are included in ACD. I will summarize. Thank you, Ken From chemistry-request@server.ccl.net Wed Jan 8 05:27:00 2003 Received: from compchem.dfh.dk ([130.225.225.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h08AQxD32616 for ; Wed, 8 Jan 2003 05:27:00 -0500 Received: (from jeremy@localhost) by compchem.dfh.dk (SGI-8.9.3/8.9.3) id LAA25844 for chemistry@ccl.net; Wed, 8 Jan 2003 11:15:40 +0100 (MET) Resent-Message-Id: <200301081015.LAA25844@compchem.dfh.dk> Date: Wed, 8 Jan 2003 11:03:15 +0100 From: "Jeremy R. Greenwood" To: GAO Yi Subject: Re: CCL:Dalton's basis function limit Message-ID: <20030108110314.A1329681@compchem.dfh.dk> References: <4367.143.89.53.94.1042008161.squirrel@sqmail.ust.hk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i In-Reply-To: <4367.143.89.53.94.1042008161.squirrel@sqmail.ust.hk>; from chgy@ust.hk on Wed, Jan 08, 2003 at 02:42:41PM +0800 Resent-From: jeremy@compchem.dfh.dk Resent-Date: Wed, 8 Jan 2003 11:15:40 +0100 Resent-To: chemistry@ccl.net Dear Gao, > When I'm doing the calculations with Dalton program, I encounter the You might like to try the Dalton users' list and its archives for Dalton-specific problems: dalton-users@kjemi.uio.no http://www.kjemi.uio.no/software/dalton/dalton.html > limitation of the basis function of 255, while the manual said it can deal > with the 1200 basis functions. Would you tell me how to overcome it? > > Gao Yi > > The output is: > > NUMBER OF BASIS FUNCTIONS IS 289 WHICH EXCEEDS > THE LIMITATION OF 255 Though you are obtaining this limit in a different calculation from the one I encountered it in, it seems to be related to the default method for handling the integrals. Kenneth Ruud kindly gave me the following advice: For an HF calculation, you can try the direct method: **DALTON INPUT .RUN PROPERTIES .DIRECT .... For an MCSCF calculation, you can try a different integral sorting program: **DALTON INPUT .RUN PROPERTIES .PRESORT He also suggests turning off London orbitals if you're using them but don't need them. Hope this helps, Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy@greenwood.net Department of Medicinal Chemistry bh +45 35306117 Pharmaceutical University of Denmark fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- A couple of months in the laboratory can frequently save a couple of hours in the library. -- Frank H. Westheimer, chemistry professor (1912-) ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Jan 8 05:15:10 2003 Received: from hpserv.imim.es ([193.144.6.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h08AF9D32390 for ; Wed, 8 Jan 2003 05:15:09 -0500 Received: by hpserv.imim.es with Internet Mail Service (5.5.2656.59) id ; Wed, 8 Jan 2003 11:18:26 +0100 Received: from imim.es (diana.imim.es [193.146.190.154]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2656.59) id CPKK1SV0; Wed, 8 Jan 2003 11:18:00 +0100 From: "Barbany, Montse" To: chemistry@ccl.net, "Villa, Jordi" Message-ID: <3E1BFA97.B3BB23DD@imim.es> Date: Wed, 08 Jan 2003 11:16:55 +0100 X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10 i686) X-Accept-Language: en MIME-Version: 1.0 Subject: MIPSim release Content-Type: multipart/alternative; boundary="------------C6BBA0D2656671ECBCF4DF1E" --------------C6BBA0D2656671ECBCF4DF1E Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit ********************************************************************** * * * MIPSim 2.1 Release * * * ********************************************************************** January 2003 The Research Group in Biomedical Informatics (GRIB) is proud to announce the release of a new version of MIPSIM. MIPSIM is a computational system developed by the GRIB at the Institut Municipal d'Investigació Mèdica (IMIM) of Barcelona for the automatic exploration of biomolecular similarities on the basis of molecular interaction potentials. MIPSIM can be used as a standalone program for the automatic exploration of biomolecular similarities but it is specially powerful when interfacing to other well-known external programs: * The quantum package GAMESS. Current version of MIPSIM has been tested with June 2001 version of GAMESS. Other versions may be compatible with the scripts distributed with MIPSIM with very few changes. * A molecular interaction potential evaluator (GRID). Current supported version of MIPSIM interfaces with GRID19 (Linux version), or Grid 20 (IRIX VERSIONS). * statistical tools for the partial least squares (PLS) calculations needed for the derivation of 3D-QSAR models (GOLPE), and * visualization packages (GOPENMOL,INSIGTHII) The current is an alpha version and may be bug free. We encourage the users to help in the development of more robust and powerful versions by reporting bugs and suggesting improvements. The program can be accessed at the web address: http://www1.imim.es/modeling/mipsim/index.html For further information, please, refer to the above mentioned page or e-mail us at mipsim@imim.es. Reference: MIPSIM: Similarity analysis of Molecular Interaction Potentials Miquel de Cáceres, Jordi Villà, Juan J. Lozano and Ferran Sanz, Bioinformatics 2000, 16, 568-569 Montse -- Montserrat Barbany Puig Computational Structural Biology Laboratory Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Pg.Marítim de la Barceloneta, 37-49; 08003 Barcelona (Spain) Tel: +34 93 224 0893 // +34 93 224 0875 e-mail: mbarbany@imim.es http://www.imim.es/grib/ --------------C6BBA0D2656671ECBCF4DF1E Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  

**********************************************************************
*                                                                                                                                                         *
*                   MIPSim 2.1 Release                                                                                                 *
*                                                                                                                                                         *
**********************************************************************

January 2003

The Research Group in Biomedical Informatics (GRIB) is proud to announce the
release of a new version of MIPSIM.
MIPSIM is a computational system developed by the GRIB at the
Institut Municipal d'Investigació Mèdica (IMIM) of Barcelona for
the automatic exploration of biomolecular similarities on the basis
of molecular interaction potentials.

MIPSIM can be used as a standalone program for the automatic exploration
of biomolecular similarities but it is specially powerful when interfacing
to other well-known external programs:

    * The quantum package GAMESS. Current version of MIPSIM has been
      tested with June 2001 version of GAMESS. Other versions may be
      compatible with the scripts distributed with MIPSIM with very few
      changes.
    * A molecular interaction potential evaluator (GRID). Current supported
      version of MIPSIM interfaces with GRID19 (Linux version), or Grid 20
      (IRIX VERSIONS).
    * statistical tools for the partial least squares (PLS) calculations
      needed for the derivation of 3D-QSAR models (GOLPE), and
    * visualization packages (GOPENMOL,INSIGTHII)

The current is an alpha version and may be bug free. We encourage the
users to help in the development of more robust and powerful versions
by reporting bugs and suggesting improvements.

The program can be accessed at the web address:

http://www1.imim.es/modeling/mipsim/index.html

For further information, please, refer to the above mentioned page or
e-mail us at mipsim@imim.es.

Reference:
MIPSIM: Similarity analysis of Molecular Interaction Potentials
Miquel de Cáceres, Jordi Villà, Juan J. Lozano and Ferran Sanz,
Bioinformatics 2000, 16, 568-569
 

Montse 

-- 
Montserrat Barbany Puig

Computational Structural Biology Laboratory
Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
Pg.Marítim de la Barceloneta, 37-49; 08003 Barcelona (Spain)
Tel: +34 93 224 0893 // +34 93 224 0875
e-mail: mbarbany@imim.es         http://www.imim.es/grib/
  --------------C6BBA0D2656671ECBCF4DF1E-- From chemistry-request@server.ccl.net Tue Jan 7 11:54:11 2003 Received: from sandmail01.sd.accelrys.com ([209.120.169.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h07GsAD25030 for ; Tue, 7 Jan 2003 11:54:10 -0500 MIME-Version: 1.0 To: chemistry@ccl.net Cc: elizabethc@accelrys.com Subject: Accelrys Customer Training Events X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: jnauss@accelrys.com Date: Tue, 7 Jan 2003 08:54:09 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 01/07/2003 08:54:11 AM, Serialize complete at 01/07/2003 08:54:11 AM Content-Type: text/plain; charset="us-ascii" Accelrys Inc. will be holding the following training workshops at locations in the US and Europe during late February and March 2003. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $450 per day for government and $330 per day for academic. 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Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Wed Jan 8 05:16:27 2003 Received: from lipid.biocomp.unibo.it ([137.204.193.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h08AGRD32427 for ; Wed, 8 Jan 2003 05:16:27 -0500 Received: from atp.biocomp.unibo.it (atp.biocomp.unibo.it [137.204.193.243]) by lipid.biocomp.unibo.it (Postfix) with ESMTP id 13E1F27A7F for ; Wed, 8 Jan 2003 11:21:43 +0100 (CET) Date: Wed, 8 Jan 2003 11:16:06 +0100 (CET) From: Ivan Rossi To: CompChem Mailing List Subject: Program updated: ESF School on structural genomics Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII University of Bologna and European Science Foundation are pleased to announce the: Bologna Winter School on Biotechnology 2003 HOT TOPICS IN STRUCTURAL GENOMICS http://www.biocomp.unibo.it/school/html2003/ 9-15 February 2003, Bologna - Italy http://www.biocomp.unibo.it/school/html2003/ email : school2003@biocomp.unibo.it The main topic will be the state of the art of protein structure prediction after CASP 5 (Critical Assessment of Techniques for Protein Structure Prediction, Asilomar, December 2002). Focus will be on comparative modelling, low homology protein modelling, new fold recognition, ab initio structure prediction, protein-protein and protein-DNA interaction, prediction of protein function and structure prediction of membrane proteins. LECTURERS Patrick Aloy EMBL Heidelberg, DE Pierre Baldi University of California Irvine, CA, USA Nir Ben-Tal Tel Aviv University Tel Aviv, IL Soren Brunak Technical University of Denmark Lyngby, DK Chris Bystroff Rensselaer Polytechnic Institute Troy, NY, USA Raffaele Calogero University of Torino Torino, IT Rita Casadio University of Bologna Bologna, IT Daniel Fischer Ben Gurion University Be'er Sheva, IL Manuela Helmer-Citterich University "Tor Vergata" Roma, IT Joel Janin LEBS, CNRS Gif sur Ivette, FR Sue Jones EBI Hinxton, UK David T. Jones University College London, UK Arthur M. Lesk University of Cambridge Cambridge, UK Henriette Molinari University of Verona Verona, IT John Moult University of Maryland Rockville, MD, USA Bruno Samori' University of Bologna Bologna, IT Jeffrey Skolnick Buffalo Center for BioinformaticsBuffalo, NY, USA Mike Taussig The Babraham Institute Cambridge, UK Anna Tramontano University "La Sapienza" Roma IT Alfonso Valencia National Center of Biotechnology Cantoblanco, ES Gunnar von Hejine University of Stockholm Stockholm, SE Richard Wagner University of Osnabrueck Osnabrueck, DE Stephen White University of California Irvine, USA Program is available at http://www.biocomp.unibo.it/school/html2003/ For Application send a short C.V. to school2003@biocomp.unibo.it. You will be notified by e-mail of acceptance. Deadline for application is January 10, 2003 The School is partially granted by the European Science Foundation (Integrated Approaches for Functional Genomics programme) FOR LIVING EXPENSES AN OFFER IS AVAILABLE: a package of 500 EURO that covers lunches, coffee breaks and social dinner. TWO OFFERS FOR THE ACCOMODATION AT THE ERASMUS COLLEGE, IN DOWNTOWN BOLOGNA, ARE ALSO AVAILABLE: 160 EURO per person for a double room (6 nights) 260 EURO per person for a single room, if available (6 nights). Dues will be payed upon acceptance with modalities to be specified. University of Bologna CIRB, INTERDEPARTMENTAL CENTER FOR BIOTECHNOLOGY CORSO DI LAUREA IN BIOTECNOLOGIE European Science Foundation Consorzio Interuniversitario Biotecnologie Consiglio Nazionale per le Ricerche Marino Golinelli Foundation O.N.L.U.S. Organisation: AIRBBC Associazione Italiana per la Ricerca in Biofisica e Biologia Computazionale From chemistry-request@server.ccl.net Wed Jan 8 03:44:19 2003 Received: from galileo.fis.unipr.it ([192.135.11.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h088iJD17182 for ; Wed, 8 Jan 2003 03:44:19 -0500 Received: from fis.unipr.it (pc116.fis.unipr.it [160.78.33.116]) by galileo.fis.unipr.it (8.11.6/8.11.6) with ESMTP id h088iAA28546; Wed, 8 Jan 2003 09:44:10 +0100 Message-ID: <3E1BE611.8050909@fis.unipr.it> Date: Wed, 08 Jan 2003 09:49:21 +0100 From: Eugenia Polverini Organization: Dip. Fisica Universita' di Parma User-Agent: Mozilla/5.0 (Windows; U; Win 9x 4.90; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Atchara Wijitkosoom , CCL Subject: Re: CCL:Superimpose program References: <3E1B0B99.3DF839A0@mercury.hec.utah.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi! There is DeepView-SwissPdbViewer at http://www.expasy.org/spdbv/ that can do this. Regards Eugenia Atchara Wijitkosoom wrote: >To whom it may concern, > >Does anybody know about the superimpose program that can deal with the >structures that have different length? > >Thank you very much in advance. > >Yours, >Atchara > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > -- Eugenia Polverini, Ph.D. Dept. of Physics University of Parma Parco Area delle Scienze, 7/A 43100 Parma ITALY Phone: +39 0521 905254 Fax: +39 0521 905223 E-Mail: eugenia.polverini@fis.unipr.it From chemistry-request@server.ccl.net Tue Jan 7 11:36:27 2003 Received: from smtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h07GaPD24354 for ; Tue, 7 Jan 2003 11:36:26 -0500 Received: from pak3 (unknown [140.232.202.227]) by smtp01.sohu.com (Postfix) with ESMTP id 4B2CA53D4B; Wed, 8 Jan 2003 00:05:38 +0800 (CST) Message-ID: <051501c2b66a$42ac9370$e3cae88c@pak3> From: "Alan Leo" To: , =?iso-8859-1?Q?Holger_Clau=DFen?= , "Mireille Krier" , "Joe Leonard" References: <005401c2b55c$c5dd2b60$2700000a@lapsigma> Subject: Summary: FLEXX error message from ligand MOL2 read Date: Tue, 7 Jan 2003 11:31:38 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Hi, All: Here is summary of my question related to my questions, thanks Holger, Mireille, Joe 's help. At last, I resolved this problem. It is because of mol2 file error. When I generated the mol2 file, I should double check the file format and atom_type. I used Babel to generate the mol2 file from x-ray pdb file. Don't believe in software completely, one should double check the file before using FLEXX. Best, Alan ___________________________ Original message __________________________ Hi, All: I am using FLEXX evalution now, but when I input the ligand minimization mol2 file,the following error messgae is appeared: _____________________________________________ FLEXX> lig FLEXX/LIGAND> read TSB_min >> DATA ERROR: No molecules found. [occured in line 126 of file TSB_min] Segmentation fault (core dumped) _____________________________________________ I have three questions: 1. I don't know if there is any newsgroup related to FLEXX except chemweb newsgroup. 2. The error message above point out the error of my sybyl mol2 file error, or maybe it is because of other reasons. 3. Should I minimize the ligand structure before I generate the *_min.mol2 file? Which software I should use? Don't peng me, I am a newbie. :) Your help is much appreciated.. Best, Alan +++++++++++++++++ Answers +++++++++++++++++++++ Question 1: **** From Joe Well, I thought it was sold/supported by Tripos? If you have it from them, why not call Support? If Tripos isn't involved, how about BiosolveIT.de, the authors... **** From Holger There is currently no FlexX specific newsgroup. However, please feel free to send any comment and question to flexx-info@biosolveit.de. Question 2 **** From Joe How was the mol2 file created? As I recall, FlexX is rather specific about what it wants to see in the file, and if it's missing or not quite correct it might complain. I worked with FlexX on/off for several years, and it was rather difficult to get the program to core dump. Can something like CORINA read the mol2 file? If so, have it read/write a new mol2 file to see if anything changes (FlexX works well with Corina, I think). **** From Mireille When I used Flexx, I did it through the Sybyl FlexX interface. Recently Molecular networks , group of Gasteiger, who wrote also corina, brought out "cliff" . **** From Holger The error message indicates in fact an error in the mol2 file. There may by plenty of reasons, so that I cannot say much without the file. Question 3 **** From Joe It should not matter, as long as the bond lengths and angles of your input structure are reasonable. FlexX works in torsional space, and looks to an external program to flex rings. **** From Mireille yes I minimized the ligand structure before saving it to *_min.mol2. I did this in Sybyl. **** From Holger Ligand structures should always be minimized before docking. You can use any external force field for minimizing the ligands e.g. the Tripos force filed with comes with Sybyl. Please, note that the newes FlexX version is able to minimize ligands upon loading, if the flag AUTOMINIZISE in the config.dat is set to 1. ++++++++++++++++++++++++++++++++++++++++++++++++++++++ Joe from jle@theworld.com Mireille from mkrier@aspirine.u-strasbg.fr Holger from claussen@biosolveit.de From chemistry-request@server.ccl.net Tue Jan 7 10:03:20 2003 Received: from web12003.mail.yahoo.com ([216.136.172.211]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h07F3KD20973 for ; Tue, 7 Jan 2003 10:03:20 -0500 Message-ID: <20030107150320.11363.qmail@web12003.mail.yahoo.com> Received: from [152.3.169.5] by web12003.mail.yahoo.com via HTTP; Tue, 07 Jan 2003 07:03:20 PST Date: Tue, 7 Jan 2003 07:03:20 -0800 (PST) From: Jianping Lin Subject: the difference of this two Gaussian jobs? To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="0-1511955117-1041951800=:11072" --0-1511955117-1041951800=:11072 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Hi All, The attachments are the two Gaussian jobs I have run. I want to get the atomic charges for both of the strucure, but the file LDA* works and the BCL* file crash (the error message is that the job is terminated by l101.exe), Can someone tell me why? Thanks a lot Jianping Lin Department of Chemistry Duke University __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. 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ICAtNDkuMjkyOTk5OTk5OTk5OTk5ICAgIDc0LjI4MDAwMDAwMDAwMDAwMSAK ICAKCg== --0-1511955117-1041951800=:11072-- From chemistry-request@server.ccl.net Wed Jan 8 14:08:16 2003 Received: from anes-nt02.anes.upmc.edu ([128.147.32.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h08J8GD17183 for ; Wed, 8 Jan 2003 14:08:16 -0500 Received: by anes-nt02.anes.upmc.edu with Internet Mail Service (5.5.2653.19) id ; Wed, 8 Jan 2003 14:08:16 -0500 Message-ID: <5DE64C592075AD4EBEE86F6AB65F8C6501A6EB50@anes-nt02.anes.upmc.edu> From: "Liu, Zhanwu" To: "'chemistry@ccl.net'" Subject: NMR simulation program for protein Date: Wed, 8 Jan 2003 14:08:15 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Hi, all, Does anybody know a NMR simulation program that could simulate the HSQC and NOESY spectra of a small protein (around 130 aa residues) by input the pdb file? Thanks a lot! Yours Zhanwu ----------------------------- Zhanwu Liu, Ph.D. Department of Anesthesiology University of Pittsburgh Phone: 412-648-9137 Fax: 412-648-9587