From chemistry-request@server.ccl.net  Mon May 29 02:36:21 2000
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From: "Graham E Jackson" <jackson@psipsy.uct.ac.za>
To: chemistry@ccl.net
Date: Mon, 29 May 2000 08:40:11 SAST-2
Subject: C13 chemical shifts
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Dear CCL

I am trying  to find software which will calculate C13 chemical 
shifts from molecular structure.   I am particularly interested in 
natural products.   The package may either be semi empirical or 
quantum mechanical.   The platform is also not important.

Thanks in advance

Graham


Graham E Jackson
Associate Professor
Department of Chemistry
University of Cape Town
Cape Town
South Africa

Fax: (027 21) 6897499
Tel: (027 21) 6502531
E-mail: jackson@psipsy.uct.ac.za
http://www.uct.ac.za/depts/cem/academic/gjackson.htm

From chemistry-request@server.ccl.net  Mon May 29 05:03:10 2000
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From: John Kerkines <jkerk@arnold.chem.uoa.gr>
To: chminf-l@listserv.indiana.edu
cc: chemistry@ccl.net
Subject: Atomic Anion Energy Levels
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Sorry for the crosspostings,

Dear all,

Almost all of us are familiar with the 'legendary' Atomic Energy Levels
compilation by Charlotte Moore, and more recently the NIST Tables on the
Web.

But both compilations have energy levels for neutrals and cations. I am
aware that anions are experimentally tougher to deal with, but recently a
lot of data has started to accumulate on the anions, so I was wondering if
there exists such a compilation or something relevant for anions.

Best,
John Kerkines


From chemistry-request@server.ccl.net  Mon May 29 08:34:15 2000
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From: "Tamas E. Gunda" <tamasgunda@tigris.klte.hu>
To: "Graham E Jackson" <jackson@psipsy.uct.ac.za>
CC: <chemistry@ccl.net>
References: <E12wJ9X-0001KR-00@mail3.uct.ac.za>
Subject: Re: CCL:C13 chemical shifts
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> Dear CCL
> 
> I am trying  to find software which will calculate C13 chemical 
> shifts from molecular structure.   I am particularly interested in 
> natural products.   The package may either be semi empirical or 
> quantum mechanical.   The platform is also not important.
> 
> Thanks in advance
> 
> Graham

HyperChem 6.0 with NMR module can calculate NMR shifts  with QM method.

Best regards

Dr Tamas E. Gunda
Research Group for Antibiotics of the Hungarian Acad. Sci.
University of Debrecen, POBox 36
H-4010 Debrecen, Hungary
tel.: (+36-52) 316666/2472
fax: (+36-52) 512914
e-mail: tamasgunda@tigris.klte.hu
home-page: www.klte.hu/~gundat/gunda.htm



From chemistry-request@server.ccl.net  Mon May 29 04:54:09 2000
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Date: Mon, 29 May 2000 04:46:33 -0400
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Cornell Nano-Researchers Create Component For A "Lab On A Chip" That
Cuts DNA Separation From A Day To A Matter Of Minutes

Read more... ->

http://www.atoma.f2s.com/nanotechnews.html

Thanks alot and best wishes.


-- 
<><><><><><><><><><><><><><>
Jonathan Desp
Matter will become software
Atoma
www.atoma.f2s.com
<><><><><><><><><><><><><><>


From chemistry-request@server.ccl.net  Mon May 29 08:22:47 2000
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Dear Elena,

Here are two of our papers, which include a number of useful references:

1- Molecular diversity and its analysis.
D. Gorse, A. Rees, M. Kaczorek and R. Lahana
Drug Discovery Today, Vol.4 No. 6,  June 1999.

2- Functional diversity of compound libraries.
D. Gorse and R. Lahana
Current Opinion in Chemical Biology, Vol.4 No.3, June 2000.

Hope it helps,

Roger

****************************************************************
Dr Roger Lahana                                          Synt:em
Vice-President R&D                     Parc Scientifique G.Besse
Computational Drug Discovery                         30000 Nimes
email: rlahana@syntem.eerie.fr                            France
Tel: +33 (0)466 048 668 (Direct)         Fax: +33 (0)466 048 667
****************************************************************
            Discover New Drugs, Discover Synt:em
                   http://www.syntem.com
****************************************************************




From chemistry-request@server.ccl.net  Mon May 29 19:16:28 2000
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Date: Mon, 29 May 2000 20:15:45 -0300 (BSC)
From: andre mauricio de oliveira <amolive@dedalus.lcc.ufmg.br>
To: Haitao Ji <caddk@online.sh.cn>
cc: "chemistry@ccl.net" <chemistry@ccl.net>
Subject: Re: CCL:DNA protein complex minimization
In-Reply-To: <20000521122029.DAEN22228.fep5.online.sh.cn@cadd>
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Dear Dr Song,

		Our group is used to achieved MM calculations for
biopolymer such as drug-DNA and protein-DNA complexes using AMBER
Forcefield, pursuing MM-DM-MM routine: a minimizaion of the complex
(Steepest Descent followed by Polak-Ribiere algorithm), a 300K and 10ps,
1.5fs-step and a final minimization of the complex. Continuous solvent
models are desirable (we use the e = 4r model). The quality of the
analysis is evaluated comparing the final structure with the x-ray one.

Cheers. 


On Mon, 22 May 2000, Haitao Ji wrote:

> Hello everybody!
>     I have a problem with DNA protein complex minimization.I think it a challenge,because it is quite difficult to maintain the inter-strand H-Bonds
> when relax all the complex.Can you give me some suggestions on the details ,such as forcefields,strategy and minimization procedure?
> If I have to add some kind of constraints,can you tell me the exact parameters?
> 
>     Any information from you will be appreciated !
> 
>     sincerely yours,
> 
> yunlong song,PhD
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> Dept. of Medicinal Chemistry
> College of pharmacy
> Second military medical university
> 325 Guohe Road, Shanghai 200433
> P. R. China
> e-mail: songyunlong@263.net  
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -= 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
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> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net
> 
> 
> 
> 
> 
> 

Andre Mauricio de Oliveira

VOICE +55-031-374-1325
      +55-031-499-5765 
FAX   +55-031-499-5700
 
Laboratorio de QSAR e Modelagem Molecular
Nucleo de Estudos em Quimica Medicinal (NEQUIM)
NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim
Departamento de Quimica ICEx
Federal University of Minas Gerais
Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901
Belo Horizonte MG Brazil 


From chemistry-request@server.ccl.net  Mon May 29 21:04:10 2000
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From: "Keisuke Ishida" <ishida@taiho.co.jp>
To: "CCL" <chemistry@ccl.net>
Subject: How to convert MDL's SD-file automatically.
Date: Tue, 30 May 2000 00:30:31 +0900
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Hi,
I want to convert a partial structure in a SD-file that contains many
compounds
to other structure automatically.
For example,
1. Search a partial structure in a SD-file.
2. Convert a partial structure to other structure automatically.
(ex. cyclehexane ring ---> benzene ring)
Please tell me some idea or information.
Thanks.

**************************************************
Keisuke Ishida
Chemistry Laboratory, Taiho Pharmaceutical Co.,Ltd.
Hanno, Saitama, 357-8527 Japan
TEL. +81-429-72-8900
FAX. +81-429-72-8913
E-mail. ishida@taiho.co.jp
**************************************************


From chemistry-request@server.ccl.net  Mon May 29 18:12:27 2000
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Reply-To: "Jim Kress" <kresslists@kressworks.com>
From: "Jim Kress" <kresslists@kressworks.com>
To: "CCL" <chemistry@ccl.net>
References: <000b01bfc52c$79367c30$0300a8c0@mindspring>
Subject: CCL:G98W and dual processors on NT
Date: Mon, 29 May 2000 18:12:22 -0400
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On May 23 I asked the list about the "low memory" warning and significant
thrashing I get with Gaussian 98W on a dual processor NT machine.

The responses I received are given below (I even got one from Gaussian!).

I also did some testing on my computer.  It appears that G98W exhibits
interesting behavior with NT (maybe all 32 bit) systems where the swap file
exceeds (approximately) 2200MB.

I found the following:

SFS = swap file size (MB)
-M- = -M- parameter in default.rou (MB)
LMW = Low memory warning
TH = thrashing

SFS       -M-   Result
2500      960   LMW and TH
2500      250   no LMW
2200      960   no LMW

For SFS between 2200MB and 2500MB, G98W exhibits some very strange behavior.
For some SFS values (e.g 2250MB) when G98W is invoked it will respond with
an "Insufficient
free memory.  Need 4 MB minimum" error message and then terminate.

Also, as the SFS approaches 2200MB (from 2500MB) the difference between the
"memory needed" and "memory available" in the "Low Memory Warning" message
decreases.

This behavior is reminiscent of some of the disk i/o observations in G98W
that result from the 32 bit integer word size.

In addition, I have found that there is a significant interaction between
the -M- parameter in the default.rou file, the SFS, and cpu time necessary
to run the test case (qs.gjf).  Here are some results (cpu time is in
seconds):

SFS    -M-  cpu time
2000   960   106
2000     96     10
1400   960     98
1400   240     17
1400   128     11
1400     ns        8

-M- of ns implies not specified in default.rou so used G98W default
established upon installation of the software (install program stated that
default.rou set up for machine with > 48 MB memory).  Larger values of -M-
result in thrashing (SFS is fixed and larger than -M-).  It appears the
memory management in G98W is unkind to jobs that are small relative to the
value of -M-.

In any event, it appears that I've identified the source of the error
message.  Take the information as you will.

Thanks for the help from the people who responded!

Jim

Check out my web site  http://www.kressworks.com/


----- Original Message -----
From: Jim Kress <jimkress@kressworks.com>
To: CCL <chemistry@ccl.net>
Sent: Tuesday, May 23, 2000 11:02 PM
Subject: CCL:G98W and dual processors on NT


> I am using G98W on a dual processor WinNT4.0SP5 machine with 1GB of RAM.
I
> do NOT specify MKL_NPROCS to be 2.
>
> However, when I run G98W, it pauses with a 'low memory' warning.  It
states
> that I need 480MB of RAM to continue (which is the amount specified in the
> default.rou file) but that I have only (approx.) 231MB.  If I allow it to
> proceed, it thrashes badly.  If I specify a memory value of LE 256MB in
the
> default.rou file, the program runs normally with no warnings or thrashing.
>
> The problem is not resolved by specification of MKL_NPROCS to be 1
>
> In all cases I am using the qs.gjf example from the C:\G98W\quick
> subdirectory.
>
> Anybody know what I need to do to get this to run properly with the larger
> default.rou memory specification?  I've asked Gaussian but they have not
> replied ...
>
> Thanks and I will summarize.
>
> Jim
>
> Check out my web site  http://www.kressworks.com/
>
>
Response 1:

I am not sure about G98W, but GAMESS would do that if the amount of the swap
space was low. It should be 2xRAM or more. With GAMESS I could run a job
with  720 MB RAM on a 768 MB machine with 2GB of swap space.

Slawomir Janicki
janicki1@earthlink.net

Response 2:

Dr. Kress,

   We have attempted to model this on a Win2000 machine with 512MB and dual
processors using various sizes of virtual memory.  With small virtual memory
settings, 128MB, we do see a loss of efficiency but never a 'low memory'
warning.  Running with 750MB of virtual memory this seems to run fine with
a memory request of 400MB.

   What setting do you have in place for your virtual memory?

--

  Douglas J. Fox
  Technical Support
  Gaussian, Inc.
  help@gaussian.com

Response 3:

Well, I don't know what is happening. Loosing cache coherency perhaps? You
would think that GAUSSIAN could make their software SMP friendly...

Slawomir Janicki
janicki1@earthlink.net

----- Original Message -----
From: "Jim Kress" <jimkress@kressworks.com>
To: "Slawomir Z. Janicki" <janicki1@earthlink.net>
Sent: Tuesday, May 23, 2000 11:12 PM
Subject: Re: G98W and dual processors on NT


> Thanks for the info.
>
> Actually, pcGAMESS is my preferred software.  Unfortunately, pcGAMESS
> doesn't have DFT capabilities and that is why I'm using G98W.
>
> Also, it's not a matter of swap space.  I have 2.5GB of swap to go with
the
> 1GB of RAM.  I never had these problems with G98W until I put in the 2nd
> processor.
>
> Jim
>
> Check out my web site  http://www.kressworks.com/
>












From chemistry-request@server.ccl.net  Mon May 29 19:57:25 2000
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From: Rajkumar Buyya <rajkumar@csse.monash.edu.au>
To: "beowulf@beowulf.org" <beowulf@beowulf.org>
Subject: CCGrid2001 Preliminary Call For Papers 
Date: Mon, 29 May 2000 22:34:14 +1000

 
Dear Colleagues,

Please find enclosed cfp of the 2001 version of Cluster Computing symposium
with scope extended to Grid. The 2000 symposium is held in Beijing, China
along with HPC ASIA'2000, May 14-17. A well received symposium opening 
keynote was delivered by Prof. Jack Dongarra. The next year symposium 
scheduled to be held in Brisbane, Australia, 16-18 May 2001:

 CCGrid2001: IEEE International Symposium on Cluster Computing and the Grid
   http://www.ccgrid2001.qut.edu.au
   http://www.ccgrid.org

is going to be  interesting one as a number of key leaders (including
Jack Dongarra, Greg Pfister, Albert Zomaya,...*see cfp*) in this area 
are actively involved in symposium organisational efforts.

The CCGrid'2001 is going to feature special sessions/workshops and those 
interested in organising one, please contact me/PC-chair--we will let you know
the logistics involved in organising special sessions/workshops.

I would like to take this opportunity to request you to consider this
symposium as a venue for presenting your research. I also request your help 
in publicising the enclosed cfp among your colleagues and encourage them 
to submit their work. 

Thank you very much.

Sincerely Yours,
Raj

--------------------------------------------------------------------------
CCGrid2001: IEEE International Symposium on Cluster Computing and the Grid
**************************************************************************

(IEEE support pending final approval)

16-18 May 2001 in Brisbane, Australia

http://www.ccgrid2001.qut.edu.au
http://www.ccgrid.org


PRELIMINARY CALL FOR PAPERS

The growing popularity of the Internet along with the availability of
powerful computers and  high-speed networks as low-cost commodity components
are changing the way we do computing.  Two advanced computing themes have
emerged: "cluster computing" and "global network  computing" (grid
computing).

CCGrid2001, sponsored by the IEEE Computer Society (final approval pending),
is designed to  bring together international cluster and network-based
computing researchers, developers,  and users. The symposium will also serve
as a forum to present the latest work, and  highlight related activities
>from around the world.

The following topics concerning Cluster or Grid computing are of interest,
but not limited to:

* Hardware and Software (based on PCs, Workstations, SMPs or Supercomputers)
* Middleware for Clusters and Grids
* File Systems and Parallel I/O
* Scheduling and Load Balancing
* Programming Models, Tools, and Environments
* Communication systems such as: Message Passing Systems e.g. MPI and PVM or
Shared Memory  Systems
* Programming Languages and System Software for supporting Grids and
Clusters
* System Management and Administration
* Performance Evaluation and Modelling
* Resource Management and Scheduling
* Computational, Data, and Information Grid
* Computational Economy
* Problem Solving Environments
* Data Structure and Algorithms
* Scientific, Engineering, and Commercial Applications for Clusters and
  Grids
* Portal Computing / Science Portals

PAPER SUBMISSION

Authors are invited to submit papers of not more than 10 pages of double
column text using  single spaced 10 point size type on 8.5 x 11 inch pages,
as per IEEE 8.5 x 11 manuscript  guidelines, see:
http://www.computer.org/cspress/instruct.htm. Authors should submit a
PostScript (level 2) or PDF file that will print on a PostScript printer.
Paper submission instructions will be placed on
http://www.ccgrid2001.qut.edu.au. Queries may be directed to the PC chair:
p.roe@qut.edu.au. It is expected that the proceedings will be published by
the IEEE Computer Society Press, USA.


WORKSHOPS/SPECIAL SESSIONS

We invite proposals for organising workshops or special sessions as part of
CCGrid2001. These special events are expected to be highly specialiased and
focused, and all 
selected papers will be published in the CCGrid2001 proceedings. Those
interested in organising special events, please contact workshops/special
sessions chair. 

CHAIRS & COMMITTEES

Honorary Chairs

Jack Dongarra, University of Tennessee (UTK)/Oak Ridge National Laboratory
(ORNL), Knoxville, USA.
Greg Pfister, IBM Server Technologies Division, Austin, Texas, USA.

General Chairs

George Mohay, Queensland University of Technology, Australia.
Rajkumar Buyya, Monash University, Australia.

Program Committee Chair

Paul Roe, Queensland University of Technology, Australia.

Program Committee Vice Chairs

David Bader, University of New Mexico, USA.
Mark Baker, University of Portsmouth, UK.
Hai Jin, University of Southern California, USA.
Alexander Reinefeld, ZIB, Germany.
Albert Zomaya, University of Western Australia, Australia.

IMPORTANT DATES

Papers Due: 4 November 2000
Notification of Acceptance: 20 December 2000
Camera Ready Papers Due: 24 January 2001


PROGRAM COMMITTEE MEMBERS


* David Abramson, Monash University, Australia.
* Ishfaq Ahmad, The Hong Kong University of Science and Technology, China.
* Srinivas Aluru, Iowa State University, USA
* Cosimo Anglano, Universita' del Piemonte Orientale, Italy.
* Amy Apon, University of Arkansas, USA.
* Hamid Arabnia, University of Georgia, USA.
* David Bader, University of New Mexico, USA.
* Mark Baker, University of Portsmouth, UK.
* Francine Berman, UCSD, USA.
* Robert G. Brown, Duke University, USA.
* Marian Bubak, Institute of Computer Science, AGH, Poland.
* Franck Cappello, Université de Paris Sud, France.
* Toni Cortés, Universidad Politecnica de Catalunya, Barcelona, Spain.
* Paul J Darwen, University of Queensland, Australia.
* Fikret Ercal, University of Missouri-Rolla, USA.
* Ian Foster, Argonne National Laboratory, USA.
* Dennis Gannon, Indiana University and NASA Ames Research Center, USA.
* Al Geist, Oak Ridge National Lab., USA.
* Alan D. George, University of Florida, USA.
* Wolfgang Gentzsch, GRIDware Inc., Germany.
* Andrzej Goscinski, Deakin University, Australia.
* Salim Hariri, The University of Arizona, USA.
* Ken Hawick, The University of Adelaide, Australia.
* Hermann Hellwagner, Uni. of Klagenfurt, Austria.
* Chris Ho Stuart, Queensland University of Technology, Australia.
* Yutaka Ishikawa, Real World Computing partnership, Japan.
* Heath James, University of Adelaide, Australia.
* Hai Jin, University of Southern California, USA.
* Chris Johnson, Australian National University, Australia.
* Pete Keleher, University of Maryland, USA.
* Wayne Kelly, Queensland University of Technology, Australia.
* Chung-Ta King, National Tsing Hua University, Taiwan.
* Domenico Laforenza, CNUCE-Institute of the Italian National Research
Council, Italy.
* Francis Lau, University of Hong Kong, China.
* Craig A. Lee, The Aerospace Corp., USA.
* Thomas Ludwig, Technical Uni. of Munich, Germany.
* Glenn Luecke, Iowa State University, USA.
* Bruce Maggs, Carnegie Mellon Uni., USA.
* Sam Makki, Queensland University of Technology, Australia.
* Evangelos Markatos, ICS-FORTH and University of Crete, Greece.
* Satoshi Matsuoka, Tokyo Institute of Technology, Japan.
* John O'Callaghan, Australian Partnership for Advanced Computing,
Australia.
* Stephan Olariu, Old Dominion University, USA.
* Marcin Paprzycki, University of Southern Mississippi, USA.
* Ira Pramanick, Sun Microsystems, USA.
* Viktor K. Prasanna, University of Southern California, USA.
* C.P. Ravikumar, Indian Institute of Technology, New Delhi, India.
* Daniel A. Reed,  University of Illinois at Urbana-Champaign.
* Alexander Reinefeld, Konrad-Zuse-Zentrum für Informationstechnik Berlin
(ZIB), Germany.
* Paul Roe, Queensland University of Technology, Australia
* Stephen Scott, Oak Ridge National Lab., USA.
* Jenny Schopf, Northwestern University, USA.
* Hong Shen, Griffith University, Australia.
* Thomas Sterling, California Institute of Technology, USA.
* Ivan Stojmenovic, University of Ottawa, Canada.
* El-ghazali Talbi, University of Lille, France.
* Domenico Talia,  ISI- CNR, Italy.
* Kenji Takeda, University of Southampton, UK.
* Valerie Taylor, Northwestern University, USA.
* Rajeev Thakur, Argonne National Laboratory, Chicago, USA.
* Putchong Uthayopas, Kasetsart University, Thailand.
* Mateo Valero, Politecnica de Catalunya, Spain.
* Cho Li Wang, Uni. of Hong Kong, China.
* Zhiwei Xu, Chinese Academy of Sciences, China.
* Xiaodong Zhang, The College of William and Mary, USA.
* Hee Yong Youn, Information and Communication University, Korea.
* Chung-Kwong Yuen, National University of Singapore, Singapore.
* Albert Zomaya, Uni. of Western Australia, Australia.
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