From chemistry-request@ccl.net Fri Apr  1 00:39:40 2005
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From: "yu, chung, yang" <ychyou.tw * yahoo.com.tw>
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Subject: W:troublebout freq job running gassian03 
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Hi, I meet a problem when I use Gaussian03 running a little big molecule's freq, as below          S
                    phC   CPh
                       C-C
                    2hC   Ch2
                       O-S
                          O
The error message is "Erroneous write during file extend. write 172031 instead of 4096 Probably out of disk space. Write error in NtrExt1". Strangely, the HD space is enough(200MB,only 2% used). Then I try to divide rwf file, the Commandline and Routepath is "%rwf=/scratch1/ycy/temp/a.rwf,600Mb,/scratch1/temp/b.rwf,600Mb,/scratch/ycy/g03/c.rwf,600MB%nosave%chk=/scratch1/ycy/chk/57DPTPS3axi.chk%mem=600MB p freq ub3lyp/6-31++g(d,p)" and the result is " No file to extend for IUnit=  1 -- out of disk space.Error termination in NtrErr: NtrErr called from NtrExt." Is somebody can tell me how to do? And another one is the job about running freq only how to ues chk file to restart. I always fail in trying it. My way is freq=restart.


I am a student in Taiwan. My name is Yang Chung-Yu and calling me ycy is OK. My email: ychyou.tw * yahoo.com.tw I hope someone can give me a hand. Thanks.


From chemistry-request@ccl.net Fri Apr  1 11:19:20 2005
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To: "=?gb2312?q?=B9=F9=CE=C4=C6=BD?=" <ybyygu ~~ yahoo.com.cn>, chemistry ~~ ccl.net
Subject: Re: CCL:Gaussian Warning:"explicit consideration of  33 degrees of
 freedom as vibrations may cause significant error"
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From: Georgina Aitken <g.d.c.aitken ~~ sussex.ac.uk>
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Dear Wenping Guo,

I have had a similar problem when I do frequency calculations on large 
floppy molecules in both G03 and G98.
Using the opt=tight or opt=verytight keywords can reduce the number of 
degrees of freedom that have low frequencies and using the 
freq=HinderedRotor keyword can also help. In most cases you can freeze out 
these vibrations by doing a frequency calculation at a low temperature e.g. 
10K.
However I would be interested to hear if you manage to get rid of the first 
warning message in the thermochemistry section of your output.

Back in november I posted the following question on CCL and had three 
useful responses to the post, all of which is summarised below:

Dear CCLers,

I am a PhD student and have been getting the following warning messages in
the thermochemistry section of my Gaussian frequency outputs for various 
divalent Pb-ligand complexes:

"Principal axes and moments of inertia in atomic units:
                           1         2         3
     EIGENVALUES --  4494.802316560.791727501.25369
           X            0.99998   0.00350   0.00560
           Y           -0.00289   0.99445  -0.10519
           Z           -0.00593   0.10517   0.99444
 This molecule is an asymmetric top.
 Rotational symmetry number  1.
 Warning -- assumption of classical behavior for rotation
           may cause significant error
 Rotational temperatures (Kelvin)      0.01927     0.01320     0.01155
 Rotational constants (GHZ):           0.40152     0.27508     0.24059
 Zero-point vibrational energy     647177.6 (Joules/Mol)
                                  154.67917 (Kcal/Mol)
 Warning -- explicit consideration of  23 degrees of freedom as
           vibrations may cause significant error "

Does this mean that the zero point energy correction is not reliable? What
can I do about it?

Thanks in advance,

Georgina Aitken

1.
Hi Georgina,
that means you have ltos of frequencies (23 of them) which are very small
and harmonic approximation may not be valid you can read more about it  at 
the G03 web site white papers:
http://www.gaussian.com/g_whitepap/white_pap.htm

some of these modes correspond to rotational motion of ligands (like 
hindered rotation)

If you optimized using the tight criteria some of those low frequenices 
will go away.  For large molecules there will always be some low frequency 
modes..

Shaji

2.
Georgina,

The warning ("explicit consideration of  23 degrees of freedom as 
vibrations may
cause significant error") means that 23 of the computed vibrational 
temperatures
are below some threshold value calculated by Gaussian to correspond to an 
ideal
gas. This threshold, for STP conditions, corresponds to vibrational 
frequencies
of around 625 cm**(-1), so if your low frequencies are only slightly below 
this
mark, there shouldn't be a problem with your zero-point correction.

How many degrees of freedom are in this system? Are you using constraints 
on any
of the atoms?

Ryan

3.
Georgina,

The second warning:

 "Warning -- explicit consideration of  23 degrees of freedom as
           vibrations may cause significant error"

is displayed whenever there are vibrational frequencies below a certain 
wavenumber.  The purpose of this warning is to remind the user that 
treatment of hindered rotations (such as those of the C-C bonds in ethane 
or propane) as "vibrations" may affect the thermodynamic calculations.

I don't think this error has any significant effect at 0K since these 
rotations are "frozen out" and hence really do act as vibrations.  At 
298.15K, however, there may be a noticeable (but still usually small) 
difference in heat capacity and entropy.

There is an option freq=hindrot which identifies the internal rotations and 
uses a different approximation which is usually better than treating these 
as vibrations.

--

As for the first warning:

"Warning -- assumption of classical behavior for rotation
           may cause significant error"

I've not encountered it before.  I suppose this means that the rigid rotor 
approximation is likely to be inaccurate, but I don't have a fix for that.

And even worse, this possibly could affect zero-point energy.  By how much, 
I have no idea.

--David Shobe, Ph.D., M.L.S.



--On Monday, March 28, 2005 11:37:17 +0800 
"=?gb2312?q?=B9=F9=CE=C4=C6=BD?=" <ybyygu ~~ yahoo.com.cn> wrote:

> Dear CCLers;
> I performed an freq calculation with G98 from a
> optimized structure.
> When finished, I found the following warnings in the
> output:
>
> Warning -- assumption of classical behavior for
> rotation
>            may cause significant error
>
> Warning -- explicit consideration of  33 degrees of
> freedom as
>            vibrations may cause significant error
>
> I am wondering what the warnings mean? Can I just
> neglect them, or how
> can I correct this situation?
>
> I would greatly appreciate any suggestion.
> Best wishes,
>
> Wenping Guo
>
> ------------------------------------------
> Path:     /China/Gansu/LanzhouUniversity/
> Address:  4006 ~~ physchem.lzu.edu.cn
>           ybyygu ~~ hotmail.com  # MSN
>           ybyygu ~~ yahoo.com.cn # Yahoo!
> -------------------------------------------
>
> _________________________________________________________
> Do You Yahoo!?
> W"2aJ@=gR;AwF7VJ5DQE;"Cb7Q5gSJ
> http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/
>
>
> -= This is automatically added to each message by the mailing script =-
> To send e-mail to subscribers of CCL put the string CCL: on your Subject:
> line and send your message to:  CHEMISTRY ~~ ccl.net
>
> Send your subscription/unsubscription requests to:
> CHEMISTRY-REQUEST ~~ ccl.net  HOME Page: http://www.ccl.net   | Jobs Page:
> http://www.ccl.net/jobs
>
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> use the Web based form from CCL Home Page
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>
>
>
>
>

Georgina Aitken

DPhil Student
University of Sussex
BN1 9QS
U.K




From chemistry-request@ccl.net Fri Apr  1 12:53:09 2005
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Subject: ChemAxon User Group Meeting (May 19-20, Budapest) - Program posted
 and poster submission deadline extended
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Appologies for multiple postings

ChemAxon anounces "Program posting" for it's first User Group Meeting 
taking place on May 19-20 at the Danubius Gellert Hotel 
<http://www.danubiushotels.com/hotels/hotel.php?id=13&lang=en>, 
Budapest, Hungary.

The meeting will present the latest implementations and research 
experience of our users as well as focused technical and scientific 
presentations on each of the ChemAxon toolkits by ChemAxon staff. There 
will be a development rountable session, a poster session for new 
posters and older posters which remain relevant and a hacker room for 
informal discussion and problem solving. For further information please 
visit the UGM home page <http://www.chemaxon.com/UGM/05/index.html>, to 
see the program please visit this link 
<http://www.chemaxon.com/UGM/05/program.html> or see below.

We have a full social program for attendees to enjoy with an informal 
garden party at ChemAxon's offices on the evening of the 18th and a 
winetasting and banquet within Buda Castle for the evening of the 19th. 
There will also be early morning visits to the thermal spa facilities 
situated at the hotel.

We have extended the poster submission deadline until May 15th. Any 
attendees wishing to submit original or previously presented posters at 
the event should submit abstracts before May 15th. For registration and 
poster submission form please see this link 
<http://www.chemaxon.hu/forum/ftopic272.html>

If you would like to register for the event please complete the 
registration form <http://www.chemaxon.hu/forum/ftopic272.html>. 
Attendees intending to stay at the meeting hotel are urged to reserve 
accommodation <http://www.chemaxon.hu/forum/ftopic261.html> before April 
25th - when the block booking will lapse.

I look forward to seeing you in May

Alex Allardyce

Meeting home page: http://www.chemaxon.com/UGM/05/index.html
Event program: http://www.chemaxon.com/UGM/05/program.html
To register or submit a poster abstract: 
http://www.chemaxon.hu/forum/ftopic272.html
Poster submission guidelines: http://www.chemaxon.hu/forum/ftopic295.html
Accomodation booking: http://www.chemaxon.hu/forum/ftopic261.html

If you do not wish to recieve any further notifications related to 
ChemAxon's User Group Meeting. Please reply to this mail with the 
subject line "Remove"

-- 
Alex Allardyce
Communications Director

Chemaxon Ltd
Maramaros kvz 3/a
Budapest, 1037 Hungary
Tel.: +361 4532658
Fax.: +361 4532659

e-mail: aa (a) chemaxon.com

*UGM Program in full:*

_Thursday, May 19th - morning_

9:00 Welcome

9:15 Virtual Classrooms and E-Learning: Bringing Cheminformatics 
Training Into Academic and Industrial Settings. TJ O'Donnell, O'Donnell 
Associates

9:45 What is Marvin and how to..? Szilard Dorant,Tamas Vertse, ChemAxon

10:30 BREAK

11:00 Developing a Compact Chemical Database System Using Marvin Tools. 
C. Deniz Akyuz, Merck Research Laboratories

11:30 Structural search using ChemAxon tools. Szabolcs Csepregi, ChemAxon

12:00 ChemAxon's Java Components in a Heterogeneous, Server-Centric 
Application Environment. Mark Runyan, CTI Scientific Systems

12:30 LUNCH and poster session

Afternoon

13:30 A Reagent Management System for Requests & Purchasing using JChem. 
Robert D. Feinstein, Kelaroo, Inc.

14:00 JChem Base - structure database engine. Szilard Dorant, ChemAxon

14:40 BREAK

15:10 LeadMarker. - an integrated suite for managing chemical and 
biological information. Tim Dudgeon, Informatics Matters Ltd

15:40 Compound storage and retrieval with JChem Cartridge for Oracle. 
Peter Kovacs, ChemAxon

16:10 Closing comments

_Friday May 20th - morning _

9:30 Using ChemAxon Toolkits in the GNF Lead Discovery Database. Yingyao 
Zhou, Genomics Institute of the Novartis Research Foundation

10:00 Predicting structure properties with Calculator Plugins. Nora 
Mate, Jozsef Szegezdi, ChemAxon

10:30 Electronic Notebooks - How ChemAxon tools enable the Chemically 
Intelligent Electronic Notebook. Paul
Denny-Gouldson (CEO) / Kevin Gill (tbc), Deffinity Solutions Ltd .

11:00 BREAK

11:30 Workflow Cheminformatics. Kanishka Karunanayake, Inforsense

12:00 Automatic generation of 3D structures and conformers of molecules 
in Marvin - Clean/3D (latest developments). Odon Farkas, ChemAxon

12:15 MarvinSpace - pre-product demonstration. Miklos Vargyas, Judit 
Papp, ChemAxon

12:30 LUNCH and Discussion Roundtable

Afternoon

14:00 Seurat: A Tool for navigating SAR. James Baxendale, Celera Genomics

14:30 Artificial synthesis. Gyorgy Pirok, ChemAxon

15:00 Improved Virtual Screening Strategies and Enrichment of Focused 
Libraries in Active Compounds Using Target-Oriented Databases. Ismail 
Ijjaali, Aureus-Pharma

15:30 BREAK

16:00 VS Explorer - analysing large scale docking experiments. Marc 
Zimmermann, Fraunhofer-Institute for Algorithms and Scientific Computing 
(SCAI)

16:30 Focused set profiling. Miklos Vargyas, ChemAxon

17:00 closing comments - end of meeting

--------------060602030904090004090503
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</head>
<body bgcolor="#ffffff" text="#000000">
Appologies for multiple postings<br>
<br>
ChemAxon anounces "Program posting" for it's first User Group Meeting
taking place<span class="postbody"> on May 19-20 at the <a
 href="http://www.danubiushotels.com/hotels/hotel.php?id=13&amp;lang=en"
 target="_blank" class="postlink2">Danubius Gellert Hotel</a>,
Budapest, Hungary. <br>
<br>
The meeting will present the latest implementations and research
experience of our users as well as focused technical and scientific
presentations on each of the ChemAxon toolkits by ChemAxon staff. There
will be a development rountable session, a poster session for new
posters and older posters which remain relevant and a hacker room for
informal discussion and problem solving. For further information please
visit the <a href="http://www.chemaxon.com/UGM/05/index.html">UGM home
page</a>, to see the program please visit <a
 href="http://www.chemaxon.com/UGM/05/program.html">this link</a> or
see below.</span><span class="postbody"><br>
<br>
We have a full social program for attendees to enjoy with an informal
garden party at ChemAxon's offices on the evening of the 18th and a
winetasting and banquet within Buda Castle for the evening of the 19th.
There will also be early morning visits to the thermal spa facilities
situated at the hotel. <br>
<br>
We have extended the poster submission deadline until May 15th. Any
attendees wishing to submit original or previously presented posters at
the event should submit abstracts before May 15th. For registration and
poster submission form please see <a
 href="http://www.chemaxon.hu/forum/ftopic272.html">this link</a><br>
<br>
If you would like to register for the event please complete the <a
 href="http://www.chemaxon.hu/forum/ftopic272.html">registration form</a>.
Attendees intending to stay at the meeting hotel are urged to <a
 href="http://www.chemaxon.hu/forum/ftopic261.html">reserve
accommodation</a> before April 25th - when the block booking will lapse.<br>
<br>
I look forward to seeing you in May<br>
<br>
Alex Allardyce<br>
<br>
</span><small>Meeting home page:
<a class="moz-txt-link-freetext"
 href="http://www.chemaxon.com/UGM/05/index.html">http://www.chemaxon.com/UGM/05/index.html</a><br>
<span class="postbody">Event program:
<a class="moz-txt-link-freetext"
 href="http://www.chemaxon.com/UGM/05/program.html">http://www.chemaxon.com/UGM/05/program.html</a></span><br>
To register or submit a poster abstract:
<a class="moz-txt-link-freetext"
 href="http://www.chemaxon.hu/forum/ftopic272.html">http://www.chemaxon.hu/forum/ftopic272.html</a><br>
Poster submission guidelines:
<a class="moz-txt-link-freetext"
 href="http://www.chemaxon.hu/forum/ftopic295.html">http://www.chemaxon.hu/forum/ftopic295.html</a><br>
Accomodation booking: <a class="moz-txt-link-freetext"
 href="http://www.chemaxon.hu/forum/ftopic261.html">http://www.chemaxon.hu/forum/ftopic261.html</a><br>
</small><br>
If you do not wish to recieve any further notifications related to
ChemAxon's User Group Meeting. Please reply to this mail with the
subject line "Remove"
<pre class="moz-signature" cols="72">-- 
Alex Allardyce
Communications Director

Chemaxon Ltd
M&aacute;ramaros k&ouml;z 3/a
Budapest, 1037 Hungary
Tel.: +361 4532658
Fax.: +361 4532659

e-mail: <a class="moz-txt-link-abbreviated"
 href="mailto:aa (a) chemaxon.com">aa (a) chemaxon.com</a>

</pre>
<big><b>UGM Program in full:</b></big><br>
<br>
<u>Thursday, May 19th - morning</u><br>
<br>
9:00 Welcome<br>
<br>
9:15 Virtual Classrooms and E-Learning: Bringing Cheminformatics
Training Into Academic and Industrial Settings. TJ O'Donnell, O'Donnell
Associates <br>
<br>
9:45 What is Marvin and how to..? Szilard Dorant,Tamas Vertse, ChemAxon
<br>
<br>
10:30 BREAK <br>
<br>
11:00 Developing a Compact Chemical Database System Using Marvin Tools.
C. Deniz Akyuz, Merck Research Laboratories <br>
<br>
11:30 Structural search using ChemAxon tools. Szabolcs Csepregi,
ChemAxon <br>
<br>
12:00 ChemAxon's Java Components in a Heterogeneous, Server-Centric
Application Environment. Mark Runyan, CTI Scientific Systems<br>
<br>
12:30 LUNCH and poster session<br>
<br>
Afternoon <br>
<br>
13:30 A Reagent Management System for Requests &amp; Purchasing using
JChem. Robert D. Feinstein, Kelaroo, Inc.<br>
<br>
14:00 JChem Base - structure database engine. Szilard Dorant, ChemAxon<br>
<br>
14:40 BREAK<br>
<br>
15:10 LeadMarker&reg; - an integrated suite for managing chemical and
biological information. Tim Dudgeon, Informatics Matters Ltd<br>
<br>
15:40 Compound storage and retrieval with JChem Cartridge for Oracle.
Peter Kovacs, ChemAxon <br>
<br>
16:10 Closing comments <br>
<br>
<u>Friday May 20th - morning </u><br>
<br>
9:30 Using ChemAxon Toolkits in the GNF Lead Discovery Database.
Yingyao Zhou, Genomics Institute of the Novartis Research Foundation <br>
<br>
10:00 Predicting structure properties with Calculator Plugins. Nora
Mate, Jozsef Szegezdi, ChemAxon <br>
<br>
10:30 Electronic Notebooks &#8211; How ChemAxon tools enable the Chemically
Intelligent Electronic Notebook. Paul<br>
Denny-Gouldson (CEO) / Kevin Gill (tbc), Deffinity Solutions Ltd . <br>
<br>
11:00 BREAK<br>
<br>
11:30 Workflow Cheminformatics. Kanishka Karunanayake, Inforsense <br>
<br>
12:00 Automatic generation of 3D structures and conformers of molecules
in Marvin - Clean/3D (latest developments). Odon Farkas, ChemAxon <br>
<br>
12:15 MarvinSpace - pre-product demonstration. Miklos Vargyas, Judit
Papp, ChemAxon <br>
<br>
12:30 LUNCH and Discussion Roundtable <br>
<br>
Afternoon<br>
<br>
14:00 Seurat: A Tool for navigating SAR. James Baxendale, Celera
Genomics <br>
<br>
14:30 Artificial synthesis. Gyorgy Pirok, ChemAxon <br>
<br>
15:00 Improved Virtual Screening Strategies and Enrichment of Focused
Libraries in Active Compounds Using Target-Oriented Databases. Ismail
Ijjaali, Aureus-Pharma <br>
<br>
15:30 BREAK <br>
<br>
16:00 VS Explorer - analysing large scale docking experiments. Marc
Zimmermann, Fraunhofer-Institute for Algorithms and Scientific
Computing (SCAI) <br>
<br>
16:30 Focused set profiling. Miklos Vargyas, ChemAxon<br>
<br>
17:00 closing comments - end of meeting <br>
</body>
</html>

--------------060602030904090004090503--


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                                                              DFT2005
               11th International Conference on the Applications of Density Functional Theory
                                                    in Chemistry and Physics
-----------------------------------------------------------------------------------------------------

We have already informed you on the organization of

the 11th International Conference on the Applications of Density Functional Theory in Chemistry
and Physics (DFT2005) which be held September 11-15, 2005, in Geneva, Switzerland.

This edition succeeds previous such biennial events organized in Brussels (2003), Madrid (2001),
Rome (1999), Vienna (1997), ... The DFT2005 Conference will be devoted to both 
fundamental and applied aspects of Density Functional Theory (DFT) in Chemistry and Physics.

The main topics covered by the Conference will be recent advances in:

- Fundamental aspects of DFT
- New exchange-correlation and kinetic energy functionals
- Conceptual DFT
- Weak interactions
- Magnetic properties
- Photochemical and photophysical properties
- Reacrivity
- Materials
- Biosystems
- Dynamics
- Etc.

All the informations concerning Conference program, Committees, Registration, Accommodation,
etc., may be found on the web site http://DFT2005.unige.ch

PLEASE NOTE THAT THE DEADLINE FOR SUBMITTING ABSTRACTS OF 
CONTRIBUTIONS HAS BEEN EXTENDED TO APRIL, 15, 2005.

IN ADDITION, AN AD HOC PROCEDURE FOR SUBMITTING REQUESTS FOR GRANTS
ALLOWING CONFERENCE PARTICIPATION IS DESCRIBED ON OUR WEB PAGES. 
THE DEADLINE FOR SUBMITTING THESE REQUESTS IS ALSO APRIL, 15, 2005.

On the behalf of the Organizing Committee:

Prof. Jacques Weber
Department of Physical Chemistry
University of Geneva
30 quai Ernest-Ansermet
CH-1211 Geneva 4, Switzerland
E-mail: DFT2005 _(a)_ sciences.unige.ch

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



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Cc: openbabel-discuss list <openbabel-discuss >< lists.sourceforge.net>
From: Geoff Hutchison <grh25 >< cornell.edu>
Subject: Open Babel Test File Repository
Date: Fri, 1 Apr 2005 14:33:25 -0500
To: chemistry >< ccl.net
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April 1, 2005

Announcing the Open Babel Chemical Test File Repository
-------------------------------------------------------

Today, the Open Babel project is pleased to announce the introduction 
of the Chemical Test File Repository. Many computational chemistry 
packages today support a wide variety of native and exchange file 
formats. Some of these formats have open, formal specifications, but 
realistically, the problem of exchanging molecular and chemical 
computer files and interconverting between formats remains a problem 
even in 2005. File formats evolve over time, files are exchanged which 
do not adhere to published specifications (particularly "PDB" files), 
and formal specifications are not always clear without example files to 
consider.

The test file repository offers an open resource of test files in 
various chemical file formats. All have been made available either 
under the GNU General Public License (GPL) or a Creative Commons 
license which permits reuse and distribution (with attribution).


Importantly these files can be used for testing import/export routines 
in many chemical programs, open and proprietary, not just Open Babel. 
By providing such a resource, we hope that developers of chemical 
software will minimize bugs when translating chemical and molecular 
data between different file formats and different representations. 
Additionally, we hope to encourage the community of chemical software 
developers to support open, well-defined file formats to facilitate 
interconversion and collaboration.


Contributions are requested in a wide variety of chemical and molecular 
file formats -- preferably with a pointer towards a file format 
specification. Contributions MUST include a full description  of the 
program used to generate the file and the name of the format used. The 
more information made available, the better. A form for contributing 
files will be made available shortly.

More details to come:
http://openbabel.sourceforge.net/repository/

Suggestions, comments, and further questions are welcome:
openbabel-discuss >< lists.sourceforge.net

Cheers,
-Geoff