From Geoffrey@averell.umh.ac.be Mon Nov 3 03:34:52 1997 Received: from averell.umh.ac.be for Geoffrey@averell.umh.ac.be by www.ccl.net (8.8.3/950822.1) id DAA24230; Mon, 3 Nov 1997 03:02:34 -0500 (EST) From: Received: by averell.umh.ac.be (AIX 4.1/UCB 5.64/4.03) id AA31796; Mon, 3 Nov 1997 09:03:28 +0100 Message-Id: <9711030803.AA31796@averell.umh.ac.be> Subject: SUMMARY for: Convention for the d orbitals in G94 To: chemistry@www.ccl.net (CCL Computational Chemistry List) Date: Mon, 3 Nov 1997 09:03:28 +0100 (NFT) X-Mailer: ELM [version 2.4 PL0] Content-Type: text Dear CCl'ers, A few weeks ago, I posted a question about the convention for the matching between the labeling that Gaussian 94 uses to describe the LCAO coefficients of the d orbitals and the classical description of d orbitals. Thank you to those who replied me. You will find below the summary of the replies that I got. Thanks. Geoffrey ================================================== Geoffrey Pourtois, PhD student - Assistant ------------------------------------------------ University of Mons-Hainaut Service de Chimie des Materiaux Nouveaux 20, Place du parc 7000 Mons Belgium ------------------------------------------------ e-mail : Geoffrey@averell.umh.ac.be tel : +32 65 37 3363 fax : +32 65 37 3366 http://morris.umh.ac.be/ ================================================== From - Tue Oct 7 16:29:47 1997 Received: from am.appstate.edu by averell.umh.ac.be (AIX 4.1/UCB 5.64/4.03) id AA33638; Tue, 7 Oct 1997 15:54:08 +0200 Received: from conrad.appstate.edu (SYSTEM@conrad.appstate.edu [152.10.1.1]) by am.appstate.edu (8.8.5/8.8.5) with ESMTP id JAA21802 for ; Tue, 7 Oct 1997 09:52:44 -0400 (EDT) Received: from dft ("port 4077"@dft.chem.appstate.edu) by conrad.appstate.edu (PMDF V5.1-8 #26327) with SMTP id <01IOIRS2P9468ZELTW@conrad.appstate.edu> for Geoffrey@averell.umh.ac.be; Tue, 7 Oct 1997 09:52:41 DST Date: Tue, 07 Oct 1997 09:52:42 -0400 From: Steve Williams Subject: CCL:G:Convention for the d orbitals in G94 X-Sender: willsd@pop.appstate.edu To: Geoffrey@averell.umh.ac.be Message-Id: <3.0.32.19971007095242.009edc80@pop.appstate.edu> Mime-Version: 1.0 X-Mailer: Windows Eudora Pro Version 3.0 (32) Content-Type: text/plain; charset="us-ascii" Status: O X-Mozilla-Status: 0005 Content-Length: 1309 Dear CCLers, Is there anybody who could give me the matching between the labeling that Gaussian 94 uses to describe the LCAO coefficents of the d orbitals and the classical description of d orbitals (dZ2,dXY,DX2-Y2,...). I put below the labeling i got into the output of G94. D 0 -> D+1 -> D-1 -> D+2 -> D-2 -> Geoffrey The notation that G94 uses is the standard notation for the spherical harmonics; these are the angular parts of the atomic wavefunctions obtained by solving the schrodinger equation forthe H atom. These are complex functions. It is possible to construct an equivalent set of functions that are real valued from these, and it is this set of commonly used real valued functions that you refer to. The real functions are linear combinations of the complex valued ones. Except for normalizations and possible multiplications by i, the connections that you want are: D0 = dz^2 D+1 + D-1 = dxz D+1 - D-1 = dyz D+2 + D-2 = dx^2-y^2 D+2 - D-2 = dxy Hope this helps, Steve ***************************************** Steve Williams F F F Chemistry \ / \ / Appalachian State University Al Al Boone, NC 28608 / \ / \ USA F F F willsd@appstate.edu From - Wed Oct 8 08:29:39 1997 Received: from hp.rz.uni-potsdam.de by averell.umh.ac.be (AIX 4.1/UCB 5.64/4.03) id AA14476; Tue, 7 Oct 1997 18:24:07 +0200 Received: from tc1.chem.uni-potsdam.de by hp.rz.uni-potsdam.de with SMTP (1.37.109.10G/16.2) id AA293824991; Tue, 7 Oct 1997 18:23:11 +0100 Received: by tc1.chem.uni-potsdam.de (AIX 3.2/UCB 5.64/4.03) id AA18352; Tue, 7 Oct 1997 17:23:22 +0100 From: ritschel@tc1.chem.uni-potsdam.de (Thomas S. Ritschel) Message-Id: <9710071623.AA18352@tc1.chem.uni-potsdam.de> Subject: CCL:G:Convention for the d orbitals in G94 To: Geoffrey@averell.umh.ac.be Date: Tue, 7 Oct 1997 17:23:22 +0100 (MET) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Status: X-Mozilla-Status: 0001 Content-Length: 758 Dear Geoffrey, > Is there anybody who could give me the matching between the labeling > that Gaussian 94 uses to describe the LCAO coefficents of the d orbitals > and the classical description of d orbitals (dZ2,dXY,DX2-Y2,...). > I put below the labeling i got into the output of G94. In my opinion the right labeling is as written below: D 0 -> DZ2 D+1 -> DXZ D-1 -> DYZ D+2 -> DX2-Y2 D-2 -> DXY Hope I could help you, Thomas. ---------------------------------------- Thomas Ritschel Universitaet Potsdam Institut fuer Physikalische und Theoretische Chemie ritschel@tc1.chem.uni-potsdam.de ----------------------------------1997-- From - Wed Oct 8 08:29:40 1997 Received: from relay2.UU.NET by averell.umh.ac.be (AIX 4.1/UCB 5.64/4.03) id AA28184; Wed, 8 Oct 1997 01:06:45 +0200 Received: from uucp1.UU.NET by relay2.UU.NET with SMTP (peer crosschecked as: uucp1.UU.NET [192.48.96.39]) id QQdkhg03203; Tue, 7 Oct 1997 19:06:11 -0400 (EDT) Message-Id: Received: from m10.UUCP by uucp1.UU.NET with UUCP/RMAIL ; Tue, 7 Oct 1997 19:05:54 -0400 Received: by m10.lorentzian.com; Tue, 7 Oct 1997 19:00:15 -0400 Received: by mousse.gaussian.com; Tue, 7 Oct 1997 15:17:59 -0400 From: gaussian.com!fox@lorentzian.com (Doug Fox) Subject: Re: CCL:G:Convention for the d orbitals in G94 To: uunet!averell.umh.ac.be!Geoffrey%lorentzian.com@uunet.uu.net (Geoffrey) Date: Tue, 7 Oct 1997 15:17:59 -0400 (EDT) In-Reply-To: <343A0473.41C6@averell.umh.ac.be> from "Geoffrey" at Oct 7, 97 11:44:19 am X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Status: X-Mozilla-Status: 0011 Content-Length: 687 Geoffrey, This data is also available on our web site and the Summer 1993 issue of Gaussian News (on the Web as well) has F functions as well. > > Is there anybody who could give me the matching between the labeling > that Gaussian 94 uses to describe the LCAO coefficents of the d orbitals > and the classical description of d orbitals (dZ2,dXY,DX2-Y2,...). > I put below the labeling i got into the output of G94. > > D 0 -> Z**2 > D+1 -> XZ > D-1 -> YZ > D+2 -> X**2 - Y**2 > D-2 -> XY > > I will sumarize the answers. > Thank you very much. > > Geoffrey Douglas J. Fox Director of Technical Support help@gaussian.com From - Wed Oct 8 14:28:09 1997 Received: from sg1503.Chemie.Uni-Marburg.DE by averell.umh.ac.be (AIX 4.1/UCB 5.64/4.03) id AA35344; Wed, 8 Oct 1997 10:38:02 +0200 Received: from ps1515.chemie.uni-marburg.de (ps1515.Chemie.Uni-Marburg.DE [137.248.151.39]) by mail.chemie.uni-marburg.de (8.8.7/8.8.7.ts) with ESMTP id KAA10710 for ; Wed, 8 Oct 1997 10:37:11 +0200 (CEST) Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.20); 8 Oct 97 10:39:07 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.20); 8 Oct 97 10:39:05 GMT+2 From: "Stefan Fau" To: Geoffrey Date: Wed, 8 Oct 1997 10:39:04 MDT Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:G:Convention for the d orbitals in G94 Return-Receipt-To: "Stefan Fau" Priority: normal X-Mailer: Pegasus Mail for Windows (v2.01) Message-Id: <30226E5E97@ps1515.chemie.uni-marburg.de> Status: X-Mozilla-Status: 0011 Content-Length: 500 Hi, G94 has the following convention: d0 = dz2 d+1 = dxz d-1 = dyz d+2 = dx2-y2 d-2 = dxy Stefan __________________________________________________________ | Stefan Fau fau@mailer.uni-marburg.de | | | | FB Chemie der Philipps-Universitaet Marburg | | Hans-Meerwein-Str. | | D-35032 Marburg | ------------------------------------------------------- From - Wed Oct 8 08:29:40 1997 Received: from wavefun.com by averell.umh.ac.be (AIX 4.1/UCB 5.64/4.03) id AA30556; Tue, 7 Oct 1997 19:45:00 +0200 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for Geoffrey@averell.umh.ac.be id AA18647; Tue, 7 Oct 97 10:45:37 -0700 Received: from bmw.wavefun.com(198.147.95.5) by volvo.wavefun.com via smap (V1.3) id sma018621; Tue Oct 7 10:44:32 1997 Received: by bmw.wavefun.com (931110.SGI/930416.SGI.AUTO) for @volvo.wavefun.com:Geoffrey@averell.umh.ac.be id AA05443; Tue, 7 Oct 97 10:41:06 -0700 From: "Liang Lou" Message-Id: <9710071041.ZM5441@bmw.wavefun.com> Date: Tue, 7 Oct 1997 10:41:01 -0700 In-Reply-To: Geoffrey "CCL:G:Convention for the d orbitals in G94" (Oct 7, 11:44am) References: <343A0473.41C6@averell.umh.ac.be> Reply-To: liang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: Geoffrey Subject: Re: CCL:G:Convention for the d orbitals in G94 Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Status: X-Mozilla-Status: 0011 Content-Length: 1892 On Oct 7, 11:44am, Geoffrey wrote: > Subject: CCL:G:Convention for the d orbitals in G94 > Dear CCLers, > > Is there anybody who could give me the matching between the labeling > that Gaussian 94 uses to describe the LCAO coefficents of the d orbitals > and the classical description of d orbitals (dZ2,dXY,DX2-Y2,...). > I put below the labeling i got into the output of G94. > > D 0 -> > D+1 -> > D-1 -> > D+2 -> > D-2 -> > > I will sumarize the answers. > Thank you very much. > > Geoffrey > -- > ================================================== > Geoffrey Pourtois, PhD student - Assistant > ------------------------------------------------ > University of Mons-Hainaut > Service de Chimie des Materiaux Nouveaux > 20, Place du parc > 7000 Mons > Belgium > ------------------------------------------------ > e-mail : Geoffrey@averell.umh.ac.be > tel : +32 65 37 3363 > fax : +32 65 37 3366 > http://morris.umh.ac.be/ > > ================================================== > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: Geoffrey@averell.umh.ac.be > -- Original Sender From: Address: Geoffrey@averell.umh.ac.be > 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 > >-- End of excerpt from Geoffrey In any math textbook for physics and chemistry applications, you can find descriptions of "spherical harmonic functions" (Ylm). By making appropriate linear combinations to eliminate the imaginary parts, and converting back to cartesian space, you will obtain the correspondence you need. Liang Lou From alsenoy@uia.ua.ac.be Mon Nov 3 06:34:54 1997 Received: from inch.uia.ac.be for alsenoy@uia.ua.ac.be by www.ccl.net (8.8.3/950822.1) id FAA24545; Mon, 3 Nov 1997 05:46:21 -0500 (EST) Received: from localhost by inch.uia.ac.be; (8.8.6/1.1.8.2/22Feb95-0943AM) id LAA07735; Mon, 3 Nov 1997 11:29:53 +0100 (MET) Date: Mon, 3 Nov 1997 11:29:52 +0100 (MET) From: Kris Van Alsenoy X-Sender: alsenoy@inch.uia.ac.be To: "G. Rechtsteiner" cc: chemistry@www.ccl.net Subject: Re: CCL:G:Vibrational Visualization of Gaussian Outputs In-Reply-To: <3.0.3.32.19971031094714.00915820@mercury.chem.nwu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 31 Oct 1997, G. Rechtsteiner wrote: > Hello: > > I am currently looking for a program (free or inexpensive, sorry, I am > still a graduate student), that will help me to visualize the vibrational > modes of a molecule from a Gaussian 94 (or 92) output file. I am aware > of Re_view for MOPAC files, but of none for Gaussian. May I suggest to give gar2ped a try ? You can find it in the CCL archive, so its free. sincerely, kris > > Thank you, > > Greg > > -- > > Greg Rechtsteiner > Northwestern University > g-recht@chem.nwu.edu > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: g-recht@chem.nwu.edu > -- Original Sender From: Address: g-recht@chem.nwu.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 > > --------------------------------------------------------------------------- Kris Van Alsenoy, Structural Chemistry Group, Department of Chemistry, University of Antwerp (UIA), Universiteitsplein 1, B-2610 Antwerp, Belgium E-mail : alsenoy@uia.ua.ac.be / Phone : +32(3)8202366 / Fax : +32(3)8202356 --------------------------------------------------------------------------- From Jeffrey.Gosper@brunel.ac.uk Mon Nov 3 07:34:55 1997 Received: from eros.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA24639; Mon, 3 Nov 1997 06:34:36 -0500 (EST) From: Received: from molnir.brunel.ac.uk by eros.brunel.ac.uk with SMTP-BRUNEL (PP); Mon, 3 Nov 1997 11:33:57 +0000 Message-Id: <1847.199711031133@molnir.brunel.ac.uk> Subject: Re: CCL:G:Vibrational Visualization of Gaussian Outputs To: g-recht@chem.nwu.edu (G. Rechtsteiner) Date: Mon, 3 Nov 1997 11:33:56 +0000 (GMT) Cc: chemistry@www.ccl.net In-Reply-To: <3.0.3.32.19971031094714.00915820@mercury.chem.nwu.edu> from "G. Rechtsteiner" at Oct 31, 97 09:47:14 am X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > > Hello: > > I am currently looking for a program (free or inexpensive, sorry, I am > still a graduate student), that will help me to visualize the vibrational > modes of a molecule from a Gaussian 94 (or 92) output file. I am aware > of Re_view for MOPAC files, but of none for Gaussian. > > Thank you, > > Greg Dear Greg and other interested parties, Re_View2 is able to visualize G94 vibrations. You''ll need a the extra file converter GvivView that is supplied on Re_View2's CDROM. For further details on re_View2 see: http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view2.htmi From che5jwc@titan.vcu.edu Mon Nov 3 13:34:58 1997 Received: from titan.vcu.edu for che5jwc@titan.vcu.edu by www.ccl.net (8.8.3/950822.1) id NAA26456; Mon, 3 Nov 1997 13:31:45 -0500 (EST) From: Received: from [128.172.182.152] by titan.vcu.edu (AIX 4.1/UCB 5.64/4.03) id AA80948; Mon, 3 Nov 1997 13:28:26 -0500 Message-Id: <345E17ED.696B@titan.vcu.edu> Date: Mon, 03 Nov 1997 13:29:01 -0500 Reply-To: che5jwc@titan.vcu.edu Organization: VCU X-Mailer: Mozilla 3.01Gold (Win95; I) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: CCL:Babel Charges (from *.hin) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am trying to convert HyperChem (*.hin) files to a format readable by Insight that includes CHARGES on the atoms using Bable1.06. My system includes a heteroatom (Pt) that is not recognized by some file types, and *.pdb files do not incorporate charges. That is not a problem, the heteroatom type can be assigned manually. However, when using Babel to produce a different file format (*.mol, *.mol2, etc.) from the original *.hin file, the charges are not retained. Any suggestions? Advance thanks. Cheers, John Cox Virginia Commonwealth University Richmond, Virginia, USA From smb@smb.chem.niu.edu Mon Nov 3 15:34:59 1997 Received: from cz2.chem.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.8.3/950822.1) id PAA26897; Mon, 3 Nov 1997 15:10:20 -0500 (EST) Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA07401; Mon, 3 Nov 97 13:49:41 -0600 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA16805; Mon, 3 Nov 97 14:06:53 -0600 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) for id OAA11783; Mon, 3 Nov 1997 14:09:31 -0600 Sender: smb@smb.chem.niu.edu Message-Id: <345E2F7B.794B@smb.chem.niu.edu> Date: Mon, 03 Nov 1997 14:09:31 -0600 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) Mime-Version: 1.0 To: computational chemistry list Subject: ECCC4 Now Open Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The Fourth Electronic Computational Chemistry Conference (ECCC-4) is now open. The conference has approximately 60 articles spanning the range of computational chemistry. Articles are being delivered in two manners this year. The first is simply to distribute the articles as written by the authors, just like we have done in the past. The second method makes use of our custom article server which will allow a great deal of end-user customization along with a common look-and-feel to the articles. This article server will be incorporated into the Internet Journal of Chemistry (http://www.ijc.com/), the new electronic journal which will launch in January 1998. You are welcome to read the articles and participate in the discussions. Registration is free and all are welcome. The conference home page is located at http://hackberry.chem.niu.edu/ECCC4/ We hope to have a European server operational in the next day or so. Steve -- Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From churca@opium.q1.fcen.uba.ar Mon Nov 3 20:35:01 1997 Received: from opium.q1.fcen.uba.ar for churca@opium.q1.fcen.uba.ar by www.ccl.net (8.8.3/950822.1) id TAA27963; Mon, 3 Nov 1997 19:48:13 -0500 (EST) Received: from localhost (churca@localhost) by opium.q1.fcen.uba.ar (8.8.0/8.8.0) with SMTP id VAA15895; Mon, 3 Nov 1997 21:21:39 -0300 Date: Mon, 3 Nov 1997 21:21:39 -0300 (ARST) From: Adrian Turjanski To: chemistry@www.ccl.net cc: chemistry@www.ccl.net Subject: MOLDEN PROBLEM In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII t Hi: I have some problems using MOLDEN3.2. When I enter to the Z-MATRIX editor and I want to submit a mopac file, The program says 'MOPAC_ROOT Enviromental variable not set ! ' . I could not compile MOLDEN on my PC so I download the executable. So I don't know how to submit the mopac file. Any help please. Thanks. From yubofan@guomai.sh.cn Sun Nov 2 11:34:45 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id LAA22263; Sun, 2 Nov 1997 11:20:28 -0500 (EST) Received: from ------ (PPP-30 [202.96.206.84]) by gm-email.guomai.sh.cn (8.8.7/8.8.7) with ESMTP id AAA20029 for ; Mon, 3 Nov 1997 00:18:04 +0800 (CST) Message-ID: <345CA849.9CED74FF@guomai.sh.cn> Date: Mon, 03 Nov 1997 00:20:25 +0800 From: Yubo Fan X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 To: Computational Chemistry List Subject: Guide of SMILE X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, CCLers, I have met SMILE format many times, but I don't know how to write it by a simplest text editor. Gould you please give me a detail guide? Thank you very much. Y. Fan -- ======================================================== FAN, Yubo Department of Chemistry E-Mail: yubofan@guomai.sh.cn Fudan University yubofan@fudan.edu.cn Shanghai, 200433 P. R. China Voice(86-21)65643978 ======================================================== From lavelle@mbi.ucla.edu Sun Nov 2 22:34:49 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id WAA23621; Sun, 2 Nov 1997 22:19:12 -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 TAA82986 for ; Sun, 2 Nov 1997 19:19:04 -0800 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA05420; Sun, 2 Nov 1997 19:19:03 -0800 Message-Id: <3.0.32.19971102192050.00a1b3d0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Sun, 02 Nov 1997 19:20:50 -0800 To: chemistry@www.ccl.net From: Laurence Lavelle Subject: INCREASING CPU UTILIZATION WITH NT4 Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" HI, I HAVE A DUAL PENTIUM 133MHZ WITH NT4 WORKSTATION RUNNING VERY CPU INTENSIVE CALCULATIONS (AB INITIO IN HYPERCHEM 5.02) FROM DAYS TO WEEKS IN DURATION. 196 MB RAM 5GB VIRTUAL MEMORY (ALL SCSI HD'S WITH A SUSTAINED DATA TRANSFER RATE OF 10MB/S.) (The machine could be upgraded to dual 200MMX.) HOWEVER TASK MANAGER SHOWS CPU UTILIZATION AT A CONSTANT 54%. ONLY WHEN I USE OTHER ADDITIONAL SOFTWARE DOES THE CPU UTILIZATION GO ABOVE 54% AND UP TO 100%. HOW DO I OBTAIN HIGHER (100% ?) CPU UTILIZATION WITH ONLY THE COMPUTATIONAL SOFTWARE RUNNING? THANKS IN ADVANCED. 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 lavelle@mbi.ucla.edu Sun Nov 2 23:34:49 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id XAA23670; Sun, 2 Nov 1997 23:07:25 -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 UAA92092; Sun, 2 Nov 1997 20:07:16 -0800 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA10020; Sun, 2 Nov 1997 20:07:16 -0800 Message-Id: <3.0.32.19971102200903.00a1b100@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Sun, 02 Nov 1997 20:09:03 -0800 To: chemistry@www.ccl.net, hyperchem@hyper.com From: Laurence Lavelle Subject: AND TO ANSWER MY OWN QUESTION ON INCREASING CPU UTILIZATION WITH NT4 Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Hi, Just remembered that Task Manager was showing the average of the two CPU's. After showing each CPU activity I realized what I already knew. HyperChem is a single thread application and no matter how many CPU's there are only one is used by HC. So one CPU is working 100% and totally dedicated to HC while the second CPU is dealing with the small OS overhead (~8%), giving an average CPU utilization of 54%. Of course when I use other software the second CPU is then utilized. 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 csc@imb-jena.de Thu Oct 30 03:34:03 1997 Received: from macke.imb-jena.de for csc@imb-jena.de by www.ccl.net (8.8.3/950822.1) id DAA18648; Thu, 30 Oct 1997 03:00:44 -0500 (EST) Received: by macke.imb-jena.de (951211.SGI.8.6.12.PATCH1502/951211.SGI/hsk) for chemistry@www.ccl.net id JAA29884; Thu, 30 Oct 1997 09:00:32 +0100 From: csc@imb-jena.de (Christoph Schneider) Message-Id: <199710300800.JAA29884@macke.imb-jena.de> Subject: Re: CCL:tRNA modelling To: chemistry@www.ccl.net Date: Thu, 30 Oct 1997 09:00:32 +0100 (MET) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Ryszard Czerminski, you wrote: > > Dear All, > > I am looking for information about tRNA modelling. > In particular for MD simulations > and parametrization of rare nucleotides (pseudo-uracil > etc...) > > Ryszard Czerminski phone : (617)354-3124 x 13 > Moldyn, Inc. fax : (617)491-4522 > 955 Massachusetts Avenue e-mail: ryszard@moldyn.com > Cambridge MA, 02139-3180 or ryszard@photon.com > > @ARTICLE{auffinger96a, AUTHOR = {P. Auffinger; E. Westhof}, TITLE = {H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations}, JOURNAL = {Biophys J}, YEAR = {1996}, VOLUME = {71}, PAGES = {940-954} } @ARTICLE{auffinger97, AUTHOR = {P. Auffinger; E. Westhof}, TITLE = {RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNAAsp anticodon hairpin}, JOURNAL = {J. Mol. Biol.}, YEAR = {1997}, VOLUME = {269}, PAGES = {326-341} } @ARTICLE{auffinger95, AUTHOR = {P. Auffinger; S. Louise-May; E. Westhof}, TITLE = {Multiple molecular dynamics simulations of the anticodon loop of tRNAAsp in aqueous solution with counterions}, JOURNAL = {J. Amer. Chem. Soc.}, YEAR = {1995}, VOLUME = {117}, PAGES = {6720-6726} } @ARTICLE{auffinger96b, AUTHOR = {P. Auffinger; S. Louise-May; E. Westhof}, TITLE = {Hydration of C-H groups in tRNA}, JOURNAL = {Faraday Discuss}, YEAR = {1996}, VOLUME = {103}, PAGES = {151-173} } @ARTICLE{auffinger96c, AUTHOR = {P. Auffinger; S. Louise-May; E. Westhof}, TITLE = {Molecular dynamics simulations of the anticodon hairpin of tRNAAsp: Structuring effects of C-H...O hydrogen bonds and of long-range hydration forces}, JOURNAL = {J. Am. Chem. Soc.}, YEAR = {1996}, VOLUME = {118}, PAGES = {1181-1189} } @ARTICLE{louise96, AUTHOR = {S. Louise-May; P. Auffinger; E. Westhof}, TITLE = {Calculations of nucleic acid conformations}, JOURNAL = {Curr Opin Struct Biol}, YEAR = {1996}, VOLUME = {6}, PAGES = {289-298} } I listed some papers of Pascal, he did the most work published on tRNA MD. Contact me if you have further questions, best regards C. -- Christoph Schneider csc@imb-jena.de Institute for Molecular Biotechnology Beutenbergstrasse 11, -Biocomputing- Tel.: +49-3641-65-6205 P.O. Box 100 813, D-07708 Jena, Germany Fax: +49-3641-65-6210 From ccl@www.ccl.net Thu Oct 30 07:34:06 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id GAA19423; Thu, 30 Oct 1997 06:34:53 -0500 (EST) Received: from rrzs2.rz.uni-regensburg.de for herbert.homeier@chemie.uni-regensburg.de by bedrock.ccl.net (8.8.6/950822.1) id GAA08973; Thu, 30 Oct 1997 06:34:41 -0500 (EST) Received: from rchs1.chemie.uni-regensburg.de (rchs1.chemie.uni-regensburg.de [132.199.48.1]) by rrzs2.rz.uni-regensburg.de (8.8.5/8.8.5) with SMTP id MAA01953; Thu, 30 Oct 1997 12:34:33 +0100 (MET) Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA02422; Thu, 30 Oct 97 13:26:31 +0100 Date: Thu, 30 Oct 97 13:26:31 +0100 From: Herbert Homeier t4720 Message-Id: <9710301226.AA02422@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Scientific Questions and Answers Database (#2) Cc: csc@imb-jena.de, noertema@theochem.tu-muenchen.de Reply-To: herbert.homeier@na-net.ornl.gov Dear colleagues, I am sorry that there was an error in the announced URL for the database. This has now been fixed. Sorry for any inconvenience caused. And many thanks to all those who sent me the information that the URL was faulty. Please try now http://www.chemie.uni-regensburg.de/pub/QA or http://www.chemie.uni-regensburg.de/QA I hope that the database will grow fast according to your participation. Enjoy. Herbert -------------------------------------------------------------- Priv.-Doz. Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg, D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX: +49-941-943 4719/+49-941-943 2305 email: herbert.homeier@na-net.ornl.gov WWW: http://www.chemie.uni-regensburg.de/~hoh05008 From ccl@www.ccl.net Thu Oct 30 09:34:18 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id IAA19941; Thu, 30 Oct 1997 08:44:14 -0500 (EST) Received: from fstgvs09 for hassler@fstgvs09.tu-graz.ac.at by bedrock.ccl.net (8.8.6/950822.1) id IAA10306; Thu, 30 Oct 1997 08:43:55 -0500 (EST) From: Date: Thu, 30 Oct 1997 14:45:44 +0200 Message-Id: <97103014454411@fstgvs09.tu-graz.ac.at> To: chemistry@ccl.net Subject: complex NCA X-VMS-To: SMTP%"chemistry@ccl.net" Dear members of CCL! Do there exist programs one can use to perform normal coordinate analyses for molecules having point groups with complex characters? (easiest example C3)? This necessarily implies the use of complex symmetry coordinates! Any help is highly acknowledged! Best wishes to everyone! K. Hassler (Department of inorganic chemistry, TU Graz, Austria) present e-mail: hassler@ftug01.tu-graz.ac.at From ccl@www.ccl.net Thu Oct 30 10:34:07 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA20519; Thu, 30 Oct 1997 09:49:00 -0500 (EST) Received: from ssci.liv.ac.uk for chen@ssci.liv.ac.uk by bedrock.ccl.net (8.8.6/950822.1) id JAA11980; Thu, 30 Oct 1997 09:48:46 -0500 (EST) Received: by ssci.liv.ac.uk (8.6.12/SMI-4.1) id OAA20955; Thu, 30 Oct 1997 14:52:04 GMT Date: Thu, 30 Oct 1997 14:52:04 GMT From: chen@ssci.liv.ac.uk (Chen Qiao) Message-Id: <199710301452.OAA20955@ssci.liv.ac.uk> To: chemistry@ccl.net Subject: PES in Gaussian 94 Dear sir, I don't know whether it's the right place to send my net poster. I am using Gaussian94. I want to know the decomposation PES of nitrobenzene on Cu atom using MP2 method. The calculation is stoped halfway in the scan at N-O distance about 3 Anstroms which said **** Fatal Problem: The smallest beta delta epsilon is -0.45527929D-01 It's a open shell system. There is a spin transition in the transition state. What is the problem? How can I solve it? Another question is also related to it: When we do scan=opt or opt=z-Matrix in scan the PES, can we updata the optimized the parameters step by step, rather than always optimise from the input parameter at each step? PS. regarding the first problem, UHF calculation was very successful. Thanks for attention. From rivelino@ufba.br Thu Oct 30 18:34:13 1997 Received: from abrolhos.ufba.br for rivelino@ufba.br by www.ccl.net (8.8.3/950822.1) id SAA24859; Thu, 30 Oct 1997 18:07:33 -0500 (EST) Received: from canudos.ufba.br by abrolhos.ufba.br (AIX 4.1/UCB 5.64/4.03) id AA22368; Thu, 30 Oct 1997 21:07:02 -0200 Received: from localhost by ufba.br (AIX 4.1/UCB 5.64/4.03) id AA85822; Thu, 30 Oct 1997 20:04:42 -0300 Date: Thu, 30 Oct 1997 20:04:42 -0300 (GRNLNDST) From: Roberto Rivelino de Melo Moreno Reply-To: Roberto Rivelino de Melo Moreno To: chemistry@www.ccl.net Subject: Li2 data Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL readers. Does anyone Know where i can search experimental data for the Li2 molecule? Thanks in advance. Roberto R. M. Moreno From melchers@chemie.fu-berlin.de Fri Oct 31 05:34:17 1997 Received: from mail.chemie.fu-berlin.de for melchers@chemie.fu-berlin.de by www.ccl.net (8.8.3/950822.1) id FAA26971; Fri, 31 Oct 1997 05:25:04 -0500 (EST) Received: from Bose.Chemie.FU-Berlin.DE(bose.chemie.fu-berlin.de[160.45.26.10]) (1910 bytes) by mail.chemie.fu-berlin.de via smail with P:smtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Fri, 31 Oct 1997 11:24:45 +0100 (MET) (Smail-3.2.0.98 1997-Oct-16 #12 built 1997-Oct-28) Received: by Bose.Chemie.FU-Berlin.DE (Smail3.2.0.98) id ; Fri, 31 Oct 1997 11:24:28 +0100 (MET) Message-Id: From: melchers@chemie.fu-berlin.de (Bernd Melchers) Subject: CCL:Raster3D on Linux (fwd) To: CHEMISTRY@www.ccl.net Date: Fri, 31 Oct 1997 11:24:28 +0100 (MET) X-Mailer: ELM [version 2.4 PL24 ME8d] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit ----- Forwarded message from Konrad Hinsen ----- Did anyone succeed in making Raster3D work under Linux? With some modifications I got most programs (all except normal3d) to compile, but neither render nor avs2ps works (render produces incorrect output files, and avs2ps empty ones). It would be nice if someone had a working binary distribution... -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr ----- End of forwarded message from Konrad Hinsen ----- I did this for version 3.2b and i am now working on the current version 3.2D. - You have to delete the Q-Format statements and their corresponding arguments. Q is NOT standard f77, so nobody should use this in portable programs. - I don't use f2c but g77. All g77 versions have little bugs (g77 is beta Release Software!), but mostly it works. f2c is slower. In one or two weeks i have some time to work further on the program. Ciao Bernd Melchers -- Bernd Melchers | melchers@FU-Berlin.DE Freie Universitaet Berlin | "We don't write software, we compose it." AG Macromelecular Modelling - Prof. Dr. E.W. Knapp for more information see http://www.chemie.fu-berlin.de/~melchers From ccl@www.ccl.net Fri Oct 31 09:34:19 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA27995; Fri, 31 Oct 1997 09:21:06 -0500 (EST) Received: from fstgvs09 for hassler@fstgvs09.tu-graz.ac.at by bedrock.ccl.net (8.8.6/950822.1) id JAA09727; Fri, 31 Oct 1997 09:20:50 -0500 (EST) From: Date: Fri, 31 Oct 1997 15:22:37 +0200 Message-Id: <97103115223787@fstgvs09.tu-graz.ac.at> To: chemistry@ccl.net Subject: complex NCA X-VMS-To: SMTP%"chemistry@ccl.net" Dear members of CCL! Do there exist programs one can use to perform normal coordinate analyses for molecules having point groups with complex characters? (easiest example C3)? This necessarily implies the use of complex symmetry coordinates! Any help is highly acknowledged! Best wishes to everyone! K. Hassler (Department of inorganic chemistry, TU Graz, Austria) present e-mail: hassler@ftug01.tu-graz.ac.at From g-recht@chem.nwu.edu Fri Oct 31 11:42:12 1997 Received: from mercury.chem.nwu.edu for g-recht@chem.nwu.edu by www.ccl.net (8.8.3/950822.1) id KAA28530; Fri, 31 Oct 1997 10:36:50 -0500 (EST) Received: from nano (nano.chem.nwu.edu [129.105.14.190]) by mercury.chem.nwu.edu (8.8.5/8.8.5) with SMTP id JAA28166 for ; Fri, 31 Oct 1997 09:36:01 -0600 (CST) Message-Id: <3.0.3.32.19971031093934.0090b390@mercury.chem.nwu.edu> X-Sender: g-recht@mercury.chem.nwu.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Fri, 31 Oct 1997 09:39:34 -0600 To: chemistry@www.ccl.net From: "G. Rechtsteiner" Subject: Surface Area Summary Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Thanks to everyone who responded to my question concerning the solvent accessible surface area of proteins. The responses are summarized below. Greg 1. Goto the EMBL website, they have the software for free. www.embl-heidelberg.de/argos/ASC.21/asc2.html Groeten, David. ________________________________________________________________________ Dr. Ir. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2. Here are some URLs I found helpful: If you get other responses, I'd be very grateful for a summary. Thanks. http://hyper.stanford.edu/~mbg/ftp/SurfaceVolumes/ Get the source code archive near the bottom of the page. It's a C package and compiles under linux without problem. http://www.embl-heidelberg.de/~eisenhab/ Some more routines for surface/volume info. http://csbmet.csb.yale.edu/people/core/pjf/pjf_hm.html See ACCESS. The CCP4 package has SURFACE and VOLUME utilities you may look into them, but it'll be a bit of work getting the the whole CCP4 suite up on linux just for those two. http://sjh.bi.umist.ac.uk/naccess.html This is a Fortran package. I had to contact the author to get it to compile under linux (UniFix 2.0 Kernal2.0.18) Michael merckel@mpibp-frankfurt.mpg.de 3. Consider the package MOLSV by Graham Smith (Calculation of Molecular Volume and Surface Area), available from QCPE. The QCPE reference number is QCMP053, and can run on a PC. Have a good day. Cherif Matta Chemistry Dept. McMaster University Hamitlon, Ontario, Canada. 4. The VMD program allows you to calculate and also display the solvent accessible surface of any protein. It's freely distributed and it's written in C++. See http://www.ks.uiuc.edu/Research/VMD Or you can use the Grasp program from Barry Honig's lab (I don't know the URL for it) which, as far as I know, it's not free but is not expensive either. Good luck. Dorina --------------------------------------------------------- Theoretical Biophysics Group Email: dorina@ks.uiuc.edu Beckman Institute, UIUC Phone: (217) 244-8946 405 North Mathews Ave. Fax: (217) 244-6078 Urbana, IL 61801, USA http://www.ks.uiuc.edu/ --------------------------------------------------------- 5. ICMlite is such a program. It will also let you display it, calculate area by residue or by atom, plot the values etc. ICMlite is free for academic institutions. Our site is http://www.molsoft.com Sincerely, Rita, Molsoft, LLC