From nkhaledi@attila.stevens-tech.edu Sat Nov 15 14:33:15 1997 Received: from attila.stevens-tech.edu for nkhaledi@attila.stevens-tech.edu by www.ccl.net (8.8.3/950822.1) id NAA10862; Sat, 15 Nov 1997 13:42:59 -0500 (EST) Received: from localhost (nkhaledi@localhost) by attila.stevens-tech.edu (8.8.5/8.8.3.1) with SMTP id NAA05738; Sat, 15 Nov 1997 13:42:54 -0500 (EST) Date: Sat, 15 Nov 1997 13:42:54 -0500 (EST) From: Nilofar Khaledi To: Ahmed Bouferguene cc: chemistry@www.ccl.net Subject: Re: CCL:Advice for purchasing PC In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII i r On Thu, 13 Nov 1997, Ahmed Bouferguene wrote: > Hi all, > > Our department is interested in purchasing some PCs to be used for > numerical computation~(in physics and chemistry) and graphical > representations. However, we do not have a thorough experience with > PCs and we would like to have your comments about a good configuration and > of course about any good software that would be worth to have. > > > Thanks all. > > Ahmed Bouferguene > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: boufer@cennas.nhmfl.gov > -- Original Sender From: Address: boufer@CeNNAs.nhmfl.gov > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From nkhaledi@attila.stevens-tech.edu Sat Nov 15 14:57:34 1997 Received: from attila.stevens-tech.edu for nkhaledi@attila.stevens-tech.edu by www.ccl.net (8.8.3/950822.1) id NAA10852; Sat, 15 Nov 1997 13:40:42 -0500 (EST) Received: from localhost (nkhaledi@localhost) by attila.stevens-tech.edu (8.8.5/8.8.3.1) with SMTP id NAA04527; Sat, 15 Nov 1997 13:40:40 -0500 (EST) Date: Sat, 15 Nov 1997 13:40:40 -0500 (EST) From: Nilofar Khaledi To: Oliver Kohlbacher cc: chemistry@www.ccl.net Subject: Re: CCL:ab-initio calculation of UV/VIS-spectra In-Reply-To: <199711131536.QAA11369@mpii-ol.ag1.mpi-sb.mpg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear oliver, it seems like you may need to review one of the abinitio calcualtion books becuase it seems to be a difficult task but it think it should be calculated from the orbital energies based on raman efefct and Jabolanski diagram and other methods of calcualtion the enrgy levels. best, Nili kahledi On Thu, 13 Nov 1997, Oliver Kohlbacher wrote: > Dear CLLers, > > what possibilities do exist to predict UV/VIS spectra of > aromatic compounds? To my understanding, it should be possible > to predict them from the orbital energies obtained by a > CI calculation. How difficult is this task? > And how to get intensities? > > Thanks for any advice, > Oliver > > > -- > ---- > Oliver Kohlbacher (oliver@mpi-sb.mpg.de) > Max-Planck-Institut fuer Informatik, Im Stadtwald, 66121 Saarbruecken > Tel.: 0681-9325-505 Fax: 0681-9325-199 > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: oliver@mpi-sb.mpg.de > -- Original Sender From: Address: oliver@mpi-sb.mpg.de > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From lavelle@mbi.ucla.edu Wed Nov 12 13:32:38 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id NAA12428; Wed, 12 Nov 1997 13:04:11 -0500 (EST) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by rho.ben2.ucla.edu (8.8.5/8.8.5) with SMTP id KAA58630 for ; Wed, 12 Nov 1997 10:04:11 -0800 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA22260; Wed, 12 Nov 1997 10:04:10 -0800 Message-Id: <3.0.32.19971112100757.00a24210@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 12 Nov 1997 10:07:58 -0800 To: chemistry@www.ccl.net From: Laurence Lavelle Subject: Improving ab initio computational speed Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" On Nov 8 I posted the message below but have had no responses. If requested I will summarize and post replies that I receive. Two possible ways to speed up ab initio calculations are: 1) Use a bases set with fewer bases functions first. Then, after convergence, use a bases set with more bases functions. Repeat this process until convergence is obtained with the (largest) bases set that was originally intended. 2) Use the largest bases set with a higher 2e integral cuttoff point (e.g. 10^-7 Hartree) and after convergence decrease the 2e integral cuttoff point. Repeat until convergence is obtained with the originally intended 2e integral cuttoff point (e.g. 10^-11 Hartree). Do either of these approaches have potential downfalls? Is one approach better than the other? Thanks Laurence Lavelle
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read.
From L330@SUEARN2.bitnet Wed Nov 12 15:32:38 1997 Received: from plearn.edu.pl for L330@SUEARN2.bitnet by www.ccl.net (8.8.3/950822.1) id PAA13074; Wed, 12 Nov 1997 15:31:59 -0500 (EST) Message-Id: <199711122031.PAA13074@www.ccl.net> Received: from SUEARN2.BITNET by plearn.edu.pl (IBM VM SMTP V2R2) with BSMTP id 8636; Wed, 12 Nov 97 21:29:32 CET Date: Wed, 12 Nov 97 23:28 MSK To: chemistry@www.ccl.net From: L330%SUEARN2.BITNET@plearn.edu.pl Subject: request of SPP1600 Dear CCLers ! We need second hand HP/Convex SPP1600 computer for research in area of quantum chemistry programs parallelization. As I know, these computers will be throw out in the frames of upgrade program to new HP Enterprise servers. Please don't throw out them ! We'll be very appreciate if somebody may propose us like server. Dr. Nick Anikin, N.D.Zelinsky Institute of Organic Chemistry Russian Academy of Sci., Moscow, Russia From ccl@www.ccl.net Thu Nov 13 13:32:52 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA26367; Thu, 13 Nov 1997 12:47:30 -0500 (EST) Received: from theory.tc.cornell.edu for richard@tc.cornell.edu by bedrock.ccl.net (8.8.6/950822.1) id MAA06990; Thu, 13 Nov 1997 12:47:29 -0500 (EST) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id MAA09527 for ; Thu, 13 Nov 1997 12:47:30 -0500 Sender: richard@TC.Cornell.EDU Message-ID: <346B3D33.1CFB@tc.cornell.edu> Date: Thu, 13 Nov 1997 12:47:31 -0500 From: Richard Gillilan X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Rigid body dynamics Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit A number of programs (like XPLOR) have implemented the virtual rigid body dynamics of T. Head-Gordon and C. Brooks (Biopolymers vol 31, 77-100 (1991). I've seen a few notes on CCL about "Moldy" that sound like it too can do this. Does anyone have info about the program? Also: 1. Does anyone know of recent studies using this technique, particularly applied to the protein-protein docking? 2. How does it compare with SHAKE type constraint methods: faster/slower or just different? Will summarize. Thanks Richard Gillilan Cornell Theory Center From shenkin@still3.chem.columbia.edu Thu Nov 13 14:40:39 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id NAA26693; Thu, 13 Nov 1997 13:54:29 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id NAA23250 for <@smtp.columbia.edu:chemistry@www.ccl.net>; Thu, 13 Nov 1997 13:54:30 -0500 (EST) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id NAA13910; Thu, 13 Nov 1997 13:54:29 -0500 From: "Peter Shenkin" Message-Id: <9711131354.ZM13908@still3.chem.columbia.edu> Date: Thu, 13 Nov 1997 13:54:29 -0500 In-Reply-To: "Bill Kraus" "CCL:Re: CCL:Sequence Classes and CORBA Servers" (Nov 11, 9:54am) References: <01bceeca$eb975820$04899ccc@Best.best.com> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:Sequence Classes and CORBA Servers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Nov 11, 9:54am, Bill Kraus wrote: > Subject: CCL:Re: CCL:Sequence Classes and CORBA Servers > I must add my support to what Konrad is saying. As a commercial software > developer who has written bioinformatics apps (e.g. MacVector, AssemblyLIGN) > as well as others (e.g. Adobe PageMill), and as someone who has been > architecting systems using OO technology for the last ten years (even doing > time at the ill-fated Taligent effort), using OO technology is no guarantee. > In fact, it's been my experience that there is a significant risk to > standardizing object interfaces - the resulting APIs can either be too > constraining or so generalized as to be useless. I also agree with this, having considered the use of the ASN.1 structures defined by NCBI for use in general-purpose molecular modeling and having participated to some extent in the CEX effort a few years back. Still, there are two aspects of such technologies: the syntactical/ methodological and the semantic. The "consortium" approach to standardizing interfaces or object classes or data structures for a particular field of use seeks to define semantics, or at least should seek to do so! This is often not as successful as one might hope for the reasons Bill mentioned. However, the underlying infrastructure might still be highly useful for one's own purposes, even if the object or data-structure definitions are your own private ones. And, if you made enough of what you've done visible (ASN.1 syntax, for example), and make the semantics clear to your users, then your users can also use the technology to interface other applications with your own. Thus, I'm more interested in using CORBA, ASN.1 and similar technologies myself, as I see fit, using my own definitions, than in buying into the defintions provided by a consortium or external organization. Even in this more limited context, the technologies themselves are very powerful. -P. -- ****************** Sir Isaiah Berlin, 1909 - 1997, RIP ******************** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From toukie@zui.unizh.ch Fri Nov 14 07:33:00 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id GAA01038; Fri, 14 Nov 1997 06:46:53 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA26119; Fri, 14 Nov 1997 12:46:51 +0100 Message-Id: <3.0.3.32.19971114124937.00688408@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Fri, 14 Nov 1997 12:49:37 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Software for adding partial atomic charges? Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; Does anyone know of DOS/Win3.x/Win95 software that can take a PDB file containing the atomic identities and coordinates of biomacromolecules such as proteins, polysaccharides, nucleic acids, and/or lipid bilayers and add partial atomic charges to the atoms? If so, kindly advise of details. Thanks, S. Shapiro toukie@zui.unizh.ch From ccl@www.ccl.net Fri Nov 14 14:33:03 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id NAA03480; Fri, 14 Nov 1997 13:57:23 -0500 (EST) Received: from origin.gig.usda.gov for srheller@gig.usda.gov by bedrock.ccl.net (8.8.6/950822.1) id NAA07299; Fri, 14 Nov 1997 13:57:22 -0500 (EST) Received: by origin.gig.usda.gov (5.x/SMI-SVR4) id AA16257; Fri, 14 Nov 1997 13:46:27 -0500 Date: Fri, 14 Nov 1997 13:46:26 -0500 (EST) From: "Stephen R. Heller" To: chemistry@ccl.net, chemweb@ic.ac.uk, CHMINF-L@LISTSERV.INDIANA.EDU., orgchem@extreme.chem.rpi.edu Subject: WANTED - Chemical and Physical Property data Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII November 14, 1997 I have just started a new project to help collect high quality databases of chemical and physical properties here at NIST (US National Institute of Standards and Technology). The main interest is in adding EI mass and other spectral data, and property data such a logP, Henry's law constants, and boiling points. (For those who want to see what there is now go to the url: http://webbook.nist.gov/chemistry/). If you have any such data and would like to provide it to NIST or collaborate with NIST on this project, please contact me by e-mail or phone - PLEASE do not reply to this list. Thanx Steve Heller Steve Heller, NIST Bldg. 221, Room A111 Gaithersburg, MD 20899 USA Phone: 301-975-3338 or 2204 FAX: 301-975-3670 E-mail: srheller@gig.usda.gov WWW: www.hellers.com/~steve From giesen@mozart.rl.kodak.com Fri Nov 14 17:33:04 1997 Received: from kodakr.kodak.com for giesen@mozart.rl.kodak.com by www.ccl.net (8.8.3/950822.1) id QAA05680; Fri, 14 Nov 1997 16:51:16 -0500 (EST) Received: from mail.rl.kodak.com by kodakr.kodak.com with SMTP id AA15564 (5.67b/IDA-1.5 for ); Fri, 14 Nov 1997 16:48:40 -0500 Received: from mozart.rl.kodak.com by mail.rl.kodak.com (8.8.3/1.1.10.5/17Jan97-0515PM) id RAA12562; Fri, 14 Nov 1997 17:03:42 -0500 (EST) Received: from berlioz.rl.kodak.com (berlioz.rl.kodak.com [150.220.76.26]) by mozart.rl.kodak.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id QAA22115; Fri, 14 Nov 1997 16:51:54 -0500 Sender: giesen@kodak.com Message-Id: <346CC7F9.41C6@mozart.rl.kodak.com> Date: Fri, 14 Nov 1997 16:51:53 -0500 From: David Giesen Organization: Eastman-Kodak X-Mailer: Mozilla 3.02 (X11; I; IRIX64 6.2 IP21) Mime-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: SUMMARY: Web-based Molecule Builder Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thanks to all who replied to my question about a web-based molecule builder. Unfortunately, it seems as though there are no magic bullets currently out there. Here is a summary in my own words of responses to date: Dr. Vladimir Gusev has a nice java builder for MCM-41 crystal structures. Find it at http://pluto.njcc.com/~vgusev Dr. Wolf-D. Ihlenfeldt has a very advanced 2-D sketcher. Find it at http://www2.organik.uni-erlangen.de/services/3d.html ChemSymphony looks like a very interesting set of java tools for rendering/rotating/measuring molecules (but not building) inside a web page. Find it at http://www.cherwell.com/chemsymphony/index.html. MicroSimulations has a slick 3-D builder called AccuModel (not web-based) which I like a lot. Find it at http://www.microsimulations.com. AccuModel is licensed by Interactive Simulations as part of their package with Sculpt that works with Chime and ISIS (they call their licensed version Chembuilder). Find it at http://www.intsim.com. And there is WebLab Viewer Pro from Molecular Simulations Inc, a nice package which is built to work with their Web Software Developer's Kit. Find it at http://www.msi.com. Thanks again to all who replied, and I'm still interested in hearing if there are any 3-D web-based molecular builders out there. Dave