From owner-chemistry@ccl.net Tue Dec  7 09:23:00 2010
From: "Esteban Gabriel Vega Hissi egvega++gmail.com" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: mopac09 segmentation fault with NOANCI
Message-Id: <-43293-101207091958-16078-dd/qhvoo6wlJ+yQz5t5gKw[a]server.ccl.net>
X-Original-From: Esteban Gabriel Vega Hissi <egvega!^!gmail.com>
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Date: Tue, 7 Dec 2010 11:19:10 -0300
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Sent to CCL by: Esteban Gabriel Vega Hissi [egvega|,|gmail.com]
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Hello,

Does anyone know why mopac2009 (linux) gives me a segmentation fault when
using PM6-DH2 and NOANCI keywords?

Thanks in advance

Esteban G. Vega-Hissi
UNSL
Argentine

--20cf3054a2e171bc1f0496d2b1fd
Content-Type: text/html; charset=ISO-8859-1

Hello,<br><br>Does anyone know why mopac2009 (linux) gives me a segmentation fault when using PM6-DH2 and NOANCI keywords?<br><br>Thanks in advance<br><br>Esteban G. Vega-Hissi<br>UNSL<br>Argentine<br>

--20cf3054a2e171bc1f0496d2b1fd--


From owner-chemistry@ccl.net Tue Dec  7 10:43:00 2010
From: "Wagener, M. \(Markus\) markus.wagener*_*spcorp.com" <owner-chemistry()server.ccl.net>
To: CCL
Subject: CCL: 2nd Call for Papers: 9th International Conference on Chemical Structures (ICCS)
Message-Id: <-43294-101207103615-7817-PQFb5la+pQw498Z44gXhmg()server.ccl.net>
X-Original-From: "Wagener, M. \(Markus\)" <markus.wagener#%#spcorp.com>
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Sent to CCL by: "Wagener, M. \(Markus\)" [markus.wagener . spcorp.com]
                         C A L L   F O R   P A P E R S
                 9th International Conference on Chemical Structures
             NH Leeuwenhorst Conference Hotel, Noordwijkerhout, The
Netherlands
                                 5-9 June 2011

Submission of abstracts and registration to the conference is now open
on the conference website at www.int-conf-chem-structures.org

The 9th International Conference on Chemical Structures (ICCS) is
seeking presentations of novel research and emerging technologies for
the following plenary sessions:

   o Cheminformatics
        > advances in structure representation
        > reaction handling and electronic lab notebooks (ELNs)
        > molecular similarity and diversity
        > chemical information visualization

   o Structure-Activity and Structure-Property Prediction
        > graphical methods for SAR analysis
        > industrialized and large-scale model building
        > multi-property prediction and multi-objective optimization

   o Structure-Based Drug Design and Virtual Screening
        > new docking and scoring approaches
        > improved understanding of protein-ligand interactions
        > pharmacophore definition and search
        > modeling of challenging targets

   o Analysis of Large Chemistry Spaces
        > mining of chemical literature and patents
        > design, profiling and comparison of compound collections and
screening sets
        > machine learning and knowledge extraction from databases

   o Integrated Chemical Information
        > advances in chemogenomics
        > integration of medical and biological information
        > semantic technologies as a driver of integration
        > translational informatics

   o Dealing with Biological Complexity
        > analysis and prediction of poly-pharmacology
        > in-silico analysis of toxicology, drug safety, and adverse
events
        > pathways and biological networks
        > druggability of targets

Besides the scientific program the conference will feature free
workshops from several companies including BioSolveIT
(www.biosolveit.de), The Chemical Computing Group (www.chemcomp.com),
and Tripos (www.tripos.com).

Joint Organizers:
   o Division of Chemical Information of the American Chemical Society
(CINF)
   o Chemical Structure Association Trust (CSA Trust)
   o Division of Chemical Information and Computer Science of the
Chemical Society of Japan (CSJ)
   o Chemistry-Information-Computer Division of the German Chemical
Society (GDCh)
   o Royal Netherlands Chemical Society (KNCV)
   o Chemical Information Group of the Royal Society of Chemistry (RSC)
   o Swiss Chemical Society (SCS)

We encourage the submission of papers on both applications and case
studies as well as on method development and algorithmic work. The final
program will be a balance of these two aspects.

> From the submissions the program committee and the scientific advisory
board will select about 30 papers for the plenary sessions. All
submissions that cannot be included in the plenary sessions will
automatically be considered for the poster session.

Contributions can be submitted for any of the above and related areas,
but we also welcome contributions in any aspect of the computer handling
of chemical structure information, such as:

   o automatic structure elucidation
   o combinatorial chemistry, diversity analysis
   o web technology and its effect on chemical information
   o electronic publishing
   o MM or QM/MM simulations
   o practical free energy calculations
   o modeling of ADME properties
   o material sciences
   o analysis and prediction of crystal structures
   o grid and cloud computing in cheminformatics

Visit the conference website at www.int-conf-chem-structures.org for
more information, including details on procedures for online abstract
submission and conference registration.

The deadline for the submission of abstracts is 31 January 2011.

We hope to see you in Noordwijkerhout.

Keith T Taylor, ICCS Chair
Markus Wagener, ICCS Chair

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 Tue Dec  7 12:30:00 2010
From: "Alex Allardyce aa!A!chemaxon.com" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: JChem and Marvin 5.4 launched - 64 bit, multi-threading, enhanced transformations, R-group ordering, new predictor plugin, ECFP, expanded reaction library, disconnected MCS
Message-Id: <-43295-101207111032-4181-O4RShB0BzUy61YVrC2/BZg|server.ccl.net>
X-Original-From: Alex Allardyce <aa ~ chemaxon.com>
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Date: Tue, 07 Dec 2010 16:57:09 +0100
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Sent to CCL by: Alex Allardyce [aa^chemaxon.com]
This is a multi-part message in MIME format.
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Please excuse cross postings

We are pleased to announce the launch of Marvin and JChem 5.4. The major 
new features are listed below along with links to download. JChem for 
Excel and Instant JChem will be released in the next weeks.

Marvin & JChem are software suites of application programming 
interfaces  (API's) and graphic user interfaces (GUI's) used to build 
chemically aware,  platform independent and web ready enterprise 
informatics systems.
Marvin includes structure and reaction editing, visualization and 
structure based property prediction; JChem includes structure management 
and search, library enumeration and library profiling.

Marvin major changes and features
* Full 64 bit support
* Multiple, ordered R-group attachment points - Up to 9 attachment 
points, the order of the attachment points can be  easily changed, and 
the display follows the IUPAC recommendations.
* Enhanced 3D transformations - Rotation around specified axes, 3D 
Plane, mirror, inversion, directed merge of fragments, displaying of 
degree of rotation.
* Context based attached data editing - Attach data to bonds, atoms, 
fragments etc.
* Search for the structure on the canvas as substructure in PubChem 
directly from MarvinSketch.
* Configurable clipboard handling - Control of file formats available 
for copy & paste.
* Fused output option in Markush enumerator - First 100 of enumerated 
structures are shown as a single fused molecule.
* A new command line tool is available for batch mode checking - New 
structure checkers introduced: Empty Structure, Metallocene, Covalent 
Counterion, Ring Strain Error, etc.
* New GUI for training of calculator plugins - Train and run your own 
molecular property prediction with Predictor plugin.
* Industry standard MMFF94 forcefield options - In Conformer Generator 
and 3D Molecular Properties.

Marvin download [http://www.chemaxon.com/download/marvin/]
Release notes [http://www.chemaxon.com/marvin/release-notes.html]
History of changes (all features and bugfixes) 
[http://www.chemaxon.com/marvin/help/developer/changes.html]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JChem major changes and features

JChem Base (database management and chemical search)
* Full 64 bit support
* New similarity search result highlighting using Maximum Common Edge 
Substructure (MCES).
* New stereo search options: enantiomer and improved double bond stereo 
options
* Similarity search is now multi-threaded and results are returned faster
* Fingerprint screening and ABAS are now running in parallel to return 
first results faster.
* More flexible tautomer search - non-tautomer search can consider 
tautomer duplicate tables
* Tables with same name in different databases are supported in 
structure cache
Markush search: New homology groups and properties for Thomson Reuters' 
MMS (Merged Markush Service) database
JChem Web Services: All JChem Manager functionality available
Structure Checker (structure file checking and automated fixing): 
Command line tool 'structurecheck' and new checkers introduced.
Reactor: New virtual reaction library containing systematically listed 
and designed synthetic reactions. 
[http://www.chemaxon.com/jchem/doc/user/Reactor.html#reactionlib]
Standardizer: Built in mesomer and solvent removal transforms
Screen - (Fast/robust 2D and now 3D ligand-based virtual screening)
* extended connectivity fingerprint (ECFP) now available (includes FCFP)
* available both as hashed binary fingerprint and as a list of integer 
features
JKlustor (MCS and other clustering methods)
* New Maximum Common Edge Substructure algorithm;
  + faster and more robust than previous MCS implementation
  + capable of finding disconnected common substructures
  + pair-wise matching of two sets of structures

JChem download [http://www.chemaxon.com/download/jchem/]
Release notes [http://www.chemaxon.com/jchem/release-notes.html]
History of changes [http://www.chemaxon.com/jchem/changes.html](all 
features and bugfixes)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Evaluation:
Registered forum users can automatically generate 2 week evaluation 
licenses for all products: http://www.chemaxon.com/my-chemaxon/
Non commercial academic users can obtain free licenses for all products, 
information and application form: 
http://www.chemaxon.com/forum/ftopic193.html
-- 
*Alex Allardyce*
Marketing Dir.
*ChemAxon**Ltd*.
Maramaros koz 3/A, Budapest, 1037 Hungary
http://www.chemaxon.com
Tel: +361 453 0435
Fax: +361 4532659
mailto:aa[#]chemaxon.com

--------------020404050405050906020708
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
  <head>
    <meta http-equiv="content-type" content="text/html;
      charset=ISO-8859-1">
  </head>
  <body bgcolor="#ffffff" text="#000000">
    Please excuse cross postings<br>
    <br>
    We are pleased to announce the launch of Marvin and JChem 5.4. The
    major new features are listed below along with links to download.
    JChem for Excel and Instant JChem will be released in the next
    weeks.<br>
    <br>
    Marvin &amp; JChem are software suites of application programming
    interfaces&nbsp; (API's) and graphic user interfaces (GUI's) used to
    build chemically aware,&nbsp; platform independent and web ready
    enterprise informatics systems.<br>
    Marvin includes structure and reaction editing, visualization and
    structure based property prediction; JChem includes structure
    management and search, library enumeration and library profiling.<br>
    <br>
    Marvin major changes and features<br>
    * Full 64 bit support&nbsp; <br>
    * Multiple, ordered R-group attachment points - Up to 9 attachment
    points, the order of the attachment points can be&nbsp; easily changed,
    and the display follows the IUPAC recommendations.<br>
    * Enhanced 3D transformations - Rotation around specified axes, 3D
    Plane, mirror, inversion, directed merge of fragments, displaying of
    degree of rotation.<br>
    * Context based attached data editing - Attach data to bonds, atoms,
    fragments etc.<br>
    * Search for the structure on the canvas as substructure in PubChem
    directly from MarvinSketch.<br>
    * Configurable clipboard handling - Control of file formats
    available for copy &amp; paste.<br>
    * Fused output option in Markush enumerator - First 100 of
    enumerated structures are shown as a single fused molecule.<br>
    * A new command line tool is available for batch mode checking - New
    structure checkers introduced: Empty Structure, Metallocene,
    Covalent Counterion, Ring Strain Error, etc.<br>
    * New GUI for training of calculator plugins - Train and run your
    own molecular property prediction with Predictor plugin.<br>
    * Industry standard MMFF94 forcefield options - In Conformer
    Generator and 3D Molecular Properties.<br>
    <br>
    Marvin download [<a class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/download/marvin/">http://www.chemaxon.com/download/marvin/</a>]<br>
    Release notes [<a class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/marvin/release-notes.html">http://www.chemaxon.com/marvin/release-notes.html</a>]<br>
    History of changes (all features and bugfixes) [<a
      class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/marvin/help/developer/changes.html">http://www.chemaxon.com/marvin/help/developer/changes.html</a>]<br>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
    JChem major changes and features<br>
    <br>
    JChem Base (database management and chemical search)<br>
    * Full 64 bit support <br>
    * New similarity search result highlighting using Maximum Common
    Edge Substructure (MCES).<br>
    * New stereo search options: enantiomer and improved double bond
    stereo options<br>
    * Similarity search is now multi-threaded and results are returned
    faster<br>
    * Fingerprint screening and ABAS are now running in parallel to
    return first results faster.<br>
    * More flexible tautomer search - non-tautomer search can consider
    tautomer duplicate tables<br>
    * Tables with same name in different databases are supported in
    structure cache<br>
    Markush search: New homology groups and properties for Thomson
    Reuters' MMS (Merged Markush Service) database<br>
    JChem Web Services: All JChem Manager functionality available<br>
    Structure Checker (structure file checking and automated fixing):
    Command line tool 'structurecheck' and new checkers introduced.<br>
    Reactor: New virtual reaction library containing systematically
    listed and designed synthetic reactions. [<a
      class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/jchem/doc/user/Reactor.html#reactionlib">http://www.chemaxon.com/jchem/doc/user/Reactor.html#reactionlib</a>]<br>
    Standardizer: Built in mesomer and solvent removal transforms<br>
    Screen - (Fast/robust 2D and now 3D ligand-based virtual screening)<br>
    * extended connectivity fingerprint (ECFP) now available (includes
    FCFP)<br>
    * available both as hashed binary fingerprint and as a list of
    integer features<br>
    JKlustor (MCS and other clustering methods)<br>
    * New Maximum Common Edge Substructure algorithm; <br>
    &nbsp;+ faster and more robust than previous MCS implementation<br>
    &nbsp;+ capable of finding disconnected common substructures<br>
    &nbsp;+ pair-wise matching of two sets of structures<br>
    <br>
    JChem download [<a class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/download/jchem/">http://www.chemaxon.com/download/jchem/</a>]<br>
    Release notes [<a class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/jchem/release-notes.html">http://www.chemaxon.com/jchem/release-notes.html</a>]
    <br>
    History of changes [<a class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/jchem/changes.html">http://www.chemaxon.com/jchem/changes.html</a>](all

    features and bugfixes)<br>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
    <br>
    Evaluation:<br>
    Registered forum users can automatically generate 2 week evaluation
    licenses for all products: <a class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/my-chemaxon/">http://www.chemaxon.com/my-chemaxon/</a><br>
    Non commercial academic users can obtain free licenses for all
    products, information and application form: <a
      class="moz-txt-link-freetext"
      href="http://www.chemaxon.com/forum/ftopic193.html">http://www.chemaxon.com/forum/ftopic193.html</a><br>
    <div class="moz-signature">-- <br>
      <div class="moz-signature">
        <title></title>
        <small><font color="#077179" face="Verdana"><small><b>Alex
                Allardyce</b></small></font></small><br>
        <div class="moz-signature"><small><font face="Verdana"><font
                color="#666666"><small>Marketing Dir.</small></font><br>
            </font><font color="#fca311"><small><small><font
                    face="Verdana"><b><big>ChemAxon</big></b></font></small></small></font><font
              face="Verdana"><font color="#fca311"><small> <b>Ltd</b>.</small></font><br>
              <small><font color="#666666">Maramaros koz 3/A, Budapest,
                  1037 Hungary</font><br>
                <font color="#6b6f40"><span
                    class="moz-txt-link-freetext"><a
                      moz-do-not-send="true"
                      class="moz-txt-link-freetext"
                      href="http://www.chemaxon.com/">http://www.chemaxon.com</a></span></font><br>
                <font color="#666666">Tel: +361 453 0435<br>
                  Fax: +361 4532659</font><br>
                <font color="#6b6f40"><span
                    class="moz-txt-link-freetext"><a
                      moz-do-not-send="true"
                      class="moz-txt-link-freetext"
                      href="mailto:aa[#]chemaxon.com">mailto:aa[#]chemaxon.com</a></span></font></small></font>
          </small></div>
      </div>
    </div>
  </body>
</html>

--------------020404050405050906020708--


From owner-chemistry@ccl.net Tue Dec  7 13:05:00 2010
From: "Jevahcel Strong jevahcel ~~ hotmail.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL:G: Can anyone help
Message-Id: <-43296-101207122348-14852-IUvi+NwhUtjJ9X94q3glPw:server.ccl.net>
X-Original-From: "Jevahcel  Strong" <jevahcel=hotmail.com>
Date: Tue, 7 Dec 2010 12:23:47 -0500


Sent to CCL by: "Jevahcel  Strong" [jevahcel.:.hotmail.com]
Dear all,
I am currently doing a harmonic frequencies computation at SCRF-B3LYP/6-31G** level with COSMO model, but it died and the message output as below, your kind help will be very grateful.
Sincerely
Jevah


 Leave Link 1102 at Tue Dec  7 05:49:35 2010, MaxMem=  629145600 cpu:       0.6
 (Enter /usr/local/apps//g03/l1110.exe)
 Forming Gx(P) for the SCF density, NAtomX=    62.
 Integral derivatives from FoFDir, PRISM(SPDF).
 Do as many integral derivatives as possible in FoFDir.
 G2DrvN: MDV=     629145102.
 G2DrvN: will do   63 centers at a time, making    1 passes doing MaxLOS=2.
 Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0.
 FoFCou: FMM=T IPFlag=           0 FMFlag=      100000 FMFlg1=           1
 NFxFlg=           0 DoJE=F BraDBF=F KetDBF=F FulRan=T.
 Symmetry not used in FoFCou.
 FMM levels:  10  Number of levels for PrismC:   9
 PrismC:  NFx=      2048 NFxT=         5 NFxU=         5.
 PrismC:  NFx=      2048 NFxT=         5 NFxU=         5.
 PrismC:  NFx=      2048 NFxT=         5 NFxU=         5.
 PrismC:  NFx=      2048 NFxT=         5 NFxU=         5.
 FoFDir/FoFCou used for L=0 through L=2.
 No F1PCM for iterative CSMder.
 Error termination via Lnk1e in /usr/local/apps//g03/l1110.exe at Tue Dec  7 06:51:52 2010.


From owner-chemistry@ccl.net Tue Dec  7 13:39:00 2010
From: "Jimmy Stewart MrMOPAC~!~att.net" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: mopac09 segmentation fault with NOANCI
Message-Id: <-43297-101207115643-28771-bBbNVY0lrjEARmZSWNQiIQ(0)server.ccl.net>
X-Original-From: Jimmy Stewart <MrMOPAC:_:att.net>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Date: Tue, 07 Dec 2010 09:56:37 -0700
Mime-Version: 1.0


Sent to CCL by: Jimmy Stewart [MrMOPAC,,att.net]

>Esteban G. Vega-Hissi reported:

>Does anyone know why mopac2009 (linux) gives me a segmentation fault when 
>using PM6-DH2 and NOANCI keywords?

If an example data set that shows a possible bug in MOPAC2009 is sent to 
me, I will attempt to resolve the issue.

Users of MOPAC2009 are encouraged to sent bug reports directly to me, along 
with example data sets and information on the platform used.

Best wishes,

Jimmy



                          ( || || )
  .-----------------oOOo----(_)----oOOo--------------------------------------.
  | James J. P. Stewart               |                                      |
  | Stewart Computational Chemistry   | E-mail:  MrMOPAC||OpenMOPAC.net       |
  | 15210 Paddington Circle           |  39/03/15 N, 104/49/29 W             |
  | Colorado Springs CO 80921-2512    | http://openmopac.net/                |
  | USA                               | SKYPE: Jimmy.Stewart2 GMT 1500 - 0200|
  |                      .ooo0        | Phone: USA +(719) 488-9416           |
  |                      (   )   Oooo.|                                      |
  .-----------------------\ (----(   )---------------------------------------.
                           \_)    ) /
                                 (_/


From owner-chemistry@ccl.net Tue Dec  7 21:45:00 2010
From: "Tsung-Wen Yen peter308~~gmail.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: I am applying to Phys Phd program at USA, need your advice.
Message-Id: <-43298-101207214323-11834-EfSnuIES4i4+8Elo/U4gZg*_*server.ccl.net>
X-Original-From: "Tsung-Wen  Yen" <peter308,,gmail.com>
Date: Tue, 7 Dec 2010 21:43:21 -0500


Sent to CCL by: "Tsung-Wen  Yen" [peter308%a%gmail.com]
Dear CCLers:
My research is about Metallic clusters, I studied its geometry, thermal properties,dynamics and time-correlation properties. Recently, I am studying its magnetism using DFT and I have discovered how cluster's symmetry induce its magnetism. I planned to apply for PHD in the phyics department in USA. However, I searched over the universities and find several groups which has the same research topic as mine. For example, Prof Landman in GIT and Prof.Bloomfield in U of Virgina, and many others. I just want to consult you that are there other research groups in USA that are well-knowed for their research in metallic clusters?( theory and simulation). Appreciated if you could give me some suggestions. I spend a lot of time searching on google and scholar google. I just want to confirm if I missed any researchers in this field. Please give me feedbacks if you think I am asking a dumb question. Many thanks!





                                                       With Best Regards
                                                       Tsung-Wen Yen