From chemistry-request@server.ccl.net Mon Aug 5 23:56:54 2002 Received: from web12807.mail.yahoo.com ([216.136.174.42]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g763usl05543 for ; Mon, 5 Aug 2002 23:56:54 -0400 Message-ID: <20020806035653.93080.qmail@web12807.mail.yahoo.com> Received: from [203.87.150.242] by web12807.mail.yahoo.com via HTTP; Mon, 05 Aug 2002 20:56:53 PDT Date: Mon, 5 Aug 2002 20:56:53 -0700 (PDT) From: amor san juan Subject: Software for viewing docked ligand+protein To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi to all! Would anyone please advice me softwares to view a docking output from ligand bounded to macromolecule( >5000atoms). Thanks so much. Amor __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Tue Aug 6 08:46:42 2002 Received: from wrzx35.rz.uni-wuerzburg.de ([132.187.3.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g76Ckfl16182 for ; Tue, 6 Aug 2002 08:46:42 -0400 Received: from wrzx34.rz.uni-wuerzburg.de (wrzx34.rz.uni-wuerzburg.de [132.187.3.34]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.05) with ESMTP id OAA21088 for ; Tue, 6 Aug 2002 14:46:41 +0200 (MET DST) Received: from localhost (localhost [127.0.0.1]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id DCCC380D3 for ; Tue, 6 Aug 2002 14:46:40 +0200 (CEST) Received: from wrzx07.rz.uni-wuerzburg.de (wrzx07.rz.uni-wuerzburg.de [132.187.1.7]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id C3E7380BA for ; Tue, 6 Aug 2002 14:46:40 +0200 (CEST) Received: from pserv.pharmazie.uni-wuerzburg.de (wpor01.pharmazie.uni-wuerzburg.de [132.187.70.201]) by wrzx07.rz.uni-wuerzburg.de (Postfix) with ESMTP id B54643DB for ; Tue, 6 Aug 2002 14:46:40 +0200 (CEST) Received: from prgsrv2 (prgsrv2.pharmazie.uni-wuerzburg.de [132.187.74.36]) by pserv.pharmazie.uni-wuerzburg.de (8.9.3/8.9.3/uniwue-M-1.0) with ESMTP id OAA01394 for ; Tue, 6 Aug 2002 14:46:39 +0200 (MESZ) Received: from wpzn86.pharmazie.uni-wuerzburg.de ([132.187.74.86]) by prgsrv2 (MailMonitor for SMTP v1.1.0 ) ; Tue, 6 Aug 2002 14:46:38 +0200 (W. Europe Daylight Time) Message-ID: <3D4FC421.523F5AE4@pharmazie.uni-wuerzburg.de> Date: Tue, 06 Aug 2002 14:42:09 +0200 From: Nik X-Mailer: Mozilla 4.77 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: holes in molecular surface when using mds from QCPE Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS (Rechenzentrum Universitaet Wuerzburg) Hi all, I am using the mds.f program obtained from QCPE about three years ago. It is running under SuSE Linux 8.0 and is compiled with g77. Since the g77 compiler is very strict I needed to change the line break in the source code. Except for this I didn't change anything. Now my problem: When I convert the obtained the dots file into a displayable format I find large holes in the surface calculated. I had a look in the source code, but since I am mainly a perl and c++ programmer I couldn't find anything obvious. Has anyone observed something similar ? Cheers Nik ------ Nik Stiefl University of Wuerzburg Department of Pharmacy Gemrnay nik@pharmazie.uni-wuerzburg.de From chemistry-request@server.ccl.net Mon Aug 5 11:23:38 2002 Received: from sd.accelrys.com ([64.165.22.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g75FNcl04547 for ; Mon, 5 Aug 2002 11:23:38 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g75FWpB18823 for chemistry@ccl.net; Mon, 5 Aug 2002 08:32:51 -0700 From: Jeffrey Nauss Received: from sandmail01.sd.accelrys.com (sandmail01.sd.accelrys.com [172.30.160.90]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g75FWpf18814 for ; Mon, 5 Aug 2002 08:32:51 -0700 To: chemistry@ccl.net Subject: Accelrys Announces a series of Cheminformatics Training in Cambridge, UK for September 2002 MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: Date: Mon, 5 Aug 2002 08:23:32 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 08/05/2002 08:23:33 AM, Serialize complete at 08/05/2002 08:23:33 AM Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g75FNcl04551 Accelrys Inc. will be holding a series of Cheminformatics workshops at their European Headquarters in Cambridge during September 2002. On September 2-3, the "Accord Developer Studio" workshop will be offered. This course includes an overview of the Accord SDK & Chemistry Control and how to use them to develop chemically-aware applications using your favourite programming environment, such as C++, Delphi or VB. Consideration will be given to the chemical toolkit functionality supported. Knowledge of programming language, ideally VB is required. On September 4, the workshop "Accord for Oracle" workshop will be conducted. This course covers the installation and use of Accord for Oracle. Participants will learn how to store, index and search chemistry alongside alphanumeric data in an Oracle database. Various ways of accessing and displaying the data stored in the database will also be discussed. Knowledge of Oracle 8.1 is required along with a familiarity of PL/SQL and SQL Statements. Knowledge of Accord Developer Studio would be an advantage. On September 5, the workshop "Accord Grid Control" workshop will be offered. This course introduces the participant to the Accord Grid Control. Using this control the participant will be able to create chemically aware applications allowing the display of chemistry in lists and tables. Knowledge of VB/VBA and experience with ActiveX controls would be an advantage. On September 6, the workshop "Accord CombiChem Add-on " workshop will be conducted. This course is an extension to the Accord SDK training course and covers the use of the CombiChem Add-On to enumerate combinatorial libraries and the use of Accord Visual Objects to produce front-end applications. Attendance at an Accord Developer Studio Workshop is required. Fees for the 2-day course are $1200 commercial, $900 government, and $660 academic. For the 1-day courses the fees are $600 commercial, $450 government, and $330 academic. Registration is on-line at URL http://www.accelrys.com/training/cheminf/registration_sep02.php. Further detailed information about these and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training). Please do not hesitate to contact us should you have any questions. Thank you very much. Elizabeth Crookenden Training Coordinator + 44 (0) 1223 228691 and Dr Judith Madeley Director of Training Accelrys Ltd 334 Cambridge Science Park Cambridge CB4 0WN Telephone number: +44 (0) 1223 228609 Fax number: +44 (0) 1223 228501 Mobile: +44 (0) 77717 61146 Web: http://www.accelrys.com From chemistry-request@server.ccl.net Mon Aug 5 15:17:56 2002 Received: from dqf.ufpe.br ([150.161.5.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g75JHnl11874 for ; Mon, 5 Aug 2002 15:17:55 -0400 Received: from npd.ufpe.br ([150.161.5.215]) by dqf.ufpe.br (8.11.4/8.11.4) with ESMTP id g75IkDc09218 for ; Mon, 5 Aug 2002 15:46:13 -0300 Message-ID: <3D4ED04A.3B5C3A9@npd.ufpe.br> Date: Mon, 05 Aug 2002 16:21:46 -0300 From: Bosco X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Problems with BSSE in B3LYP H-bond calculations Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear collegues I am calculating the XH---Pyrazine system, with X = F, CN, Cl, NC and CCH. The H-bond energies calculated using the 6-31++G(d,p) basis set at HF, B3LYP and MP2 levels predict the following order of stability: FH > CNH > Cl > NCH > HCCH. The procedure of Boys and Bernadi for calculating the BSSE decreases the H-bond energy when using RHF and MP2 methods. However, for DFT/B3LYP method, the corrected H-bond energies (i.e., including BSSE) for the complexes with XH = FH, CNH and ClH are slightly larger than the corresponding uncorrected values. Do you know something similar (reference) or a justification for that? Thanks in advance, Bosco -- Prof. João Bosco Paraiso da Silva e-mail: paraiso@npd.ufpe.br Bosco´s Homepage: www.dqf.ufpe.br/Professores/Bosco/Bosco.html Departamento de Química Fundamental Universidade Federal de Pernambuco 50740.250 - Recife (PE) - Brazil DQF´s Homepage: www.dqf.ufpe.br Phone: +55 81 3271-8441 ext. 5009 Fax: +55 81 271-8442 From chemistry-request@server.ccl.net Tue Aug 6 11:27:55 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g76FRtl20708 for ; Tue, 6 Aug 2002 11:27:55 -0400 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g76FRtg11288 for ; Tue, 6 Aug 2002 10:27:55 -0500 (CDT) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id KAA29699 for chemistry@ccl.net; Tue, 6 Aug 2002 10:27:55 -0500 (CDT) Date: Tue, 6 Aug 2002 10:27:55 -0500 From: John Stone To: chemistry@ccl.net Subject: Structural Biology Software Database updated... Message-ID: <20020806102752.F29525@geneseo.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.19i Dear CCL, It has been a while since I last mentioned it, but I wanted to let people know that we've been updating entries in our structural biology software database over the last few months. The database now contains 329 software application entries in 22 categories. The database home page is here: http://www.ks.uiuc.edu/Development/biosoftdb/ As always, if you would like see new software packages added to the database, please use the "submit" link on the DB web page. Your comments and feedback are also appreciated. Enjoy, John Stone biosoftdb@ks.uiuc.edu -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Tue Aug 6 09:21:04 2002 Received: from mh1-cam.cam.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g76DL3l17403 for ; Tue, 6 Aug 2002 09:21:03 -0400 Received: from camdmail01.cam.accelrys.com ([172.27.160.90]) by mh1-cam.cam.accelrys.com with esmtp (Exim 3.12 #1 (Debian)) id 17c4Gf-0000Z9-00 for ; Tue, 06 Aug 2002 14:20:57 +0100 To: chemistry@ccl.net Subject: Accelrys Catalyst and Cerius2 Training in San Diego MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.10 March 22, 2002 Message-ID: From: tluu@accelrys.com Date: Tue, 6 Aug 2002 14:20:52 +0100 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 08/06/2002 01:20:53 PM, Serialize complete at 08/06/2002 01:20:53 PM Content-Type: multipart/alternative; boundary="=_alternative 0049520C80256C0D_=" This is a multipart message in MIME format. --=_alternative 0049520C80256C0D_= Content-Type: text/plain; charset="us-ascii" Accelrys Inc. will be holding a series of workshops involving the Catalyst and Cerius2 user interfaces at our Corporate Headquarters in San Diego, CA in September 2002. On September 24-25, the "Pharmacophore Generation with Catalyst" workshop will be presented. This workshop is intended to introduce customers to pharmacophore generation and to the Catalyst user interface. The workshop begins with the basics of the Catalyst interface and builds to simple pharmacophore generation, selection of training sets, and three-dimensional database searching. Methods used within Catalyst for automatic hypothesis generation and manual hypothesis construction will be discussed. Some optimisation of training sets and database searching will be covered as well. Attendees should possess knowledge of basic UNIX commands and have a basic understanding of QSAR theory. The "Introduction to Cerius2 for Life Sciences Workshop" will be offered on September 26-27. This course provides an overview of molecular modelling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modelling experience is not assumed making this course a great place to learn molecular modelling with Cerius2. On September 30 - October 1, the "Library Design and Analysis Workshop" will be held. This course will cover the basics of combinatorial library design, > from initial library specification through to library analysis techniques. Various approaches to library subsetting will be described, including methods to select chemically diverse subsets from a virtual library, as well as techniques for lead explosion, after initial SAR data has been determined. Other topics covered will include methods for library-library comparison and several approaches to hole-filling of an existing library. Familiarity with the Cerius2 environment is required for attendance to this workshop. Fees for each 2-day course are $1200 commercial, $900 government, and $660 academic. Registration is on-line at URL http://www.accelrys.com/training/rdd/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/rdd/schedule.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Judith Madeley +44 1223 228 609 Tien Luu +44 1223 228 608 --=_alternative 0049520C80256C0D_= Content-Type: text/html; charset="us-ascii"
Accelrys Inc. will be holding a series of workshops involving the Catalyst and
Cerius2 user interfaces at our Corporate Headquarters in San Diego, CA in
September 2002.

On September 24-25, the "Pharmacophore Generation with Catalyst" workshop
will be presented.  This workshop is intended to introduce customers to
pharmacophore generation and to the Catalyst user interface.  The workshop
begins with the basics of the Catalyst interface and builds to simple
pharmacophore generation, selection of training sets, and three-dimensional
database searching.  Methods used within Catalyst for automatic hypothesis
generation and manual hypothesis construction will be discussed.  Some
optimisation of training sets and database searching will be covered as
well.  Attendees should possess knowledge of basic UNIX commands and have a
basic understanding of QSAR theory.

The "Introduction to Cerius2 for Life Sciences Workshop" will be offered on
September 26-27.  This course provides an overview of molecular modelling
techniques for life sciences applications using Cerius2.  The workshop will
focus on basic skills for use of the interface and will explore various
modules in the areas of rational-drug design, structure-based drug design,
and combinatorial chemistry.  Prior modelling experience is not assumed
making this course a great place to learn molecular modelling with Cerius2.

On September 30 - October 1, the "Library Design and Analysis Workshop"
will be held.  This course will cover the basics of combinatorial library design,
from initial library specification through to library analysis techniques.
Various approaches to library subsetting will be described, including
methods to select chemically diverse subsets from a virtual library, as well
as techniques for lead explosion, after initial SAR data has been
determined. Other topics covered will include methods for library-library
comparison and several approaches to hole-filling of an existing library.
Familiarity with the Cerius2 environment is required for attendance to this
workshop.

Fees for each 2-day course are $1200 commercial, $900 government,
and $660 academic.

Registration is on-line at URL
http://www.accelrys.com/training/rdd/registration.php.  Further detailed
information about this and other Accelrys training workshops can be found
at the Accelrys website
(http://www.accelrys.com/training/rdd/schedule.html).

Please do not hesitate to contact us should you have any questions.

Thank you very much.
Judith Madeley
+44 1223 228 609

Tien Luu
+44 1223 228 608
 --=_alternative 0049520C80256C0D_=--