From owner-chemistry@ccl.net Tue Jun 19 07:28:01 2007
From: "Guermoune Abdeladim lguermoune,+,hotmail.com" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: AIM calculation
Message-Id: <-34512-070619072530-23827-8tlCOveDtdhP1Qvbt71e9g---server.ccl.net>
X-Original-From: "Guermoune  Abdeladim" <lguermoune ~ hotmail.com>
Date: Tue, 19 Jun 2007 07:25:27 -0400


Sent to CCL by: "Guermoune  Abdeladim" [lguermoune(0)hotmail.com]
Dear Netters,
I have asked a few days ago about AIM, and I have proposed my problem. So up to now the problem has not been resolved. Fortunately used of NBO analysis with resonance keyword, it gives some good results.
Thank you everyone who answered my question, and raising an interesting remarks about AIM calculation.

Guermoune Abdeladim.
University Cadi Ayyad Marrakech
Morocco.


From owner-chemistry@ccl.net Tue Jun 19 10:22:01 2007
From: "Amandeep S. Sidhu asidhu^biomap.org" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: CFP: 2007 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2007)
Message-Id: <-34513-070618175407-21528-o6QdU0kPSCDdHYuddmRVVA/a\server.ccl.net>
X-Original-From: "Amandeep S. Sidhu" <asidhu|-|biomap.org>
Content-Transfer-Encoding: 8bit
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Date: Tue, 19 Jun 2007 06:53:39 +1000
MIME-Version: 1.0


Sent to CCL by: "Amandeep S. Sidhu" [asidhu,+,biomap.org]

2007 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM
2007)
(co-located  with IEEE/WCI/ACM WI-IAT 07 and IEEE GrC 07)

http://www.cis.drexel.edu/faculty/thu/bibm/index.php.htm

San Jose, CA, USA    Nov 2-4, 2007

IEEE BIBM 2007 will provide a general forum for disseminating the latest
research in bioinformatics and biomedicine. It is a multidisciplinary conference
that brings together academic and industrial scientists from computer science,
biology, chemistry, medicine, mathematics and statistics. It will exchange
research results and address open issues in all aspects of bioinformatics and
biomedicine and  provide a forum for the presentation of work in  databases,
algorithms, interfaces, visualization, modeling, simulation, ontology  and other
computational methods, as applied to life science  problems, with emphasis on
applications in high throughput data-rich areas in biology, biomedical
engineering. IEEE BIBM 2007   intends to attract a balanced combination of
computer scientists, biologists, biomedical engineers, chemist, data analyzer,
statistician. 

Topics of interests

We are soliciting high quality original research papers (including significant
works-in-progress) in any aspect of bioinformatics and biomedicine. New
computational  techniques and methods in machine learning; data mining; text
analysis; pattern recognition; knowledge representation; databases; data
modeling; combinatorics; stochastic modeling; string and graph algorithms;
linguistic methods; robotics; constraint satisfaction; data visualization;
parallel computation; data integration; modeling and simulation and heir
application in life science domain  are especially encouraged. Relevant topics
included, but are not limited to: 
•	Biological Data Mining
•	High Performance Bio-computing
•	Genomics, Comparative Genomics
•	Biological Databases & Data Integration
•	Biological Data Visualization
•	Evolution and Phylogeny
•	Molecular sequence analysis 
•	Healthcare Informatics
•	Recognition of genes and regulatory elements 
•	Molecular evolution 
•	Proteomics, Protein structure, Computational proteomics 
•	Gene networks, Computational genetics 
•	Combinatorial libraries and drug design 
•	Computational systems biology 
•	Microarray design and data analysis 
•	BioOntologies
•	Sequence Analysis
•	Structural and functional genomics
•	Synthetic Biological Systems
•	Pathways, Networks , Systems Biology
•	Text Mining & Information Extraction
•	Transcriptomics
•	BioMedical Devices with Embedded Computers 
•	Signal and Image Processing in BioMedicine 
•	BioMedical Image Segmentation and Compression 
•	BioMedical Intelligence and Data Warehousing 
•	BioMedical Databases & Information Systems , BioMedical Information 
•	Multimedia Biomedical Databases 
•	Intelligent Biomedical Knowledge Discovery 
•	Modeling signalling network
•	Temporal and spatial mining of clinic data including medical images

MEETING ORGANIZATION:


GENERAL CO-CHAIRS:
Prof. Yi Pan 
Department of Computer Science
Georgia State University
34 Peachtree Street, Suite 1450
Atlanta, GA 30302-4110, USA

Prof. Carmelina Ruggiero
Editor-in-chief of IEEE Trans. on NanoBioscience
Professor of Bioengineering
DIST University of Genoa
Via Opera Pia 13  Genoa, 16145, Italy

Prof. Aydin Tozeren
Distinguished Professor and Director, 
Center for Integrated Bioinformatics,
School of Biomedical Engineering, Science & Health Systems 
Drexel University, Philadelphia, PA 19104, USA

PROGRAM CO-CHAIRS:
Prof. Xiaohua Hu
College of Information Science & Technology
Drexel University
Philadelphia, PA 19104 USA

Prof. Zoran Obradovic
Center for Information Science and Technology,
Temple University, 
303 Wachman Hall (038-24),
1805 N. Broad St.,
Philadelphia, PA 19122, USA. 

Prof. Ion Mandoiu
Computer Science & Engineering Department
University of Connecticut
371 Fairfield Way, Unit 2155
Storrs, CT 06269-2155
Office: ITEB 261

WORKSHOP CHAIRS:
Jinyan Li              Institute for Infocomm Research, Singapore
Xue-Wen Chen           Univ. of Kansas, USA 
Tharam S. Dillon       Curtin University of Technology, Australia

TUTORIAL CHAIR:
Sun Kim                Indiana University, USA

LOCAL ACCOMMODATION CO-CHAIRS:
David Scot Taylor       San José State University, USA
Tom Qi Zhang            Google, USA

PUBLICITY CO-CHAIRS:
Amandeep S. Sidhu        Curtin University of Technology, Australia
Shuigeng Zhou            Fudan University, China

IEEE BIBM CO-CHAIRS/DIRECTORS:
Xiaohua Hu          Drexel University, USA
Yi Pan              Georgia State University, USA

IEEE BIBM STEERING COMMITTEE:

Xiaohua Hu           Drexel University, USA
Vipin Kumar          Univ. of Minnesota, USA
Michael Ng           HongKong Baptist University, China
Zoran Obradovic      Temple University, USA
Yi  Pan              Georgia State University, USA
Jose Principe        Univ. of Florida, USA
Carmelina Ruggiero   DIST University of Genoa, Italy
Niilo Saranummi      VTT Information Technology, Finland
Shusaku Tsumoto      Shimane University, Japan

SUBMISSION REQUIREMENTS:


Please submit a  full  length paper (not exceeding 5000 words) thorough the
online submission system (The paper format is very flexible, if you prefer to
prepare your paper in IEEE 2-column format, you can download the format
instruction here for Latex or word).  Electronic submissions (in PDF or
Postscript format) are required.  Accepted papers will be published in the
conference proceedings by the IEEE Computer Society Press that are indexed by
EI. The Best papers selected from the IEEE BIBM 07 will be published as a
special issue in related IEEE Transactions  and other journals such as IJDMB,
IJBRA etc.


IMPORTANT DATES:

Paper submission:     June 30, 2007
Notification:         August 1, 2007
Camera-ready due:     August 20, 2007


From owner-chemistry@ccl.net Tue Jun 19 11:00:01 2007
From: "Kanchana Thanthiriwatte sahanchem^yahoo.com" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL:G: Spherical <--> Cartesian interconversion
Message-Id: <-34514-070619023530-18284-lph1d/9M5cpjiJA+e9QFsw|,|server.ccl.net>
X-Original-From: "Kanchana  Thanthiriwatte" <sahanchem~~yahoo.com>
Date: Tue, 19 Jun 2007 02:35:26 -0400


Sent to CCL by: "Kanchana  Thanthiriwatte" [sahanchem*o*yahoo.com]
Dear CCLers,

I need to convert Cartesian values to Spherical Harmonics 
values and again Spherical Harmonics values to Cartesian values. I 
have found following paper. (H.B. Schlegel, M.J. Frisch, Int. J. 
Quantum. Chem., (1995),54, 83-87.). I need to know that the transformation matrix is same for following Cartesian to spherical conversions.

1) Cartesian Gaussian primitives <-->spherical Gaussian primitives
2) Cartesian integrals <--> Spherical integrals
3) Cartesian multipoler moments <-->  Spherical multipoler moments

The above paper explains  Cartesian Gaussian primitives <-->spherical 
Gaussian primitives. I consider Cartesian integrals and 
multipoler moments. Does the transformation matrix same for other two types (integrals and moments)? Or if it is different how do I convert them?

Regards,
-Sahan-

Kanchana S. Thanthiriwatte
Department of Chemistry
Mississippi State University
Box 9573
Mississippi State, MS 39762


From owner-chemistry@ccl.net Tue Jun 19 11:34:00 2007
From: "Ken W. Browne kbrowne^_^technologynetworks.net" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: Virtual Discovery Conference, London, 24-26 Oct
Message-Id: <-34515-070619042836-31650-pn+ZGqAgxEFDqIVJSDK/rA%a%server.ccl.net>
X-Original-From: "Ken W. Browne" <kbrowne a technologynetworks.net>
Date: Tue, 19 Jun 2007 04:28:32 -0400


Sent to CCL by: "Ken W. Browne" [kbrowne- -technologynetworks.net]
I would just like to draw your attention to this conference which may be interest to the group. It will include presentations on virtual screening, in silico ADMET and aspects of computational chemistry and cheminformatics.

Speakers will include:
Martin Harrison
Associate Principal Scientist
AstraZeneca

Hugo Kubinyi
Professor of Pharmaceutical Chemistry
University of Heidelberg

Paul Malthouse Professor
Head of Biochemistry
University College Dublin 

Malcolm Walkinshaw
Professor of Structural Biochemistry
University of Edinburgh
 

The full agenda has just been released on www.VirtualDiscovery.net 

Best Wishes,
Ken


From owner-chemistry@ccl.net Tue Jun 19 12:32:00 2007
From: "Jennifer Clare Brookes ucapjcb a ucl.ac.uk" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL:G: Conformer calculations
Message-Id: <-34516-070619122741-27715-63TLnH6DkIfUvT50SxGRnw:-:server.ccl.net>
X-Original-From: "Jennifer Clare Brookes" <ucapjcb(_)ucl.ac.uk>
Date: Tue, 19 Jun 2007 12:27:38 -0400


Sent to CCL by: "Jennifer Clare Brookes" [ucapjcb ~~ ucl.ac.uk]

Hi everyone,

I am looking at the flexibility of 6-membered rings, in particular that of methyl-R-gamma cyclogeranate, using Gaussian 03. What I would like to do is increment the dihedral angle between 4 of the atoms in this molecule (by about 2 degrees) so that it switches from boat to chair. At each geometry change I would like to fix the coordinates of these atoms and do a constrained optimization on the rest of the molecule. This using a semi-emperical method like AM1. It looks like I can use Model Builder in Gaussian to increment the dihedral and then fix these atoms as constants, and the rest as variables and optimize. I have had a look at the manual, but I am stuck as to how to go about this, please does anyone have any tips or examples?

Thank you for any advice!

Jenny


From owner-chemistry@ccl.net Tue Jun 19 13:18:01 2007
From: "John McKelvey jmmckel^_^gmail.com" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: Various hardware for DFT and TDDFT calculation
Message-Id: <-34517-070619112852-21206-soeyZvYaGV439UAMqSy5PQ[-]server.ccl.net>
X-Original-From: "John McKelvey" <jmmckel/./gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_99685_3300298.1182266923633"
Date: Tue, 19 Jun 2007 11:28:43 -0400
MIME-Version: 1.0


Sent to CCL by: "John McKelvey" [jmmckel-.-gmail.com]
------=_Part_99685_3300298.1182266923633
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit
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Folks,

I have two linux boxes, a dual XEON/2.4GHZ, and a dual-dual AMD/2.0. [which
I really like, and got the latter complete system cpu box  with 4gigs memory
for a little over $$2100]..  Am now looking at a dual-Quad/2.33 Intel box
for less than $3000.  Anyone have any comments about relative timngs on the
dual-Quad intel box vs the dual-dual AMD box?  I know that the memory
controller issue is better for the AMD.  Don't expect to see the dual-Quad
to be twice as fast, as the AMD, but am curious about relative timings.

Many thanks!

John McKelvey

PS:  If you are looking for a very reliable vendor who builds to specs and
backs up their 3-year warranty dependably and with no hassle, look at
www.jncs.com.  I've bought 7 mobos or systems from them and have had to
exchange only two memory sticks, which they let cross in the mail during the
exchange.  They pack things for shipping very, very reliably, including
complete systems.

------=_Part_99685_3300298.1182266923633
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Folks,<br><br>I have two linux boxes, a dual XEON/2.4GHZ, and a dual-dual AMD/2.0. [which I really like, and got the latter complete system cpu box&nbsp; with 4gigs memory for a little over $$2100]..&nbsp; Am now looking at a dual-Quad/2.33 Intel box for less than $3000.&nbsp; Anyone have any comments about relative timngs on the dual-Quad intel box vs the dual-dual AMD box?&nbsp; I know that the memory controller issue is better for the AMD.&nbsp; Don&#39;t expect to see the dual-Quad to be twice as fast, as the AMD, but am curious about relative timings.&nbsp; 
<br><br>Many thanks!<br><br>John McKelvey<br><br>PS:&nbsp; If you are looking for a very reliable vendor who builds to specs and backs up their 3-year warranty dependably and with no hassle, look at <a href="http://www.jncs.com">
www.jncs.com</a>.&nbsp; I&#39;ve bought 7 mobos or systems from them and have had to exchange only two memory sticks, which they let cross in the mail during the exchange.&nbsp; They pack things for shipping very, very reliably, including complete systems.
<br> 

------=_Part_99685_3300298.1182266923633--


From owner-chemistry@ccl.net Tue Jun 19 15:10:01 2007
From: "Alex A. Granovsky gran * classic.chem.msu.su" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: Various hardware for DFT and TDDFT calculation
Message-Id: <-34518-070619144244-27740-EsNfr6an51/cN72tvjlIVA]~[server.ccl.net>
X-Original-From: "Alex A. Granovsky" <gran|,|classic.chem.msu.su>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0076_01C7B2C4.E5EAE860"
Date: Tue, 19 Jun 2007 22:55:14 +0400
MIME-Version: 1.0


Sent to CCL by: "Alex A. Granovsky" [gran{:}classic.chem.msu.su]
This is a multi-part message in MIME format.

------=_NextPart_000_0076_01C7B2C4.E5EAE860
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	charset="ISO-8859-1"
Content-Transfer-Encoding: quoted-printable

Hi,

the PC GAMESS homepage at MSU has lots of benchmark data, including DFT =
ones.=20

http://classic.chem.msu.su/gran/gamess

Best regards,
Alex Granovsky



  ----- Original Message -----=20
  From: John McKelvey jmmckel^_^gmail.com=20
  To: Granovsky, Alex, A. =20
  Sent: Tuesday, June 19, 2007 7:28 PM
  Subject: CCL: Various hardware for DFT and TDDFT calculation


  Folks,

  I have two linux boxes, a dual XEON/2.4GHZ, and a dual-dual AMD/2.0. =
[which I really like, and got the latter complete system cpu box  with =
4gigs memory for a little over $$2100]..  Am now looking at a =
dual-Quad/2.33 Intel box for less than $3000.  Anyone have any comments =
about relative timngs on the dual-Quad intel box vs the dual-dual AMD =
box?  I know that the memory controller issue is better for the AMD.  =
Don't expect to see the dual-Quad to be twice as fast, as the AMD, but =
am curious about relative timings. =20

  Many thanks!

  John McKelvey

  PS:  If you are looking for a very reliable vendor who builds to specs =
and backs up their 3-year warranty dependably and with no hassle, look =
at www.jncs.com.  I've bought 7 mobos or systems from them and have had =
to exchange only two memory sticks, which they let cross in the mail =
during the exchange.  They pack things for shipping very, very reliably, =
including complete systems.=20


------=_NextPart_000_0076_01C7B2C4.E5EAE860
Content-Type: text/html;
	charset="ISO-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
<META content=3D"MSHTML 5.00.3314.2100" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Hi,</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>the PC GAMESS homepage at MSU has lots=20
of&nbsp;benchmark data, including DFT ones. </FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2><A=20
href=3D"http://classic.chem.msu.su/gran/gamess">http://classic.chem.msu.s=
u/gran/gamess</A></FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Best regards,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Alex Granovsky</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<BLOCKQUOTE=20
style=3D"BORDER-LEFT: #000000 2px solid; MARGIN-LEFT: 5px; MARGIN-RIGHT: =
0px; PADDING-LEFT: 5px; PADDING-RIGHT: 0px">
  <DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
  <DIV=20
  style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
  <A href=3D"mailto:owner-chemistry[#]ccl.net" =
title=3Downer-chemistry[#]ccl.net>John=20
  McKelvey jmmckel^_^gmail.com</A> </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>To:</B> <A=20
  href=3D"mailto:gran[#]classic.chem.msu.su"=20
  title=3Dgran[#]classic.chem.msu.su>Granovsky, Alex, A. </A> =
</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Tuesday, June 19, 2007 =
7:28=20
PM</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Subject:</B> CCL: Various hardware =
for DFT=20
  and TDDFT calculation</DIV>
  <DIV><BR></DIV>Folks,<BR><BR>I have two linux boxes, a dual =
XEON/2.4GHZ, and a=20
  dual-dual AMD/2.0. [which I really like, and got the latter complete =
system=20
  cpu box&nbsp; with 4gigs memory for a little over $$2100]..&nbsp; Am =
now=20
  looking at a dual-Quad/2.33 Intel box for less than $3000.&nbsp; =
Anyone have=20
  any comments about relative timngs on the dual-Quad intel box vs the =
dual-dual=20
  AMD box?&nbsp; I know that the memory controller issue is better for =
the=20
  AMD.&nbsp; Don't expect to see the dual-Quad to be twice as fast, as =
the AMD,=20
  but am curious about relative timings.&nbsp; <BR><BR>Many =
thanks!<BR><BR>John=20
  McKelvey<BR><BR>PS:&nbsp; If you are looking for a very reliable =
vendor who=20
  builds to specs and backs up their 3-year warranty dependably and with =
no=20
  hassle, look at <A =
href=3D"http://www.jncs.com">www.jncs.com</A>.&nbsp; I've=20
  bought 7 mobos or systems from them and have had to exchange only two =
memory=20
  sticks, which they let cross in the mail during the exchange.&nbsp; =
They pack=20
  things for shipping very, very reliably, including complete systems.=20
<BR></BLOCKQUOTE></BODY></HTML>

------=_NextPart_000_0076_01C7B2C4.E5EAE860--


From owner-chemistry@ccl.net Tue Jun 19 15:53:01 2007
From: "sachin tyagi sachintyagi1#,#gmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: subscription cancellation
Message-Id: <-34519-070619154547-15773-62EiRe2DRUvfAAOGsrDjPA,+,server.ccl.net>
X-Original-From: sachin tyagi <sachintyagi1*gmail.com>
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Date: Tue, 19 Jun 2007 13:45:59 -0500
MIME-Version: 1.0


Sent to CCL by: sachin tyagi [sachintyagi1^^gmail.com]
Dear Administrator,
   I want to unsuscribe from your portal.

Thanks

Sachin


From owner-chemistry@ccl.net Tue Jun 19 20:38:00 2007
From: "Mohamed Z Rishard rishiz{:}hotmail.com" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: Time dependent DFT calculation of 2-cyclopentenone
Message-Id: <-34520-070619165603-20446-bzQCqE8FTruU3rS6kyKiyQ+/-server.ccl.net>
X-Original-From: "Mohamed  Z Rishard" <rishiz^^hotmail.com>
Date: Tue, 19 Jun 2007 16:56:00 -0400


Sent to CCL by: "Mohamed  Z Rishard" [rishiz=-=hotmail.com]
I want to do a TD-DFT calculation for the lowest excited singlet state of the above molecule. The route section is as follows:

p TD=(nstates=4,root=1) B3LYP/6-311++G(d,p) opt freq pop=full

However I keep getting a message stating that there is an error. Does anybody have a comment?