From owner-chemistry@ccl.net Mon Nov 21 00:11:01 2005
From: "Geoffrey Hutchison grh25^cornell.edu" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: info about .MOL files needed
Message-Id: <-30017-051120021929-443-pn+ZGqAgxEFDqIVJSDK/rA{}server.ccl.net>
X-Original-From: Geoffrey Hutchison <grh25%x%cornell.edu>
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Sent to CCL by: Geoffrey Hutchison [grh25^cornell.edu]
Well, MDL Molfiles have a published specification:
http://www.mdl.com/downloads/public/ctfile/ctfile.jsp

If you're looking for an open package to parse MDL Molfiles, there  
are several (off the top of my head), depending on what you want. For  
example Open Babel is a flexible converter for a wide range of  
chemistry file formats:
Open Babel http://openbabel.sourceforge.net/
CDK        http://cdk.sourceforge.net/
JOELib     http://joelib.sourceforge.net/
Rosetta    http://octetsource.org/

Of course in practice, there are Molfiles which don't adhere to the  
standard, so if you're writing a parser, you might want to be  
flexible about what files you accept.

Cheers,
-Geoff

--
-Dr. Geoffrey Hutchison        <grh25(-)cornell.edu>
Cornell University, Department of Chemistry and Chemical Biology
Abruņa Group                http://abruna.chem.cornell.edu/

On Nov 19, 2005, at 5:30 PM, Roman Garcia nykros]|[gmail.com wrote:

> Sent to CCL by: Roman Garcia [nykros|,|gmail.com]
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>
> Hi,
>   I=B4m new to CCL, sorry if this question has been previously  
> answered, bu=
> t
> CCL search capabilities seems to be disabled. I would like to know  
> if anyon=
> e
> can help me: I need the specification of .MOL files to build a  
> parser to
> extract molecule information. Is there a free parser available?
>  Any usefull information will be apreciated.
>   Thank you in advance. Roman Garcia.
>
> ------=_Part_15806_31969803.1132417002248
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> <div>Hi,</div>
> <div>&nbsp;</div>
> <div>&nbsp; I=B4m new to CCL, sorry if this question has been  
> previously an=
> swered, but CCL search capabilities seems to  
> be&nbsp;disabled.&nbsp;I would=
>  like&nbsp;to know if anyone can&nbsp;help me: I&nbsp;need the  
> specificatio=
> n of .MOL files to build a parser to extract molecule information.  
> Is there=
>  a free parser available?
> </div>
> <div>&nbsp; Any usefull information will be apreciated.</div>
> <div>&nbsp;</div>
> <div>&nbsp; Thank you in advance. Roman Garcia.</div>
> <div>&nbsp;</div>
>
> ------=_Part_15806_31969803.1132417002248--
>
>
>
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From owner-chemistry@ccl.net Mon Nov 21 03:32:00 2005
From: "Van Dam, HJJ \(Huub\) h.j.j.vandam-,-dl.ac.uk" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: Computation of density gradients on Lebedev grids
Message-Id: <-30018-051121032054-7163-Ph8lMWaIPUMF4XZgN1PYMA%a%server.ccl.net>
X-Original-From: "Van Dam, HJJ \(Huub\)" <h.j.j.vandam%dl.ac.uk>
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Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam%%dl.ac.uk]
Hi Rick,

Are you planning to compute the gradient of the density with respect to
the angular coordinates? If so, why? All the codes I know simply compute
the gradient of the density at a grid point with respect to the
cartesian coordinates. For molecular quadratures there seems to be
little reason in doing it any other way.

Best wishes,

   Huub van Dam
   CCLRC Daresbury Laboratory

-----Original Message-----
> From: owner-chemistry%ccl.net [mailto:owner-chemistry%ccl.net] 
Sent: 19 November 2005 12:34
To: Vandam, Huub 
Subject: CCL: Computation of density gradients on Lebedev grids

Sent to CCL by: "Rick Muller" [rmuller=sandia.gov] Can anyone point me
to a reference for the calculation of density gradients on Lebedev
grids? I suspect that one computes the multipole moments of the density
and gets the gradients from there, but I haven't actually ever found a
reference for this, and would be interested in seeing one.

Thanks in advance,

Rick

Rick Muller
rmuller..sandia.govhttp://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 Mon Nov 21 04:17:01 2005
From: "Patrik Jens Johansson patrikj#,#fy.chalmers.se" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: MC routine for relative orientation of two or more molecules
Message-Id: <-30019-051121041511-9539-UDco7DVutMfiE/Iav+VehA!^!server.ccl.net>
X-Original-From: "Patrik Jens Johansson" <patrikj=fy.chalmers.se>


Sent to CCL by: "Patrik Jens Johansson" [patrikj-#-fy.chalmers.se]
Dear CCLers,

I would like to investigate two molecules orientation with respect to each other i.e. let one of them rotate and contact the other in all possible ways - distances / angles etc. Preferrably I would like to make lots of HF or higher single point calcs, both molecules treated "stiff", and then choose among these results for further optimisations to final structures. 
Any suggestions of a routine or subroutine in an existing software?
(The GLOBOP option in GAMESS does not allow two QM units to be used)

Sincerely
/Patrik
patrikj===fy.chalmers.se
Chalmers Univ. of Technology


From owner-chemistry@ccl.net Mon Nov 21 04:51:00 2005
From: "Sergio Emanuel Galembeck segalemb-*-usp.br" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL:G: TDDFT in G03
Message-Id: <-30020-051121043205-20416-9DbSq+bLXGF155Y4Wlr/1Q===server.ccl.net>
X-Original-From: Sergio Emanuel Galembeck <segalemb[a]usp.br>
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Sent to CCL by: Sergio Emanuel Galembeck [segalemb{=}usp.br]
Dear Evgeniy,

   The keyword for these calculations is only TD and 
you combine this with your prefered functional and
basis set (e.g. B3LYP/6-31+G(d,p)).

            Best regards,

                         Sergio
 

Citando "Evgeniy Gromov Evgeniy.Gromov]=[tc.pci.uni-heidelberg.de"
<owner-chemistry.===.ccl.net>:

> Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov]~[tc.pci.uni-heidelberg.de]
> Dear All,
> 
> I wonder whether it is possible to perform TDDFT
> calculation for excited states using Gaussian03.
> I did not find any proper keyword at Gaussian web
> page. I will very appreciate if someone shows me
> an example of Gaussian input for a TDDFT
> calculation. Thanks a lot!
> 
> Best,
> Evgeniy
> 
> -- 
> _______________________________________
> Dr. Evgeniy Gromov
> Theoretische Chemie
> Physikalisch-Chemisches Institut
> Im Neuenheimer Feld 229
> D-69120 Heidelberg
> Germany
> 
> Telefon: +49/(0)6221/545263
> Fax: +49/(0)6221/545221
> E-mail: evgeniy|-|tc.pci.uni-heidelberg.de
> _______________________________________> 
> 
> 
>


From owner-chemistry@ccl.net Mon Nov 21 05:36:00 2005
From: "Noel O Boyle no228]=[cam.ac.uk" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL: Interpretation of Excited States
Message-Id: <-30021-051121052920-23445-IJU5tTo3Ph5S+qd0mwNyPw[#]server.ccl.net>
X-Original-From: "Noel O'Boyle" <no228:-:cam.ac.uk>
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Sent to CCL by: "Noel O'Boyle" [no228{=}cam.ac.uk]
> Question1) Symmetry of orbital No.12 is A1G. Can electron excite 
> gerade representation to gerade representation? (A1G to E1G ?)
Question (1) As far as I know, electronic transitions between orbitals of the same symmetry are forbidden. That is why excited state 7, which is 'G' (i.e. involves a transition between orbitals of the same symmetry), has oscillator strength of 0.
> Question2) Each value of right side of orbital number is wave-function 
> coefficients. Does the plus/minus sign of these coefficients have any 
> quantum meaning for excitaion? 
> If one should pay attention to plus values, "13 -> 47  0.00297" is
> the most effective component of these four relation? Or, when one 
> takes absolute value, "13 -> 22   -0.02923" is the most effective 
> component?
I think you should take the absolute value, or the square of the value.
Note that the square of the values does not add to exactly 100% but
should be in the neighbourhood of 100%.

Noel


From owner-chemistry@ccl.net Mon Nov 21 06:10:00 2005
From: "Michel Petitjean ptitjean{}itodys.jussieu.fr" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: MC routine for relative orientation of two or more molecules
Message-Id: <-30022-051121054212-4021-2ArmIxMqLF0rLFlhs6YDNA,+,server.ccl.net>
X-Original-From: Michel Petitjean <ptitjean(!)itodys.jussieu.fr>
Date: Mon, 21 Nov 2005 11:42:05 +0100 (MET)


Sent to CCL by: Michel Petitjean [ptitjean#%#itodys.jussieu.fr]
To: <chemistry{=}ccl.net>
Subject: CCL: Re: MC routine for relative orientation of two or more molecules

There is an infinity of relative orientations, i.e. rotating and
translating one of the molecule, the other having fixed coordinates.
May be you could sample: random rotations (isotropic law), and random
translations (probability law to be defined carefully).
Other problem, how would you like to rank the results, so that you
select the best ones?

Michel Petitjean,                     Email: petitjean{=}itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)                      ptitjean{=}ccr.jussieu.fr
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html

Sent to CCL by: "Patrik Jens Johansson" [patrikj-#-fy.chalmers.se]
>Dear CCLers,
>
>I would like to investigate two molecules orientation with respect to each other i.e. let one of them rotate and contact the other in all possible ways - distances / angles etc. Preferrably I would like to make lots of HF or higher single point calcs, both molecules treated "stiff", and then choose among these results for further optimisations to final structures. 
>Any suggestions of a routine or subroutine in an existing software?
>(The GLOBOP option in GAMESS does not allow two QM units to be used)
>
>Sincerely
>/Patrik
>patrikj(~)fy.chalmers.se
>Chalmers Univ. of Technology


From owner-chemistry@ccl.net Mon Nov 21 08:40:00 2005
From: "Sean Mooney sdmooney- -iupui.edu" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: CCL and Google Base or Wikipedia
Message-Id: <-30023-051121045953-6897-NHXMecq/YyhWVpGE5z1TKw*_*server.ccl.net>
X-Original-From: Sean Mooney <sdmooney~!~iupui.edu>
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Sent to CCL by: Sean Mooney [sdmooney]^[iupui.edu]
Anyone who has worked with academic computational chemistry software 
knows that bugs/errors in docs do occur.  The nice thing about wiki's is 
that these errors can be fixed immediately after discovery.  In addition 
to protocols, 'factbook' like content is also useful.  Wikipedia may not 
be the appropriate place for this, because anyone can change anything 
(including unregistered users) and there is no required structure of the 
documents (like the references mentioned below).  However, it is pretty 
easy to install the open source MediaWiki software (the tools that drive 
Wikipedia) if someone were so motivated.   This may be attractive 
because required structure can be imposed using templates and limiting 
user access is possible (even if only to registered users, to prevent 
spam).  It is also extensible (after overcoming a learning curve), so 
that developers can imbed their own functionality.  There are other 
reasons that curent wiki's may not be appropriate for scientific 
knowledgebases.  Like the poor controlled vocabulary or ontology 
support, for example.

If anyone is interested in installing and using a wiki feel free to 
email me offline and I would be happy to chat about some of the issues 
we looked at.

-Sean

Perry E. Metzger perry(!)piermont.com wrote:

>Sent to CCL by: "Perry E. Metzger" [perry/a\piermont.com]
>
>"Jim Kress ccl_nospam###kressworks.com" <owner-chemistry_-_ccl.net> writes:
>  
>
>>Sent to CCL by: "Jim Kress" [ccl_nospam]![kressworks.com]
>>Except that recent examination has shown Wikipedia to be riddled with
>>errors, for example:
>>
>>http://arstechnica.com/staff/palatine.ars/2005/10/20/1580
>>
>>So, I would be unwilling to rely on it for any serious purpose.
>>    
>>
>
>I routinely correct errors in chemical factboxes on Wikipedia. In
>general, they aren't too bad. They need more references, the way most
>of Wikipedia does. I find it is often a good place to go for quick
>information, errors or no.
>
>Perry>
>
>
>  
>


From owner-chemistry@ccl.net Mon Nov 21 09:15:01 2005
From: "A. Rajendran raji]-[anal.chem.tohoku.ac.jp" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL:G: TDDFT calculation using g03
Message-Id: <-30024-051121003951-3446-Fv+6OpthzZlI0xc86DQKNg a server.ccl.net>
X-Original-From: "A.  Rajendran" <raji|-|anal.chem.tohoku.ac.jp>


Sent to CCL by: "A.  Rajendran" [raji[*]anal.chem.tohoku.ac.jp]
Dear CCL members,
I have a basic doubt in TDDFT calculation using gaussian03. Can you please explain me the following:
If the Input file for geom opt is:
B3LYP/6-311+G(d) test fopt pop=full gfprint SCRF=(CPCM, Solvent=Water)

Then which one of the following is correct for TDDFT (Singlet) calculation :
 TD(NStates=15, Singlets, Direct)/6-311+G(d) test guess=read geom=check SCRF=(CPCM, Solvent=Water)
         (OR)
 TD(NStates=15, Singlets, Direct) B3LYP/6-311+G(d) Pop(full) test guess=read geom=check SCRF=(CPCM, Solvent=Water)

Being a beginer, it will be very helful for me, if you give me your comments.You can also send mails to raji/at/anal.chem.tohoku.ac.jp  Thanks in advance.
Raj, Japan.


From owner-chemistry@ccl.net Mon Nov 21 09:50:00 2005
From: "Zhao Yuan ccl^^mail.sioc.ac.cn" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL: info about .MOL files needed
Message-Id: <-30025-051121014957-16790-DtAmMLLO0lDDc3/R3Evatg[#]server.ccl.net>
X-Original-From: "Zhao Yuan" <ccl-.-mail.sioc.ac.cn>
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Date: Mon, 21 Nov 2005 14:49:38 +0800
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Sent to CCL by: "Zhao Yuan" [ccl-,-mail.sioc.ac.cn]

--------------Boundary-00=_QMLAQL80000000000000
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I have a paper about MDL file format.  If you need it, I can mail it to y=
ou.=0D
 =0D
-------Original Message-------=0D
 =0D
> From: Roman Garcia nykros]|[gmail.com=0D
Date: 11/20/05 07:15:37=0D
To: Wang, Renxiao =0D
Subject: CCL: info about .MOL files needed=0D
 =0D
Sent to CCL by: Roman Garcia [nykros|,|gmail.com]=0D
------=3D_Part_15806_31969803.1132417002248=0D
Content-Type: text/plain; charset=3DISO-8859-1=0D
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 =0D
Hi,=0D
  I=3DB4m new to CCL, sorry if this question has been previously answered=
, bu=3D=0D
t=0D
CCL search capabilities seems to be disabled. I would like to know if any=
on=3D=0D
e=0D
can help me: I need the specification of .MOL files to build a parser to=0D
extract molecule information. Is there a free parser available?=0D
  Any usefull information will be apreciated.=0D
  Thank you in advance. Roman Garcia.=0D
 =0D
------=3D_Part_15806_31969803.1132417002248=0D
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<div>Hi,</div>=0D
<div>&nbsp;</div>=0D
<div>&nbsp; I=3DB4m new to CCL, sorry if this question has been previousl=
y an=3D=0D
swered, but CCL search capabilities seems to be&nbsp;disabled.&nbsp;I wou=
ld=3D=0D
  like&nbsp;to know if anyone can&nbsp;help me: I&nbsp;need the
specificatio=3D=0D
n of .MOL files to build a parser to extract molecule information. Is the=
re=3D=0D
  a free parser available?=0D
</div>=0D
<div>&nbsp; Any usefull information will be apreciated.</div>=0D
<div>&nbsp;</div>=0D
<div>&nbsp; Thank you in advance. Roman Garcia.</div>=0D
<div>&nbsp;</div>=0D
 =0D
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<DIV>I have a paper about MDL file format.&nbsp;&nbsp;If you need it, I c=
an mail it to you.</DIV>
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IV>
<DIV>&nbsp;</DIV>
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<DIV dir=3Dltr style=3D"FONT-SIZE: 11pt"><I><B>From:</B></I> <A href=3D"m=
ailto:owner-chemistry\a/ccl.net">Roman Garcia nykros]|[gmail.com</A></DIV>
<DIV dir=3Dltr style=3D"FONT-SIZE: 11pt"><I><B>Date:</B></I> 11/20/05 07:=
15:37</DIV>
<DIV dir=3Dltr style=3D"FONT-SIZE: 11pt"><I><B>To:</B></I> <A href=3D"mai=
lto:ccl\a/mail.sioc.ac.cn">Wang, Renxiao </A></DIV>
<DIV dir=3Dltr style=3D"FONT-SIZE: 11pt"><I><B>Subject:</B></I> CCL: info=
 about .MOL files needed</DIV></DIV>
<DIV>&nbsp;</DIV>
<DIV>Sent to CCL by: Roman Garcia [nykros|,|gmail.com]</DIV>
<DIV>------=3D_Part_15806_31969803.1132417002248</DIV>
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<DIV>Hi,</DIV>
<DIV>&nbsp;&nbsp;I=3DB4m new to CCL, sorry if this question has been prev=
iously answered, bu=3D</DIV>
<DIV>t</DIV>
<DIV>CCL search capabilities seems to be disabled. I would like to know i=
f anyon=3D</DIV>
<DIV>e</DIV>
<DIV>can help me: I need the specification of .MOL files to build a parse=
r to</DIV>
<DIV>extract molecule information. Is there a free parser available?</DIV=
>
<DIV>&nbsp; Any usefull information will be apreciated.</DIV>
<DIV>&nbsp;&nbsp;Thank you in advance. Roman Garcia.</DIV>
<DIV>&nbsp;</DIV>
<DIV>------=3D_Part_15806_31969803.1132417002248</DIV>
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<DIV>&lt;div&gt;&amp;nbsp; I=3DB4m new to CCL, sorry if this question has=
 been previously an=3D</DIV>
<DIV>swered, but CCL search capabilities seems to be&amp;nbsp;disabled.&a=
mp;nbsp;I would=3D</DIV>
<DIV>&nbsp; like&amp;nbsp;to know if anyone can&amp;nbsp;help me: I&amp;n=
bsp;need the specificatio=3D</DIV>
<DIV>n of .MOL files to build a parser to extract molecule information. I=
s there=3D</DIV>
<DIV>&nbsp; a free parser available?</DIV>
<DIV>&lt;/div&gt;</DIV>
<DIV>&lt;div&gt;&amp;nbsp; Any usefull information will be apreciated.&lt=
;/div&gt;</DIV>
<DIV>&lt;div&gt;&amp;nbsp;&lt;/div&gt;</DIV>
<DIV>&lt;div&gt;&amp;nbsp; Thank you in advance. Roman Garcia.&lt;/div&gt=
;</DIV>
<DIV>&lt;div&gt;&amp;nbsp;&lt;/div&gt;</DIV>
<DIV>&nbsp;</DIV>
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From owner-chemistry@ccl.net Mon Nov 21 10:25:00 2005
From: "Eileen McKelvey eomckel]*[attglobal.net" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL:G: TDDFT in G03
Message-Id: <-30026-051121052807-22597-yYe1GfABltLLr2SCVvIS7g[]server.ccl.net>
X-Original-From: Eileen McKelvey <eomckel(~)attglobal.net>
Content-Transfer-Encoding: 7bit
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Date: Mon, 21 Nov 2005 04:49:29 -0500
MIME-Version: 1.0


Sent to CCL by: Eileen McKelvey [eomckel\a/attglobal.net]
Probably not there..  Definitely in Turbomole...

Evgeniy Gromov Evgeniy.Gromov]=[tc.pci.uni-heidelberg.de wrote:

>Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov]~[tc.pci.uni-heidelberg.de]
>Dear All,
>
>I wonder whether it is possible to perform TDDFT
>calculation for excited states using Gaussian03.
>I did not find any proper keyword at Gaussian web
>page. I will very appreciate if someone shows me
>an example of Gaussian input for a TDDFT
>calculation. Thanks a lot!
>
>Best,
>Evgeniy
>
>  
>


From owner-chemistry@ccl.net Mon Nov 21 11:00:01 2005
From: "Zhijian Wu zhijw**hotmail.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: TDDFT in G03
Message-Id: <-30027-051121012129-30789-kc3HqW59mMwSJpvAgqos6Q++server.ccl.net>
X-Original-From: "Zhijian Wu" <zhijw.:.hotmail.com>
Content-Type: text/html; format=flowed
Date: Mon, 21 Nov 2005 00:34:09 -0500
Mime-Version: 1.0


Sent to CCL by: "Zhijian Wu" [zhijw,+,hotmail.com]
<html><div style='background-color:'><DIV class=RTE>
<P>Hi,</P>
<P>&nbsp;</P>
<P>A simple input file will look like:</P>
<P>&nbsp;</P>
<P>b3lyp/6-31g(d) td(nstates=...)</P>
<P>&nbsp;</P>
<P>But I do not know if it is possible to optimize the excited states using TDDFT.</P>
<P>&nbsp;</P>
<P>Regards,</P>
<P>&nbsp;</P>
<P>Wu<BR><BR></P></DIV>
<DIV></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #a0c6e5 2px solid; MARGIN-RIGHT: 0px"><FONT style="FONT-SIZE: 11px; FONT-FAMILY: tahoma,sans-serif">
<HR color=#a0c6e5 SIZE=1>

<DIV></DIV>From:&nbsp;&nbsp;<I>"Evgeniy Gromov Evgeniy.Gromov]=[tc.pci.uni-heidelberg.de" &lt;owner-chemistry*ccl.net&gt;</I><BR>Reply-To:&nbsp;&nbsp;<I>"CCL Subscribers" &lt;chemistry*ccl.net&gt;</I><BR>To:&nbsp;&nbsp;<I>"Wu, Zhijian " &lt;zhijw*hotmail.com&gt;</I><BR>Subject:&nbsp;&nbsp;<I>CCL:G: TDDFT in G03</I><BR>Date:&nbsp;&nbsp;<I>Mon, 21 Nov 2005 00:13:29 -0500</I><BR>&gt;Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov]~[tc.pci.uni-heidelberg.de]<BR>&gt;Dear All,<BR>&gt;<BR>&gt;I wonder whether it is possible to perform TDDFT<BR>&gt;calculation for excited states using Gaussian03.<BR>&gt;I did not find any proper keyword at Gaussian web<BR>&gt;page. I will very appreciate if someone shows me<BR>&gt;an example of Gaussian input for a TDDFT<BR>&gt;calculation. Thanks a 
lot!<BR>&gt;<BR>&gt;Best,<BR>&gt;Evgeniy<BR>&gt;<BR>&gt;--<BR>&gt;_______________________________________<BR>&gt;Dr. Evgeniy Gromov<BR>&gt;Theoretische Chemie<BR>&gt;Physikalisch-Chemisches Institut<BR>&gt;Im Neuenheimer Feld 229<BR>&gt;D-69120 Heidelberg<BR>&gt;Germany<BR>&gt;<BR>&gt;Telefon: +49/(0)6221/545263<BR>&gt;Fax: +49/(0)6221/545221<BR>&gt;E-mail: evgeniy|-|tc.pci.uni-heidelberg.de<BR>&gt;_______________________________________<BR>&gt;<BR>&gt;<BR>&gt;<BR>&gt;<BR>&gt;<BR>&gt;<BR>&gt;<BR>&gt;<BR>&gt;<BR>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<BR>&gt;<BR>&gt;<BR>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<BR>&gt;<BR>&gt;Subscribe/Unsubscribe:<BR>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<BR>&gt;<BR>&gt;<BR>&gt;<BR>&gt;Job advertisements: http://www.ccl.net/jobs<BR>&gt;<BR>&gt;<BR>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<BR>&gt;<BR>&gt;<BR>&gt;<BR>&gt;<BR>&gt;<BR></FONT></BLOCKQUOTE></div></html>


From owner-chemistry@ccl.net Mon Nov 21 11:35:01 2005
From: "Jamie Platts platts a Cardiff.ac.uk" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: info about .MOL files needed
Message-Id: <-30028-051121111800-21753-QptQ5L36p/GdBmb65zYScw:_:server.ccl.net>
X-Original-From: "Jamie Platts" <platts%a%Cardiff.ac.uk>
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Date: Mon, 21 Nov 2005 15:17:06 +0000
Mime-Version: 1.0


Sent to CCL by: "Jamie Platts" [platts|*|Cardiff.ac.uk]
Try

www.mdl.com/downloads/public/ctfile/ctfile.pdf 

Jamie

>>> owner-chemistry[#]ccl.net 11/21/05 2:59 pm >>>

Hi,
  Im new to CCL, sorry if this question has been previously answered, but
CCL search capabilities seems to be disabled. I would like to know if anyone
can help me: I need the specification of .MOL files to build a parser to
extract molecule information. Is there a free parser available?
  Any usefull information will be apreciated.
  Thank you in advance. Roman Garcia.


From owner-chemistry@ccl.net Mon Nov 21 12:10:00 2005
From: "errol lewars elewars[]trentu.ca" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL:G: TDDFT in G03
Message-Id: <-30029-051121095959-16354-KVxv/chnu9XZDecI+fRKAw^_^server.ccl.net>
X-Original-From: errol lewars <elewars(a)trentu.ca>
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Date: Mon, 21 Nov 2005 09:57:16 -0500
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Sent to CCL by: errol lewars [elewars++trentu.ca]
2005 Nov 21

Hello,

Here is an input for a TDDFT calc with Gaussian 98; it's likely the same 
with G03:

%Mem=4000000
 # B3P86/6-311++G** TD=(Singlets,NStates=6)
   Maxdisk=240000000

TDDFT UV of acetone, using AM1 geom.

0 1
 6   1.264222744   0.000000000  -0.156750059
 6   0.000000000   0.000000000   0.641444070
 8   0.000000000   0.000000000   1.876769041
 6  -1.264222744   0.000000000  -0.156750059
 1  -2.158188121   0.000000000   0.512875067
 1  -1.299017032  -0.907246026  -0.807615755
 1  -1.299017032   0.907246026  -0.807615755
 1   2.158188121   0.000000000   0.512875067
 1   1.299017032   0.907246026  -0.807615755
 1   1.299017032  -0.907246026  -0.807615755

E. Lewars
====


Evgeniy Gromov Evgeniy.Gromov]=[tc.pci.uni-heidelberg.de wrote:

>Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov]~[tc.pci.uni-heidelberg.de]
>Dear All,
>
>I wonder whether it is possible to perform TDDFT
>calculation for excited states using Gaussian03.
>I did not find any proper keyword at Gaussian web
>page. I will very appreciate if someone shows me
>an example of Gaussian input for a TDDFT
>calculation. Thanks a lot!
>
>Best,
>Evgeniy
>
>  
>


From owner-chemistry@ccl.net Mon Nov 21 12:45:01 2005
From: "Mariusz Sterzel msterzel_._buffalo.edu" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL:G: TDDFT in G03
Message-Id: <-30030-051121121510-13192-0rmuPxuXf8bntmyVVdYw+Q_._server.ccl.net>
X-Original-From: Mariusz Sterzel <msterzel(a)buffalo.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Mon, 21 Nov 2005 11:14:59 -0500 (EST)
MIME-Version: 1.0


Sent to CCL by: Mariusz Sterzel [msterzel_-_buffalo.edu]
If you mean TDDFT geometry optimization for excited states Turbomole is 
the right answer but you can also do numerical geometry optimization using 
gaussian. Take a look at:

http://kekule.osc.edu/cgi-bin/ccl/message.cgi?2002+04+11+009

It uses Z-matrix but is terribly slow because of numerical gradients. The 
other disadvantage is you cannot calculate frequencies for excited state.


Mariusz




--
Mariusz Sterzel
Email: msterzel/^at^\buffalo.edu



On Mon, 21 Nov 2005, Eileen McKelvey eomckel]*[attglobal.net wrote:

> Sent to CCL by: Eileen McKelvey [eomckel\a/attglobal.net]
> Probably not there..  Definitely in Turbomole...
>
> Evgeniy Gromov Evgeniy.Gromov]=[tc.pci.uni-heidelberg.de wrote:
>
>> Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov]~[tc.pci.uni-heidelberg.de]
>> Dear All,
>>
>> I wonder whether it is possible to perform TDDFT
>> calculation for excited states using Gaussian03.
>> I did not find any proper keyword at Gaussian web
>> page. I will very appreciate if someone shows me
>> an example of Gaussian input for a TDDFT
>> calculation. Thanks a lot!
>>
>> Best,
>> Evgeniy
>>
>>
>>


From owner-chemistry@ccl.net Mon Nov 21 16:56:00 2005
From: "Roman Garcia nykros : gmail.com" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: info about .MOL files needed
Message-Id: <-30031-051121155359-4110-7h+0ITqyyx1mi5cFVsm06A[*]server.ccl.net>
X-Original-From: Roman Garcia <nykros++gmail.com>
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Mon, 21 Nov 2005 17:53:54 -0300
MIME-Version: 1.0


Sent to CCL by: Roman Garcia [nykros*o*gmail.com]
  Thanks for all your responses. The .mol files are very well
documented, but It seems I will be reinventing the wheel if I program
another parser. I was pointed to OpenBabel, CDK, JOELib and Rosetta.
What are your personal experiences with  these opensource pakages?
JOELib looks pretty inpresive. What kind of performace can i expect
> from JAVA libraries? (CDK, JOELib and Rosetta are written in JAVA).

  Thanks in advance. Roman.


From owner-chemistry@ccl.net Mon Nov 21 18:05:01 2005
From: "Brian Salter-Duke b_duke**octa4.net.au" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: CCL and Google Base or Wikipedia
Message-Id: <-30032-051121165553-12204-Cy4+2zRZ8g945Kzv/5SbnA(_)server.ccl.net>
X-Original-From: Brian Salter-Duke <b_duke]_[octa4.net.au>
Content-Disposition: inline
Content-Type: text/plain; charset=us-ascii
Date: Tue, 22 Nov 2005 08:55:11 +1100
Mime-Version: 1.0


Sent to CCL by: Brian Salter-Duke [b_duke*|*octa4.net.au]
On Mon, Nov 21, 2005 at 09:08:13AM -0500, Sean Mooney sdmooney- -iupui.edu wrote:
> Sent to CCL by: Sean Mooney [sdmooney]^[iupui.edu]
> Anyone who has worked with academic computational chemistry software 
> knows that bugs/errors in docs do occur.  The nice thing about wiki's is 
> that these errors can be fixed immediately after discovery.  In addition 
> to protocols, 'factbook' like content is also useful.  Wikipedia may not 
> be the appropriate place for this, because anyone can change anything 
> (including unregistered users) and there is no required structure of the 
> documents (like the references mentioned below).  However, it is pretty 
> easy to install the open source MediaWiki software (the tools that drive 
> Wikipedia) if someone were so motivated.   This may be attractive 
> because required structure can be imposed using templates and limiting 
> user access is possible (even if only to registered users, to prevent 
> spam).  It is also extensible (after overcoming a learning curve), so 
> that developers can imbed their own functionality.  There are other 
> reasons that curent wiki's may not be appropriate for scientific 
> knowledgebases.  Like the poor controlled vocabulary or ontology 
> support, for example.

I think you underestimate the strength of the open source approach in
Wikipedia. Anyone can alter stuff, but there are users and those
designated as administrators who keep a pretty close eye on changes and 
fix "spam" changes quickly. Also "spam" changes are not common, particularly
in scientific and technical pages. There is a kind of structure and
plenty of peer pressurte to make pages fit the standards.

A good example of how it works is indeed the Bill Gates page. Have a
look at that page now. It is excellent.

How do you propose to "impose' structure? Who imposes it? Who decides on
the structure? If there is structure and imposition, people will
probably not do it for free. Who is going to pay them?

I think the aswer is for us, as a community, to work to improve
wikipedia. Of course not everything suits wikipedia. It is, after all, a
"pedia". Another wiki might be usefull for another purpose, but for
"pedia"-like entries, wikipedia is great and can be better.


> If anyone is interested in installing and using a wiki feel free to 
> email me offline and I would be happy to chat about some of the issues 
> we looked at.
> 
> -Sean
> 
> Perry E. Metzger perry(!)piermont.com wrote:
> 
> >Sent to CCL by: "Perry E. Metzger" [perry/a\piermont.com]
> >
> >"Jim Kress ccl_nospam###kressworks.com" <owner-chemistry_-_ccl.net> writes:
> >  
> >
> >>Sent to CCL by: "Jim Kress" [ccl_nospam]![kressworks.com]
> >>Except that recent examination has shown Wikipedia to be riddled with
> >>errors, for example:
> >>
> >>http://arstechnica.com/staff/palatine.ars/2005/10/20/1580
> >>
> >>So, I would be unwilling to rely on it for any serious purpose.
> >>    
> >>
> >
> >I routinely correct errors in chemical factboxes on Wikipedia. In
> >general, they aren't too bad. They need more references, the way most
> >of Wikipedia does. I find it is often a good place to go for quick
> >information, errors or no.
> >
> >Perry> 
> 
> 

-- 
         Brian Salter-Duke (Brian Duke) b_duke!A!octa4.net.au  
       Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia
    Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/
Honorary Researcher, Chem., Melbourne Univ. & Med. Chem., Monash Univ.