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Subject: Objects in Bio- & Chem-Informatics 2001, Boston (USA), July 9-10
To: biopython-announce-l@biopython.org, chemweb@ic.ac.uk,
   bioinformatics@sdsc.edu, tc@omg.org, lifesciences@omg.org,
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We apologize to those who receive multiple copies of this email.
Please distribute this call to all interested parties.
--------------------------------------------------------------------------------------------------
                      Objects in Bio- & Chem-Informatics 2001 (OiBC)
                                  July 9 and 10, 2001
                    Sheraton Ferncroft Resort, Danvers, Massachusetts, USA
                             http://www.omg.org/lsr/oibc/


Following in the tradition of the successful 'Objects in Bioinformatics'
conferences held in Hinxton, UK in 1997 and 98 and in San Jose, California
in 1999, Objects in Bio- & Chem-informatics 2001 focuses on the role of
object-oriented technology, reusable software components, ontologies,
design patterns, and distributed computing in life sciences research. The
conference is aimed at developers, integrators, and users of
object-oriented software for the biological and chemical research community
in both academia and industry. The overall theme of the conference is
sharing best practices for implementing object-based systems in life
sciences research. The conference will include lectures and poster sessions
on the application of these technologies to bioinformatics,
cheminformatics, genomics, structural biology, proteomics, computational
biology, and related disciplines.

The program will include presentations of current work from:

· ArQule                                 · NetGenics
· Azara                                  · Object Management Group
· BioAnalyte                             · open-bio.org
· Biogen                                 · Physiome Sciences
· Blackstone Technology Group            · San Diego Supercomputer Center
· Crystallics                            · Sandia National Laboratories
· Doubletwist                            · Sanger Centre
· European Bioinformatics Institute      · Scripps Research Institute
· GlaxoSmithKline                        · Synomics
· IBM Research                           · Thermo LabSystems
· Incyte Genomics                        · 3rd Millennium
· Keio University                        · University of Cambridge
· Life Science Informatics Solutions     · University of Colorado
· LION Bioscience                        · University of Connecticut
· Los Alamos National Laboratory         · University of Massachusetts
Lowell
· Millennium Pharmaceuticals             · Virtek
· National Institute of                  · Weizmann Institute of Science
   Standards and Technology              · Wyeth Ayerst Research

OiBC 2001 will be held in conjunction with OMG's Technical Committee (TC)
Meeting Week in Danvers, Massachusetts (19 miles north of Boston).
Attendees of OiBC-2001 are also invited to attend the OMG TC Meeting in its
entirety and view first hand OMG's standards adoption process in action.
During these meeting weeks, members will apply OMG's open, vendor-neutral,
consensus-building standardization process to set industry software
standards in domains such as Life Sciences Research, Telecommunications,
Manufacturing, Human Resources, and Healthcare.

The full agenda and presentation abstracts, as well as hotel and
registration information for OiBC 2001 are available at
www.omg.org/lsr/oibc.  To learn more about the initiatives underway with
the Life Science Research Domain Task Force, see their roadmap at
www.omg.org/lsr.




From chemistry-request@server.ccl.net Tue Jun  5 21:47:17 2001
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To: "chemistry@ccl.net" <chemistry@ccl.net>
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Hello:

I would like to review info about the hepatic first pass effect, as well
as find some database of clearance values and other pharmacokinetics
data. Any sugestions?



--
Greatings
Prof. Juan Alexander Padron Garcia
Centro de Quimica Farmaceutica
La Havana Cuba
padrongj@cqf.co.cu




From chemistry-request@server.ccl.net Tue Jun  5 15:53:53 2001
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Subject: CCL:Crystal Accuarcy
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--------------AD1E60F01EEEABD03F432459
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Dear CCL'ers,

Does anyone know how to increase, in a consitent manner

the accuracy of Crystal98 ??

I have the Input deck below:

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Diamond-2 STO-3G
CRYSTAL
0 0 0
227
3.57
1
6  0.1250000000     0.1250000000   0.1250000000
END
6 2
0 0 3 2.  1.
71.6168370      0.15432897
13.0450960      0.53532814
3.53051220      0.44463454
0 1 3 4.  1.
2.94124940     -0.09996723      0.15591627
0.68348310      0.39951283      0.60768372
0.22228990      0.70011547      0.39195739
99 0
END
DFT
BASIS
0
6 2
1 0 18  0.4445  143.2340
1 4 18  0.4445  143.2340
99 0
EXCHANGE
LDA
END
TOLINTEG
12 12 1 1 1
NOBIPOLA
END
1 0 1
TOLSCF
11 11
MAXCYCLE
50
FMIXING
40
END

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

I have tried to do this by decreasing the tolerences of the overlap and penetration of the colomb integrals
(from 7 to 14).  I do not get a consistent convergence of the total energy. Has anyone seen this and
What am I doing wrong ??

CJ Tymczak
=========================================================
|  Dr. C. J. Tymczak                                    |
|  Group T-12   MS 268                                  |
|  Los Alamos National Laboratory                       |
|  Phone:(505)-667-3881                                |
=========================================================



--------------AD1E60F01EEEABD03F432459
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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>

<pre>Dear CCL'ers,

Does anyone know how to increase, in a consitent manner

the accuracy of Crystal98 ??&nbsp;

I have the Input deck below:&nbsp;

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++&nbsp;

Diamond-2 STO-3G&nbsp;
CRYSTAL&nbsp;
0 0 0&nbsp;
227&nbsp;
3.57&nbsp;
1&nbsp;
6&nbsp; 0.1250000000&nbsp;&nbsp;&nbsp;&nbsp; 0.1250000000&nbsp;&nbsp; 0.1250000000&nbsp;
END&nbsp;
6 2&nbsp;
0 0 3 2.&nbsp; 1.&nbsp;
71.6168370&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.15432897&nbsp;
13.0450960&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.53532814&nbsp;
3.53051220&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.44463454&nbsp;
0 1 3 4.&nbsp; 1.&nbsp;
2.94124940&nbsp;&nbsp;&nbsp;&nbsp; -0.09996723&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.15591627&nbsp;
0.68348310&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.39951283&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.60768372&nbsp;
0.22228990&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.70011547&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.39195739&nbsp;
99 0&nbsp;
END&nbsp;
DFT&nbsp;
BASIS&nbsp;
0&nbsp;
6 2&nbsp;
1 0 18&nbsp; 0.4445&nbsp; 143.2340&nbsp;
1 4 18&nbsp; 0.4445&nbsp; 143.2340&nbsp;
99 0&nbsp;
EXCHANGE&nbsp;
LDA&nbsp;
END&nbsp;
TOLINTEG&nbsp;
12 12 1 1 1&nbsp;
NOBIPOLA&nbsp;
END&nbsp;
1 0 1&nbsp;
TOLSCF&nbsp;
11 11&nbsp;
MAXCYCLE&nbsp;
50&nbsp;
FMIXING&nbsp;
40&nbsp;
END&nbsp;

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++&nbsp;

I have tried to do this by decreasing the tolerences of the overlap and penetration of the colomb integrals&nbsp;
(from 7 to 14).&nbsp; I do not get a consistent convergence of the total energy. Has anyone seen this and&nbsp;
What am I doing wrong ??&nbsp;

CJ Tymczak&nbsp;
=========================================================
|&nbsp; Dr. C. J. Tymczak&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |
|&nbsp; Group T-12&nbsp;&nbsp; MS 268&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |
|&nbsp; Los Alamos National Laboratory&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |
|&nbsp; Phone:(505)-667-3881&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |
=========================================================</pre>
&nbsp;</html>

--------------AD1E60F01EEEABD03F432459--



From chemistry-request@server.ccl.net Tue Jun  5 21:52:46 2001
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Date: Mon, 11 Jun 2001 18:54:26 -0700
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From: "Benjamin J Moritz" <bmoritz@asu.edu>
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Dear CCLers,

I have a question about performing frequency calculations in G98.  We have 
optimized several structures using the Amsterdam Density Functional (ADF) 
program and would now like to perform seperate frequency calculations on 
only a certain section of the optimized structure.  My question to CCL is 
can I create an input file with the optimized internal coordinates from 
ADF, and freeze a section of the structure and have Gaussian 98 perform 
frequency calculations on the unfrozen atoms?  Any help is greatly 
appreciated.  Thank you.



****************************************************************
Benjamin J. Moritz                                       home (602) 453-9411
Dept. of Chemistry & Biochemistry                 work (480) 965-8509
Arizona State University                                Mailto:bmoritz@asu.edu
P. O. Box 871604
Tempe, AZ  85287-1604
****************************************************************

"Karma is justice without the satisfaction."

--=====================_2171156==_.ALT
Content-Type: text/html; charset="us-ascii"

<html>
Dear CCLers,<br>
<br>
I have a question about performing frequency calculations in G98.&nbsp;
We have optimized several structures using the Amsterdam Density
Functional (ADF) program and would now like to perform seperate frequency
calculations on only a certain section of the optimized structure.&nbsp;
My question to CCL is can I create an input file with the optimized
internal coordinates from ADF, and freeze a section of the structure and
have Gaussian 98 perform frequency calculations on the unfrozen
atoms?&nbsp; Any help is greatly appreciated.&nbsp; Thank you.<br>
<br>
<br>
<x-sigsep><p></x-sigsep>
<font size=3 color="#00FF00">****************************************************************<br>
</font><font size=3>Benjamin J.
Moritz<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
home (602) 453-9411<br>
Dept. of Chemistry &amp;
Biochemistry&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
work (480) 965-8509<br>
Arizona State
University&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</font><a href="mailto:bmoritz@asu.edu" eudora="autourl"><font size=3 color="#0000FF">Mailto:bmoritz@asu.edu</a><br>
</font><font size=3>P. O. Box 871604<br>
Tempe, AZ&nbsp; 85287-1604<br>
</font><font size=3 color="#00FF00">****************************************************************<br>
<br>
</font><font size=3>&quot;Karma is justice without the
satisfaction.&quot;<br>
</font></html>

--=====================_2171156==_.ALT--



From chemistry-request@server.ccl.net Wed Jun  6 02:36:25 2001
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Date: Wed, 6 Jun 2001 14:35:40 +0800
From: Song Yun-long <songyunlong@263.net>
To: "chemistry@ccl.net" <chemistry@ccl.net>
Subject: orbital component
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Dear sir,
I am a novice of quantum chemistry.I need to analysis the component of HOMO or LUMO orbital,ie,
which atom and which orbital compose the HOMO orbital.I know it can be calculated from the molecular
coefficient of the HOMO orbital.But I didn't know the details.Can you help me?
I wonder if there is some freeware to solve the problem?
Besides, I used MOPAC6.0 interfaced with Sybyl program package!

Thank you in advance!

             Song Yun-long
            songyunlong@263.net


From chemistry-request@server.ccl.net Wed Jun  6 03:04:25 2001
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To: Marc BAADEN <baaden@smplinux.de>
cc: CHEMISTRY@ccl.net, jose.faraldo-gomez@christ-church.ox.ac.uk
Subject: Re: CCL:tri-fluor-ethanol (TFE) solvent force field parameters and
 coordinates
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On Tue, 5 Jun 2001, Marc BAADEN wrote:

>
>Dear All,
>
>below I forward a message from a colleague. You can either reply directly
>to him (mailto:jose.faraldo-gomez@christ-church.ox.ac.uk), or I will forward
>any responses.
M. Fioroni, K. Bruger, A.E. Mark and D. Roccatano A new
         2,2,2-trifluoroethanol model for molecular dynamics simulations. 
         J. Phys. Chem. B, 104 (2000), 12347-12354. 

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: spoel@xray.bmc.uu.se	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From chemistry-request@server.ccl.net Wed Jun  6 07:27:06 2001
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Date: Wed, 6 Jun 2001 01:26:51 +0200
From: a3arzi <Arturas.Ziemys@vaidila.vdu.lt>
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To: Song Yun-long <songyunlong@263.net>
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Subject: Re: CCL:orbital component
In-reply-To: <20010606063546.GMBO21008.fep2.online.sh.cn@169>
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Hi,

Try contact with S.I.Gorelsky (serge@yorku.ca) for "MOMIX" software.... It is suitible for
MO analysis over fragments of molecules ...

Good luck
Arturas Z.



From chemistry-request@server.ccl.net Wed Jun  6 06:00:25 2001
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From: zalesny@wb486.ch.pwr.wroc.pl (Robert Zalesny)
To: escr@klingon.uab.es, rrashid@unlserve.unl.edu
Subject: Re: CCL:Hyperpolarizability calculations.
Cc: chemistry@ccl.net

There is a review related to calculations of nonlinear optical
properties written by Kurtz:
* Kurtz,H.A.;Dudis,D.S. in "Review in Computational Chemistry" Vol.12
  Ed. K.B.Lipkowitz
One may also looks for a review in:
* Chemical Review (1994),Vol.94
All the number is concerned to nonlinear optical properties of molecules.

To my best knowledge the freeware programs that have capabilities of
calculations above mentioned properties are:
GAMESS
DALTON
These are the most famous.

==================================
Robert Zalesny
Quantum Chemistry Group
Wroclaw University of Technology
Poland
==================================


From chemistry-request@server.ccl.net Wed Jun  6 07:49:22 2001
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> Hello:
>
> I would like to review info about the hepatic first pass effect, as well
> as find some database of clearance values and other pharmacokinetics
> data. Any sugestions?
>
> --
> Greatings
> Prof. Juan Alexander Padron Garcia
> Centro de Quimica Farmaceutica
> La Havana Cuba
> padrongj@cqf.co.cu
>



From chemistry-request@server.ccl.net Wed Jun  6 13:56:35 2001
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From: Eric Scerri <scerri@chem.ucla.edu>
Subject: phase information/orbitals question
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At the risk of re-opening the debate on the observation of orbitals,

I recently had a communication informing me that several experiments 
have provided  phase information involving electrons in atoms and 
molecules and that this can be regarded as evidence for wavefunctions 
as opposed to electron density.

I wonder if anyone has any views on this and/or whether they might 
provide examples of this kind of work.

eric scerri
-- 


Dr. Eric Scerri ,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri@chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.wkap.nl/journalhome.htm/1386-4238

Also see International Society for the Philosophy of Chemistry
http://www.georgetown.edu/earleyj/ISPC.html

From chemistry-request@server.ccl.net Wed Jun  6 13:44:03 2001
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Date: Wed, 6 Jun 2001 18:43:26 +0100 (WEST)
From: Sofia Godinho <sgodinho@itqb.unl.pt>
To: CCL <chemistry@ccl.net>
Subject: nth-order saddle point, n>1
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Dear CCLers,
I wonder what is the chemical/physical meaning of a nth-order
saddle point (n>1)?
That is...for instance, when I get four immaginary frequencies
does it mean that I have to "pass through" four vibrational modes
to arrive to a minimum? (Or to three to get to a transition state?)
Or it simply has nothing to do with it and it is only a mathematical
definition of a saddle point?
Or...?

May I thank you in advance for any help, 
	Sofia

Sofia Godinho
Ph-D student
ITQB-UNL-Portugal
email: sgodinho@itqb.unl.pt



From chemistry-request@server.ccl.net Wed Jun  6 16:36:24 2001
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Date: Wed, 6 Jun 2001 15:36:22 -0500 (CDT)
From: =?iso-8859-1?q?Miguel=20Balderas?= <nyfgmaba@yahoo.com.mx>
Subject: phD in electrochemical theoretical (calculations)
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Dear CCLs:
 
I would like to get some references of electrochemical
calculations and  who is working in this area.
 Does anyone can help me?

Thanks in advance,
 
Miguel A. Balderas

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