From L.Yee@unsw.edu.au Tue May 13 00:42:48 1997 Received: from sam.comms.unsw.EDU.AU for L.Yee@unsw.edu.au by www.ccl.net (8.8.3/950822.1) id AAA26613; Tue, 13 May 1997 00:40:32 -0400 (EDT) Received: from superam.ceic.unsw.edu.au ([129.94.144.149]) by sam.comms.unsw.EDU.AU (8.8.5/8.7.5.kenso-central) with SMTP id OAA04157 for ; Tue, 13 May 1997 14:40:17 +1000 (EST) Message-Id: <3.0.1.32.19970513144111.00694e80@pop3.unsw.edu.au> X-Sender: p2121821@pop3.unsw.edu.au X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Tue, 13 May 1997 14:41:11 +1000 To: chemistry@www.ccl.net From: Lachlan H Yee Subject: CCL: Transition State Optimisation Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Theoretical Chemists, I am struggling to find the transition state between to simple molecules. I am using Gaussian94 and keep coming up with two imaginary frequencies when solving for frequencies. I am wondering if someone could advise me on how to direct the program to follow the 2nd imaginary frequency, which I believe to be the one corresponds to the First Order Saddle Point I seek. Any help would be appreciated, Lachlan Yee. ____________________________ Lachlan H Yee B.Sc. Postgraduate Student Polymer Science Univesity of NSW Sydney 2052 Australia Ph (02) 9385 5512 Fx (02) 9385 5966 Email: l.yee@unsw.edu.au From edvard@fagmed.uit.no Tue May 13 01:42:50 1997 Received: from kvikk.uit.no for edvard@fagmed.uit.no by www.ccl.net (8.8.3/950822.1) id BAA26848; Tue, 13 May 1997 01:40:07 -0400 (EDT) From: Received: from petrus.fagmed.uit.no (petrus.fagmed.uit.no [129.242.44.243]) by kvikk.uit.no (8.8.5/8.8.5) with ESMTP id HAA22116 for ; Tue, 13 May 1997 07:40:08 +0200 (METDST) Received: from fa13.imb.fm.uit.no (atf3 [129.242.48.45]) by petrus.fagmed.uit.no (8.8.5/8.7.3) with SMTP id HAA01077 for ; Tue, 13 May 1997 07:39:16 +0200 Received: by fa13.imb.fm.uit.no (SMI-8.6/ABaa-2.0mini) id HAA29992; Tue, 13 May 1997 07:35:33 +0100 Date: Tue, 13 May 1997 07:35:33 +0100 Message-Id: <199705130635.HAA29992@fa13.imb.fm.uit.no> To: CHEMISTRY@www.ccl.net Subject: Re: Forcefield for carbohydrates Reply-to: edvard@fagmed.uit.no Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-MD5: nFZkdYNe99RkRWbLo4xY6A== CHARMM22 carbohydrate extension: J. Comput. Chem. 17(4):450-68 (1996). =D8yvind. edvard@fagmed.uit.no From lestaw.k.bieniasz@uni-tuebingen.de Tue May 13 04:42:57 1997 Received: from outmail.zdv.uni-tuebingen.de for lestaw.k.bieniasz@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id EAA27820; Tue, 13 May 1997 04:09:42 -0400 (EDT) Received: from echem5.orgchemie.chemie (echem5.orgchemie.chemie.uni-tuebingen.de) by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AA16420; Tue, 13 May 97 10:09:15 MES Date: Tue, 13 May 1997 10:07:53 +0200 (W. Europe Daylight Time) From: "Lestaw K. Bieniasz" To: Paul Beroza Cc: CHEMISTRY@www.ccl.net, Gerald.Loeffler@univie.ac.at Subject: Re: CCL:Numerically Solving Partial Differential Equations In-Reply-To: <199705121540.IAA10348@euler.scripps.edu> Message-Id: X-X-Sender: coibi01@mailserv.uni-tuebingen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 12 May 1997, Paul Beroza wrote: > can all be used to solve the Poisson-Boltzmann equation. I would > recommend "Numerical Recipes" as a good introduction to numerical > methods to solve partial differential equations. "Numerical Recipes" are a bit trivial if one wants to make a real thing. I would rather recommend: Lapidus L. & Pinder G.F., Numerical Solution of Partial Differential Equations in Science and Engineering, Wiley, New York, 1982 and Smith G.D. Numerical Solution of Partial Differential Equations: Finite Difference Methods (3rd edition), Clarendon, Oxford, 1985. Both combine rigorous discussion with clarity of presentation and practical usefullness. HTH, L.B. *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz | | temporary address: (3rd April 1997 - 31st August 1997) | | Institut fuer Organische Chemie, Universitaet Tuebingen | | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | *-------------------------------------------------------------------* | permanent address: | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | E-mail: nbbienia@cyf-kr.edu.pl | *-------------------------------------------------------------------* From pino@jsbach.dichi.unina.it Tue May 13 05:42:52 1997 Received: from jsbach.dichi.unina.it for pino@jsbach.dichi.unina.it by www.ccl.net (8.8.3/950822.1) id EAA28041; Tue, 13 May 1997 04:58:37 -0400 (EDT) From: Received: by jsbach.dichi.unina.it (AIX 3.2/UCB 5.64/4.03) id AA12018; Wed, 7 Feb 1996 10:53:27 +0100 Date: Wed, 7 Feb 1996 10:53:27 +0100 Message-Id: <9602070953.AA12018@jsbach.dichi.unina.it> To: chemistry@www.ccl.net Subject: Core Potentials of halogens Content-Type: text/plain Mime-Version: 1.0 X-Mailer: NCSA Mosaic 2.7b4 on RS/6000 AIX X-Url: http://www.ccl.net/ccl/welcome.text.html#2 I would appreciate to receive informations about appropriate effective core potentials for halogens atoms for Van Deer Waals complex calculations. From gsartor@ipruniv.cce.unipr.it Tue May 13 06:42:52 1997 Received: from ipruniv.cce.unipr.it for gsartor@ipruniv.cce.unipr.it by www.ccl.net (8.8.3/950822.1) id FAA28310; Tue, 13 May 1997 05:53:34 -0400 (EDT) Received: by ipruniv.cce.unipr.it (AIX 3.2/UCB 5.64/4.03) id AA38529; Tue, 13 May 1997 11:49:13 +0100 Date: Tue, 13 May 1997 11:49:13 +0100 (NFT) From: Giorgio Sartor Subject: PEPFLEX To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, could anyone point me were to find some references to PEPFLEX-I and II by B.D. Sykes and coworkers? Thanks Giorgio Sartor -- +----------------------------------------+ | Giorgio Sartor | | Istituto di Chimica Biologica | | Universita' degli Studi di Parma | | Via Gramsci, 14 | | 43100 Parma - ITALY | | Tel ++39-(0)521-290363 | | FAX 988952 | | http://www.unipr.it/~gsartor | +----------------------------------------+ From rprf526-int@intccop1.intevep.pdv.com Tue May 13 09:42:55 1997 Received: from firewall.intevep.pdv.com for rprf526-int@intccop1.intevep.pdv.com by www.ccl.net (8.8.3/950822.1) id JAA29322; Tue, 13 May 1997 09:15:34 -0400 (EDT) Received: by firewall.intevep.pdv.com (4.1/SMI-4.1) id AA19893; Tue, 13 May 97 09:15:17-040 Received: from intevep.intevep.pdv.com(129.90.18.4) by firewall.intevep.pdv.com via smap (V1.3) id sma019889; Tue May 13 09:15:16 1997 Received: from intccop1.intevep.pdv.com by intevep (5.x/SMI-SVR4) id AA03113; Tue, 13 May 1997 09:05:51 -0400 Received: from ccMail by intccop1.intevep.pdv.com (SMTPLINK V2.11) id AA863529632; Tue, 13 May 97 09:17:02 EST Date: Tue, 13 May 97 09:17:02 EST From: "RPRF526-INT" Encoding: 14 Text Message-Id: <9704138635.AA863529632@intccop1.intevep.pdv.com> To: chemistry@www.ccl.net Return-Receipt-To: rprf526-int@intccop1.intevep.pdv.com Subject: MNDO parameters for Fe In the article "Application of the MNDO method for fe and Mo compounds" by M. Czerwinski. Mol.cryst.liq. Cryst., 1996, vol 281, p 171. We can found parameters for these metals, the problem is with the keyword EXTERNAL. I construct the "external file" following the MOPAC 6.0 manual instructions, with the names for the parameters uss, upp, udd, zs ... etc., let a empty line at the begining, but the program don't recognize the data. Does someone know how construct the file exactly? Any help is welcome. Thanks in advance, Sincerely, Manuel J. Goncalves Intevep, s.A. From gford@post.smu.edu Tue May 13 11:42:56 1997 Received: from post.cis.smu.edu for gford@post.smu.edu by www.ccl.net (8.8.3/950822.1) id LAA03702; Tue, 13 May 1997 11:17:46 -0400 (EDT) Received: by post.cis.smu.edu (/\==/\ Smail3.1.28.1 #28.3) id ; Tue, 13 May 97 10:17 CDT Message-Id: Date: Tue, 13 May 97 10:17 CDT From: "George P. Ford" Reply-To: "George P. Ford" To: CHEMISTRY@www.ccl.net Subject: Babel - fractional coordinates According to the Manual Babel accepts an input format described as "Free Form Fractional". Does anyone know exactly what this format looks like? A short example would be much appreciated. George P. Ford ============================================================================ George P. Ford | email: gford@smu.edu Department of Chemistry | web: http://www.smu.edu/~gford/ Southern Methodist University | telephone: (214)768-2479 Dallas, Texas 75275 | fax: (214)768-4089 ============================================================================ From daizadeh@indigo.ucdavis.edu Tue May 13 12:42:55 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id MAA04486; Tue, 13 May 1997 12:41:09 -0400 (EDT) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id JAA20105; Tue, 13 May 1997 09:48:41 -0700 From: "Iraj Daizadeh" Message-Id: <9705130948.ZM20103@indigo.ucdavis.edu> Date: Tue, 13 May 1997 09:48:27 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: 3-D Imaging Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. Would anyone know an easy-to-learn program that allows for visualizing data >from a file in 3-dimension Euclidean space something that looks like a fluid dynamics simulation? I started to write such a piece of code using Tcl/Tk but speed is of the essence (as always). Thanks in advance. Iraj Daizadeh Department of Chemistry University of California Davis, CA 95616 From bdavis@yorku.ca Tue May 13 12:50:03 1997 Received: from sungod.ccs.yorku.ca for bdavis@yorku.ca by www.ccl.net (8.8.3/950822.1) id LAA04028; Tue, 13 May 1997 11:53:59 -0400 (EDT) Received: from dekan.phoenix.yorku.ca (MCsSFXD9jYsdFgqowvxHrxnO65SeE0of@dekan.phoenix.yorku.ca [130.63.236.46]) by sungod.ccs.yorku.ca (8.8.5/8.8.5) with ESMTP id LAA03525 for ; Tue, 13 May 1997 11:53:59 -0400 (EDT) Received: from localhost (bdavis@localhost) by dekan.phoenix.yorku.ca (8.8.5/8.6.12) with SMTP id LAA18020 for ; Tue, 13 May 1997 11:53:59 -0400 X-Authentication-Warning: dekan.phoenix.yorku.ca: bdavis owned process doing -bs Date: Tue, 13 May 1997 11:53:58 -0400 (EDT) From: Bill Davis X-Sender: bdavis@dekan.phoenix.yorku.ca To: chemistry@www.ccl.net Subject: micelles Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone! Does anyone know if there is any published work on the stability of micelles or reverse micelles in liquid media. More specifically, their stability when the liquid boils? Thanks for the help. Regards, ************************************************************************* Dr. William M. Davis Phone: (416) 736-2100 ext. 77767 Dept. Of Chemistry Fax: (416) 736-5936 York University Email: bdavis@yorku.ca 4700 Keele St. North York, Ontario CANADA M3J 1P3 ************************************************************************* From hinsen@lmspc2.ibs.fr Tue May 13 13:42:56 1997 Received: from ibs.ibs.fr for hinsen@lmspc2.ibs.fr by www.ccl.net (8.8.3/950822.1) id NAA04876; Tue, 13 May 1997 13:35:05 -0400 (EDT) Received: from lmspc2.ibs.fr (lmspc2.ibs.fr [192.134.36.142]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id TAA14788; Tue, 13 May 1997 19:36:11 +0200 Received: (from hinsen@localhost) by lmspc2.ibs.fr (8.8.5/8.8.5) id TAA04267; Tue, 13 May 1997 19:35:03 +0200 Date: Tue, 13 May 1997 19:35:03 +0200 Message-Id: <199705131735.TAA04267@lmspc2.ibs.fr> From: Konrad Hinsen To: daizadeh@indigo.ucdavis.edu CC: CHEMISTRY@www.ccl.net In-reply-to: <9705130948.ZM20103@indigo.ucdavis.edu> (daizadeh@indigo.ucdavis.edu) Subject: Re: CCL:3-D Imaging > Would anyone know an easy-to-learn program that allows for visualizing data > from a file in 3-dimension Euclidean space something that looks like a fluid > dynamics simulation? I started to write such a piece of code using Tcl/Tk but > speed is of the essence (as always). One possibility for almost all visualization tasks is to write a simple program to transform the data to a VRML file and then use a VRML browser to visualize it. For more information about VRML, look at the VRML repository (http://www.sdsc.edu/vrml/). For an example of code that generates VRML, look at the VRML module on my Python page (http://www.yi.com/home/HinsenKonrad/python.html). -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From pwalters@portal.vpharm.com Tue May 13 13:49:12 1997 Received: from portal.vpharm.com for pwalters@portal.vpharm.com by www.ccl.net (8.8.3/950822.1) id NAA04790; Tue, 13 May 1997 13:22:40 -0400 (EDT) Received: from neoprene.vpharm.com by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA10044; Tue, 13 May 1997 13:14:21 -0400 Sender: pwalters@portal.vpharm.com Message-Id: <3378A77F.2781@portal.vpharm.com> Date: Tue, 13 May 1997 10:40:15 -0700 From: Pat Walters Organization: Vertex Pharmaceuticals X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Mime-Version: 1.0 To: "George P. Ford" Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Babel - fractional coordinates References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit George P. Ford wrote: > > According to the Manual Babel accepts an input format described as "Free Form > Fractional". Does anyone know exactly what this format looks like? A short > example would be much appreciated. line 1 - #_of_atoms alpha beta gamma a b c line 2 - title lines 3 to end - element x y z Spacing is not important. It's ok to put numbers after the element labels (C4,N6,etc.) ================================================ 15 90.00 106.07 90.00 9.692 7.371 15.345 COLHOA N .66250 .17070 .54240 N .68230 .13160 .63460 C .81750 .07680 .66390 C .88940 .08180 .59630 C .78970 .14220 .52040 C .87640 .02170 .76120 O .79880 .16750 .43530 N .53740 .28850 .40510 C .53360 .24250 .48830 N .42660 .25480 .52670 C .30740 .32860 .47090 C .29980 .38880 .38540 C .41710 .36570 .35180 C .18280 .35130 .51080 C .42110 .42850 .26060 ================================================ Have fun, Pat -- W. Patrick Walters, Ph.D. Staff Scientist, Computational Chemistry and Molecular Modeling Vertex Pharmaceuticals, Inc., 130 Waverley St., Cambridge, MA 02139 Voice: (617)577-6000 FAX: (617)577-6400 From psv8b@watt.seas.virginia.edu Tue May 13 15:43:03 1997 Received: from mail.virginia.edu for psv8b@watt.seas.virginia.edu by www.ccl.net (8.8.3/950822.1) id OAA05635; Tue, 13 May 1997 14:44:04 -0400 (EDT) Received: from watt.seas.virginia.edu by mail.virginia.edu id aa27361; 13 May 97 14:44 EDT Received: from localhost (psv8b@localhost) by watt.seas.Virginia.EDU (8.8.5/8.6.6) with SMTP id OAA93190 for ; Tue, 13 May 1997 14:44:03 -0400 Date: Tue, 13 May 1997 14:44:03 -0400 (EDT) From: "Venkataraman P.S." To: chemistry@www.ccl.net Subject: CCL: Software for print quality images Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I am looking for a "free" software that would read XYZ co-ordinates of molecules and produce print quality images in black & white. The software should preferably have the following additional features : 1. The names of the atoms should be displayed. Otherwise it is difficult to identify atoms in grey-scale. A ball and stick image would be great. 2. The software should allow translation/rotation of the structure to obtain a suitable view. 3. A unix/PC based application is preferred. If anyone is aware of such a software, kindly let me know directly. I shall be glad to summarize the responses for the benefit of others. Thanks in advance. Venkat ******************************* Venkataraman P.S. Department of chemical engineering University of Virginia Charlottesville Va 22903 ******************************** From brunob@helix.nih.gov Tue May 13 17:42:57 1997 Received: from mgcct6.nci.nih.gov for brunob@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id QAA06486; Tue, 13 May 1997 16:59:47 -0400 (EDT) Received: from mgcct6 (localhost [127.0.0.1]) by mgcct6.nci.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id SAA01205 for ; Tue, 13 May 1997 18:27:40 -0400 Sender: brunob@helix.nih.gov Message-ID: <3378EADC.2781@helix.nih.gov> Date: Tue, 13 May 1997 18:27:40 -0400 From: Bruno Bienfait Organization: National Cancer Institute X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Hexadecane/water partition coefficients Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi ! I am looking for a program that can predict the hexadecane/water partition coefficients for organic molecules. Also, is there any database available containing exprimental values ? Thank you in advance,, Bruno -- [ Bruno Bienfait, Ph. D. Laboratory of Medicinal Chemistry ] [ National Cancer Institute ] [ Email : brunob@helix.nih.gov National Institutes of Health ] [ Phone : (301) 402-3111 Building 37, Room 5B20 ] [ Fax : (301) 496-5839 Bethesda Maryland 20892 , USA ] [ WWW : http://schiele.organik.uni-erlangen.de/Bruno_Bienfait ] From online@mactech.com Tue May 13 18:07:56 1997 Received: from xenon.chem.ucla.edu for online@mactech.com by www.ccl.net (8.8.3/950822.1) id QAA06430; Tue, 13 May 1997 16:48:16 -0400 (EDT) Received: from [128.97.76.42] ([128.97.76.42]) by xenon.chem.ucla.edu (8.6.9/8.6.9) with ESMTP id NAA00619; Tue, 13 May 1997 13:52:23 -0700 X-Sender: nick@xenon.chem.ucla.edu Message-Id: In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 13 May 1997 13:48:05 -0700 To: "Venkataraman P.S." From: "nick.c" Subject: Re: CCL:Software for print quality images Cc: chemistry@www.ccl.net Venkataraman, I have always used Chem3D for geneating postscript files of 3D molecular structures. It is configurable to have atom labels or numbers on the atoms, exports postcript form, allows free rotation/translation of structures and fragments, and imports xyz data. There is a Macintosh freeware version of this software available from CamSci at: I've always used the commercial mac version, but they also have a commercial PC version. I'm uncertain what features are available in their freeware version. Hope this helps, ____Nicholas C. DeMello, Ph.D.________________________________________ Online at MacTech Magazine, the Journal of Macintosh Programming http://www.MacTech.com/ _/ _/ _/ _/_/_/ _/ _/ Chemistry: Nick@chem.UCLA.edu _/_/ _/ _/ _/ _/ _/_/_/ MacTech: Online@MacTech.com _/ _/_/ _/ _/ _/ _/ http://www.chem.ucla.edu/~nick/ _/ _/ _/_/_/ _/ _/