From owner-chemistry@ccl.net Wed Jul 25 05:47:01 2007
From: "Christoph Steinbeck c.steinbeck ~ uni-koeln.de" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: 3. German Conference on Chemoinformatics - Second Call for Papers
Message-Id: <-34792-070725052635-11123-BiL21x1fDol12XcdN5tYxQ[*]server.ccl.net>
X-Original-From: Christoph Steinbeck <c.steinbeck-$-uni-koeln.de>
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Sent to CCL by: Christoph Steinbeck [c.steinbeck#%#uni-koeln.de]
Dear Colleagues,

this is the second call for papers for the 3. German Conference on
Chemoinformatics (http://www.gcc-cic.de) to be held in Goslar, Germany,
November 11-13, 2007. The conference language is English.

We are inviting the submission of abstracts for talks and posters in the
following areas

* Chemoinformatics and Drug Development
* Chemical Information
* Molecular Modeling
* Computational Material Science and Nanotechnology

Conference Web site:
http://www.gcc-cic.de

The conference website has links to the abstract submission interface, a
PDF version of the first circular as well as additional information.

Conference Venue:
Hotel Der Achtermann, Rosentorstrae 20, D-38640 Goslar, Germany
Goslar is located at the heart of Germany and famous for its ore mine
(UNESCO World Heritage Site) and its old town.
http://www.hotel-der-achtermann.de

Invited Speakers:
Juergen Bajorath
Thomas Frauenheim
Steve Heller
Alexander Hillisch
Tudor Oprea
Alexander Tropsha

Dead Lines:
Submission of oral contribution: 31.07.2007
Submission of posters: 31.07.2007
Scholarship: 02.08.2007
Submission of last-minute-poster: 05.11.2007

Contact:
Gesellschaft Deutscher Chemiker e.V.
Congressteam/ GCC 2007
Membership / Scientific and Regional Divisions
P. O. Box 90 04 40
60444 Frankfurt am Main
GERMANY
Phone: +49/69/7917-358 (Simone Schmidt)
Fax:     +49/69/7917-475
E-Mail: tg:_:gdch.de

Information about the scientific programme:
Prof. Dr. Achim Zielesny
Fachhochschule Gelsenkirchen
Fachbereich Angewandte Naturwissenschaften
August-Schmidt-Ring 10
45665 Recklinghausen
GERMANY
Phone: +49 2361 915-530
Fax:     +49 2361 915-484
E-Mail: achim.zielesny:_:fh-gelsenkirchen.de

Information about the exhibition:
Dr. Frank Oellien
Intervet Innovation GmbH
Zur Probstei
55270 Schwabenheim
GERMANY
Phone: +49 6130 948-365
Fax:     +49 6130 948-517
E-Mail:frank.oellien:_:intervet.com

Regards,

Christoph Steinbeck
(Chairman CIC)

-- 
PD Dr. Christoph Steinbeck (christoph.steinbeck:_:uni-tuebingen.de)
Lecturer in Chemoinformatics Univ. Tuebingen, WSI-RA, Sand 1, D-72076
Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax: (+49/0)
7071-29-5091 What is man but that lofty spirit - that sense of
enterprise. ... Kirk, "I, Mudd," stardate 4513.3..


From owner-chemistry@ccl.net Wed Jul 25 08:43:01 2007
From: "Narendra narendrax++gmail.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL: Hi
Message-Id: <-34793-070724085219-1005-w4tUXVfBNyCTL+PbHV8l4A..server.ccl.net>
X-Original-From: Narendra <narendrax]=[gmail.com>
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Sent to CCL by: Narendra [narendrax{:}gmail.com]
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Hi every one! can any one suggest me any good software too to create
z-matrix input files to run calculations in Gauss03.

Thank for your attention

Narendra

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<div>Hi every one! can any one suggest me any good software too to create z-matrix input files to run calculations in Gauss03.</div>
<div>&nbsp;</div>
<div>Thank for your attention&nbsp;</div>
<div>&nbsp;<br>Narendra<br>&nbsp;</div>

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From owner-chemistry@ccl.net Wed Jul 25 11:01:00 2007
From: "Yubo Fan yubofan|-|mail.chem.tamu.edu" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: hydroxide for dock
Message-Id: <-34794-070725105103-29764-iOp7WLDunAWG1bU8y4Dvig+*+server.ccl.net>
X-Original-From: "Yubo Fan" <yubofan##mail.chem.tamu.edu>
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Sent to CCL by: "Yubo Fan" [yubofan[A]mail.chem.tamu.edu]

This is a multi-part message in MIME format.

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Hi, everyone,

I'm preparing structures with Chimera for docking with Dock6. There is a =
Zn-coordinating hydroxide that I want to keep in the structure. When I =
prepare dock files, Chimera always treat it as a water. Is there any way =
to define it as a hydroxide in Chimera?

Thanks,

Yubo
=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=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
Dr. Yubo Fan               Email: yubofan{}mail.chem.tamu.edu
Department of Chemistry    Tel:   1-979-845-5237
Texas A&M University
College Station, TX 77843
=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=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
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.6000.16481" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Hi, everyone,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I'm preparing structures with Chimera =
for docking=20
with Dock6. There is a Zn-coordinating hydroxide that I want to keep in =
the=20
structure. When I prepare dock files, Chimera always treat it as a =
water. Is=20
there any way to define it as a hydroxide in Chimera?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thanks,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Yubo</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>=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=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<BR>Dr. Yubo=20
Fan&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;=20
Email: <A=20
href=3D"mailto:yubofan{}mail.chem.tamu.edu">yubofan{}mail.chem.tamu.edu</A>=
<BR>Department=20
of Chemistry&nbsp;&nbsp;&nbsp; Tel:&nbsp;&nbsp; 1-979-845-5237<BR>Texas =
A&amp;M=20
University<BR>College Station, TX=20
77843<BR>=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=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</FONT></DIV></BODY></HTML>

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From owner-chemistry@ccl.net Wed Jul 25 11:36:00 2007
From: "Marcin Krol mykrol:_:cyf-kr.edu.pl" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL:G: Hi
Message-Id: <-34795-070725111644-5961-SCiQN1fFY7RJCjB32AOGOw---server.ccl.net>
X-Original-From: Marcin Krol <mykrol^cyf-kr.edu.pl>
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Date: Wed, 25 Jul 2007 15:37:49 +0100
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Sent to CCL by: Marcin Krol [mykrol[#]cyf-kr.edu.pl]
If you want to build molecules from scratch using a database of 
templates try ebuilder 
(http://ecce.emsl.pnl.gov/cgi-bin/help/toolhelp?builder).
Molden is also very good (http://www.cmbi.ru.nl/molden/molden.html)
I think that you can also get DS Studio viewer for free from accelrys 
which you can use to build molecules from scratch.
Remember that you don't need to create z-matrix files to run g03 jobs, 
simple xyz file is fine.
Hope this helps
Marcin

> Hi every one! can any one suggest me any good software too to create 
> z-matrix input files to run calculations in Gauss03.
>  
> Thank for your attention 
>  
> Narendra
>


From owner-chemistry@ccl.net Wed Jul 25 12:11:00 2007
From: "Ramon Crehuet rcsqtc.*_*.iiqab.csic.es" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL:G: electric field and MP2
Message-Id: <-34796-070725113713-16331-htjth6KDOE13Obn5B+J3vg*_*server.ccl.net>
X-Original-From: Ramon Crehuet <rcsqtc(0)iiqab.csic.es>
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Date: Wed, 25 Jul 2007 17:36:47 +0200
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Sent to CCL by: Ramon Crehuet [rcsqtc#%#iiqab.csic.es]
Sorry, my last post was scrambled for an unknown reason...

Dear all,
We would like to perform an MP2 calculation under an external uniform 
electric field (FIELD keyword) in gaussian 03.
Although the manual does not state that this is impossible, we get an 
error message saying that only single point, force and scan calculations 
are possible (which seems to suggest that gradients are available...) 
Besides, other groups seem to have performed geometry optimisations with 
MP2 and a field (see for instance JCP, 124, 094308, (2006)). I was 
wondering if it may depend on the gaussian version, though I could not 
find anything on the on-line release notes. In our supercomputing center 
we have the Gaussian 03 C02.
Thanks for your attention,
Ramon

PS. This is an example of a problematic input:

#N MP2/6-31+G(d)
opt=z-matrix nosymm field=z+120

h2

0 1
H
H 1 r1

r1 0.8


From owner-chemistry@ccl.net Wed Jul 25 12:46:00 2007
From: "Elaine Meng meng]*[cgl.ucsf.edu" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: hydroxide for DOCK
Message-Id: <-34797-070725120258-3113-o/3LJNpzR+8/BpbyMYDK7A||server.ccl.net>
X-Original-From: "Elaine  Meng" <meng .. cgl.ucsf.edu>
Date: Wed, 25 Jul 2007 12:02:55 -0400


Sent to CCL by: "Elaine  Meng" [meng]^[cgl.ucsf.edu]
Dear Yubo,
I could answer more precisely if I could see the file, but without seeing
it, I recommend:

(a) looking at the residue name of the hydroxide in the text of the file.
Is it WAT or HOH?  If so, you could edit it to a different name, say XOH
or HOM.
  
(b) then, run Dock Prep in Chimera including hydrogen addition and all the
steps before that (but don't assign charges or write the Mol2 file).

(c) check the structure; if hydrogen is added where you didn't want it,
simply delete it.  For example, Ctrl-click to select an atom and use
"Actions... Atoms/Bonds... delete" in the menu to delete it.

The protonation states are intended to be reasonable at physiological pH,
but if a group is expected to have a perturbed pKa (for example, in an
active site or near an ion), it is a good idea to check it and manually
add/delete hydrogens as needed. ( more details in
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html
)

(d) run Dock Prep again with only the steps AFTER hydrogen addition 
(charge assignment and Mol2 file output) turned on.  If it asks for the
net charge of XOH (or whatever you named it), indicate -1.

(e) that procedure will use Antechamber to calculate the partial charges on
the hydroxide O and H.  If, however, you already know the charges you want
to use for these atoms, you can edit the charge values in the output
Mol2 file.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng/a\cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html

p.s. questions like this could be sent to chimera-users/a\cgl.ucsf.edu or
 dock-fans/a\docking.org ... I will send a copy to the former


From owner-chemistry@ccl.net Wed Jul 25 13:30:00 2007
From: "Raymond C. Fort Jr. rcfort|*|maine.edu" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL:G: Hi
Message-Id: <-34798-070725124715-5139-HxjZhPvHZpN2K99ziqu/lg-$-server.ccl.net>
X-Original-From: "Raymond C. Fort Jr." <rcfort---maine.edu>
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Date: Wed, 25 Jul 2007 11:46:54 -0400
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Sent to CCL by: "Raymond C. Fort Jr." [rcfort#%#maine.edu]
At 07:56 AM 7/24/2007, you wrote:
>Hi every one! can any one suggest me any good software too to create 
>z-matrix input files to run calculations in Gauss03.
>
>Thank for your attention
>
>Narendra

The best thing about Z-matrices is that you can write them by hand.  See

http://chemistry.umeche.maine.edu/Modeling/Gaussian.html



>

Professor Ray Fort Jr.                  rcfort]^[maine.edu
Department of Chemistry         chemistry.umeche.maine.edu/fort.html
University of Maine                     Voice: (207)-581-1180
Orono, ME 04469                 FAX: (207)-581-1191

Computer modeling of organic and biomolecules; chemistry of lignin 
and cellulose


From owner-chemistry@ccl.net Wed Jul 25 14:18:00 2007
From: "Hoa Nguyen hoagiaonguyen|,|yahoo.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL:G: Hi
Message-Id: <-34799-070725140127-24867-YWhLm4nzs4gos34oDW1vDQ]*[server.ccl.net>
X-Original-From: Hoa Nguyen <hoagiaonguyen-.-yahoo.com>
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Sent to CCL by: Hoa Nguyen [hoagiaonguyen%%yahoo.com]
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MolDesign from cse-online.net can help you creat z-matrix structure from cartesian structure in a gaussian input.

Hoa Nguyen
Department of Chemistry
University of Utah

"Narendra narendrax++gmail.com" <owner-chemistry/./ccl.net> wrote: Hi every one! can any one suggest me any good software too to create z-matrix input files to run calculations in Gauss03.
  
 Thank for your attention 
  
Narendra
 
 

       
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MolDesign from cse-online.net can help you creat z-matrix structure from cartesian structure in a gaussian input.<br><br>Hoa Nguyen<br>Department of Chemistry<br>University of Utah<br><br><b><i>"Narendra narendrax++gmail.com" &lt;owner-chemistry/./ccl.net&gt;</i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> <div>Hi every one! can any one suggest me any good software too to create z-matrix input files to run calculations in Gauss03.</div> <div>&nbsp;</div> <div>Thank for your attention&nbsp;</div> <div>&nbsp;<br>Narendra<br>&nbsp;</div> </blockquote><br><p>&#32;
      <hr size=1>Choose the right car based on your needs.  
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--0-829562442-1185382879=:74732--


From owner-chemistry@ccl.net Wed Jul 25 14:53:00 2007
From: "DONALD MKHONTO mkhonto++wisc.edu" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: SURFACE ENERGY CALCULATION FROM FORCITE
Message-Id: <-34800-070725131650-26826-s3MeTf3BJvDvEX8NgB5rVw%a%server.ccl.net>
X-Original-From: DONALD MKHONTO <mkhonto#wisc.edu>
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Sent to CCL by: DONALD MKHONTO [mkhonto_._wisc.edu]
Hi Alexander

Thank your responce and the for the paper. I like the comparison in there and is usefull to me. I apreciate.

Donald

----- Original Message -----
> From: "Dr. Alexander Hofmann ah^-^chemie.hu-berlin.de" <owner-chemistry*ccl.net>
Date: Tuesday, July 24, 2007 3:24 am
Subject: CCL: SURFACE ENERGY CALCULATION FROM FORCITE
To: "Mkhonto, Donald " <mkhonto*wisc.edu>


>  Sent to CCL by: "Dr. Alexander Hofmann" [ah**chemie.hu-berlin.de]
>  Hi Donald,
>  
>  I cannot exactly answer the question, but I like the way they do in 
> the 
>  following article:
>  
>  V. Fiorentini and M. Methfessel, J. Phys.: Condens. Matter, 1996, 8, 
> 6525.
>  
>  They compare different approaches and discuss the convergence 
> behaviour. 
>  Very useful and general!
>  
>  Best regards
>  
>  Alexander
>  
>  Donald mkhonto mkhonto_._wisc.edu wrote:
>  > Sent to CCL by: "Donald  mkhonto" [mkhonto**wisc.edu]
>  > Does anyone know how to calculate surface energy using the FORCITE 
> software from accelrys materials studio. The surface energy is U = 
> (U-surface - U-bulk)/Area, where U-surface is the energy of the 
> surface and U-bulk is the energy of the bulk (species equal in number 
> to the species contained in the surface) and is devided by the surface 
> area. I am trying to figure out how the energy of the bulk can be 
> calculated from FORCITE when the surface has been constructed to be a 
> 3D crystal with a vaccum slab. Could be the same with a 2D slab I 
> guess. Programes like METADISE and MRVIN would reprouce "the same" 
> surface energy and am looking at ways of using accelrys to do the same 
> and add some organic adsorbates on surfaces. I'll appreciate your help 
> and I hope my question will be clear to everyone.
>  > 
>  > Donald
>  > mkhonto|,|wisc.edu> 
>  > 
>  > 
>  
>  -- 
>  
>  Dr. Alexander Hofmann
>  
>  Humboldt-Universitaet zu Berlin
>  Institut fuer Chemie
>  Arbeitsgruppe Quantenchemie
>  
>  Post:     Unter den Linden 6
>             10099 Berlin
>  Visitors: Brook-Taylor-Strasse 2
>             12489 Berlin
>  
>  ah chemie.hu-berlin.de
>     **
>  
>  Tel.: +49-30-2093-7138
>  Fax.: +49-30-2093-7136
>  
>  http://www.chemie.hu-berlin.de/ag_sauer/index.html
>  
>  PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35
>  
>  
>  
>  -= This is automatically added to each message by the mailing script 
> =->  
>  
>  
>


From owner-chemistry@ccl.net Wed Jul 25 17:49:01 2007
From: "Young Leh youngleh++gmail.com" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: Reaction Rate Theory in Solution
Message-Id: <-34801-070725174748-9806-SILgWe0tlQOudVxlRewCAg=-=server.ccl.net>
X-Original-From: "Young  Leh" <youngleh(!)gmail.com>
Date: Wed, 25 Jul 2007 17:47:44 -0400


Sent to CCL by: "Young  Leh" [youngleh=-=gmail.com]
Dear CCLer,

I am thinking of estimating reaction rate in solutions.  Will transition state theory or absolute rate theory work  in this case?  Any difference with gas phase reaction?