From chemistry-request@ccl.net Wed Jun  8 23:52:12 2005
Received: from mailhub2.uq.edu.au (mailhub2.uq.edu.au [130.102.149.128])
	by server.ccl.net (8.13.1/8.13.1) with ESMTP id j593q7bN022026
	for <chemistry |a| ccl.net>; Wed, 8 Jun 2005 23:52:08 -0400
Received: from smtp2.uq.edu.au (newsmtp2.uq.edu.au [130.102.149.129])
	by mailhub2.uq.edu.au (8.13.3/8.13.3) with ESMTP id j593EJdX096207
	for <chemistry |a| ccl.net>; Thu, 9 Jun 2005 13:14:20 +1000 (EST)
Received: from uq.edu.au (mail2b.soe.uq.edu.au [130.102.3.91])
	by smtp2.uq.edu.au (8.13.3/8.13.3) with ESMTP id j593EJEq096164
	for <chemistry |a| ccl.net>; Thu, 9 Jun 2005 13:14:19 +1000 (EST)
Received: from [152.98.207.35] by negative.soe.uq.edu.au (mshttpd); Thu,
 09 Jun 2005 13:14:17 +1000
From: Dr Seth OLSEN <s.olsen1 |a| uq.edu.au>
To: chemistry |a| ccl.net
Message-ID: <18026317e7e1.17e7e1180263 |a| uq.edu.au>
Date: Thu, 09 Jun 2005 13:14:17 +1000
X-Mailer: iPlanet Messenger Express 5.2 HotFix 2.05 (built Mar  3 2005)
MIME-Version: 1.0
Content-Language: en
Subject: CCL: electronic overlaps at different configurations 
X-Accept-Language: en
Priority: normal
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
X-Scanned-By: MIMEDefang 2.51 on UQ Mailhub on 130.102.149.128
X-Spam-Status: No, score=1.1 required=5.0 tests=TRACKER_ID autolearn=no 
	version=3.0.3
X-Spam-Level: *
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net


Hi CCLers,

I'm curious about what it would take to calculate products of electronic
state overlaps at neighboring geometries that look like:

  <psi(r1)>|psi(r2)><psi(r2)|psi(r3><psi(r3)|psi(r1)>

where psi is an electronic wavefunction of a given adiabatic state over
all degrees of freedom, or alternatively

<psi(r1)| P(r2)P(r3) |psi(r1)>

where P(ri) are density operators for a given electronic adiabatic state.  

Particularly, I'm curious to know how one would go about doing this with
an electronic wavefunction defined in the usual 'ab initio' way, as sums
of configurations over molecular orbitals defined in an atom-centered
gaussian basis set.  Even without bulk rotations (in the sense that the
directions of the eigenvectors of the rotational inertial don't change)
and translations (that is, the neighboring points are different vectors
in the internal nuclear coordinate space), it seems it wouldn't be
straightforward due to the parametric dependence of the electronic basis
on the nuclear configuration.  For example, if the symmetry group
changes between configurations.

Can someone point me the direction of references that might relate to
this problem?

Cheers,

Seth


ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1 |a| uq.edu.au
Web: www.ccms.uq.edu.au 

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms





From chemistry-request@ccl.net Wed Jun  8 23:16:02 2005
Received: from mailhub1.uq.edu.au (mailhub1.uq.edu.au [130.102.148.128])
	by server.ccl.net (8.13.1/8.13.1) with ESMTP id j593FsPc020487
	for <chemistry |a| ccl.net>; Wed, 8 Jun 2005 23:15:55 -0400
Received: from smtp2.uq.edu.au (newsmtp2.uq.edu.au [130.102.149.129])
	by mailhub1.uq.edu.au (8.13.3/8.13.3) with ESMTP id j592Y06A009005
	for <chemistry |a| ccl.net>; Thu, 9 Jun 2005 12:34:00 +1000 (EST)
Received: from uq.edu.au (mail2b.soe.uq.edu.au [130.102.3.91])
	by smtp2.uq.edu.au (8.13.3/8.13.3) with ESMTP id j592XxDc046451
	for <chemistry |a| ccl.net>; Thu, 9 Jun 2005 12:33:59 +1000 (EST)
Received: from [152.98.207.35] by negative.soe.uq.edu.au (mshttpd); Thu,
 09 Jun 2005 12:33:59 +1000
From: Dr Seth OLSEN <s.olsen1 |a| uq.edu.au>
To: chemistry |a| ccl.net
Message-ID: <173c2b17879a.17879a173c2b |a| uq.edu.au>
Date: Thu, 09 Jun 2005 12:33:59 +1000
X-Mailer: iPlanet Messenger Express 5.2 HotFix 2.05 (built Mar  3 2005)
MIME-Version: 1.0
Content-Language: en
Subject: CCL: Simplex optimizations in curvilinear internals
X-Accept-Language: en
Priority: normal
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
X-Scanned-By: MIMEDefang 2.51 on UQ Mailhub on 130.102.148.128
X-Spam-Status: No, score=1.1 required=5.0 tests=TRACKER_ID autolearn=no 
	version=3.0.3
X-Spam-Level: *
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net


Hi CCL,

I was thinking about what a pain it can be to do numerical
gradient-driven optimizations and my thoughts turned to so-called
'simplex' methods.  It would seem that a simplex method would be quite
easy to do in cartesians, but I don't know what it would gain you. 
Mostly this is because one really wants to do optimizations in internal
coordinates, in which the energy function can take a more natural form.  

At the same time it would seem that if you create a simplex in 3N
cartesians (a total of 3N+1 points) and can project bulk rotations and
translations out of the simplex, than you would have some redundant
information that can be used to extract some (limited) gradient
information.  So for the same size simplex as the cartesian case, one
might be able to do a pseudo-gradient-guided simplex optimization in
internal coordinates that could work better.  One might be able, even,
to use the fact that curvilinear internals are usually only orthogonal
in the differential sense, not globally.

Does anyone know on the list of references, sources relating to simplex
optimization methods in curvilinear (perhaps redundant) coordinate sets?
 I've heard that simplex methods are sometimes used in molecular
dynamics simulation, but I don't know if its done in cartesians usually
or what.  Has anyone used them for quantum chemistry?

Cheers,

Seth

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia

tel (617) 33653732
fax (617) 33654623
email: s.olsen1 |a| uq.edu.au
Web: www.ccms.uq.edu.au 

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms





From chemistry-request@ccl.net Wed Jun  8 21:23:43 2005
Received: from relay4.delfa.net (relay4.delfa.net [193.125.210.9])
	by server.ccl.net (8.13.1/8.13.1) with ESMTP id j591Nbvx016588
	for <chemistry %a% ccl.net>; Wed, 8 Jun 2005 21:23:38 -0400
X-Envelope-To: ReichertD %a% mir.wustl.edu
Received: from [192.168.5.1] (CPE0050bfacfe11-CM00122573bb18.cpe.net.cable.rogers.com [24.42.82.45])
	(authenticated bits=0)
	by sycorax.delfa.net (8.13.3/8.13.3/Sycorax.Delfa) with ESMTP id j590YNjC020046
	(version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO);
	Thu, 9 Jun 2005 04:34:25 +0400
Message-ID: <42A78E8E.80605 %a% xenon.spb.ru>
Date: Wed, 08 Jun 2005 20:34:22 -0400
From: Dmitri Rozmanov <dima %a% xenon.spb.ru>
User-Agent: Debian Thunderbird 1.0.2 (X11/20050331)
X-Accept-Language: en-us, en
MIME-Version: 1.0
To: ReichertD %a% mir.wustl.edu, CCL <chemistry %a% ccl.net>
Subject: Re: CCL:Monte Carlo and solvent structure ?
References: <OF3A2B9478.3ADD3398-ON86257019.0065DF60-86257019.006746BD %a% msnotes.wustl.edu>
In-Reply-To: <OF3A2B9478.3ADD3398-ON86257019.0065DF60-86257019.006746BD %a% msnotes.wustl.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
Content-Transfer-Encoding: 7bit
X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed 
	version=3.0.3
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net

Hi there,

One of the definition of the first coordination  number is that: it is the integral of the rdf 
> from 0 till the first minimum. So, you can try just this.

Regards,

	--- Dmitri Rozmanov.



ReichertD %a% mir.wustl.edu wrote:
> Hi all,
> I'm trying to repeat some published research in order to better 
> familiarize with Monte Carlo modeling using BOSS. I'm looking at the 
> solvation of Gd 3+ in TIP3P waters using the parameters of van Veggel 
> and Reinhoudt ( Chem. Eur. J. 5(1) 1999 p90 ). I'm trying to get a feel 
> for the structure and number of waters in the first solvation shell, so 
> with a relatively small simulation I generate the rdf which seems 
> reasonable and compares well to the published data. Here's where I 
> become clueless, how do I determine the number of water molecules in the 
> first solvation shell ? Now the BOSS output following the rdf spits out 
> "Gamma(R) and Coordination Numbers" with "Actual CN = CN x Atom Density" 
> following but I can't figure out what this is and or what to do with it. 
> My admittedly limited understanding is that the integral of the rdf can 
> provide this, any help/pointers would be greatly appreciated.
> thanks in advance,
> -david
> David Reichert, Ph.D.
> Asst. Professor Radiology
> Washington University School of Medicine
> 510 S. Kingshighway, Campus Box 8225
> St Louis, MO 63110
> 
> e-mail: reichertd %a% wustl.edu
> voice: (314) 362-8461
> fax: (314) 362-9940
> 



From chemistry-request@ccl.net Thu Jun  9 04:49:06 2005
Received: from mail.biovertis.com (81-223-198-148.arsenal.xdsl-line.inode.at [81.223.198.148])
	by server.ccl.net (8.13.1/8.13.1) with ESMTP id j598n1Mj011758
	for <CHEMISTRY=at=ccl.net>; Thu, 9 Jun 2005 04:49:01 -0400
Received: from mail.biovertis.com (localhost [127.0.0.1])
	by localhost (Postfix) with ESMTP
	id 17117FB29A; Thu,  9 Jun 2005 09:44:14 +0200 (CEST)
Received: by mail.biovertis.com (Postfix, from userid 65534)
	id 99541FB29C; Thu,  9 Jun 2005 09:44:13 +0200 (CEST)
Received: from bvmail.biovertis.intern (bvmail.biovertis.intern [192.168.1.5])
	(using TLSv1 with cipher EDH-RSA-DES-CBC3-SHA (168/168 bits))
	(Client did not present a certificate)
	by mail.biovertis.com (Postfix) with ESMTP
	id 03246FB29A; Thu,  9 Jun 2005 09:44:11 +0200 (CEST)
Received: from bvmail.biovertis.intern (localhost [127.0.0.1])
	by bvmail.biovertis.intern (8.12.10/8.12.10/SuSE Linux 0.7) with ESMTP id j597i9Ap004771;
	Thu, 9 Jun 2005 09:44:10 +0200
Received: from bvmail.biovertis.intern (root@localhost)
	by bvmail.biovertis.intern (8.12.10/8.12.10/Submit) with ESMTP id j597i9sP004770;
	Thu, 9 Jun 2005 09:44:09 +0200
Date: Thu, 9 Jun 2005 09:44:08 +0200
From: "Dirk Classen-Houben" <Dirk.Classen-Houben=at=biovertis.com>
Sender: "Dirk Classen-Houben" <Dirk.Classen-Houben=at=biovertis.com>
To: CHEMISTRY=at=ccl.net, gustavo.seabra=at=gmail.com, jlabanow=at=nd.edu
Message-ID: <H0000069000593f4.1118303047.bvmail.biovertis.intern@MHS>
Subject: RE: CCL:Reflections about the list
x-scalix-Hops: 1
MIME-Version: 1.0
Content-Type: text/plain;
	charset="US-ASCII"
Content-Disposition: inline
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net
X-Spam-Level: 
X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO 
	autolearn=failed version=3.0.3
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j598n6Mj011767

Hi,

The problem with many questions and few answers in the list is, that only few people are able to collect the answers they get and and post a summary in the list. 
The advantage of collecting answers by one person (who wrote the question) and posting a summary is, that everybody doesn't have to read so many answers, only the summar.
The advantage of a reply to the list is, that you can see immediately if anybody has given a good answer and different people don't write answers other people already did.

Dirk.


Dirk Classen-Houben

BV-Biotechnologies GmbH
Biovertis AG
Campus Vienna Biocenter 6
1030 Wien, Austria

Phone: +43-1-7989 303 110
Fax:   +43-1-7989 303 400 

> -----Original Message-----
> From: Jan K Labanowski [mailto:jlabanow=at=nd.edu] 
> Sent: Donnerstag, 09. Juni 2005 00:31
> To: Gustavo Seabra
> Cc: CCL
> Subject: CCL:Reflections about the list
> 
> 
> Dear Gustavo,
> I added the Reply-To: chemistry=at=ccl.net
> header to CCL messages. As to reasons...
> The idea was that once people get a bunch of answers
> they will post a "summary" to CCL (please do!!!).
> This would limit the traffic on the list. With the amount
> of spam that we get every day, people are trying to limit
> the amount of email they receive. What usually happens
> is that we unsubscribe from the busy lists that we
> CAN CONTROL and still receive tons of spam that
> we cannot control. Moreover, we are all swamped with
> "memos"  at our institutions that we cannot control either. 
> This has the unfortunate effect that many of us slowly end 
> our participation in the lists since we are overwhelmed with 
> the amount of mail and spam. As a result, however, we end up 
> with the pure spam in our mailboxes.
> 
> We will see in a few days how the default "reply to CCL"
> works. If subscribers start yelling at me, I will just 
> restore the old default, i.e, replies by default will go to 
> the original author.
> 
> Jan
> --
> Jan K. Labanowski, Ph.D.                   Tel. (574) 631-5465
> Science Computing Facility                FAX (574) 631-9293
> University of Notre Dame
> 225 Nieuwland Science Hall
> Notre Dame, IN 46556-5670
> 
> 
> 
> Quoting Gustavo Seabra <gustavo.seabra=at=gmail.com>:
> 
> > Dear All,
> >
> > I just have a questio that I would appreciate to hear your opinions.
> >
> > I participate in other mailing lists, and what is common there is 
> > that, whenever you reply to a message, your reply 
> automatically goes 
> > to the list, not to the personal e-mail of the original poster. The 
> > exceptions would be when he or she have defined a "reply 
> to" address, 
> > in which case it also goes to that  address. But, it 
> **always** goes 
> > to the list as well.
> >
> > Here in CCL this doesn't happen, unless you are careful enough to 
> > select "reply all" instead of simply "reply". As a consequence, my 
> > mailbox gets filled with questions, and just a few answers.
> >
> > My personal opinion is in favor of the common way of the 
> other lists, 
> > and the reason is that I have learned **a lot** from the answers to 
> > question posted by other people as well as to my questions. 
> Sometimes 
> > I just like to follow a thread, even if I don't know any 
> answer to it, 
> > and end up knowing more than before. That just doesn't happen 
> > naturally with CCL, unless it's a thread that people are 
> being careful 
> > to send the reply to all (we do see this in some general interest 
> > issues), if we ask the poster for a summary or if he 
> voluntarily posts 
> > a summary. Otherwise, only he learns from the answers.
> >
> > Would anybody know why the CCL behavior is different? Is 
> there anybody 
> > else here who feels he could learn more by following other 
> threads as 
> > well?
> >
> > Thanks,
> >
> > --
> >
> --------------------------------------------------------------
> -------------------------------
> > Gustavo Seabra                                    
> Postdoctoral Associate
> > Quantum Theory Project                             
> University of Florida
> > Registered Linux user number 381680
> > Say NO! to software patents: http://www.nosoftwarepatents.com
> >
> --------------------------------------------------------------
> -------------------------------
> > If at first you don't succeed...
> >                               ...skydiving is not for you.
> >
> >
> >
> >
> > Send your subscription/unsubscription requests to: 
> CHEMISTRY-REQUEST=at=ccl.net
> > HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs
> >
> > use the Web based form from CCL Home Page
> >
> >
> >
> >
> >
> >
> 
> 
> 
> 
> 
> -= This is automatically added to each message by the mailing 
> script =- To send e-mail to subscribers of CCL put the string 
> CCL: on your Subject: line and send your message to:  
> CHEMISTRY=at=ccl.net
> 
> Send your subscription/unsubscription requests to: 
> CHEMISTRY-REQUEST=at=ccl.net 
> HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs 
> 
> If your is mail bouncing from ccl.net domain due to spam 
> filters, please use the Web based form from CCL Home Page 
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> -+-+-+-+-+
> 
> 
> 
> 
> 
> 




From chemistry-request@ccl.net Thu Jun  9 06:21:05 2005
Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129])
	by server.ccl.net (8.13.1/8.13.1) with ESMTP id j59AKw0m015416
	for <CHEMISTRY=at=ccl.net>; Thu, 9 Jun 2005 06:20:59 -0400
Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13])
          by shiva.jussieu.fr (8.12.11/jtpda-5.4) with ESMTP id j59AKvcs040888
          for <CHEMISTRY=at=ccl.net>; Thu, 9 Jun 2005 12:20:57 +0200 (CEST)
X-Ids: 168
Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM)
	id j59AKqj8357350; Thu, 9 Jun 2005 12:20:52 +0200 (MEST)
Date: Thu, 9 Jun 2005 12:20:52 +0200 (MEST)
From: Michel Petitjean <ptitjean=at=itodys.jussieu.fr>
Message-Id: <200506091020.j59AKqj8357350=at=ds10.itodys.jussieu.fr>
To: CHEMISTRY=at=ccl.net
Subject: CCL: Re: Reflections about the list
X-Greylist: Sender IP whitelisted, not delayed by milter-greylist-1.7.2 (shiva.jussieu.fr [134.157.0.168]); Thu, 09 Jun 2005 12:20:57 +0200 (CEST)
X-Antivirus: scanned by sophie at shiva.jussieu.fr
X-Miltered: at shiva.jussieu.fr with ID 42A81809.001 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)!
X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed 
	version=3.0.3
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net

To: CCL <CHEMISTRY=at=ccl.net>
Subj: CCL: Re: Reflections about the list

Personally, I never use the automatic reply, even for a single
sender. I read emails with the unix mail command, save the message,
edit it and most time delete parts of it to shorten the size of
my reply, then send the reply with the command mail.
Note that this procedure avoids any action of viruses,
even if the viruses are runnable on my unix host. Furthermore,
the virus cannot be propagated. Finally, I can read and send
messages via any Xterm emulator, without using graphical
functionalities.
Webmail users may have a different opinion.
For the CCL, replying to the whole list is a good idea: I learn
more from replies than from questions.

/* I do not like software patents */

Michel Petitjean                      Email: petitjean=at=itodys.jussieu.fr
entropy=at=mdpi.org                             ptitjean=at=ccr.jussieu.fr
Editor-in-Chief of Entropy            http://www.mdpi.org/entropy
FIS2005 coordinator                   http://www.mdpi.org/fis2005
ITODYS (CNRS, UMR 7086)
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html
......................................................................
> From owner-chemistry=at=ccl.net Wed Jun  8 23:56:48 2005
Message-ID: <f79359b60506081425ebc00a4=at=mail.gmail.com>
Date: Wed, 8 Jun 2005 17:25:58 -0400
From: Gustavo Seabra <gustavo.seabra=at=gmail.com>
X-Reply-To: 
Subject: CCL:Reflections about the list

Dear All,

I just have a questio that I would appreciate to hear your opinions.

I participate in other mailing lists, and what is common there is
that, whenever you reply to a message, your reply automatically goes
to the list, not to the personal e-mail of the original poster. The
exceptions would be when he or she have defined a "reply to" address,
in which case it also goes to that  address. But, it **always** goes
to the list as well.

Here in CCL this doesn't happen, unless you are careful enough to
select "reply all" instead of simply "reply". As a consequence, my
mailbox gets filled with questions, and just a few answers.

My personal opinion is in favor of the common way of the other lists,
and the reason is that I have learned **a lot** from the answers to
question posted by other people as well as to my questions. Sometimes
I just like to follow a thread, even if I don't know any answer to it,
and end up knowing more than before. That just doesn't happen
naturally with CCL, unless it's a thread that people are being careful
to send the reply to all (we do see this in some general interest
issues), if we ask the poster for a summary or if he voluntarily posts
a summary. Otherwise, only he learns from the answers.

Would anybody know why the CCL behavior is different? Is there anybody
else here who feels he could learn more by following other threads as
well?

Thanks,

-- 
---------------------------------------------------------------------------------------------
Gustavo Seabra                                    Postdoctoral Associate
Quantum Theory Project                             University of Florida
Registered Linux user number 381680
Say NO! to software patents: http://www.nosoftwarepatents.com
---------------------------------------------------------------------------------------------


From chemistry-request@ccl.net Thu Jun  9 15:03:58 2005
Received: from neptune.tranzyme.com (neptune.tranzyme.com [132.210.158.201])
	by server.ccl.net (8.13.1/8.13.1) with ESMTP id j59J3vVP032225
	for <chemistry|at|ccl.net>; Thu, 9 Jun 2005 15:03:57 -0400
Received: from mercure.tranzyme.com (dcsher01.tranzyme.com [10.32.2.3])
	by neptune.tranzyme.com (8.12.10/8.12.10) with ESMTP id j59IEDc4028100
	for <chemistry|at|ccl.net>; Thu, 9 Jun 2005 14:14:13 -0400
X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0
Content-class: urn:content-classes:message
MIME-Version: 1.0
Content-Type: multipart/alternative;
	boundary="----_=_NextPart_001_01C56D1F.14B76D0A"
Subject: NMR structure determination software
Date: Thu, 9 Jun 2005 14:14:30 -0400
Message-ID: <C94F931D92788D4EBD498B740AA5F7E123B395|at|dcsher01.tranzyme.com>
X-MS-Has-Attach: 
X-MS-TNEF-Correlator: 
Thread-Topic: NMR structure determination software
Thread-Index: AcVtHxRj2cw6wKTjRxWoENlW9ePQ5A==
From: "Axel Mathieu" <AMathieu|at|tranzyme.com>
To: <chemistry|at|ccl.net>
X-Scanned-By: MIMEDefang 2.48 on 10.32.2.1
X-Spam-Status: No, score=0.0 required=5.0 tests=HTML_MESSAGE autolearn=failed 
	version=3.0.3
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net

This is a multi-part message in MIME format.

------_=_NextPart_001_01C56D1F.14B76D0A
Content-Type: text/plain;
	charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

Greetings CCL'ers:
=20
I was wondering if any of you were willing to share your expert opinion
on the type of minimal and hopefully rather inexpensive software set-up
needed to solve NMR solution structures (including visualization). I'm
currently using MOE which I really like for all my modeling needs but it
really has too many bells and whistles for just the NMR structure
determination that we want to accomplish now.
=20
I do understand that there exist many algorithms to solve NMR structures
- many of which are "free" to non-profit organizations - and I do not
want to embark on a discussion of how and which software is better. I
simple want to see if there is a @simple@ cost-effective NMR structure
determination set-up for commercial organizations.
=20
If any of you offer such solutions, please do not hesitate to contact me
as I am interested.
Again many thanks to the community for the immense help,
=20
APM
=20

------_=_NextPart_001_01C56D1F.14B76D0A
Content-Type: text/html;
	charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:o=3D"urn:schemas-microsoft-com:office:office" =
xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns:st1=3D"urn:schemas-microsoft-com:office:smarttags" =
xmlns=3D"http://www.w3.org/TR/REC-html40">

<head>
<meta http-equiv=3DContent-Type content=3D"text/html; =
charset=3Dus-ascii">
<meta name=3DProgId content=3DWord.Document>
<meta name=3DGenerator content=3D"Microsoft Word 11">
<meta name=3DOriginator content=3D"Microsoft Word 11">
<link rel=3DFile-List href=3D"cid:filelist.xml@01C56CFD.8D4F5740">
<o:SmartTagType =
namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
 name=3D"PersonName"/>
<!--[if gte mso 9]><xml>
 <o:OfficeDocumentSettings>
  <o:DoNotRelyOnCSS/>
 </o:OfficeDocumentSettings>
</xml><![endif]--><!--[if gte mso 9]><xml>
 <w:WordDocument>
  <w:SpellingState>Clean</w:SpellingState>
  <w:GrammarState>Clean</w:GrammarState>
  <w:DocumentKind>DocumentEmail</w:DocumentKind>
  <w:EnvelopeVis/>
  <w:ValidateAgainstSchemas/>
  <w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
  <w:IgnoreMixedContent>false</w:IgnoreMixedContent>
  <w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
  <w:Compatibility>
   <w:BreakWrappedTables/>
   <w:SnapToGridInCell/>
   <w:WrapTextWithPunct/>
   <w:UseAsianBreakRules/>
   <w:UseWord2002TableStyleRules/>
  </w:Compatibility>
  <w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel>
 </w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
 <w:LatentStyles DefLockedState=3D"false" LatentStyleCount=3D"156">
 </w:LatentStyles>
</xml><![endif]--><!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{mso-style-parent:"";
	margin:0cm;
	margin-bottom:.0001pt;
	mso-pagination:widow-orphan;
	font-size:12.0pt;
	font-family:"Times New Roman";
	mso-fareast-font-family:"Times New Roman";}
a:link, span.MsoHyperlink
	{color:blue;
	text-decoration:underline;
	text-underline:single;}
a:visited, span.MsoHyperlinkFollowed
	{color:purple;
	text-decoration:underline;
	text-underline:single;}
span.EmailStyle17
	{mso-style-type:personal-compose;
	mso-style-noshow:yes;
	mso-ansi-font-size:10.0pt;
	mso-bidi-font-size:10.0pt;
	font-family:Arial;
	mso-ascii-font-family:Arial;
	mso-hansi-font-family:Arial;
	mso-bidi-font-family:Arial;
	color:windowtext;}
span.SpellE
	{mso-style-name:"";
	mso-spl-e:yes;}
@page Section1
	{size:612.0pt 792.0pt;
	margin:72.0pt 90.0pt 72.0pt 90.0pt;
	mso-header-margin:35.4pt;
	mso-footer-margin:35.4pt;
	mso-paper-source:0;}
div.Section1
	{page:Section1;}
-->
</style>
<!--[if gte mso 10]>
<style>
 /* Style Definitions */=20
 table.MsoNormalTable
	{mso-style-name:"Table Normal";
	mso-tstyle-rowband-size:0;
	mso-tstyle-colband-size:0;
	mso-style-noshow:yes;
	mso-style-parent:"";
	mso-padding-alt:0cm 5.4pt 0cm 5.4pt;
	mso-para-margin:0cm;
	mso-para-margin-bottom:.0001pt;
	mso-pagination:widow-orphan;
	font-size:10.0pt;
	font-family:"Times New Roman";
	mso-ansi-language:#0400;
	mso-fareast-language:#0400;
	mso-bidi-language:#0400;}
</style>
<![endif]-->
</head>

<body lang=3DEN-US link=3Dblue vlink=3Dpurple =
style=3D'tab-interval:36.0pt'>

<div class=3DSection1>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Greetings <st1:PersonName w:st=3D"on"><span =
class=3DSpellE>CCL</span></st1:PersonName><span
class=3DSpellE>&#8217;ers</span>:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I was wondering if any of you were willing to share =
your
expert opinion on the type of minimal and hopefully rather inexpensive =
software
set-up needed to solve NMR solution structures (including =
visualization). I&#8217;m
currently using MOE which I really like for all my modeling needs but it =
really
has too many bells and whistles for just the NMR structure determination =
that
we want to accomplish now.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I do understand that there exist many algorithms to =
solve
NMR structures &#8211; many of which are &#8220;free&#8221; to =
non-profit
organizations - and I do not want to embark on a discussion of how and =
which
software is better. I simple want to see if there is a @simple@ =
cost-effective NMR
structure determination set-up for commercial =
organizations.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>If any of you offer such solutions, please do not =
hesitate
to contact me as I am interested.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Again many thanks to the community for the immense =
help,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>APM<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

</div>

</body>

</html>

------_=_NextPart_001_01C56D1F.14B76D0A--


From chemistry-request@ccl.net Thu Jun  9 13:04:30 2005
Received: from uis-gumail-9-stage2.georgetown.edu (postoffice-4.georgetown.edu [141.161.88.216])
	by server.ccl.net (8.13.1/8.13.1) with ESMTP id j59H4MeK028252
	for <chemistry = ccl.net>; Thu, 9 Jun 2005 13:04:22 -0400
Received: from uis-gumail-9.georgetown.edu (postoffice-4.georgetown.edu [141.161.88.216])
	by uis-gumail-9-stage2.georgetown.edu (8.12.10/8.12.10) with ESMTP id j59Fvtm9029516
	for <chemistry = ccl.net>; Thu, 9 Jun 2005 11:57:58 -0400 (EDT)
Received: from imap.georgetown.edu (uis-gumail-5.georgetown.edu [141.161.88.141])
	by uis-gumail-9.georgetown.edu (8.12.10/8.12.10) with ESMTP id j59FviLe029395
	for <chemistry = ccl.net>; Thu, 9 Jun 2005 11:57:44 -0400 (EDT)
Received: from [141.161.233.111] by imap.georgetown.edu (mshttpd); Thu,
 09 Jun 2005 11:57:44 -0400
From: Sivanesan Dakshanamurthy <sd233 = georgetown.edu>
To: chemistry = ccl.net
Message-ID: <4cb6864c71e5.4c71e54cb686 = imap.georgetown.edu>
Date: Thu, 09 Jun 2005 11:57:44 -0400
X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.26 (built Mar 31 2004)
MIME-Version: 1.0
Content-Language: en
Subject: Re: CCL:Reflections about the list
X-Accept-Language: en
Priority: normal
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
X-GU-FilterVersion: 1.26
X-Scanned-By: MIMEDefang 2.39
X-Spam-Status: No, score=0.5 required=5.0 tests=FROM_ENDS_IN_NUMS 
	autolearn=no version=3.0.3
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net

I too agree with the Dr.Michel Petitjean, replying to the whole list is a good idea.
-Siva  

D.Sivanesan, Ph.D.
E401, New Research Building,
Macromolecular Core & Dept. of Oncology,
Lombardi Cancer Center (NCI Comprehensive Cancer Center), 
Georgetown University, Washington DC 20057
Phone: 202-687-2347


----- Original Message -----
From: Michel Petitjean <ptitjean = itodys.jussieu.fr>
Date: Thursday, June 9, 2005 6:20 am
Subject: CCL:Reflections about the list

> To: CCL <CHEMISTRY = ccl.net>
> Subj: CCL: Re: Reflections about the list
> 
> Personally, I never use the automatic reply, even for a single
> sender. I read emails with the unix mail command, save the message,
> edit it and most time delete parts of it to shorten the size of
> my reply, then send the reply with the command mail.
> Note that this procedure avoids any action of viruses,
> even if the viruses are runnable on my unix host. Furthermore,
> the virus cannot be propagated. Finally, I can read and send
> messages via any Xterm emulator, without using graphical
> functionalities.
> Webmail users may have a different opinion.
> For the CCL, replying to the whole list is a good idea: I learn
> more from replies than from questions.
> 
> /* I do not like software patents */
> 
> Michel Petitjean                      Email: 
> petitjean = itodys.jussieu.frentropy@mdpi.org                        
>     ptitjean = ccr.jussieu.fr
> Editor-in-Chief of Entropy            http://www.mdpi.org/entropy
> FIS2005 coordinator                   http://www.mdpi.org/fis2005
> ITODYS (CNRS, UMR 7086)
> 1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
> 75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
> http://petitjeanmichel.free.fr/itoweb.petitjean.html
> >......................................................................
> > From owner-chemistry = ccl.net Wed Jun  8 23:56:48 2005
> Message-ID: <f79359b60506081425ebc00a4 = mail.gmail.com>
> Date: Wed, 8 Jun 2005 17:25:58 -0400
> From: Gustavo Seabra <gustavo.seabra = gmail.com>
> X-Reply-To: 
> Subject: CCL:Reflections about the list
> 
> Dear All,
> 
> I just have a questio that I would appreciate to hear your opinions.
> 
> I participate in other mailing lists, and what is common there is
> that, whenever you reply to a message, your reply automatically goes
> to the list, not to the personal e-mail of the original poster. The
> exceptions would be when he or she have defined a "reply to" address,
> in which case it also goes to that  address. But, it **always** goes
> to the list as well.
> 
> Here in CCL this doesn't happen, unless you are careful enough to
> select "reply all" instead of simply "reply". As a consequence, my
> mailbox gets filled with questions, and just a few answers.
> 
> My personal opinion is in favor of the common way of the other lists,
> and the reason is that I have learned **a lot** from the answers to
> question posted by other people as well as to my questions. Sometimes
> I just like to follow a thread, even if I don't know any answer to it,
> and end up knowing more than before. That just doesn't happen
> naturally with CCL, unless it's a thread that people are being careful
> to send the reply to all (we do see this in some general interest
> issues), if we ask the poster for a summary or if he voluntarily posts
> a summary. Otherwise, only he learns from the answers.
> 
> Would anybody know why the CCL behavior is different? Is there anybody
> else here who feels he could learn more by following other threads as
> well?
> 
> Thanks,
> 
> -- 
> -------------------------------------------------------------------
> --------------------------
> Gustavo Seabra                                    Postdoctoral 
> AssociateQuantum Theory Project                             
> University of Florida
> Registered Linux user number 381680
> Say NO! to software patents: http://www.nosoftwarepatents.com
> -------------------------------------------------------------------
> --------------------------
> 
> 
> -= This is automatically added to each message by the mailing 
> script =-
> To send e-mail to subscribers of CCL put the string CCL: on your 
> Subject: line
> and send your message to:  CHEMISTRY = ccl.net
> 
> Send your subscription/unsubscription requests to: CHEMISTRY-
> REQUEST = ccl.net 
> HOME Page: http://www.ccl.net   | Jobs Page: 
> http://www.ccl.net/jobs 
> 
> If your is mail bouncing from ccl.net domain due to spam filters, 
> pleaseuse the Web based form from CCL Home Page 
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
> +-+-+
> 
> 
> 
> 
> 
> 



From chemistry-request@ccl.net Thu Jun  9 16:10:52 2005
Received: from bradbury.acpub.duke.edu (bradbury.acpub.duke.edu [152.3.233.54])
	by server.ccl.net (8.13.1/8.13.1) with ESMTP id j59KAks9004307
	for <CHEMISTRY^at^ccl.net>; Thu, 9 Jun 2005 16:10:46 -0400
Received: from pohl.acpub.duke.edu (pohl.acpub.duke.edu [152.3.233.64])
	by bradbury.acpub.duke.edu (8.12.10/8.12.10/Duke-5.0.0) with ESMTP id j59Hn2YN029628
	for <CHEMISTRY^at^ccl.net>; Thu, 9 Jun 2005 13:49:02 -0400
Received: from godzilla.acpub.duke.edu (godzilla.acpub.duke.edu [152.3.233.25])
	by pohl.acpub.duke.edu (8.12.11/8.12.10/Duke-5.0.0) with ESMTP id j59HmwB2020715
	for <CHEMISTRY^at^ccl.net>; Thu, 9 Jun 2005 13:48:58 -0400
Received: (from jz7@localhost)
	by godzilla.acpub.duke.edu (8.12.10/8.12.9/Submit) id j59Hmtgb015500;
	Thu, 9 Jun 2005 13:48:55 -0400 (EDT)
Date: Thu, 9 Jun 2005 13:48:55 -0400 (EDT)
From: jz7^at^duke.edu
Sender: jz7^at^duke.edu
To: CHEMISTRY^at^ccl.net
Subject: about excess electron transfer theoretical study
Message-ID: <Pine.GSO.4.58.0506091121180.29276^at^godzilla.acpub.duke.edu>
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
X-PMX-Version: 4.7.1.128075, Antispam-Engine: 2.0.3.2, Antispam-Data: 2005.6.9.19
X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no 
	version=3.0.3
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net

Dear all,

I am reading about study on excess electron transfer (mainly thgouth DNA
or pi-stack system). Although there are more and more experiments on this,
I didn't find much theoretical reference talking about method study it. Is
there really no such publication? Anyone who has seen it or know where I
can find it please give me some help! Any information would be helpful,
even reference on the conducticity of DNA would be helpful.

Thanks a lot!

Jeny


From chemistry-request@ccl.net Thu Jun  9 16:48:37 2005
Received: from rm-rstar.sfu.ca (rm-rstar.sfu.ca [142.58.101.21])
	by server.ccl.net (8.13.1/8.13.1) with ESMTP id j59KmWc0006173
	for <chemistry)at(ccl.net>; Thu, 9 Jun 2005 16:48:36 -0400
Received: from cultus.sfu.ca (cultus.sfu.ca [142.58.101.5])
	by rm-rstar.sfu.ca (8.12.10/8.12.5/SFU-5.0H) with ESMTP id j59JvxCk020875
	for <chemistry)at(ccl.net>; Thu, 9 Jun 2005 12:57:59 -0700 (PDT)
Message-Id: <200506091957.j59JvxCk020875)at(rm-rstar.sfu.ca>
Content-Type: text/html
Content-Disposition: inline
Content-Transfer-Encoding: binary
X-Mailer: SFUwebmail 2.70
X-Sender: justinz)at(popserver.sfu.ca
To: chemistry)at(ccl.net
MIME-Version: 1.0
From: justinz)at(sfu.ca
Subject: Mopac7 installation in Solaris
Date: Thu, 09 Jun 2005 12:57:59 -0700
Reply-To: justinz)at(sfu.ca
X-Virus-Scanned: by antibody.sfu.ca running antivirus scanner
X-Spam-Status: No, score=1.7 required=5.0 tests=HTML_10_20,HTML_MESSAGE,
	HTML_MIME_NO_HTML_TAG,MIME_HTML_ONLY,NO_REAL_NAME autolearn=no 
	version=3.0.3
X-Spam-Level: *
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net

Hi All:<br>
<br>
I want to install a Mopac 7 in Sun Sparc Solaris system. What version I can download? What dependency packages are required for its installations? May I use " g77 -O *.f -o mopac.exe " to compile the source files?&nbsp;<br>
<br>
thanks,<br>
<br>
Justin<br>
<br>



From chemistry-request@ccl.net Thu Jun  9 18:35:37 2005
Received: from ithnet.com (mail-a01.ithnet.com [217.64.83.96])
	by server.ccl.net (8.13.1/8.13.1) with SMTP id j59MZWmF010915
	for <chemistry [a] ccl.net>; Thu, 9 Jun 2005 18:35:33 -0400
Received: (qmail 19121 invoked by uid 0); 9 Jun 2005 21:35:32 -0000
Received: from rer [a] panet.de by mail-a01 
 (Processed in 0.437013 secs); 09 Jun 2005 21:35:32 -0000
X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO 
	autolearn=failed version=3.0.3
X-Virus-Status: No
Received: from unknown (HELO panet.de) (84.145.189.131)
  by mail-a01.ithnet.com with SMTP; 9 Jun 2005 21:35:31 -0000
X-Sender-Authentication: SMTP AUTH verified <guenther.meinrath [a] pa-net.de>
Message-ID: <42A8B644.E7E39774 [a] panet.de>
Date: Thu, 09 Jun 2005 22:36:04 +0100
From: rer <rer [a] panet.de>
X-Mailer: Mozilla 4.75 [de]C-CCK-MCD QXW0325a  (Win98; U)
X-Accept-Language: de,en
MIME-Version: 1.0
To: chemistry [a] ccl.net
Subject: Re: Reflection about the list
References: <4cb6864c71e5.4c71e54cb686 [a] imap.georgetown.edu>
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit
X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net

Dear CCL list members,

the communication about 'reflections on the list'
meanwhile has generated some traffic. As a pretty
recent member of the list, this discussion is a
bit surprising to me. Being attached to several
mailing lists, the CCL list is the only list whee
this kind of discussion has arisen. In the other
lists (e.g. RADCH-L, ENVIRON) the questions and
responses are transfered to all subscribers. To
identify interesting topics and enjoying an
intelligent and meaningful discussion seems to be
a main motivation to join a list. Imagine: reading
an interesting question of a list member - and
never getting to know the answers! For a
scientist, this seems to me an efficient technique
of torture... 

Some days ago, I was looking for some information
about including lanthanide ions into Gaussian98
calculations. One of the hits in the search engine
directed to 'server.ccl...'. The linked post in
CCL was very intersting to me (doing Gaussian
calculations as a kind of 'hobby'), especially
because the person posting the question was kind
enough to summarize the answers. Otherwise the
responses would not have been available. May be
the poster has aso received some answer that where
not of interest to him - but possibly to me and
other subscribers of the CCL list.

If only the question would have been available,
what help this post would offer to others (the
community 'being the list')? In short: Replying to
the list should be a natural choice.

Dr. habil. Guenther Meinrath
Technische Universitdt Bergakademie Freiberg
Institute of Inorganic Chemistry
Leipziger Str. 27
D-09596 Freiberg
&
RER Consultants Passau
Schiesstattweg 3a
D-94032 Passau

         


Sivanesan Dakshanamurthy schrieb:
> 
> I too agree with the Dr.Michel Petitjean, replying to the whole list is a good idea.
> -Siva
> 
> D.Sivanesan, Ph.D.
> E401, New Research Building,
> Macromolecular Core & Dept. of Oncology,
> Lombardi Cancer Center (NCI Comprehensive Cancer Center),
> Georgetown University, Washington DC 20057
> Phone: 202-687-2347
>