From chemistry-request@server.ccl.net Thu Jun 14 03:31:13 2001 Received: from mcmail.cis.mcmaster.ca (mattacf@[130.113.64.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5E7VD530635 for ; Thu, 14 Jun 2001 03:31:13 -0400 Received: from localhost (mattacf@localhost) by mcmail.cis.mcmaster.ca with ESMTP id DAA20991 for ; Thu, 14 Jun 2001 03:31:13 -0400 (EDT) Date: Thu, 14 Jun 2001 03:31:13 -0400 (EDT) From: "C.F. Matta" To: CHEMISTRY@ccl.net Subject: Program to Calculate Delocalization Indeces (AIMDELOC) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, Several discussions on the CCL were concerned with the description of delocalization between bonded atoms. This message is to announce the availability of a UNIX/LINUX based program called AIMDELOC that compute the delocalization indeces between any two atoms within a molecule (bonded or not). The delocalisation indeces are defined in terms of the Fermi hole within the context of the quantum theory of atoms in molecules (AIM) developed by Bader and coworkers. The program input consists of the intergation files generated by the AIMPAC suite of programs. AIMDELOC program is available from the Quantum Chemistry Program Exchange (QCPE) Chemistry department, Indiana University, at a small administrative charge at: http://qcpe.chem.indiana.edu/ Author: Cherif F. Matta ======= Date of deposition at QCPE: 2001 =========================== Program title and Number: ========================= AIMDELOC 01 (LNUX101): A program to calculate the localization and delocalization indeces according to the quantum theory of Atoms-In-Molecules (AIM)"; QCPE0802. A detailed manual can be obtained from myself or from the web-site of QCPE. AIMPAC suite of programs is available free of charge at: http://www.chemistry.mcmaster.ca/aimpac/ Cheers, Cherif ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ___________________________________________________________________________ From chemistry-request@server.ccl.net Thu Jun 14 09:35:24 2001 Received: from hermes.csd.unb.ca (root@[131.202.3.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5EDZO516258 for ; Thu, 14 Jun 2001 09:35:24 -0400 Received: from mailserv.unb.ca (root@mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.9.3/8.9.3) with ESMTP id KAA11505 for ; Thu, 14 Jun 2001 10:35:24 -0300 (ADT) Received: from unb.ca ([131.202.164.145]) by mailserv.unb.ca (8.8.8+Sun/8.8.8) with ESMTP id KAA01912 for ; Thu, 14 Jun 2001 10:35:23 -0300 (ADT) Message-ID: <3B28BE50.6020004@unb.ca> Date: Thu, 14 Jun 2001 10:38:24 -0300 From: Martin Gillis User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:0.9.1) Gecko/20010607 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: sgi office apps??? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi all, I am curious if anyone knows of an office package for a sgi machine. Apps, such as, doc. processing, spreadsheets, etc.... Thanks, Martin Gillis From chemistry-request@server.ccl.net Thu Jun 14 10:59:08 2001 Received: from uldns1.unil.ch ([130.223.8.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5EEx8517972 for ; Thu, 14 Jun 2001 10:59:08 -0400 Received: from localhost ([127.0.0.1] helo=uldns1.unil.ch) by uldns1.unil.ch with esmtp (Exim 3.14 #1) id 15AYaL-00035B-00; Thu, 14 Jun 2001 16:59:01 +0200 Received: from pcbch3207h.unil.ch ([130.223.143.63] helo=pcbch3207h ident=aborel) by uldns1.unil.ch with esmtp (Exim 3.14 #1) id 15AYaK-000359-00; Thu, 14 Jun 2001 16:59:00 +0200 Message-ID: X-Mailer: XFMail 1.4.0 on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit MIME-Version: 1.0 In-Reply-To: <3B28BE50.6020004@unb.ca> Date: Thu, 14 Jun 2001 16:59:00 +0200 (MET DST) Reply-To: Alain Borel Organization: University of Lausanne Sender: aborel@pcbch3207h From: Alain Borel To: Martin Gillis Subject: RE: CCL:sgi office apps??? Cc: chemistry@ccl.net On 14-Jun-01 Martin Gillis wrote: > Hi all, > > I am curious if anyone knows of an office package for a sgi machine. > Apps, such as, doc. processing, spreadsheets, etc.... Maybe you can find IRIX binaries of StarOffice or OpenOffice? http://www.openoffice.org Otherwise: AbiWord, Gnumeric (from the Gnome project http://www.gnome.org). And of course, unbeatable for document preparation: LaTeX ---------------------------------- Alain Borel Date: 14-Jun-01 Time: 16:56:11 From chemistry-request@server.ccl.net Thu Jun 14 04:38:11 2001 Received: from mel.ruc.dk ([130.225.220.27]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5E8c8525654 for ; Thu, 14 Jun 2001 04:38:09 -0400 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id KAA23692; Thu, 14 Jun 2001 10:38:07 +0200 (MET DST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id KAA01856; Thu, 14 Jun 2001 10:18:20 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 14 Jun 01 10:38:07 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 14 Jun 01 10:38:04 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Benjamin.Moritz@asu.edu Date: Thu, 14 Jun 2001 10:38:04 +0100 Subject: CCL:Large Mass Atoms CC: chemistry@ccl.net X-Confirm-Reading-To: "Jens Spanget-Larsen" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <12FF457C3E36@virgil.ruc.dk> Benjamin.Moritz@asu.edu: > I was wondering if anyone can help me out with an isotope problem > in G98. I want to set the value of some of my atoms to a very > large mass, but I'm not sure how the input file should look. Do I > need two seperate jobs to do this? Any help will be greatful. Dear Benjamin, in order to specify nuclear masses different from the atomic default values, you need to activate the option 'readiso' to the 'freq' keyword. Additional input is then required, placed after the definition of molecular coordinates in the input stream. The additional input consists of: First one line with two numbers: temperature (in K) and a scaling factor (say, unity). Then one line per atom, with specification of the nuclear mass (amu) to be applied in the calculation of molecular vibrations ('freq'). In the sample input below, the molecular geometry is read from the chk-file ('geom=check'), and also the force constant matrix is read > from this file ('readfc' option to the 'freq' keyword). Hence, the job assumes that a previous run has stored the appropriate date from 'opt' and 'freq' calculations in the chk-file. The job specified below only takes a second or two, since the force constant matrix need not to be recalculated. - In this example, the nuclear masses are entered as whole numbers (for simplicity); Gaussian then selects the appropriate values for the isotopes in question. If you don't input whole number values, Gaussian adopts the value entered "as is". Good Luck, Jens >--< ------------------------------------------------ %chk=PhO_VTZ #t B3LYP/cc-pVTZ Freq(ReadFC,ReadISO) Geom=Check O(18) Phenoxyl Radical 0 2 298.150 1.00000 12 12 12 12 12 12 18 1 1 1 1 1 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Jun 14 04:14:15 2001 Received: from iris6.chimica.unical.it ([160.97.42.125]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5E8EE520926 for ; Thu, 14 Jun 2001 04:14:14 -0400 Received: from chpcrs6 (chpcrs6.chimica.unical.it [160.97.42.132]) by iris6.chimica.unical.it (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id HAA26582; Thu, 14 Jun 2001 07:37:18 +0200 Message-ID: <001401c0f4aa$229ebd20$842a61a0@chpcrs6> From: "Nino Russo" To: Cc: Subject: post-doc position Date: Thu, 14 Jun 2001 10:15:11 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0011_01C0F4BA.E520CB80" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_0011_01C0F4BA.E520CB80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 Postdoc: Computational bio-organic and bio-inorganic Sciences, Dipartimento di Chimica, Universit=E0 della Calabria, I-98030 = Arcavacata di Rende, Italy A postdoctoral position in computational chemistry is available to be started immediately in the group of Professor N. Russo(computational and theoretical chemistry) at = Dipartimento di Chimica, Universit=E0 della Calabria In this computational project, structural, electronic and dynamic = properties of a series of molecules with biochemical significance will = be studied by modern empirical, semiempirical and ab-initio methods. The successful applicant will have a strong background in chemistry or physics and experience with: Molecular mechanics, molecular = dynamics quantum mechanical methods. =20 Applicants should send a CV to Professor Russo by email (nrusso@unical.it)=20 ------=_NextPart_000_0011_01C0F4BA.E520CB80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 

Postdoc:=20 Computational bio-organic and bio-inorganic=20 Sciences,
          = Dipartimento=20 di Chimica, Universit=E0 della Calabria, I-98030 Arcavacata di Rende, = Italy
A=20 postdoctoral position in computational chemistry
is available to be = started=20 immediately in the group of
Professor N. Russo(computational and = theoretical=20 chemistry) at Dipartimento di Chimica, Universit=E0 della Calabria
In = this=20 computational project, structural, electronic and dynamic properties of = a series=20 of molecules with biochemical significance will be studied by modern = empirical,=20 semiempirical and ab-initio methods.
The successful applicant will = have a=20 strong background in
chemistry or physics and experience with: = Molecular=20 mechanics, molecular dynamics quantum mechanical methods.
 
Applicants should send a CV = to=20 Professor Russo
by email (nrusso@unical.it)

------=_NextPart_000_0011_01C0F4BA.E520CB80-- From chemistry-request@server.ccl.net Thu Jun 14 10:15:04 2001 Received: from uscmail.usc.es ([193.144.75.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5EEF3517023 for ; Thu, 14 Jun 2001 10:15:04 -0400 Received: from qfcronos (qfcronos.usc.es [193.144.74.154]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id QAA08441 for ; Thu, 14 Jun 2001 16:15:02 +0200 (MET DST) Message-ID: <000e01c0f4dc$ef986ba0$9a4a90c1@usc.es> From: =?iso-8859-1?Q?Jes=FAs_Rodr=EDguez_Otero?= To: Subject: IGLO program Date: Thu, 14 Jun 2001 16:18:51 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000B_01C0F4ED.B2EEE100" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_000B_01C0F4ED.B2EEE100 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers How can I get the IGLO program of Kutzelnigg and Schindler ?? Jesus Rodriguez-Otero ------=_NextPart_000_000B_01C0F4ED.B2EEE100 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers
 
How can I get the IGLO program of = Kutzelnigg and=20 Schindler ??
 
Jesus = Rodriguez-Otero
------=_NextPart_000_000B_01C0F4ED.B2EEE100-- From chemistry-request@server.ccl.net Thu Jun 14 01:55:16 2001 Received: from mail.etang.com ([202.101.42.207]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5E5tF528695 for ; Thu, 14 Jun 2001 01:55:15 -0400 Received: from lizhenhua (unknown [202.108.240.3]) by mail.etang.com (Postfix) with ESMTP id 7BE421C8A7EC3 for ; Thu, 14 Jun 2001 14:05:20 +0800 (CST) Message-ID: <005901c0f496$c226ac40$c40b140a@lizhenhua> From: "Zhenhua Li" To: "CCL" References: Subject: Re: CCL:Fwd: phase/orbitals Date: Thu, 14 Jun 2001 13:56:25 +0800 Organization: Chem. Dept. Fudan Univ. Shanghai, China MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2462.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2462.0000 Einstein once said that it is theory that determines what we can observe. So although orbital or whatever is just a mathematical concept, maybe one day we can really design some methods to observe them experimentally. But what is physical, it is hard to say. ----- Original Message ----- From: To: Sent: Thursday, June 14, 2001 11:40 AM Subject: CCL:Fwd: phase/orbitals > > >From: "N. Sukumar" > >Date: Wed, 13 Jun 2001 21:26:05 -0400 > >To: chemistry@ccl.net > >Subject: CCL:phase/orbitals > >Sender: "Computational Chemistry List" > > > >The approximate nature of orbitals in many-electron systems is indeed a very > >different issue from the question of "observability" or "physical reality". > > > > Note that physical methods such as electron momentum spectroscopy > (EMS) can probe the momentum distributions of orbitals (especially > valence orbitals) and in that sense allows one to 'visualize' them. > It is possible to get extremely nice agreement between the > theoretical momentum distributions from DFT calculations, for > example, and the experimentally observed MDs. > > > -- > Cheers, > > Dave > > Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au > Senior Principal Research Scientist Voice: 61-3-9545-2477 > CSIRO Molecular Science Fax: 61-3-9545-2446 > Private Bag 10,Clayton South MDC 3169 http://www.csiro.au > Australia http://www.molsci.csiro.au > > For the World Chemical Congress in Brisbane, July 2001 check the details at > http://www.ccm.com.au/wcc > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@osc.e du > > > > > From chemistry-request@server.ccl.net Thu Jun 14 18:09:31 2001 Received: from relay1.scripps.edu ([137.131.200.29]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5EM9V525480 for ; Thu, 14 Jun 2001 18:09:31 -0400 Received: from helios.scripps.edu (helios.scripps.edu [137.131.20.56]) by relay1.scripps.edu (8.11.0/TSRI-4.0r) with ESMTP id f5EM9O114338; Thu, 14 Jun 2001 15:09:24 -0700 (PDT) Received: from scripps.edu (localhost [127.0.0.1]) by helios.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id PAA171747; Thu, 14 Jun 2001 15:09:27 -0700 (PDT) Sender: weber@scripps.edu Message-ID: <3B293617.D1BBC3BD@scripps.edu> Date: Thu, 14 Jun 2001 15:09:27 -0700 From: Christoph Weber Organization: The Scripps Research Institute X-Mailer: Mozilla 4.76C-SGI [en] (X11; U; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Martin Gillis CC: chemistry@ccl.net Subject: Re: CCL:sgi office apps??? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Alain Borel wrote: > > On 14-Jun-01 Martin Gillis wrote: > > Hi all, > > > > I am curious if anyone knows of an office package for a sgi machine. > > Apps, such as, doc. processing, spreadsheets, etc.... > > Maybe you can find IRIX binaries of StarOffice or OpenOffice? > http://www.openoffice.org > > Otherwise: AbiWord, Gnumeric (from the Gnome project http://www.gnome.org). > And of course, unbeatable for document preparation: LaTeX There's a GUI on top of LaTeX, Lyx, which makes working with LaTeX far easier for the novice and lets one concentrate on creating content rather than wrestle with software or text formatting. LaTeX and Lyx are available on SGI's freeware CD and web site. Christoph -- | Dr. Christoph Weber Sen. Applications Specialist | Research Computing, TPC21 858-784-9869 (phone) | The Scripps Research Institute 858-784-9301 (FAX) | La Jolla CA 92037-1027 weber@scripps.edu | http://www.scripps.edu/~weber/ When asked whether there any inherently unknowable laws of physics, Nobel laureate Eugene Wigner replied: "I don't know of any." From chemistry-request@server.ccl.net Thu Jun 14 19:06:51 2001 Received: from mailhost.msi.com ([146.202.0.242]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5EN6o526346 for ; Thu, 14 Jun 2001 19:06:50 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id PAA03425 for ; Thu, 14 Jun 2001 15:41:56 -0700 (PDT) Received: from unknown(146.202.5.50) by mailhost.msi.com via smap (V2.0) id xmac03382; Thu, 14 Jun 01 15:41:48 -0700 Message-Id: <5.1.0.14.0.20010614150210.00a89ec0@pop3.norton.antivirus> X-Sender: jnauss/sparky2.msi.com@pop3.norton.antivirus X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 14 Jun 2001 15:10:08 -0400 To: chemistry@ccl.net From: Jeff Nauss Subject: InsightII and Cerius2 workshops in August Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed On 1 June, Molecular Simulations Inc., Synopsys, Oxford Molecular, and GCG joined together to become Accelrys. Now, we would like to announce four customer training workshops for August in the United States. Two will be held in San Diego, and two will be held in New Jersey. In San Diego, at the San Diego Supercomputer Center, two advanced InsightII workshops will be offered. On August 7-8, the "CHARMm Workshop" will be offered. This workshop will provide a more in-depth coverage of molecular mechanics and dynamics focusing on the use of CHARMm. Both command line usage as well as use in InsightII will be covered. No experience is necessary but knowledge of InsightII will be helpful. On August 9-10, also in San Diego, the workshop "Structure-Based Drug Design with InsightII" will be conducted. This workshop is for experienced users of InsightII who are interested in docking and drug design. The focus will be on detailed studies of single ligand interactions with specific receptors. Extensive experience or completion of the "Introduction to Life Science Modeling with InsightII" workshop is required. That same week, two workshops will be offered at Rutgers University, New Brunswick, NJ. On August 7-8, the "Introduction to Cerius2 for Life Sciences Workshop" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modeling experience is not assumed making this course a great place to learn molecular modeling with Cerius2. Also, in New Brunswick on August 9-10, the "Small Molecule and Drug Design with Cerius2" workshop will be offered. This workshop is aimed at our customers in the pharmaceutical industry and who are involved in drug design and who would like to make more effective use of modeling in their research. The course will focus on QSAR techniques and methodologies as well as structure-based drug design. Familiarity with the Cerius2 environment is required for attendance to this workshop. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for more than one course and receive a 25% discount for the each additional course. Further detailed information about this and other Accelrys training workshops, as well as on-line course registration, can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/index.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss 858-799-5555 Chris Arzt 858-799-5340 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 On June 1, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Accelrys is a subsidiary of Pharmacopeia, Inc.