From owner-chemistry@ccl.net Wed Mar 26 04:40:00 2008
From: "Justin Finnerty justin.finnerty!=!uni-oldenburg.de" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: Cannot allocate memory for Gaussian.
Message-Id: <-36548-080326043535-29168-WLKTcWMloimdmWILcHdCGA**server.ccl.net>
X-Original-From: Justin Finnerty <justin.finnerty-x-uni-oldenburg.de>
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Date: Wed, 26 Mar 2008 09:35:00 +0100
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Sent to CCL by: Justin Finnerty [justin.finnerty!A!uni-oldenburg.de]
On Tue, 2008-03-25 at 16:51 -0400, Roman D Gorbunov
rgorbuno]^[aecom.yu.edu wrote:
> Sent to CCL by: "Roman D Gorbunov" [rgorbuno++aecom.yu.edu]
> Dear CCL Subscribers,
> 
> I try to allocate memory for the Gaussian program (I put "%mem=3000MB" in the Gaussian input file). As the result I get:
> galloc:  could not allocate memory.: Cannot allocate memory
> 
> It is strange since with top-command I can see the following:
> Mem:   4050152k total,   870400k used,  3510500k free,    98756k buffers

Check what the OS limits are (ulimit -a or ulimit -m).  We get this
error under a PBS queuing system when the user attempts to allocate more
memory than asked for in the job request because the queue system sets
the memory limit.  I have noticed that some linux distributions are
setting these limits auto"magic"ally (eg core dump size = 0k).

Cheers
	Justin


-- 
Dr Justin Finnerty
Rm W3-1-165         Ph 49 (441) 798 3726
Carl von Ossietzky Universität Oldenburg


From owner-chemistry@ccl.net Wed Mar 26 06:25:01 2008
From: "Andrzej Eilmes eilmes[-]chemia.uj.edu.pl" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: CTTC V abstract submission
Message-Id: <-36549-080326062130-28765-gK1ftkuwBwW0CU+N/IJaxg%%server.ccl.net>
X-Original-From: Andrzej Eilmes <eilmes() chemia.uj.edu.pl>
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Date: Wed, 26 Mar 2008 11:21:13 +0100 (CET)
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Sent to CCL by: Andrzej Eilmes [eilmes*|*chemia.uj.edu.pl]
Dear CCL subscribers,

Deadline for abstract submission (1 April 2008) for the Conference "Current 
Trends in Theoretical Chemistry V" is approaching. The CTTC V Conference 
will take place in Krakow, Poland 6-10 July 2008. 

All information about the conference (including the list of invited 
speakers) is available at the conference web page:
http://www.chemia.uj.edu.pl/cttc5/

The on-line registration form and the guidelines for abstract preparation 
are accesible at the same URL. 

We are looking forward to welcoming you in Krakow in July,

Andrzej Eilmes and Jacek Korchowiec, CTTC V Chairmen

--
Current Trends in Theoretical Chemistry V
6-10 July 2008, Krakow, Poland

http://www.chemia.uj.edu.pl/cttc5/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- 
----------------------------------------------------------------
 dr hab. Andrzej Eilmes                 eilmes^^chemia.uj.edu.pl
 Wydzial Chemii, Uniw. Jagiellonski, Ingardena 3, 30-060 Krakow
 Faculty of Chemistry,  Jagiellonian University, Krakow, Poland
 Phone: (48-12) 6632030                    Fax: (48-12) 6340515
----------------------------------------------------------------


From owner-chemistry@ccl.net Wed Mar 26 08:35:00 2008
From: "may abdelghani may01dz]|[yahoo.fr" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: NBO3.1 vr NBO 5.0 transition metals binding treatment
Message-Id: <-36550-080326071816-24082-t1IUmQLoq/k3C7ABacrNqQ^server.ccl.net>
X-Original-From: may abdelghani <may01dz ~~ yahoo.fr>
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Date: Wed, 26 Mar 2008 11:23:35 +0100 (CET)
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Sent to CCL by: may abdelghani [may01dz%a%yahoo.fr]
dear CCL'ers
I know that the fifth version of NBO program ( NBO
5.0), contains extensive capabilities related
transition metal bonding, I ask if the old one, NBO
3.1, have this capability, is can described the
transition metals binding (metallic bond)?
thanks,
may abdelghani



      _____________________________________________________________________________ 
Envoyez avec Yahoo! Mail. Capacité de stockage illimitée pour vos emails. http://mail.yahoo.fr


From owner-chemistry@ccl.net Wed Mar 26 09:45:01 2008
From: "Tommy Ohyun Kwon ohyun.kwon*o*chemistry.gatech.edu" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: TiO2 nanocluster coordinates
Message-Id: <-36551-080326083226-31371-rsHEOiLM8Kroy5ID8Dt9Uw**server.ccl.net>
X-Original-From: Tommy Ohyun Kwon <ohyun.kwon_-_chemistry.gatech.edu>
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Date: Wed, 26 Mar 2008 08:02:31 -0400
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Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon[a]chemistry.gatech.edu]
Dear CCLers'
I would greatly appreciate it if anyone could send me the xyz coordinates or
cif files of TiO2 nanoclusters. Larger size cluster such as (TiO2)38 would be
ok.
Thank you very much for your kind attention.
Looking forward to hearing from you soon.

Sincerely,

Tommy

--
Tommy Ohyun Kwon, Ph.D
School of Chemistry and Biochemistry
Georgia Institute of Technology
Atlanta Georgia, 30332
Email: ohyun.kwon_-_chemistry.gatech.edu


From owner-chemistry@ccl.net Wed Mar 26 14:35:00 2008
From: "David Price d.w.price/./reading.ac.uk" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian03 BIG memory problem
Message-Id: <-36552-080326143231-28560-37K8EDXne2BYxfhFMQsZfQ!^!server.ccl.net>
X-Original-From: "David  Price" <d.w.price:+:reading.ac.uk>
Date: Wed, 26 Mar 2008 14:32:25 -0400


Sent to CCL by: "David  Price" [d.w.price/a\reading.ac.uk]

      I am trying a reasonably big problem with Gaussian03 rev D.02 at the unrestricted MP4 level.  The problem needs about 130 GB of memory to store all the integrals etc in core.  I am running on an SGI Altix (Itanium II)with 1 TB of RAM over 8 CPUs (PEs).  The calculation completes if I run with any memory up to 80 GB (and stores about 100 GB of .rwf files).  If I use 96GB or 128 MB (or more!) the the calculation fails to complete and crashes without any errors. I have tries many combinations of keywords (incore, etc) with no luck.
      Anyone have any (good) ideas?
      Cheers,
             Dave


From owner-chemistry@ccl.net Wed Mar 26 17:35:01 2008
From: "Nuno A. G. Bandeira nuno.bandeira(a)ist.utl.pt" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: {Spam?} Re: CCL: TiO2 nanocluster coordinates
Message-Id: <-36553-080326155152-25082-fA+22vO2sbYOEdAewBZhOw[*]server.ccl.net>
X-Original-From: "Nuno A. G. Bandeira" <nuno.bandeira]-[ist.utl.pt>
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Date: Wed, 26 Mar 2008 18:44:58 +0000
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Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira===ist.utl.pt]
Tommy Ohyun Kwon ohyun.kwon*o*chemistry.gatech.edu escreveu:
> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon[a]chemistry.gatech.edu]
> Dear CCLers'
> I would greatly appreciate it if anyone could send me the xyz coordinates or
> cif files of TiO2 nanoclusters. Larger size cluster such as (TiO2)38 would be
> ok.
> Thank you very much for your kind attention.
> Looking forward to hearing from you soon
There are 125 xray structures for TiO2 in the Karlsruhe ICSD database. 
Could you be more specific ?

-- 
Nuno A. G. Bandeira, AMRSC  
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group, 
Faculty of Science 
University of Lisbon - C8 building, Campo Grande, 
1749-016 Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html 
Doctoral student ~~ IST,Lisbon
--


From owner-chemistry@ccl.net Wed Mar 26 18:29:00 2008
From: "aa aa(!)chemaxon.hu" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL: ChemAxon Chinese cheminformatics overview and Free Academic Package seminar series: April 21-24, Chengdu, Changsha, Beijing, Hangzhou, China
Message-Id: <-36554-080326182715-27465-3BJK3toJGOsUzCaMkOZIEQ-.-server.ccl.net>
X-Original-From: aa <aa+*+chemaxon.hu>
Content-Type: multipart/alternative;
 boundary="------------070300020609050807070302"
Date: Wed, 26 Mar 2008 18:26:52 -0400
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Sent to CCL by: aa [aa*_*chemaxon.hu]
This is a multi-part message in MIME format.
--------------070300020609050807070302
Content-Type: text/plain; charset=iso-8859-1; format=flowed
Content-Transfer-Encoding: 7bit

Please excuse cross postings. To see Chinese language version of this 
information please visit: http://www.chemaxon.com/kanji2/China_0408.html

*ChemAxon announces a series of lectures and demonstrations taking place 
between April 21st and 24th at Universities in Chengdu, Changsha, 
Beijing and Hangzhou, China.*

Dr. Zhenbin Li will present "Cheminformatics and Its Role in Biological 
and Pharmaceutical Research and Development" which will be followed by 
"An Introduction to ChemAxon's Free Academic Package" and demonstration 
of ChemAxon software by Alex Allardyce of ChemAxon. All presentations 
are in Chinese or with Chinese translation.

The seminars are open to all comers.

Locations and timings:

    * April 21st 9:30 Chemistry building, College of Chemistry, Sichuan
      University, Chengtu, China
    * April 22nd 9:30 College of Chemistry and Chemical Engineering,
      Central South University, Changsha, China
    * April 23rd 14:30 Institute of Process Engineering Chinese Academy
      of Sciences, Beijing, China
    * April 24th 14:30 Department of Chemistry, Zhejiang University,
      Hangzhou, China

Topics to include

    * What is cheminformatics?
    * Drug discovery process and its reality
    * Components and methodologies
    * SAR, QSAR, and drug-like properties
    * Modeling, CAMD, and optimization
    * Challenges pharmaceutical and biotechnology companies are facing
    * Technologies and expertise biotechnology and pharmaceutical
      companies are seeking
    * Tools commercially available
    * Live demonstration of ChemAxon functionality
    * ChemAxon?s free Academic Package and other free provision of software

To confirm attendance and receive notifications of event location please 
email "aa__,__chemaxon__.__com".

To find out more about ChemAxon's free software and Academic Package and 
to download, please visit: http://www.chemaxon.com/prices.html

Please do forward this message to those of interest.

Many thanks.

Alex
--

Alex Allardyce
Dir. Marketing, ChemAxon


--------------070300020609050807070302
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 7bit

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
</head>
<body bgcolor="#ffffff" text="#000000">
Please excuse cross postings. To see Chinese language version of this
information please visit: <a moz-do-not-send="true"
 href="http://www.chemaxon.com/kanji2/China_0408.html">http://www.chemaxon.com/kanji2/China_0408.html</a><br>
<br>
<b>ChemAxon announces a series of lectures and demonstrations taking
place between April 21st and 24th at Universities in Chengdu, Changsha,
Beijing and Hangzhou, China.</b><br>
<br>
Dr. Zhenbin Li will present "Cheminformatics and Its Role in Biological
and Pharmaceutical Research and Development" which will be followed by
"An Introduction to ChemAxon's Free Academic Package" and demonstration
of ChemAxon software by Alex Allardyce of ChemAxon. All presentations
are in Chinese or with Chinese translation. <br>
<br>
The seminars are open to all comers. <br>
<br>
Locations and timings:
<ul>
  <li>April 21st 9:30 Chemistry building, College of Chemistry, Sichuan
University, Chengtu, China</li>
  <li>April 22nd 9:30 College of Chemistry and Chemical Engineering,
Central South University, Changsha, China</li>
  <li>April 23rd 14:30 Institute of Process Engineering Chinese Academy
of Sciences, Beijing, China</li>
  <li>April 24th 14:30 Department of Chemistry, Zhejiang University,
Hangzhou, China</li>
</ul>
Topics to include
<ul>
  <li>What is cheminformatics?</li>
  <li>Drug discovery process and its reality</li>
  <li>Components and methodologies</li>
  <li>SAR, QSAR, and drug-like properties</li>
  <li>Modeling, CAMD, and optimization</li>
  <li>Challenges pharmaceutical and biotechnology companies are facing</li>
  <li>Technologies and expertise biotechnology and pharmaceutical
companies are seeking</li>
  <li>Tools commercially available</li>
  <li>Live demonstration of ChemAxon functionality</li>
  <li>ChemAxon&#146;s free Academic Package and other free provision of
software</li>
</ul>
To confirm attendance and receive notifications of event location
please email <a class="moz-txt-link-rfc2396E" href="mailto:aa__,__chemaxon__.__com">"aa__,__chemaxon__.__com"</a>.<br>
<br>
To find out more about ChemAxon's free software and Academic Package
and to download, please visit: <a moz-do-not-send="true"
 href="http://www.chemaxon.com/prices.html">http://www.chemaxon.com/prices.html</a><br>
<br>
Please do forward this message to those of interest.<br>
<br>
Many thanks.<br>
<br>
Alex<br>
<font color="#7f7f7f">--<br>
<br>
Alex Allardyce<br>
Dir. Marketing, ChemAxon</font><br>
<br>
</body>
</html>

--------------070300020609050807070302--


From owner-chemistry@ccl.net Wed Mar 26 19:11:00 2008
From: "JunJun Liu ljjlp03]~[gmail.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL: similarity of different molecules
Message-Id: <-36555-080326190232-14965-62EiRe2DRUvfAAOGsrDjPA..server.ccl.net>
X-Original-From: "JunJun Liu" <ljjlp03(a)gmail.com>
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Date: Wed, 26 Mar 2008 18:02:05 -0400
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Sent to CCL by: "JunJun Liu" [ljjlp03\a/gmail.com]
Hello everybody,

I want to know how similar two different molecules are. Does anybody know  
how to do this? Any suggestions regarding algorithms or softwares are  
highly appreciated!

Thanks in advance!

Junjun


From owner-chemistry@ccl.net Wed Mar 26 20:29:00 2008
From: "Pavlina KOSINOVA nu.pavlina^^centrum.cz" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL:G: PCM problems
Message-Id: <-36556-080326122811-15246-WH7Wy0qVOtcaqKHrypIjew!=!server.ccl.net>
X-Original-From: "Pavlina  KOSINOVA" <nu.pavlina!^!centrum.cz>
Date: Wed, 26 Mar 2008 12:28:07 -0400


Sent to CCL by: "Pavlina  KOSINOVA" [nu.pavlina::centrum.cz]
Dear CCL Subscribers,

I am using PCM for radical calculations, i.e., I am just using, as an input command, the default parameters:  

#p ub3p86/6-31g(d) opt freq scrf=(iefpcm,solvent=water) geom=connectivity

Some of my caculations crashed with the following error message: 

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=   22.
                        Tesserae with average area of 0.200 Ang**2.
 1st derivatives      : Analytical V*U(x)*V algorithm (CHGder, D1EAlg=0).
                        Cavity 1st derivative terms included.
 Solvent              : Water, Eps     =  78.390000
                               Eps(inf)=   1.776000
                               RSolv   =   1.385000 Ang.
 ------------------------------------------------------------------------------
 AdVTs1: ISph=  500 is engulfed by JSph=  501 but Ae(  500) is not yet zero!
 Error termination via Lnk1e in /opt/gaussian/g03/l301.exe at Fri Mar 14 20:01:07 2008.

Please could anyone help me to solve this problem ?

Thank you very much for your help. 

Best wishes.
Pavlina KOSINOVA 
(Ph.D. student)


From owner-chemistry@ccl.net Wed Mar 26 21:25:00 2008
From: "Rajarshi Guha rguha~!~indiana.edu" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL: similarity of different molecules
Message-Id: <-36557-080326212204-19858-6B+q8iuLoo9qqyczmVCjlw(~)server.ccl.net>
X-Original-From: Rajarshi Guha <rguha]=[indiana.edu>
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Sent to CCL by: Rajarshi Guha [rguha:_:indiana.edu]
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Hash: SHA1


On Mar 26, 2008, at 6:02 PM, JunJun Liu ljjlp03]~[gmail.com wrote:

>
> Sent to CCL by: "JunJun Liu" [ljjlp03\a/gmail.com]
> Hello everybody,
>
> I want to know how similar two different molecules are. Does  
> anybody know how to do this? Any suggestions regarding algorithms  
> or softwares are highly appreciated!

There are lots of tools that will do this. On the OSS side you could use

CDK http://almost.cubic.uni-koeln.de/cdk/cdk_top
OpenBabel http://openbabel.org/wiki/Main_Page

Of course it also depends on what type of similarity you're  
considering. You could use fingerprints (which either of the above  
will generate) or some type of real-valued descriptor.

If you have a few molecules and just want the Tanimoto similarity  
using CDK fingerprints, you can try http:// 
cheminfo.informatics.indiana.edu/~rguha/code/java/cdkws/sim.html  
which will give you the similrity matrix for a set of SMILES

- -------------------------------------------------------------------
Rajarshi Guha  <rguha : indiana.edu>
GPG Fingerprint: D070 5427 CC5B 7938 929C  DD13 66A1 922C 51E7 9E84
- -------------------------------------------------------------------
In matrimony, to hesitate is sometimes to be saved.
        -- Butler


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From owner-chemistry@ccl.net Wed Mar 26 22:00:00 2008
From: "Guanna Li gnli^^^dicp.ac.cn" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: nbo&nboview
Message-Id: <-36558-080326215400-5356-y0BoHQIMTg6YJrjtnADDhQ**server.ccl.net>
X-Original-From: "Guanna Li" <gnli*o*dicp.ac.cn>
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	charset="gb2312"
Date: Thu, 27 Mar 2008 09:54:33 +0800
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Sent to CCL by: "Guanna Li" [gnli{:}dicp.ac.cn]
Dear colleagues,
is there a free nbo&nboview program for PC-windows-xp operating systerm?
Thanks!
 				
Best wishes 
Guanna Li
 
State Key Laboratory of Catalysis
Dalian Institute of Chemical Physics
Chinese Academy of Sciences
 
457 Zhongshan Road, Dalian 116023, China
 
Tel: +86-411-8437 9302
Email: gnli{=}dicp.ac.cn