From antunez@chem.cinvestav.mx Thu Jul 31 01:14:34 1997 Received: from latina.chem.cinvestav.mx for antunez@chem.cinvestav.mx by www.ccl.net (8.8.3/950822.1) id AAA00856; Thu, 31 Jul 1997 00:50:09 -0400 (EDT) Received: by latina.chem.cinvestav.mx (SMI-8.6/SMI-SVR4) id WAA15226; Wed, 30 Jul 1997 22:48:20 -0600 Date: Wed, 30 Jul 1997 22:48:19 -0600 (CST) From: Sandra Antunez To: Mike Kotelyanskii cc: Jeffrey.Nauss@UC.Edu, chemistry@www.ccl.net Subject: Re: CCL:Molecular Modeling hardware In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A couple of years ago in usenet and at the HotWired site, there was some discussion as to whether SGI could survive the Wintel onslaught. Technical issues such as system bus speed and polygon processing, as well as the ability of big-time users to have the actual operating system modified to suit their needs made it obvious that wintel boxes were precluded from the high end. At the time I expressed the worry that the low and medium ends were exposed, and would soon succumb. OpenGL is native in NT these days, and $1000 will get you some fairly reasonable polygon processing power. At this point, I suspect the main hurdle to be overcome in porting traditional SGI sw to NT is not graphics, but issues peculiar to UNIX such as process management, signals and other low-level programming thigs that differ between Unix and NT. NT 4.0 is the first "decent" MS operating system, which can support most of the functionality you expected from IRIX or Solaris. Intergraph and others now sell big-time graphics software on NT. SGI-based developers will have to do the same. I suspect the market will go to wintel over the course of two or three years to do both mainstream modelling and parallelized numbercrunching. Toy Story is doable on wintel boxes, the only thing missing is a port of the software. A note of caution, though. From a strictly visceral point of view, NT "feels" bulkier or klunkier than unix variants. It seems you need quite a lot more memory to get the same job done. Heinz Hemken hhemken@franchiseloan.com From ckbsjuin@giascl01.vsnl.net.in Thu Jul 31 06:14:36 1997 Received: from giascl01.vsnl.net.in for ckbsjuin@giascl01.vsnl.net.in by www.ccl.net (8.8.3/950822.1) id GAA01816; Thu, 31 Jul 1997 06:07:30 -0400 (EDT) Received: from [202.54.52.117] by giascl01.vsnl.net.in; (5.65v3.2/1.1.8.2/27May97-1036AM) id AA31477; Thu, 31 Jul 1997 15:39:43 +0500 Date: Thu, 31 Jul 1997 15:39:43 +0500 Message-Id: <9707311039.AA31477@giascl01.vsnl.net.in> X-Sender: ckbsjuin@giascl01.vsnl.net.in X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: ghoshal Subject: Reaction Simulation Using Hyperchem Dear friends, I am using hyperchem for windows release 3. I want to simulate an addition reaction eg., reaction of vinylamine with ethylene .I have studied the method suggested in the Hyperchem FAQ , but it does not seem to work. I guess somebody has already solved the problem and appreciate some advise. Thanking you in anticipation. (Ms) N. Ghoshal, Medicinal Chemistry Division, Indian Institute of Chemical Biology, Calcutta-700032,India (nghoshal@hotmail.com) (ckbsjuin@giascl01.vsnl.net.in) ****************************************** Tapan Kumar Ghoshal, Professor E.E, Coordinator, Centre for Knowledge Based System, Jt Director, School of Education Technology, Jadavpur University, Calcutta-700032, India Snail Mail: as above ; Fax: +91-33-472-7723 Voice Phone:+91-33-473-6129 (office), -412-5704 (home) ========== Peace of mind comes from the knowledge that in this world even the minutest flutter of a leaf is predestined. ++++++++++++++++++++++++++++++++++++++++++++++ From s.hogg@ic.ac.uk Thu Jul 31 08:14:39 1997 Received: from romeo.ic.ac.uk for s.hogg@ic.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA02107; Thu, 31 Jul 1997 07:39:02 -0400 (EDT) Received: from helen.mt.ic.ac.uk [155.198.96.140] by romeo.ic.ac.uk with smtp (Exim 1.62 #1) id 0wttZM-0007Jg-00; Thu, 31 Jul 1997 12:39:01 +0100 Message-Id: <3.0.1.32.19970731123558.0072a4e4@155.198.100.1> X-Sender: seth@155.198.100.1 X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Thu, 31 Jul 1997 12:35:58 +0100 To: chemistry@www.ccl.net From: Simon Hogg Subject: Existence of Babel-1.7 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Somebody mentioned to me the existence of babel-1.7 that is an 'enhanced' version of babel. However, I have been unable to find any trace of this on CCL or many other places I have looked and searched. Can anybody confirm the existence of babel-1.7 ?? -- Simon Hogg, Imperial College, London, UK Tel. +44 171 589 5111 ext. 56721 Fax. +44 171 584 3194 Email: s.hogg@ic.ac.uk Glass-List: glass-list@ic.ac.uk From s.hogg@ic.ac.uk Thu Jul 31 08:22:06 1997 Received: from romeo.ic.ac.uk for s.hogg@ic.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA02163; Thu, 31 Jul 1997 07:57:01 -0400 (EDT) Received: from helen.mt.ic.ac.uk [155.198.96.140] by romeo.ic.ac.uk with smtp (Exim 1.62 #1) id 0wttqn-0007Ov-00; Thu, 31 Jul 1997 12:57:01 +0100 Message-Id: <3.0.1.32.19970731125359.006d9150@155.198.100.1> X-Sender: seth@155.198.100.1 X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Thu, 31 Jul 1997 12:53:59 +0100 To: chemistry@www.ccl.net From: Simon Hogg Subject: Summary of .xyz -> .pdb -> .povray (Overdue!!) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Here is a summary of the replies I received some time ago regarding easy transfer of .xyz files produced with Tinker (http://dasher.wustl.edu) to povray files for md trajectory animation. My original question was: > Is there a way to produce POVRAY .pov files from an XYZ input file? I > actually have a concatenated series of xyz data points from an MD > simulation and would like them, so that when read, they would make a > 'movie'. > > I would like to put them into POVRAY in sequence, and render them as a > movie, but what is the best way of doing that? > > I don't really want to have to de-concatenate them, use babel, then > PDB2POV and then render them. I *think* I have seen someone do this, > but can't remember who it was, but if anyone can give me a kick in the > right direction, I would be very grateful. And here are some replies; ***From Ernst-Udo Wallenborn you just described it. use babel to make a series babel -ix foo.xyz all -op foo.pdb then use pdb2pov (or povchem) to render them. i know povchem is scriptable, so you can pipe in the commands from a perl or shell script. Real paranoids btw use babel again on each single pdb and convert it from pdb to com and back (to give it a defined standard orientation) and later on don't render the povchem output directly but process the pov files (which can also be automated eg with perl). Then you get a series of images and all you need is something like mpeg_encode. *** ***From: Thomas Wagener you can use REVIEW to convert xyz files to pov. The older version of the program is available for free. As far as I remember the adress is: http://www.chemsoft.com *** ***From: Jeffrey Gosper Re_View will do exactly this and the original version is still free for individual user! Re_View automates the POV interface and will automatically create AAWin animations. Its also extremely easy to generate Mpegs. If you want to depict multiple/partial bonds as well and automatic Mpgeg production then Re_View2 is what you need. *** ***From: "Andrew Dalke" You might be interested in a program I helped develop, VMD (http://www.ks.uiuc.edu/Research/vmd/), which reads and animates xyz files and can save the images to POV-Ray. There is an example of how to generate movies (in this case for Raster3D) at http://www.ks.uiuc.edu/Research/vmd/workshop/movie.html which you might find useful. VMD works best on SGIs and is somewhat on the slow side for most Linux machines. There is also an HP version. ***END*** -- Simon Hogg, Imperial College, London, UK Tel. +44 171 589 5111 ext. 56721 Fax. +44 171 584 3194 Email: s.hogg@ic.ac.uk Glass-List: glass-list@ic.ac.uk From ccl@www.ccl.net Tue Jul 29 03:33 EDT 1997 Date: Thu, 24 Jul 1997 00:38:42 +0200 From: Shu-Kun Lin To: chemistry@www.ccl.net Subject: 97.09.01 1st Electronic Conf. on Synthetic Organic Chem Dear colleague, Can you please tell me how can I subscribe to chemistry@www.ccl.net? Please do me a favour by forwarding the following message to it: Dear colleagues: The First Electronic Conference on Synthetic Organic Chemistry (ECSOC-1) will be held on the Internet and Web during September 1- 30, 1997. The conference website is http://mdpi.org/ecsoc-1.htm in the US and http://www.unibas.ch/mdpi/ecsoc-1.htm in Europe The deadline for sending abstracts for consideration is extended to 30 July 1997. The Deadline for sending posters will be 15 August 1997. Sincerely, Shu-Kun Lin ecsoc-1@mdpi.org From magan@aec.co.za Thu Jul 31 11:14:41 1997 Received: from firewall.aec.co.za for magan@aec.co.za by www.ccl.net (8.8.3/950822.1) id LAA03677; Thu, 31 Jul 1997 11:04:30 -0400 (EDT) Received: by firewall.aec.co.za; id KAA13190; Wed, 25 Jun 1997 10:42:16 +0200 (SAT) Received: from aec.co.za(168.206.10.91) by firewall.aec.co.za via smap (3.2) id xma013187; Wed, 25 Jun 97 10:42:06 +0200 Received: from UNIXBACK/SpoolDir by aec.co.za (Mercury 1.21); 25 Jun 97 10:43:55 +0200 Received: from SpoolDir by UNIXBACK (Mercury 1.30); 25 Jun 97 10:43:52 +0200 Received: from MaganG.aec.co.za by aec.co.za (Mercury 1.30); 25 Jun 97 10:43:42 +0200 Received: by MaganG.aec.co.za with Microsoft Mail id <01BC8187.26968CE0@MaganG.aec.co.za>; Wed, 25 Jun 1997 16:45:12 -0700 Message-ID: <01BC8187.26968CE0@MaganG.aec.co.za> From: Magan Govender To: "'chemistry@www.ccl.net'" Subject: RE: UF6 Calculations Date: Wed, 25 Jun 1997 16:45:06 -0700 Return-Receipt-To: MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Netters I am interested in running calculations on UF6 using the basis set of Hay et al, with the G94W, E program. Does anyone know of recent work done on UF6 using the ab initio methods. Many Thanks Magan From jkl@ccl.net Thu Jul 31 13:13:29 1997 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.8.3/950822.1) id NAA04496; Thu, 31 Jul 1997 13:11:46 -0400 (EDT) Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.6/950822.1) id NAA03601; Thu, 31 Jul 1997 13:11:44 -0400 (EDT) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id NAA00661; Thu, 31 Jul 1997 13:11:43 -0400 (EDT) Date: Thu, 31 Jul 1997 13:11:43 -0400 (EDT) Message-Id: <199707311711.NAA00661@krakow.ccl.net> To: chemistry@www.ccl.net Subject: Silicon Graphics response to our CCL discussion Cc: jkl@ccl.net Dear CCL, In response to our discussion about Silicon Graphics, I received an e-mail from David Zirl containing an official position from Gary L. Lauer, the president of World Trade Corporation, on this issue. I enclose the plain text transcript of this letter below. Since the transcript may contain errors, please refer to the original PostScript file which is available in CCL archives as: ftp://www.ccl.net/pub/chemistry/hardware/sgi/sgilett.ps Quoting from the letter of David Zirl: > Dear Colleages > > I've attached a letter from the President of our sales > organization that I hope helps alleviate some of the concerns about > Silicon Graphics. If you are unable to read this file and if you have > further questions regarding SGI's committment to the molecular modeling > market including our committment to the software vendors and most > importantly our committment to you, our customers, please contact me > directly. > > You can read about our Q4 results at: > > http://www.sgi.com/Headlines/1997/July/Q4_results.html > > Thanks > > David > -- > > David M. Zirl, PhD > Silicon Graphics, Inc. > Mailstop 8L-580 e-mail dzirl@sgi.com > Chemistry Market Manager http://www.sgi.com/ChemBio > 2011 N. Shoreline Boulevard office: (415) 933-6577 > Mountain View, CA 94043-1389 fax: (415) 932-6577 I am posting this information to CCL hoping that it will contribute to a balanced view about Silicon Graphics situation. Jan Labanowski jkl@ccl.net ---- /* The original letter is in sgilett.ps -- This is a transcript which * may contain errors. When in doubt, please consult the original * Jan Labanowski */ /LOGO/ Silicon Graphics Computer Systems/Cray Research 2011 N. Shoreline Boulevard Mountain View, California 94043-1389 Telephone (415) 960-1980 Fax (415) 961 0590 July 31, 1997 Computational Chemistry List c/o Jan Labanowski Dear Colleagues: You may have read the recent Business Week article on Silicon Graphics. It is ironic that the issue hit the stands the day after we reported the best quarter in our history. Frankly speaking, most of the story was old news and missed the point where Silicon Graphics is today. Yes, Silicon Graphics has had some problems over the past couple of years. We recongnized those problems, we accepted responsibility, and our management team has been working hard to address them. Strong actions have been taken and we are seeing the results as evidenced by our outstanding 4th quarter. We are also very optimistic about this coming year and beyond. This quarter was a reflection of our ability to execute. Our product transition is complete, we are shipping our entire product line without significant constraints and most imnportantly, the new products are finding strong acceptance by you, our customer. We are entering the new fiscal year with our entire organization aligned to build on this success. Most importantly, we are committed to providing you with the best products and solutions in the industry. Moving forward, we have renewed our commitment to make customer service and satisfaction our number one priority. I am confident that as a most valued customer you will continue to experience the dedication and creativity of the entire Silicon Graphics organization. Thank you for your business. Sincerely, /-/ Gary L. Lauer President World Trade Corporation From desingh@syr.edu Thu Jul 31 15:14:43 1997 Received: from mailbox.syr.edu for desingh@syr.edu by www.ccl.net (8.8.3/950822.1) id OAA05018; Thu, 31 Jul 1997 14:26:12 -0400 (EDT) Received: from dirac.syr.edu (syru33-128.syr.edu [128.230.33.128]) by mailbox.syr.edu (8.8.5/8.8.5) with SMTP id OAA08539 for ; Thu, 31 Jul 1997 14:26:11 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <33E0F9EE.59E2@syr.edu> Date: Thu, 31 Jul 1997 16:47:42 -0400 From: Deepak Singh Organization: Dept. of Chemistry & W. M. Keck Center for molecular electronics X-Mailer: Mozilla 3.0SC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: computational chem list Subject: Joining the list Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello everyone, I have recently started doing computational work and would like to get onto the list. How do I do this? Thank you -- Deepak. ---------------------------------------------------------------------- Deepak Singh Graduate Student Department of Chemistry & W. M. Keck Center for Molecular Electronics Syracuse University Syracuse, NY 13244 Voice: (315) 443 5928, 443 1739 email:desingh@syr.edu Fax : (315) 443 4070 URL:http://web.syr.edu/~desingh ----------------------------------------------------------------------- From baker@terminator.chem.uiowa.edu Thu Jul 31 16:14:43 1997 Received: from ns-mx.uiowa.edu for baker@terminator.chem.uiowa.edu by www.ccl.net (8.8.3/950822.1) id PAA05282; Thu, 31 Jul 1997 15:52:29 -0400 (EDT) Received: from terminator.chem.uiowa.edu (terminator.chem.uiowa.edu [128.255.69.76]) by ns-mx.uiowa.edu (8.8.5/8.8.5) with SMTP id OAA24942 for <@ns-mx.uiowa.edu:chemistry@www.ccl.net>; Thu, 31 Jul 1997 14:52:29 -0500 Received: by terminator.chem.uiowa.edu (940816.SGI.8.6.9/940406.SGI) id OAA09502; Thu, 31 Jul 1997 14:53:33 -0700 Date: Thu, 31 Jul 1997 14:53:32 -0700 (PDT) From: "Nathan A. Baker" To: chemistry@www.ccl.net Subject: Gaussian 94's "Standard Orientation" Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi -- I was wondering if anyone knew the rules for G94's transformation of the input coorindates into the standard orientation printed out by Link L301. I have a charge distribution that needs to be transformed into standard orientation and it would be nice to know what Gaussian is doing. Thanks! ----------------------------------------------- Nathan Baker * baker@terminator.chem.uiowa.edu HELP! MY TYPEWRITER IS BROKEN! -- E. E. CUMMINGS ----------------------------------------------- From ccl@www.ccl.net Mon Jul 28 15:14:03 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id OAA14836; Mon, 28 Jul 1997 14:45:59 -0400 (EDT) Received: from wugate.wustl.edu for reichertd@mirlink.wustl.edu by bedrock.ccl.net (8.8.6/950822.1) id OAA03156; Mon, 28 Jul 1997 14:45:57 -0400 (EDT) Received: from mirlink.wustl.edu (mirlink.wustl.edu [128.252.155.1]) by wugate.wustl.edu (8.8.5/8.8.5) with SMTP id NAA26172 for ; Mon, 28 Jul 1997 13:45:59 -0500 (CDT) Message-ID: Date: 28 Jul 1997 13:43:44 -0500 From: "David Reichert" Subject: MM parameter development To: "CCL post" X-Mailer: Mail*Link SMTP-MS 3.0.2 I'm looking for some info and/or code to help automate the development of forcefield parameters. Given a set of x-ray or NMR structures and/or results from ab initio calculations are there programs that can automate the development of parameters for a given forcefield, ie eq bondlengths, angles, stretching constants etc... Any pointers would be greatly appreciated. (I'm getting tired of doing this by hand, there must be a better tool somewhere !) thanks, ************************************************ * David E. Reichert, Ph.D. * * Mallinckrodt Inst. of Radiology * * Div. Radiological Sciences, * * Washington University School of Medicine * * 510 S. Kingshighway Blvd., Campus Box 8225 * * St. Louis, MO 63110 * * * * phone: (314)362-8461 * * fax: (314)362-9940 * * e-mail: reichertd@mirlink.wustl.edu * ************************************************ From ep7@dent.okayama-u.ac.jp Mon Jul 28 22:14:08 1997 Received: from deews1.dent.okayama-u.ac.jp for ep7@dent.okayama-u.ac.jp by www.ccl.net (8.8.3/950822.1) id VAA17558; Mon, 28 Jul 1997 21:34:40 -0400 (EDT) From: Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.7.5+2.6Wbeta6/3.3W9) with SMTP id JAA25681 for ; Tue, 29 Jul 1997 09:43:53 +0900 (JST) Message-Id: <199707290043.JAA25681@deews1.dent.okayama-u.ac.jp> Date: Tue, 29 Jul 1997 09:49:37 +0900 To: CHEMISTRY@www.ccl.net Subject: Re: Gauss View MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Hello, I received a answer for the following questions: I would like to ask you about Gauss View. How can I use Gauss View ? For example, must we compile Gauss View with Gaussian 94 ? Please replay to me. Date: Mon, 07 Jul 1997 08:53:32 -0700 (PDT) From: Wayne Steinmetz Subject: Re: CCL:CCL: Gauss View To: ep7@dent.okayama-u.ac.jp Content-type: TEXT/PLAIN; CHARSET=US-ASCII We run GAuss View on a Silicon Graphics workstation. Gaussian is finally following the example of most software vendors and ships an executable for Gauss View. Hence, you do not have to compile anything in order to use Gauss View. However, Gauss View requires the latest version of Gaussian and you will need the updates. Unfortunately, Gaussian only ships source code for Gaussian 94. My related questions are: Gaussian 94 Revision C.3 or Revision D.3 are OK ? What you feel about Gauss View ? Date: Sun, 20 Jul 1997 20:58:41 -0700 (PDT) From: Wayne Steinmetz Subject: Re: Gauss View To: ep7@dent.okayama-u.ac.jp Content-type: TEXT/PLAIN; CHARSET=US-ASCII Sorry about the delay. Gauss View requires the e2 version of Gaussian to run properly. That is we are running the g94e2 executable. When we ordered Gaussian, we received the previous version. Since the order for Gauss View was placed shortly thereafter we were not charged for the required upgrades to Gauss View. We are quite pleased with the performance of Gauss View and now use it as the entry point for most Gaussian calculations. We have used Sybyl to prepare the input file. That works too but ordering Sybyl just as a GUI for Gaussian would not be a very cost-effective solution. If you do not have licenses for other packages which are compatible with Gaussian, Gauss View is a very good solution. We are glad that we made the investment. Wayne Steinmetz Pomona College From chan@uni-muenster.de Tue Jul 29 05:14:10 1997 Received: from asterix.uni-muenster.de for chan@uni-muenster.de by www.ccl.net (8.8.3/950822.1) id FAA19337; Tue, 29 Jul 1997 05:11:23 -0400 (EDT) Received: from localhost (chan@localhost) by asterix.uni-muenster.de (8.7.5/8.7.5) with SMTP id LAA66552 for ; Tue, 29 Jul 1997 11:11:19 +0200 X-Authentication-Warning: asterix.uni-muenster.de: chan owned process doing -bs Date: Tue, 29 Jul 1997 11:11:19 +0200 (MES) From: "Jerry C.C. Chan" To: CHEMISTRY@www.ccl.net Subject: Diffuse and Polarization functions for TZV basis set Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers, We are working on DFT calculations of molecules containing C, F, etc, using TZVP basis set (UniChem_basis). Could anyone please tell us where we can get some appropriate diffuse and polarization functions for the first two row elements? I will summarize. Many thanks, Jerry ****************************************************************** * Jerry Chun Chung CHAN chan@moorea.uni-muenster.de * * * * Universitaet Muenster phone: 0049-251-83-29156 * * Institut fuer Physikalische Chemie fax: 0049-251-83-29159 * * Schlossplatz 4-7 * * D-48149 Muenster * * Germany * ****************************************************************** From choic@gusun.georgetown.edu Tue Jul 29 11:14:15 1997 Received: from gusun.georgetown.edu for choic@gusun.georgetown.edu by www.ccl.net (8.8.3/950822.1) id LAA20818; Tue, 29 Jul 1997 11:05:17 -0400 (EDT) Received: from molmod.georgetown.edu (molmod.chem.georgetown.edu [141.161.23.55]) by gusun.georgetown.edu (8.8.5/8.8.5) with SMTP id LAA11394 for ; Tue, 29 Jul 1997 11:03:21 -0400 (EDT) Message-Id: <199707291503.LAA11394@gusun.georgetown.edu> From: "Cheol Ho Choi" To: Subject: SUMMARY of NICS Date: Tue, 29 Jul 1997 11:05:58 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0000_01BC9C0F.64664E00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.71.1008.3 X-MimeOle: Produced By Microsoft MimeOLE Engine V4.71.1008.3 This is a multi-part message in MIME format. ------=_NextPart_000_0000_01BC9C0F.64664E00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, Below is a summary of responses to the "NICS(Negative = nucleus-independent chemical shift)". In the pursuit of the reliable = definition of "aromaticity", Schleyer and coworkers have proposed the = NICS (JACS 1996, 118, 6317). Thanks to all who have responded.=20 1) I am not 100% sure that I have calculated NICS correctly, but I = believe I have. Using Gaussian, it is trivial to include a ghost atom (symbol Bq) at the geometric center of a ring, or wherever one wishes to measure the chemical shift. By default, this atom will have no basis functions, but will be used as a point at which to calculate any desired property. = Then, by running a normal NMR calculation, one obtains the chemical shifts for = all atoms, including the ghost atom. Using this method, I have = reproduced results from the recent Jial et al. paper in JACS 1997, 119, 5921 - = 5929, as well as the original NICS paper (Schleyer et al. JACS 1996, 118, 6317 = - 6318), so I believe I am doing it correctly. Regards, Eric #########################################################################= >From the desk of: Dr. Eric V. Patterson=20 Postdoctoral Associate=20 Department of Chemistry voice: (612) 624-1535 University of Minnesota FAX: (612) 626-7541 207 Pleasant St. SE email: patter@pollux.chem.umn.edu Minneapolis, MN 55455 WWW: http://pollux.chem.umn.edu/~patter 2) After reading your NICS-question, I hope that I can give you a brief = view of calculating NICS. With Gaussian94 (also Gaussian92/DFT) it is very easy. A input for = benzene is given below. It is like a normal Gaussian job. $RunGauss # RHF/6-31+G* NMR Test Name=3DXXX C6H6//RBECKE3LYP 6-31G(D)=20 0 1 C 0.00000 0.00000 0.00000 C 1.39659 0.00000 0.00000 C 2.09488 1.20948 0.00000 C 1.39659 2.41896 0.00000 C 0.00000 2.41896 0.00000 C -0.69829 1.20948 0.00000 H -0.54351 -0.94139 0.00000 H 1.94010 -0.94139 0.00000 H 3.18190 1.20948 0.00000 H 1.94010 3.36035 0.00000 H -0.54351 3.36035 0.00000 H -1.78532 1.20948 0.00000 Bq 0.69829 1.20948 0.00000 (in the center) Bq 0.69829 1.20948 0.50000 (0.5A above the center) Bq 0.69829 1.20948 1.00000 (0.5A above the center) Bq 0.69829 1.20948 1.50000 (1.0A above the center) Bq 0.69829 1.20948 2.00000 (1.5A above the center) Bq 0.69829 1.20948 2.50000 (2.0A above the center) You can calculat the NICS not only at the ring center, but also above = the ring center (also every point you wish) We recommand the 6-31+G* basis set, but you can use another basis sets = dependingon the systems used and your CPU time. In the keyword line, NMR means by default NMR=3DGIAO.=20 In the output file, you will find the calculated magnetic shielding = constant at the every point you have chosen. With sign conversion, e.g., the = negative of the magnetic shielding is the NICS (in agreement with 1H chemical = shifts). For the regular and plane molecules, it is not difficult to find the = geometricalpoint, but you will have trouble with non-plane or = 3D-molecules. For this purpose, I strongly recommand the molecule = program written by Dr. Hommes. This programhas many advantage over many = other softwares. You can contact him to get more information (hommes@ccc.uni-erlangen.de). This will help not only for = NICS calculations, but also for generating Gaussian inputs, as well as for = visualizing your optimized geometry and vibration model, and drawing = high quality plots for your publication. If you have another question, please let me know. Sincerely yours Dr. Haijun Jiao=20 Computer Chemistry Center Institut fuer Organische Chemie Universitaet Erlangen-Nuernberg Henkestr. 42 91054-Erlangen Germany e-mail: haijun@ccc.uni-erlangen.de Fax: 0049-9131-85-6533 ------=_NextPart_000_0000_01BC9C0F.64664E00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

 Dear = CCLers,
Below is a = summary of responses=20 to the "NICS(Negative nucleus-independent chemical = shift)".  In=20 the pursuit of the reliable definition of "aromaticity", = Schleyer and=20 coworkers have proposed the NICS (JACS 1996, 118, 6317). = Thanks to all who = have=20 responded. 

 

1) I am not 100% sure = that I have=20 calculated NICS correctly, but I believe I
have.  Using = Gaussian, it is=20 trivial to include a ghost atom (symbol Bq)
at the geometric center = of a=20 ring, or wherever one wishes to measure the
chemical shift.  By = default,=20 this atom will have no basis functions, but
will be used as a point = at which=20 to calculate any desired property.  Then,
by running a normal = NMR=20 calculation, one obtains the chemical shifts for
all atoms, = including the=20 ghost atom.  Using this method, I have reproduced
results from = the=20 recent Jial et al. paper in JACS 1997, 119, 5921 - 5929,
as well as = the=20 original NICS paper (Schleyer et al. JACS 1996, 118, 6317 -
6318), so = I=20 believe I am doing it=20 correctly.

Regards,
Eric

###############################= ##########################################

>From=20 the desk of:

Dr. Eric V. Patterson
Postdoctoral Associate=20

Department of Chemistry voice: (612) 624-1535
University of = Minnesota=20 FAX: (612) 626-7541
207 Pleasant St. SE email: patter@pollux.chem.umn.edu=
Minneapolis,=20 MN 55455 WWW: http://pollux.chem.umn.edu/~p= atter

 

2) After = reading your=20 NICS-question, I hope that I can give you a brief view
of calculating = NICS.

With Gaussian94 (also Gaussian92/DFT) it is very easy. A = input for=20 benzene
is given below. It is like a normal Gaussian=20 job.

$RunGauss
# RHF/6-31+G* NMR Test = Name=3DXXX

C6H6//RBECKE3LYP=20 6-31G(D)

0 1
C 0.00000 0.00000 0.00000
C 1.39659 0.00000=20 0.00000
C 2.09488 1.20948 0.00000
C 1.39659 2.41896 0.00000
C = 0.00000=20 2.41896 0.00000
C -0.69829 1.20948 0.00000
H -0.54351 -0.94139=20 0.00000
H 1.94010 -0.94139 0.00000
H 3.18190 1.20948 0.00000
H = 1.94010=20 3.36035 0.00000
H -0.54351 3.36035 0.00000
H -1.78532 1.20948=20 0.00000
Bq 0.69829 1.20948 0.00000 (in the center)
Bq 0.69829 = 1.20948=20 0.50000 (0.5A above the center)
Bq 0.69829 1.20948 1.00000 (0.5A = above the=20 center)
Bq 0.69829 1.20948 1.50000 (1.0A above the center)
Bq = 0.69829=20 1.20948 2.00000 (1.5A above the center)
Bq 0.69829 1.20948 2.50000 = (2.0A=20 above the center)

You can calculat the NICS not only at the ring = center,=20 but also above the
ring center (also every point you wish)

We=20 recommand the 6-31+G* basis set, but you can use another basis sets = dependingon=20 the systems used and your CPU time.

In the keyword line, NMR = means by=20 default NMR=3DGIAO.

In the output file, you will find the = calculated=20 magnetic shielding constant at
the every point you have chosen. With = sign=20 conversion, e.g., the negative of
the magnetic shielding is the NICS = (in=20 agreement with 1H chemical shifts).

For the regular and plane = molecules,=20 it is not difficult to find the geometricalpoint, but you will have = trouble with=20 non-plane or 3D-molecules. For this purpose, I strongly recommand the = molecule=20 program written by Dr. Hommes. This programhas many advantage over many = other=20 softwares. You can contact him to get more
information (hommes@ccc.uni-erlangen.de= ). This=20 will help not only for NICS
calculations, but also for generating = Gaussian=20 inputs, as well as for visualizing your optimized geometry and vibration = model,=20 and drawing high quality plots for your publication.


If you = have=20 another question, please let me know.

Sincerely yours

Dr. = Haijun=20 Jiao
Computer Chemistry Center
Institut fuer Organische=20 Chemie
Universitaet Erlangen-Nuernberg
Henkestr.=20 42
91054-Erlangen
Germany

e-mail: haijun@ccc.uni-erlangen.de=
Fax:=20 0049-9131-85-6533
 ------=_NextPart_000_0000_01BC9C0F.64664E00-- From hofmann@thkin.pci.uni-leipzig.de Tue Jul 29 12:14:15 1997 Received: from pcjan.chemie.uni-leipzig.de for hofmann@thkin.pci.uni-leipzig.de by www.ccl.net (8.8.3/950822.1) id LAA21069; Tue, 29 Jul 1997 11:28:28 -0400 (EDT) Received: from localhost (hofmann@localhost) by pcjan.chemie.uni-leipzig.de (8.8.5/8.8.5) with SMTP id RAA12137 for ; Tue, 29 Jul 1997 17:30:11 +0200 X-Authentication-Warning: pcjan.chemie.uni-leipzig.de: hofmann owned process doing -bs Date: Tue, 29 Jul 1997 17:30:10 +0200 (MEST) From: Alexander Hofmann X-Sender: hofmann@pcjan.chemie.uni-leipzig.de To: chemistry@www.ccl.net Subject: Basisset for Pt with f-functions Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello together, a collegue is searching for a Pt basis with f-functions and (if available) the related ECP for the core would be great. Thank you very much Alex ------------------------------------------------------------------------- | | | | Alexander Hofmann | Phone (office) +49-341-97-36337 | | Institut fuer Physikalische | Fax (office) +49-341-97-30099 | | und Theoretische Chemie | | | Augustusplatz 10-11 | hofmann@thkin.pci.uni-leipzig.de | | | | | D-04109 Leipzig | http://www.uni-leipzig.de/~quant | | | /hofmann/alex.html | ------------------------------------------------------------------------- From dzirl@sgi.com Wed Jul 30 16:28:18 1997 Received: from sgi.sgi.com for dzirl@sgi.com by www.ccl.net (8.8.3/950822.1) id QAA29355; Wed, 30 Jul 1997 16:11:34 -0400 (EDT) Received: from cthulhu.engr.sgi.com (cthulhu.engr.sgi.com [192.26.80.2]) by sgi.sgi.com (950413.SGI.8.6.12/970507) via ESMTP id NAA02688 for <@sgi.engr.sgi.com:chemistry@www.ccl.net>; Wed, 30 Jul 1997 13:11:34 -0700 env-from (dzirl@sgi.com) Received: from nyknicks.engr.sgi.com (nyknicks.engr.sgi.com [198.29.106.29]) by cthulhu.engr.sgi.com (950413.SGI.8.6.12/960327.SGI.AUTOCF) via ESMTP id NAA00923 for <@cthulhu.engr.sgi.com:chemistry@www.ccl.net>; Wed, 30 Jul 1997 13:10:58 -0700 Received: from nyknicks (localhost [127.0.0.1]) by nyknicks.engr.sgi.com (950413.SGI.8.6.12/960327.SGI.AUTOCF) via SMTP id MAA10910 for ; Wed, 30 Jul 1997 12:55:08 -0700 Sender: dzirl@sgi.com Message-ID: <33DF9C1C.15FB@sgi.com> Date: Wed, 30 Jul 1997 12:55:08 -0700 From: David Zirl X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Silicon Graphics Content-Type: multipart/mixed; boundary="------------59E21CFB3F54" This is a multi-part message in MIME format. --------------59E21CFB3F54 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleages I've attached a letter from the President of our sales organization that I hope helps alleviate some of the concerns about Silicon Graphics. If you are unable to read this file or if you have further questions regarding SGI's continued committment to the molecular modeling market including our committment to the software vendors and most importantly our committment to you, our customers, please contact me directly. You can read about our Q4 results at: http://www.sgi.com/Headlines/1997/July/Q4_results.html Thanks David -- David M. Zirl, PhD Silicon Graphics, Inc. Mailstop 8L-580 e-mail dzirl@sgi.com Chemistry Market Manager http://www.sgi.com/ChemBio 2011 N. Shoreline Boulevard office: (415) 933-6577 Mountain View, CA 94043-1389 fax: (415) 932-6577 --------------59E21CFB3F54 Content-Type: application/postscript; name="jan.ps" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="jan.ps" %!PS-Adobe-3.0 %%BoundingBox: 54 72 558 720 %%Creator: Mozilla (NetScape) HTML->PS %%DocumentData: Clean7Bit %%Orientation: Portrait %%Pages: 1 %%PageOrder: Ascend %%Title: file:/disk2/khw/Projects/Gary_Letter/gary_letter_7_29_97.html %%EndComments %%BeginProlog [ /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /space /exclam /quotedbl /numbersign /dollar /percent /ampersand /quoteright /parenleft /parenright /asterisk /plus /comma /hyphen /period /slash /zero /one /two /three /four /five /six /seven 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fffffffffffffffffffffffffffffffffffffffffffffffffffffffefffffefffffefffffeffff fefffffeffffffffefffffefffffefffffeffffffffeffffffffeffffffffeffffffffffffffef fffffffeffffffffefffffefffffefffffefffffeffffffffefffffefffffeffff0 grestore 353.2 702.3 moveto 8 f2 (2011 N. Shoreline Boulevard) show 353.3 693.6 moveto 8 f2 (Mountain View, California 94043-1389) show 353.2 684.9 moveto 8 f2 (Telephone \(415\) 960-1980) show 353.2 676.2 moveto 8 f2 (Fax \(415\) 961-0590) show 0 653.2 moveto 12 f0 (July 31, 1997) show 0 626.6 moveto 12 f0 (Computational Chemistry List) show 0 613.3 moveto 12 f0 (c/o Jan Labanowski) show 0 600 moveto 12 f0 () show 0 586.7 moveto 12 f0 ( ) show 0 560.1 moveto 12 f0 (Dear Colleagues: ) show 0 533.5 moveto 12 f0 (You may have read the recent Business Week article on Silicon Graphics. It is ironic that the issue hit) show 0 520.2 moveto 12 f0 (the stands the day after we reported the best quarter in our history. ) show 0 493.6 moveto 12 f0 (Frankly speaking, most of the story was old news and missed the point of where Silicon Graphics is) show 0 480.3 moveto 12 f0 (today. Yes, Silicon Graphics has had some problems over the past couple of years. We recognized those) show 0 467 moveto 12 f0 (problems, we accepted responsibility, and our management team has been working hard to address) show 0 453.7 moveto 12 f0 (them. Strong actions have been taken and we are seeing the results as evidenced by our outstanding 4th) show 0 440.4 moveto 12 f0 (quarter. ) show 0 413.8 moveto 12 f0 (We are also very optimistic about this coming year and beyond. This quarter was a reflection of our) show 0 400.5 moveto 12 f0 (ability to execute. Our product transition is complete, we are shipping our entire product line without) show 0 387.2 moveto 12 f0 (significant constraints and most importantly, the new products are finding strong acceptance by you, our) show 0 373.9 moveto 12 f0 (customer. We are entering the new fiscal year with our entire organization aligned to build on this) show 0 360.6 moveto 12 f0 (success. ) show 0 334 moveto 12 f0 (Most importantly, we are committed to providing you with the best products and solutions in the) show 0 320.7 moveto 12 f0 (industry. Moving forward, we have renewed our commitment to make customer service and satisfaction) show 0 307.4 moveto 12 f0 (our number one priority. ) show 0 280.8 moveto 12 f0 (I am confident that as a most valued customer you will continue to experience the dedication and) show 0 267.5 moveto 12 f0 (creativity of the entire Silicon Graphics organization. ) show 0 240.9 moveto 12 f0 (Thank you for your business. ) show 0 214.3 moveto 12 f0 (Sincerely, ) show gsave /rowdata 272 string def 0 157.8 translate 126.7 40.6 scale 181 58 4 [181 0 0 -58 0 58] smartimage12rgb ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff 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ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff0 grestore 126.7 157.8 moveto 12 f0 ( ) show 0 144.5 moveto 12 f0 (Gary L. Lauer) show 0 131.2 moveto 12 f0 (President) show 0 117.9 moveto 12 f0 (World Trade Corporation) show pagelevel restore showpage %%EOF --------------59E21CFB3F54-- From ccl@www.ccl.net Wed Jul 30 17:14:30 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id QAA29433; Wed, 30 Jul 1997 16:23:01 -0400 (EDT) Received: from bioc1.msi.com for dgregory@msi.com by bedrock.ccl.net (8.8.6/950822.1) id QAA11010; Wed, 30 Jul 1997 16:22:59 -0400 (EDT) Received: by bioc1.msi.com (5.64/0.0) id AA19117; Wed, 30 Jul 97 13:22:29 -0700 Received: from biff.msi.com(146.202.0.225) by bioc1.msi.com via smap (V2.0) id xma019106; Wed, 30 Jul 97 13:22:19 -0700 Received: from dxg-pc.msi.com by biff.msi.com.biosym.com (4.1/SMI-4.1) id AA25755; Wed, 30 Jul 97 13:21:30 PDT Message-Id: <3.0.32.19970730132134.0074a5dc@146.202.0.225> X-Sender: dgregory@146.202.0.225 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 30 Jul 1997 13:21:35 -0700 To: chemistry@ccl.net (Comp. Chem. List) From: Don Gregory Subject: Re: CCL:CHM:Trajectory animation Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi Brian, Jakob Hallaska has done some very fine work with Quanta/CHARMm animations. I'd encourage you to have a look at: http://www.molbio.su.se/~jakob/COMPLETE_QUANTA.html Don Gregory **************************************************** At 11:27 AM 7/25/97 -0700, you wrote: > > How are people out there animating CHARMM trajectory (.dcd) files? > > I know this is a FAQ, but in scanning the archives I saw only > the use of VMD/NAMD (which I'm not knocking, I intend to try > them). > > I could kludge together a script which takes the output of > a number of programs in order to extract frames the CHARMM trajectory > and then save them as say MPEGs, but I'd rather not reinvent the > wheel if I don't have to. > > I know QUANTA animates trajectories nicely. Can you take a > screen movie on SGI's like you can take a snapshot? Does anyone > have experience doing this and could give me pointers. > > I will of course summarize if there's interest. > > -Brian > >-- >============================================================================= >| .---------.| Brian W. Beck | E-mail Addresses: | >|/\ | || Biochem/Biophysics | brian@bert.chem.wsu.edu | >|| \\ WSU || Washington St. Univ| brian_beck@wsu.edu | >|\ - *|| 639 Fulmer | URL http://elmo.chem.wsu.edu/~brian | >| | || Pullman, WA, USA | VOICE (509) 335-4083 | >| \___________|| 99164-4660 | FAX (509) 335-9688 | >============================================================================= > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: brian@bert.chem.wsu.edu >-- Original Sender From: Address: brian@bert.chem.wsu.edu >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 iguana@one.net Wed Jul 30 22:14:33 1997 Received: from one.net for iguana@one.net by www.ccl.net (8.8.3/950822.1) id VAA00649; Wed, 30 Jul 1997 21:56:26 -0400 (EDT) Received: from shell.one.net (iguana@shell.one.net [206.112.192.106]) by one.net (8.8.4/8.7.5) with ESMTP id VAA15359 for ; Wed, 30 Jul 1997 21:56:20 -0400 Received: from localhost (iguana@localhost) by shell.one.net (8.8.6/8.7.3) with SMTP id VAA10337 for ; Wed, 30 Jul 1997 21:56:20 -0400 X-Authentication-Warning: shell.one.net: iguana owned process doing -bs Date: Wed, 30 Jul 1997 21:56:18 -0400 (EDT) From: Ray Crawford To: chemistry@www.ccl.net Subject: xspread In-Reply-To: <33DC42B9.41C6@h1tw0036.hoechst.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Sorry to reply to the list, but I deleted the originating message... The xspread program source can be retrieved from: http://www.freebsd.org/ports/math.html#xspread-2.1 Later, Ray Crawford The Procter & Gamble Company crawford.ra@pg.com