From chemistry-request@ccl.net Wed Jul 14 03:14:27 2004
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Date: Wed, 14 Jul 2004 10:23:34 +0200
From: "Joerg K. Wegner" <wegnerj<<at>>informatik.uni-tuebingen.de>
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To: "O. Hucke" <ohucke<<at>>u.washington.edu>
Cc: chemistry<<at>>ccl.net
Subject: Re: CCL:SAR database software
References: <Pine.A41.4.58.0407131232030.146436<<at>>homer11.u.washington.edu>
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Dear Dr. Hucke,

have a look at:
http://joelib.sf.net
and decide on your own.
JDBC and web interfaces with Java are really good. Descriptors and 2D/3D 
structures are possible.

Kind regards, Joerg

> Dear CCLers,
> 
> we are looking for a (ideally free, of course) database software for the
> storage and the work with SAR data. Ideally the program should be able to
> o store 3D structures of inhibitors
> o perform substructure searches
> o provide a web interface for online access (?)
> 
> Any hints are highly appreciated.
> 
> Thanks,
> 
> Oliver
> 
> _________________________
> 
> Oliver Hucke, Dr.
> 
> University of Washington
> Dept. of Biochemistry
> Seattle, WA 98195
> _________________________
> 
> 
> -= This is automatically added to each message by the mailing script =-
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> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:wegnerj<<at>>informatik.uni-tuebingen.de
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)


From chemistry-request@ccl.net Wed Jul 14 08:30:29 2004
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Date: Wed, 14 Jul 2004 15:36:12 +0200
From: Ferenc Csizmadia <fcsiz|at|chemaxon.com>
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To: chemistry|at|ccl.net
CC: "O. Hucke" <ohucke|at|u.washington.edu>
Subject: Re: CCL:SAR database software (fwd)
References: <Pine.LNX.4.58.0407132311460.4572@Moon>
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Oliver,

You can consider using JChem Base 
(http://www.chemaxon.com/products.html#JChemBase) , which is a Java tool 
for the development of applications that supports chemical registration 
and fast structure searching. JChem Base can integrate a variety of 
database systems (Oracle, MySQL, MS SQL Server, PostrgeSQL, etc.) with 
web interfaces and provides substructure, similarity, and exact search 
engine. Structures are stored in database tables. Structural and 
non-structural data can be combined. Several file formats, like SMILES, 
SDF, and RDF can be imported and exported. The system includes Marvin, a 
Java based chemical editor and viewer applet and image generation 
functionality.
Some examples: http://www.jchem.com/examples.html

We are just putting together a special package for academic institutions 
that would provide all of our tools (not just JChem Base) free with some 
restrictions. Please let me know if you are interested.

Best regards,
Ferenc

-- 
Dr. Ferenc Csizmadia
ChemAxon Ltd.
http://www.chemaxon.com




>we are looking for a (ideally free, of course) database software for the
>storage and the work with SAR data. Ideally the program should be able to
>o store 3D structures of inhibitors
>o perform substructure searches
>o provide a web interface for online access (?)
>
>Any hints are highly appreciated.
>
>Thanks,
>
>Oliver
>
>_________________________
>
>Oliver Hucke, Dr.
>
>University of Washington
>Dept. of Biochemistry
>Seattle, WA 98195
>_________________________
>
>
>-= 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
>
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>HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs
>
>If your mail is bouncing from CCL.NET domain send it to the maintainer:
>Jan Labanowski,  jlabanow|at|nd.edu (read about it on CCL Home Page)
>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>
>
>
>
>
>  
>



From chemistry-request@ccl.net Wed Jul 14 09:22:47 2004
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To: chemistry{at}ccl.net
Subject: Assigning aa to random atoms
Date: Wed, 14 Jul 2004 16:30:20 +0200
From: "Filipe Maia" <filipe{at}xray.bmc.uu.se>
Organization: BMC
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Hi!

Is there any program other than WARP that can assign aminoacids(and  
consequently bonds)
to a group of atoms for which we only know the position and the atom type?
And if we also know the sequence?
Thanks in advance.

Best regards,
Filipe


-- 
Don't go around saying the world owes you a living.
The world owes you nothing.  It was here first.
          -- Mark Twain



From chemistry-request@ccl.net Wed Jul 14 08:41:20 2004
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Date: Wed, 14 Jul 2004 09:47:22 -0300
From: Paul Momoh <momohpo/at/mail1.vcu.edu>
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Good morning,
I initially performed a stability job (STABLE) on a DFT (B3LYP) job. I
got the message RHF-> UHF instability. I then performed another
stabilty test (using Stable=repopt). The instability was subsequently
corrected (I got a lower abs energy). Where/how can I get the
corrected coordinates and/or multiplicity and/or method used for the
corrected structure?

Paul Momoh.
Lab. of Nanotechnology Research,
Virginia Commonwealth University
P.O. BOX 842006
804 827 1222


From chemistry-request@ccl.net Wed Jul 14 07:06:08 2004
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Message-ID: <40F52813.3070703)at(chem.ethz.ch>
Date: Wed, 14 Jul 2004 14:33:23 +0200
From: angelo vargas <vargas)at(chem.ethz.ch>
Organization: ETHZ
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To: chemistry)at(ccl.net
Subject: Z-matrix orientation and standard orientation
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Hallo
I have a small problem with G98.
it happens that two jobs with an identical route sections produce in one 
case both Z-matrix and standard orientations, while in the other case 
only the standard orientation (with loss of infos of the original form 
of the Z-mat.
Explicit addition of IOP(2/11=0) that should force printout of both 
Z-matrix and standard orientations (at every opt step) does not help. I 
can patch the problem I guess but would like to know what is the control 
procedure for matrix output.....
Both initial Z-matrixes contain dummies and geometrical constraints.

The route sections (identical) are

JOB 1

Gaussian 98:  HP-PARisc-HPUX-G98RevA.7 11-Apr-1999
                     13-Jul-2004
  **************************************************
  ------------------------------------------------------------
  # HF/STO-3g Opt=Z-Matrix gfinput gfprint IOP(6/7=3) pop=full
  ------------------------------------------------------------
  1/10=7,18=40,38=1/1,3;
  2/17=6,18=5/2;
  3/11=9,24=11,25=1,30=1/1,2,3;
  4//1;
  5/5=2,38=4/2;
  6/7=3,28=1/1;
  7/29=1/1,2,3,16;
  1/10=7,18=40/3(1);
  99//99;
  2//2;
  3/11=9,25=1,30=1/1,2,3;
  4/5=5,16=2/1;
  5/5=2,38=4/2;
  7//1,2,3,16;
  1/18=40/3(-5);
  2//2;
  6/7=3,19=2,28=1/1;
  99/9=1/99;


JOB 2

**************************************************
  Gaussian 98:  HP-PARisc-HPUX-G98RevA.7 11-Apr-1999
                     13-Jul-2004
  **************************************************
  ------------------------------------------------------------
  # HF/STO-3g Opt=Z-Matrix gfinput gfprint IOP(6/7=3) pop=full
  ------------------------------------------------------------
  1/10=7,18=40,38=1/1,3;
  2/17=6,18=5/2;
  3/11=9,24=11,25=1,30=1/1,2,3;
  4//1;
  5/5=2,38=4/2;
  6/7=3,28=1/1;
  7/29=1/1,2,3,16;
  1/10=7,18=40/3(1);
  99//99;
  2//2;
  3/11=9,25=1,30=1/1,2,3;
  4/5=5,16=2/1;
  5/5=2,38=4/2;
  7//1,2,3,16;
  1/18=40/3(-5);
  2//2;
  6/7=3,19=2,28=1/1;
  99/9=1/99;



Thanks
Angelo

_______________________________________________________________________
Angelo Vargas
Institute for Chemical and Bio Engineering
Swiss Federal Institute of Technology (ETHZ)
ETH Hvnggerberg,   Telefon:  0041/1/633 42 32, Room HCl E 129
Z|rich - Switzerland       Fax:      0041/1/632 11 63
E-mail:   vargas)at(chem.ethz.ch
________________________________________________________________________




From chemistry-request@ccl.net Wed Jul 14 08:05:13 2004
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From: Dmitry Rozmanov <dima)at(xenon.spb.ru>
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To: CCL <chemistry)at(ccl.net>
Subject: force constants of diatomics
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Hello CCL.

I have calculated some diatomics in Gaussian03 for self educational purpose and 
stuck with a problem.

I got some meaningful constans for HF, HCl, HBr (10.66, 5.22, 4.19, 3.23 
mDyne/A). I found somewhere these constants as 9.70, 4.80, 4.10 and 3.20. Then 
there is no problem here.

However, for CO and NO I got something strange, 41.34 and 39.29. While I have 
found 18.60 and 15.30 mDyne/A for these species. This is the problem. Why are 
they two times greater?

Have anybody seen such a behaviour before?

The calculations were RHF/6-31G (ROHF for NO and LanL2DZ for HI).
I have tried MP2/6-31++G(d,p) for CO and got 35.18 force constant. The same 
thing anyway.

I was told that G98 produces the same results. By unknown reason.

What do I do wrong?
How to overcome the problem?

Thank you in advance.
Best wishes.

	---Dmitry.



From chemistry-request@ccl.net Wed Jul 14 06:05:47 2004
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Date: Wed, 14 Jul 2004 11:08:06 +0000 (UTC)
From: C J Kenneth Tan -- OptimaNumerics <cjtan!at!OptimaNumerics.com>
To: Ian Hovell <HOVELL!at!cetem.gov.br>
cc: "'chemistry'" <chemistry!at!ccl.net>
Subject: CCL:Summary Choice of computer for G03
In-Reply-To: <4DB0991764FED5119A2A000475B057CA1C57BD@CELEBRIS04>
Message-ID: <Pine.LNX.4.60.0407141031220.1329!at!krylov.OptimaNumerics.com>
References: <4DB0991764FED5119A2A000475B057CA1C57BD@CELEBRIS04>
Organization: "OptimaNumerics"
URL: http://www.OptimaNumerics.com
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Another component to pay attention to is the availability of
well-tuned numerical libraries for the platform.  It is important to
remember that:

- one implementation of a numerical library does not necessarily equal
  to another implementation
- hardware vendor-supplied numerical libraries often perform better than
  open source/public domain numerical libraries
- specialist third-party numerical libraries can outperform hardware
  vendor-supplied numerical libraries

The LAPACK implementation in OptimaNumerics Libraries can outperform
hardware vendors' libraries by up to 13x on Intel Xeon and Itanium II
machines.  This is the performance level achieved in the current
version.  In the benchmarks for the next release (3.0), OptimaNumerics
LAPACK routines have been shown to outperform hardware vendors'
libraries by an even higher gain fold on the Intel Xeon EM64T (Nocona)
machines.


Kenneth Tan
-----------------------------------------------------------------------
C. J. Kenneth Tan, Ph.D.
OptimaNumerics Ltd.
E-mail: cjtan!at!OptimaNumerics.com      Telephone: +44 798 941 7838
Web: http://www.OptimaNumerics.com    Facsimile: +44 289 066 3015
-----------------------------------------------------------------------


On 2004-07-13 13:48 -0300 Ian Hovell (HOVELL!at!cetem.gov.br) wrote:

> Date: Tue, 13 Jul 2004 13:48:17 -0300
> From: Ian Hovell <HOVELL!at!cetem.gov.br>
> To: 'chemistry' <chemistry!at!ccl.net>
> Subject: CCL:Summary Choice of computer for G03
> 
> As promised here is a summary to the following question
> 
> >I'm looking for the ideal computer for running G03. I was wondering what
> >people on the list, when buying a new computer dedicated to Gaussian03,
> >would go fo? Would people go for cpu speed, cache memory, RAM or hard disk.
> >Where would the emphasise be? And what OS would you opt for. I'm sure these
> >questions have been asked for before so if any body can point me to a URL
> >they know, okay.
> >Thanks for your help and time.
> 
> The answers;
> 
> I don't believe you will get definite answers to your question. I've seen
> people on this list using computers of all kinds, single or multi
> processors, Linux, Windows, Mac, etc... running Gaussian. Maybe the most
> important question is what kind of simulations do you want to do on this
> computer?
> 
> Of course, I'd go for the best computer possible, ant that means best CPU,
> with large cache,  maximum RAM and a large HD. Especially, if you plan on
> doing ab-initio calculations on large molecules, you will need lots of HD
> space, and maybe consider a 62 bit processor.
> 
> As for OS, I'd definetely go for Linux, unless you choose a multi-processor
> computer for which Linux isn't available.
> 
> HTH,
>           Gustavo Seabra.
> 
> Ian, I have grown fond of Mac's again, since OS X is the only operating
> system where I can do both professional development in C and Python
> alongside Word - all without an emulator and/or dual booting.  The prices
> for dual processors are comparable to what Dell has, if not a little cheaper
> (list prices, YMMV).
> Whatever you get, there are a number of things to consider:
> 1)	People forget that there are things like memory bandwidth and
> disk/IO bandwidth.  Thus, they purchase the fastest processor(s) they can,
> and wonder why their jobs don't run as fast as they'd expected.  I'd plan
> for 1 job per 1 or 2 processors for maximum efficiency.  If you have to use
> integral files, I'd investigate fast disks, SCSI, etc.
> 2)	Compilers make a HUGE difference.  gcc/g77 are way slower than
> machine-specific compilers (Intel/PC or IBM/Mac).  While it costs a little
> $$, getting 20-50% faster run-time is a cheap upgrade.  Some compilers also
> have difficulties with some parallel libraries, or don't offer them - check
> with Gaussian if there's any good or bad purchases.
> 3)	The safe recommendation is that one should get as much memory and
> disk as possible.  See (1) for kinds and/or speeds of disk.  Regarding
> cache, I don't know how particular portions of Gaussian relate to cache
> hits/misses - they should know this.  Of course, running more than a single
> job on the box is quite a bit worse re: cache than differences with a single
> job.  And I think people now feel that machines should NEVER page (some turn
> off the option in Linux), so lots and lots of RAM is required.
> 4)	Do you want to be your own system manager?  Do you have access to
> one who is competent?  If not, maybe Linux will be a bother - nothing's real
> good out of the box as I understand things.  I run off-the-shell OS X to
> success.
> 5)	Do you need any kind of compatibility with PC/Mac/Linux/...?  Does
> the machine have to have a graphics head or is it merely a server - the
> latter is WAY easier to configure and maintain.  I'm not sure how PC's
> communicate with
> Mac/Linux/Unix, but the latter three seem to talk to each other well.
> Hope this helps...
> Joe
> 
> I've used various versions of Gaussian on various machines at supercomputing
> centers for many years (at least 18 years).  My current favorite machine is
> SGI's itantuim/altix machine.  It is shared memory so gaussian speed-up is
> nearly linear (at least up to 8 processors, as many as I have tried), and
> the 64 bit system makes file size limitations no longer an issue.  I have
> been able to optimizations/frequency calculations on molecules with nearly
> 150 atoms, including Re atoms, using good quality DFT methods, as well as
> MP2 calculations that choked other machines I have used.
> Steve Williams
> 
> I hope that helps
> Ian Hovell 
> 
> 
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> 
> 
> 
> 
> 
> 
> 


From chemistry-request@ccl.net Wed Jul 14 12:23:23 2004
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Date: Sat, 12 Jun 2004 15:52:27 +0000 (UTC)
From: C J Kenneth Tan -- OptimaNumerics <cjtan^at^OptimaNumerics.com>
To: Marc Noguera Julian <marc^at^klingon.uab.es>
cc: CCL <chemistry^at^ccl.net>
Subject: CCL:cooling needs
In-Reply-To: <3EE6F1E2.5020003^at^klingon.uab.es>
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Marc,

> I need to stablish some kind fo relation between number of PC's running and
> the cooling needed for them (number of frigories). Can anyone help
> Thanks in advance

I don't think this is a simple question.  What kind of machines are
you putting in?  Are the rack-mounted?  How many CPUs in a single 1U
or 2U unit?  Who made the machines?  What is the air flow condition in
the room?  

There was a talk by Steve Smith (Dell) at ICCSA 2004 last month, that
illustrated some of the complexities of machine configuration in a
machine room.  He also covered the associated issue of efficiency of
code and the cost of computation.  The slides are available for
download at the conference web site:
http://iccsa2004.unipg.it/plenary/SteveSmith.zip


Kenneth Tan

P/S: This is not meant to be an advert for OptimaNumerics, but Steve
did mention OptimaNumerics in the presentation.  
-----------------------------------------------------------------------
C. J. Kenneth Tan, Ph.D.
OptimaNumerics Ltd.
E-mail: cjtan^at^OptimaNumerics.com      Telephone: +44 798 941 7838
Web: http://www.OptimaNumerics.com    Facsimile: +44 289 066 3015
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From chemistry-request@ccl.net Wed Jul 14 10:51:02 2004
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To: scerri..at..chem.ucla.edu
From: "Dr. N. SUKUMAR" <nagams..at..rpi.edu>
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Subject: Re: CCL:Question on molecular structure and QM
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I have a slightly different take on this. While the Born-Oppenheimer
separation of electronic and nuclear motions is central to the chemist's
concept of molecular structure, I would say that molecular structure IS
defined beyond/without the B-O approximation, in the same way that
"electronic structure" is defined within the B-O approximation. This "quantum
mechanical" concept of molecular structure is different from the "chemist's"
concept of molecular structure. The latter is an approximation and can be
"extracted" from the former. In the QM description, we could visualize both
electrons and nuclei as charge clouds moving together in space ("wave
packets"). Bond lengths and bond angles can be extracted from the total
wavefunction through the reduced 2-particle and 3-particle densities: lengths
appear as peaks in the radial distribution functions and angles as peaks in
the angular ones (a series of such computations, with electrons in electronic
orbitals and protonic orbitals was, in fact, carried out by I.L.Thomas et al
in the '70s). The "chemist's" concept of molecular structure is only one of
several possible approximations, however; considerations in momentum space
lead to different, equally valid approximations.

However, the molecular structure extracted from pure QM does NOT necesarily
bear a unique 1:1 correspondance with chemists's B-O molecular structures.
Thus different structural and geometric isomers are mixed into the SAME total
wavefunction. In fluxional molecules and other situations where B-O does
breakdown, there is the additional complication that the energies of the B-O
states are close enough to be inseparable. Rather than look upon this as a
limitation, this gives us a window to expand the chemist's popular concept of
molecular structure. Already we talk of 2-D structure (specification of
topology alone) and 3-D structure. Anybody who has dealt with proteins
realizes the advantages of a broader definition, encompassing families of
related 3-D structures.

For a physicist, a molecule is simply a collision that takes too long. If by
molecule, we mean a stoichiometric collection of interacting electrons and
nuclei (canonical ensemble), then yes, molecular structure is defined even
without B-O. If we want to further specify a limited range of energy
(microcanonical ensemble), we are often left with a single B-O structure or a
small set of fluxional structures, which can be extracted from the QM
solution.

Dr. N. Sukumar
Rensselaer Polytechnic Institute

On Sat, 10 Jul 2004 16:31:14 -0700 Eric Scerri wrote:

> 
> Thanks for your interesting response Brian and all others who have 
> responded off-list.  Please keep your replies coming.
> 
> Your point about structure being reduced to physics, if not pure QM 
> with no B-O, is well taken.  I see little point in trying to 
> demarcate between QM and physics in this context.  For example the 
> status of the Pauli Exclusion principle vis a vis QM has never been 
> quite settled.  And yet nobody would claim that introducing the spin 
> quantum number to Schrodinger's non-relativistic model represents a 
> problem with the reduction of chemistry to QM.
> 
> Here is another thought on the subject which I hope is not too 
> trivial.  The importation of B-O allows the molecule to have some 
> structure but of course does not in itself dictate the details of the 
> molecular structure.	It just allows the calculation to get off the 
> ground, so to speak.	It is not as if the calculations are 
> semi-empirical as when certain experimental data are introduced 
> although they are semi empirical in the broad sense of saying that 
> nuclei are much heavier than electrons.
> 
> What is behind this thinking is that there are many claims to a lack 
> of full reduction of chemical phenomena to QM (or physics).  I am 
> trying to weight up whether the molecular shape question is more or 
> less serious than say the inability to strictly predict chemical 
> periodicity without using the experimental order of orbital filling 
> (n + l rule).  Also discussed in the Lowdin volume and something you 
> and I have talked about.
> 
> regards,
> eric
> 
> 
> >On Thu, Jul 08, 2004 at 11:59:33PM -0700, Eric Scerri wrote:
> >  >
> >>
> >>  The following is a somewhat general philosophical question.
> >>  I would very much appreciate the comments of computational chemists.
> >>
> >>  In the philosophy of chemistry literature much has been made of the
> >>  fact that molecular structure cannot be strictly deduced from QM.  I
> >>  am referring to the work of Guy Wooley in the UK and Hans Primas at
> >>  the ETH.
> >>
> >>  The basis of this claim is that structure comes after applying the
> >>  Born-Oppenheimer approximation to fix the nuclei.  These authors
> >>  claim that in this sense molecular structure has not been "reduced"
> >>  to QM.
> >>
> >>  They point to the fact that the Hamiltonians for two isomers of an
> >>  organic compound, for example, are identical in the absence of the
> >>  B-O approximation and they conclude that a strictly QM calculation
> >>  cannot therefore distinguish between the two structures in question.
> >>
> >>  I would be happy to pull some references together for anyone
> >>  interested in studying the original articles.  But I just wanted to
> >>  hear some general reactions to such claims.
> >
> >I think your conclusions are essentially correct. It is what we do with
> >them that is the problem.
> >
> >A key point that I like to demonstrate this and which I owe to Brian
> >Sutcliffe is the point that quantum mechanics says that all identical
> >particles are indistinguishable. The Born-Oppenheimer approximation
> >changes a system where all electrons are indisdinquishable and all like
> >nuclei are indistinguishable to one of indistinquishable electrons in
> >the field of distiquishable like nuclei. For example CO2 with two O-16
> >isotopes has two indisquishable O nuclei and we teach students that this
> >leads to alternate lines in the rotational fine structure of the IR
> >spectrum to be missing. However the standard quantum chemistry methods
> >have the two O nuclei as distinguishable. There is a lot that has to be
> >worked out here. See Brian Surcliffe's article in the Lowdin memorial
> >volume.
> >
> >Molecular structure is not as of now reducible to pure quantum mechanics
> >but this does not mean it is not reducible to physics since the
> >Born-Oppenheimer approximation is part of physics and the calculations
> >agree with experiment.
> >
> >I am not so clear about the point about isomers. A pure non-B-O
> >calculation would lead to all isomers and the dynamics of
> >interconversion I think. Maybe people who do non-B-O calculations on
> >small sytems could comment.
> ---------------







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----- Forwarded message from Godefroid Gahungu <ggahungu/at/yahoo.fr> -----
    Date: Wed, 14 Jul 2004 07:51:45 +0200 (CEST)
    From: Godefroid Gahungu <ggahungu/at/yahoo.fr>
Reply-To: ggahungu/at/yahoo.fr
 Subject: Gaussian output treatment!
      To: jlabanow/at/nd.edu

My greetings first,
 
 
 
      I am a new user of Gaussian program. I was navigating when I saw your site something
very interesting for from your site. In fact, I was looking for a help with Guassian 98
calculation, but haven`t been able to ask my questions to the Users. The following was my
question:
 
      From a  Single Point calculation or let`s say an structural optimization out file,
how can I extract or calculate the Percent Compositions (% atomic contribution) of
Molecular orbitals (e.g for the HOMO and LUMO)? Can any one suggests  another way to
solve this problem?
 
     Thanks alot for your coming help.

		
---------------------------------
Criez gratuitement votre Yahoo! Mail avec 100 Mo de stockage !
Criez votre Yahoo! Mail

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Dear CCLers,

I am using the program FLO/QXP - a great program btw.

Can anybody tell me how to save more than the default 25 solutions of 
the mcdock run? I tried the -W flag but it did not work...

Thanks very much,
Oliver

-- 
_______________________________________________________________

Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke!at!u.washington.edu
_______________________________________________________________



From chemistry-request@ccl.net Wed Jul 14 17:09:11 2004
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From: "Phil Hultin" <hultin..at..cc.umanitoba.ca>
To: "Computational Chemistry List" <chemistry..at..ccl.net>
Subject: Gaussian Dipole Output
Date: Wed, 14 Jul 2004 17:15:19 -0500
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A colleague asked me why the dipole data in the "archive" portion of a
Gaussian output file is not the same as the dipole data expressed only a few
lines above where all the multipole moments are displayed.  I had to admit
that I had not observed this before but on checking all my output files I
see that this is indeed the case.

Can anyone explain why these entries differ?  Is it simply that the
"archive" is not expressed in Debye?  If so, what unit is it expressed in?
Dr. Philip G. Hultin
Associate Professor of Chemistry
University of Manitoba
Winnipeg, MB, Canada R3T 2N2
(vox) 204-474-9814
(fax) 204-474-7608
mailto:hultin..at..cc.umanitoba.ca
http://www.umanitoba.ca/chemistry/


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<DIV><FONT face=3DArial size=3D2><SPAN class=3D312385821-14072004>A =
colleague asked me=20
why the dipole data in the "archive" portion of a Gaussian output file =
is not=20
the same as the dipole data expressed only a few lines above where all =
the=20
multipole moments are displayed.&nbsp; I had to admit that I had not =
observed=20
this before but on checking all my output files I see that this is =
indeed the=20
case.</SPAN></FONT></DIV>
<DIV><FONT face=3DArial size=3D2><SPAN=20
class=3D312385821-14072004></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2><SPAN class=3D312385821-14072004>Can =
anyone explain=20
why these entries differ?&nbsp; Is it simply that the "archive" is not =
expressed=20
in Debye?&nbsp; If so, what unit is it expressed in?</SPAN></FONT></DIV>
<P><FONT size=3D2>Dr. Philip G. Hultin<BR>Associate Professor of=20
Chemistry<BR>University of Manitoba<BR>Winnipeg, MB, Canada R3T =
2N2<BR>(vox)=20
204-474-9814<BR>(fax) 204-474-7608<BR><A=20
href=3D"mailto:hultin..at..cc.umanitoba.ca">mailto:hultin..at..cc.umanitoba.ca</A><=
BR><A=20
href=3D"http://www.umanitoba.ca/chemistry/"=20
target=3D_blank>http://www.umanitoba.ca/chemistry/</A> </FONT></P>
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From chemistry-request@ccl.net Wed Jul 14 20:07:52 2004
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Date: Wed, 14 Jul 2004 21:13:54 -0400
From: Rick Venable <rvenable(at)pollux.cber.nih.gov>
To: chemistry(at)ccl.net
Subject: CCL: gauche+ convention
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I've been trying to track down references to the convention used to
define the gauche+ torsion state in degrees, and have noted that two
conventions seem to be in use.  From what I can infer,

gauche+ = +60	IUPAC convention
gauche+ = -60	IUPAC-IUB convention

where the latter is used for biological macromolecules.

Is this correct?  Are there any useful references or web sites which can
elaborate on either or both conventions?  Can anyone shed any light on
the history of this dichotomy?

Regards,

=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   Rick_Venable(at)nih.gov
ALT email:  rvenable(at)speakeasy.org
-------------------------------------
"Don't blame me, I voted for Kang."
                         Homer
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=