From owner-chemistry@ccl.net Wed Jan 30 07:59:01 2008
From: "Sergio Emanuel Galembeck segalemb||usp.br" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: problem with aim calculation.
Message-Id: <-36158-080130064603-12492-MnBHrtrGKrx3ioJ2o5B+3Q[-]server.ccl.net>
X-Original-From: Sergio Emanuel Galembeck <segalemb===usp.br>
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Date: Wed, 30 Jan 2008 08:43:30 -0200
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Sent to CCL by: Sergio Emanuel Galembeck [segalemb,+,usp.br]
Dear Guermoune,
Do not forget the 6D 10F in your input line:
#p B3P86 6-311++G(3df,2p) aim=3Dall density=3Dcurrent scf=3D(tight,save)
output=3Dwfn scfcyc=3D250 guess=3Dhuckel 6d 10f
Best regards,
Sergio
>>> I used as keywords in the input file:
>>>
>>> #p B3P86 6-311++G(3df,2p) aim=3Dall density=3Dcurrent scf=3D(tight,save)
>>> output=3Dwfn scfcyc=3D250 guess=3Dhuckel
>>>
>>> Can any one have suggestions to result this problem?
>>> (sorry for my English, its the third foreigner language for me)
>>> Yours,
>>>
>>> -----------------------------------
>>> GUERMOUNE Abdeladim.
>>> University Cadi Ayyad
>>> Morocco.>
>>>
>>>
>>
>>
>> --
>> Krzysztof Zborowski
>> Faculty of Chemistry
>> Jagiellonian University
>> 3 Ingardena Street
>> 30-060 Krakow
>> Poland
>> phone: +48(12)632-4888 ext. 2064 or 2067
>> fax: +48(12)634-05-15
>> email: zborowsk*|*chemia.uj.edu.pl
>> ICQ 158385743
>> gg 3817259
>> skype kzys70
>>
>>
>>
>> -=3D This is automatically added to each message by the mailing script =
=3D->
>>
>>
>
>
>
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From owner-chemistry@ccl.net Wed Jan 30 08:46:00 2008
From: "simone Brogi brogi32^^unisi.it" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: RESP CHARGES
Message-Id: <-36159-080129110057-4645-kZXU/ArCNoFNzzsbC3o55A^-^server.ccl.net>
X-Original-From: "simone Brogi" <brogi32(0)unisi.it>
Date: Tue, 29 Jan 2008 11:00:53 -0500
Sent to CCL by: "simone Brogi" [brogi32(!)unisi.it]
Hi, you have ever used like input for find Resp charges in Amber package a Jaguar ESP output file????? thanks
From owner-chemistry@ccl.net Wed Jan 30 09:21:01 2008
From: "Christophe Morell cmorell(_)ujf-grenoble.fr" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL:G: densities in gaussian cube files
Message-Id: <-36160-080130033142-24826-csXal33ncOqXBmQSDxqEhw]-[server.ccl.net>
X-Original-From: Christophe Morell <cmorell-*-ujf-grenoble.fr>
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Date: Wed, 30 Jan 2008 08:33:44 +0100
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Sent to CCL by: Christophe Morell [cmorell[*]ujf-grenoble.fr]
Dear All,
I'm trying to use cube file from Gaussian to visualize local
descriptors such as Fukui functions.
However, it appears that densities written in cube files does not
comply with normalization conditions such as:
somme of the densities=number of electrons
Somme of the densities of the Fukui Function = 1
Am I making a conceptual mistake?
Any suggestion is welcome.
Regards
--
Christophe Morell
_____________________________
French Nuclear Agency (CEA)
INaC/SCIB/LAN
17, Rue des Martyrs
38017 GRENOBLE CEDEX
00 (33) 4 38 78 39 17
Christophe.morell(_)cea.fr
_____________________________
Seek for simplicity- and then distrust it
(A.F. Whitehead)
From owner-chemistry@ccl.net Wed Jan 30 09:56:00 2008
From: "John McKelvey jmmckel-,-gmail.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL:G: problem with aim calculation.
Message-Id: <-36161-080130090712-19315-xvv5JyBnFTLHgcCe4VRfCQ/./server.ccl.net>
X-Original-From: "John McKelvey" <jmmckel:-:gmail.com>
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Sent to CCL by: "John McKelvey" [jmmckel() gmail.com]
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Dear Guermoune,
I do not know the size of your system; I do notice thet a very large basis
set is being used , that the initial guess is Hueckel, and that as many as
250 SCF cycles might be needed.
Could I suggest starting with a much smaller basis set, run the SCF, then
use those SCF MO's to rerun using a somewhat larger basis set, and so-on,
until you get to the basis set you want. This can all be done in a single,
multi-step job, where the same checkpoint file is used for each step and is
saved, and then used for the AIM step. This amy well save a chuck of cpu
time, and help assure solid SCF convergence.
Then, in a second job rerun the last run using the MO's generated there for
the guess, adding the AIM keyword.
Multi-step jobs are quite easy to set up in Gaussian, and are probably well
documented by Gaussian.
Best regards,
John McKelvey
On Jan 30, 2008 5:43 AM, Sergio Emanuel Galembeck segalemb||usp.br <
owner-chemistry*|*ccl.net> wrote:
>
> Sent to CCL by: Sergio Emanuel Galembeck [segalemb,+,usp.br]
> Dear Guermoune,
>
> Do not forget the 6D 10F in your input line:
>
> #p B3P86 6-311++G(3df,2p) aim=all density=current scf=(tight,save)
> output=wfn scfcyc=250 guess=huckel 6d 10f
>
> Best regards,
>
> Sergio
>
> >>> I used as keywords in the input file:
> >>>
> >>> #p B3P86 6-311++G(3df,2p) aim=all density=current scf=(tight,save)
> >>> output=wfn scfcyc=250 guess=huckel
> >>>
> >>> Can any one have suggestions to result this problem?
> >>> (sorry for my English, its the third foreigner language for me)
> >>> Yours,
> >>>
> >>> -----------------------------------
> >>> GUERMOUNE Abdeladim.
> >>> University Cadi Ayyad
> >>> Morocco.>
> >>>
> >>>
> >>
> >>
> >> --
> >> Krzysztof Zborowski
> >> Faculty of Chemistry
> >> Jagiellonian University
> >> 3 Ingardena Street
> >> 30-060 Krakow
> >> Poland
> >> phone: +48(12)632-4888 ext. 2064 or 2067
> >> fax: +48(12)634-05-15
> >> email: zborowsk*|*chemia.uj.edu.pl
> >> ICQ 158385743
> >> gg 3817259
> >> skype kzys70
> >>
> >>
> >>
> >> -= This is automatically added to each message by the mailing script
> =->
> > Job: http://www.ccl.net/jobsConferences:
> > http://server.ccl.net/chemistry/announcements/conferences/
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Dear Guermoune,<br><br>I do not know the size of your system; I do notice thet a very large basis set is being used , that the initial guess is Hueckel, and that as many as 250 SCF cycles might be needed.<br><br>Could I suggest starting with a much smaller basis set, run the SCF, then use those SCF MO's to rerun using a somewhat larger basis set, and so-on, until you get to the basis set you want. This can all be done in a single, multi-step job, where the same checkpoint file is used for each step and is saved, and then used for the AIM step. This amy well save a chuck of cpu time, and help assure solid SCF convergence.<br>
<br> <br><br>Then, in a second job rerun the last run using the MO's generated there for the guess, adding the AIM keyword.<br><br>Multi-step jobs are quite easy to set up in Gaussian, and are probably well documented by Gaussian.<br>
<br>Best regards,<br><br><br>John McKelvey<br><div class="gmail_quote">On Jan 30, 2008 5:43 AM, Sergio Emanuel Galembeck segalemb||usp.br <<a href="mailto:owner-chemistry*|*ccl.net">owner-chemistry*|*ccl.net</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>Sent to CCL by: Sergio Emanuel Galembeck [segalemb,+,<a href="http://usp.br" target="_blank">usp.br</a>]<br>
Dear Guermoune,<br><br> Do not forget the 6D 10F in your input line:<br><br>#p B3P86 6-311++G(3df,2p) aim=all density=current scf=(tight,save)<br> output=wfn scfcyc=250 guess=huckel 6d 10f<br><br> Best regards,<br>
<br> Sergio<br><br>>>> I used as keywords in the input file:<br>>>><br>>>> #p B3P86 6-311++G(3df,2p) aim=all density=current scf=(tight,save)<br>>>> output=wfn scfcyc=250 guess=huckel<br>
>>><br>>>> Can any one have suggestions to result this problem?<br>>>> (sorry for my English, its the third foreigner language for me)<br>>>> Yours,<br>>>><br>>>> -----------------------------------<br>
>>> GUERMOUNE Abdeladim.<br>>>> University Cadi Ayyad<br>>>> Morocco.><br>>>><br>>>><br>>><br>>><br>>> --<br>>> Krzysztof Zborowski<br>>> Faculty of Chemistry<br>
>> Jagiellonian University<br>>> 3 Ingardena Street<br>>> 30-060 Krakow<br>>> Poland<br>>> phone: +48(12)632-4888 ext. 2064 or 2067<br>>> fax: +48(12)634-05-15<br>>> email: zborowsk*|*<a href="http://chemia.uj.edu.pl" target="_blank">chemia.uj.edu.pl</a><br>
>> ICQ 158385743<br>>> gg 3817259<br>>> skype kzys70<br>>><br>>><br>>><br>>>><br>>><br>>><br>
><br>><br>><br>><a href="http://www.ccl.net/chemistry/sub_unsub.shtml" target="_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a>><br>
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From owner-chemistry@ccl.net Wed Jan 30 10:32:00 2008
From: "Carlo Gatti c.gatti(a)istm.cnr.it" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: European Charge Density Meeting 5, ECDM-5 , Lake of Como, Italy
Message-Id: <-36162-080130090911-20618-1NZwHioIRXlSkqcjZVBJMQ[a]server.ccl.net>
X-Original-From: "Carlo Gatti" <c.gatti*|*istm.cnr.it>
Date: Wed, 30 Jan 2008 09:09:07 -0500
Sent to CCL by: "Carlo Gatti" [c.gatti]=[istm.cnr.it]
5th European Charge Density Meeting
Gravedona, Lake of Como (Italy) 6-11 June 2008
http://www.ecdm5.istm.cnr.it/
Please visit this site for all information concerning the meeting.
Topics and keynote lecturers
1) New directions in QTAIM and bond descriptors (A. Martin Pendas, Oviedo)
2) Chemical applications of charge density (D. Stalke, Goettingen)
3) Quantum Chemistry progresses for charge density studies (R. Dovesi, Torino)
4) Effects of extreme environments on chemical bonding (A. Oganov, Zurich)
5) New directions in refinement (B. Dittrich)
6) Intermolecular Interactions Part A: theory of molecular aggregation (A. Gavezzotti, Milano)
7) Intermolecular interactions Part B: a multipolar model approach (P. Coppens, Buffalo)
8) Charge and spin densities in materials science (S. Dahaoui, Nancy)
9) Charge density in the life sciences (P. Luger, Berlin)
10)Large facilities: opportunities and challenges (B. B. Iversen, Aarhus)
Topics and chairs of the ECDM5 Micro-Symposia
1)Chemical bonding in extreme environments: Crystallography under high pressure or electric field (chair: U. Pietsch)
2) Charge, Spin, and Momentum densities in Materials Science (chair: Y. Wang)
3)Large facilities and charge density in the life sciences (chair: J. Helliwell)
4)New functions and descriptors for chemical bonding (chair: M. Kohout)
5)New directions in charge density refinement and density matrix reconstructions (in memory of Niels Hansen) (chair: F. Larsen)
6)Static and dynamical aspects of charge density (chair: R.F.W. Bader.)
7)Molecular interactions : the charge density viewpoint (chair: M. Spackman)
Poster sessions
Each poster will be exposed and discussed for the whole duration of the meeting
Prices
Early registration (Senior: 280 Euro; Junior: 140 Euro)
Travel grants for junior participants
More details on the meeting website http://www.ecdm5.istm.cnr.it/
I'm welcoming you all on the beautiful shores of the Lake of Como in North Italy
Arrivederci,
Carlo Gatti (CNR-ISTM, via Golgi 19, 20133 Milano, Italy)
e-mail : c.gatti*istm.cnr.it
From owner-chemistry@ccl.net Wed Jan 30 12:39:00 2008
From: "Mike Smith scu98rkr_._hotmail.com" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Transition State + Reactions without a Barrier
Message-Id: <-36163-080130120230-574-tU4U4YUR734TGvaTKHH6Ng^^server.ccl.net>
X-Original-From: "Mike Smith" <scu98rkr*_*hotmail.com>
Date: Wed, 30 Jan 2008 12:02:26 -0500
Sent to CCL by: "Mike Smith" [scu98rkr|-|hotmail.com]
Hi,
I've been looking at the addition of O2/OH/HO2 to C5H5.
I can find a transition state for C5H5 + O2. If I then do an IRC calculation you can see a saddle point for the transition state between C5H5+O2 -> C5H5O2.
If I then run a Scan job using opt=z-matrix slowly increasing the O-C bond length, between the C5H5 and the O2. A saddle point is also shown, with a structure very similar to the Transition State.
However with OH/HO2 I can not find a Transition State. Also if I run a Scan job using opt=z-matrix slowly increasing the O-C bond length no saddle point is shown.
Presumably there is no barrier for these reactions ? Therefore no transition state as there is "no saddle point where there is a minimum in all dimensions but one" ?
1. Why is there a transition state for the first case but not the others ? Is it because the Oxygen has a lower heat of formation and is more stable than OH and HO2 radicals and therefore the saddle point is representing the disruption of the stable Oxygen molecule rather than anything to do with the C5H5 ring ?
2. What would be the best way to stop me wasting time looking for transition states for reactions without a barrier. Would a opt=z-matrix scan at along the relevant bond/motion to check for a barrier be a good idea ? Or should my chemistry just be better ?
Thanks
From owner-chemistry@ccl.net Wed Jan 30 13:14:00 2008
From: "Katrin Spiegel katrin.spiegel|gmail.com" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: RESP CHARGES
Message-Id: <-36164-080130115927-32475-4UdI9v1MfI3K0+knb0yOeg() server.ccl.net>
X-Original-From: "Katrin Spiegel" <katrin.spiegel]=[gmail.com>
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Date: Wed, 30 Jan 2008 16:01:24 +0000
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Sent to CCL by: "Katrin Spiegel" [katrin.spiegel- -gmail.com]
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Hi Simone,
try an input file for jaguar like this (changing the method to what you want
and adding the coordinates)
title
&gen
basis=6-31G*
numd=5
dftname=B3LYP
gcharge=-2
wispc=0.75
icfit=1
scalfr=0.9614
ip172=2
&
You'll get an jaguar-esp file in the correct format except for the first
line. You need to put the number of atoms and esp-fit centers on the first
line in 2I5 format.
This should be readable by the resp-module of amber.
best,
Katrin
On Jan 29, 2008 4:00 PM, simone Brogi brogi32^^unisi.it <
owner-chemistry]-[ccl.net> wrote:
>
> Sent to CCL by: "simone Brogi" [brogi32(!)unisi.it]
>
> Hi, you have ever used like input for find Resp charges in Amber package a
> Jaguar ESP output file????? thanks>
>
>
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Hi Simone,<br><br>try an input file for jaguar like this (changing the method to what you want and adding the coordinates)<br><br>title<br>&gen<br>basis=6-31G*<br>numd=5<br>dftname=B3LYP<br>gcharge=-2<br>wispc=0.75<br>
icfit=1<br>scalfr=0.9614<br>ip172=2<br>&<br><br>You'll get an jaguar-esp file in the correct format except for the first line. You need to put the number of atoms and esp-fit centers on the first line in 2I5 format.<br>
This should be readable by the resp-module of amber.<br><br>best,<br><br>Katrin<br><br><br><div class="gmail_quote">On Jan 29, 2008 4:00 PM, simone Brogi brogi32^^<a href="http://unisi.it">unisi.it</a> <<a href="mailto:owner-chemistry]-[ccl.net">owner-chemistry]-[ccl.net</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>Sent to CCL by: "simone Brogi" [brogi32(!)unisi.it]<br><br>Hi, you have ever used like input for find Resp charges in Amber package a Jaguar ESP output file????? thanks<br>
<br><br><br<br<br<br<br><br>E-mail to subscribers: <a href="mailto:CHEMISTRY]-[ccl.net">CHEMISTRY]-[ccl.net</a> or use:<br> <a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target="_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
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From owner-chemistry@ccl.net Wed Jan 30 16:48:01 2008
From: "Abdeladim guermoune lguermoune#hotmail.com" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL:G: problem with aim calculation
Message-Id: <-36165-080130164630-27498-lOoBmwHePe0LzTpODSHIFQ[a]server.ccl.net>
X-Original-From: "Abdeladim guermoune" <lguermoune*hotmail.com>
Date: Wed, 30 Jan 2008 16:46:26 -0500
Sent to CCL by: "Abdeladim guermoune" [lguermoune!=!hotmail.com]
Dear members,
I have use the suggested instruction :
#P B3P86 6-311++G(3DF,2P) DENSITY=CURRENT SCF=(TIGHT,SAVE)
ouTPUT=WFN SCFCYC=250
Without aim keyword, so the wfn file is empty.
Lets remember that the calculation is realized with G03 (version D). The earlier attempts abort with error : THE MOLECULAR GRAPH IS DISCONNECTED ... ABORTING! And again when I try the work as suggested : #p B3P86 6-311++G(3df,2p) aim=all density=current scf=(tight,save) output=wfn scfcyc=250 guess=huckel 6d 10f
I hope that the AIMQB program give the solution as proposed, when the chk file is treated by the program, so any additional keyword in order to get the best chk?
All suggestions are welcome.
And thanks for your help.
Guermoune.
From owner-chemistry@ccl.net Wed Jan 30 19:23:01 2008
From: "N. Sukumar nagams:_:rpi.edu" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL:G: problem with aim calculation
Message-Id: <-36166-080130190731-2212-ov8zyDGw+p7SJkV9dgawtA[#]server.ccl.net>
X-Original-From: "N. Sukumar" <nagams__rpi.edu>
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Sent to CCL by: "N. Sukumar" [nagams-,-rpi.edu]
The AIM keyword has nothing to do with the generation of the WFN file.
Writing the WFN file is controlled by the OUT=WFN keyword, which
specifies that a WFN file is to be written out to the file name specified
in the com file after the coordinate section. Did you remember to
terminate the com file with the name of the WFN file to be written out?
For example...
...coordinate section...
<blank line>
test.wfn
This will write out a test.wfn file. If you check the end of your log
file (after the chk punch file and just before the random quotation) you
will see something like:
Writing a WFN file to test.wfn.
If you didn't specify a WFN file name to write to, this will look like:
Writing a WFN file to .
because there was nowhere to write the WFN file to and g03 probably
dumped your wfn to /dev/null!
N. Sukumar
Associate Research Professor of Chemistry and Chemical Biology
Center for Biotechnology and Interdisciplinary Studies
Rensselaer Polytechnic Institute
http://reccr.chem.rpi.edu/
==============Original message text===============
On Wed, 30 Jan 2008 16:46:26 EST "Abdeladim guermoune
lguermoune#hotmail.com" wrote:
Sent to CCL by: "Abdeladim guermoune" [lguermoune!=!hotmail.com]
Dear members,
I have use the suggested instruction :
#P B3P86 6-311++G(3DF,2P) DENSITY=CURRENT SCF=(TIGHT,SAVE)
ouTPUT=WFN SCFCYC=250
Without aim keyword, so the wfn file is empty.
Lets remember that the calculation is realized with G03 (version D). The
earlier attempts abort with error : THE MOLECULAR GRAPH IS DISCONNECTED
... ABORTING! And again when I try the work as suggested : #p B3P86
6-311++G(3df,2p) aim=all density=current scf=(tight,save) output=wfn
scfcyc=250 guess=huckel 6d 10f
I hope that the AIMQB program give the solution as proposed, when the chk
file is treated by the program, so any additional keyword in order to get
the best chk?
All suggestions are welcome.
And thanks for your help.
Guermoune.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========
From owner-chemistry@ccl.net Wed Jan 30 22:06:01 2008
From: "Anatoli Korkin a_korkin{:}yahoo.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: Invitation to join ASDN.NET - edicational web portal
Message-Id: <-36167-080130220136-10894-tcVvgveEkyQWMrPBBYS+vQ]_[server.ccl.net>
X-Original-From: "Anatoli Korkin" <a_korkin[*]yahoo.com>
Date: Wed, 30 Jan 2008 22:01:32 -0500
Sent to CCL by: "Anatoli Korkin" [a_korkin-*-yahoo.com]
Dear CCL members,
We want to revitalize the venerable ASDN.NET (est. 1998) and transform it
into a lively educational Web portal for atomic and nanoscale materials
aimed at the broad audience. It was dormant for a while but has a deserved
name recognition and high search engine ranking:
http://asdn.net/
We are looking for partners among professionals (professors and teachers)
and students, on a regular basis or occasionally, who are interested
in creating some "pages" or "directories", such as "chemistry", "physics",
"life sciences", "energy", "electronics", etc., where different aspects
of fundamentals or applications of atomistics are addressed. Contributions
of original educational materials or references to useful materials
on the Internet are equally acceptable.
All materials that are incorporated into the ASDN.NET portal will be dully
credited to the respective authors and links to the original or personal
pages will be included. If needed, pages acknowledging author's work or
author personal page or resume can be also housed on the ASDN.NET.
Formal collaboration, like applying for joint grant proposals, is also
an option when a suitable call for proposals is available, along with
an adequate level of expertise and commitment.
Further details will be provided to those interested. Please,
contact me at korkin{at}nanoandgiga.com.
Thank you for your consideration!
Anatoli Korkin
korkin{at}nanoandgiga.com