From owner-chemistry@ccl.net Mon Feb 27 04:26:00 2006
From: "David Cornil cornildavid]^[yahoo.fr" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: Dipole_moment_with_AMPAC
Message-Id: <-31009-060227042428-16698-emJzYzjKai+dLCL0wdrr4Q_._server.ccl.net>
X-Original-From: "David  Cornil" <cornildavid!A!yahoo.fr>
Date: Mon, 27 Feb 2006 04:24:24 -0500


Sent to CCL by: "David  Cornil" [cornildavid(0)yahoo.fr]
Dear CCLers,

Last two week, I 've asked a question about the difference between the "Point-Charg" and "Hybrid" component on an AMPAC output. 
I transfert to you the answer to my question.

The general formalism to calculate the expectation value of some
monoelectronic operator X in the basis set of AOs (/i>, /j>) reads:

            <X> = sum (i and j) <i/X/j> D(i,j)

where <i/X/j> is the integral for the operator X calculated on the pair
of AO i and j,
and D(i,j) is an entry in the density matrix for the eigenstate
considered. See the book of Mc Weeny for details on density matrices.

In the zero differential overlap (ZDO) approximation, only diagonal
terms of the kind <i/X/i> are considered non zero (e.g. CNDO).
Applied to the dipole moment, the ZDO approximation leads to the point
charge contributions.

In the NDDO approaches (INDO, MINDO, MNDO, etc), monocentric integrals
are also retained in the approximation:
<i/X/j> if and only if /i> and /j> are centered on the same atom A.
Suppose the operator "X" is "z", required to compute the "z" dipole
component. Now, <s/z/pz> is not zero when the AOs "s" and "pz" are
centered on the same atom. Such an integral is said "hybrid" as it
reflects a true hybridization of the AOs.
These contributions might be important for atoms with one or more lone
pair(s).
Note also that with "d" AOs introduced in the basis set (MNDO/d; SAM1),
it also appears non zero "hybrid" integrals of the kind <p/z/d>.


I thank Andy Holder for his help.

Cornil David


From owner-chemistry@ccl.net Mon Feb 27 05:52:00 2006
From: "Reinaldo Pis Diez pis_diez]=[yahoo.com.ar" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: Energy differences between spin states in [Ru(bipyridine)3]+2
Message-Id: <-31010-060224150215-20407-Y/nmVs4fMdvEWGzFANnGhg/./server.ccl.net>
X-Original-From: Reinaldo Pis Diez <pis_diez * yahoo.com.ar>
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Date: Fri, 24 Feb 2006 16:03:39 -0300
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Sent to CCL by: Reinaldo Pis Diez [pis_diez#%#yahoo.com.ar]


	Dear Arvydas

> 
> Triplet state is 2.29 eV higher in comparison with singlet.
> Pentet state is  3.23 eV higher in comparison with triplet.
> Septet state is  2.55 eV higher in comparison with pentet.
>

		Well, I don't know any theoretical or experimental study on such a 
system, but I know from Inorganic Chemistry courses that Ru^{2+}, 
belonging to the second-row transition metals, tends to form low-spin 
complexes. Thus, your results (singlet state is the GS) seems to be in 
agreement with Ligand-Field Theory predictions.
		Regards,

						Reinaldo


	
	
		
___________________________________________________________ 
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From owner-chemistry@ccl.net Mon Feb 27 06:48:00 2006
From: "Arvydas Tamulis tamulis:-:mserv.itpa.lt" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: How to calculate spectrum of triplet [Ru(III)(bpy)2(bpy*-)2+]
Message-Id: <-31011-060227063850-10000-81nlJqED4BzU/h2gHouYRw(a)server.ccl.net>
X-Original-From: Arvydas Tamulis <tamulis(-)mserv.itpa.lt>
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Date: Mon, 27 Feb 2006 13:38:41 +0200 (EET)
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Sent to CCL by: Arvydas Tamulis [tamulis__mserv.itpa.lt]
Dear Reinaldo and other CCLs,

Thank you for responding to my former question.
The next question: How properly calculate spectrum of excited complex 
[Ru(III)(bpy)2(bpy*-)2+] in the triplet state ?
Which programs are suitable?
I understand that TURBOMOLE can optimize geometry in excited states but
does this package properly calculate spectrum in triplet state of
this complex?
Do you know other software which is able to calculate spectrum of
triplet [Ru(III)(bpy)2(bpy*-)2+] ?

Regards,
Arvydas


From owner-chemistry@ccl.net Mon Feb 27 07:22:01 2006
From: "Mariusz Radon mariusz.radon#%#gmail.com" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL:G: problem with PCM in g03
Message-Id: <-31012-060227071219-30249-ntk3ZLaJCaLFDVX5zajMBA::server.ccl.net>
X-Original-From: "Mariusz Radon" <mariusz.radon(0)gmail.com>
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Date: Mon, 27 Feb 2006 13:12:14 +0100
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Sent to CCL by: "Mariusz Radon" [mariusz.radon]~[gmail.com]
Hi,

I really need symmetry in this case, not only to simplify
calculations, but also to make interpretation easier, so I strongly
would like to employ it. Anyway, thanks for your advice!

I stil hope that someone knows how to overcome this bug(?) in g03
still having explicit symmetry... Any suggestions?

Thanks in advance,
Mariusz

On 2/26/06, Anthony J. H. M. Meijer a.meijer _ sheffield.ac.uk
<owner-chemistry+*+ccl.net> wrote:
> Sent to CCL by: "Anthony J. H. M. Meijer" [a.meijer/a\sheffield.ac.uk]
> On Saturday 25 February 2006 17:52, Mariusz Radon mariusz.radon%a%gmail.com
> wrote:
> > Sent to CCL by: "Mariusz Radon" [mariusz.radon]_[gmail.com]
> > ------=_Part_12633_28785460.1140889404731
> > Content-Type: text/plain; charset=ISO-8859-1
> > Content-Transfer-Encoding: quoted-printable
> > Content-Disposition: inline
> >
> > Dear CCLers,
> >
> > I'm trying to use PCM model in g03. My input is as follows
> >
> > #P B3LYP/Gen UHF SCF=3D(Fermi,Sleazy) SCRF(PCM,Solvent=3DH2O) Guess=3DRead
> > Integral(Grid=3DSG1)
> > #P GFINPUT IOP(6/7=3D3) Symmetry(PG=3DCs,Follow) Opt(loose)
> >
> > (this is rough optimisation in water). Although 2 times SCF(SCRF) has
> > converged and 2 steps of geometry optimisation has been done I got the
> > following error in the 3rd step:
> >
> >  Polarizable Continuum Model (PCM)
> >  =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
> > =3D=3D=3D=3D=3D=3D=3D=3D=3D
> >  Model                : PCM.
> >  Atomic radii         : UA0 (Simple United Atom Topological Model).
> >  Polarization charges : Total charges.
> >  Charge compensation  : None.
> >  Solution method      : Matrix inversion.
> >  Cavity               : GePol (RMin=3D0.200 OFac=3D0.890).
> >                         Default sphere list used, NSphG=3D   27.
> >                         Tesserae with average area of 0.200 Ang**2.
> >  1st derivatives      : Analytical V*U(x)*V algorithm (CHGder, D1EAlg=3D0).
> >                         Cavity 1st derivative terms included.
> >  Solvent              : Water, Eps=3D  78.390000.
> >
> > --------------------------------------------------------------------------=
> > ----
> >  Using symmetry in molecular cavity generation.
> >  AdVTs1: ISph=3D  281 is engulfed by JSph=3D  284 but Ae(  281) is not yet
> > = zero!
> >  Error termination via Lnk1e in /usr/local/g03/l301.exe at Thu Feb 23
> > 23:54:12 2006.
> >  Job cpu time:  0 days  7 hours  6 minutes 27.8 seconds.
> >  File lengths (MBytes):  RWF=3D    674 Int=3D      0 D2E=3D      0 Chk=3D
> > = 23
> > Scr=3D      1
> >
> > The same story is with other solvents I've tried (THF, Chlorobenzene), but
> > the error occurs earlier (in 2nd and 1st step respectively). What may be
> > th= e
> > reason? I've no idea what is wrong, particularly that the last geometry
> > doesn't seem to be spoiled in any way, moreover SCF(SCRF) can be done at
> > this geometry without any error.
> >
> > Thanks in advance.
> >
> > Best wishes,
> > Mariusz
> >
> > --
>
> Hi,
>
> I've had a similar problem in the past, which disappeared if I switched off
> symmetry using the NOSYMM option in the route section.
>
> Hope this helps,
>
> Anthony Meijer
>
>
> --
> -------------------------------------------------
> Dr. Anthony J. H. M. Meijer
> Dept. of Chemistry, Room G8a
> University of Sheffield
> Sheffield S3 7HF
> United Kingdom
>
> Email: a.meijer!A!sheffield.ac.uk
> WWW: meijer.group.shef.ac.uk
> Tel:+44-114-222-9482
> Fax:+44-114-222-9346
> PGP:0xB55B90AF (On request or at keyserver)
> -------------------------------------------------
> Nothing makes one so vain as being told that one is a sinner.
> Conscience makes egotists of us all.
>                 -- Oscar Wilde>
>
>
>


From owner-chemistry@ccl.net Mon Feb 27 08:06:00 2006
From: "Reinaldo Pis Diez pis_diez,,yahoo.com.ar" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: How to calculate spectrum of triplet [Ru(III)(bpy)2(bpy*-)2+]
Message-Id: <-31013-060227072459-8235-s3FozE7ZELazZrJurhZ2dw.@.server.ccl.net>
X-Original-From: Reinaldo Pis Diez <pis_diez,,yahoo.com.ar>
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Date: Mon, 27 Feb 2006 09:26:37 -0300
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Sent to CCL by: Reinaldo Pis Diez [pis_diez,+,yahoo.com.ar]
	Dear Arvydas,

> The next question: How properly calculate spectrum of excited complex 
> [Ru(III)(bpy)2(bpy*-)2+] in the triplet state ?
> Which programs are suitable?

		ADF can do that at the density functional level of theory. You can 
read about the program at www.scm.com.
		Regards,

					Reinaldo


	
	
		
___________________________________________________________ 
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From owner-chemistry@ccl.net Mon Feb 27 11:50:00 2006
From: "Joslyn Y Kravitz jyudenfr-x-umich.edu" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: LANL2DZ vs SDD
Message-Id: <-31014-060227114227-10735-/W6zokgh1+wZ8/FT8mSVJw++server.ccl.net>
X-Original-From: Joslyn Y Kravitz <jyudenfr..umich.edu>
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Date: Mon, 27 Feb 2006 11:42:04 -0500 (EST)
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Sent to CCL by: Joslyn Y Kravitz [jyudenfr ~ umich.edu]
SDD is a triple zeta basis set and LanL2DZ is a double zeta basis set, 
which is likely why the SDD is better. I am not sure of the difference in 
how they treat relativistic effects.

Joslyn Kravitz



On Sun, 26 Feb 2006, zjwu zjwu a imr.edu wrote:

> Sent to CCL by: "zjwu" [zjwu#imr.edu]
> Hi, all,
>
> I have maybe a naive question about the basis sets LANL2DZ and SDD which are the standard basis sets in Gaussian package. I am now using the two basis sets to calculate the systems containing 4d and 5d elements (including rare earth elements).My question is:
>
> What is the difference of the two basis sets in dealing with relativistic effects and spin-orbit coupling effect?
>
> The two basis sets use the same valence electrons for 4d and 5d elements, but it seems SDD is better than LANL2DZ.
>
> Thank you very much.
>
> Zhijian WU>
>
>
>
>
>


From owner-chemistry@ccl.net Mon Feb 27 12:58:00 2006
From: "Egon Willighagen e.willighagen%a%science.ru.nl" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: software pattents in chemistry?
Message-Id: <-31015-060227121820-29727-JSD7rJmIzQWjXFC1GEmRUg/a\server.ccl.net>
X-Original-From: Egon Willighagen <e.willighagen-#-science.ru.nl>
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Date: Mon, 27 Feb 2006 14:14:24 +0100
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Sent to CCL by: Egon Willighagen [e.willighagen]_[science.ru.nl]

Hi all,

Today I learned that software pattents have hit chemistry, chemoinformatics in 
this case:

http://v3.espacenet.com/textdoc?DB=EPODOC&IDX=WO2005001743&F=0

I have no idea on the impact of this pattent, but was wondering if others saw 
more software pattents in chemistry, and wether software pattents in 
chemistry affected work in our field. 

Anyone who has experience with software pattents in cheminformatics, 
computational chemistry and the likes?

Egon

-- 
e.willighagen^science.ru.nl
PhD student on Molecular Representation in Chemometrics
Radboud University Nijmegen
Blog: http://chem-bla-ics.blogspot.com/
http://www.cac.science.ru.nl/people/egonw/
GPG: 1024D/D6336BA6


From owner-chemistry@ccl.net Mon Feb 27 14:53:01 2006
From: "David van der Spoel spoel{:}xray.bmc.uu.se" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL: software pattents in chemistry?
Message-Id: <-31016-060227144155-5546-LYLpHJnyiZ5B+76vrDeXKA*o*server.ccl.net>
X-Original-From: David van der Spoel <spoel(0)xray.bmc.uu.se>
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Date: Mon, 27 Feb 2006 19:36:18 +0100
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Sent to CCL by: David van der Spoel [spoel- -xray.bmc.uu.se]
Egon Willighagen e.willighagen%a%science.ru.nl wrote:
> Sent to CCL by: Egon Willighagen [e.willighagen]_[science.ru.nl]
> 
> Hi all,
> 
> Today I learned that software pattents have hit chemistry, chemoinformatics in 
> this case:
> 
> http://v3.espacenet.com/textdoc?DB=EPODOC&IDX=WO2005001743&F=0
> 
> I have no idea on the impact of this pattent, but was wondering if others saw 
> more software pattents in chemistry, and wether software pattents in 
> chemistry affected work in our field. 
> 
> Anyone who has experience with software pattents in cheminformatics, 
> computational chemistry and the likes?
> 
> Egon
> 
This is bad.

I had an idea some time ago that could help to insure ourselves from 
problems related to patents. If there were a repository for software 
that is in a public place, like a scientific journal (e.g. JCC or JCTC), 
where one could upload new versions of the code (together with a 
one-page description of the software) then there would be a public 
track-record of software that can be used in patent-cases as  proof of 
prior art. Of course the software needs to be under a license that 
allows redistribution. Simultaneously this would be a great source of 
information.

How would you feel about contributing to something like this? I gather 
that if there is enough support from the community we could convince one 
of the journals to do something like this.


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel{=}xray.bmc.uu.se	spoel{=}gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From owner-chemistry@ccl.net Mon Feb 27 15:27:01 2006
From: "Andrew D. Fant fant[a]pobox.com" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL:G: software pattents in chemistry?
Message-Id: <-31017-060227145521-10303-7s2glx0U4MVwqZfrWI7/Aw*o*server.ccl.net>
X-Original-From: "Andrew D. Fant" <fant]^[pobox.com>
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Date: Mon, 27 Feb 2006 14:55:14 -0500
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Sent to CCL by: "Andrew D. Fant" [fant-$-pobox.com]
Egon Willighagen e.willighagen%a%science.ru.nl wrote:
> Sent to CCL by: Egon Willighagen [e.willighagen]_[science.ru.nl]

> I have no idea on the impact of this pattent, but was wondering if others saw 
> more software pattents in chemistry, and wether software pattents in 
> chemistry affected work in our field. 
> 
> Anyone who has experience with software pattents in cheminformatics, 
> computational chemistry and the likes?

Egon,
   I will admit that I didn't check the link for that patent, but I know that
patents have existed on various computational chemistry methods for quite a
while now..

The best advice that I can pass along, given that I am not a lawyer, and
especially not one admitted to any bar in the EU, is to not go looking at
patent databases or checking on the status of the neat idea you read about in
JCICS or JCAMD that you want to implement for cdk (or any other open-source
project).  The problem is that while you are liable for infringement if you use
a patented process without permission, if it can be shown that you KNEW it was
patented and did it anyway, you are liable for TREBLED damaged in many
jurisdictions.  Ignorance in this case really can be your best defense.

Be glad you are in the EU where they did block the software patent legislation
last year.  Make sure your MEP knows why you think software patents are a bad
idea.  And as an open-source developer, make sure that you release often and
early, so that your work can be cited as prior art if needed.

I'm sorry if this sounds like a rant.  Lets just say a nerve has been hit. I'll
withdraw back to my cave and return everyone to your regularly scheduled
gaussian support requests.

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 Feb 27 16:02:01 2006
From: "Jim Kress ccl_nospam+/-kressworks.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: software pattents in chemistry?
Message-Id: <-31018-060227145443-9480-ZtRajK/b8xT+ZLJDxu/iVg-#-server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam * kressworks.com>
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Date: Mon, 27 Feb 2006 14:54:32 -0500
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Sent to CCL by: "Jim Kress" [ccl_nospam-*-kressworks.com]
This is absurd.  There is prior art for the method described, for example,
the Qeq method of Goddard and Rappe.  This 'patent' is not enforceable.

Jim 

> -----Original Message-----
> From: Egon Willighagen e.willighagen%a%science.ru.nl 
> [mailto:owner-chemistry##ccl.net] 
> Sent: Monday, February 27, 2006 1:00 PM
> To: Kress, Jim 
> Subject: CCL: software pattents in chemistry?
> 
> Sent to CCL by: Egon Willighagen [e.willighagen]_[science.ru.nl]
> 
> Hi all,
> 
> Today I learned that software pattents have hit chemistry, 
> chemoinformatics in this case:
> 
> http://v3.espacenet.com/textdoc?DB=EPODOC&IDX=WO2005001743&F=0
> 
> I have no idea on the impact of this pattent, but was 
> wondering if others saw more software pattents in chemistry, 
> and wether software pattents in chemistry affected work in our field. 
> 
> Anyone who has experience with software pattents in 
> cheminformatics, computational chemistry and the likes?
> 
> Egon
> 
> --
> e.willighagen++science.ru.nl
> PhD student on Molecular Representation in Chemometrics 
> Radboud University Nijmegen
> Blog: http://chem-bla-ics.blogspot.com/
> http://www.cac.science.ru.nl/people/egonw/
> GPG: 1024D/D6336BA6
> 
> 
> 
> -= This is automatically added to each message by the mailing 
> script =-
> To recover the email address of the author of the message, 
> please change> Conferences: 
> http://server.ccl.net/chemistry/announcements/conferences/
> 
> Search Messages: http://www.ccl.net/htdig  (login: ccl, 
> Password: search)> 
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
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> 
> 
> 
> 
>


From owner-chemistry@ccl.net Mon Feb 27 16:37:06 2006
From: "jz7##duke.edu" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: calculating/plotting the MOs of excited states
Message-Id: <-31019-060227160329-23407-rzScLnB16JK1ng4xaeSNwg() server.ccl.net>
X-Original-From: jz7-$-duke.edu
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Date: Mon, 27 Feb 2006 14:24:04 -0500 (EST)
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Sent to CCL by: jz7,duke.edu
Dear all,

I would like to see the molecular orbitals of certain excited states of an
organic compound (about 100 atoms). Could anyone please recommend method
to calculate such excited states property and plotting those MOs?

Really appreciate the help!


From owner-chemistry@ccl.net Mon Feb 27 17:12:00 2006
From: "Jan Labanowski janl|a|speakeasy.net" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: software pattents in chemistry?
Message-Id: <-31020-060227163619-12988-5zeSk1NdbwDpR5cdakfQfA]_[server.ccl.net>
X-Original-From: "Jan Labanowski" <janl---speakeasy.net>
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Date: Mon, 27 Feb 2006 21:36:13 +0000
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Sent to CCL by: "Jan Labanowski" [janl|-|speakeasy.net]
Before we go to 100 messages on software repositories, I would like
to remind P.T. CCL Members that the software repository exists on CCL
for last 15 years (in case you wanted to ask how stable is this site...).
At the beginning, there was a lot of contributions to the CCL Archives.
Now there are very few and while I was thinking about putting some work
into it, after a COLD reception of my announcement of upload page:

http://server.ccl.net/chemistry/aboutccl/contributing/
http://server.ccl.net/chemistry/why_upload.shtml

I have put my effort of reorgenizing the CCL Archives on a back burner.
We discussed this already on the list why there is only a limited 
number of open source computational chemistry packages (though there are
several VERY GOOD open source project on freshmeat.net -- check Google:

http://www.google.com/search?hl=en&q=freshmeat+chemistry&btnG=Google+Search

In US, after the practical implementation of the Birch Bayh and Bob Dole Act
of 1980 finally took place, people at academia have to protect intellectual
property developed from Federal grants since it belongs to the parent
organization. Similar laws/practices are in Europe and elsewhere.
And therefore software developed at the University that may be "sold", 
"rented", "technology-transferred" has to be protected. 
It is not necessarily the greed of researchers and facilty.

They "work-for-hire" for their University, Inc.

There is also the element of protecting the "quality" and "the source".
THIS IS A VALID POINT!!! While there are arguments to the contrary, the
scientific fields are much different that the "general utility" software,
since beside the programming expertize, a lot of deep scientific insight
is needed to make a reliable package. For that reason, we have a number
of GPL Chemistry Viewers but only a few of GPL "ab initio" codes (though
we have some -- but do you use them?).

I will shut up here, but please do not blame everyone for software patents.
In many cases they HAD TO DO IT and have it in the faculty contract at
their institution.

Jan Labanowski
CCL Admin.


From owner-chemistry@ccl.net Mon Feb 27 17:47:01 2006
From: "Konrad Hinsen konrad.hinsen|-|cea.fr" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: software or online server to predict protein flexibility
Message-Id: <-31021-060227155431-18639-nHPyYdWWtxulPztN1lS1Hw(0)server.ccl.net>
X-Original-From: "Konrad  Hinsen" <konrad.hinsen- -cea.fr>
Date: Mon, 27 Feb 2006 15:54:25 -0500


Sent to CCL by: "Konrad  Hinsen" [konrad.hinsen!A!cea.fr]
On 27.02.2006, at 21:12, David van der Spoel spoel{:}xray.bmc.uu.se wrote:

>I had an idea some time ago that could help to insure ourselves from 
>problems related to patents. If there were a repository for software 
>that is in a public place, like a scientific journal (e.g. JCC or JCTC), 
>where one could upload new versions of the code (together with a 
>one-page description of the software) then there would be a public 
>track-record of software that can be used in patent-cases as  proof of 
>prior art. Of course the software needs to be under a license that 
>allows redistribution. Simultaneously this would be a great source of 
>information.

>How would you feel about contributing to something like this? I gather 
>that if there is enough support from the community we could convince one 
>of the journals to do something like this.

The French CNRS proposes such a repository:

	http://ciel.ccsd.cnrs.fr/

As far as I can see, its use is not restricted to the French research community, but for the moment 
most of the site is available in French only. All my published software is in there.
--
-------------------------------------------------------------------------------
Konrad Hinsen
Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: konrad.hinsen#,#cea.fr
-------------------------------------------------------------------------------


From owner-chemistry@ccl.net Mon Feb 27 18:22:01 2006
From: "Dr. Seth Olsen s.olsen1]![uq.edu.au" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: software pattents in chemistry?
Message-Id: <-31022-060227165325-29790-JzBuRS5Ru5KE5tbV9MHSfQ,+,server.ccl.net>
X-Original-From: "Dr. Seth Olsen" <s.olsen1^^uq.edu.au>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Tue, 28 Feb 2006 07:53:17 +1000
MIME-Version: 1.0


Sent to CCL by: "Dr. Seth Olsen" [s.olsen1..uq.edu.au]

Patents happen, but what bothers me most is the excessively small print 
in that flow chart.  I put it into photoshop to zoom in and read it, but 
there's just no structure at all.  Hard to avoid infringing on a patent 
that you can't bloody read.
Cheers,

Seth

Egon Willighagen e.willighagen%a%science.ru.nl wrote:

>Sent to CCL by: Egon Willighagen [e.willighagen]_[science.ru.nl]
>
>Hi all,
>
>Today I learned that software pattents have hit chemistry, chemoinformatics in 
>this case:
>
>http://v3.espacenet.com/textdoc?DB=EPODOC&IDX=WO2005001743&F=0
>
>I have no idea on the impact of this pattent, but was wondering if others saw 
>more software pattents in chemistry, and wether software pattents in 
>chemistry affected work in our field. 
>
>Anyone who has experience with software pattents in cheminformatics, 
>computational chemistry and the likes?
>
>Egon
>
>  
>


-- 
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms

Dr Seth Olsen, PhD
Postdoctoral Fellow, Biomolecular Modeling 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() uq.edu.au
Web: www.ccms.uq.edu.au 

ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms


From owner-chemistry@ccl.net Mon Feb 27 18:58:01 2006
From: "Mike Gilson gilson__verachem.com" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: patents in computational chemistry and cheminformatics
Message-Id: <-31023-060227173732-25064-n/neTkqthkc5jxkRZn0YuQ^-^server.ccl.net>
X-Original-From: "Mike  Gilson" <gilson[#]verachem.com>
Date: Mon, 27 Feb 2006 17:37:24 -0500


Sent to CCL by: "Mike  Gilson" [gilson .. verachem.com]
Since this discussion begin with a discussion of a patent application with my name on it, here are my 2-3 cents!
 
> Anyone who has experience with software pattents in cheminformatics, 
> computational chemistry and the likes?

Patents are actually quite common in this area: go to the US Patent Office search site (http://patft.uspto.gov/netahtml/search-bool.html)and search for "accelrys", "tripos", "generalized born", "protein-ligand docking", for example. You'll find patents from both companies and universities. 

> If there were a repository for software that is in a public place, like  
> a scientific journal (e.g. JCC or JCTC), where one could upload new
> versions of the code (together with a one-page description of the software) 
> then there would be a public track-record of software that can be 
> used in patent-cases as proof of prior art.

Patenting the obvious or the known is definitely a problem in the US. The patent examiners seem to check for prior art only in their databases of prior patents. They don't look at the literature or the marketplace. Unfortunately, they probably also would not look in a software repository.

> There is prior art for the method described, for example,the Qeq method of Goddard and Rappe.

Like pretty much every other patent, this one builds on the work of others, and is patentable only insofar as it goes beyond what has been done in the past.

Best regards,
Mike


From owner-chemistry@ccl.net Mon Feb 27 19:32:01 2006
From: "Osman Guner oguner*|*turquoisecons.com" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: software pattents in chemistry?
Message-Id: <-31024-060227151802-24332-6R59eHo5yTuc1cnzptpaTg##server.ccl.net>
X-Original-From: "Osman Guner" <oguner]![turquoisecons.com>
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Date: Mon, 27 Feb 2006 11:17:55 -0800
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Sent to CCL by: "Osman Guner" [oguner*_*turquoisecons.com]
This is a multi-part message in MIME format.

------=_NextPart_000_0008_01C63B8F.75C848A0
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	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Patenting pharmacophore models have been an issue for some time.  There =
are
a number of patents that are still pending, but there are also some that =
are
issued.  Those patents that are issued are not just the pharmacophore =
model
itself, but the model in conjunction with other inventions.

=20

There is a nice, but somewhat dated discussion on this at:

=20

Pieraccioli D.  "Patenting the pharmacophore", Curr. Drug. Disc. 2002,
October, pp 40-43

=20

Also some mention on this in my monologue, where I list some of the =
patents
that are pending, and some that are issued:

=20

G=FCner, O.F.  "The impact of pharmacophore modeling in drug design," =
IDrugs,
2005 8(7), 567-572.

=20

=20

Osman F, G=FCner, PhD

Principal, Turquoise Consulting

oguner-$-turquoisecons.com

http://www.turquoisecons.com

=20

-----Original Message-----
> From: owner-chemistry-$-ccl.net [mailto:owner-chemistry-$-ccl.net]=20
Sent: Monday, February 27, 2006 10:12 AM
To: Guner, Osman F 
Subject: CCL: software pattents in chemistry?

=20

Sent to CCL by: Egon Willighagen [e.willighagen]_[science.ru.nl]

=20

Hi all,

=20

Today I learned that software pattents have hit chemistry, =
chemoinformatics
in=20

this case:

=20

http://v3.espacenet.com/textdoc?DB=3DEPODOC&IDX=3DWO2005001743&F=3D0

=20

I have no idea on the impact of this pattent, but was wondering if =
others
saw=20

more software pattents in chemistry, and wether software pattents in=20

chemistry affected work in our field.=20

=20

Anyone who has experience with software pattents in cheminformatics,=20

computational chemistry and the likes?

=20

Egon

=20

--=20

e.willighagen++science.ru.nl

PhD student on Molecular Representation in Chemometrics

Radboud University Nijmegen

Blog: http://chem-bla-ics.blogspot.com/

http://www.cac.science.ru.nl/people/egonw/

GPG: 1024D/D6336BA6

=20

=20

=20

-=3D This is automatically added to each message by the mailing script =
=3D-=20http://www.ccl.net/cgi-bin/ccl/send_ccl_message

=20=20

Subscribe/Unsubscribe:=20=20=20

Job: http://www.ccl.net/jobs=20=20

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: =
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=20http://www.ccl.net/spammers.txt

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<div class=3DSection1>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Patenting pharmacophore models have been an issue for some =
time.=A0 There
are a number of patents that are still pending, but there are also some =
that
are issued.=A0 Those patents that are issued are not just the =
pharmacophore model
itself, but the model in conjunction with other =
inventions.<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>There is a nice, but somewhat dated discussion on this =
at:<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Pieraccioli D.=A0 &quot;Patenting the pharmacophore&quot;, =
<i><span
style=3D'font-style:italic'>Curr. Drug. Disc.</span></i> <b><span
style=3D'font-weight:bold'>2002</span></b>, October, pp =
40-43<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Also some mention on this in my monologue, where I list some of =
the
patents that are pending, and some that are =
issued:<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>G=FCner, O.F.=A0 &quot;The impact of pharmacophore modeling in =
drug design,&quot;
<i><span style=3D'font-style:italic'>IDrugs</span></i>, <b><span
style=3D'font-weight:bold'>2005</span></b> <i><span =
style=3D'font-style:italic'>8</span></i>(7),
567-572.<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Osman F, G=FCner, PhD<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Principal, Turquoise Consulting<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>oguner-$-turquoisecons.com<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>http://www.turquoisecons.com<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>-----Original Message-----<br>
> From: owner-chemistry-$-ccl.net [mailto:owner-chemistry-$-ccl.net] <br>
Sent: Monday, February 27, 2006 10:12 AM<br>
To: Guner, Osman F <br>
Subject: CCL: software pattents in chemistry?</span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Sent to CCL by: Egon Willighagen =
[e.willighagen]_[science.ru.nl]<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Hi all,<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Today I learned that software pattents have hit chemistry,
chemoinformatics in <o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>this case:<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>http://v3.espacenet.com/textdoc?DB=3DEPODOC&amp;IDX=3DWO200500174=
3&amp;F=3D0<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>I have no idea on the impact of this pattent, but was wondering =
if
others saw <o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>more software pattents in chemistry, and wether software =
pattents in <o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>chemistry affected work in our field. =
<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Anyone who has experience with software pattents in =
cheminformatics, <o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>computational chemistry and the =
likes?<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Egon<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>-- <o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>e.willighagen++science.ru.nl<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>PhD student on Molecular Representation in =
Chemometrics<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><st1:PlaceName w:st=3D"on"><font size=3D2 =
face=3D"Courier New"><span
 style=3D'font-size:10.0pt'>Radboud</span></font></st1:PlaceName> =
<st1:PlaceType
w:st=3D"on">University</st1:PlaceType> <st1:City w:st=3D"on"><st1:place =
w:st=3D"on">Nijmegen</st1:place></st1:City><o:p></o:p></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>Blog: =
http://chem-bla-ics.blogspot.com/<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>http://www.cac.science.ru.nl/people/egonw/<o:p></o:p></span></fon=
t></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>GPG: 1024D/D6336BA6<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
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<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
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<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
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<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
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<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
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also<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
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<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
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10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>E-mail to subscribers: CHEMISTRY-$-ccl.net or =
use:<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>=A0=A0=A0=A0=A0 =<o:p></o:p></span></font><=
/p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>E-mail to administrators: CHEMISTRY-REQUEST-$-ccl.net or =
use<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'>=A0=A0=A0=A0=A0 =<o:p></o:p></span></font><=
/p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
style=3D'font-size:
10.0pt'<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D2 face=3D"Courier New"><span =
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nt></p>

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From owner-chemistry@ccl.net Mon Feb 27 20:08:03 2006
From: "Anthony Fejes fejes,,zymeworks.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: software pattents in chemistry?
Message-Id: <-31025-060227193550-9537-HRt02wi6rU1oYmJTjOJirw . server.ccl.net>
X-Original-From: Anthony Fejes <fejes]_[zymeworks.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 27 Feb 2006 16:35:45 -0800
MIME-Version: 1.0


Sent to CCL by: Anthony Fejes [fejes_._zymeworks.com]


For what it's worth, the same figure appears to be included in their 
publication of similar name, and is entirely legible in that format:

  J Chem Inf Comput Sci. 2003 Nov-Dec;43(6):1982-97.

It appears they filed provisional patents, and then proceeded to publish 
the same material.

Anthony Fejes
Zymeworks


Dr. Seth Olsen s.olsen1]![uq.edu.au wrote:
> Sent to CCL by: "Dr. Seth Olsen" [s.olsen1..uq.edu.au]
> 
> Patents happen, but what bothers me most is the excessively small print 
> in that flow chart.  I put it into photoshop to zoom in and read it, but 
> there's just no structure at all.  Hard to avoid infringing on a patent 
> that you can't bloody read.
> Cheers,
> 
> Seth
> 
> Egon Willighagen e.willighagen%a%science.ru.nl wrote:
> 
> 
>>Sent to CCL by: Egon Willighagen [e.willighagen]_[science.ru.nl]
>>
>>Hi all,
>>
>>Today I learned that software pattents have hit chemistry, chemoinformatics in 
>>this case:
>>
>>http://v3.espacenet.com/textdoc?DB=EPODOC&IDX=WO2005001743&F=0
>>
>>I have no idea on the impact of this pattent, but was wondering if others saw 
>>more software pattents in chemistry, and wether software pattents in 
>>chemistry affected work in our field. 
>>
>>Anyone who has experience with software pattents in cheminformatics, 
>>computational chemistry and the likes?
>>
>>Egon
>>
>> 
>>
> 
> 
>


From owner-chemistry@ccl.net Mon Feb 27 20:42:00 2006
From: "Liu Tao liutao_jlu%a%126.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL:G: PCM error termination Gaussian03
Message-Id: <-31026-060227194338-13632-MVFOKb8Oy3pReD8PnUyFOA-#-server.ccl.net>
X-Original-From: "Liu  Tao" <liutao_jlu[]126.com>
Date: Mon, 27 Feb 2006 19:43:35 -0500


Sent to CCL by: "Liu  Tao" [liutao_jlu|-|126.com]
I do geometry optimizations on ~60 atom systems using B3LYP hybrid
functionals on the lanl2dz basis set. I do gas phase optimizations without any problem, but when it comes to SCRF solvation (pcm), my jobs often
crash, with error messages like:


 Polarizable Continuum Model (PCM)
 =================================
 Model                : PCM.
 Atomic radii         : UA0 (Simple United Atom Topological Model).
 Polarization charges : Total charges.
 Charge compensation  : None.
 Solution method      : Matrix inversion.
 Cavity               : GePol (RMin=0.200 OFac=0.890).
                        Default sphere list used, NSphG=   31.
                        Tesserae with average area of 0.200 Ang**2.
 Solvent              : Dichloromethane, Eps     =   8.930000
                               Eps(inf)=   2.020000
                               RSolv   =   2.270000 Ang.
 ------------------------------------------------------------------------------
 Using symmetry in molecular cavity generation.
 AdVTs1: ISph=  196 is engulfed by JSph=  201 but Ae(  196) is not yet zero!
 Error termination via Lnk1e in /usr/people/g03c02/g03/l301.exe at Mon Feb 27 13:13:44 2006.

What does this means?...How to get around it?

Could you kindly help me to solve the problem?
Many thanks!

  Tao Liu
liutao_jlu-*-126.com


From owner-chemistry@ccl.net Mon Feb 27 21:35:00 2006
From: "Ross Walker ross++rosswalker.co.uk" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: software pattents in chemistry?
Message-Id: <-31027-060227212715-15387-MlhDo5MgI87aOVuibu+VxA-*-server.ccl.net>
X-Original-From: "Ross Walker" <ross[*]rosswalker.co.uk>
Content-Transfer-Encoding: 7bit
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	charset="us-ascii"
Date: Mon, 27 Feb 2006 18:27:02 -0800
MIME-Version: 1.0


Sent to CCL by: "Ross Walker" [ross]_[rosswalker.co.uk]

> For what it's worth, the same figure appears to be included in their 
> publication of similar name, and is entirely legible in that format:
> 
>   J Chem Inf Comput Sci. 2003 Nov-Dec;43(6):1982-97.
> 
> It appears they filed provisional patents, and then proceeded 
> to publish 
> the same material.

And this is part of the problem with software patents I feel. If you are
going to patent an algorithm you can't then expect to publish work that uses
that algorithm in peer reviewed journals. The problem being that if you
patent the algorithm you use other researchers can't use that algorithm to
reproduce and verify your work and therefore such work does not belong in a
peer reviewed journal.

Copyrighted code is a very different situation, however, since even if you
use a commercial implementation of an algorithm to do the research other
scientists can simply implement the algorithm described in your paper to
reproduce the results. If the algorithm itself is patented then nobody can
verify your results without paying you royalties.

Thus perhaps the discussion should be whether publication of an algorithm,
by the authors of a patent, in scientific journals then invalidates the
scope of that patent.

Just my 2c.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross-.-rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.


From owner-chemistry@ccl.net Mon Feb 27 22:10:00 2006
From: "John McKelvey jmmckel-$-attglobal.net" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: Antivirus software and VPN clients
Message-Id: <-31028-060227145831-12874-EwnMezvXoMd7fnDrqDRjlA,,server.ccl.net>
X-Original-From: John McKelvey <jmmckel^attglobal.net>
Content-Transfer-Encoding: 7bit
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Date: Mon, 27 Feb 2006 14:53:11 -0500
MIME-Version: 1.0


Sent to CCL by: John McKelvey [jmmckel-$-attglobal.net]

CClers,

This may be off topic, Jan, but perhaps someone on the list can help.

I currently am running 2005 Norton SystemWorks Premier, which of course 
includes their antivirus package.  At the same time I am using  Nortel 
VPN client to connect to a cluster.  Now, I can not do both at the same 
time as Norton antivirus thinks that the VPN client is a worm!!!  I have 
to disable the worm protection part of Norton inorder to get through.  
Am running W2K which connects to the internet through a Netgear firewall 
router. 

Interestingly enough, [;-),  3 weeks of wrangling with various support 
groups got me nowhere in locating the above workaround.  The solution 
above was located in 3 minutes by a colleague using Google!!!

Does anyone have a suggestion for a different approach where I would not 
have to turn off worm protection?  [Have queried Norton on this, but no 
answer yet...]

Best regards, and many thanks!

John McKelvey


From owner-chemistry@ccl.net Mon Feb 27 22:44:00 2006
From: "Andrew Fant fant(-)pobox.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: Antivirus software and VPN clients
Message-Id: <-31029-060227222655-25931-JSIENBhnwSwxnF88kg2VOQ . server.ccl.net>
X-Original-From: Andrew Fant <fant^pobox.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 27 Feb 2006 22:26:44 -0500
MIME-Version: 1.0


Sent to CCL by: Andrew Fant [fant]|[pobox.com]
John McKelvey jmmckel-$-attglobal.net wrote:

> Does anyone have a suggestion for a different approach where I would not 
> have to turn off worm protection?  [Have queried Norton on this, but no 
> answer yet...]

John,
    My gut reaction would be to suggest swapping out the VPN client for ssh, or 
at least using ssh to get out beyond your system through an encrypted tunnel 
using a VNC client of some kind.  It may be impractical (I'm living in an 
essentially Unix-only zone here) but that would be where I would start.

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