From chemistry-request@server.ccl.net Tue Jun 4 00:16:21 2002 Received: from ns-0.mssm.edu ([146.203.100.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g544GLC20301 for ; Tue, 4 Jun 2002 00:16:21 -0400 Received: from CONVERSION-DAEMON.ns-0.mssm.edu by ns-0.mssm.edu (PMDF V6.1 #38773) id <0GX500G01YJ04Y@ns-0.mssm.edu> for chemistry@ccl.net; Tue, 04 Jun 2002 00:16:12 -0400 (EDT) Received: from mssm.edu ([146.203.58.157]) by ns-0.mssm.edu (PMDF V6.1 #38773) with ESMTP id <0GX500EI9YJ0JI@ns-0.mssm.edu> for chemistry@ccl.net; Tue, 04 Jun 2002 00:16:12 -0400 (EDT) Date: Tue, 04 Jun 2002 00:15:00 -0400 From: root Subject: autodock 3.05 Sender: root@ns-0.mssm.edu To: chemistry@ccl.net Message-id: <3CFC3EC4.8F40EDDF@mssm.edu> Organization: Mount Sinai School of Medicine MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-3 i686) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi All, I was installing autodock 3.05 on my linux machine (redhat 7.3) following the steps mentioned at this website: http://www.biochemistry.unimelb.edu.au/pscotney/autodock/AutoDock-HOWTO.html Everything was going well till I came to step "Make autodock". I made the changes following the author's suggestion, I am getting following error: make: *** No rule to make target `main.cc', needed by `main.o'. Stop. I would appreciate any help. Thanks Sachchi. From chemistry-request@server.ccl.net Mon Jun 3 18:35:35 2002 Received: from sandmail01.sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g53MZTC03222 for ; Mon, 3 Jun 2002 18:35:31 -0400 To: chemistry@ccl.net Cc: judith.madeley@accelrys.com Subject: Accelrys Materials Studio Workshop in Cambridge, UK MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 From: jnauss@accelrys.com Message-ID: Date: Mon, 3 Jun 2002 15:35:07 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 06/03/2002 03:35:35 PM, Serialize complete at 06/03/2002 03:35:35 PM Content-Type: text/plain; charset="us-ascii" Accelrys will be holding two Materials Studio Training Workshops in their Cambridge office in July. An Introduction to Materials Studio on July 23rd This course provides an introduction to the functionality in Materials Visualizer, the core module in the Materials Studio suite of software. Participants learn how to use the powerful sketching and building tools allowing them to build a range of structures from simple molecules to crystal interfaces. They also learn how to manipulate the visualization tools including the advanced isosurfaces tools. Further details can be found at http://www.accelrys.com/training/matsci/workshops/matstudio.html An Introduction to Polymer Modelling with Materials Studio on July 24th and 25th This course provides an introduction to the polymer modelling functionality available in Materials Studio. This will cover the basics of building polymers through to calculating properties of polymers such as diffusion and miscibility. Modules covered are Discover, Amorphous Cell, DPD and Equilibria. Further details can be found at http://www.accelrys.com/training/matsci/workshops/polymer_modeling.html Customers can register on-line at http://www.accelrys.com/training/matsci/registration.php. -- Jeffrey L. Nauss, Ph.D. Manager US Training, Global Bioinformatics and Macromolecular Modeling 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 Mon Jun 3 15:38:21 2002 Received: from mr.usu.edu ([129.123.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g53JcLC32592 for ; Mon, 3 Jun 2002 15:38:21 -0400 Received: from pc3 (pc3.chem.usu.edu [129.123.3.37]) by mr.usu.edu (Postfix) with SMTP id 48CD01D3AB for ; Mon, 3 Jun 2002 13:38:24 -0600 (MDT) Reply-To: From: "Tapas Kar" To: Subject: Semiempirical IR/Raman spectra Date: Mon, 3 Jun 2002 13:36:19 -0600 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0005_01C20B03.A4DE3A70" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0005_01C20B03.A4DE3A70 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Hi: I am looking for freely available semiempirical program (MNDO etc) programs to calculate IR and Raman spectra for large molecules. Please help me to find such program. Thanks Tapas *********************************************** "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - ---------------------------------------------------------------------------- ---- Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu Web:http://www.chem.usu.edu/faculty/Tapas/index.html ------=_NextPart_000_0005_01C20B03.A4DE3A70 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi: I am=20 looking for freely available semiempirical program (MNDO etc) programs = to=20 calculate IR and Raman spectra for large molecules. Please help me to = find such=20 program.
Thanks
Tapas

***********************************************
"We owe a lot to the Indians, who taught = us how to=20 count, without
which no worthwhile scientific discovery could have = been=20 made."
         &n= bsp;           &nb= sp;           &nbs= p;        =20 - Albert Einstein=20 -
--------------------------------------------------------------------= ------------
Tapas=20 Kar, Ph. D
Department of Chemistry & Biochemistry
Utah State=20 University
Logan, UT 84322-0300

Tel: 435-797-7230
Fax:=20 435-797-3390
Email: tapaskar@cc.usu.edu
Web:http://www.chem.usu.edu/faculty/Tapas/index.html

 
------=_NextPart_000_0005_01C20B03.A4DE3A70-- From chemistry-request@server.ccl.net Mon Jun 3 16:08:03 2002 Received: from puck.reed.edu ([134.10.2.8]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g53K81C00680 for ; Mon, 3 Jun 2002 16:08:01 -0400 Received: (qmail 27235 invoked from network); 3 Jun 2002 20:07:17 -0000 Received: from rosencrantz.reed.edu (134.10.2.31) by puck.reed.edu with SMTP; 3 Jun 2002 20:07:17 -0000 Message-id: <6458782@rosencrantz.reed.edu> Date: 03 Jun 2002 13:07:56 PDT From: Alan.Shusterman@directory.reed.edu (Alan Shusterman) Subject: RTIL bonds and viscosity To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/enriched Content-Disposition: inline I am studying the chemical and physical properties of room-temperature ionic liquids (RTIL) like N-butylimidazolium tetrafluoroborate (bmim BF4). Can anyone point me at computational studies of these compounds? I'm particularly interested in the following properties: bond energies proton affinities solvent viscosity Also, is there a good way to predict viscosity using molecular models? Any leading references would be most appreciated. Thanks, -Alan ==== Alan Shusterman Department of Chemistry Reed College 3203 S.E. Woodstock Blvd. Portland, OR 97202 503-771-1112, ext. 7699 From chemistry-request@server.ccl.net Mon Jun 3 15:54:30 2002 Received: from web21305.mail.yahoo.com ([216.136.129.141]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g53JsUC00334 for ; Mon, 3 Jun 2002 15:54:30 -0400 Message-ID: <20020603195429.78699.qmail@web21305.mail.yahoo.com> Received: from [129.109.73.75] by web21305.mail.yahoo.com via HTTP; Mon, 03 Jun 2002 12:54:29 PDT Date: Mon, 3 Jun 2002 12:54:29 -0700 (PDT) From: Bruce Roberts Subject: IEJMD: Haruo Hosoya special issue To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Call for Papers: IEJMD special issue dedicated to Professor Haruo Hosoya on the occasion of the 65th birtday Guest Editor: Professor Jun-ichi Aihara Internet Electronic Journal of Molecular Design, http://www.biochempress.com Email: iejmd@yahoo.com You are cordially invited to contribute a paper to the special issue of the Internet Electronic Journal of Molecular Design, http://www.biochempress.com, dedicated to Professor Haruo Hosoya. The topic of the paper can be any original contribution regarding computer-assisted molecular design applications in chemistry, biochemistry, biology, chemical and pharmaceutical industry. The main scientific achievements of Professor Haruo Hosoya are presented below. Pioneer of mathematical chemistry: Establishment of new mathematical concepts, methodologies and proof techniques for giving mathematical meaning and interpretation to many important empirical rules in chemistry. * Introduction of topological Index, Z (1971) (Godfather of topological index) characterization, classification, identification of graphs correlation of Z index with thermodynamic properties (bp, entropy, etc.) graph-theoretical molecular orbital theory, bond order, aromaticity, etc. QSPR study of thermodynamic properties of alkanes * Introduction of counting polynomials into chemical thinking Z-counting polynomial (1971), sextet polynomial (1975), king polynomial (1977), Wheland polynomial (1979), rotational polynomial (1988) operator technique for obtaining the recursion formulas (1983) * Graph-theoretical analysis of Hueckel molecular orbital theory extended Hueckel rule (1975), benzene character (1980), topological bond order (1976) * Quantum-chemical interpretation of oxidation number and its extension to organic molecules (1982) electron number analysis around the component atoms of molecules using ab initio MO wavefunction * Mathematical foundation of organic electron theory (Robinson and Ingold) (1999) proof of the diagramamatic recipe of organic electron theory discovery of abnormal tunneling electron transfer in large polycyclic aromatic hydrocarbons (2001) * Derivation of the closed formula giving the degeneracy of the angular parts of atomic wavefunction of n-dimensional hydrogen atom (1999) * Damping factor for rapid convergence of alternating series in the calculation of Madelung constants (1982) Haruo Hosoya was born in 1936, graduated from the University of Tokyo in 1959, obtained the D.Sc. Degree (equivalent to the Ph.D. degree in the USA) from the same university in 1964. In 1969 He was appointed Associate Professor of Ochanimizu University (Tokyo) and in 1984 promoted to (Full) Professor there. During 1990-1992 he served as Dean of the Faculty of Science (to which his chemistry department belongs). In 2002 he retired > from Ochamimizu University. ************** If you decide to contribute a paper, please note these important deadlines: Title of manuscript and authors submitted by Email to iejmd@yahoo.com : June 30, 2002 Early submission: manuscript submitted by Email to iejmd@yahoo.com : July 30, 2002 Late submission: manuscript submitted by Email to iejmd@yahoo.com : August 30, 2002 If you want to contribute a paper, but need more time for the submission, send an E-mail with an estimated time of submission. If you have any questions regarding this special issue, please contact me by E-mail at: iejmd@yahoo.com Instructions for Authors To obtain a Word file with Instructions for Authors send an Email to iejmd@yahoo.com The Internet Electronic Journal of Molecular Design publishes original contributions regarding 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 (QSPR) 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 General Only original papers are considered for publication in the Internet Electronic Journal of Molecular Design. Submission of an article is understood to imply that it has not previously been published in any language, that it is not considered for publication elsewhere, and that if accepted for publication it will not be published elsewhere. Organization of Manuscript The entire manuscript, including mathematical equations, chemical structures, tables, and figures must be prepared in electronic form and submitted as Word for Windows files. Use only fonts that come with Windows software. For the text use Times New Roman size 12. For all special characters (e.g., Greek characters) use the font Symbol. Use carriage returns only to end headings and paragraphs, not to break lines of text. Automatic hyphenation should be turned off. Do not insert spaces before punctuation. Verify the correct spelling for the final version with the Spelling and Grammar function of Word. Mathematical Equations All mathematical equations must be prepared with the equation editor from Word and placed in the proper place. The equations are labeled in the order in which they appear in the text with Arabic numbers in parentheses aligned to the left margin. In writing the equations use the following rules: vectors and matrices with bold, functions such as log, sin, cos normal, and all other mathematical symbols with italic. Tables Each table is numbered with Arabic numbers and must have a caption that briefly explains the contents of the table. Column headings should be brief and must indicate units. Explanations can be given in footnotes labeled with a, b, as italic superscripts. Figures Figures are numbered consecutively with Arabic numbers. Each figure must be referred to in the text and must have a caption that briefly explains the contents of the figure. Chemical Structures All chemical structures should be prepared with a suitable graphics program, such as: ISIS/Draw from MDL Information Systems, http://www.mdli.com/ ACD/ChemSketch from Advanced Chemistry Development, http://www.acdlabs.com/ ChemWindow from SoftShell, http://www.softshell.com/ ChemDraw from CambridgeSoft, http://www.camsoft.com/ Use the following settings for chemical drawings: text font: Times New Roman text size: 10 pt standard bond/grid length: 16 pt line width: 0.7 pt stereo bond width: 2.0 pt double/triple bond spacing: 20% of width down bond hashes: 2.5 pt All compounds must be labeled with Arabic numbers, with font Times New Roman, size 10, bold. References In the text references must be numbered sequentially in the order of their appearance with Arabic numbers in square brackets before punctuation, e.g. [1,2]; [3-6]; [1,5]. All references must be collected in numerical order at the end of the manuscript under the heading "REFERENCES". Journals. Titles of journals must be abbreviated according to the Chemical Abstracts Service Source Index. Give the list of all authors, title (with the first letter of each main word capitalized), journal (italic), year (bold), volume (italic), and pages: [1] H. Kubinyi, Variable Selection in QSAR Studies. I. An Evolutionary Algorithm, Quant. Struct.-Act. Relat. 1994, 13, 285-294. [2] J. G. Topliss and R. P. Edwards, Chance Factors in Studies of Quantitative Structure-Activity Relationships, J. Med. Chem. 1979, 22, 1238-1244. [3] W. Zheng, S. J. Cho, and A. Tropsha, Rational Design of a Targeted Combinatorial Chemical Library with Opiatelike Activity, Int. J. Quantum Chem. 1998, 69, 65- 75. Books. Give the list of all authors, title (with the first letter of each main word capitalized), publisher, town, edition (if more than one has been published), date, volume, and pages (if necessary): [4] L. B. Kier and L. H. Hall, Molecular Connectivity in Structure-Activity Analysis, Research Studies Press, Letchworth, 1986, pp. 20-25. Chapters from multi-author books. [5] H. Kubinyi, Comparative molecular field analysis (CoMFA); in: The Encyclopedia of Computational Chemistry, Eds. P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schaefer III, and P. R. Schreiner, John Wiley & Sons, Chichester, 1998, pp. 448- 460. ************** __________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com From chemistry-request@server.ccl.net Tue Jun 4 01:17:54 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g545HsC21350 for ; Tue, 4 Jun 2002 01:17:54 -0400 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.0) with ESMTP id g545Hs110542; Tue, 4 Jun 2002 01:17:54 -0400 (EDT) Date: Tue, 4 Jun 2002 01:17:53 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Your coordinator, Jan Labanowski, needs your help... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Subscribers, You may be aware that, as with other states, Ohio has been hit with a budget shortfall. Given this, I need your support more than ever. I am asking for your help in maintaining the Computational Chemistry List (CCL). When you look at our Supporters Page (http://www.ccl.net/cgi-bin/donors), you will notice that it has started to shrink (the script does not show entries that are older than a year). CCL is essentially a virus and spam-free e-mail discussion service with an associated web site containing archives, extensive document and software holding and search capability. In order to operate, CCL needs hardware, backups, upgrades, and security, which is a constant struggle with changing technologies. I employ students to help me run it, since I would not be able to do it all by myself. While they learn a lot of new things, they also need their wages. To make it easier for you to support CCL we offer two options: Option 1: Services ======== We will provide you with a quotation and invoice -- just like a normal mail-order purchase (we even can accept credit cards). You would: a) buy a set of CDs with CCL archives for $250; or b) place your job advertisement on our job site: http://www.ccl.net/jobs (you pay $100 when a candidate is found). Option 2: Donations ========= In your jurisdiction, gifts towards CCL may be tax deductible. You will get a donation letter from the Ohio State University Department of Development that can be used for tax purposes. We will accept any donation amount, but donations over $1,000 allow you to sponsor a CCL Web page of your choice and have your logo displayed there. In short, if you want to help, please look at the links from our front page: http://www.ccl.net or don't hesitate to contact me at jkl@ccl.net. I would love {:-)} to talk with you about helping CCL. Really... Ask yourself, how much is CCL worth for you? For example, did you hire someone thanks to a CCL job ad? I am getting a lot of praise for this service, because it is considered as very focused and often more successful than expensive ads in scientific journals and professional employment services. TRY IT, it costs NOTHING. But if you are happy with it, please help support us. Or how many times has a question to CCL saved you many hours of digging through research literature or past experimentations? If you are a graduate student or a postdoctoral researcher, please tell your boss about CCL and how important it is to you. Ask them to help. They should understand, given the economic climate these days. If many of you help, even with smaller amounts, we will be OK here... CCL is a real cost to Ohio Supercomputer Center. CCL is facing a certain reduction in capabilities and possible demise if we do not receive funding > from outside sources. You might think that you could live without CCL, but would you really be better off without it? I have a list of faithful supporters, who always respond to these appeals. I really hate to rely on the same people and institutions over and over again. There are about 3000 people using CCL and it must be worth something if you all use it. But last time I asked for help a few months month ago, I received a single check for $20.00 and a few e-mails: "Jan, I am not doing so great financially lately, but if you really need, I will try to help again...". I understand that you are all busy... But please help this time... Do not wait for other guys to help and put it off when you can do it at higher amount and comfortably... Help me now, with what you can -- it will be money well spent, and you will feel better knowing that we at CCL really appreciate you and that you are a part of it all. Jan Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Tue Jun 4 03:18:54 2002 Received: from relay2.softcomca.com ([168.144.1.68]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g547IOC23780 for ; Tue, 4 Jun 2002 03:18:54 -0400 Received: from M2W056 ([168.144.108.56]) by relay2.softcomca.com with Microsoft SMTPSVC(5.0.2195.4905); Tue, 4 Jun 2002 03:18:23 -0400 X-Originating-IP: 202.185.72.155 X-URL: http://www.mail2web.com/ Subject: autodock-placing ligand ; mutate structure Sender: "nepenthes@vplaces.net" From: "nepenthes@vplaces.net" Date: Tue, 4 Jun 2002 03:18:23 -0400 To: "chemistry@ccl.net" Reply-To: nepenthes@vplaces.net X-Priority: 3 X-MSMail-Priority: Normal MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Mailer: JMail 3.7.0 by Dimac (www.dimac.net) Message-ID: X-OriginalArrivalTime: 04 Jun 2002 07:18:23.0849 (UTC) FILETIME=[0352D590:01C20B98] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-Printable to 8bit by server.ccl.net id g547IsC23783 Hi CCLers, I have a question regarding Autodock usage. Does anybody find any significant difference in the docking result when it comes to placing the ligand in the grid box? I found that when I place my ligand at the corner end of the box, I can find better interactions between the docked ligand and protein as compared to placing the ligand at the binding site itself. The energy of binding found was lower and there seemed to be more conformations with interactions as found in the crystal structure. Secondly, I would like to mutant one residue of my protein manually by substituting the residue with another. Can anybody suggest how I may optimize the whole protein structure or do I need to optimize it at all? I don't expect any significant change in the structure of the protein but i'm not quite sure if I can just optimize the residue itself without affecting the whole protein. My concern is that the side chain of the new residue may not be accurately represented without some form of refinement. Thank you kindly for any suggestions/feedback. Regards, Rowyna -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From chemistry-request@server.ccl.net Tue Jun 4 04:21:46 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g548LjF25645 for ; Tue, 4 Jun 2002 04:21:46 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0GX6001AN9W8LZ@mailstudenti.unimi.it> for chemistry@ccl.net; Tue, 04 Jun 2002 10:21:44 +0200 (MEST) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0GX6009TM9W9GF@smtp.unimi.it> for chemistry@ccl.net; Tue, 04 Jun 2002 10:21:45 +0200 (MEST) Date: Tue, 04 Jun 2002 10:24:05 +0200 From: Giulio Vistoli Subject: New release of VEGA1.4.1 To: CCL Message-id: <000e01c20ba1$30d26450$424f959f@Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Content-type: multipart/alternative; boundary="Boundary_(ID_a0nYETfL22ipGq/uyur5hQ)" X-Priority: 3 X-MSMail-priority: Normal This is a multi-part message in MIME format. --Boundary_(ID_a0nYETfL22ipGq/uyur5hQ) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Dear collegues, we are glad to announce the new final release of VEGA1.4.1 ( http://users.unimi.it/~ddl ) our well known program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). New features of VEGA1.4.1: - Interaction energy evaluation for the analysis of the docking results. - New console with direct command interface. - Avanced cut, copy & paste routines. - Predator plugin for protein secondary structure prediction. - GAMESS cartesian file loader and saver. - Glass windows (Windows NT/2000/XP only). - Some bug fixes. Release 1.4.1: - GAMESS cartesian file loader and saver. - Fix: HyperChem .hin loader. - Fix: XYZ detection. - Fix: Insight surface loader. - Fix: generation of solvent cluster. - Fix: Pentium III-M CPU detection. - Win32: interaction energy evaluation for the analysis of the docking results. - Win32: new console with direct command interface. - Win32: advanced cut, copy & paste routines. - Win32: Predator plugin for protein secondary structure prediction. - Win32: glass windows (Windows NT/2000/XP only). - Win32: PLUGINGET command added. - Win32: Dhrystone plugin 1.1. - Win32: updated DevIL DLLs to 1.3.1 Giulio Vistoli & Alessandro Pedretti Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317522 Fax +39-02-50317565 giulio.vistoli@unimi.it http://users.unimi.it/~ddl --Boundary_(ID_a0nYETfL22ipGq/uyur5hQ) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
Dear collegues,

we are glad to announce the new final release of VEGA1.4.1
( http://users.unimi.it/~ddl ) our well known program to convert, manage and
visualize of 3D structures for several platforms (Win32, Linux, Irix,
AmigaOs).
 
 
 
New features of VEGA1.4.1:
 
- Interaction energy evaluation for the analysis of the docking results.
- New console with direct command interface.
- Avanced cut, copy & paste routines.
- Predator plugin for protein secondary structure prediction.
- GAMESS cartesian file loader and saver.
- Glass windows (Windows NT/2000/XP only).
- Some bug fixes.
 
 
Release 1.4.1:

- GAMESS cartesian file loader and saver.
- Fix: HyperChem .hin loader.
- Fix: XYZ detection.
- Fix: Insight surface loader.
- Fix: generation of solvent cluster.
- Fix: Pentium III-M CPU detection.
- Win32: interaction energy evaluation for the analysis of the docking results.
- Win32: new console with direct command interface.
- Win32: advanced cut, copy & paste routines.
- Win32: Predator plugin for protein secondary structure prediction.
- Win32: glass windows (Windows NT/2000/XP only).
- Win32: PLUGINGET command added.
- Win32: Dhrystone plugin 1.1.
- Win32: updated DevIL DLLs to 1.3.1

Giulio Vistoli & Alessandro Pedretti

 

Giulio Vistoli
Istituto di Chimica Farmaceutica e Tossicologica
Viale Abruzzi, 42
I-20131 Milano
Italia
Tel. +39-02-50317522
Fax +39-02-50317565
giulio.vistoli@unimi.it
http://users.unimi.it/~ddl

 

 

--Boundary_(ID_a0nYETfL22ipGq/uyur5hQ)-- From chemistry-request@server.ccl.net Tue Jun 4 04:28:17 2002 Received: from smtpscan-nl1.vscan.dsm-group.com ([163.175.162.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g548SHF25887 for ; Tue, 4 Jun 2002 04:28:17 -0400 Received: from nlgln20ntms920.GLN20.DSM-GROUP.COM (localhost [127.0.0.1]) by smtpscan-nl1.vscan.dsm-group.com (8.9.3/8.8.5-1.2.2m-19990317) with ESMTP id KAA22483 for ; Tue, 4 Jun 2002 10:28:16 +0200 (MET DST) Received: by nlgln20ntms920.gln20.dsm-group.com with Internet Mail Service (5.5.2653.19) id ; Tue, 4 Jun 2002 10:28:05 +0200 Message-ID: <6D47A7D05774D411959200508BDF739A024382FA@nlgln50ntms001.gln51.dsm-group.com> From: "Coussens, Betty" To: "'chemistry@ccl.net'" Subject: TDDFT in Gaussian Date: Tue, 4 Jun 2002 10:28:04 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="ISO-8859-1" Dear all, I have been using Gaussian98 Revision A.5 for performing a number of TDDFT calculations on norbornane and norbornane like systems. As I was performing this type of computations for the first time I tried reproducing the spectra presented in a recent paper by Ando et al. (Jpn. J. Appl. Phys. Vol 41 (2002) pp. L105-L108). Unfortunately, I was not able to do so. As I had no idea why, I contacted the authors of this paper. They were so kind to send me the output of the TDDFT computation on norbornane they performed themselves. Comparing their results with mine, it appeared that although the excitation energies were similar, the oscillator strengths were totally different. The only difference between mine and their calculation is that I was using symmetry whereas they were not. I had the plan to use their optimized norbornane structure and perform exactly the same calculation as they did. However, in the meantime, I checked the CCL for messages on TDDFT. Based on these messages, it seems that I have to conclude that the computation of oscillator strenghts was originally not correctly implemented in Gaussian. As I am using Revision A.5 whereas Ando et al. have been using revision A.9 this could probably also explain why I am not able to reproduce the results of the Ando group. Can anybody comment on this? Thanks in advance! Betty Disclaimer 1. This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. 2. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately. This e-mail is confidential and may be legally privileged. DSM does not guarantee that the information sent and/or received by or with this e-mail is correct and does not accept any liability for damages related thereto. From chemistry-request@server.ccl.net Tue Jun 4 08:30:03 2002 Received: from gwia.kvl.dk ([130.225.43.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g54CU2F31036 for ; Tue, 4 Jun 2002 08:30:02 -0400 Received: from kvl.dk (pwt.kemi.kvl.dk [130.225.43.124]) by gwia.kvl.dk; Tue, 04 Jun 2002 14:24:41 +0200 Sender: pwt@ccl.net Message-ID: <3CFCB3C0.558E5919@kvl.dk> Date: Tue, 04 Jun 2002 14:34:08 +0200 From: Peter Waaben Thulstrup Organization: Royal Veterinary and Agricultural University X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.10-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: G98 TD/CIS Opposite sign of the components of length- and velocity dipole moments? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL, I have some questions regarding the output os CIS and TD jobs in G98 (Rev. A7). I can't find anything on these issues in Gaussian documentation or past CCL posts, although the questions are rather simple. So I hope it makes sense... The output of TD and CIS calculations give the x, y, and z components of the "Ground to excited state Transition electric dipole moments", "Ground to excited state transition velocity dipole Moments", and the "Ground to excited state transition magnetic dipole Moments". 1) Why are the components of the electric and velocity derived transition dipole moments oppositely signed? I thought that they should be identical in a complete basis. I would have thought that the sign ought to be the same. Which values should I trust? 2) Is it possible to say which of the computed oscillator strengths (dipole-length or dipole-velocity derived) provide the best estimate of experimental absorption intensities? 3) I suppose that the computed electric and magnetic dipole moments are origin dependent. But are the magnetic transition dipole moments derived in a manner which make them related in to the transition velocity dipole moments, rather than the transition electric dipole moments? (e.g. in terms of origin dependence etc.) Any help or comments will be greatly appreciated! Peter -- Peter W. Thulstrup Chemistry Department / Royal Veterinary and Agricultural University Thorvaldsensvej 40 / DK-1871 Frederiksberg C / Denmark Phone: +45 35282464 / Fax: +45 35282398 / E-mail: pwt@kvl.dk From chemistry-request@server.ccl.net Tue Jun 4 11:55:22 2002 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g54FtMF03495 for ; Tue, 4 Jun 2002 11:55:22 -0400 Received: from [165.91.177.32] (account yubofan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.5.2) with ESMTP id 1604737 for CHEMISTRY@ccl.net; Tue, 04 Jun 2002 05:53:06 -0500 Sender: yubo@ccl.net Message-ID: <3CFCE2E9.6A6C3A71@mail.chem.tamu.edu> Date: Tue, 04 Jun 2002 10:55:22 -0500 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Compiling G98 A11 on Linux Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id g54FtMF03496 Dear Sir/Lady, We've got a copy of Gaussian 98 A11 and we tried to compile it on our Linux box. We used the Atlas library provided in the CD-ROM and PGI F77 to compile G98A11. After it's compiled, I tried to run test jobs but failed. G98 always gives the error message--g98: error while loading shared libraries: g98: undefined symbol: flush_. Can you help me to solve this problem? My computer is a P4 Xeon dual processor Linux box. BTW, there is only 256KB cache in our P4 chips. How can we change the default value, 512KB, into 256KB in the Atlas library? I also tried the libraries, which are optimized for P4, downloaded on the web Thank you very much. I am looking forward to receiving your reply as soon as possible. Sincerely Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Tue Jun 4 12:22:38 2002 Received: from goshen.rutgers.edu ([165.230.180.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g54GMcF04437 for ; Tue, 4 Jun 2002 12:22:38 -0400 Received: from eden.rutgers.edu (unknown [165.230.180.134]) by goshen.rutgers.edu (Postfix) with ESMTP id 356AE212E0 for ; Tue, 4 Jun 2002 12:22:38 -0400 (EDT) Received: by eden.rutgers.edu (Postfix, from userid 37805) id 0D631335C3; Tue, 4 Jun 2002 12:22:37 -0400 (EDT) Date: Tue, 4 Jun 2002 12:22:37 -0400 (EDT) From: Jianquan Chen X-Sender: jianquan@er6.rutgers.edu To: chemistry@ccl.net Subject: calculate charge using MOPAC In-Reply-To: <6D47A7D05774D411959200508BDF739A024382FA@nlgln50ntms001.gln51.dsm-group.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I need to add charge to thousands of molecules. MOPAC is free but slow and sometimes changes the moleucular structure. I don't know how MOPAC works. I have 2 questions. Can I run MOPAC without optimizing the molecular structure? Is there any way to accelate MOPAC? I don't need very accurate charges. Thanks a lot for any response. Jianquan Chen From chemistry-request@server.ccl.net Tue Jun 4 10:58:27 2002 Received: from biosino.org ([202.127.18.238]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g54EwPF02296 for ; Tue, 4 Jun 2002 10:58:26 -0400 Received: from mao [202.127.18.233] by biosino.org (SMTPD32-6.04) id A59111390200; Tue, 04 Jun 2002 22:58:25 +0800 Date: Tue, 4 Jun 2002 23:0:38 +0800 From: "xmao@biosino.org" To: "chemistry@ccl.net" Subject: reactivity of a molecule X-mailer: FoxMail 3.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Message-Id: <200206042258103.SM00279@mao> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g54EwRF02297 Hello Everyone: I wonder if there are some tutorails on the website or some references that teach how to get the reactivity of a molecule from the quantum chemistry calculation results. Ö Àñ£¡ xmao xmao@biosino.org From chemistry-request@server.ccl.net Tue Jun 4 12:11:52 2002 Received: from goshen.rutgers.edu ([165.230.180.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g54GBqF04105 for ; Tue, 4 Jun 2002 12:11:52 -0400 Received: from eden.rutgers.edu (unknown [165.230.180.134]) by goshen.rutgers.edu (Postfix) with ESMTP id D97862018E for ; Tue, 4 Jun 2002 12:11:52 -0400 (EDT) Received: by eden.rutgers.edu (Postfix, from userid 37805) id 97DF7335C2; Tue, 4 Jun 2002 12:11:52 -0400 (EDT) Date: Tue, 4 Jun 2002 12:11:52 -0400 (EDT) From: Jianquan Chen X-Sender: jianquan@er6.rutgers.edu To: chemistry@ccl.net Subject: convert 2d to 3d In-Reply-To: <6D47A7D05774D411959200508BDF739A024382FA@nlgln50ntms001.gln51.dsm-group.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I need to convert thousands of 2d sdf file to 3d mol2 files and add charges. But I met a problem. Concord and Corina is too expensive. Concord is built in the alchemy2000 that is not very expensive. I have a question before I buy Alchemy2000. Can I run Alchemy2000 in batch mode? I mean, can I use alchemy2000 to convert thousands of 2d file to 3d automatically. Thank you in advance. jianquan chen From chemistry-request@server.ccl.net Tue Jun 4 20:55:11 2002 Received: from front1.chartermi.net ([24.213.60.123]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g550tAF27713 for ; Tue, 4 Jun 2002 20:55:10 -0400 Received: from [24.247.80.10] (HELO quantumnt) by front1.chartermi.net (CommuniGate Pro SMTP 3.5.3) with SMTP id 110441054 for chemistry@ccl.net; Tue, 04 Jun 2002 20:54:46 -0400 Message-ID: <000b01c20c2b$967bd4a0$0401a8c0@quantumnt> From: "Jim Kress" To: "CCL" Subject: guess=cards in G98W Date: Tue, 4 Jun 2002 20:54:45 -0400 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 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 I am trying to read SCF vectors in G98W to do some properties analysis. I have 281 MOs to read. G98W does just fine until it gets to number 229 when it just fails with a popup that says: "Severe Error Message # 2070" "The processing of the last link ended abnormally. All processing has been aborted." I do notice that when I open the file, G98W does not load all the lines of the input file into the "Existing File Job Edit" screen. Indeed, it only loads up to part of vector 230 in the Molecule Specification field and the text area in the Molecule Specification field is grayed out and is not editable. I can find no information about this error message (or how to fix it) in the G98W documentation. Does anyone know how to fix this problem or is G98W limited with respect to the number of vectors can be read (or the number of characters allowed in the Molecule Specification field is limited)? Any help is appreciated. Edited (for brevity) input file can be found below. Jim # RHF/LanL2MB 6D guess(only,cards,nosymm) test read vectors 2,1 RU 3.0188000000 4.2740000000 4.4842000000 H 2.7252000000 2.9358000000 3.4880000000 RU 2.4127000000 1.4474000000 4.7860000000 RU 1.8666000000 4.0731000000 7.1800000000 C 1.1607000000 3.8043000000 5.1929000000 C 0.7056000000 2.6426000000 5.8480000000 H -0.2477000000 2.5314000000 5.8798000000 ... many more atoms H 0.3276000000 7.1401000000 6.5129000000 H 1.8425000000 7.5252000000 6.6282000000 (5X,5E15.8) -1 1 1 3.71689355E-03 5.54340362E-03-2.61747088E-05-4.06952110E-05 3.35982883E-05 1 2-1.71202103E-03-2.45538324E-03 2.58117751E-03-1.28530048E-03-1.17477090E-03 ... many more vectors 29 54-2.27644023E-03 1.64337289E-02-2.34432536E-02 3.76168489E-02-1.45246824E-03 29 55-2.86839519E-02-3.42897982E-02 4.69872260E-02-2.07960459E-02 1.57208327E-01 29 56-7.92854398E-02 2.49396272E-01 3.18211813E-01-4.59048732E-01 1.29009132E-01 29 57 9.79215915E-02 30 1 1.30355576E-03-8.14503723E-03 2.69564660E-04-7.45512414E-04 1.09297039E-03 30 2 1.48362124E-02-5.99025118E-02 7.33172394E-02-4.97928630E-03-7.16157921E-03 30 3 3.74119193E-03 2.42501275E-03-1.30562264E-02 9.48387741E-04 3.03738151E-03 ... many more vectors From chemistry-request@server.ccl.net Tue Jun 4 22:39:21 2002 Received: from rwcrmhc52.attbi.com ([216.148.227.88]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g552dKF30837 for ; Tue, 4 Jun 2002 22:39:21 -0400 Received: from daveg-lifebook.cachesoftware.com ([12.224.212.36]) by rwcrmhc52.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020605023915.MDLG2751.rwcrmhc52.attbi.com@daveg-lifebook.cachesoftware.com>; Wed, 5 Jun 2002 02:39:15 +0000 Message-Id: <5.1.0.14.0.20020604190716.039d3340@pop3.norton.antivirus> X-Sender: (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 04 Jun 2002 19:17:43 -0700 To: Jianquan Chen From: David Gallagher Subject: Re: calculate charge using MOPAC Cc: chemistry@ccl.net In-Reply-To: References: <6D47A7D05774D411959200508BDF739A024382FA@nlgln50ntms001.gln51.dsm-group.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Jianquan 1. MOPAC can run just an "SCF" which does not change the geometry. This is the fastest way to get partial charges. 2. The new linear-scaling versions of MOPAC can calculate up to 20,000 atoms in just a few hours on a Windows desktop computer. With "MOPAC 2002", an SCF on a 641 atom protein takes about 3 minutes on a 1000 MHz Pentium III. There is more information at http://www.cachesoftware.com/mopac/index.shtml David Gallagher, Fujitsu At 12:22 PM 6/4/2002 -0400, Jianquan Chen wrote: >Hi, >I need to add charge to thousands of molecules. MOPAC is free but slow and >sometimes changes the moleucular structure. I don't know how MOPAC >works. I have 2 questions. >Can I run MOPAC without optimizing the molecular >structure? >Is there any way to accelate MOPAC? I don't need very accurate charges. > >Thanks a lot for any response. > > >Jianquan Chen > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Jun 4 22:35:42 2002 Received: from web21303.mail.yahoo.com ([216.136.129.192]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g552ZgF30766 for ; Tue, 4 Jun 2002 22:35:42 -0400 Message-ID: <20020605023541.52016.qmail@web21303.mail.yahoo.com> Received: from [203.196.129.98] by web21303.mail.yahoo.com via HTTP; Wed, 05 Jun 2002 03:35:41 BST Date: Wed, 5 Jun 2002 03:35:41 +0100 (BST) From: =?iso-8859-1?q?Ishita=20sharma?= To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Sir, I am pooja,just joined into the field of molecular modeling in INDIA.i have a peptide which has a sequence GEWTWDDATKTWTWTEGGGGFALFALFA The first part of this sequence that is GEWTWDDATKTWTWTE is known to have a beta-hairpin structure and the other part GGGG is a linker FALFALFA forms a helix,i wish to know how the peptide will fold if i join all these together ,i ahve the pdb file for GEWTWDDATKTWTWTE and for the other part i have generated using INSIGHTII ,so i have a pdb file for the entire sequence which corresponds to a beta-beta-alpha motif,i just want to know whether it will actually make this motif using AMBER(molecular dynamics and minimisation).Is AMBER the correct choice or should i use some other software as i have been told that it is not necessary that AMBER would predict the correct structure,do you have any idea where else this kind of peptide structure prediction studies are carried out. Waiting for your reply Thanks with regards pooja __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page > from News and Sport to Email and Music Charts http://uk.my.yahoo.com From chemistry-request@server.ccl.net Tue Jun 4 22:39:30 2002 Received: from rwcrmhc52.attbi.com ([216.148.227.88]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g552dTF30850 for ; Tue, 4 Jun 2002 22:39:29 -0400 Received: from daveg-lifebook.cachesoftware.com ([12.224.212.36]) by rwcrmhc52.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020605023923.MDPY2751.rwcrmhc52.attbi.com@daveg-lifebook.cachesoftware.com>; Wed, 5 Jun 2002 02:39:23 +0000 Message-Id: <5.1.0.14.0.20020604193320.028be850@pop3.norton.antivirus> X-Sender: (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 04 Jun 2002 19:44:05 -0700 To: "xmao@biosino.org" From: David Gallagher Subject: Re: reactivity of a molecule Cc: "chemistry@ccl.net" In-Reply-To: <200206042258103.SM00279@mao> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g552dUF30851 Hi Xmao, Frontier densities and superdelocalizabilities calculated according to Fukui's method are one way to estimate or visualize reactivity such as susceptibility to electrophilic, nucleophilic or radical attack. There is a free multimedia movie on "Reactivity" at http://www.cachesoftware.com/cache/applications.shtml that includes the application of Fukui's approach as well as the use of frontier molecular orbitals and electrostatics from quantum chemistry calculations. http://www.cachesoftware.com/movies/ReactivityMovie.exe Regards, David Gallagher, Fujitsu At 11:00 PM 6/4/2002 +0800, xmao@biosino.org wrote: >Hello Everyone: > I wonder if there are some tutorails on the website or some > references that teach how to get the reactivity of a molecule from the > quantum chemistry calculation results. > > > > Ö >Àñ£¡ > > xmao > xmao@biosino.org > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Jun 4 22:14:04 2002 Received: from smtp02.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g552E3F30161 for ; Tue, 4 Jun 2002 22:14:04 -0400 Received: from clqxm (unknown [211.68.8.218]) by smtp02.sohu.com (Postfix) with ESMTP id 000E36ACA5 for ; Wed, 5 Jun 2002 10:13:47 +0800 (CST) Message-ID: <000701c20c37$8d09a7b0$da0844d3@domain> From: "ch" To: Subject: OPLSAA set for carbohydrate Date: Wed, 5 Jun 2002 10:20:15 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id g552E4F30162 Dear CCLer: I am assigning atom types to cyclodextrin. I do not make sure which types are suitable to C5-C6-O-H and C4-C5-C6-O. The OPLSAA literature (J Comp Chem 1997, 18, 1955-1970) listed torsional parameters for carbohydrates in Table 5, and said "the torsional parameters describing the C-C-O-H torsion of simple alcohols do not optimally describe the energetics of carbohydrates, so anew set was determined...." Does this mean that the torsional parameters describing the C-C-O-H and C-C-C-O torsion of simple alcohols do not optimally describe C5-C6-O-H and C4-C5-C6-O? And is there torsional parameters available for C-C-C-O in alcohols? thank you very much for any advices. Chen