From owner-chemistry@ccl.net Mon Dec 12 04:27:00 2005
From: "Eduardo Lemos de Sa edulsa^_^quimica.ufpr.br" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL: software to convolution/deconvolution
Message-Id: <-30280-051212035540-7162-l62uYMyxmNUezyHcZSu2Og]^[server.ccl.net>
X-Original-From: Eduardo Lemos de Sa <edulsa:-:quimica.ufpr.br>
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Date: Mon, 12 Dec 2005 05:49:11 -0200 (BRST)
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Sent to CCL by: Eduardo Lemos de Sa [edulsa*quimica.ufpr.br]
Dear CCLers

A friend is looking for free softwares able to perform
convolution/deconvolution of curves. Please, could you pointed to me some
one of them?

Thank you in advance

My best wishes

Eduardo

Eduardo Lemos de Saá
Dep. Química - Universidade Federal do Paraná
P. Box 19081 - Curitiba / PR / Brazil
ZIP 81531-990
fax: +55(41)3361-3186
fone: +55(41) 3361-3300


From owner-chemistry@ccl.net Mon Dec 12 09:26:01 2005
From: "Diane dsorgelo]=[vub.ac.be" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: Chemical Reactivity Symposium, Brussels, April 5-7, 2006, Second Announcement
Message-Id: <-30281-051212065937-2565-zM/6/MpLw2CVz/3084tl9A^server.ccl.net>
X-Original-From: "Diane" <dsorgelo * vub.ac.be>
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Date: Mon, 12 Dec 2005 12:18:45 +0100
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Sent to CCL by: "Diane" [dsorgelo::vub.ac.be]
Dear Colleague,

A Three Day International Symposium will be held on (Theoretical Aspects of)
of "Chemical Reactivity", at the Vrije Universiteit Brussel, Brussels,
Belgium, from April 5 to 7, 2006.

This Symposium is organized under the auspices of the Fund for Scientific
Research Flanders and the International Solvay Institutes for Physics and
Chemistry.

The aim of the conference is to give the audience an impression of
theoretical aspects of chemical reactivity, as it can now be studied
starting from the electronic structure of atoms, molecules,... using a
variety of quantum mechanical methodologies. Both more fundamental and
applied aspects (wave function vs. DFT reactivity descriptors, dynamics,
aromaticity, organic and inorganic reactions, biosystems, zeolites, ...)
will be addressed. For this purpose 13 internationally renowned speakers
will deliver invited talks (40 minutes each) on various
approaches/applications. Contributed lectures will be given by selected
number of foreign participants and representatives of a number of Belgian
research groups. A poster session will give ample space and time for
presentation of research results by all other participants.

The invited speakers (all confirmed) are:

P. W. Ayers (McMaster University Hamilton, Ontario, Canada)
P. K. Chattaraj (Indian Institute of Technology, Kharagpur, India)
D. A. Dixon (The University of Alabama, Tuscaloosa, USA)
W. Domcke (Lehrstuhl für Theoretische Chemie, Garching, Germany)
P. W. Fowler (University of Sheffield, Sheffield, UK)
J. Hutter (Universität Zürich, Zürich, Switzerland)
J.M.L. Martin (Weizmann Institute of Science, Rechovot, Israel)
R. G. Parr (University of North Carolina, Chapel Hill, USA)
U. Röthlisberger (Ecole Polytechnique Federale, Lausanne,Switzerland)
M. Solà (Universitat de Girona, Girona, Spain)
M. Sprik (University of Cambridge, United Kingdom)
R.A. van Santen (Eindhoven Technical University,The Netherlands )
P. von Rague Schleyer ( University of Georgia, Athens, USA)

Full details as well as the Registration and Abstract Submission form can be
found on the website http://www.vub.ac.be/chemicalreactivity/

A asked by quite a lot of colleagues the period of early registration and
abstract submission has been extended to January 9, 2006.

Looking forward to meet you in Brussels,

With very best regards,


Paul Geerlings
Chair of the Organizing Committee

Prof. P. GEERLINGS
Free University of Brussels
Faculty of Sciences
Department of General Chemistry (ALGC)
Pleinlaan 2
1050 Brussels
Belgium
Tel. :  +32.2.629.33.14
Fax. :  +32.2.629.33.17


From owner-chemistry@ccl.net Mon Dec 12 10:01:01 2005
From: "Noko Phala nphala|angloresearch.com" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL: Linux Cluster Building Workshops
Message-Id: <-30282-051212091442-18359-bQ7aGHtH7XKnTa6M1EqfFQ.:.server.ccl.net>
X-Original-From: "Noko Phala" <nphala%%angloresearch.com>
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Sent to CCL by: "Noko Phala" [nphala]~[angloresearch.com]
What would be a good book on building Windows clusters?

_________________________
Dr Noko Phala
Process Research
Anglo Research 
PO Box 106 Crown Mines 2025
Republic of South Africa
Tel: +27 (11) 377 4817
e-mail: nphala+/-angloresearch.com 

-----Original Message-----
> From: owner-chemistry+/-ccl.net [mailto:owner-chemistry+/-ccl.net] 
Sent: Friday, December 09, 2005 4:36 PM
To: Noko Phala
Subject: CCL: Linux Cluster Building Workshops

Sent to CCL by: Jerome PANSANEL [j.pansanel[-]pansanel.net]
I recommend this book for such workshop or anyone looking for more 
informations about HPC linux clusters:
"High Performance Linux Clusters" edited by O'Reilly

Jerome Pansanel

Le Jeudi 08 Décembre 2005 22:37, himanshu khandelia hkhandel%%cems.umn.edu a 
écrit :
> Sent to CCL by: "himanshu  khandelia" [hkhandel- -cems.umn.edu]
> Is anyone aware of any cluster building workshops that might be useful for
> engineers and scientists who are not system administrators, but are trying
> to build their own machines ?http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Mon Dec 12 10:36:00 2005
From: "Noko Phala nphala!=!angloresearch.com" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: What about an alternative CCL ?
Message-Id: <-30283-051212034843-5490-qWl1h8551uT7YWyyhNiGOA : server.ccl.net>
X-Original-From: "Noko Phala" <nphala..angloresearch.com>
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Date: Mon, 12 Dec 2005 10:46:43 +0200
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Sent to CCL by: "Noko Phala" [nphala++angloresearch.com]
Agree. The diversity of the topics in CCL are what makes it interesting, and helps bring to the fore outstanding issues in computational chemistry.

_________________________
Dr Noko Phala
Process Research
Anglo Research 
PO Box 106 Crown Mines 2025
Republic of South Africa
Tel: +27 (11) 377 4817
e-mail: nphala-#-angloresearch.com 

-----Original Message-----
> From: owner-chemistry-#-ccl.net [mailto:owner-chemistry-#-ccl.net] 
Sent: Tuesday, December 06, 2005 1:19 AM
To: Noko Phala
Subject: CCL: What about an alternative CCL ?

Sent to CCL by: "Robinson, James" [James.Robinson]^[evotec.com]
Dear list

During my part-time PhD studies and brief career in drug design, I found the list provided some inspiration and food-for-thought from simply reading comments and problems people had. Stuck in a small office, it was a comfort to realise that other people where having similar problems to my own. Sometimes the questions asked on the CCL served to provide the seed for problem solving. There is no need for an alternative CCL, its does a very good job as it is. 

James Robinson

-----Original Message-----
> From: owner-chemistry---ccl.net [mailto:owner-chemistry---ccl.net] 
Sent: 05 December 2005 20:54
To: Robinson, James
Subject: CCL: What about an alternative CCL ?

Sent to CCL by: "Shobe, David" [dshobe]![sud-chemieinc.com] Jim,

I don't consider your recent posts to be flames or trolls (since you seem to be sincere and not just posting in order to get a reaction).  But I would put them in the "personal axe-grinding" category, since you keep returning to this subject whenever you can find the least bit of connection to the actual topic of the thread.  

I don't believe in censorship.  (Another reason I don't want a second CCL--I prefer an ummoderated list to a moderated one).  The decision of what you post on CCL should be yours.  But I will *ask* you to discuss computational chemistry instead of politics.  

--David Shobe, Ph.D., M.L.S.
Süd-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a firewall.



-----Original Message-----
> From: Jim Kress [mailto:ccl_nospam ~ kressworks.com]
Sent: Saturday, December 03, 2005 1:06 PM
To: Shobe, David
Subject: FW: What about an alternative CCL ?

David,

Inasmuch as you had responded off list to me previously, I thought it appropriate I respond to you in kind (as well as to the list).  I would have just replied to you (and I apologize for my tardiness) but, since the topic re-emerged I decided to reply to the whole list.

Here is my message to our community:

-----Original Message-----
> From: Jim Kress [mailto:ccl_nospam ~ kressworks.com]
Sent: Saturday, December 03, 2005 12:14 PM
To: 'CCL Subscribers'
Subject: RE: What about an alternative CCL ?

Ah yes, let's assign bad names (flames, trolls, and personal axe-grinding) to topics about which we disagree and then suppress their expression because they have been assigned thusly.  It's a good technique.  One that's been used throughout history to suppress ideas that people didn't like or couldn't disprove. In our current social  environment it's even become a trendy way of dismissing those pesky people with whom we disagree.

Unfortunately for those who wish to ignore it, there are basic issues regarding the funding of science in our country that must be resolved.  

That may seem unimportant (or trollish or flamish or axe grinding) now.
However, in not too many years the Congress' Social Security slush fund (and it's other slush funds) is going to dry up and they won't have any funds to disperse to the scientific community (or many other places for that matter).
The annual national deficit will reach into the trillion dollar range.  The debt repayment will also reach into the trillion dollar range.  The funding system will collapse or dry up.  The economy may collapse as other nations demand repayment of the debit instruments they hold that are currently propping up our economy.

The taxpayers will NOT tolerate the extreme increases in tax rates that will be required to maintain science (and other non-Constitutionally mandated) spending at current levels and massive cuts will be enacted.  Spending on science will be among the first to fall because taxpayers will recognize and enforce the basic premise of our government, i.e. we are a Constitutionally Limited Republic where the power wielded by the government is explicitly assigned to it by the citizens (via the Constitution) and the citizens never assigned (via the Constitution) Congress the power to fund science.  The taxpayers will become more and more aware that the government is forcibly taking their money to give to other people to do work they don't care about, think is useless, and was never authorized.  They will exponentially escalate their resistance to this use of force, especially when they see their standard of living destroyed just so the government can give their money to other people.

What are you all going to do then?

That is the origination of my 'flames, trolls, and personal axe-grinding'.
That is the reason I have brought this up.

You ignore this at your own peril.  Study history.  Revolutions have started over less.

Jim


> -----Original Message-----
> From: Shobe, David dshobe%sud-chemieinc.com [mailto:owner-chemistry ~ 
> ccl.net]
> Sent: Friday, December 02, 2005 6:17 PM
> To: Kress, Jim
> Subject: CCL: What about an alternative CCL ?
> 
> Sent to CCL by: "Shobe, David" [dshobe^_^sud-chemieinc.com] I'm afraid 
> that flames, trolls, and personal axe-grinding are inherent to this 
> type of forum. :-(  A second CCL will not help.
> 
> Not that I mean to excuse such rude behavior.   
> 
> --David Shobe, Ph.D., M.L.S.
> Süd-Chemie, Inc.
> phone (502) 634-7409
> fax (502) 634-7724
> 
> Don't bother flaming me: I'm behind a firewall.
> 
> 
> -----Original Message-----
> > From: owner-chemistry__ccl.net [mailto:owner-chemistry__ccl.net]
> Sent: Friday, December 02, 2005 4:16 PM
> To: Shobe, David
> Subject: CCL: What about an alternative CCL ?
> 
> Sent to CCL by: "Dillen Jan [jlmd],[sun.ac.za]" 
> <JLMD],[sun.ac.za> I was just wondering whether it might not be the 
> time to establish an alternative to the current CCL where people can 
> ask questions about certain programs without being brand-marked as 
> freaks, where the response is not a lecture about the pros and cons of 
> capitalism, socialism, or the spending of US taxpayer's money and, 
> most importantly, where people do not find the need to apologise for 
> their bad English to avoid a lashing.
> 
> Just a thought. 
> 
> J. Dillen
> 
> 
> -----Original Message-----
> > From: owner-chemistry\a/ccl.net [mailto:owner-chemistry\a/ccl.net]
> Sent: 02 December 2005 17:22
> To: Dillen Jan <jlmd\a/sun.ac.za>
> Subject: CCL: Gauzzian Compilation
> 
> 
> Sent to CCL by: Mehdi Bounouar [mehdi.bounouar*ch.tum.de] Hum,
> 
> Well, not replying is sufficient. Beside that this Gauzzian inc.
> bashing is really annoying and does not help anyone ...
> 
> > Rather disgusting behavior for a company that charges thousands of 
> > dollars for taxpayer funded work and then refuses to provide 
> > comprehensive support for those products it has developed
> with money
> > forcibly removed from other people.
> 
> also not everyone on this list is an USA tax payer, write your 
> congressman for a Gauzzian-US version ;-)
> 
> 
> and apologies to everyone  especially to Roger (No answer
> inside) and Jim if he takes my answer as a personal attack (sorry bad
> english)
> 
> Mehdihttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www
.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.tx> tThis e-mail message may contain confidential and / or 
> privileged information. If you are not an addressee or otherwise 
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> Thank you.
> 
> 
> 
> -= This is automatically added to each message by the mailing script
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From owner-chemistry@ccl.net Mon Dec 12 11:11:01 2005
From: "andras.borosy_+_givaudan.com" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: software to convolution/deconvolution
Message-Id: <-30284-051212074607-9609-7hYizIp4k7TYEey62ssR/A]~[server.ccl.net>
X-Original-From: andras.borosy!^!givaudan.com
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Sent to CCL by: andras.borosy[a]givaudan.com
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Dear Colleagues,


>=20
> A friend is looking for free softwares able to perform
> convolution/deconvolution of curves. Please, could you pointed to me=20
some
> one of them?

In PASCAL, BASIC or ForTran see: Numerical Recipes (http://www.nr.com), in =

MatLab-like see: Octave(http://www.octave.org/)

Best wishes,

Dr. Andr=E1s Borosy
Seniour Scientist
Delivery Systems, Fragrance Research
Givaudan Schweiz AG
Ueberlandstr. 138
8600 D=FCbendorf
Switzerland
tel: + 41-1-8242164
fax: +41-1-8242926
e-mail: andras.borosy(-)givaudan.com


>=20
> Thank you in advance
>=20
> My best wishes
>=20
> Eduardo
>=20
> Eduardo Lemos de Sa=E1
> Dep. Qu=EDmica - Universidade Federal do Paran=E1
> P. Box 19081 - Curitiba / PR / Brazil
> ZIP 81531-990
> fax: +55(41)3361-3186
> fone: +55(41) 3361-3300
>=20
>=20
>=20
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<br>
<br><font size=3D2><tt>Dear Colleagues,</tt></font>
<br>
<br><font size=3D2><tt><br>
&gt; <br>
&gt; A friend is looking for free softwares able to perform<br>
&gt; convolution/deconvolution of curves. Please, could you pointed to
me some<br>
&gt; one of them?</tt></font>
<br>
<br><font size=3D2><tt>In PASCAL, BASIC or ForTran see: </tt></font><a href=
=3D"http://www.numerical-recipes.com/forum/"><font size=3D3 color=3Dblue><u=
>Numerical
Recipes</u></font></a><font size=3D3> </font><font size=3D2><tt>(http://www=
.nr.com),
in MatLab-like see: <b><u>Octave</u></b>(http://www.octave.org/)</tt></font>
<br>
<br><font size=3D2><tt>Best wishes,</tt></font>
<br>
<br><font size=3D2><tt>Dr. Andr=E1s Borosy<br>
Seniour Scientist<br>
Delivery Systems, Fragrance Research<br>
Givaudan Schweiz AG<br>
Ueberlandstr. 138<br>
8600 D=FCbendorf<br>
Switzerland<br>
tel: + 41-1-8242164<br>
fax: +41-1-8242926<br>
e-mail: andras.borosy(-)givaudan.com</tt></font>
<br>
<br><font size=3D2><tt><br>
&gt; <br>
&gt; Thank you in advance<br>
&gt; <br>
&gt; My best wishes<br>
&gt; <br>
&gt; Eduardo<br>
&gt; <br>
&gt; Eduardo Lemos de Sa=E1<br>
&gt; Dep. Qu=EDmica - Universidade Federal do Paran=E1<br>
&gt; P. Box 19081 - Curitiba / PR / Brazil<br>
&gt; ZIP 81531-990<br>
&gt; fax: +55(41)3361-3186<br>
&gt; fone: +55(41) 3361-3300<br>
&gt; <br>
&gt; <br>
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&gt; -=3D This is automatically added to each message by the mailing script
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&gt; &nbsp; &nbsp; &nbsp; http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessa=
ge<br>
&gt; <br>
&gt;<br>
&gt; &nbsp; &nbsp; &nbsp; http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessa=
ge<br>
&gt; <br>
&gt;<br>
&gt; &nbsp; &nbsp; &nbsp; http://www.ccl.net/chemistry/sub=5Funsub.shtml<br>
&gt; <br>
&gt;<br>
&gt; <br>
&gt;<br>
&gt; <br>
&gt; Search Messages: http://www.ccl.net/htdig &nbsp;(login: ccl, Password:
search)<br>
&gt; <br>
&gt;<br>
&gt; &nbsp; &nbsp; &nbsp;<br>
&gt; <br>
&gt;<br>
&gt; <br>
&gt; -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+=
-+<br>
&gt; <br>
&gt; <br>
</tt></font>
--=_alternative 003DCDEEC12570D5_=--


From owner-chemistry@ccl.net Mon Dec 12 11:45:01 2005
From: "Gustavo Seabra gustavo.seabra=-=gmail.com" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL: Wiki-like Chemical Databases
Message-Id: <-30285-051212092309-18999-qY0HNHHi3ag+/7wZA+t/+w#%#server.ccl.net>
X-Original-From: Gustavo Seabra <gustavo.seabra- -gmail.com>
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Date: Mon, 12 Dec 2005 09:16:14 -0500
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Sent to CCL by: Gustavo Seabra [gustavo.seabra|gmail.com]
AFAIK, the software used to build Wikipedia itself is free, maybe even
OpenSource. You can just download it and create your own
Wikipedia-like site.

Gustavo.

On 12/11/05, Paul Tratnyek tratnyek---ebs.ogi.edu
<owner-chemistry++ccl.net> wrote:
> Sent to CCL by: Paul Tratnyek [tratnyek__ebs.ogi.edu]
> Any examples of--or software for--implementing "open" databases of
> physicochemical data were anyone can contribute to the database via
> the web, as in the wikipedia and other wiki-based databases of other
> kinds of information. Thanks.


From owner-chemistry@ccl.net Mon Dec 12 12:21:00 2005
From: "Andrew D. Fant fant|a|pobox.com" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: Linux Cluster Building Workshops
Message-Id: <-30286-051212102940-4367-7XQA3kyJJ6E/9caoklREpQ ~~ server.ccl.net>
X-Original-From: "Andrew D. Fant" <fant+*+pobox.com>
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Date: Mon, 12 Dec 2005 10:29:18 -0500
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Sent to CCL by: "Andrew D. Fant" [fant*pobox.com]
Noko Phala nphala|angloresearch.com wrote:
> Sent to CCL by: "Noko Phala" [nphala]~[angloresearch.com]
> What would be a good book on building Windows clusters?
> 

There's really only been one serious book out on the topic.  MIT Press 
published an alternate version of their second Beowulf book for windows as 
'Beowulf Cluster Computing with Windows'.  Having said that, I would strongly 
advise against going with a Windows cluster unless you have a strong set of 
factors which make it mandatory.  Microsoft has only just released their first 
hpc/clustering version of windows, and it was rather rushed to make it for 
release at supercomputing 05.  It still has all the overhead of running windows 
  as a server os, and vendor support is, in spite of the large booth they had 
for the launch, somewhat spotty.  While MPI is supported to some degree, there 
is a goal of making..net the new API for parallel processing.  And then there 
is the cost of licensing, which is not trivial.  If you really are determined 
to go this route, you might also want to check out the Cornell Theory Center 
website at http://www.tc.cornell.edu .  They are about the only large scale HPC 
site running in a Microsoft environment.  They make it work and do some good 
research, but from what I have seen, it's akin to watching a hippopotamus tap 
dance; the appeal isn't in seeing the dance being done well, but the amazement 
that it can be done at all.

Hope This Helps.
	Andy

-- 
Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fant^^^pobox.com | That shines on me               | Disclaimer:  I don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myself


From owner-chemistry@ccl.net Mon Dec 12 12:55:02 2005
From: "James Kubicki kubicki*geosc.psu.edu" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: Wiki-like Chemical Databases
Message-Id: <-30287-051212093552-24416-AhxrOTrHxYM8iqwE37C6/w- -server.ccl.net>
X-Original-From: James Kubicki <kubicki.:.geosc.psu.edu>
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Date: Mon, 12 Dec 2005 08:42:42 -0500
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Sent to CCL by: James Kubicki [kubicki~~geosc.psu.edu]
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This is a project that Joel is working on although we are far removed from 
allowing
open input.  He is working on a chemical kinetics database for 
environmental chemistry.
Once the structure is built, we would like to open it up (slowly) to 
outside users to upload
their data as well.

At 09:33 PM 12/11/2005, you wrote:
>Sent to CCL by: Paul Tratnyek [tratnyek__ebs.ogi.edu]
>Any examples of--or software for--implementing "open" databases of
>physicochemical data were anyone can contribute to the database via
>the web, as in the wikipedia and other wiki-based databases of other
>kinds of information. Thanks.James Kubicki
335 Deike Bldg.
Dept. of Geosciences
The Pennsylvania State University
University Park, PA 16802
814-865-3951
814-574-7379 (Cell)
814-863-7823 (Fax)

--=====================_605252953==_.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<font size=3>This is a project that Joel is working on although we are
far removed from allowing<br>
open input.&nbsp; He is working on a chemical kinetics database for
environmental chemistry.<br>
Once the structure is built, we would like to open it up (slowly) to
outside users to upload<br>
their data as well.<br><br>
At 09:33 PM 12/11/2005, you wrote:<br>
<blockquote type=cite class=cite cite>Sent to CCL by: Paul Tratnyek
[tratnyek__ebs.ogi.edu]<br>
Any examples of--or software for--implementing &quot;open&quot; databases
of <br>
physicochemical data were anyone can contribute to the database via 
<br>
the web, as in the wikipedia and other wiki-based databases of other
<br>
kinds of information. Thanks.<br><br>
<br><br<br<br<br<br><br<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message" eudora="autourl">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br<br>
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<a href="http://www.ccl.net/chemistry/sub_unsub.shtml" eudora="autourl">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br><br>
Before posting, check wait time at:
<a href="http://www.ccl.net/" eudora="autourl">http://www.ccl.net</a><br><br>
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RTFI: <a href="http://www.ccl.net/chemistry/aboutccl/instructions/" eudora="autourl">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br><br</blockquote>
<x-sigsep><p></x-sigsep>
James Kubicki<br>
335 Deike Bldg.<br>
Dept. of Geosciences<br>
The Pennsylvania State University<br>
University Park, PA 16802<br>
814-865-3951<br>
814-574-7379 (Cell)<br>
814-863-7823 (Fax)<br>
</font></html>

--=====================_605252953==_.ALT--


From owner-chemistry@ccl.net Mon Dec 12 13:30:01 2005
From: "Vincent Xianlong Wang xloongw]![yahoo.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: software to convolution/deconvolution
Message-Id: <-30288-051212111018-27578-EAB/jkHCwRf76aUv791/SA%%server.ccl.net>
X-Original-From: Vincent Xianlong Wang <xloongw^^^yahoo.com>
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Date: Mon, 12 Dec 2005 08:10:08 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: Vincent Xianlong Wang [xloongw[a]yahoo.com]
Hi Eduardo,

The one I know is Origin from OriginLab that can do
this job. It is a commerical software, but you can try
its demo version.

Regards,

Vincent

--- "Eduardo Lemos de Sa edulsa^_^quimica.ufpr.br"
<owner-chemistry(~)ccl.net> wrote:

> Sent to CCL by: Eduardo Lemos de Sa
> [edulsa*quimica.ufpr.br]
> Dear CCLers
> 
> A friend is looking for free softwares able to
> perform
> convolution/deconvolution of curves. Please, could
> you pointed to me some
> one of them?
> 
> Thank you in advance
> 
> My best wishes
> 
> Eduardo
> 
> Eduardo Lemos de Saá
> Dep. Química - Universidade Federal do Paraná
> P. Box 19081 - Curitiba / PR / Brazil
> ZIP 81531-990
> fax: +55(41)3361-3186
> fone: +55(41) 3361-3300
> 
> 
> 
> -= This is automatically added to each message by
> the mailing script =-
> To recover the email address of the author of the
> message, please change
> the strange characters on the top line to the (~)
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> header.> 
> E-mail to administrators: CHEMISTRY-REQUEST(~)ccl.net
> or use> 
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> http://www.ccl.net> 
> Search Messages: http://www.ccl.net/htdig  (login:
> ccl, Password: search)
> 
> If your mail bounces from CCL with 5.7.1 error,
> check:> 
> RTFI:
> http://www.ccl.net/chemistry/aboutccl/instructions/> 
> 
> 
> 


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From owner-chemistry@ccl.net Mon Dec 12 14:43:00 2005
From: "D.BIO- Gerard Pujadas gerard.pujadas(a)urv.net" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: Is there any book/review/web to learn QSAR/QSAR-3D from the basis?
Message-Id: <-30289-051212143325-9788-XWXgvD4UZrdoGA5ohIEz0g{:}server.ccl.net>
X-Original-From: "D.BIO- Gerard Pujadas" <gerard.pujadas[#]urv.net>
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Date: Mon, 12 Dec 2005 20:33:00 +0100
Mime-Version: 1.0


Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas]^[urv.net]

Dear CCL list members,

I would appreciate if you could point me to a 
book, review, etc. where I could learn 
QSAR/3D-QSAR from the basis.

With many thanks in advances for your help

Yours sincerely

Gerard

-- 
======================== NOTE: NEW ADDRESS AND E-MAIL ========================
Dr. Gerard Pujadas
Grup de recerca en "Vi i Salut"
Dept. Bioquímica i Biotecnologia           room 106
Campus de Sant Pere Sescelades		   e-mail: gerard.pujadas/a\urv.net
Univ. Rovira i Virgili                     phone: 34-977 559565
C/ Marcel·lí Domingo                       fax: 34-977 559597
43007 Tarragona (CATALONIA)
State: Spain (European Union)
===========================================================================


From owner-chemistry@ccl.net Mon Dec 12 16:34:00 2005
From: "Sengen Sun sengensun..yahoo.com" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Apologies to Prof. Avijit Ghosh
Message-Id: <-30290-051212162802-26064-3u75LiEG5MHT0i7ESU46DA(_)server.ccl.net>
X-Original-From: Sengen Sun <sengensun:_:yahoo.com>
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Date: Mon, 12 Dec 2005 13:27:52 -0800 (PST)
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Sent to CCL by: Sengen Sun [sengensun]_[yahoo.com]
I wish to apologize to Prof. Ghosh that my words were
too harsh for his inaccurate remarks.  I had some
misunderstanding. I was over sensitive. I am not
perfect especially when I have to address so many
e-mails in a very short time. Forgive me!

So many participants have been involved in the
discussion, manifesting something. This is NOT about
one's philosophy, but unresolvable theoretical issues
at the frontier of the modern sciences.  

Publicly and privately, I received strong objections
to my remarks, "Hoffmann makes a clear statement .....
And then we all follow that." I like these strong
objections very much. It is actually ironic what I
really think. I do try to respect any one, especially
a Nobel Laureate. But it is not right that what a
Nobel Laureate said absolutely cannot be touched or
analysed by others. This point marks the distinction
of this round of discussions from any earlier ones.

It is a good thing that a discussion can go as far and
as deep as possible without limits. We had two rounds
of very hot ones in 2005. I am absolutely amazed that
the participants have driven the debates into such a
depth despite of some difficulties. The discussions
have moved a big step forward in 2005, compared to an
earlier discusion initiated by Prof. E. Lewars 5 years
ago:
http://www.ccl.net/cgi-bin/ccl/message-new?2000+08+25+007.

I am advocating free, open, fair, and equal
discussions on science. There absolutely has not been
a better place anywhere than CCL in this world. I
welcome any one to criticize my bad behaviors due to
my bad emotions or my misunderstanding of other CCL
fellows. But please do not say anything to hurt the
scientific discussions.

Again I apologize to Prof. Ghosh and wish you and all
other CCLers to have a happy holiday and a happy new
year.

Sengen








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From owner-chemistry@ccl.net Mon Dec 12 17:09:01 2005
From: "Drew McCormack da.mccormack[#]few.vu.nl" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: [ANN] Programming Course for Scientists
Message-Id: <-30291-051212162644-25954-3kdgZWOeiMAJ+iavF1t5mw(0)server.ccl.net>
X-Original-From: Drew McCormack <da.mccormack() few.vu.nl>
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Sent to CCL by: Drew McCormack [da.mccormack ~ few.vu.nl]

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I thought some people on this list may be interested in a course I  
have just finished giving called 'Programming Paradigms for  
Scientific Developers'. It is programming language agnostic,  
including Fortran 90, Python, and C++. It introduces Structured  
Programming, Object Oriented Programming, and Generic Programming, to  
Scientists that have limited familiarity with these paradigms.

Course slides can be found here:
http://www.maniacalextent.com/publications/

I have also written a blog entry covering aspects of the course here:
http://www.maniacalextent.com/blog

Drew McCormack

========================================
  Dr. Drew McCormack (Kmr. R153)
  Afd. Theoretische Chemie
  Faculteit Exacte Wetenschappen
  Vrije Universiteit Amsterdam
  De Boelelaan 1083
  1081 HV Amsterdam
  The Netherlands

  Email        		da.mccormack at few.vu.nl
  Web        		http://www.maniacalextent.com
  Blog			http://www.maniacalextent.com/blog

  Telephone      	+31 20 5987623
  Mobile        		+31 6   48321307
  Fax           		+31 20 5987629



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<HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
-khtml-line-break: after-white-space; "><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I thought =
some people on this list may be interested in a course I have just =
finished giving called 'Programming Paradigms for Scientific =
Developers'. It is programming language agnostic, including Fortran 90, =
Python, and C++. It introduces Structured Programming, Object Oriented =
Programming, and Generic Programming, to Scientists that have limited =
familiarity with these paradigms.</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">Course slides can be found =
here:</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; "><A =
href=3D"http://www.maniacalextent.com/publications/">http://www.maniacalex=
tent.com/publications/</A></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">I have also written a blog entry =
covering aspects of the course here:</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A =
href=3D"http://www.maniacalextent.com/blog">http://www.maniacalextent.com/=
blog</A></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Drew McCormack</DIV><BR><DIV> <SPAN =
class=3D"Apple-style-span" style=3D"border-collapse: separate; =
border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; =
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border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; =
font-size: 12px; font-style: normal; font-variant: normal; font-weight: =
normal; letter-spacing: normal; line-height: normal; text-align: auto; =
-khtml-text-decorations-in-effect: none; text-indent: 0px; =
-apple-text-size-adjust: auto; text-transform: none; orphans: 2; =
white-space: normal; widows: 2; word-spacing: 0px; "><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><FONT face=3D"Helvetica" size=3D"3" style=3D"font: =
12.0px =
Helvetica">=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
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margin-left: 0px; "><FONT face=3D"Helvetica" size=3D"3" style=3D"font: =
12.0px Helvetica"><SPAN class=3D"Apple-converted-space">=A0</SPAN>Dr. =
Drew McCormack (Kmr. R153)</FONT></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px Helvetica"><SPAN =
class=3D"Apple-converted-space">=A0</SPAN>Afd. Theoretische =
Chemie</FONT></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; "><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica"><SPAN =
class=3D"Apple-converted-space">=A0</SPAN>Faculteit Exacte =
Wetenschappen</FONT></DIV><DIV style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; "><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica"><SPAN =
class=3D"Apple-converted-space">=A0</SPAN>Vrije Universiteit =
Amsterdam</FONT></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; "><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica"><SPAN =
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margin-bottom: 0px; margin-left: 0px; "><FONT face=3D"Helvetica" =
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Amsterdam</FONT></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; "><FONT face=3D"Helvetica" =
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</SPAN></SPAN></SPAN></SPAN></SPAN>da.mccormack at =
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From owner-chemistry@ccl.net Mon Dec 12 17:45:00 2005
From: "Jeff Nauss jnauss_+_accelrys.com" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: Is there any book/review/web to learn QSAR/QSAR-3D from the basis?
Message-Id: <-30292-051212160147-16852-h/982r25HND5dlc134li0w_+_server.ccl.net>
X-Original-From: Jeff Nauss <jnauss:accelrys.com>
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Date: Mon, 12 Dec 2005 12:23:40 -0800
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Sent to CCL by: Jeff Nauss [jnauss,accelrys.com]
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> Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas]^[urv.net]
> 
> I would appreciate if you could point me to a 
> book, review, etc. where I could learn 
> QSAR/3D-QSAR from the basis.

One place to start might be from the master himself:

Hansch C, Leo A. 1995. Exploring QSAR: Fundamentals and Applications in 
Chemistry and Biology. Washington, DC: ACS Professional Reference Book. 
557 pp.

Please note that the book focuses mostly on the Hansch type parameters and 
does not cover the more modern descriptors very well in my opinion.

Another useful book is:

Livingstone D. 1995. Data Analysis for Chemists. Oxford: Oxford University 
Press

The latter is not strictly about QSAR but gives some of the mathematical 
background.  I found it very useful.

Jeff
--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779

Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/training



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<br><tt><font size=2>&gt; Sent to CCL by: &quot;D.BIO- Gerard Pujadas&quot;
[gerard.pujadas]^[urv.net]<br>
&gt; <br>
&gt; I would appreciate if you could point me to a <br>
&gt; book, review, etc. where I could learn <br>
&gt; QSAR/3D-QSAR from the basis.</font></tt>
<br>
<br><font size=2 face="sans-serif">One place to start might be from the
master himself:</font>
<br><font size=2 face="sans-serif"><br>
Hansch C, Leo A. 1995. <i>Exploring QSAR: Fundamentals and Applications
in Chemistry and Biology</i>. Washington, DC: ACS Professional Reference
Book. 557 pp.</font>
<br>
<br><font size=2 face="sans-serif">Please note that the book focuses mostly
on the Hansch type parameters and does not cover the more modern descriptors
very well in my opinion.</font>
<br>
<br><font size=2 face="sans-serif">Another useful book is:</font>
<br>
<br><font size=2 face="sans-serif">Livingstone D. 1995. <i>Data Analysis
for Chemists</i>. Oxford: Oxford University Press</font>
<br>
<br><font size=2 face="sans-serif">The latter is not strictly about QSAR
but gives some of the mathematical background. &nbsp;I found it very useful.</font>
<br>
<br><font size=2 face="sans-serif">Jeff</font>
<br><font size=2 face="sans-serif">--<br>
Jeffrey L. Nauss, Ph.D.<br>
Lead Training Scientist<br>
Accelrys<br>
10188 Telesis Court, Suite 100<br>
San Diego, CA 92121-4779<br>
<br>
Phone: +1-858-799-5555<br>
Fax: +1-858-799-5100<br>
http://www.accelrys.com/training<br>
</font>
<br>
<br>
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From owner-chemistry@ccl.net Mon Dec 12 19:21:00 2005
From: "Andrew D. Fant fant+/-pobox.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: Is there any book/review/web to learn QSAR/QSAR-3D from the basis?
Message-Id: <-30293-051212191600-27196-/TWbCkvGCr4ayU5Yd2GcgA . server.ccl.net>
X-Original-From: "Andrew D. Fant" <fant~~pobox.com>
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Date: Mon, 12 Dec 2005 19:15:54 -0500
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Sent to CCL by: "Andrew D. Fant" [fant-.-pobox.com]
Jeff Nauss jnauss_+_accelrys.com wrote:
> Sent to CCL by: Jeff Nauss [jnauss,accelrys.com]
>>Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas]^[urv.net]
>>
>>I would appreciate if you could point me to a 
>>book, review, etc. where I could learn 
>>QSAR/3D-QSAR from the basis.
> 
> 
> One place to start might be from the master himself:
> 
> Hansch C, Leo A. 1995. Exploring QSAR: Fundamentals and Applications in 
> Chemistry and Biology. Washington, DC: ACS Professional Reference Book. 
> 557 pp.
> 
> Please note that the book focuses mostly on the Hansch type parameters and 
> does not cover the more modern descriptors very well in my opinion.
> 
> Another useful book is:
> 
> Livingstone D. 1995. Data Analysis for Chemists. Oxford: Oxford University 
> Press
> 
> The latter is not strictly about QSAR but gives some of the mathematical 
> background.  I found it very useful.

Almost any good Medicinal Chemistry textbook will have a discussion of QSAR 
> from a practical standpoint. The mathematical rigor varies widely, of course. 
For a quick overview, Graham Patrick's "Introduction to Medicinal Chemistry" is 
a good and affordable starting point.  If you want a hernia, Burger's Medicinal 
Chemistry and Drug Discovery has a lucid chapter on the subject as well.  If 
you are more interested in descriptors and their definitions, Wiley had 
"Molecular Descriptors in QSAR/QSPR" by Karelson which can help point the way 
into the literature, although it is a few years old now.

IIRC, there are some licensing/patent issues surrounding 3D-QSAR.  Tripos holds 
  US Patents 5025388 (titled simply comparative molecular field analysis, and 
dated 6/18/1993) and 5307287 (same title, dated 4/26/1994).  The listed first 
inventor according to the USPTO is Richard D. Cramer III, if you want to do a 
literature search back to the original papers.  Given the patent, your best 
source for the theoretical underpinnings might well be in the Theory Manual of 
the Sybil documentation.  This is certainly not the only methodology for 
correlation of molecular structure with biological activity. Off the top of my 
head, 4D-QSAR and HASL are two other approaches.  One good overview on the 
subject, although somewhat dated by now, is 3D-QSAR in Drug Design (Kubinyi, 
ed.) from ESCOM in 1993.  Again, if nothing else, it gives a good jumping off 
point into the literature.

Hope This Helps,
	Andy

-- 
Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fant,+,pobox.com | That shines on me               | Disclaimer:  I don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myself


From owner-chemistry@ccl.net Mon Dec 12 19:55:01 2005
From: "Bryan Putnam bfp^-^purdue.edu" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL:G: What about an alternative CCL ?
Message-Id: <-30294-051212140619-4162-sUU5tcJaMlnVVoPY6b7vdQ|,|server.ccl.net>
X-Original-From: Bryan Putnam <bfp()purdue.edu>
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Sent to CCL by: Bryan Putnam [bfp:-:purdue.edu]
On Mon, 12 Dec 2005, Noko Phala nphala!=!angloresearch.com wrote:

> Sent to CCL by: "Noko Phala" [nphala++angloresearch.com]
> Agree. The diversity of the topics in CCL are what makes it interesting, and helps bring to the fore outstanding issues in computational chemistry.
> 
> _________________________
> Dr Noko Phala
> Process Research
> Anglo Research 
> PO Box 106 Crown Mines 2025
> Republic of South Africa
> Tel: +27 (11) 377 4817
> e-mail: nphala|,|angloresearch.com 
> 
> -----Original Message-----
> > From: owner-chemistry|,|ccl.net [mailto:owner-chemistry|,|ccl.net] 
> Sent: Tuesday, December 06, 2005 1:19 AM
> To: Noko Phala
> Subject: CCL: What about an alternative CCL ?
> 
> Sent to CCL by: "Robinson, James" [James.Robinson]^[evotec.com]
> Dear list
> 
> During my part-time PhD studies and brief career in drug design, I found 
> the list provided some inspiration and food-for-thought from simply 
> reading comments and problems people had. Stuck in a small office, it 
> was a comfort to realise that other people where having similar problems 
> to my own. Sometimes the questions asked on the CCL served to provide 
> the seed for problem solving. There is no need for an alternative CCL, 
> its does a very good job as it is.
> 
> James Robinson

I totally agree, in fact I'd like to see the ":G" notation removed from 
posts that have the word Gaussian in them. What next, a scarlet letter :G 
on the t-shirts of anyone using Gaussian? :-)

Bryan


From owner-chemistry@ccl.net Mon Dec 12 20:30:00 2005
From: "dedey*alumni.bilkent.edu.tr" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL:G: dual core opteron
Message-Id: <-30295-051212101331-18744-ZQIKqJ9Tx7cympSC3TKRug*server.ccl.net>
X-Original-From: <dedey . alumni.bilkent.edu.tr>
Date: Mon, 12 Dec 2005 16:20:35 EET


Sent to CCL by: [dedey%%alumni.bilkent.edu.tr]

Dear CCL members,

We are about to build a cluster and trying to decide about the machine configurations.
I wonder if anyone performed parallel execution of Gaussian 98 or 03 
on clusters each of which has AMD Opteron-dual core processors, running Solaris or rpm Linux.
If yes, can you inform me about the operating system. Any diffucilties, or tricks -if present- is also requested.
 

Thanks in advance.
--  
Yavuz Dede


From owner-chemistry@ccl.net Mon Dec 12 21:05:01 2005
From: "Avijit Ghosh avijit ~~ physics.drexel.edu" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL: Orbitals and Philosophy
Message-Id: <-30296-051212205816-22866-aH2zRFBrqiFkd9P2SSSQEg*o*server.ccl.net>
X-Original-From: Avijit Ghosh <avijit~~physics.drexel.edu>
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Date: Mon, 12 Dec 2005 20:58:09 -0500 (EST)
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Sent to CCL by: Avijit Ghosh [avijit###physics.drexel.edu]

> Dear Prof. Ghosh
> 
> I am not to say that orbitals are not useful, they obviously are. I
> guess that this discussion never turned into this direction, just
> because everybody all fully aware of their utility. What I mean is that from
> your mail I had an impression that you put all approximation as equally
> connected to physical reality just because they are approximations. I
> just cannot agree to give the same amount of physical sense to both
> orbitals  and wavefunctions (even purely electronic).

	Perhaps I am mistaken but the entire discussion on is "X" real 
where "X" are either orbitals or more recently the detection of phases,
seems to have revolved around 2 somewhat related issues (1) Is "X" an
observable, in the quantum mechanical sense, where if it is not then "X" 
is termed "not real" (2) Does "X" as an approximate description of 
reality deserve to have the label "real" as measured by the degree of
approximateness.

 Somewhat complicating these two statements is the fact that in
much of electronic structure theory, one sees orbitals as nothing more 
than rather useful basis sets to do more reasonable calculations.
	
	I dont think (1) is a good way of categorizing things into 
"real" and "not real" because it inherently depends on how one defines the 
system and (2) is problematic as it is an expression of an opinion and may 
even change as we become interested in different things (where I somewhat 
inadequately used  BO as an illustration).

	Again I have to say this viewpoint is a personal opinion and
the only reason I jumped in here was I got the impression someone
was doing around changing or requesting changes in textbooks. 

To me  pink unicorns  are not real and intelligent design is not real. 
Orbitals, on the otherhand,  are an approximate description of reality 
much like many other  approximate  descriptions  of reality that dont 
deserve the somewhat  perjorative  label "not  real". Especially as in 
practicality orbitals  provide the  basis of doing what is essentially 
"hand waving" QM for  people like  organic  chemists  (hybridization, 
bonding) w/out actually  having to stare at the time indep. schroedinger 
eq. 

	To extend the analogy in the opposite direction, the 
fact that particles are  approximations to reality (taken as a given by 
quantum mechanics) more  properly encompassed in QFT as localized 
excitations of fields doesn't necessarily require the immediate 
disclaimer that "particles" are not  real in textbooks or (in parallel to 
the recent experimental articles on orbitals) as commentary admonishing 
the use of the word "electrons" in journal articles as if they  were 
actual defined unchangeable entities or particles.

	As I haven't really said anything new on this post than the
last email and I'll let this rest but I wanted to put my vote out for 
"real" if anyone is vote counting :)


	-all the best,
	-avi

_____________________________________________________________________
Avijit Ghosh, Ph.D.		   Drexel University, Dept of Physics
Asst. Professor                                      3141 Chestnut st
Phone: 215-895-2726                            Philadelphia, PA 19104
Fax: 215-895-5934                  Web: http://bio.physics.drexel.edu


From owner-chemistry@ccl.net Mon Dec 12 21:40:01 2005
From: "Schrodinger Announcements announce=-=schrodinger.com" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: Schrodinger releases Maestro for academic use
Message-Id: <-30297-051212213805-17253-oatAmKE087cx0nEMscctvw=-=server.ccl.net>
X-Original-From: "Schrodinger  Announcements" <announce/./schrodinger.com>


Sent to CCL by: "Schrodinger  Announcements" [announce##schrodinger.com]
Schrodinger is pleased to announce the availability of Maestro, a powerful, 
all-purpose molecular modeling and visualization program, for use at no charge 
to all academic users.

Maestro is able to build and modify a wide range of chemical structures, view 
them in a variety of rendering styles, and output high-quality images for use 
in print and/or presentations. Maestro's project facility can be used as an 
electronic notebook to record important properties associated with each 
structure. Maestro is easy to learn and yet powerful - inclusion of the Python 
scripting language allows the user to configure complex tasks into simple 
operations. In addition, Maestro drives all of Schrodinger's industry-leading 
computational programs: Glide, for accurate ligand-receptor docking; Prime, 
for protein structure prediction (homology modeling and threading) as well as 
prediction of ligand-induced fit effects in flexible receptors; Phase, for 
pharmacophore modeling; CombiGlide, for focused library design; MacroModel, 
for versatile, full-featured classical mechanical modeling; Jaguar, for rapid 
ab initio electronic calculations; and many more.

Maestro is available for Linux and SGI; to find out more, and to obtain your 
free copy, please visit www.schrodinger.com.


Schrodinger Announcements


From owner-chemistry@ccl.net Mon Dec 12 22:15:01 2005
From: "Samuel Flores samuel.flores===yale.edu" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL:G: mmtsb for charmm?
Message-Id: <-30298-051212220604-10342-7roQBTiN/qsjs2fl/pDAYw%server.ccl.net>
X-Original-From: "Samuel Flores" <samuel.flores^_^yale.edu>
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	charset="US-ASCII"
Date: Mon, 12 Dec 2005 21:29:16 -0500
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Sent to CCL by: "Samuel Flores" [samuel.flores,+,yale.edu]
Hi Guys,

Has anyone used mmtsb's program 'mdCHARMM.pl'?  It puts out an energy file
with eight nonzero numerical columns.  I think the rightmost of these,
column 8, contains the total energy, but I can't be sure.  Can anyone tell
me where the file format is explained?

Thanks

Sam

Samuel Flores
Graduate Student
Gerstein Lab 
 
Office:
Bass 437
266 Whitney Avenue
New Haven, CT 06520 
203.432.5405
 
Home: 
28 Pearl Street
New Haven, CT 06511
cell: 203.747.2682 

-----Original Message-----
> From: owner-chemistry]_[ccl.net [mailto:owner-chemistry]_[ccl.net] 
Sent: Monday, December 12, 2005 8:57 PM
To: Flores, Samuel 
Subject: CCL:G: dual core opteron

Sent to CCL by: [dedey%%alumni.bilkent.edu.tr]

Dear CCL members,

We are about to build a cluster and trying to decide about the machine
configurations.
I wonder if anyone performed parallel execution of Gaussian 98 or 03 
on clusters each of which has AMD Opteron-dual core processors, running
Solaris or rpm Linux.
If yes, can you inform me about the operating system. Any diffucilties, or
tricks -if present- is also requested.
 

Thanks in advance.
--  
Yavuz Dedehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Mon Dec 12 23:23:01 2005
From: "Steve Bowlus chezbowlus_._goldrush.com" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: Is there any book/review/web to learn QSAR/QSAR-3D from the basis?
Message-Id: <-30299-051212231956-12715-bWBoTAynOXOHqv1kOwkGxg(-)server.ccl.net>
X-Original-From: Steve Bowlus <chezbowlus**goldrush.com>
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Date: Mon, 12 Dec 2005 20:18:39 -0800
MIME-Version: 1.0


Sent to CCL by: Steve Bowlus [chezbowlus|*|goldrush.com]
Well, for getting started, I think you should go back to the real 
beginning of the "linear free energy relationship" - most textbooks on 
physical organic chemistry will have discussions of the Hammett 
relationship, thence discussions of the various substituent constants 
(Hammett, Taft, etc.).  Classical, "Hansch-approach" QSAR is an elegant 
extension of this methodology.  What Hansch and Leo talk about in their 
books (must read!) will make a lot more sense with this basis.

Also at the basis is a good understanding of statistics - not just the 
arithmetic, but how statistical models are derived, the meaning of 
fitting statistics (for regression equations and for individual terms), 
outlier detection, and so on.  It is crucial you understand the 
statistical concepts and how they tie into the chemistry/biology you are 
doing (correlation is numerology, causation is science).  So in addition 
to regression and related techniques, you should also understand 
hypothesis testing and inference in the general way.  Take a look at 
"The Biostatistical Cookbook" by Michelson and Schofield, if you can 
find a copy.

Most of the modern methods (chemomethrics, 3D-QSAR) build on this 
foundation.  We use things like principle component regression and/or 
partial least squares (projection of latent structures) as means to 
reduce descriptor dimensionality, but the final activity models must 
meet the same statistical tests as those from regression techniques. 
Rather than rely on regression alone to select variables, we may use 
neural networks or genetic algorithms to do the variable selection - 
again the models must meet the same, fundamental statistical tests.  All 
of these topics are exhaustively reported and reviewed in the literature 
> from the mid-1980's on.

BTW, do not fall into the trap of thinking that QSAR is something 
magically different from "QSPR" or "ADME" modeling:  in most cases, we 
are taking some structural descriptor(s) (broadly including interaction 
fields) and correlating these with some observable, biological response. 
    I tend to think more in terms of a general, property-performance 
relationship, where the properties are structural metrics and the 
performance is some biological (or pharmacokinetic) response.

sb


D.BIO- Gerard Pujadas gerard.pujadas(a)urv.net wrote:
> Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas]^[urv.net]
> 
> Dear CCL list members,
> 
> I would appreciate if you could point me to a 
> book, review, etc. where I could learn 
> QSAR/3D-QSAR from the basis.
> 
> With many thanks in advances for your help
> 
> Yours sincerely
> 
> Gerard
>