From owner-chemistry@ccl.net Thu May  8 00:46:01 2008
From: "Joe L m68_x*hotmail.com" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: newbie question on geo opt heavy water
Message-Id: <-36907-080507170924-14694-ww3Y/YDiW707xdxzrmwppw- -server.ccl.net>
X-Original-From: "Joe  L" <m68_x() hotmail.com>
Date: Wed, 7 May 2008 17:09:21 -0400


Sent to CCL by: "Joe  L" [m68_x(_)hotmail.com]
dear netters

I am sorry for this newbie question, I am trying to optimize the geometry of heavy water, the problem is with the isotopes, regular water works fine, but somehow the bond length and angle are the same if i use the isotopes, if someone can give me some help, that'd be greatly appreciated.

thanks

joe
----
this is the job file
#p hf/6-31g opt

hf/6-31g optimization of water

0 1
o
h(iso=2) 1 oh
h(iso=2) 1 oh 2 aoh

oh=0.9
aoh=104.0

298.15 1.0
16
2
2


From owner-chemistry@ccl.net Thu May  8 02:07:01 2008
From: "Hod Greeley hod-ccl/./greeley.org" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: Using FORK and WAIT on typical linux boxes
Message-Id: <-36908-080508020339-11700-ui+blySKpQ3Q1biC0HaDcQ||server.ccl.net>
X-Original-From: "Hod Greeley" <hod-ccl{}greeley.org>
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Date: Wed, 7 May 2008 20:53:11 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: "Hod Greeley" [hod-ccl*greeley.org]
I've written code like this before, although not for fork or wait in
particular.  It's really not hard.  About the only tricky bits are
figuring out the symbol conventions so you can get the Fortran and C to
link and, as mentioned, dealing with the difference in string handling.

Best,
Hod Greeley

> I've seen short C 'wrapper' routines used for this sort of thing; the C
> routine makes the actual call to one of the myriad OS utility routines,
> and provides a Fortran callable interface.  The wrapper usually has to
> handle string conversion, if strings are being passed as arguments.
>
> --
> Rick Venable    5635FL/T906
> Membrane Biophysics Section
> NIH/NHLBI Lab. of Computational Biology
> Bethesda, MD  20892-9314   U.S.A.
> (301) 496-1905  venabler AT nhlbi*nih*gov
>
>
>
> -----Original Message-----
>> From: John McKelvey jmmckel.]|[.gmail.com
>> [mailto:owner-chemistry]|[ccl.net]
> Sent: Wed 07-May-08 5:46 PM
> To: Venable, Richard (NIH/NHLBI) [E]
> Subject: CCL: Using FORK and WAIT on typical linux boxes
>
> CCLERs
>
> Most linux compiler such as gnu and Intel do not have fork and wait in
> their
> libraries.  Is is possib;le to compile the fortran program calling these
> with the Intel fortran compiler, and include the Intel C libraries at link
> time?   Any other suggestions?
>
> Looks like the Lahey/Fujitsu linux fortarn compilers avoid the problem,
> but
> $$$.
>
>
> Thanks!
>
> John McKelvey
>
>


From owner-chemistry@ccl.net Thu May  8 07:15:00 2008
From: "Lukasz Cwiklik cwiklik!A!gmail.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: newbie question on geo opt heavy water
Message-Id: <-36909-080508071121-4391-gWlfLFT5a0AoDbfxHml3xw:server.ccl.net>
X-Original-From: "Lukasz Cwiklik" <cwiklik/a\gmail.com>
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Date: Thu, 8 May 2008 14:11:09 +0300
MIME-Version: 1.0


Sent to CCL by: "Lukasz Cwiklik" [cwiklik : gmail.com]
On Thu, May 8, 2008 at 12:09 AM, Joe L m68_x*hotmail.com
<owner-chemistry++ccl.net> wrote:
>
>  Sent to CCL by: "Joe  L" [m68_x(_)hotmail.com]
>  dear netters
>
>  I am sorry for this newbie question, I am trying to optimize the geometry of heavy water, the problem is with the isotopes, regular water works fine, but somehow the bond length and angle are the same if i use the isotopes, if someone can give me some help, that'd be greatly appreciated.
>
Dear Joe,
Your optimization results are correct. In Born-Oppenheimer
approximation only an electronic structure and nuclei charges matter
and they are identical for both H2O and D2O. Roughly speaking,
only the calculations including kinetic energy of nuclei would be affected
(for instance, vibrational/rotational analysis, molecular dynamics, dG
of solvation).
Best,
Lukasz


-- 
Lukasz Cwiklik
http://cwiklik.wordpress.com


From owner-chemistry@ccl.net Thu May  8 08:08:00 2008
From: "Steve Williams willsd-*-appstate.edu" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: newbie question on geo opt heavy water
Message-Id: <-36910-080508080005-27270-hI3/eA85KRQIAavSg8um4Q=-=server.ccl.net>
X-Original-From: Steve Williams <willsd**appstate.edu>
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Date: Thu, 08 May 2008 07:56:00 -0400
MIME-Version: 1.0


Sent to CCL by: Steve Williams [willsd- -appstate.edu]
I think that all general purpose quantum chemistry programs are based on 
the Born-Oppenheimer approximation (any counter example programs?).  The 
basis for this is the much smaller mass (and much higher velocity) of 
electrons relative to nuclei.  For the lightest nucleus (H) the mass 
ratio is nearly 2000:1 and is significantly larger than this for other 
nuclei.  This means that nuclei move so slowly compared to electrons 
that they can be considered stationary for the purposes of solving the 
electronic Schrodinger equation.  You can regard this as treating every 
nucleus (including H and D) as having the same (infinite) mass.  The 
electronic properties (energies and energy derivatives) are thus 
completely independent of nuclear mass and you'll get the same structure 
for H2O and D2O (or T2O for that matter).  The nuclear masses DO play a 
role in the conversion of energy second derivatives into vibrational 
frequencies, so the (quite useful) prediction of isotopic shifts in IR 
and Raman spectra is possible.
I'm sure you'll find good descriptions of this in any quantum chemistry 
and most computational chemistry text books.
Steve Williams

Joe L m68_x*hotmail.com wrote:
> Sent to CCL by: "Joe  L" [m68_x(_)hotmail.com]
> dear netters
>
> I am sorry for this newbie question, I am trying to optimize the geometry of heavy water, the problem is with the isotopes, regular water works fine, but somehow the bond length and angle are the same if i use the isotopes, if someone can give me some help, that'd be greatly appreciated.
>
> thanks
>
> joe
> ----
> this is the job file
> #p hf/6-31g opt
>
> hf/6-31g optimization of water
>
> 0 1
> o
> h(iso=2) 1 oh
> h(iso=2) 1 oh 2 aoh
>
> oh=0.9
> aoh=104.0
>
> 298.15 1.0
> 16
> 2
> 2>
>
>


From owner-chemistry@ccl.net Thu May  8 09:48:01 2008
From: "Ingo Reulecke ingo.reulecke+*+carus-it.com" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: Chemical programming frameworks
Message-Id: <-36911-080508051320-25839-DpuOjxH2pCKBFTqt0Z8frQ!=!server.ccl.net>
X-Original-From: "Ingo  Reulecke" <ingo.reulecke_._carus-it.com>
Date: Thu, 8 May 2008 05:13:17 -0400


Sent to CCL by: "Ingo  Reulecke" [ingo.reulecke*carus-it.com]
Hello,

I am currently involved in a commercial software project with focus on pharmaceutical research. Part of my responsibility is the choice of an appropriate chemical programming framework which should be able to adress the following problems:

- Import and export of standard chemical file formats (mol2, sdf, pdb, canonical smiles, InChI, structure diagrams)

- Handling and processing of chemical structures

- Normalization (standardization) of chemical structures

- Handling and enumeration of equivalent tautomeric forms and different protonation states

- Calculation of molecular properties (molecular weight, partition coefficient, Hydrogen bond functions, hybridization, aromaticity, molecular fingerprints and measures of similarity)

- Generation of 3D conformation

- Graphical representation (2D structure diagrams, interactive 3D visualization)

- Structure diagram drawing

- Searching capabilities (equality, similarity, substructure, SMARTS, molecular properties)

- Efficient data handling, database support

The software will be implemented in Java and will probably utilze a web-based GUI.

I would appreciate any kind of suggestions, please feel free to contact me directly via email.

Thanks,
Ingo Reulecke

c.a.r.u.s. HMS
Hamburg
Germany


From owner-chemistry@ccl.net Thu May  8 10:27:01 2008
From: "Carsten Wittekindt wittekindt]^[cosmologic.de" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: Announcement: Release of COSMOfrag Version 3.1
Message-Id: <-36912-080508102009-16657-SyRiFbMDgTgNYq5qCWjzkw^^^server.ccl.net>
X-Original-From: Carsten Wittekindt <wittekindt{:}cosmologic.de>
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
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  charset="us-ascii"
Date: Thu, 8 May 2008 15:23:32 +0200
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Sent to CCL by: Carsten Wittekindt [wittekindt__cosmologic.de]

---------------------------------------
COSMOlogic is pleased to

Announce the Release of 

COSMOfrag Version 3.1.
---------------------------------------



COSMOfrag is a tool that enables the use of COSMOtherm for high-throughput 
calculation of physicochemical properties. 
The basic idea of COSMOfrag is to replace the time consuming calculation of 
sigma-profiles with DFT/COSMO calculations by an approximate composition of 
the sigma-profile from fragments of precalculated DFT/COSMO files. 

Among the broad area of application of COSMOfrag, the fast and reliable 
prediction of relevant ADME properties are of special interest for life 
sciences projects. Models for several ADME properties are available for high 
throughput calculations:
	-- Intestinal Absorption Coefficient,
	-- Blood-Brain Partitioning Coefficient,
	-- Binding to Human Serum Albumin,
	-- Octanol-Water Partition Coefficient,
	-- Partition Coefficient between almost any two liquid phases
	-- Water solubility.
	-- Solubility in almost any solvent or solvent mixture

New features of COSMOfrag version 3.1 include:
	-- Improved treatment of large cyclic systems of up to 16 ring atoms.
	-- Improved 1-octanol water partition coefficient prediction.
	-- The COSMofrag database now consists of more then 65000 molecules.
	-- New features to handle stereo centers and E/Z isoers of double bonds.

Pipeline Pilot components are available for standard applications. New 
components can easily be created.

Please contact wittekindt[at]cosmologic.de or  info[at]cosmologic.de for free 
a trial version.
 For further details about our methods and applications refer to our web page 
www.cosmologic.de and www.cosmologic.de/LifeScience/main_LifeScience.html .

-- 
Dr. Carsten Wittekindt
COSMOlogic GmbH & Co. KG		Phone	+49-2171-363667
Burscheider Str. 515 				Fax	+49-2171-73168-9
D-51381 Leverkusen				Email	wittekindt=-=cosmologic.de
Germany						Web	http://www.cosmologic.de


From owner-chemistry@ccl.net Thu May  8 11:02:00 2008
From: "andras.borosy:+:givaudan.com" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: Chemical programming frameworks
Message-Id: <-36913-080508102432-19727-PQpIwvNQopYT19nGeOWqnQ|-|server.ccl.net>
X-Original-From: andras.borosy^givaudan.com
Content-Type: multipart/alternative; boundary="=_alternative 004F1EA8C1257443_="
Date: Thu, 8 May 2008 16:24:11 +0200
MIME-Version: 1.0


Sent to CCL by: andras.borosy(_)givaudan.com
This is a multipart message in MIME format.
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Content-Transfer-Encoding: quoted-printable

Dear Mr. Reulecke,

There are several applications which are capable for that. Why would we=20
need one more?

Sincerely yours,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -=
=20
Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http://www.givaudan.com




"Ingo Reulecke ingo.reulecke+*+carus-it.com" <owner-chemistry^^^ccl.net>=20
Sent by: owner-chemistry^^^ccl.net
08.05.2008 11:13
Please respond to
"CCL Subscribers" <chemistry^^^ccl.net>


To
"Borosy, Andras " <andras.borosy^^^givaudan.com>
cc

Subject
CCL: Chemical programming frameworks







Sent to CCL by: "Ingo  Reulecke" [ingo.reulecke*carus-it.com]
Hello,

I am currently involved in a commercial software project with focus on=20
pharmaceutical research. Part of my responsibility is the choice of an=20
appropriate chemical programming framework which should be able to adress=20
the following problems:

- Import and export of standard chemical file formats (mol2, sdf, pdb,=20
canonical smiles, InChI, structure diagrams)

- Handling and processing of chemical structures

- Normalization (standardization) of chemical structures

- Handling and enumeration of equivalent tautomeric forms and different=20
protonation states

- Calculation of molecular properties (molecular weight, partition=20
coefficient, Hydrogen bond functions, hybridization, aromaticity,=20
molecular fingerprints and measures of similarity)

- Generation of 3D conformation

- Graphical representation (2D structure diagrams, interactive 3D=20
visualization)

- Structure diagram drawing

- Searching capabilities (equality, similarity, substructure, SMARTS,=20
molecular properties)

- Efficient data handling, database support

The software will be implemented in Java and will probably utilze a=20
web-based GUI.

I would appreciate any kind of suggestions, please feel free to contact me =

directly via email.

Thanks,
Ingo Reulecke

c.a.r.u.s. HMS
Hamburg
Germany



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<br><font size=3D2 face=3D"sans-serif">Dear Mr. Reulecke,</font>
<br>
<br><font size=3D2 face=3D"sans-serif">There are several applications which
are capable for that. Why would we need one more?</font>
<br>
<br><font size=3D2 face=3D"sans-serif">Sincerely yours,</font>
<br>
<br><font size=3D2 face=3D"sans-serif">Dr. Andr=E1s P=E9ter Borosy<br>
Scientific Modelling Expert<br>
Fragrance Research<br>
Givaudan Schweiz AG &nbsp;- &nbsp;Ueberlandstrasse 138 &nbsp;- &nbsp;CH-8600
&nbsp;- &nbsp;D=FCbendorf &nbsp;- &nbsp;Switzerland<br>
T:+41-44-824 2164 &nbsp;- &nbsp;F:+41-44-8242926 &nbsp; &nbsp;- &nbsp;http:=
//www.givaudan.com</font>
<br>
<br>
<br>
<br>
<table width=3D100%>
<tr valign=3Dtop>
<td width=3D40%><font size=3D1 face=3D"sans-serif"><b>&quot;Ingo Reulecke i=
ngo.reulecke+*+carus-it.com&quot;
&lt;owner-chemistry^^^ccl.net&gt;</b> </font>
<br><font size=3D1 face=3D"sans-serif">Sent by: owner-chemistry^^^ccl.net</fo=
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<p><font size=3D1 face=3D"sans-serif">08.05.2008 11:13</font>
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<div align=3Dcenter><font size=3D1 face=3D"sans-serif">Please respond to<br>
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<br>
<br>
<br><tt><font size=3D2><br>
Sent to CCL by: &quot;Ingo &nbsp;Reulecke&quot; [ingo.reulecke*carus-it.com=
]<br>
Hello,<br>
<br>
I am currently involved in a commercial software project with focus on
pharmaceutical research. Part of my responsibility is the choice of an
appropriate chemical programming framework which should be able to adress
the following problems:<br>
<br>
- Import and export of standard chemical file formats (mol2, sdf, pdb,
canonical smiles, InChI, structure diagrams)<br>
<br>
- Handling and processing of chemical structures<br>
<br>
- Normalization (standardization) of chemical structures<br>
<br>
- Handling and enumeration of equivalent tautomeric forms and different
protonation states<br>
<br>
- Calculation of molecular properties (molecular weight, partition coeffici=
ent,
Hydrogen bond functions, hybridization, aromaticity, molecular fingerprints
and measures of similarity)<br>
<br>
- Generation of 3D conformation<br>
<br>
- Graphical representation (2D structure diagrams, interactive 3D visualiza=
tion)<br>
<br>
- Structure diagram drawing<br>
<br>
- Searching capabilities (equality, similarity, substructure, SMARTS, molec=
ular
properties)<br>
<br>
- Efficient data handling, database support<br>
<br>
The software will be implemented in Java and will probably utilze a web-bas=
ed
GUI.<br>
<br>
I would appreciate any kind of suggestions, please feel free to contact
me directly via email.<br>
<br>
Thanks,<br>
Ingo Reulecke<br>
<br>
c.a.r.u.s. HMS<br>
Hamburg<br>
Germany<br>
<br>
<br>
<br>
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From owner-chemistry@ccl.net Thu May  8 11:37:00 2008
From: "Rajarshi Guha rguha**indiana.edu" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL: Chemical programming frameworks
Message-Id: <-36914-080508112117-30775-QAfQONfEGdhTx1zgaDzgNQ~!~server.ccl.net>
X-Original-From: Rajarshi Guha <rguha/a\indiana.edu>
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Sent to CCL by: Rajarshi Guha [rguha[a]indiana.edu]
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1


On May 8, 2008, at 5:13 AM, Ingo Reulecke ingo.reulecke+*+carus- 
it.com wrote:
>
> Sent to CCL by: "Ingo  Reulecke" [ingo.reulecke*carus-it.com]
> Hello,
>
> I am currently involved in a commercial software project with focus  
> on pharmaceutical research. Part of my responsibility is the choice  
> of an appropriate chemical programming framework which should be  
> able to adress the following problems:

There are many such toolkits available. On the commercial side, the  
ChemAxon toolkit probably supports all the requirements you list. An  
alternative is the OpenEye toolkit, which is C++, but has Java bindings.

On the open source side, the CDK which is an LGPL Java toolkit  
satisfies a number of the requirements but not all. Since it's open  
source you could add/implement missing stuff, depending on  
inclination and feasibility.

You could also look at RDKit or OpenBabel, but these are C or C++  
toolkits.

I've indicate what features are supported by the CDK (as I know it  
more than the others).

> - Import and export of standard chemical file formats (mol2, sdf,  
> pdb, canonical smiles, InChI, structure diagrams)

Supported by the CDK

> - Handling and processing of chemical structures

Supported by CDK

> - Normalization (standardization) of chemical structures

Supported by CDK

> - Handling and enumeration of equivalent tautomeric forms and  
> different protonation states

Not supported by CDK

> - Calculation of molecular properties (molecular weight, partition  
> coefficient, Hydrogen bond functions, hybridization, aromaticity,  
> molecular fingerprints and measures of similarity)

Supported by CDK

> - Generation of 3D conformation

Not support by CDK (there are a variety of open source tools for this  
including smi23d and OpenBabel)

> - Graphical representation (2D structure diagrams, interactive 3D  
> visualization)

Supported by CDK (2D depiction) and Jmol (3D visualization)

> - Structure diagram drawing

Supported by CDK (via JChemPaint)

> - Searching capabilities (equality, similarity, substructure,  
> SMARTS, molecular properties)

Supported by CDK

> - Efficient data handling, database support

This is not really part of the toolkit, but it's easy to interface  
with JDBC etc. If working with databases, you may also want to  
consider cheminformatics cartridges that integrate toolkits with the  
database (Tigress for PostgreSQL, MyChem for MySQL, gNova for  
PostgreSQL)

- -------------------------------------------------------------------
Rajarshi Guha  <rguha++indiana.edu>
GPG Fingerprint: D070 5427 CC5B 7938 929C  DD13 66A1 922C 51E7 9E84
- -------------------------------------------------------------------
I saw Elvis.  He sat between me and Bigfoot on the UFO.


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From owner-chemistry@ccl.net Thu May  8 16:54:00 2008
From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas . chem.elte.hu" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: Chemical programming frameworks
Message-Id: <-36915-080508165125-4726-Mw+KlHeJCzABDgPI7JDWaQ|*|server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas <farkas#chem.elte.hu>
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Date: Thu, 08 May 2008 21:14:23 +0200
Mime-Version: 1.0


Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas:-:chem.elte.hu]
Hi Ingo,

I think you should check out ChemAxon's cheminformatics programs
portfolio (GUI, Java API, applets, etc.) at
http://www.chemaxon.com/products.html .
These are free for academia, for free web pages, etc.

Good luck.

Best wishes,

Ödön

On Thu, 2008-05-08 at 05:13 -0400, Ingo Reulecke ingo.reulecke+*
+carus-it.com wrote:
> Sent to CCL by: "Ingo  Reulecke" [ingo.reulecke*carus-it.com]
> Hello,
> 
> I am currently involved in a commercial software project with focus on pharmaceutical research. Part of my responsibility is the choice of an appropriate chemical programming framework which should be able to adress the following problems:
> 
> - Import and export of standard chemical file formats (mol2, sdf, pdb, canonical smiles, InChI, structure diagrams)
> 
> - Handling and processing of chemical structures
> 
> - Normalization (standardization) of chemical structures
> 
> - Handling and enumeration of equivalent tautomeric forms and different protonation states
> 
> - Calculation of molecular properties (molecular weight, partition coefficient, Hydrogen bond functions, hybridization, aromaticity, molecular fingerprints and measures of similarity)
> 
> - Generation of 3D conformation
> 
> - Graphical representation (2D structure diagrams, interactive 3D visualization)
> 
> - Structure diagram drawing
> 
> - Searching capabilities (equality, similarity, substructure, SMARTS, molecular properties)
> 
> - Efficient data handling, database support
> 
> The software will be implemented in Java and will probably utilze a web-based GUI.
> 
> I would appreciate any kind of suggestions, please feel free to contact me directly via email.
> 
> Thanks,
> Ingo Reulecke
> 
> c.a.r.u.s. HMS
> Hamburg
> Germany> 
> 
-- 
Ödön Farkas
Associate professor
Deparment of Organic Chemistry and
Laboratory of Chemical Informatics,
Institute of Chemistry,
Eötvös Loránd University, Budapest
Address: 1/A Pázmány Péter sétány,
H-1117 Budapest, Hungary
Phone: +36-1-372-2570
Cell phone: +36-30-255-3111
Fax: +36-1-372-2620
URL: http://organ.elte.hu/farkas


From owner-chemistry@ccl.net Thu May  8 17:32:00 2008
From: "Oellien, F (Frank) Frank.Oellien#%#Intervet.com" <owner-chemistry()server.ccl.net>
To: CCL
Subject: CCL: 4. German Conference on Chemoinformatics - Call for Papers
Message-Id: <-36916-080508172934-22899-rtT1OHlLGJVqBW7/EztKpA()server.ccl.net>
X-Original-From: "Oellien, F (Frank)" <Frank.Oellien- -Intervet.com>
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Date: Thu, 8 May 2008 23:29:16 +0200
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Sent to CCL by: "Oellien, F (Frank)" [Frank.Oellien^^Intervet.com]

                              CALL FOR PAPERS
                 4th German Conference on Chemoinformatics
                  Hotel 'Der Achtermann', Goslar, Germany
                           9 - 11 November 2008

Dear Colleagues,

The CIC division of the German Chemical Society announces the 4. German =
Conference on Chemoinformatics (http://www.gdch.de/gcc2008) to be held =
in Goslar, Germany, November 9 - 11, 2008.

We are inviting the submission of abstracts for talks and posters in the =
following plenary sessions:

* Chemoinformatics and Drug Development
* Chemical Information
* Molecular Modelling
* Computational Material Science and Nanotechnology=20
and other highlights in the field of Computational Chemistry.

We encourage the submission of papers on both applications and case =
studies as well as on method development and algorithmic work.=20

Visit the conference website at www.gdch.de/gcc2008 for more =
information, including a link to the online abstract submission =
interface, a more detailed, downloadable PDF version of the 1. circular =
as well as additional information.

The deadline for the submission of abstracts is 29 July 2008.

Invited Speakers are:
J=FCrgen Bajorath, University of Bonn/D
Michael Berthold, University of Konstanz/D=20
Marcus Elstner, University of Braunschweig/D=20
Robert Glen, Cambridge University/GB=20
Kurt Varmuza, Technical University of Vienna/A=20
Brian Vickery, Chemistry Central, London/GB

Because of the strong increase of the number of attendees during the =
last two conferences, we have had to impose a limit for the number of =
conference participants this year (200 max). So please register early.

http://www.gdch.de/vas/tagungen/tg/circular1.pdf

I hope to see you in Goslar.

Frank Oellien, Conference Chairman

Mit freundlichen Gr=FC=DFen / With kind regards=20

Dr. Frank Oellien
BioChemInformatics Scientist
Intervet Innovation GmbH
Zur Propstei
55270 Schwabenheim, Germany

E-Mail:   	frank.oellien^^intervet.com
Phone:	+49 (6130) 948 365	=09
Fax:	+49 (6130) 948 517	=09
=20
Home    	http://www.intervet.com

Sitz der Gesellschaft: Schwabenheim 	     Amtsgericht Mainz, HRB 23 166	 =
 Gesch=E4ftsf=FChrer: Dr. Peter Schmid

--------------------------------------
This message and any attachments are solely for the intended recipient.

If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited



-- please immediately and permanently delete.
--------------------------------------


From owner-chemistry@ccl.net Thu May  8 18:07:01 2008
From: "David Hughes dwhfelice+/-gmail.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: New software for searching the web for chemical information
Message-Id: <-36917-080508113009-4795-+rWKkXBrzPIeh0pjOJhYaw{=}server.ccl.net>
X-Original-From: "David Hughes" <dwhfelice|gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_17338_18233016.1210253579977"
Date: Thu, 8 May 2008 15:32:59 +0200
MIME-Version: 1.0


Sent to CCL by: "David Hughes" [dwhfelice~~gmail.com]
------=_Part_17338_18233016.1210253579977
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

A friend recently showed me an interesting chemistry application that I
thought members of CCL would like to know about. This application searches
over "all" chemical information that is freely-available on the web,
including the internet itself, using a single search. It is quite easy to
use -- you simply draw a chemical structure, and start a search. You can
also use SDfiles to submit a series of compounds as separate
queries, simplifying searches for starting materials or test compounds.

The application is called "CWM Global Search". You can find information
about it at http://www.akosgmbh.de/globalsearch/index.htm, including a movie
showing the use of Global Search. I note that you can now use this
application for free for 7 days -- a convenient way to see if it would be
helpful to you.

Cheers,
David

David Hughes
Basel, Switzerland

(Apologies for "cross-posting", but I really think this is useful software
to consider.)

------=_Part_17338_18233016.1210253579977
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

<div>A friend recently showed me an interesting chemistry application that I thought members of CCL would like to know about. This application searches over &quot;all&quot; chemical information that is freely-available on the web, including the internet itself, using a single search. It is quite easy to use -- you simply draw a chemical structure, and start a search. You can also use SDfiles to submit a series of compounds as separate queries,&nbsp;simplifying searches for starting materials or test compounds.<br>
&nbsp;<br>The application is called &quot;CWM Global Search&quot;. You can find information about it at <a href="http://www.akosgmbh.de/globalsearch/index.htm">http://www.akosgmbh.de/globalsearch/index.htm</a>, including a movie showing the use of Global Search. I note that you can now use this application for free for 7 days -- a convenient way to see if it would be helpful to you.<br>
&nbsp;<br>Cheers,<br>David<br>&nbsp;<br>David Hughes<br>Basel, Switzerland</div>
<div>&nbsp;</div>
<div>(Apologies for &quot;cross-posting&quot;, but I really think this is useful software to consider.)</div>

------=_Part_17338_18233016.1210253579977--


From owner-chemistry@ccl.net Thu May  8 18:42:01 2008
From: "priscila sarcinelli dos santos priscilasarcinelli]|[yahoo.com.br" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL:G: PES scan
Message-Id: <-36918-080507143713-28086-/MWbWL/AsRsw0laBZtNizA.@.server.ccl.net>
X-Original-From: "priscila sarcinelli dos santos" <priscilasarcinelli]*[yahoo.com.br>
Date: Wed, 7 May 2008 14:37:10 -0400


Sent to CCL by: "priscila sarcinelli dos santos" [priscilasarcinelli[#]yahoo.com.br]

 
 When I doing a PES scan in Gaussian package, I got an error message below.

 DE(Corr)= -0.30544820     E(CORR)=     -397.15055266     Delta= 1.16D-06
 NORM(A)=   0.10934414D+01
 DE(Corr)= -0.30544741     E(CORR)=     -397.15055187     Delta= 7.91D-07
 NORM(A)=   0.10934568D+01
 DE(Corr)= -0.30543967     E(CORR)=     -397.15054413     Delta= 7.74D-06
 NORM(A)=   0.10934495D+01
 DE(Corr)= -0.30544947     E(CORR)=     -397.15055393     Delta=-9.80D-06
 NORM(A)=   0.10934428D+01
 DE(Corr)= -0.30544855     E(CORR)=     -397.15055301     Delta= 9.21D-07
 NORM(A)=   0.10934389D+01
 DE(Corr)= -0.30544816     E(CORR)=     -397.15055262     Delta= 3.82D-07
 NORM(A)=   0.10934358D+01
  *************
 *MAX. CYCLES*
 *************
 Dominant configurations:
 ***********************
 Spin Case        I    J    A    B          Value
   ABAB          13   12   14   13       0.226493D+00
 Largest amplitude= 2.26D-01
 Error termination via Lnk1e in C:\G03W\l913.exe at Tue May 06 21:51:33 2008.
 Job cpu time:  0 days  1 hours 46 minutes 31.0 seconds.

      What keywords should I add, or What can I do to let the calculation go on?
      Any reply will be appreciated. Thank you very much in
  advance!

          Priscila Sarcinelli dos Santos


From owner-chemistry@ccl.net Thu May  8 20:17:00 2008
From: "Antony Williams tony,chemspider.com" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: New software for searching the web for chemical information
Message-Id: <-36919-080508201449-21701-kHFpkl7C2Iv+RIxPaBmfiw{}server.ccl.net>
X-Original-From: "Antony Williams" <tony\a/chemspider.com>
Content-class: urn:content-classes:message
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	boundary="----_=_NextPart_001_01C8B164.2C0F28B5"
Date: Thu, 8 May 2008 19:35:13 -0400
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Sent to CCL by: "Antony Williams" [tony---chemspider.com]
This is a multi-part message in MIME format.

------_=_NextPart_001_01C8B164.2C0F28B5
Content-Type: text/plain;
	charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

David,

I took an early look at this application and was asked whether we were
okay with having ChemSpider as part of the search and I of course agreed
in keeping with our recent Creative Commons announcement.here
http://www.chemspider.com/blog/chemspider-adopts-creative-commons-licens
es.html.

=20

As a user of the system I am interested in your experiences relative to
the online services such as ChemSpider, PubChem or  the Chemical
Structure Lookup Service. What are the advantages from your point of
view (please feel free to connect with me offline).

=20

One comment, and I am sure that people are aware of it, is that the
advertised 100 million structures are of course not unique structures.
The PubChem dataset is on ChemSpider and ChemSpider is on PubChem
(http://www.chemspider.com/blog/pubchem-deposition-of-chemspider-data-is
-well-underway-my-favorite-color-is-green.html). There is a lvery large
amount of overlap between all of the datasets and I based on experience
I would estimate the number of unique structures at around 25-30
million. Do you happen to know what the real number of unique structures
is?

=20

Best wishes

=20

PS. There was an interesting article about ChemSpider published in
Nature yesterday - these systems of "global chemistry searching" are
growing in number.
http://www.chemspider.com/blog/nature-writes-about-chemspider.html

=20

=20

Antony Williams,
URL: www.chemspider.com <http://www.chemspider.com/>=20

Email: antony.williams|,|chemspider.com

Phone: (919) 341-8375

Mobile: (919) 201-1516
Fax: (919) 300-5321

=20

CONFIDENTIALITY NOTICE

Unless expressly stated otherwise, this message is confidential and is
intended for the addressee(s) only.

If you are not an addressee, please inform the sender immediately or
contact feedback|,|chemspider.com.

=20

________________________________

> From: owner-chemistry|,|ccl.net [mailto:owner-chemistry|,|ccl.net]=20
Sent: Thursday, May 08, 2008 9:33 AM
To: Antony Williams
Subject: CCL: New software for searching the web for chemical
information

=20

A friend recently showed me an interesting chemistry application that I
thought members of CCL would like to know about. This application
searches over "all" chemical information that is freely-available on the
web, including the internet itself, using a single search. It is quite
easy to use -- you simply draw a chemical structure, and start a search.
You can also use SDfiles to submit a series of compounds as separate
queries, simplifying searches for starting materials or test compounds.
=20
The application is called "CWM Global Search". You can find information
about it at http://www.akosgmbh.de/globalsearch/index.htm, including a
movie showing the use of Global Search. I note that you can now use this
application for free for 7 days -- a convenient way to see if it would
be helpful to you.
=20
Cheers,
David
=20
David Hughes
Basel, Switzerland

=20

(Apologies for "cross-posting", but I really think this is useful
software to consider.)


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<div class=3DSection1>

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

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>I took an early look at this =
application
and was asked whether we were okay with having ChemSpider as part of the =
search
and I of course agreed in keeping with our recent Creative Commons
announcement.here <a
href=3D"http://www.chemspider.com/blog/chemspider-adopts-creative-commons=
-licenses.html">http://www.chemspider.com/blog/chemspider-adopts-creative=
-commons-licenses.html</a>.<o:p></o:p></span></font></p>

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

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>As a user of the system I am =
interested in
your experiences relative to the online services such as ChemSpider, =
PubChem or
&nbsp;the Chemical Structure Lookup Service. What are the advantages =
> from your
point of view (please feel free to connect with me =
offline).<o:p></o:p></span></font></p>

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

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>One comment, and I am sure that =
people are
aware of it, is that the advertised 100 million structures are of course =
not
unique structures. The PubChem dataset is on ChemSpider and ChemSpider =
is on
PubChem (<a
href=3D"http://www.chemspider.com/blog/pubchem-deposition-of-chemspider-d=
ata-is-well-underway-my-favorite-color-is-green.html">http://www.chemspid=
er.com/blog/pubchem-deposition-of-chemspider-data-is-well-underway-my-fav=
orite-color-is-green.html</a>).
There is a lvery large amount of overlap between all of the datasets and =
I based
on experience I would estimate the number of unique structures at around =
25-30
million. Do you happen to know what the real number of unique structures =
is?<o:p></o:p></span></font></p>

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

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

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

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>PS. There was an interesting =
article about
ChemSpider published in Nature yesterday &#8211; these systems of =
&#8220;global
chemistry searching&#8221; are growing in number. <a
href=3D"http://www.chemspider.com/blog/nature-writes-about-chemspider.htm=
l">http://www.chemspider.com/blog/nature-writes-about-chemspider.html</a>=
<o:p></o:p></span></font></p>

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

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

<div>

<p class=3DMsoNormal><st1:City w:st=3D"on"><st1:place =
w:st=3D"on"><b><font size=3D1
  color=3Dnavy face=3DVerdana><span =
style=3D'font-size:8.0pt;font-family:Verdana;
  =
color:navy;font-weight:bold'>Antony</span></font></b></st1:place></st1:Ci=
ty><b><font
size=3D1 color=3Dnavy face=3DVerdana><span =
style=3D'font-size:8.0pt;font-family:Verdana;
color:navy;font-weight:bold'> Williams,</span></font></b><font size=3D1
color=3Dnavy face=3DVerdana><span =
style=3D'font-size:8.0pt;font-family:Verdana;
color:navy'><br>
<b><span style=3D'font-weight:bold'>URL:</span></b> <a
href=3D"http://www.chemspider.com/" =
title=3D"blocked::http://www.chemspider.com/">www.chemspider.com</a><o:p>=
</o:p></span></font></p>

<p class=3DMsoNormal><b><font size=3D1 color=3Dnavy face=3DVerdana><span
style=3D'font-size:8.0pt;font-family:Verdana;color:navy;font-weight:bold'=
>Email: </span></font></b><font
size=3D1 color=3Dnavy face=3DVerdana><span =
style=3D'font-size:8.0pt;font-family:Verdana;
color:navy'><a href=3D"mailto:antony.williams|,|chemspider.com"
title=3D"blocked::mailto:antony.williams|,|chemspider.com">antony.williams|,|=
chemspider.com</a><o:p></o:p></span></font></p>

<p class=3DMsoNormal><b><font size=3D1 color=3Dnavy face=3DVerdana><span
style=3D'font-size:8.0pt;font-family:Verdana;color:navy;font-weight:bold'=
>Phone:</span></font></b><font
size=3D1 color=3Dnavy face=3DVerdana><span =
style=3D'font-size:8.0pt;font-family:Verdana;
color:navy'> (919) 341-8375<o:p></o:p></span></font></p>

<p class=3DMsoNormal><st1:place w:st=3D"on"><st1:City =
w:st=3D"on"><b><font size=3D1
  color=3Dnavy face=3DVerdana><span =
style=3D'font-size:8.0pt;font-family:Verdana;
  =
color:navy;font-weight:bold'>Mobile</span></font></b></st1:City></st1:pla=
ce><b><font
size=3D1 color=3Dnavy face=3DVerdana><span =
style=3D'font-size:8.0pt;font-family:Verdana;
color:navy;font-weight:bold'>:</span></font></b><font size=3D1 =
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face=3DVerdana><span =
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(919) 201-1516<br>
<b><span style=3D'font-weight:bold'>Fax:</span></b> (919) =
300-5321<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D1 color=3Dnavy face=3DVerdana><span =
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<div>

<p class=3DMsoNormal><b><font size=3D1 color=3Dnavy face=3DVerdana><span
style=3D'font-size:8.0pt;font-family:Verdana;color:navy;font-weight:bold'=
>CONFIDENTIALITY
NOTICE<o:p></o:p></span></font></b></p>

<p class=3DMsoNormal><font size=3D1 color=3Dnavy face=3DVerdana><span =
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style=3D'font-size:
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please
inform the sender immediately or contact <a
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title=3D"blocked::mailto:feedback|,|chemspider.com&#10;mailto:info|,|acdlabs.=
com">feedback|,|chemspider.com</a>.<o:p></o:p></span></font></p>

<p class=3DMsoNormal =
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size=3D3
face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>

<hr size=3D2 width=3D"100%" align=3Dcenter tabindex=3D-1>

</span></font></div>

<p class=3DMsoNormal><b><font size=3D2 face=3DTahoma><span =
style=3D'font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font =
size=3D2
face=3DTahoma><span style=3D'font-size:10.0pt;font-family:Tahoma'>
owner-chemistry|,|ccl.net [mailto:owner-chemistry|,|ccl.net] <br>
<b><span style=3D'font-weight:bold'>Sent:</span></b> Thursday, May 08, =
2008 9:33
AM<br>
<b><span style=3D'font-weight:bold'>To:</span></b> Antony Williams<br>
<b><span style=3D'font-weight:bold'>Subject:</span></b> CCL: New =
software for
searching the web for chemical information</span></font><o:p></o:p></p>

</div>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<div>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>A friend recently showed me an interesting chemistry application =
that I
thought members of CCL would like to know about. This application =
searches over
&quot;all&quot; chemical information that is freely-available on the =
web,
including the internet itself, using a single search. It is quite easy =
to use
-- you simply draw a chemical structure, and start a search. You can =
also use
SDfiles to submit a series of compounds as separate =
queries,&nbsp;simplifying
searches for starting materials or test compounds.<br>
&nbsp;<br>
The application is called &quot;CWM Global Search&quot;. You can find
information about it at <a =
href=3D"http://www.akosgmbh.de/globalsearch/index.htm">http://www.akosgmb=
h.de/globalsearch/index.htm</a>,
including a movie showing the use of Global Search. I note that you can =
now use
this application for free for 7 days -- a convenient way to see if it =
would be
helpful to you.<br>
&nbsp;<br>
Cheers,<br>
David<br>
&nbsp;<br>
David Hughes<br>
<st1:place w:st=3D"on"><st1:City w:st=3D"on">Basel</st1:City>, =
<st1:country-region
 =
w:st=3D"on">Switzerland</st1:country-region></st1:place><o:p></o:p></span=
></font></p>

</div>

<div>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;<o:p></o:p></span></font></p>

</div>

<div>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>(Apologies for &quot;cross-posting&quot;, but I really think =
this is
useful software to consider.)<o:p></o:p></span></font></p>

</div>

</div>

</div>

</body>

</html>

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From owner-chemistry@ccl.net Thu May  8 21:59:01 2008
From: "Bryan Bishop kanzure-*-gmail.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Chemical programming frameworks
Message-Id: <-36920-080508195623-20249-37K8EDXne2BYxfhFMQsZfQ^_^server.ccl.net>
X-Original-From: "Bryan Bishop" <kanzure=gmail.com>
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Thu, 8 May 2008 17:51:28 -0500
MIME-Version: 1.0


Sent to CCL by: "Bryan Bishop" [kanzure]![gmail.com]
On Thu, May 8, 2008 at 4:13 AM, Ingo Reulecke
ingo.reulecke+*+carus-it.com <owner-chemistry:_:ccl.net> wrote:
> Part of my responsibility is the choice of an appropriate chemical programming framewor

You may be interested in:
http://heybryan.org/mediawiki/index.php/Comp_chem_linkdump

It's my notes on computational chemistry packages. Please feel free to
dump more links on the page, I know that I havent' scouted the entire
web re: the simulation frameworks, so there's more to do.

- Bryan