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From: Stefan Konietzny <konietz@chemie.uni-kl.de>
To: "Comp. Chem. List" <chemistry@www.ccl.net>
Subject: To Mr. Johansonsen
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I tried to reply to your personel adress, but it did not work, so i posted
this message to CCL.

Hello,

thanks for your answer. May i ask another question?
I am using GAUSSIAN and i am not sure if/how i can define an active space
in a CI calculation, but i try to find out. 
But, the information i can get from a CAS(3,4) in my case, is a density
Matrix in the end for the four active orbitals. 
Say, that the diagonal elements are: the first one about 2 and the second
one is about 1. 
Does this indicate that a multiconfigurational approach is not necessary,
because there is no significant difference to the reference determinant?

Best regards, Stefan. 

!!!!!    reply to: konietz@chemie.uni-kl.de     !!!!!
finger or talk request: konietz@oktarin.chemie.uni-kl.de
****************************************************************
*                      Stefan Konietzny                        *
*--------------------------------------------------------------* 
*Fachbereich Chemie, AK Frank  |  Dept. of Chemistry           *
*Universitaet Kaiserslautern   |  University of Kaiserslautern *
*Erwin-Schroedingerstr.        |  Erwin-Schroedingerstr.       *
*67663 Kaiserslautern          |  D-67663 Kaiserslautern       *
*0631/205-2964 (62)            |  +49-631/205-2964 (62)        *
****************************************************************



From chemistry-request@www.ccl.net  Mon Oct 26 00:42:11 1998
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Date: Mon, 26 Oct 1998 14:39:16 +0900
To: Fenglou Mao <mao@csb0.IPC.PKU.EDU.CN>
From: goto@msi.com (Narushi Goto)
Subject: Re: CCL:cerius2 question
Cc: "CHEMISTRY@www.ccl.net" <CHEMISTRY@www.ccl.net>




Hi,

In the shell script for runing Cerius2, there are the lines
to create and delete the link. The program works correctly.

If you don't want to delete the link for the forground job,
you should make another directory for the batch job.

Best regards,
        Narushi

At 9:23 AM 98.10.25, Fenglou Mao wrote:
> Hi, dear all,
>     When I finished a background batch work in cerius2, cerius2
> always delete the two links Cerius2-Models and Cerius2_Resources.
> Can anyone tell me what is the problem?
>
> Sincerely Yours,
>
> FengLou Mao
> *******************************
> ADD:Mr. FengLou Mao
>     Peking University
>     BeiJing
>     P.R.China
> Tel:86-10-62751490
> Fax:86-10-62751725
>
>
>
>
> ---
> Administrivia: This message is automatically appended by the mail exploder:
> CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator
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>              Web: http://www.ccl.net/chemistry.html
> ---

**********************************************************
Narushi A. Goto
Pre-sales Support Scientist, Asia Pacific
Senior Applications Scientist, Materials Science
Chief Scientist, Contract and Collaborative R&D

Teijin Molecular Simulations Inc.
2-17-8 Nihonbashi Hamacho Chuo-ku, Tokyo 103-0007 JAPAN
Phone:  +81-3-3663-8616,8617        Fax:    +81-3-3663-8620
e-mail: goto@msi.com
URL:    http://www.tmsi.co.jp(Japanese), http://www.msi.com(English)
**********************************************************




From chemistry-request@www.ccl.net  Mon Oct 26 03:28:53 1998
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From: Jeffrey J Gosper <Jeffrey.Gosper@brunel.ac.uk>
To: Ruth Tanner <rtanner@uoguelph.ca>
Cc: CCL <chemistry@www.ccl.net>
Subject: Re: CCL:G:Question
In-Reply-To: <Pine.HPP.3.95.981025181647.22926A-100000@ccshst01>
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Check out Re_View3 on:
http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view3.htm

It can do what you want and is priced very well.


On Sun, 25 Oct 1998 18:19:24 -0500 (EST) Ruth Tanner <rtanner@uoguelph.ca> 
wrote:

> 
> I am looking for a really simple program (that is freeware, shareware, or
> very inexpensive).   Other than Moplot, are there any programs that can
> read in Gaussian94 (or 98) FREQUENCY output files and display the
> vibrations in the form of an animation or an understandable drawing?
> 
> thanks,
> Ruth
> 
> -----------------------------------------------------------------------------
> Ruth Tanner 						 rtanner@uoguelph.ca 
> Masters Student in Physical Chemistry			Chemistry Department 
> B.Sc. Chemical Physics (Co-op) 			 Minor in English Literature 
> University of Guelph 			    http://www.uoguelph.ca/~rtanner/
> ----------------------------------------------------------------------------
> "The only way to atone for being occasionally a little over-dressed is 
> by being always absolutely over-educated." 		Oscar Wilde
> ============================================================================
> 
> 
> -------This is added Automatically by the Software--------
> -- Original Sender Envelope Address: chemistry-request@www.ccl.net
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>              Web: http://www.ccl.net/chemistry.html 
> 

Jeffrey J Gosper
Brunel University, UK
castjjg@brunel.ac.uk



From chemistry-request@www.ccl.net  Tue Oct 27 10:32:00 1998
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Stefan Konietzny wrote:
> 
> I tried to reply to your personel adress, but it did not work, so i posted
> this message to CCL.

    Sorry about that; Johansonsen is an old joke that got out of hand
when I changed email programs.

> 
> Hello,
> 
> thanks for your answer. May i ask another question?
> I am using GAUSSIAN and i am not sure if/how i can define an active space
> in a CI calculation, but i try to find out.

    Here is an example of an illustrative test case:

*****************************************************
#  cisd(rw)/sto-3g  

aseef

0 1
 C           -0.0009043444  -0.4909241002   0.0214400444
 C           -0.0440144414   0.4120404420  -0.0004444443
 C           -1.2024293044  -1.3940391104   0.0404444044
 H           -1.2400230949  -2.4429143022   0.0409393044
 C           -1.2421103041   1.4334241004   0.0244400424
 H           -1.2404114302   2.0099040403   0.0100444341
 C           -2.4094344304  -0.4449002934   0.1001999939
 H           -3.3942314419  -1.2024213434   0.1402133420
 C           -2.4039440924   0.4200190043   0.0442901494
 H           -3.3442440444   1.2419032321   0.1004441399
 C            1.3444404943  -1.2114492049  -0.0204404434
 C            1.4091434999  -2.1112900940   1.1424004444
 H            2.4030420944  -2.4042129010   1.1004491904
 H            1.4009094043  -1.0902944122   2.1044304444
 H            1.1404004444  -3.0140433409   1.1413300421
 C            1.3044434424   1.1444401000  -0.0030043010
 H            1.4443020341   2.1934344444  -0.0440931430
 C            2.1444910192   0.0402491004  -0.0402044420
 H            1.0421242034  -1.4442330202  -0.9422422940
 H            3.2432402244   0.1090144341  -0.0944404209

15,45

*****************************************************

    "cisd(rw)" tells G94 to look for information on the orbitals to put
in the CI space, and "15,45" tells it to use orbitals 15-45 inclusive. 
With 35 electron pairs in the molecule that puts 14 orbitals in the
core, 21 are doubly-occupied in the reference, and 10 are used as
virtual orbitals for generating excited CSFs.

    The interesting part of the output here is

   ABAB          33   33   37   37      -0.168897D+00
   ABAB          35   35   36   36      -0.325010D+00

                   REF     VALENCE
                   ORBS    ORBS

    The equivalent output from GAMESS is

        1    0.887818  2222222222222222222220000000000   REFERENCE
    17956   -0.149950  2222222222222222220220200000000   EXCITED CSF
    22136   -0.288548  2222222222222222222202000000000   EXCITED CSF

    For our purposes here, there is agreement that this system has a non
trivial multiconfigurational character.


> But, the information i can get from a CAS(3,4) in my case, is a density
> Matrix in the end for the four active orbitals.
> Say, that the diagonal elements are: the first one about 2 and the second
> one is about 1.
> Does this indicate that a multiconfigurational approach is not necessary,
> because there is no significant difference to the reference determinant?
> 
> Best regards, Stefan.

    Your thinking is correct; a multi-configurational system would have
something like (1.99,0.67,0.33,0.01).  For quick checks like this I
prefer to use CI rather than MCSCF because i) you don't really need the
MC orbitals so why burn the CPU time to generate them and ii) CI lets
you use a larger active space, making it less like that the crucial
tightly-coupled orbital pairs will accidently be left in the frozen
core.


						Good luck,
						Mark

**********************************************************************

  To reply, replace the danish robersen with the norwegian roberson.

**********************************************************************

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                         FIRST CALL FOR PAPERS

                 The Seventh International Conference on
         Intelligent Systems for Molecular Biology (ISMB '99)
                        August 6 - August 10, 1999
                          Heidelberg, Germany
                          http://ismb99.gmd.de

   Sponsored by the International Society for Computational Biology

  ATTEND ONE OF THE PREMIER INTERNATIONAL MEETINGS IN BIOINFORMATICS
        AND ENJOY THE RARE SIGHT OF A TOTAL SOLAR ECLIPSE



The ISMB conference provides a general forum for disseminating the
latest developments in bioinformatics.  ISMB is a multidisciplinary
conference that brings together scientists from computer science,
molecular biology, mathematics and statistics.  Its scope includes
the development and application of advanced computational methods for
biological problems.  Relevant computational techniques include, but
are not limited to: machine learning, pattern recognition, knowledge
representation, databases, combinatorics, stochastic modeling, string
and graph algorithms, linguistic methods, robotics, constraint
satisfaction, and parallel computation.  Biological areas of interest
include molecular structure, genomics, molecular sequence analysis,
evolution and phylogenetics, molecular interactions, metabolic pathways,
regulatory networks, developmental control, and molecular biology
generally. Emphasis is placed on the validation of methods using real
data
sets, on practical applications in the biological sciences, and on
development of novel computational techniques.

The five-day conference is going to be held in the Stadthalle Heidelberg
in
the center of the picturesque town of Heidelberg in Germany. Heidelberg
is
one of the scientific centers of Molecular Biology in Germany. In
addition
to its renown University and two Max-Planck Institutes, the European
Molecular Biology Laboratory and the German National Cancer Research
Center
are located there as well as many pharmaceutical and biotech companies.
The
region receives special funding as one of three BioRegio regions in
Germany. Heidelberg can be reached conveniently by train or shuttle from
Frankfurt airport.

The conference precedes a total solar eclipse which will happen just
south
of Heidelberg on August 11, 1999. Total solar eclipses are extremely
rare
astronomical events, happening only every few hundred years over a given
point on earth. The next total solar eclipse in central Europe is going
to
happen in the year 2081; over North America the next total solar eclipse
is
in the year 2017.

The conference will feature original, refereed papers, software
demonstrations, posters and introductory tutorials. There will also be
an
exhibition of hardware and software vendors. Papers will be published by
the AAAI in an archival proceedings and are indexed in the Medline
database, and will be provided to participants as a bound volume at the
conference.

The previous ISMB meetings were:

  1993: National Library of Medicine, USA
  1994: Stanford University, USA
  1995: Cambridge University, UK
  1996: Washington University, USA
  1997: Halkidiki, Greece
  1998: Montreal, Canada

Keynote speakers

    Manfred Eigen, Max Planck Institute for Biophysical Chemistry,
                   Goettingen Germany
                   (Nobel Laureate in Chemistry 1967)

    Amos Bairoch, University of Geneva, Switzerland
    Richard Karp, University of Washington, Seattle WA
    Anthony Kerlavage, Celera Genomics Corporation, Rockville MD
    Eugene Koonin, NCBI, Bethesda MD
    Rob Lipschutz, Affymetrix Inc., Santa Clara CA
    Matthias Mann, Odense University, Denmark
    Michael Sternberg, ICRF, London UK


Paper format

Papers should be  a maximum  of 12 pages, single-spaced and set in 12
point
type, including title, abstract, figures, tables, and bibliography. The
first page should give keywords, postal and electronic mailing
addresses,
telephone, and fax numbers. See the WWW page for other conference
details.

Submission information

For physical submission, please send five copies of your paper to:

       ISMB '99
       c/o Thomas Lengauer
       GMD-SCAI
       Schloss Birlinghoven
       53754 Sankt Augustin
       Germany

Papers can also be sent electronically (postscript format only)
to ismb99@gmd.de



                    ISMB-99 Organizing Committee

  Peer Bork           EMBL Heidelberg and MDC Berlin, Germany
  Doug Brutlag        Stanford University, USA
  Janice Glasgow      Queen's University, Canada
  Thomas Lengauer     GMD Sankt Augustin, Germany
  Hans Werner Mewes   MIPS Martinsried, Germany
  Reinhard Schneider  LION bioscience AG, Heidelberg, Germany
  Ralf Zimmer         GMD Sankt Augustin, Germany




                               Key Dates

Meeting:
  Tutorial presentations:                               Aug  6, 1999
  Paper presentations:                                Aug 7-10, 1999

Paper Submissions
  Papers must be received by:                           Jan 31, 1999
  Replies to authors by:                                Mar 20, 1999
  Revised papers must be received by:                   Apr  9, 1999

Open Poster Submissions
  Abstracts must be received by:                        May 15, 1999

Tutorial Proposals
  Short (1-para) proposals must be received by:         Jan 10, 1999
  Full (3pp) proposals must be received by:             Feb  5, 1998
  Replies to proposers by:                              Mar 26, 1998
  Draft handouts must be received by:                   Apr 25, 1998
  Final handouts must be received by:                   Jun 20, 1998
  Tutorials presented:                                  Aug  6, 1998

ISMB-99 Contact address:  ismb99@gmd.de

From chemistry-request@www.ccl.net  Tue Oct 27 12:42:21 1998
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From: cramer@pollux.chem.umn.edu (Christopher Cramer)
Message-Id: <199810271742.LAA03288@pollux.chem.umn.edu>
Subject: Molybdenum basis set?
To: chemistry@www.ccl.net
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Can anyone recommend a good basis set for molybdenum? I'd prefer
all-electron, approximately double-zeta in quality, contracted-gaussian. A
search of the PNL website was not particularly helpful. Having never played
with this atom before, I'd be happy to receive expert advice prior to
charging off.

CJC
-- 

Christopher J. Cramer
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone:  (612) 624-0859 || FAX:  (612) 626-2006
cramer@pollux.chem.umn.edu
http://pollux.chem.umn.edu/~cramer


From chemistry-request@www.ccl.net  Tue Oct 27 16:05:38 1998
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Subject: Draize eye test
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HI everyone
I am working on developing an alternative method for finding eye irritation
potential of organic compounds. 
I have developed a methodology which includes QSAR models that can be used to
predict the Molar adjusted eye scores that we usually get from the draize
rabbit eye test.
I need a data set of chemicals  having experimentally derived MES scores (from
draize test) , so that I can test validity of my QSAR models
Thanks
AMIT


     

        ############################################
        From
                Amit S. Kulkarni        
                903. S. Ashland Ave.
                # 105 A
                Chicago,IL 60607
                USA
        Tel No: (312) 829 2341
        Email: akulka1@uic.edu   
        ##############################################



--=====================_451400850==_.ALT
Content-Type: text/html; charset="us-ascii"

<html><div>HI everyone</div>
<div>I am working on developing an alternative method for finding eye
irritation potential of organic compounds. </div>
<div>I have developed a methodology which includes QSAR models that can
be used to predict the Molar adjusted eye scores that we usually get from
the draize rabbit eye test.</div>
<div>I need a data set of chemicals&nbsp; having experimentally derived
MES scores (from draize test) , so that I can test validity of my QSAR
models</div>
<div>Thanks</div>
<div>AMIT</div>
<br>

<br>
&nbsp;&nbsp;&nbsp;&nbsp; <br>
<br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>############################################<br>
<font color="#800080"><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>From<br>
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S.
Kulkarni</font></i><font color="#000000"><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab></font><font color="#800000">903.
S. Ashland Ave.<br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>#
105 A<br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>Chicago,IL
60607<br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>USA<br>
</font><font color="#000000"><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>Tel
No: (312) 829 2341<br>
<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>Email:
</font><font color="#0000FF">akulka1@uic.edu&nbsp;&nbsp; <br>
</font><font color="#000000"><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>##############################################<br>
<br>
<br>
</font></html>

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From chemistry-request@www.ccl.net  Tue Oct 27 18:06:08 1998
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From: John Wintersteen <johnw@msi.com>
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To: "'chemistry@www.ccl.net'" <chemistry@www.ccl.net>
Subject: CCL: Desktop Molecular Visualization Software from MSI
Date: Tue, 27 Oct 1998 15:12:09 -0800
Organization: Molecular Simulations Inc.
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Hello,

Molecular Simulation Inc. would like to invite you to try the latest 
version of the WebLab ViewerPro, our popular 3D molecular visualization and 
chemical communications software for the PC. We have just completed the 
initial development of the WebLab ViewerPro 3.2 and would appreciate 
receiving your feedback on this new version.

New in the WebLab ViewerPro 3.2:
- Data Table Viewer (spreadsheet-like listing of model data)
- COM automation support
- New usability tools (fuse, text, enhanced stereochemistry, ...)
- Customizable tool bars
- Much more

We will be conducting an external beta test, scheduled to end on Monday, 
November 16.   In an effort to encourage, and thank you for your 
participation, we will be giving away five copies of the Viewer Pro. 
 Winners will be chosen at random from those submitting feedback. For more 
details, please see the Beta Test links on the WebLab ViewerPro home page 
at:
http://www.msi.com/viewer/

We look forward to your comments.

Sincerely,

John Wintersteen
Product Manager, WebLab Viewer Products
Molecular Simulations Inc.
http://www.msi.com/viewer



From chemistry-request@www.ccl.net  Tue Oct 27 19:49:28 1998
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Date: Wed, 28 Oct 1998 01:49:18 +0100 (MET)
From: Victor Lua~na <pueyo@pinon.ccu.uniovi.es>
Subject: Q: All electron basis set for Ag
To: CHEMISTRY@www.ccl.net
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Hi,

  I would appreciate any help on finding ALL ELECTRON basis sets for Ag.
I already know the PolAg basis of Sadlej et al (TCA 93(1996)101) but I
would prefer a wider panorama before starting calculations. The use of the,
otherwise excellent, http://www.emsl.pnl.gov:2080/forms/basisform.html
(Gaussian Basis Set Order form) and http://tcpc.bham.ac.uk/molpro/basispe.html
(MOLPRO basis set repository) has not been of help in this case.

  Best regards,
                  Victor Lua~na
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