From owner-chemistry@ccl.net Tue Oct 13 04:56:01 2009
From: "Tatsiana Kirys nushki : mail.ru" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: Conversion from Torsion Space to Cartesian Conversion from Torsion Spa
Message-Id: <-40452-091013045325-11651-/5skQuMtzqQRhsvn7AvhcQ _ server.ccl.net>
X-Original-From: "Tatsiana  Kirys" <nushki(a)mail.ru>
Date: Tue, 13 Oct 2009 04:53:21 -0400


Sent to CCL by: "Tatsiana  Kirys" [nushki[a]mail.ru]
I need to convert amino acid conformation from torsion space
(chi_1, chi_2, etc) to cartesian space, but couldn't find any programm
on the internet available.

could you please suggest any?

-- 
With regards,
Tatsiana Kirys
Ph.D. student
UIIP NAS of Belarus            mailto:kirys*o*newman.bas-net.by


From owner-chemistry@ccl.net Tue Oct 13 09:38:01 2009
From: "Oellien, F (Frank) frank.oellien()sp.intervet.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: GCC2009 - Last call for registration
Message-Id: <-40453-091013085722-9761-O94Snn+rO+ShSnqXfe7hxQ#,#server.ccl.net>
X-Original-From: "Oellien, F (Frank)" <frank.oellien * sp.intervet.com>
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Date: Tue, 13 Oct 2009 14:57:08 +0200
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Sent to CCL by: "Oellien, F (Frank)" [frank.oellien%a%sp.intervet.com]

Dear Colleague,

The CIC division of the German Chemical Society wants to inform you =
about the upcoming 5. German Conference on Chemoinformatics to be held =
in Goslar, Germany, November 8 - 10,  2009 (http://www.gdch.de/gcc2009 =
). The international conference covers plenary talk, regular talks, and =
posters in the following sessions:

*	Chemoinformatics and Drug Discovcery
*	Chemical Information, Patents, and Databases=20
*	Molecular Modelling=20
*	Computational Material Science and Nanotechnology=20

Please register now by using the online registration form =
(http://www.gdch.de/vas/tagungen/tg/5358/anmeld__e.htm) on our =
conference website at www.gdch.de/gcc2009. The final deadline for =
registration is October 16, 2009.

The scientific programm is available as PDF =
(http://www.gdch.de/vas/tagungen/tg/5358/gcc_prog_2009.pdf) or online =
under http://www.gdch.de/vas/tagungen/tg/5358/program__e.htm

Please consider the conference dinner on Tuesday evening during your =
travel planing.

In addition, there will be 3 workshops in front of the conference on =
Sunday afternoon by Chemical Computing Group, CCDC and the OCHEM team, =
Helmholtz Zentrum, Munich. We will inform you about the details (times, =
lecture halls, ..) on website.
Furthermore, a free-software session will be held on Sunday afternoon.

Visit the conference website at www.gdch.de/gcc2009 for more information =
or access directly the Call-for-Paper PDF =
http://www.gdch.de/vas/tagungen/tg/einlad5358.pdf


I hope to see you in Goslar.=20

Frank Oellien
GDCh CIC Division Chair=20


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::sp.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.
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From owner-chemistry@ccl.net Tue Oct 13 10:13:00 2009
From: "Serghei Glinca glinca*staff.uni-marburg.de" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: Ligand Docking - NAD at active site
Message-Id: <-40454-091013093659-12757-ZY/7HEncFmbVLSTqt46L5Q|-|server.ccl.net>
X-Original-From: "Serghei  Glinca" <glinca(a)staff.uni-marburg.de>
Date: Tue, 13 Oct 2009 09:36:55 -0400


Sent to CCL by: "Serghei  Glinca" [glinca=staff.uni-marburg.de]
Hi everybody,

I want to carry out some docking studies for a protein, where NAD is bound at the active site. How should I treat the binding site? Docking with or without the cofactor? It seems to me that docking with the cofactor at the active site make more sense, if the cofactor is strongly bound. 

I would greatly appreciate any kind of reference!

 
Best regards,
Serghei


From owner-chemistry@ccl.net Tue Oct 13 12:29:01 2009
From: "Ivanciuc, Ovidiu I. oiivanci],[UTMB.EDU" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: Conversion from Torsion Space to Cartesian Conversion from Torsion Spa
Message-Id: <-40455-091013121450-10309-ozpQPf2HSyyzuzE0tQK06w-#-server.ccl.net>
X-Original-From: "Ivanciuc, Ovidiu I." <oiivanci[A]UTMB.EDU>
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Date: Tue, 13 Oct 2009 10:04:15 -0500
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Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci(~)UTMB.EDU]

>>>I need to convert amino acid conformation from torsion space
>>>(chi_1, chi_2, etc) to cartesian space
See MolMol:
http://www.mol.biol.ethz.ch/groups/wuthrich_group/software
Read as DIANA torsion angle file -> Save as PDB

________________________________________
> From: owner-chemistry+oiivanci=3D=3Dutmb.edu(~)ccl.net [owner-chemistry+oiiva=
nci=3D=3Dutmb.edu(~)ccl.net] On Behalf Of Tatsiana Kirys nushki : mail.ru [ow=
ner-chemistry(~)ccl.net]
Sent: Tuesday, October 13, 2009 3:53 AM
To: Ivanciuc, Ovidiu I.
Subject: CCL: Conversion from Torsion Space to Cartesian Conversion from To=
rsion Spa

Sent to CCL by: "Tatsiana  Kirys" [nushki[a]mail.ru]
I need to convert amino acid conformation from torsion space
(chi_1, chi_2, etc) to cartesian space, but couldn't find any programm
on the internet available.

could you please suggest any?

--
With regards,
Tatsiana Kirys
Ph.D. student
UIIP NAS of Belarus            mailto:kirys|,|newman.bas-net.by



-=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Tue Oct 13 14:09:01 2009
From: "David Gallagher gallagher.da=-=gmail.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: COSMOtherm Training Course, USA, 10 Nov 2009
Message-Id: <-40456-091013135051-10932-slb1eHxcP5Gleo4bsz58YA-x-server.ccl.net>
X-Original-From: David Gallagher <gallagher.da:gmail.com>
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Date: Tue, 13 Oct 2009 10:50:46 -0700
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Sent to CCL by: David Gallagher [gallagher.da**gmail.com]
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Training Course:
COSMOtherm hands-on introductory training course with 30 minutes 
presentation and 90 minutes hands-on exercises.

What is <http://cacheresearch.com/cosmo.html>COSMOtherm:
A software tool for a priori prediction of thermodynamic properties 
(such as solubility and phase equilibria), including for complex 
mixtures.  COSMOtherm is based on quantum mechanics and statistical 
thermodynamics methods, and provides a fast and easy method to screen 
thermodynamic properties of compounds, for example, for drug 
solubilities or process chemistry, etc.

Who should attend:
First-time users and those wishing to learn more about 
<http://cacheresearch.com/cosmo.html>COSMOtherm and the prediction of 
thermodynamic properties for solubilities, phase equilibria, process 
chemistry, ionic liquids, etc.

<http://cacheresearch.com/aiche.html#training>Venue and time:
Venue - AIChE in Nashville, TN, USA at Gaylord Opryland Hotel, Room Belmont C.
Time - Tuesday 10 November 2009,  7PM - 9PM.

Cost & prerequisites:
There is no fee, but please bring your own laptop.  A copy of 
COSMOtherm will be provided for your laptop (Windows or Macintosh).

Registration:
To reserve a space, please send an Email to David Gallagher at 
<mailto:Cosmo=-=CACheResearch.com>Cosmo=-=CACheResearch.com with your 
name, institution, location, and application area of interest.

       ----------------------------------------------------------

--=====================_4529437==.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<body>
<b>Training Course:<br>
</b>COSMOtherm hands-on introductory training course with 30 minutes
presentation and 90 minutes hands-on exercises.<br><br>
<b>What is
<a href="http://cacheresearch.com/cosmo.html">COSMOtherm</a>:<br>
</b>A software tool for <i>a priori </i>prediction of thermodynamic
properties (such as solubility and phase equilibria), including for
complex mixtures.&nbsp; COSMOtherm is based on quantum mechanics and
statistical thermodynamics methods, and provides a fast and easy method
to screen thermodynamic properties of compounds, for example, for drug
solubilities or process chemistry, etc.<br><br>
<b>Who should attend:<br>
</b>First-time users and those wishing to learn more about
<a href="http://cacheresearch.com/cosmo.html">COSMOtherm</a> and the
prediction of thermodynamic properties for solubilities, phase
equilibria, process chemistry, ionic liquids, etc. <br><br>
<b><a href="http://cacheresearch.com/aiche.html#training">Venue and
time</a>:<br>
</b>Venue - AIChE in Nashville, TN, USA at Gaylord Opryland Hotel, Room
Belmont C.<br>
Time - Tuesday 10 November 2009,&nbsp; 7PM - 9PM. <br><br>
<b>Cost &amp; prerequisites:<br>
</b>There is no fee, but please bring your own laptop.&nbsp; A copy of
COSMOtherm will be provided for your laptop (Windows or
Macintosh).<br><br>
<b>Registration:<br>
</b>To reserve a space, please send an Email to David Gallagher at
<a href="mailto:Cosmo=-=CACheResearch.com">Cosmo=-=CACheResearch.com</a> with
your name, institution, location, and application area of
interest.<br><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
----------------------------------------------------------<br>
</body>
</html>

--=====================_4529437==.ALT--


From owner-chemistry@ccl.net Tue Oct 13 15:38:00 2009
From: "Alexander Hoepker achoepker[-]gmail.com" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: choice of basis set
Message-Id: <-40457-091013153538-15637-fzj4V11CQTJequlnA00rZQ^-^server.ccl.net>
X-Original-From: Alexander Hoepker <achoepker+*+gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Tue, 13 Oct 2009 15:35:26 -0400
MIME-Version: 1.0


Sent to CCL by: Alexander Hoepker [achoepker~!~gmail.com]
I am calculating geometries and energies of organolithium species
consisting of only second row elements (C,N,Li,O,H) using the B3LYP
functional. So far I have used the standard 6-31G(d) basis set but
have begun to question the activation barriers because I am computing
transition state structures in which an N-Li bond is cleaved. This
would result in considerable charge separation compared to the ground
state and my basis set my not be able to handle such systems.

I am considering diffuse functions as well as additional
polarizations: 6-31++G(d,p)

Could anyone comment on the choice of basis set? Could electron
correlation play a key role that may warrant an augmented cc-PVTZ
basis set?
(To give you a sense of our computational resources: my structures
consist of ~35 heavy atoms for which a frequency calculation on our
computers requires about five hours).


Thanks for your help,

Alexander Hoepker
Cornell University