From hutschka@quantix.u-strasbg.fr Wed Apr 17 04:47:20 1996 Received: from quantix.u-strasbg.fr for hutschka@quantix.u-strasbg.fr by www.ccl.net (8.7.1/950822.1) id EAA13554; Wed, 17 Apr 1996 04:25:29 -0400 (EDT) From: Received: by quantix.u-strasbg.fr (AIX 3.2/UCB 5.64/4.03) id AA18765; Wed, 17 Apr 1996 10:25:29 +0200 Date: Wed, 17 Apr 1996 10:25:29 +0200 Message-Id: <9604170825.AA18765@quantix.u-strasbg.fr> To: CHEMISTRY@www.ccl.net Subject: Input Gaussian 92 Hello, I have a simple question: I'm using g92 and I use a pseudopotential that I put in my input file (PSEUDO=CARDS) The problem is that I've got 55 atoms and the first line in the pseudo input card is not long enough to write the numbers (7 and 9) used to specify which atom is described with the pseudo. Does anybody knows how to do this ?? Thanks . HUTSCHKA Francois Laboratory of Quantum Chemistry STRASBOURG FRANCE E-Mail:hutschka@quantix.u-strasbg.fr From ragno@serifos.caspur.it Wed Apr 17 05:03:21 1996 Received: from serifos.caspur.it for ragno@serifos.caspur.it by www.ccl.net (8.7.1/950822.1) id DAA13310; Wed, 17 Apr 1996 03:46:41 -0400 (EDT) Received: by serifos.caspur.it; id AA25697; Wed, 17 Apr 1996 09:46:16 +0200 Date: Wed, 17 Apr 1996 09:46:16 +0200 (MET DST) From: Gianluca Sbardella To: chemistry@www.ccl.net Cc: jkl@ccl.net Subject: Re: CCL:MAILIG LISTS (again ?!) (fwd) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here is the key of the mistery!! Thank you, John-M. ***************************************************************** * * * Dr. Gianluca Sbardella E-mail: ragno@kea.caspur.it * * Dip. Studi Farmaceutici ragno@serifos.caspur.it * * Universita' "La Sapienza" Phone: 39-6-49913814 * * P.le A. Moro, 5 Fax: 39-6-491491 * * 00185 Roma * * ITALY * ***************************************************************** ---------- Forwarded message ---------- Date: Tue, 16 Apr 1996 15:42:48 -0300 (ADT) From: John-M. Sichel To: Gianluca Sbardella Cc: Jan Labanowski Subject: Re: CCL:MAILIG LISTS (again ?!) On Tue, 16 Apr 1996, Gianluca Sbardella wrote: > Hi again, > I already sent a CCL message with the list in ASCII format. > Anyway, if anybody didn't receive it, please write me back and I'll send > him (or her) again. I have solved the mystery of your missing message. I didn't receive the ASCII message either, so I looked in the CCL archives on the WWWeb. It is in the _reject_ file of messages which are not posted to the list but only archived. I don't know why it is in the reject file, but you could ask the list co-ordinator = Jan Labanowski (jkl@ccl.net). Perhaps he doesn't like your sending the same message twice, but for people like me who can't read MIME the ASCII version is much better. Anyway your list looks very useful, thank you. I succeeded in downloading the file from the Archives so I don't need another copy. John-M. Sichel Dept. de chimie et biochimie Universite de Moncton Moncton NB, Canada E1A 3E9 Tel: (506-)858-4313 E-mail: SICHELJ@UMONCTON.CA I know you believe you understand what you think I said, but I am not sure you realize that what you heard is not what I meant. (Gaussian92) From golb@osi.lanet.lv Wed Apr 17 05:48:16 1996 Received: from sg.osi.lanet.lv for golb@osi.lanet.lv by www.ccl.net (8.7.1/950822.1) id FAA14705; Wed, 17 Apr 1996 05:37:24 -0400 (EDT) Received: from localhost (golb@localhost) by sg.osi.lanet.lv (8.7.4/8.7.3) with SMTP id LAA02874; Wed, 17 Apr 1996 11:03:30 +0300 X-Authentication-Warning: sg.osi.lanet.lv: golb owned process doing -bs Date: Wed, 17 Apr 1996 11:03:29 +0300 (EET DST) From: Alexander Golbraikh To: "Brian W. Beck" cc: chemistry@www.ccl.net Subject: Re: CCL:Inside or outside of a polyhedron In-Reply-To: <9604161535.AA22114@bert.chem.wsu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 16 Apr 1996, Brian W. Beck wrote: > Alexander Golbraikh wrote: > : > : > : > : Take any ray beginning at the given point. Count the number of > : points of intersection of this ray with polyhedron surface. If it is > : even, then the point is outside the polyhedron, if it is odd, then inside. > : One precaution: the ray may slide on some edges of the polyhedron. > : > : Best regards, > : Alexander Golbraikh > : > : > ^ / > |/ > < As you say, the ray may slide. The "o" point at the left is > |\ outside the "polyhedron" yet passes through the polyhedron > | \ surface only once if you send the ray only through the vertices > o \ defined by... say the Calphas of a protein. > > -Brian > -- Thank you for your remark. I mean the point must be taken into account in case the ray crosses the surface of the polyhedron, i.e. when any whatever small segment of the ray containing this point contains also points both in the inside and in the outside of the polyhedron. Both cases could be easily discriminated. You may also ask what to do if the given point belongs to the polyhedron surface. In this case all depends on which polyhedron we consider: the closed or the open one. (If we consider that the border (the surface) of the polyhedron belongs to the polyhedron, it is closed). If it is closed, the point belongs to the polyhedron (but isn't its inner point), if it is open, the point doesn't belong to the polyhedron. Alexander +----------------------------------------------------------------------+ + Dr. Alexander Golbraikh Email: golb@osi.lanet.lv + + Group of Molecular Biophysics + + Latvian Institute of Organic Synthesis FAX: + (371) 7-821-038 + + 21 Aizkraukles st. + + Riga LV-1006 Phone: + (371) 7-552-354 + + LATVIA + +----------------------------------------------------------------------+ From ASZYM@ichuwr.chem.uni.wroc.pl Wed Apr 17 08:47:24 1996 Received: from indigo2 for ASZYM@ichuwr.chem.uni.wroc.pl by www.ccl.net (8.7.1/950822.1) id IAA15718; Wed, 17 Apr 1996 08:24:04 -0400 (EDT) Received: from ichuwr.chem.uni.wroc.pl by indigo2 via SMTP (940816.SGI.8.6.9/930416.SGI) for id OAA00715; Wed, 17 Apr 1996 14:24:52 GMT Received: from ICHUWR/SMTPQueue by ichuwr.chem.uni.wroc.pl (Mercury 1.11); Wed, 17 Apr 96 14:23:37 +0100 Received: from Mailqueue by ICHUWR (Mercury 1.11); Wed, 17 Apr 96 14:23:09 +0100 From: "Andrzej Szymoszek" To: chemistry@www.ccl.net Date: Wed, 17 Apr 1996 14:23:00 GMT+1 Subject: Re: Inside or outside of a polyhedron Priority: normal X-mailer: Pegasus Mail v3.1 (R1) Message-ID: <11CEB9C1F2C@ichuwr.chem.uni.wroc.pl> Dear Netters, Shouldn't be noticed that if you have n points in space, it isn't determined what kind of polyhedron you actually have? This is the non-convex case. Imagine 4 points in 2D: .4 3. 1. 2. You can go 1-2-4-3-1, or 1-3-4-2-1, or 1-3-2-4-1. So the problem is in this case quite complicated. For the "convex" case, staying by 2D (generalization to 3D is straightforward, hopefully :-) I have an idea first to find a gravity centre of the polygon. This is the point we are sure it is inside. Then you join g.c. with the point in question- and determine whether it crosses the border (point outside) or not (inside). Andrzej Szymoszek aszym@ichuwr.chem.uni.wroc.pl From toukie@zui.unizh.ch Wed Apr 17 09:47:12 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.1/950822.1) id JAA16776; Wed, 17 Apr 1996 09:37:32 -0400 (EDT) Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA16547; Wed, 17 Apr 96 15:37:19 +0200 X-Nupop-Charset: Swiss Date: Wed, 17 Apr 1996 15:38:05 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <56285.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: ? re H-bonds Dear Colleagues; I have a series of compounds for which I wish to be able to estimate strengths of intramolecular hydrogen bonds. These compounds all have the following basic structure: H R / / X :O | / C----C | ------ and I would like to be able to calculate the approximate intramolecular hy- drogen bond energy between the H atom and the :O atom. I know the distance between H and O and between H and the lone electron pair (:); I also know the values of the torsion angles corresponding to H-X-C-C, :-O-C-C, O-C-C-X, R-O-C-C, X-H-:-O, and H-:-O-C. Given this information, is there a formula for estimating the strength of the intramolecular hydrogen bond H---: or H---O? Of course, any relevant references would also be most welcome. Thanks in advance to all responders. Sincerely, S. Shapiro ZH toukie@zui.unizh.ch From craig@occam.gh.wits.ac.za Wed Apr 17 12:47:33 1996 Received: from occam.gh.wits.ac.za for craig@occam.gh.wits.ac.za by www.ccl.net (8.7.1/950822.1) id MAA20437; Wed, 17 Apr 1996 12:01:00 -0400 (EDT) Received: (from craig@localhost) by occam.gh.wits.ac.za (8.6.12/8.6.9) id RAA04099; Wed, 17 Apr 1996 17:59:24 +0200 Date: Wed, 17 Apr 1996 17:59:24 +0200 (GMT+0200) From: Craig Taverner X-Sender: craig@occam.gh.wits.ac.za To: Rui Luo cc: Robert Fraczkiewicz , chemistry@www.ccl.net Subject: Re: CCL:Inside or outside of a polyhedron In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Just an idea. It's very efficient, but not sure it's right. Sorry, but it won't work. > First transform the current coordinate system to one with the given point > (x,y,z) as the origin. I.e. subtrate (xi,yi,zi), where i=1,...,N, by > (x,y,z). This can be done very fast. > > Second look at the sign of the transformed coordinates of all vertices. > If all xi's, where i=1,...,N, have the same sign, the point is outside > of the polyhedron. The statement holds for all yi's or all zi's. So if any > one of the three conditions holds, the point will be outside. Otherwise if > none of the conditions hold, it's inside. If any one of your test conditions is true (eg, all x positive or all x negative) then yes the point is outside the polyhedron, however, if any number of tests is false, the point can still be outside the polyhedron. The tests only work one way. Just consider a square on a 2-d surface with all sides at 45 degrees to the axes. Place the origin just outside one side, and notice that your have points with both positive and negative values for both x and y axes. Cheers, Craig "Imagine if every Thursday your shoes exploded if you tied them the usual way. This happens to us all the time with computers, and nobody thinks of complaining." -- Jeff Raskin, interviewed in Doctor Dobb's Journal Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa tel: +27-11-716-2290 fax: +27-11-716-3826 email: craig@hobbes.gh.wits.ac.za www: http://www.gh.wits.ac.za/craig From info@anny.psgvb.com Wed Apr 17 13:47:42 1996 Received: from anny.psgvb.com for info@anny.psgvb.com by www.ccl.net (8.7.1/950822.1) id NAA20934; Wed, 17 Apr 1996 13:09:00 -0400 (EDT) Received: by anny.psgvb.com (931110.SGI/920502.SGI.AUTO) for chemistry@www.ccl.net id AA04475; Wed, 17 Apr 96 09:55:32 -0700 Date: Wed, 17 Apr 96 09:55:32 -0700 From: info@anny.psgvb.com (Info at Schrodinger Inc.) Message-Id: <9604171655.AA04475@anny.psgvb.com> To: chemistry@www.ccl.net Subject: Schrodinger, Inc. Seminar series Schrodinger, Inc. announces a seminar series: Recent Advances in Many Body Quantum Mechanics Performance of the PS-GVB ab initio Electronic Structure Program Speakers: Professor William A. Goddard III, Caltech Professor Richard A. Friesner, Columbia Dr. Murco Ringnalda, President, Schrodinger, Inc. Dates and Locations: Tuesday, May 7 : Paris, France Wednesday, May 8 : Frankfurt, Germany Thursday, May 9 : London, England For more information, contact: Paris: Guy Desmarquets, guy@psgvb.com, 33-88-95-6852 Frankfurt: Heinz Hofmann, heinz@psgvb.com, 49-9241-91216 London: Ed Baily, ed@psgvb.com, 44-1823-681006 -- Schrodinger, Inc. / phone 503-299-1150 / fax 503-299-4532 121 SW Morrison, Suite 1212, Portland, OR 97204 / info@psgvb.com From fgonzale@lauca.usach.cl Wed Apr 17 14:47:33 1996 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.7.1/950822.1) id OAA22412; Wed, 17 Apr 1996 14:09:45 -0400 (EDT) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.6.11/8.6.9) with ESMTP id PAA01625 for ; Fri, 17 Apr 1992 15:11:55 -0500 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.12/8.6.12) id OAA19197 for chemistry@www.ccl.net; Wed, 17 Apr 1996 14:12:10 -0400 From: Fdo Danilo Gonzalez Nilo Message-Id: <199604171812.OAA19197@lauca.usach.cl> Subject: winemu To: chemistry@www.ccl.net Date: Wed, 17 Apr 96 14:12:06 AST Hi! Anybody have any free emulator of windows 3.x for LINUX (eg. winemu, etc) I need it so much, if anybody have it, please send it me to my address or give me an ftp address for taking it thank a lot!! Danilo Gonzalez N. University of Santiago of Chile Faculty of Chemistry and Biology casilla 307, Santiago-2, Chile fono: 681 2575 E-mail : fgonzale@lauca.usach.cl fax : (562) 681 2108 *************************************************************************x From tvd@iris69.msi.com Wed Apr 17 19:47:17 1996 Received: from bioc1.msi.com for tvd@iris69.msi.com by www.ccl.net (8.7.1/950822.1) id TAA26053; Wed, 17 Apr 1996 19:31:20 -0400 (EDT) Received: from iris69.biosym.com by bioc1.msi.com (5.64/0.0) id AA09987; Wed, 17 Apr 96 16:36:25 -0700 Received: by iris69.msi.com (940816.SGI.8.6.9/930416.SGI) id QAA20990; Wed, 17 Apr 1996 16:30:48 -0700 Date: Wed, 17 Apr 1996 16:30:48 -0700 From: tvd@msi.com (Ton van Daelen) Message-Id: <199604172330.QAA20990@iris69.msi.com> To: chemistry@www.ccl.net Subject: Cerius-2 software developer's kit: a series of hands-on workshops Cc: tvd@iris69.msi.com Hello all, In the month of May we will offer six workshops on the Cerius2 software developer's kit. This might be of interest to any computational chemist that is doing in house code development, and wants to link an application to a graphical user interface. The workshop is free (!) and features hands-on training on how to use the developer's kit. Please check out the attached information as well as our web site (http://www.msi.com). Registration is required as we have to limit the number of participants to 40 per workshop. Hope to see you there ! Ton van Daelen ====================================================================== Molecular Simulations Inc. and Silicon Graphics Present The Software Developer's Kit A Toolkit for Integrating Chemistry Applications in a Standard Environment A Hands-On Scientific Workshop > Maximize the Value of In-House Chemistry Code If you use or write computational chemistry applications, then you will appreciate the advantages that a standard user interface can provide. Cerius2 and the Software Developer's Kit (C2*SDK) from Molecular Simulations Inc. can help you increase your development efficiency by allowing you to integrate your chemistry application in a user friendly graphical interface. > Receive Hands-On C2*SDK Training * Explore how your research group can benefit from easier access to external code developed from academic collaborations using C2*SDK. * See how the visibility of your integrated applications is increased because they "plug-and-play" into any Cerius2 installation. * Learn how to interface your code into a common environment for visualization and data exchange with scientific applications from MSI and third-parties. * Experience how the Software Developer's Kit in Cerius2 is used to develop scientific applications and solve research problems in areas such as polymer science, rational drug design, catalysis, chemical reactions, combinatorial chemistry, and crystal growth. * See Cerius2*SDK demonstrated on the latest Silicon Graphics workstations. Silicon Graphics is the leading manufacturer of high-performance visual and enterprise computing systems. ------------------------------ Seminar Dates ------------------------------ Monday, May 13 San Diego, CA Wednesday, May 15 Chicago, IL Friday, May 17 Parsippany, NJ Monday, May 20 London, England Wednesday, May 22 Paris, France Thursday, May 23 Frankfurt, Germany ------------------------------ Seminar Day ------------------------------ 9:30 a.m. Registration and Coffee 10 a.m. to 3:30 p.m. Seminar and hands-on sessions ------------------------------ How to Register ------------------------------ Fax or e-mail this registration form today. We will fax you a confirmation notice and directions for your workshop. Registration is required, as space is limited. Lunch will be provided. In Europe Fax: Severine Capely Fax: +33 1 69419909 (Paris, France) In the United States Fax: Mike Weitz Fax: (619) 597-9777 (San Diego, CA) E-mail: seminars@msi.com __ I am unable to attend, but I would like to receive more information. __ Please register me for this free workshop: Workshop Location (city/date): Parsippany, NJ Name: Title: Company: Address: City: State: Zip: Country: E-mail: Phone: Fax: For more information, visit our web site at http://www.msi.com, e-mail seminars@msi.com, or call Severine Capely at +33 1 694 19908 (Paris), or Mike Weitz at (619) 597-9709 (San Diego, CA). Ton van Daelen Product Manager Software Developer's Kit workshop registration: seminars@msi.com __o E: tvd@biosym.com _`\<,_ Molecular Simulations P: -1-619-546-5329 (*)/ (*) 9685 Scranton Road F: -1-619-458-0136 /\/\/\/\/\/\ San Diego, CA 92121 W: http://www.msi.com