From ep7@dent.okayama-u.ac.jp Tue May 26 03:22:47 1998 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA15432 Tue, 26 May 1998 03:22:41 -0400 (EDT) From: ep7@dent.okayama-u.ac.jp Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id QAA18506 for ; Tue, 26 May 1998 16:23:59 +0900 (JST) Message-Id: <199805260723.QAA18506@deews1.dent.okayama-u.ac.jp> Date: Tue, 26 May 1998 16:39:23 +0900 To: CHEMISTRY@www.ccl.net Subject: ESP MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Sir: I would like to ask about determination of atomic charges from ab initio electrostatic potentials: For example, in CHELP, CHELPG, and Merz and Kollman, various points were normally putted at the van der Waals contact region surrounding the molecule ? Thank you. Masao Masamura Preventive Dentistry Okayama University Dental School Shikata-cho, 2-5-1 Okayama 700 Japan FAX: 81-86-235-6714 e-mail: ep7@dent.okayama-u.ac.jp From boufer@cennas.nhmfl.gov Tue May 26 09:39:12 1998 Received: from cennas.nhmfl.gov (cennas.nhmfl.gov [146.201.220.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA17182 Tue, 26 May 1998 09:39:12 -0400 (EDT) Received: from localhost (boufer@localhost) by cennas.nhmfl.gov (8.8.5/8.8.5) with SMTP id JAA07471 for ; Tue, 26 May 1998 09:39:41 -0400 (EDT) Date: Tue, 26 May 1998 09:39:41 -0400 (EDT) From: Ahmed Bouferguene X-Sender: boufer@cennas To: chemistry@www.ccl.net Subject: CPHF~(A good reference) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings all, I wonder if anybody can suggest a good reference~(review paper) about the CPHF procedure. Thanks a lot. -- Ahmed Bouferguene ----------------------------------------------------------------------- Ce n'est pas par ce que les choses sont difficiles que nous n'osons pas les faire. C'est parce que nous n'osons pas les faire qu'elles sont difficiles. From daizadeh@kappa.ucdavis.edu Tue May 26 10:38:22 1998 Received: from kappa.ucdavis.edu (kappa.ucdavis.edu [128.120.7.55]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA17640 Tue, 26 May 1998 10:38:21 -0400 (EDT) Received: (from daizadeh@localhost) by kappa.ucdavis.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id HAA24724; Tue, 26 May 1998 07:38:43 -0700 From: "Iraj Daizadeh" Message-Id: <9805260738.ZM24722@kappa.ucdavis.edu> Date: Tue, 26 May 1998 07:38:43 -0700 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Youngsters and Science. Cc: grad@indigo.ucdavis.edu, catolbert@ucdavis.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. Last week I sent a message concerning Science-By-Mail, an educational experience linking school kids and ``working'' scientists. Those interested in this opportunity, i.e. for anyone interested in sharing scientific understanding for those just entering the field, can take a look at: http://www.mos.org/mos/sbm/sciencemail.html or Call (617) 589-0437 or (800) 729-3300 (Monday-Friday 9-5 EST). Their email is: sbm@mos.org for more information. Iraj. -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 530.754.8695 Fax: 530.752.8995 email: daizadeh@kappa.ucdavis.edu From rschmid@acs.ucalgary.ca Mon May 25 17:28:13 1998 Received: from ds11.acs.ucalgary.ca (root@ds11.acs.ucalgary.ca [136.159.244.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA13311 Mon, 25 May 1998 17:28:12 -0400 (EDT) Received: from localhost by acs1.acs.ucalgary.ca (AIX 4.1/UCB 5.64/4.03) id AA78834; Mon, 25 May 1998 15:27:27 -0600 Date: Mon, 25 May 1998 15:27:26 -0600 (MDT) From: Rochus Schmid Reply-To: Rochus Schmid To: ccl Subject: summary: molecular builder In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi netters, thanks to all who responded to my question. there is not much to summarize and I won't list all the answers I've got here. Most replies are roughly: "we've been looking for that kind of software, too. Couldn't find anything." BUT: I was pointed to molden3.3 http://www.caos.kun.nl/~schaft/molden/molden.html and looked at it again. It's not exactly what I wanted but it's worth to consider. The problem is: you can easily edit a z-matrix with it. but in order to change *any* internal coordinate this must be defined in terms of the z-mat. so if I start from xyz and the auto z-mat builder doesn't make a z-mat which includes this int. coordinate I have to reedit the whole z-mat. this is all I have, sorry ;-) greetings, rochus P.S. what about if all those people (including me), who want to have such a software think about "creating" it? I was thinking about using a openGL extended scripting language like tcl (or maybe python) for the job. since I have no clue about tcl I was wondering if someone could supply a "viewport" which just displays a ball and stick model which can be rotated etc.? if you want to comment this idea or have any (definetly better ;-) ones please reply *directly* to me, since we don't want to waste the bandwidth on ccl. On Tue, 12 May 1998, Rochus Schmid wrote: > > > > > Dear Netters, > > Please forgive me for asking that question, which came up a couple of > times already, I know. But I am desperate and my question is rather > specific: > > I am searching for a (simple!!!, 3D!) molecular builder: > > - it should run under UNIX/X and be free (I know cerius2 and insightII > and and and ....) > > - it should be very simple (I don't need ruberbands, rayshading etc. and > it is only for a couple of atoms and not for > proteins) > > - it should be able to add or delete atoms by mouse and change bond > length, angles and dihedrals by selecting the atoms. > > - it should be able to read and write the stuff as pdb or xyz or whatever > > > > I follow this mailing list for quite a while now and similar questions > came up quite often, I know. > > So I know about gopenmol and xmol and viewmol and molden and vmd and a > couple more. But none of these programs is what I'm looking for. > > To make that more clear: > I really like xmol. It's simple and free etc. but you can't build > molecules. > > And I really liked the UNICHEM interface by Cray. This was perfect to me > but it is not free ;-) > > Is there anything on this beautifull world like that?? > I can't believe, that I'm the only one who needs that kind of software. > > Thanks in advance for any comment or hint. > Happy computing, > > > Rochus > > > > > ******************************************************************** > Rochus Schmid Phone: (403) 220-3232 > University of Calgary Fax: (403) 289-9488 > Department of Chemistry Email: rschmid@acs.ucalgary.ca > 2500 University Drive N.W. > Calgary, Alberta > Canada T2N 1N4 > http://www.chem.ucalgary.ca/groups/ziegler/ > ******************************************************************** > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 richard@tc.cornell.edu Tue May 26 17:02:30 1998 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA20494 Tue, 26 May 1998 17:02:30 -0400 (EDT) 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 RAA38042; Tue, 26 May 1998 17:02:30 -0400 Sender: richard@tc.cornell.edu Message-ID: <356B2DE6.7AAE@tc.cornell.edu> Date: Tue, 26 May 1998 17:02:30 -0400 From: Richard Gillilan X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: richard@tc.cornell.edu Subject: Multipole expansion error bounds Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Does anyone have a reference to error bounds for truncating multipole expansions of 3D point charge sets? I have Greengard's 87 paper which gives 2D results. Are they also correct for 3D? (the library seems to have misplaced his more recent book!!). Also, any ideas on optimal position for expansion center? The 2D bound indicates one should minimize the distance from center to farthest charge independent of charge value or distribution, but it seems like some kind of charge-weighted center would be better. Thanks Richard Gillilan Cornell Theory Center richard@tc.cornell.edu From p.morrison@which.net Tue May 26 17:29:22 1998 Received: from mail1-gui.server.which.net (mail1-gui.server.which.net [194.168.97.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA20623 Tue, 26 May 1998 17:29:19 -0400 (EDT) Received: from packard-bell ([194.168.99.74]) by mail1-gui.server.which.net (Post.Office MTA v3.1.2 release (PO203-101c) ID# 0-33929U70000L2S50) with SMTP id AAA19816 for ; Tue, 26 May 1998 22:29:02 +0100 Message-ID: <356B33AB.7EDD@which.net> Date: Tue, 26 May 1998 22:27:08 +0100 From: Admin Kit User Reply-To: p.morrison@which.net X-Mailer: Mozilla 3.01C-Mozilla (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: cd-roms chemistry set +elements +high school chem Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit could you please send reviews of the above, also with details of ordering please. Regards, Paul Morrison From jonarg@patra.hellasnet.gr Tue May 26 20:33:38 1998 Received: from pop.patra.netor.gr (pop.patra.Hellasnet.GR [193.218.117.126]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA21689 Tue, 26 May 1998 20:33:36 -0400 (EDT) Received: from patra.netor.gr ([193.218.117.113]) by pop.patra.netor.gr (Netscape Mail Server v2.02) with ESMTP id AAA264 for ; Wed, 27 May 1998 03:28:18 +0300 Message-ID: <356B604C.C5032F80@patra.netor.gr> Date: Wed, 27 May 1998 03:37:32 +0300 From: jonarg@patra.hellasnet.gr (Koklas Gerasimos) Organization: HOME X-Mailer: Mozilla 4.02 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Graphs Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 7bit Hi! Is there any topological index (like Randic,Balaban,...) that can include information about double bonds in the system? -- jonarg@patra.netor.gr