From chemistry-request@ccl.net Wed Oct 20 17:07:17 2004 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9KM7GL3017616 for ; Wed, 20 Oct 2004 17:07:16 -0500 Received: from [130.126.120.206] (vancouver.ks.uiuc.edu [130.126.120.206]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i9KMJTxk010634 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Wed, 20 Oct 2004 17:19:29 -0500 (CDT) Message-ID: <4176E3D1.3060003-.at.-ks.uiuc.edu> Date: Wed, 20 Oct 2004 17:16:49 -0500 From: "David P. Brandon" Reply-To: brandon-.at.-ks.uiuc.edu User-Agent: Mozilla Thunderbird 0.7.2 (Windows/20040707) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry-.at.-ccl.net Subject: "Hands-On" Workshop on Computational Biophysics - Boston Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit 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 "Hands-On" Workshop on Computational Biophysics http://www.ks.uiuc.edu/Training/Workshop/Boston/ Application Deadline: November 9, 2004 The Theoretical and Computational Biophysics Group, an NIH Resource for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu ) at the University of Illinois at Urbana-Champaign (www.uiuc.edu ), will organize a "'Hands-On' Workshop on Computational Biophysics" to be held December 5 to December 9, 2004 at The Colonnade Hotel in Boston, Massachusetts. The workshop will explore a wide range of physical models and computational approaches for the simulation of biological systems. The workshop will be based on case studies including the properties of membranes and membrane proteins, mechanism of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Physical concepts, mathematical techniques, and computational methods required will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, steered molecular dynamics simulations, and combined quantum mechanical - molecular mechanical calculations The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which participants will be able to set up and run simulations. Applications to the workshop are due by November 9, 2004. Selection and notification of participants from the application pool will be completed by November 11, 2004. Those selected to attend must register and pay a workshop fee by November 15, 2004. The base registration fee is $115 for students, $175 for non-student academics, and $250 for all other applicants. Housing and course materials are included in the fee. Due to space and equipment constraints, the workshop is limited to 20 participants. For further information, and online application, go to http://www.ks.uiuc.edu/Training/Workshop/Boston/ . We look forward to receiving your application. Please note that we cannot help with travel expenses or arrangements. Workshop Organizers E-mail: workshop+boston-.at.-ks.uiuc.edu From chemistry-request@ccl.net Tue Oct 19 14:22:10 2004 Received: from web53910.mail.yahoo.com (web53910.mail.yahoo.com [206.190.36.220]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i9JJM81d021664 for ; Tue, 19 Oct 2004 14:22:09 -0500 Message-ID: <20041019193418.33073.qmail[at]web53910.mail.yahoo.com> Received: from [129.128.136.71] by web53910.mail.yahoo.com via HTTP; Tue, 19 Oct 2004 15:34:18 EDT Date: Tue, 19 Oct 2004 15:34:18 -0400 (EDT) From: "A. Boufarik" Subject: Slater Basis Set To: "Comp. Chem. List" MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1223684522-1098214458=:28734" X-Spam-Status: No, hits=1.8 required=7.5 tests=FROM_ENDS_IN_NUMS,HTML_MESSAGE, MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-1223684522-1098214458=:28734 Content-Type: text/plain; charset=us-ascii Greetings all, In the past years, I have seen many people trying to use Slater orbitals as a basis set in the molecular calculations. Two main arguments have been put forward: [1] Theoretical: Shrodinger equation has solutions that are closer to Slater orbitals that Gaussians. As an example, hydrogen functions all have an exponential terms exp(-x) rather than exp(-x*x) [2] Practical : It has been argued that for CI calculations, we better have a small basis set so to allow scan larger configurations spaces. Two questions are in my mind : [1] Have any of the Gaussian experts met a problem for which the basis was too large to be handled during CI. Something that may support statement (2) [2] From a chemistry point of view, is there any benefit for using Slater orbitals. I mean by this, will there be any new physics/chemistry that can only be detected by a Slater basis. Or, is this just another way to do the same old chemistry with an extra 10^(-15) accuracy instead of 10^(-13) with gaussians. Thanks for your comments and ideas, Boufarik --------------------------------- Post your free ad now! Yahoo! Canada Personals --0-1223684522-1098214458=:28734 Content-Type: text/html; charset=us-ascii
Greetings all,
 
In the past years, I have seen many people trying to use Slater orbitals as a basis set in the molecular calculations. Two main arguments have been put forward:
[1] Theoretical: Shrodinger equation has solutions that are closer to Slater orbitals that Gaussians. As an example, hydrogen functions all have an exponential terms exp(-x) rather than exp(-x*x)
 
[2] Practical : It has been argued that for CI calculations, we better have a small basis set so to allow scan larger configurations spaces.
 
Two questions are in my mind : 
 
[1] Have any of the Gaussian experts met a problem for which the basis was too large to be handled during CI. Something that may support statement (2)
 
[2] From a chemistry point of view, is there any benefit for using Slater orbitals. I mean by this, will there be any new physics/chemistry that can only be detected by a Slater basis. Or, is this just another way to do the same old chemistry with an extra 10^(-15) accuracy instead of 10^(-13) with gaussians.
 
Thanks for your comments and ideas,
 
Boufarik 


Post your free ad now! Yahoo! Canada Personals
--0-1223684522-1098214458=:28734-- From chemistry-request@ccl.net Tue Oct 19 17:56:43 2004 Received: from web53907.mail.yahoo.com (web53907.mail.yahoo.com [206.190.36.217]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i9JMugL3007948 for ; Tue, 19 Oct 2004 17:56:42 -0500 Message-ID: <20041019230842.1774.qmail:at:web53907.mail.yahoo.com> Received: from [129.109.59.107] by web53907.mail.yahoo.com via HTTP; Tue, 19 Oct 2004 16:08:42 PDT Date: Tue, 19 Oct 2004 16:08:42 -0700 (PDT) From: IEJMD Subject: Internet Electronic Conference of Molecular Design 2004 To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii 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 Call for papers Internet Electronic Conference of Molecular Design 2004 IECMD 2004, November 29 - December 12 http://www.biochempress.com An electronic conference for presenting and discussing recent developments in Molecular Design will be held between November 29 and December 12, 2004. IECMD 2004 covers all areas of molecular design and uses the Internet for exchanging information. IECMD 2003 accepts electronic papers in the following categories: Posters Research notes Communications Full papers Reviews Paper Submission Papers should be prepared with a Word template from http://www.biochempress.com and submitted by E-mail to iejmd:at:yahoo.com. All papers will be peer reviewed. Accepted papers will be published as PDF files on the IECMD 2004 Web site, http://www.biochempress.com. There will be no registration for visitors of IECMD 2004, and all PDF papers will be free for download. After the Conference, all accepted papers will be published in IEJMD - the Internet Electronic Journal of Molecular Design, http://www.biochempress.com. Important Dates November 15, 2004 - Final papers due November 29, 2004 - Conference begins December 12, 2004 - Conference ends For detailed Instructions for Authors, see the Word template at http://www.biochempress.com IECMD 2004 will cover all aspects of computer-assisted molecular design applications in chemistry, biochemistry, biology, chemical and pharmaceutical industry, including: Computer-aided organic synthesis Chemical structure and reactivity investigated with molecular mechanics, quantum chemistry, and molecular dynamics methods Definition, calculation and evaluation of novel structural descriptors Chemical database searching, clustering, similarity and diversity measure Prediction of physico-chemical properties with Quantitative Structure-Property Relationships (QSPR) Quantitative Structure-Activity Relationships (QSAR) models for biological activity, toxicity, mutagenicity, and carcinogenicity Prediction of chromatographic retention parameters and design of stationary phases for chromatography Modeling of bioorganic compounds, such as proteins, enzymes, and nucleic acids New algorithms for modeling chemical and biochemical phenomena, such as global optimization methods, simulated annealing, neural networks, genetic algorithms, ant colony algorithm Design of special materials, catalysts, high energy compounds, polymers, molecular machines Best regards, John Paul T. Smith Assistant Editor Internet Electronic Journal of Molecular Design (IEJMD) ISSN 1538-6414 Publisher: BioChem Press http://www.biochempress.com __________________________________ Do you Yahoo!? Read only the mail you want - Yahoo! Mail SpamGuard. http://promotions.yahoo.com/new_mail From chemistry-request@ccl.net Wed Oct 20 13:17:28 2004 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9KIHLL3005929; Wed, 20 Oct 2004 13:17:24 -0500 In-Reply-To: To: "Tom Cao" Cc: chemistry:at:ccl.net, "Computational Chemistry List" Subject: Re: CCL:Questions about InsightII and Quanta MIME-Version: 1.0 Sensitivity: X-Mailer: Lotus Notes Release 6.5.1 January 21, 2004 Message-ID: From: Rita Wilby Date: Wed, 20 Oct 2004 11:29:30 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.5.2|June 01, 2004) at 10/20/2004 11:29:49 AM, Serialize complete at 10/20/2004 11:29:49 AM Content-Type: multipart/alternative; boundary="=_alternative 0065956488256F33_=" X-Spam-Status: No, hits=1.8 required=7.5 tests=HTML_MESSAGE, MAILTO_TO_SPAM_ADDR,MK_BAD_HTML_04 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 multipart message in MIME format. --=_alternative 0065956488256F33_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Hello Tom, Thank you for your question on Insight II and QUANTA, which are now=20 provided by Accelrys. Insight II, originally from Biosym, is primarily a macromolecular modeling = application. Insight II functionality includes simulations, homology=20 modeling, protein structure analysis, de novo design, and docking.=20 Specific modules within Insight II are comprehensively listed on our=20 website: http://www.accelrys.com/insight/ QUANTA, originally from MSI, is primarily a macromolecular structure=20 determination tool for X-ray crystallographers. Additional functionality=20 includes simulations, homology modeling, protein structure analysis, and=20 de novo design.=20 http://www.accelrys.com/quanta/ Insight II has two de novo design tools, namely MCSS and Ludi. Each method = has a different approach to the placement of fragments for de novo design. = MCSS was developed in Martin Karplus' laboratory at Harvard and uses=20 CHARMm-based energies to explore and rank fragment binding sites starting=20 with a large number of potential locations for selected fragments on of=20 ligands. More information on MCSS is available in the originators'=20 publications and Accelrys documentation: 1. Miranker, A., Karplus, M. 1991. Functionality maps of binding sites: a=20 multiple copy simultaneous search method. Proteins: Struc. Func. Gen,=20 11:29-34=20 2. Caflisch, A., Miranker, A., Karplus, M. 1993. Multiple copy=20 simultaneous search and construction of ligands in binding sites:=20 application to inhibitors of HIV-1 aspartic proteinase. J. Med. Chem.=20 36:2142-67 3. http://www.accelrys.com/insight/mcss.html 4. http://www.accelrys.com/doc/pdf/mcss2K.pdf Ludi was developed by Hans-Joachim Boehm at BASF. Ludi places fragments=20 according to matches with interaction sites, which are then prioritised by = its internal scoring function. The pre-computed interaction sites may be=20 derived from an alignment of known active ligands or from a rules-based=20 complementary image of a macromolecular binding site. Ludi functionality=20 is documented in=20 1. H.-J. B=F6hm,?The Computer Program Ludi:A New Method for the De Novo=20 Design of Enzyme Inhibitors,? J. Comp. Aided Molec. Design, 6, 61-78,=20 1992. 2. H-J. B=F6hm,?The Development of a Simple Empirical Scoring Function to=20 Estimate the Binding Constant for a Protein Ligand Complex of Known=20 Three-dimensional Structure?, J. Comp. Aided Molec. Design, 8, 243-356, 1994. 3. H.-J. B=F6hm,?Ludi: Rule-based Automatic Design of New Substituents for = Enzyme Inhibitor Leads?, J. Comp. Aided Molec. Design, 6, 593-606, 1992. Boehm, H.-J. "Towards the automatic design of synthetically accessible=20 protein ligands: peptides, amides, and peptidomimetics," J. Comput.- Aided = Molec. Des., 1996, 10, 265-272.=20 http://www.accelrys.com/insight/ludi.html http://www.accelrys.com/doc/pdf/ligand2K.pdf A detailed comparative analysis of Ludi and MCSS is available if you are=20 interested. MCSS/Hook was developed by Rod Hubbard's laboratory in University of York. = MCSS/Hook, available only in QUANTA, includes MCSS functionality and=20 extends MCSS by connecting selected fragments that are already favorably=20 placed. More information on MCSS/Hook is available from: 1. M.B. Eisen, D.C. Wiley, M. Karplus and R.E. Hubbard "HOOK: A program=20 for finding novel molecular architectures that satisfy the chemical and=20 steric requirements of a macromolecule binding site." Proteins Structure,=20 Function and Genetics, 1994, 19, 199-221. 2. http://www.accelrys.com/quanta/mcss=5Fhook.html 3. http://www.accelrys.com/doc/life/quanta2K/pdf/mcss-hook=5Fbook.pdf Ludi and MCSS/Hook have parallel functionalities also. Ludi will connect=20 two or three separate fragments in a site if it can find a fragment that=20 matches available link sites, similar to Hook. We will be happy to discuss any or all of these questions with you=20 off-line, to avoid spamming CCL. Regards, Rita Marguerita Lim-Wilby, B.Pharm., Ph.D. Product Manager, Structure-Based Design Accelrys Inc., http://www.accelrys.com Tel: (858) 799-5486 Cell: (858) 344-0156 Fax: (928) 752-8479 email: rwilby:at:accelrys.com "Tom Cao" =20 Sent by: "Computational Chemistry List" 10/19/2004 10:59 AM To chemistry:at:ccl.net cc Subject CCL:Questions about InsightII and Quanta Dear All, I have a couple of questions regarding InsightII and Quanta made by MSI.=20 Thank you in advance for your help. 1) Both of the InsightII and Quanta are molecular modeling software,=20 what's=20 the real difference between them? for example force field enigen ...?=20 What's=20 the advantage of each of them? 2) InsightII has Ludi, Quanta has MCSS and HOOK, what's the advantage=20 between these two de novo design methods? Thanks again for your help. Sincerely Tom =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F FREE pop-up blocking with the new MSN Toolbar get it now!=20 http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ -=3D This is automatically added to each message by the mailing script =3D- To send e-mail to subscribers of CCL put the string CCL: on your Subject:=20 line and send your message to: CHEMISTRY:at:ccl.net Send your subscription/unsubscription requests to:=20 CHEMISTRY-REQUEST:at:ccl.net=20 HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs=20 If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow:at:nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --=_alternative 0065956488256F33_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Hello Tom,

Thank you for your question on Insig= ht II and QUANTA, which are now provided by Accelrys.

Insight II, originally from Biosym, is primarily a macromolecular modeling application. Insight II functionality includes simulations, homology modeling, protein structure analysis, de novo design, and docking. Specific modules within Insight II are comprehens= ively listed on our website:
http://www.accelrys.com/insight/

QUANTA, originally from MSI, is prim= arily a macromolecular structure determination tool for X-ray crystallographers. Additional functionality includes simulations, homology modeling, protein structure analysis, and de novo design.
http://www.accelrys.com/quanta/

Insight II has two de novo design to= ols, namely MCSS and Ludi. Each method has a different approach to the placement of fragments for de novo design.

MCSS was developed in Martin Karplus' laboratory at Harvard and uses CHARMm-based energies to explore and rank fragment binding sites starting with a large number of potential locations for selected fragments on of ligands. More information on MCSS is available in the originators' publications and Accelrys documentation:
1. Miranker, A., Karplus, M. 1991. F= unctionality maps of binding sites: a multiple copy simultaneous search method. Proteins: Struc. Func. Gen, 11:29-34
2. Caflisch, A., Miranker, A., Karpl= us, M. 1993. Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. J. Med. Chem. 36:2142-67
3. http://www.accelrys.com/insight/m= css.html
4. http://www.accelrys.com/doc/pdf/m= css2K.pdf

Ludi was developed by Hans-Joachim B= oehm at BASF. Ludi places fragments according to matches with interaction sites, which are then prioritised by its internal scoring function. The pre-comput= ed interaction sites may be derived from an alignment of known active ligands or from a rules-based complementary image of a macromolecular binding site. Ludi functionality is documented in
1. H.-J. B=F6hm,“The Computer = Program Ludi:A New Method for the De Novo Design of Enzyme Inhibitors,” J. Co= mp. Aided Molec. Design, 6, 61-78, 1992.
2. H-J. B=F6hm,“The Developmen= t of a Simple Empirical Scoring Function to Estimate the Binding Constant for a Protein Ligand Complex of Known Three-dimensional Structure”, J. Co= mp. Aided Molec.
Design, 8, 243-356, 1994.
3. H.-J. B=F6hm,“Ludi: Rule-ba= sed Automatic Design of New Substituents for Enzyme Inhibitor Leads”, J. Comp. Aided Molec. Design, 6, 593-606, 1992.
Boehm, H.-J. "Towards the autom= atic design of synthetically accessible protein ligands: peptides, amides, and peptidomimetics," J. Comput.- Aided Molec. Des., 1996, 10, 265-272.
http://www.accelrys.com/insight/ludi= .html
http://www.accelrys.com/doc/pdf/liga= nd2K.pdf

A detailed comparative analysis of L= udi and MCSS is available if you are interested.

MCSS/Hook was developed by Rod Hubba= rd's laboratory in University of York. MCSS/Hook, available only in QUANTA, includes MCSS functionality and extends MCSS by connecting selected fragmen= ts that are already favorably placed. More information on MCSS/Hook is availab= le from:
1. M.B. Eisen, D.C. Wiley, M. Karplus and R.E. Hubbard "HOOK: A program for finding novel molecular architec= tures that satisfy the chemical and steric requirements of a macromolecule binding site." Proteins Structure, Function and Genetics, 1994, 19, 199-221.
2. http://www.accelrys.com/quanta/mc= ss=5Fhook.html
3. http://www.accelrys.com/doc/life/= quanta2K/pdf/mcss-hook=5Fbook.pdf

Ludi and MCSS/Hook have parallel fun= ctionalities also. Ludi will connect two or three separate fragments in a site if it can find a fragment that matches available link sites, similar to Hook.

We will be happy to discuss any or a= ll of these questions with you off-line, to avoid spamming CCL.

Regards,
Rita


Marguerita Lim-Wilby, B.Pharm., Ph.D= .
Product Manager, Structure-Based Design
Accelrys Inc., http://www.accelrys.com

Tel: (858) 799-5486
Cell: (858) 344-0156
Fax: (928) 752-8479
email: rwilby:at:accelrys.com



"Tom Cao" &= lt;tomc1234:at:hotmail.com>
Sent by: "Computational Chemist= ry List" <chemistry-request:at:ccl.net>

10/19/2004 10:59 AM

To
chemistry:at:ccl.net
cc
Subject
CCL:Questions about Ins= ightII and Quanta



Dear All,

I have a couple of questions regarding InsightII and Quanta made by MSI.
Thank you in advance for your help.

1) Both of the InsightII and Quanta are molecular modeling software, what's
the real difference between them? for example force field enigen ...? What's
the advantage of each of them?

2) InsightII has Ludi, Quanta has MCSS and HOOK, what's the advantage
between these two de novo design methods?

Thanks again for your help.

Sincerely

Tom

=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F
FREE pop-up blocking with the new MSN Toolbar   get it now!
http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/



-=3D This is automatically added to each message by the mailing script =3D-=
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
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--=_alternative 0065956488256F33_=-- From chemistry-request@ccl.net Tue Oct 19 16:22:53 2004 Received: from mail.mdli.com ([208.200.221.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9JLMp1d002052 for ; Tue, 19 Oct 2004 16:22:51 -0500 Received: from exch-sl02.mdli.com (exch-sl02.mdli.com [172.16.3.10]) by mail.mdli.com (Postfix) with ESMTP id D2BBCB734F for ; Tue, 19 Oct 2004 14:33:44 -0700 (PDT) Received: by exch-sl02.mdli.com with Internet Mail Service (5.5.2657.72) id <45Y6T84R>; Tue, 19 Oct 2004 14:33:44 -0700 Message-ID: From: Terry Wright To: CHEMISTRY$at$ccl.net Subject: Call for papers - ACS San Diego March 13-17, 2005 : Informatics Challenges for Start-Up Companies Date: Tue, 19 Oct 2004 14:33:39 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4B623.4C6D7D59" X-Spam-Status: No, hits=5.1 required=7.5 tests=HTML_60_70, HTML_FONTCOLOR_UNKNOWN,HTML_FONT_BIG,HTML_MESSAGE,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 This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C4B623.4C6D7D59 Content-Type: text/plain All those interested are cordially invited to submit abstracts for this symposium. National ACS Meeting: San Diego March 13-17 2005 Informatics Challenges for Start-Up Companies Division of Chemical Information This symposium is intended for discussion of the unique informatics challenges facing start-up companies. Talks for this symposium may deal on any aspect of cheminformatics, bioinorganics, or management of other scientific information. This includes such topics as. 1) Managing information with limited resources (money and support staff) 2) Commercial versus customized information management systems for your workplace. 3) Making applications from different sources work together. 4) How to efficiently share information across different groups or departments 5) Integrating information with partners or other collaborators. 6) Standardizing hardware/software for increased efficiency. 7) Registration systems for internal databases Talks may focus on either solutions for these issues, or discussion of the problems that still confront organizations in informatics handling. Speakers are not limited to those working at start-ups. Anyone with knowledge in this area is welcome to submit an abstract. Until November 23, abstracts may be entered electronically, via the OASYS system on the ACS web site (www.oasys.acs.org), then select Division of Chemical Information (CINF). After that date or, if you have problems, please send abstracts directly to me (terryw$at$mdli.com). Thanks for your interest. Terry Terry Wright MDL Information Systems 14600 Catalina Street San Leandro, CA 94577 Phone: 510-357-2222 ext. 1392 Email: terryw$at$mdli.com ------_=_NextPart_001_01C4B623.4C6D7D59 Content-Type: text/html

All those interested are cordially invited to submit abstracts for this symposium.

 

 

 

National ACS Meeting: San Diego   March 13-17 2005

 

Informatics Challenges for Start-Up Companies

Division of Chemical Information

 

This symposium is intended for discussion of the unique informatics challenges facing start-up companies. Talks for this symposium may deal on any aspect of cheminformatics, bioinorganics, or management of other scientific information. This includes such topics as.

 

1)   Managing information with limited resources (money and support staff)

2)   Commercial versus customized information management systems for your workplace.

3)   Making applications from different sources work together.

4)   How to efficiently share information across different groups or departments

5)   Integrating information with partners or other collaborators.

6)   Standardizing hardware/software for increased efficiency.

7)   Registration systems for internal databases

 

Talks may focus on either solutions for these issues, or discussion of the problems that still confront organizations in informatics handling. Speakers are not limited to those working at start-ups. Anyone with knowledge in this area is welcome to submit an abstract.

 

Until November 23, abstracts may be entered electronically, via the OASYS system on the ACS web site (www.oasys.acs.org), then select Division of Chemical Information (CINF). After that date or, if you have problems, please send abstracts directly to me (terryw$at$mdli.com).

 

Thanks for your interest.

 

Terry

 

 

Terry Wright

MDL Information Systems

14600 Catalina Street

San Leandro, CA 94577

 

Phone: 510-357-2222 ext. 1392

Email: terryw$at$mdli.com

 

------_=_NextPart_001_01C4B623.4C6D7D59-- From chemistry-request@ccl.net Wed Oct 20 13:53:50 2004 Received: from hotmail.com (bay4-dav27.bay4.hotmail.com [65.54.171.57]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9KIrnL3007816 for ; Wed, 20 Oct 2004 13:53:49 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 20 Oct 2004 12:06:01 -0700 Received: from 206.81.149.244 by BAY4-DAV27.phx.gbl with DAV; Wed, 20 Oct 2004 19:05:42 +0000 X-Originating-IP: [206.81.149.244] X-Originating-Email: [rwoodphd^at^msn.com] X-Sender: rwoodphd^at^msn.com From: "Richard Wood" To: Subject: Tinker questions Date: Wed, 20 Oct 2004 13:05:38 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0326_01C4B6A5.7EDF77D0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Message-ID: X-OriginalArrivalTime: 20 Oct 2004 19:06:01.0410 (UTC) FILETIME=[D6F94220:01C4B6D7] X-Spam-Status: No, hits=3.6 required=7.5 tests=HTML_30_40,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_0326_01C4B6A5.7EDF77D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all I have some questions about the use of Tinker. 1) I have a box of water that I'm trying to convert from a pdb file = into a Tinker xyz file. However, I'm having difficulty with the file = when it asks me to pick a forcefield. What should I do here? =20 2) When I originally installed the GUI, and ran dynamics, I could see = each step of the calculation on the screen. I then tried to get the = program to write to an arc file, which wouldn't work. Since then, all a = dynamics calculation does is write each step to a file. How can I go = back to seeing each step on the screen? 3) If I run dynamics from a command line, it generates an arc file, but = the GUI won't read it. Is there a reason for this? I suspect the = number of frames my be a problem? TIA, Richard Richard L. Wood, Ph. D. Computational Chemist Hyrum, UT 84319 ------=_NextPart_000_0326_01C4B6A5.7EDF77D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all
 
I have some questions about the use of=20 Tinker.
 
1)  I have a box of water that I'm = trying to=20 convert from a pdb file into a Tinker xyz file.  However, I'm = having=20 difficulty with the file when it asks me to pick a forcefield.  = What should=20 I do here? 
 
2) When I originally installed the GUI, = and ran=20 dynamics, I could see each step of the calculation on the = screen.  I=20 then tried to get the program to write to an arc file, which wouldn't=20 work.  Since then, all a dynamics calculation does is write each = step to a=20 file.  How can I go back to seeing each step on the = screen?
 
3) If I run dynamics from a command = line, it=20 generates an arc file, but the GUI won't read it.  Is there a = reason for=20 this?  I suspect the number of frames my be a problem?
 
TIA,
Richard
 
Richard L. Wood, Ph. = D.
Computational=20 Chemist
Hyrum, UT 84319
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