From chemistry-request@server.ccl.net Wed Mar 15 15:56:33 2000 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA31660 for ; Wed, 15 Mar 2000 15:56:32 -0500 Received: from [130.126.120.117] (maccupertino.ks.uiuc.edu [130.126.120.117]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id OAA22135; Wed, 15 Mar 2000 14:56:32 -0600 (CST) User-Agent: Microsoft Outlook Express Macintosh Edition - 5.01 (1630) Date: Wed, 15 Mar 2000 14:56:33 -0600 Subject: BioCoRE - a structural biology portal From: Gila Budescu To: Message-ID: In-Reply-To: <200003152041.OAA06464@venezia.ks.uiuc.edu> Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Please look at http://www.ks.uiuc.edu/Research/collaboratory/ for an instant fulfillment of your wishes. The project started on 2/99 and first official release was announced on 2/2000. We are looking forward to supporting your work. Gila Budescu regarding Liew Fui fah's message: >From owner-chemistry@server.ccl.net Tue Mar 14 23:12 CST 2000 Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id XAA19730; Tue, 14 Mar 2000 23:12:20 -0600 (CST) Received: (from root@localhost) by server.ccl.net (8.8.7/8.8.7) id XAA25314 for ccl3; Tue, 14 Mar 2000 23:47:35 -0500 Received: from gw5smtp.um.edu.my ([202.185.112.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id WAA24979 for ; Tue, 14 Mar 2000 22:29:05 -0500 Received: from Gwdom1-Message_Server by gw5smtp.um.edu.my with Novell_GroupWise; Wed, 15 Mar 2000 11:29:06 +0800 Message-Id: X-Mailer: Novell GroupWise 5.5 Date: Wed, 15 Mar 2000 11:28:44 +0800 From: "Liew Fui fah" To: Subject: CCL:Molecular Modeling - expert opinion needed Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id WAA24980 Sender: "Computational Chemistry List" Errors-To: chemistry-request@ccl.net Precedence: bulk Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 3801 Dear CCLers, Nowadays, Internet has become a tool for scientists in order to perform their work efficiently. Almost every one of us relies on the Internet to have discussion, looking for information and communicating with others. Indeed, through Internet we are effectively engaged with research, publications and information sharing that need collaboration with geographically dispersed colleagues. With a thought of fully utilizing the strength of Internet, I foresee there is a possibility to develop a web based molecular modeling station/portal, that would allow chemists to carry out experiment work, share information and modeling results with just a simple login to the server through an Internet browser. The molecular modeling engine, computing facilities and the working space are provided by the station. In order to carry out an analysis on this idea, I need expert opinion from fellow CCLers as to inspect the need and how should such a web based molecular modeling station perform. Please kindly give your opinions from a user or developer*s perspective with respect to the following aspects. (These are some basic guidelines for the survey, you are most welcome to add additional comments) A. Interface - What are the interface features that you would like to see and use when manipulating your structure? Beside the common editing and browsing tools, you are welcome to suggest new feature the meet your requirements. - Would you like to have an interface setting that match the way you want to work? - How do you like the information of transition states, molecular properties, orbitals, vibration, electronic spectrum, etc to be displayed? - Which molecular modeling package(s) that has the user interface that you like most. B. Modeling Methods - What are the general features / methods that are a *must* for a molecular modeling package? - What modeling methods are you using? - What are the advance characteristics of a molecular modeling package that will meet you requirements? - Please suggest the molecular modeling package(s) that you like to use most in terms of it accuracy and ease to use. C. Platform - Since it will be a web based molecular modeling station, it is ideal to have access from multi-platform machine. As a reference, please suggest the platforms that most of the chemists engage with while they carry out their work. - Would you like to have a direct access to the web based station at your current working platform? - What platform do you think that is most capable to operate as a server which can handle large amount of job load and provide enough storage? D. Technologies - Do you think that Java will meet most of the web based application requirements while incorporating various plug-ins and formats (e.g. XML, SVG). What is your comment on this particular technology? - Please suggest other technologies that you think is powerful in developing a web based chemical application. (if any) E. Database - What are the existing databases that you would like to use in your searches? Please provide references. F. General - What do you think about a web based molecular modeling station/portal? - Will it be convenient to do molecular modeling job in a remote machine through Internet? Your opinions and comments are very useful to my research, please kindly reply to fuifah@um.edu.my Thanks. Regards, Liew Fui Fah, University Malaya, Malaysia. fuifah@um.edu.my -= 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 -- Barry Isralewitz Theoretical Biophysics Group Beckman 3121 Office Phone: (217) 244-1612 Home Phone: (217) 337-6364 email: barryi@ks.uiuc.edu http://www.ks.uiuc.edu/~barryi From chemistry-request@server.ccl.net Thu Mar 16 04:39:43 2000 Received: from myamlak.ch.uj.edu.pl (myamlak.ch.uj.edu.pl [149.156.71.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA02339 for ; Thu, 16 Mar 2000 04:39:28 -0500 Received: from localhost (borowski@localhost) by myamlak.ch.uj.edu.pl (8.9.3/8.9.3) with ESMTP id KAA15508; Thu, 16 Mar 2000 10:32:00 +0100 (MET) Date: Thu, 16 Mar 2000 10:32:00 +0100 (MET) From: Tomasz Borowski X-Sender: borowski@myamlak.ch.uj.edu.pl To: Dirk Uwe Neumann cc: chemistry@ccl.net Subject: Re: CCL:energies of natural orbitals In-Reply-To: <38C66A00.F486315A@chemie.hu-berlin.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dirk, I'am not absolutely sure, but as far as I remember the natural orbitals are not eigenvectors of any one-electron Hamiltonian, they are eigenvectors of one-electron density matrix, thus there are no energies conected with them. Tomek Borowski From chemistry-request@server.ccl.net Thu Mar 16 01:43:13 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA01440 for ; Thu, 16 Mar 2000 01:43:12 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id WAA16383; Wed, 15 Mar 2000 22:43:34 -0800 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14544.33430.480569.185041@lrz.uni-muenchen.de> Date: Wed, 15 Mar 2000 22:43:34 -0800 (PST) To: Gila Budescu Cc: Subject: CCL:BioCoRE - a structural biology portal In-Reply-To: References: <200003152041.OAA06464@venezia.ks.uiuc.edu> X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid So, how many truckloads of DEC (Compaq) Alphas have been shipped to UIUC recently? ;) Seriously, for system sizes and user numbers beyond the trivial we're talking serious amounts of tightly coupled iron here (you do mention "Interactive MD" in "Description"). Also, (with the possible exception of server-side Java), Java VM implementations are known to be so buggy and slow to be unusable in practice. I haven't missed the frequent occurance of "distributed" in your overview article, but does it really work in practice? (I know VMD/NAMD does, but your approach seems to be different, both because of use of nonlocal networking with necessarily poor latency and throughput, and trivial portability at the price of very poor performance due to Java). Could you perhaps elaborate further on your interesting approach? Gila Budescu writes: > Please look at http://www.ks.uiuc.edu/Research/collaboratory/ > for an instant fulfillment of your wishes. The project started on 2/99 and > first official release was announced on 2/2000. We are looking forward to > supporting your work. > Gila Budescu > > > > regarding Liew Fui fah's message: > [...] From chemistry-request@server.ccl.net Thu Mar 16 04:46:23 2000 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA02419 for ; Thu, 16 Mar 2000 04:46:22 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id JAA19708 for ; Thu, 16 Mar 2000 09:48:28 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Thu, 16 Mar 2000 09:48:28 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Gradient Corrections - summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I was asked to summarise the responses to my questions about gradient corrections. The questions were: > 1) Is exchange better described by gradient corrections than correlation > (i.e. would implementing just Becke exchange be a worthwhile move)? > > 2) Is the correct choice of functional very problem dependent? Is there > one choice that gives better *overall* results than the others? > > 3) Are there other methodologies for improving on LDA besides gradient > corrections? If so, what (dis)advantages do they have? Most of the answers appear to exist in the recent paper A. J. Cohen and N. C. Handy, "Assessment of exchange correlation functionals", Chemical Physics Letters vol 316, p 160 (2000). Many thanks to Stefan Grimme for this reference. The responses I obtained are: -------------------------------------------------------------------------------- From: Matt Challacombe (1) No, and thankfully the signs on the errors are different. My opinion is current xc functionals work well because of opposing and roughly equal errors. (2) Yes, a bit. I think one of the best functionals is the PBE functional, which is ab initio, respects all the correct asymptotics etc. (3) You might check out the new functionals by Perdew, Becke and also Scuseria that use the kinetic energy density. These are supposed to get exchange better. -------------------------------------------------------------------------------- From: Stefan Grimme after some testing and experience over some years I strongly recommend Handy and Cohen's parametrisation of Beckes B97 without exact exchange (b97-1gga). Look at C c gammas from Becke 97 paper: C Becke A. D. Density-functional thermochemistry. V. C Systematic optimization of exchange-correlation functionals, C J. Chem. Phys., 1997, 107, 8554-8560 C C HCTH: JCP 109 (1999) 6264 C -> b97-1, b97-1gga: -> Cohen and Handy, CPL 316 (2000), 160 C C HCTH120 and HCTH147 C Boese, Doltsinis, Handy, Sprik C JCP 112 (2000) 1670 C 1) I think Ex and C should be treated on equal footing. 2) I would say that there is little problem dependence (depends, however, on your accuracy requirements) 3) Include Hessian of rho or kinetic energy density terms, but improvemnts are quite marginal -------------------------------------------------------------------------------- From: Thomas Bligaard Pedersen I would like to recommend the PKZB meta-GGA of Perdew, Kurth, Zupan and Blaha; which gives excellent results for a very broad range of systems like crystals, surfaces, etc. This functional can even compete with B3LYP for thermochemical calculations on molecules. It uses both the spin-dependent derivative of the density and the derivative of the wavefunctions. The latter makes the exchange-correlation potential orbital dependent. -------------------------------------------------------------------------------- Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Thu Mar 16 06:59:06 2000 Received: from nmr-v.ioc.ac.ru (val@nmr-v.ioc.ac.ru [193.233.3.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA03826 for ; Thu, 16 Mar 2000 06:59:05 -0500 Received: from localhost (val@localhost) by nmr-v.ioc.ac.ru (8.8.7/8.8.7) with SMTP id PAA10691 for ; Thu, 16 Mar 2000 15:04:10 +0300 Date: Thu, 16 Mar 2000 15:04:09 +0300 (MSK) From: Val To: CHEMISTRY@ccl.net Subject: netropsin & distamycin electronic structures Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, I would appreciate if someone can point me out the references on ab-initio or density functional study of Netropsin and Distamycin molecules. regards, Valentin. ==================================================================== , , , , Valentine P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Thu Mar 16 09:49:01 2000 Received: from nmr.utmb.edu (dggin1.utmb.edu [129.109.73.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA04776 for ; Thu, 16 Mar 2000 09:49:01 -0500 Received: from nmr.utmb.edu (morass.utmb.edu [129.109.73.39]) by nmr.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id IAA09221; Thu, 16 Mar 2000 08:51:22 -0600 Sender: bruce@nmr.utmb.edu Message-ID: <38D0F4B5.4B55F1BA@nmr.utmb.edu> Date: Thu, 16 Mar 2000 08:50:29 -0600 From: "Bruce A. Luxon" Reply-To: bruce@nmr.utmb.edu Organization: Sealy Center for Structural Biology X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: License Transfer Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I've just recently received a new SGI and want to transfer our FELIX license >from the old slow machine to the new fast machine. MSI just quoted me $500 just to transfer the license - a seemingly trivial task. This seems outrageous to me. Is this typical? As an academic user I am having increasing difficulty supporting the use of commercial software at these prices. Any comments or advice? Thanks, Bruce -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Bruce A. Luxon, Ph.D. Associate Professor Sealy Center for Structural Biology Dept. of Human Biological Chemistry & Genetics University of Texas Medical Branch Galveston, TX 77555-1157 (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ http://www.nmr.utmb.edu/ mailto:bruce@nmr.utmb.edu =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Mar 16 11:46:05 2000 Received: from igor.wag.caltech.edu (igor.wag.caltech.edu [131.215.33.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA05531 for ; Thu, 16 Mar 2000 11:46:04 -0500 Received: from wag.caltech.edu (DHCP-26-202.wag.caltech.edu [131.215.26.202]) by igor.wag.caltech.edu (8.9.3/8.9.3) with ESMTP id IAA595438; Thu, 16 Mar 2000 08:44:36 -0800 (PST) Message-ID: <38D10EFF.5D2CC945@wag.caltech.edu> Date: Thu, 16 Mar 2000 08:42:39 -0800 From: "Richard P. Muller" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: "Dr. Sudhir A. Kulkarni" CC: chemistry@ccl.net Subject: Re: CCL:Dreiding validation suite References: <38CF5EEC.27C4742D@mahindrabt.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The original Dreiding paper was: Dreiding: A Generic Force Field for Molecular Simulations S. L. Mayo, B. D. Olafson, and W. A. Goddard, III JPC 94, 8897 (1990) You also might be interested in UFF: A Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations. A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard, III, and W. M. Skiff JACS 114, 10024 (1992) "Dr. Sudhir A. Kulkarni" wrote: > > Hello, > Can some one send me references, pointers for validation of Dreiding > > Force Field method by W. A. Goddard? > Thanks in advance. > > Sudhir