From owner-chemistry@ccl.net Tue Jun 27 00:27:00 2006 From: "Igor Schweigert igor.schweigert()gmail.com" To: CCL Subject: CCL: Schwartz-like inequality on Coulomb and exchange integrals Message-Id: <-32019-060626120814-24701-W2OYbZhCPGGDsppjaLWivg(_)server.ccl.net> X-Original-From: "Igor Schweigert" Content-Type: multipart/alternative; boundary="----=_Part_52700_31643313.1151338075388" Date: Mon, 26 Jun 2006 09:07:55 -0700 MIME-Version: 1.0 Sent to CCL by: "Igor Schweigert" [igor.schweigert : gmail.com] ------=_Part_52700_31643313.1151338075388 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Sudhir, Thanks for the references, I have looked up the JCP and truly enjoyed reading it as it may give me a lead towards other issues I had. I need to spend more time following the references therein. Igor On 6/25/06, Dr. Sudhir A. Kulkarni sudhirk(_)vlifesciences.com < owner-chemistry*ccl.net> wrote: > > Sent to CCL by: "Dr. Sudhir A. Kulkarni" [sudhirk(a)vlifesciences.com] > Igor, > > Look at following papers. > Rigorous bounds to molecular electron repulsion and electro-static > potential integrals: > S.R. Gadre, S.A. Kulkarni, R.K. Pathak J. Chem. Phys. 91, 3596-3602 > (1989). > > Some aspects of parallelization of two-electron integrals in molecular > orbital programs > S.R. Gadre, S.A. Kulkarni, A.C. Limaye, R.N. Shirsat Z. Phys.D-Atoms, > Molecules and Clusters 18, 357-363 (1991) > > If you don't get these papers yourself write a request to Professor Gadre > at > gadre,+,chem.unipune.ernet.in > > Hope this is useful. > Regards. > > Sudhir > > Igor Schweigert ischweig-.-uci.edu wrote: > > >Sent to CCL by: "Igor Schweigert" [ischweig[a]uci.edu] > >------=_Part_26477_20075059.1151085235334 > >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >Content-Transfer-Encoding: 7bit > >Content-Disposition: inline > > > >Hi, > > > >I wonder if someone knows a reference to a discussion of the inequality > >between the Coulomb- and exchange-type ERI of two basis functions : > > > >(ij|ji) <= (ii|jj) (Mulliken notation) > > > >I know I've seen it discussed somewhere but cannot recall where. I've > tried > >Web of Science and Google Scholar searches but to no avail (most matches > >lead to the Schwartz condition on the four-index ERI). > > > >Thanks in advance, > >Igor > > > >------=_Part_26477_20075059.1151085235334 > >Content-Type: text/html; charset=ISO-8859-1 > >Content-Transfer-Encoding: 7bit > >Content-Disposition: inline > > > >Hi,
> >
> >I wonder if someone knows a reference to a discussion of > >the inequality between the Coulomb- and exchange-type ERI of two basis > >functions :
> >
> >(ij|ji) <= (ii|jj)  (Mulliken notation)
> >
> >I know I've seen it discussed somewhere but > >cannot recall where. I've tried Web of Science and Google Scholar > >searches but to no avail (most matches lead to the Schwartz condition on > the four-index ERI).
> >
> >Thanks in advance,
> >Igor
> >
> >
> >
> > > >------=_Part_26477_20075059.1151085235334--> > > > > > > > > > > > > -- > Sudhir A. Kulkarni, Ph.D. > VLife Sciences Technologies Pvt. Ltd. > 1 Akshay, 50 Anand Park > Aundh, Pune 411007 > INDIA > Tel: +91-20-2588-6737 > > > ---------------------------------------------------------------------------------------------------------------------------------------- > VLife Sciences Technologies Pvt Ltd.(VLife); Mail Disclaimer: This e-mail > and any files transmitted with it are confidential and the views expressed > in the same are not necessarily the views of VLife, and its Directors, > Management, Employees or Associates. This communication represents the > originator's personal views and opinions. If you are not the intended > recipient or the person responsible for delivering the e-mail to the > intended recipient, be advised that you have received this e-mail by error, > and that any use, dissemination, forwarding, printing, or copying of this > e-mail is strictly prohibited. You shall be under obligation to keep the > contents of this e-mail, strictly confidential and shall not disclose, > disseminate or divulge the same to any Person, Company, Firm or Entity. > Please ensure you have adequate virus protection before you open or detach > any documents from this transmission. VLife does not accept any liability > for virus. If you received this e-mail in ! > error, please immediately notify info,+,VLifeSciences.com. The rights to > monitor all e-mail communication through our network are reserved with us. > > ----------------------------------------------------------------------------------------------------------------------------------------> > > > ------=_Part_52700_31643313.1151338075388 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Sudhir,

Thanks for the references, I have looked up the JCP and truly enjoyed reading it as it may give me a lead towards other issues I had. I need to spend more time following the references therein.

Igor


On 6/25/06, Dr. Sudhir A. Kulkarni sudhirk(_)vlifesciences.com <owner-chemistry*ccl.net> wrote:
Sent to CCL by: "Dr. Sudhir A. Kulkarni" [sudhirk(a)vlifesciences.com]
Igor,

Look at following papers.
Rigorous bounds to molecular electron repulsion and electro-static
potential integrals:
S.R. Gadre, S.A. Kulkarni, R.K. Pathak J. Chem. Phys. 91, 3596-3602 (1989).

Some aspects of parallelization of two-electron integrals in molecular
orbital programs
S.R. Gadre, S.A. Kulkarni, A.C. Limaye, R.N. Shirsat Z. Phys.D-Atoms,
Molecules and Clusters 18, 357-363 (1991)

If you don't get these papers yourself write a request to Professor Gadre at
gadre,+,chem.unipune.ernet.in

Hope this is useful.
Regards.

Sudhir

Igor Schweigert ischweig-.-uci.edu wrote:

>Sent to CCL by: "Igor Schweigert" [ischweig[a]uci.edu]
>------=_Part_26477_20075059.1151085235334
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>Content-Transfer-Encoding: 7bit
>Content-Disposition: inline
>
>Hi,
>
>I wonder if someone knows a reference to a discussion of the inequality
>between the Coulomb- and exchange-type ERI of two basis functions :
>
>(ij|ji) <= (ii|jj)  (Mulliken notation)
>
>I know I've seen it discussed somewhere but cannot recall where. I've tried
>Web of Science and Google Scholar searches but to no avail (most matches
>lead to the Schwartz condition on the four-index ERI).
>
>Thanks in advance,
>Igor
>
>------=_Part_26477_20075059.1151085235334
>Content-Type: text/html; charset=ISO-8859-1
>Content-Transfer-Encoding: 7bit
>Content-Disposition: inline
>
>Hi,<br>
><br>
>I wonder if someone knows a reference to a discussion of
>the inequality between the Coulomb- and exchange-type ERI of two basis
>functions :<br>
><br>
>(ij|ji) &lt;= (ii|jj)&nbsp; (Mulliken notation)<br>
><br>
>I know I've seen it discussed somewhere but
>cannot recall where. I've tried Web of Science and Google Scholar
>searches but to no avail (most matches lead to the Schwartz condition on the four-index ERI). <br>
><br>
>Thanks in advance,<br>
>Igor<br>
><br>
><br>
><br>
>
>------=_Part_26477_20075059.1151085235334-->
>
>
>
>
>

--
Sudhir A. Kulkarni, Ph.D.
VLife Sciences Technologies Pvt. Ltd.
1 Akshay, 50 Anand Park
Aundh, Pune 411007
INDIA
Tel: +91-20-2588-6737

----------------------------------------------------------------------------------------------------------------------------------------
VLife Sciences Technologies Pvt Ltd.(VLife); Mail Disclaimer: This e-mail and any files transmitted with  it are confidential and the views expressed in the same are not necessarily the  views of VLife, and its Directors, Management, Employees or Associates. This communication represents the originator's personal views and opinions. If you are not the intended recipient or the person responsible for delivering the e-mail to the intended recipient, be advised that you have received this e-mail by error, and that any use, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. You shall be under obligation to keep the contents of this e-mail, strictly confidential and shall not disclose, disseminate or divulge the same to any Person, Company, Firm or Entity. Please ensure you have adequate virus protection before you open or detach any documents from this transmission. VLife does not accept any liability for virus. If you received this e-mail in !
error, please immediately notify info,+,VLifeSciences.com. The rights to monitor all e-mail communication through our network are reserved with us.
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------=_Part_52700_31643313.1151338075388-- From owner-chemistry@ccl.net Tue Jun 27 04:15:01 2006 From: "Orlin Blajiev blajiev_-_vub.ac.be" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32020-060627041056-15169-Hgy/nodtYijSnfRONwBHdA!^!server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 27 Jun 2006 10:10:36 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be] Hi, I will appreciate some help with the following question. I have the following input for Gaussian-how can I ask for a individual basis set for Ag as 6-31 is not available for it. %chk=clBHA.chk %mem=20000000 # opt freq b3lyp/6-31g(d) formcheck output=wfn XX clBHAN311.log 0 1 O 1.03535 -1.04284 0.02249 C 0.41990 0.04621 0.23888 C -1.06633 0.06016 0.14887 C -1.75191 -1.11823 0.41903 C -3.13397 -1.16168 0.35358 C -3.82195 -0.01875 0.00104 C -3.16803 1.15775 -0.29437 C -1.78409 1.19172 -0.22084 N 1.03103 1.15471 0.56393 H 0.53306 1.97165 0.81387 O 2.41620 1.28733 0.63971 Ag 3.35043 -0.74343 0.20642 H -1.19437 -1.99336 0.67135 H -3.66278 -2.06484 0.56731 Cl -5.62080 -0.06847 -0.08841 H -3.71992 2.02505 -0.58447 H -1.27777 2.09764 -0.48124 Best regards, Orlin -- Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 From owner-chemistry@ccl.net Tue Jun 27 05:18:00 2006 From: "Marius Retegan marius.retegan|,|yahoo.com" To: CCL Subject: CCL:G: plot interatomic distances from a gaussian optimization log Message-Id: <-32021-060627051547-9905-UdeME4FFagwTagvkHB4xAw+/-server.ccl.net> X-Original-From: Marius Retegan Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1589413850-1151399739=:31513" Date: Tue, 27 Jun 2006 02:15:39 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Marius Retegan [marius.retegan]~[yahoo.com] --0-1589413850-1151399739=:31513 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL Does anybody know a free software that can plot the values of a distance from a gaussian optimization log. I know that gOpenMol can do this but it requires a fchk and I don't have a the chk. Thank you --0-1589413850-1151399739=:31513 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL

Does anybody know a free software that can plot the values of a distance from a gaussian optimization log. I know that gOpenMol can do this but it requires a fchk and I don't have a the chk.

Thank you
 --0-1589413850-1151399739=:31513-- From owner-chemistry@ccl.net Tue Jun 27 06:15:00 2006 From: "=?iso-8859-1?q?=D6d=F6n_Farkas?= farkas()chem.elte.hu" To: CCL Subject: CCL: Free conformer generators Message-Id: <-32022-060627010807-22486-W2OYbZhCPGGDsppjaLWivg-*-server.ccl.net> X-Original-From: =?iso-8859-1?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 26 Jun 2006 20:19:45 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?q?=D6d=F6n_Farkas?= [farkas!=!chem.elte.hu] Hi Paul, I made a post on Thursday already about 3D structure generation (Subject: CCL: Request for a program code), the same applies to conformer search. Conformer generation is available in Chemaxon's Marvin, which is free for academic users, free websites and evaluation: http://www.chemaxon.com/marvin The latest developments (including conformer search) are available in alpha stage (Marvin 4.1): http://www.chemaxon.com/shared/alpha/marvin/ Best wishes, Ödön -- Odon Farkas Research Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány Péter sétány H-1117 Budapest, Hungary From owner-chemistry@ccl.net Tue Jun 27 06:49:01 2006 From: "kefalidi(a)chem.auth.gr" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32023-060627063231-20333-RW0Y2I1bb1XY8dnYJsgzNA,server.ccl.net> X-Original-From: kefalidi]^[chem.auth.gr Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-7; format="flowed" Date: Tue, 27 Jun 2006 12:29:19 +0300 MIME-Version: 1.0 Sent to CCL by: kefalidi-*-chem.auth.gr Hi Orlin, The basis set you asked for the Ag atom is not available because Ag is a second row transition metal. For information about all the basis set that you can use for the Ag atom or any other atom, you can visit the site http://www.emsl.pnl.gov/forms/basisform.html Christos Quoting "Orlin Blajiev blajiev_-_vub.ac.be" : > Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be] > Hi, > > I will appreciate some help with the following question. I have the > following input for Gaussian-how can I ask for a individual basis set > for Ag as 6-31 is not available for it. > > %chk=clBHA.chk > %mem=20000000 > # opt freq b3lyp/6-31g(d) formcheck output=wfn > > XX clBHAN311.log > > 0 1 > O 1.03535 -1.04284 0.02249 > C 0.41990 0.04621 0.23888 > C -1.06633 0.06016 0.14887 > C -1.75191 -1.11823 0.41903 > C -3.13397 -1.16168 0.35358 > C -3.82195 -0.01875 0.00104 > C -3.16803 1.15775 -0.29437 > C -1.78409 1.19172 -0.22084 > N 1.03103 1.15471 0.56393 > H 0.53306 1.97165 0.81387 > O 2.41620 1.28733 0.63971 > Ag 3.35043 -0.74343 0.20642 > H -1.19437 -1.99336 0.67135 > H -3.66278 -2.06484 0.56731 > Cl -5.62080 -0.06847 -0.08841 > H -3.71992 2.02505 -0.58447 > H -1.27777 2.09764 -0.48124 > > Best regards, > Orlin > > -- > Orlin Blajiev > Department of Metallurgy, Electrochemistry and Materials Science > Faculty of Applied Science > Vrije Universiteit Brussel > Pleinlaan 2, B-1050 Brussels > Belgium > > http://www.vub.ac.be/META/ > > tel.: 32-(0)2-6293538 > fax : 32-(0)2-6293200> > > Christos E. Kefalidis PhD Student Laboratory of Applied Quantum Chemistry Department of Chemistry Aristotle University of Thessaloniki From owner-chemistry@ccl.net Tue Jun 27 07:24:01 2006 From: "Gilles Frapper gilles.frapper^^univ-poitiers.fr" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32024-060627051412-9740-UeiMiEo8EMuEkxIrnAwoQA\a/server.ccl.net> X-Original-From: Gilles Frapper Content-Type: multipart/alternative; boundary="------------050002010301060703040905" Date: Tue, 27 Jun 2006 11:13:59 +0200 MIME-Version: 1.0 Sent to CCL by: Gilles Frapper [gilles.frapper|-|univ-poitiers.fr] This is a multi-part message in MIME format. --------------050002010301060703040905 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Bonjour, use the keyword *genecp* et define the pseudo and basis set below the "geometry" section. see the onlne manual . Bonne journée. Gilles # b3lyp/genecp opt freq formcheck output=wfn XX clBHAN311.log 0 1 O 1.03535 -1.04284 0.02249 C 0.41990 0.04621 0.23888 . . C H 0 6-31G(d) **** Ag 0 SDD (or Lanl2dz or ...) **** Ag 0 SDD (or Lanl2dz or ...) ----- Orlin Blajiev blajiev_-_vub.ac.be a écrit : >Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be] >Hi, > >I will appreciate some help with the following question. I have the >following input for Gaussian-how can I ask for a individual basis set >for Ag as 6-31 is not available for it. > >%chk=clBHA.chk >%mem=20000000 ># opt freq b3lyp/6-31g(d) formcheck output=wfn > >XX clBHAN311.log > > 0 1 >O 1.03535 -1.04284 0.02249 >C 0.41990 0.04621 0.23888 >C -1.06633 0.06016 0.14887 >C -1.75191 -1.11823 0.41903 >C -3.13397 -1.16168 0.35358 >C -3.82195 -0.01875 0.00104 >C -3.16803 1.15775 -0.29437 >C -1.78409 1.19172 -0.22084 >N 1.03103 1.15471 0.56393 >H 0.53306 1.97165 0.81387 >O 2.41620 1.28733 0.63971 >Ag 3.35043 -0.74343 0.20642 >H -1.19437 -1.99336 0.67135 >H -3.66278 -2.06484 0.56731 >Cl -5.62080 -0.06847 -0.08841 >H -3.71992 2.02505 -0.58447 >H -1.27777 2.09764 -0.48124 > >Best regards, >Orlin > > > -- Gilles Frapper groupe chimie quantique appliquée UMR CNRS 6503 - LACCO - Université de Poitiers 40, av. recteur Pineau 86022 Poitiers cedex tel : 05 49 45 35 74 - mel : gilles.frapper*o*univ-poitiers.fr site : http://labo.univ-poitiers.fr/yargla --------------050002010301060703040905 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Bonjour,

use the keyword genecp et define the pseudo and basis set below the "geometry" section.
see the onlne manual .

Bonne journée.
Gilles

# b3lyp/genecp opt freq  formcheck output=wfn

XX clBHAN311.log

  0  1
O           1.03535        -1.04284         0.02249
C           0.41990         0.04621         0.23888
.
.

C H 0
6-31G(d)
****
Ag 0
SDD                    (or Lanl2dz or ...)
****

Ag 0
SDD                   (or Lanl2dz or ...)
-----


Orlin Blajiev blajiev_-_vub.ac.be a écrit : 
Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be]
Hi,

I will appreciate some help with the following question. I have the 
following input for Gaussian-how can I ask for a  individual  basis set 
for Ag as 6-31 is not available for it.

%chk=clBHA.chk
%mem=20000000
# opt freq b3lyp/6-31g(d) formcheck output=wfn

XX clBHAN311.log

  0  1
O           1.03535        -1.04284         0.02249
C           0.41990         0.04621         0.23888
C          -1.06633         0.06016         0.14887
C          -1.75191        -1.11823         0.41903
C          -3.13397        -1.16168         0.35358
C          -3.82195        -0.01875         0.00104
C          -3.16803         1.15775        -0.29437
C          -1.78409         1.19172        -0.22084
N           1.03103         1.15471         0.56393
H           0.53306         1.97165         0.81387
O           2.41620         1.28733         0.63971
Ag          3.35043        -0.74343         0.20642
H          -1.19437        -1.99336         0.67135
H          -3.66278        -2.06484         0.56731
Cl         -5.62080        -0.06847        -0.08841
H          -3.71992         2.02505        -0.58447
H          -1.27777         2.09764        -0.48124

Best regards,
Orlin

  


-- 
Gilles Frapper
groupe chimie quantique appliquée
UMR CNRS 6503 - LACCO - Université de Poitiers
40, av. recteur Pineau 86022 Poitiers cedex
tel : 05 49 45 35 74 - mel : gilles.frapper*o*univ-poitiers.fr
site : http://labo.univ-poitiers.fr/yargla
--------------050002010301060703040905-- From owner-chemistry@ccl.net Tue Jun 27 08:00:00 2006 From: "Orlin Blajiev blajiev=-=vub.ac.be" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32025-060627073906-13170-zgh25tqwrZSEExbjTO2RLw:-:server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 27 Jun 2006 13:39:16 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [blajiev_+_vub.ac.be] Hi, Thank you for the answer. I was wondering is not it possible to have an individual basis set assingment for Ag in particular or for each atom in the structure. It is a possibility in the case of GAMESS, for example. There every atom can be given its own basis set. Therefore, 6-31 can be used for light ones and lesser for the transition metals. Orlin kefalidi(a)chem.auth.gr wrote: > Sent to CCL by: kefalidi-*-chem.auth.gr > Hi Orlin, > > The basis set you asked for the Ag atom is not available because Ag is > a second > row transition metal. For information about all the basis set that you can use > for the Ag atom or any other atom, you can visit the site > http://www.emsl.pnl.gov/forms/basisform.html > > Christos > > Quoting "Orlin Blajiev blajiev_-_vub.ac.be" : > > >> Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be] >> Hi, >> >> I will appreciate some help with the following question. I have the >> following input for Gaussian-how can I ask for a individual basis set >> for Ag as 6-31 is not available for it. >> >> %chk=clBHA.chk >> %mem=20000000 >> # opt freq b3lyp/6-31g(d) formcheck output=wfn >> >> XX clBHAN311.log >> >> 0 1 >> O 1.03535 -1.04284 0.02249 >> C 0.41990 0.04621 0.23888 >> C -1.06633 0.06016 0.14887 >> C -1.75191 -1.11823 0.41903 >> C -3.13397 -1.16168 0.35358 >> C -3.82195 -0.01875 0.00104 >> C -3.16803 1.15775 -0.29437 >> C -1.78409 1.19172 -0.22084 >> N 1.03103 1.15471 0.56393 >> H 0.53306 1.97165 0.81387 >> O 2.41620 1.28733 0.63971 >> Ag 3.35043 -0.74343 0.20642 >> H -1.19437 -1.99336 0.67135 >> H -3.66278 -2.06484 0.56731 >> Cl -5.62080 -0.06847 -0.08841 >> H -3.71992 2.02505 -0.58447 >> H -1.27777 2.09764 -0.48124 >> -- Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 From owner-chemistry@ccl.net Tue Jun 27 08:54:00 2006 From: "FAVRE Georges 210344 georges.favre_+_cea.fr" To: CCL Subject: CCL:G: Gaussian "gauopt utility" Message-Id: <-32026-060627064952-1163-IXLlLCPy2/egdQlEs+AXBg[*]server.ccl.net> X-Original-From: "FAVRE Georges 210344" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 27 Jun 2006 12:01:59 +0200 MIME-Version: 1.0 Sent to CCL by: "FAVRE Georges 210344" [georges.favre:cea.fr] Dear CCL I am trying to use the Gaussian "gauopt" utility, which is typically used to optimize parameters such as basis functions for which there is no standard optimization method implemented within Gaussian. An example of optimization of the scale factors in the STO-2G expansion of a minimal basis set for water is given on the Gaussian Website to make the concepts clearer, but I don't understand some points. Here below are reported the STO-2G basis set for O atom and the "gauopt" example: BASIS="STO-2G" O 0 S 2 1.00 49.9809710 0.430128000 8.89658800 0.678914000 SP 2 1.00 1.94523700 0.494720000E-01 0.511541000 0.493363000 0.963782000 0.612820000 **** "gauopt" Example 3 3 T 0.0 0.0 7.66V 2.25V 1.24V # RHF/Gen Test Water RHF/STO-2G basis with optimized scale factors 0,1 O H,1,r H,1,r,2,a r 0.96 a 104.5 1 0 sto 1s 2 <1 12.10> sto 2sp 2 <2 12.10> **** 2 0 sto 1s 2 <3 12.10> **** 3 0 sto 1s 2 <3 12.10> **** What does the parameter 12.10 mean? I don't understand these values since they don't have any appearance in the STO-2G basis. Another point which bothers me is the values used for the variables: 7.66V 2.25V 1.24V Does anyone could explain me what these values correspond to? Thanks and have a great day! Regards, Georges Favre From owner-chemistry@ccl.net Tue Jun 27 09:29:00 2006 From: "VITORGE Pierre 094605 Pierre.VITORGE]![cea.fr" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32027-060627053042-20838-bP80qyjeyaNQQXdqqsnzsg^^^server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 27 Jun 2006 10:53:16 +0200 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE(_)cea.fr] use keyword gen -----Message d'origine----- De : owner-chemistry(-)ccl.net [mailto:owner-chemistry(-)ccl.net] Envoyé : mardi 27 juin 2006 10:27 Ŕ : VITORGE Pierre 094605 Objet : CCL:G: Gaussian individual basis set Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be] Hi, I will appreciate some help with the following question. I have the following input for Gaussian-how can I ask for a individual basis set for Ag as 6-31 is not available for it. %chk=clBHA.chk %mem=20000000 # opt freq b3lyp/6-31g(d) formcheck output=wfn XX clBHAN311.log 0 1 O 1.03535 -1.04284 0.02249 C 0.41990 0.04621 0.23888 C -1.06633 0.06016 0.14887 C -1.75191 -1.11823 0.41903 C -3.13397 -1.16168 0.35358 C -3.82195 -0.01875 0.00104 C -3.16803 1.15775 -0.29437 C -1.78409 1.19172 -0.22084 N 1.03103 1.15471 0.56393 H 0.53306 1.97165 0.81387 O 2.41620 1.28733 0.63971 Ag 3.35043 -0.74343 0.20642 H -1.19437 -1.99336 0.67135 H -3.66278 -2.06484 0.56731 Cl -5.62080 -0.06847 -0.08841 H -3.71992 2.02505 -0.58447 H -1.27777 2.09764 -0.48124 Best regards, Orlin -- Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200http://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 Tue Jun 27 10:04:01 2006 From: "Barry Hardy barry.hardy+*+tiscalinet.ch" To: CCL Subject: CCL: eCheminfo Meeting, Bryn Mawr, 16-19 October - Preliminary Program, Early Registration Message-Id: <-32028-060627090645-10581-vL31YAvN8dGXH07XH4ohFg:-:server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="=====================_20461179==_.ALT" Date: Tue, 27 Jun 2006 15:06:36 +0200 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy#tiscalinet.ch] --=====================_20461179==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed The eCheminfo Community of Practice InterAction Meeting "Latest Advances in Drug Discovery Design & Planning Methods" will take place 16-19 October 2006, Bryn Mawr, Philadelphia, USA Program themes include Structure-based Drug Design, Screening & Docking, Cheminformatics & Modeling supporting Medicinal Chemistry, Pharmacophores, Metabolomics, Quantum Biochemistry, Knowledge Management, Electronic Lab Notebooks, Critical Path Innovation in Drug Development, Biomarkers, Predictive Toxicology & ADME. In addition to morning presentations and panel discussions, workshops will run each afternoon expanding on the discussion of topics and methods and working through the application of new methods and software to drug discovery & development problems, with bbq, social activity and poster sessions running on campus during the evenings. The preliminary program and schedule is available at: http://www.echeminfo.com/COMTY_conferences/ Reduced rates apply for early registration through 30 June. Academic discounts apply. All registrants are eligible to submit an abstract (ca. 300 words) for the poster sessions. Please address any questions related to the conference, exhibition or workshop program to me. Registration enquiries should be directed to eCheminfo [at] douglasconnect.com best regards Barry Hardy eCheminfo Community of Practice Douglas Connect Baermeggenweg 14, Zeiningen CH-4314, Switzerland Tel: +41 61 851 0170 Confirmed Speakers at the Bryn Mawr meeting include: Frank Hollinger (Locus Pharmaceuticals), Erin Duffy (Rib-X), Mike Malams (Wyeth), Debananda Das (NCI), Max Cummings (Johnson & Johnson PR&D), Lance Westerhoff (QuantumBio), Jose Duca (Schering-Plough), Osman Guner (Turquoise Consulting), Hege Beard (Schrodinger), Stan Young (NISS), John Irwin (UCSF), William Douglas Figg (NCI), Daryll Reid (Simbiosys), Gregory Warren (GlaxoSmithKline), Deepak Bandyopadhyay (Johnson & Johnson PR&D), Paul Hawkins (OpenEye), Chris Cooper (BMS), James Arnold (Astra-Zeneca), Phil Edwards (Astra-Zeneca), Pete Connolly (Johnson & Johnson PR&D), Dimitris Agrafiotis (Johnson & Johnson PRD), Jim Wikel (Coalesix), Tudor Oprea (Univ. New Mexico), Alex Tropsha (UNC), Curt Breneman (RPI), Sanji Bhal (ACD/Labs), Michael Bolger (Simulations Plus), Bob Clark (Tripos), Gilles Klopman (Multicase), Navita Mallalieu (Roche Pharmaceuticals), Deepak Bandyopadhyay (Johnson & Johnson PR&D), Zentam Tsuchihashi (BMS), Peter Henstock (Pfizer), Darius Dziuda (Multivariate bioMarkers Discovery), Keith Elliston (Genstruct), Michael Liebman (Windber Research Institute), Jonathan Sheldon (InforSense), Duane Shugars (Concentia Digital), Jian Wang (Biofortis), Peter Gates (Johnson & Johnson PR&D), Barry Hardy (Douglas Connect), Dennis Underwood (Praxeon), Jeff Spitzner (Rescentris), David Mosenkis (Spotfire), Joel Hoffman (IntraSphere), Delia Wolf (Harvard Medical School), Craig Liddell (Realtime Science), Joseph Bitran (Enterprizer), Alvin Berger (Metabolon), Gregory Banik (Bio-RAD), George Harrigan (Monsanto), Rick Beger (NCTR, FDA), Don Robertson (Pfizer), Teresa Garret (Duke University), Laszlo Boros (SIDMAP), Bruce Kristal (Cornell University), Andrew Lane (JG Brown Cancer Center, U. Louisville), Oliver Fiehn (UC Davis Genome Center), Susan Connor (Glaxo SmithKline) --=====================_20461179==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
The eCheminfo Community of Practice InterAction Meeting "Latest Advances in Drug Discovery Design & Planning Methods" will take place 16-19 October 2006, Bryn Mawr, Philadelphia, USA

Program themes include Structure-based Drug Design, Screening & Docking, Cheminformatics & Modeling supporting Medicinal Chemistry, Pharmacophores, Metabolomics, Quantum Biochemistry, Knowledge Management, Electronic Lab Notebooks, Critical Path Innovation in Drug Development, Biomarkers, Predictive Toxicology & ADME. In addition to morning presentations and panel discussions, workshops will run each afternoon expanding on the discussion of topics and methods and working through the application of new methods and software to drug discovery & development problems, with bbq, social activity and poster sessions running on campus during the evenings.

The preliminary program and schedule is available at:
htt= p://www.echeminfo.com/COMTY_conferences/

Reduced rates apply for early registration through 30 June. Academic= discounts apply.

All registrants are eligible to submit an abstract (ca. 300 words) for the= poster sessions.

Please address any questions related to the conference, exhibition or= workshop program to me.  Registration enquiries should be directed to= eCheminfo [at] douglasconnect.com

best regards
Barry Hardy
eCheminfo Community of Practice

Douglas Connect
Baermeggenweg 14, Zeiningen
CH-4314, Switzerland
Tel: +41 61 851 0170

Confirmed Speakers at the Bryn Mawr meeting include:
Frank Hollinger (Locus Pharmaceuticals), Erin Duffy (Rib-X), Mike Malams= (Wyeth), Debananda Das (NCI), Max Cummings (Johnson & Johnson= PR&D), Lance Westerhoff (QuantumBio), Jose Duca (Schering-Plough),= Osman Guner (Turquoise Consulting), Hege Beard (Schrodinger), Stan Young= (NISS), John Irwin (UCSF), William Douglas Figg (NCI), Daryll Reid= (Simbiosys), Gregory Warren (GlaxoSmithKline), Deepak Bandyopadhyay= (Johnson & Johnson PR&D), Paul Hawkins (OpenEye), Chris Cooper= (BMS), James Arnold (Astra-Zeneca), Phil Edwards (Astra-Zeneca), Pete= Connolly (Johnson & Johnson PR&D), Dimitris Agrafiotis (Johnson= & Johnson PRD), Jim Wikel (Coalesix), Tudor Oprea (Univ. New Mexico),= Alex Tropsha (UNC), Curt Breneman (RPI), Sanji Bhal (ACD/Labs), Michael= Bolger (Simulations Plus), Bob Clark (Tripos), Gilles Klopman (Multicase),= Navita Mallalieu (Roche Pharmaceuticals), Deepak Bandyopadhyay (Johnson= & Johnson PR&D), Zentam Tsuchihashi (BMS), Peter Henstock (Pfizer),= Darius Dziuda (Multivariate bioMarkers Discovery), Keith Elliston= (Genstruct), Michael Liebman (Windber Research Institute), Jonathan Sheldon= (InforSense), Duane Shugars (Concentia Digital), Jian Wang (Biofortis),= Peter Gates (Johnson & Johnson PR&D), Barry Hardy (Douglas= Connect), Dennis Underwood (Praxeon), Jeff Spitzner (Rescentris), David= Mosenkis (Spotfire), Joel Hoffman (IntraSphere), Delia Wolf (Harvard= Medical School), Craig Liddell (Realtime Science), Joseph Bitran= (Enterprizer), Alvin Berger (Metabolon), Gregory Banik (Bio-RAD), George= Harrigan (Monsanto), Rick Beger (NCTR, FDA), Don Robertson (Pfizer), Teresa= Garret (Duke University), Laszlo Boros (SIDMAP), Bruce Kristal (Cornell= University), Andrew Lane (JG Brown Cancer Center, U. Louisville), Oliver= Fiehn (UC Davis Genome Center), Susan Connor (Glaxo SmithKline)

--=====================_20461179==_.ALT-- From owner-chemistry@ccl.net Tue Jun 27 10:38:00 2006 From: "Lukasz Cwiklik lukasz.cwiklik=uochb.cas.cz" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32029-060627103047-31643-zOwLTmhGM9k2N/kC23QQCg*server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 27 Jun 2006 16:30:44 +0200 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [lukasz.cwiklik-#-uochb.cas.cz] On 6/27/06, Orlin Blajiev blajiev=-=vub.ac.be wrote: > Sent to CCL by: Orlin Blajiev [blajiev_+_vub.ac.be] > Hi, > > Thank you for the answer. I was wondering is not it possible to have an > individual basis set assingment for Ag in particular or for each atom > in the structure. It is a possibility in the case of GAMESS, for > example. There every atom can be given its own basis set. Therefore, > 6-31 can be used for light ones and lesser for the transition metals. > > Orlin Hi, Of course individual basis set assingment is possible. See: http://www.gaussian.com/g_ur/k_gen.htm Basis for individual atoms can be downloaded from: http://www.emsl.pnl.gov/forms/basisform.html (choose Gaussian94 format if you are using Gaussian03). Best, Lukasz Cwiklik -- Lukasz Cwiklik http://www.molecular.cz/~cwiklik From owner-chemistry@ccl.net Tue Jun 27 11:13:00 2006 From: "Eva B lter eva.berssen()mail.uni-oldenburg.de" To: CCL Subject: CCL:G: NBO visualization Message-Id: <-32030-060627072854-30261-QFUlcUN75T8SuYkR43Hxvg[]server.ccl.net> X-Original-From: "Eva B lter" Date: Tue, 27 Jun 2006 07:28:51 -0400 Sent to CCL by: "Eva B lter" [eva.berssen|*|mail.uni-oldenburg.de] Hello! I want to plot some G03-generated NBO results with regular programms like Chem3D or others. Trying to visualize some Orbitals ore binding parameters with Molekel failed because of the choice of the basis sets (I used the gen key). The normal fchk-files only plot the mulliken informations. Is it possible to verify the calculations to get the wanted NBO-informations in an fchk file ore are there other possibilties to plot the informations? Thank you and greetings Eva Blter From owner-chemistry@ccl.net Tue Jun 27 11:49:02 2006 From: "Alessandro Contini alessandro.contini-.-unimi.it" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32031-060627095322-3796-gHGqa4PijV0577EZP92P/A.:.server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 7BIT Content-type: text/plain Date: Tue, 27 Jun 2006 14:53:04 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini]=[unimi.it] Hi Orlin, this is possible in gaussian by using the keyword gen, as in the following input example: %chk=test.chk %mem=256MB %nproc=1 # opt freq b3lyp/gen geom=checkpoint guess=read title 0 1 C H O 0 6-31G(d) **** Fe 0 6-311+G(3df,2p) **** In this case the 6-31G* basis is applied to carbon oxigen (and H) atoms, while a more extended basis is applied to iron (NB just an example!!) It's also possible to apply a basis set on single atoms by specifing their number (see the on line manual at http://www.gaussian.com/g_ur/k_gen.htm. ) Hope this help Alessandro Il giorno mar, 27/06/2006 alle 08.08 -0400, Orlin Blajiev blajiev=-=vub.ac.be ha scritto: > Sent to CCL by: Orlin Blajiev [blajiev_+_vub.ac.be] > Hi, > > Thank you for the answer. I was wondering is not it possible to have an > individual basis set assingment for Ag in particular or for each atom > in the structure. It is a possibility in the case of GAMESS, for > example. There every atom can be given its own basis set. Therefore, > 6-31 can be used for light ones and lesser for the transition metals. > > Orlin > > > > > > kefalidi(a)chem.auth.gr wrote: > > Sent to CCL by: kefalidi-*-chem.auth.gr > > Hi Orlin, > > > > The basis set you asked for the Ag atom is not available because Ag is > > a second > > row transition metal. For information about all the basis set that you can use > > for the Ag atom or any other atom, you can visit the site > > http://www.emsl.pnl.gov/forms/basisform.html > > > > Christos > > > > Quoting "Orlin Blajiev blajiev_-_vub.ac.be" : > > > > > >> Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be] > >> Hi, > >> > >> I will appreciate some help with the following question. I have the > >> following input for Gaussian-how can I ask for a individual basis set > >> for Ag as 6-31 is not available for it. > >> > >> %chk=clBHA.chk > >> %mem=20000000 > >> # opt freq b3lyp/6-31g(d) formcheck output=wfn > >> > >> XX clBHAN311.log > >> > >> 0 1 > >> O 1.03535 -1.04284 0.02249 > >> C 0.41990 0.04621 0.23888 > >> C -1.06633 0.06016 0.14887 > >> C -1.75191 -1.11823 0.41903 > >> C -3.13397 -1.16168 0.35358 > >> C -3.82195 -0.01875 0.00104 > >> C -3.16803 1.15775 -0.29437 > >> C -1.78409 1.19172 -0.22084 > >> N 1.03103 1.15471 0.56393 > >> H 0.53306 1.97165 0.81387 > >> O 2.41620 1.28733 0.63971 > >> Ag 3.35043 -0.74343 0.20642 > >> H -1.19437 -1.99336 0.67135 > >> H -3.66278 -2.06484 0.56731 > >> Cl -5.62080 -0.06847 -0.08841 > >> H -3.71992 2.02505 -0.58447 > >> H -1.27777 2.09764 -0.48124 > >> > > -- Dr. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Universita' degli Studi di Milano, Facolta' di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini : unimi.it skype alessandrocontini From owner-chemistry@ccl.net Tue Jun 27 12:23:01 2006 From: "=?iso-8859-1?q?=D6d=F6n_Farkas?= farkas..chem.elte.hu" To: CCL Subject: CCL: Gaussian individual basis set Message-Id: <-32032-060627091457-12567-4WLyKnmTvisihr/UdHqQ8Q_+_server.ccl.net> X-Original-From: =?iso-8859-1?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 27 Jun 2006 13:29:51 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?q?=D6d=F6n_Farkas?= [farkas_-_chem.elte.hu] Hi Orlin, The basis set is your choice, but I can ive you an example, how to set up the input: #P Freq B3LYP 6D GenECP SCRF=(Solvent=Acetonitrile) Temperature=313 2-N (-) Imaginary frequences: 0 Total energy: 0.0000000 0 1 C 0.0219078528 -0.0379317850 0.0154822299 H -0.0039891653 0.0066547527 1.1018420498 H 1.0375904885 0.0065468998 -0.3710188335 H -0.5243615117 -0.8953702820 -0.3707895090 I -1.0166940893 1.7610922660 -0.7188493007 C H 0 6-31G(d) **** I 0 SDD **** I 0 MWB46 Best wishes, Ödön -- Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány Péter sétány H-1117 Budapest, Hungary From owner-chemistry@ccl.net Tue Jun 27 12:59:00 2006 From: "Igor Schweigert ischweig[A]uci.edu" To: CCL Subject: CCL: answer to why Kij <= Jij ? Message-Id: <-32033-060627115213-22333-JulwBGzs4E1ASkLE0T+sNw##server.ccl.net> X-Original-From: "Igor Schweigert" Content-Type: multipart/alternative; boundary="----=_Part_71409_15818332.1151423530875" Date: Tue, 27 Jun 2006 08:52:10 -0700 MIME-Version: 1.0 Sent to CCL by: "Igor Schweigert" [ischweig{}uci.edu] ------=_Part_71409_15818332.1151423530875 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Pierre, Thank you for your response. I may need to spend more time on the second point of your proof (T, 1-T). Math aside, the statement "exp. values of the permutation operator is bound by 1" adds the flavor of formality to what one thinks intuitively, therefore it's good enough for a physicist! Igor On 6/26/06, Pierre Archirel pierre.archirel|-|lcp.u-psud.fr < owner-chemistry]^[ccl.net> wrote: > > Sent to CCL by: Pierre Archirel [pierre.archirel!A!lcp.u-psud.fr] > This is an answer to I. Schweigert. > I find the following reasoning in the lecture, I had in the past from G. > Bessis: > 1- set a_ij=f_i(1).f_j(2).r_12**(-1/2), > then J_ij = and K_ij = > where p(ij) is the transposition operator for i and j. > 2- prove that the mean value of a transposition is ruled by: > -1 <= <= +1 > (use T_ij=1/2(1-p_ij), prove it is idempotent and positive defined, > also use 1-T in the same way) > 3- this implies <= > and eventually proves the statement. > Best wishes > P.A. > ------=_Part_71409_15818332.1151423530875 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Pierre,

Thank you for your response. I may need to spend more time on the second point of your proof (T, 1-T). Math aside, the statement "exp. values of the permutation operator is bound by 1" adds the flavor of formality to what one thinks intuitively, therefore it's good enough for a physicist!

Igor

 
On 6/26/06, Pierre Archirel pierre.archirel|-|lcp.u-psud.fr <owner-chemistry]^[ccl.net> wrote:
Sent to CCL by: Pierre Archirel [pierre.archirel!A!lcp.u-psud.fr]
This is an answer to I. Schweigert.
I find the following reasoning in the lecture, I had in the past from G.
Bessis:
1- set a_ij=f_i(1).f_j(2).r_12**(-1/2),
then J_ij = <a_ij|a_ij> and K_ij = <a_ij|p(i,j)|a_ij>
where p(ij) is the transposition operator for i and j.
2- prove that the mean value of a transposition is ruled by:
-1 <= <p(ij)> <= +1
(use T_ij=1/2(1-p_ij), prove it is idempotent and positive defined,
also use 1-T in the same way)
3- this implies <a_ij|p(i,j)|a_ij> <= <a_ij|a_ij>
and eventually proves the statement.
Best wishes
P.A.

------=_Part_71409_15818332.1151423530875-- From owner-chemistry@ccl.net Tue Jun 27 13:33:00 2006 From: "Dipankar Roy dipankarroy++iitb.ac.in" To: CCL Subject: CCL:G: NBO visualization Message-Id: <-32034-060627125228-32085-QUYTrSrp9L7mZchAfJ2zPg=server.ccl.net> X-Original-From: "Dipankar Roy" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 27 Jun 2006 22:21:45 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dipankar Roy" [dipankarroy . iitb.ac.in] Hi, Try NBOVIEW. It is available from NBO5.0 web page and is not FREE. -dipankar roy > Sent to CCL by: "Eva B lter" [eva.berssen|*|mail.uni-oldenburg.de] > Hello! > > I want to plot some G03-generated NBO results with regular programms like > Chem3D or others. Trying to visualize some Orbitals ore binding parameters > with Molekel failed because of the choice of the basis sets (I used the > gen key). > The normal fchk-files only plot the mulliken informations. Is it possible > to verify the calculations to get the wanted NBO-informations in an fchk > file ore are there other possibilties to plot the informations? > Thank you and greetings > > Eva Blter> > > > *********************************************** Dipankar Roy Graduate Student of Prof. R. B. Sunoj Computational Chemistry Laboratoty Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) URL: http://www.geocities.com/dipankar_roy79/dipankar.html *********************************************** GETTING A SIMPLE ANSWER FROM A PROFESSOR IS LIKE GETTING A THIMBLE OF WATER FROM A FIRE HYDRANT. - PROF. LEN SHAPIRO, NDSU From owner-chemistry@ccl.net Tue Jun 27 14:09:02 2006 From: "Brian Popp bvpopp^wisc.edu" To: CCL Subject: CCL:G: NBO visualization Message-Id: <-32035-060627135130-17643-HaamKafta64er9bmmaUKig]~[server.ccl.net> X-Original-From: Brian Popp Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 27 Jun 2006 12:52:04 -0500 MIME-version: 1.0 Sent to CCL by: Brian Popp [bvpopp|,|wisc.edu] Eva, In G03, there are two ways to generate nbo's in the chk file. 1: Use the pop keyword: pop=nbosave 2: Use pop=nboread and then specify in the NBO input -- $NBO aonbo=c $END The latter is my preferred choice and is also applicable for other NBO derived items such as NLMOs - check the NBO 5.0 manual for further details. Check the G03 input ordering to ensure that the NBO specific input is correctly positioned in your input file. I use Gaussview to view my results. The NBO ordering will be at the end of the NBO section of the output. Try generating a cub file of one of the first NBOs in the list. Visualize it to make sure it makes chemical sense and to verify that nbo has overwritten the standard mo orbitals which is what the aonbo=c keyword is suppose to do. Hope this helps. Brian Popp Chemistry Department University of Wisconsin-Madison 1101 University Ave. Madison, WI 53706 On Jun 27, 2006, at 10:16 AM, Eva B lter eva.berssen()mail.uni- oldenburg.de wrote: > Sent to CCL by: "Eva B lter" [eva.berssen|*|mail.uni-oldenburg.de] > Hello! > > I want to plot some G03-generated NBO results with regular > programms like Chem3D or others. Trying to visualize some Orbitals > ore binding parameters with Molekel failed because of the choice of > the basis sets (I used the gen key). > The normal fchk-files only plot the mulliken informations. Is it > possible to verify the calculations to get the wanted NBO- > informations in an fchk file ore are there other possibilties to > plot the informations? > Thank you and greetings > > Eva Blter > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Tue Jun 27 14:55:06 2006 From: "Nuno A. G. Bandeira nuno.bandeira::ist.utl.pt" To: CCL Subject: CCL: NBO visualization Message-Id: <-32036-060627145359-23837-Gm9TXRY9fCMIhXZ//7tUjg]*[server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Date: Tue, 27 Jun 2006 14:53:58 -0400 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira-*-ist.utl.pt] Use Pop=(SaveNBOs), that will punch NBOs in the checkpoint file. Cheers, -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student ++ IST,Lisbon -- From owner-chemistry@ccl.net Tue Jun 27 15:30:11 2006 From: "Kaliappan Muthukumar muthukumar2k3,yahoo.com" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32037-060627100228-7280-qj8hBybcH91rCkkPcsiivA-*-server.ccl.net> X-Original-From: Kaliappan Muthukumar Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1770479829-1151413342=:57951" Date: Tue, 27 Jun 2006 14:02:22 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Kaliappan Muthukumar [muthukumar2k3()yahoo.com] --0-1770479829-1151413342=:57951 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Orlin, More obviously, I hope ONIUM method could help you in G03. Here you could assign various basis set for various atoms along with gen keyword. Visit http://www.gaussian.com/g_ur/k_oniom.htm for details. Hope this helps you. Regards, Muthu "Orlin Blajiev blajiev=-=vub.ac.be" wrote: Sent to CCL by: Orlin Blajiev [blajiev_+_vub.ac.be] Hi, Thank you for the answer. I was wondering is not it possible to have an individual basis set assingment for Ag in particular or for each atom in the structure. It is a possibility in the case of GAMESS, for example. There every atom can be given its own basis set. Therefore, 6-31 can be used for light ones and lesser for the transition metals. Orlin kefalidi(a)chem.auth.gr wrote: > Sent to CCL by: kefalidi-*-chem.auth.gr > Hi Orlin, > > The basis set you asked for the Ag atom is not available because Ag is > a second > row transition metal. For information about all the basis set that you can use > for the Ag atom or any other atom, you can visit the site > http://www.emsl.pnl.gov/forms/basisform.html > > Christos > > Quoting "Orlin Blajiev blajiev_-_vub.ac.be" : > > >> Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be] >> Hi, >> >> I will appreciate some help with the following question. I have the >> following input for Gaussian-how can I ask for a individual basis set >> for Ag as 6-31 is not available for it. >> >> %chk=clBHA.chk >> %mem=20000000 >> # opt freq b3lyp/6-31g(d) formcheck output=wfn >> >> XX clBHAN311.log >> >> 0 1 >> O 1.03535 -1.04284 0.02249 >> C 0.41990 0.04621 0.23888 >> C -1.06633 0.06016 0.14887 >> C -1.75191 -1.11823 0.41903 >> C -3.13397 -1.16168 0.35358 >> C -3.82195 -0.01875 0.00104 >> C -3.16803 1.15775 -0.29437 >> C -1.78409 1.19172 -0.22084 >> N 1.03103 1.15471 0.56393 >> H 0.53306 1.97165 0.81387 >> O 2.41620 1.28733 0.63971 >> Ag 3.35043 -0.74343 0.20642 >> H -1.19437 -1.99336 0.67135 >> H -3.66278 -2.06484 0.56731 >> Cl -5.62080 -0.06847 -0.08841 >> H -3.71992 2.02505 -0.58447 >> H -1.27777 2.09764 -0.48124 >> -- Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtMr. Kaliappan Muthukumar, Computational Modelling Group, Tyndall National Institute, University College Cork, Lee Maltings, Prospect Row, Cork, Ireland Phone : ++ 353 21 4904201 Mobile : 00 353 851616568 E- Mail : muthukumar2k3() yahoo.com, kmkumar() tyndall.ie Website : http://www.tyndall.ie/research/computational-modelling-group/members.html --------------------------------- Yahoo! India Answers: Share what you know. Learn something new Click here Catch all the FIFA World Cup 2006 action on Yahoo! India Click here --0-1770479829-1151413342=:57951 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear Orlin,
 
More obviously, I hope ONIUM method could help you in G03. Here you could assign various basis set for various atoms along with gen keyword.
 
 
Hope this helps you.
 
Regards,
Muthu

"Orlin Blajiev blajiev=-=vub.ac.be" <owner-chemistry() ccl.net> wrote:
Sent to CCL by: Orlin Blajiev [blajiev_+_vub.ac.be]
Hi,

Thank you for the answer. I was wondering is not it possible to have an
individual basis set assingment for Ag in particular or for each atom
in the structure. It is a possibility in the case of GAMESS, for
example. There every atom can be given its own basis set. Therefore,
6-31 can be used for light ones and lesser for the transition metals.

Orlin





kefalidi(a)chem.auth.gr wrote:
> Sent to CCL by: kefalidi-*-chem.auth.gr
> Hi Orlin,
>
> The basis set you asked for the Ag atom is not available because Ag is
> a second
> row transition metal. For information about all the basis set that you can use
> for the Ag atom or any other atom, you can visit the site
> http://www.emsl.pnl.gov/forms/basisform.html
>
> Christos
>
> Quoting "Orlin Blajiev blajiev_-_vub.ac.be" :
>
>
>> Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be]
>> Hi,
>>
>> I will appreciate some help with the following question. I have the
>> following input for Gaussian-how can I ask for a individual basis set
>> for Ag as 6-31 is not available for it.
>>
>> %chk=clBHA.chk
>> %mem=20000000
>> # opt freq b3lyp/6-31g(d) formcheck output=wfn
>>
>> XX clBHAN311.log
>>
>> 0 1
>> O 1.03535 -1.04284 0.02249
>> C 0.41990 0.04621 0.23888
>> C -1.06633 0.06016 0.14887
>> C -1.75191 -1.11823 0.41903
>> C -3.13397 -1.16168 0.35358
>> C -3.82195 -0.01875 0.00104
>> C -3.16803 1.15775 -0.29437
>> C -1.78409 1.19172 -0.22084
>> N 1.03103 1.15471 0.56393
>> H 0.53306 1.97165 0.81387
>> O 2.41620 1.28733 0.63971
>> Ag 3.35043 -0.74343 0.20642
>> H -1.19437 -1.99336 0.67135
>> H -3.66278 -2.06484 0.56731
>> Cl -5.62080 -0.06847 -0.08841
>> H -3.71992 2.02505 -0.58447
>> H -1.27777 2.09764 -0.48124
>>


--
Orlin Blajiev
Department of Metallurgy, Electrochemistry and Materials Science
Faculty of Applied Science
Vrije Universiteit Brussel
Pleinlaan 2, B-1050 Brussels
Belgium

http://www.vub.ac.be/META/

tel.: 32-(0)2-6293538
fax : 32-(0)2-6293200


http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml
http://www.ccl.net/spammers.txt






Mr. Kaliappan Muthukumar,
Computational Modelling Group,
Tyndall National Institute,
University College Cork,
Lee Maltings, Prospect Row,
Cork, Ireland
 
Phone    : ++  353 21 4904201 Mobile : 00 353 851616568

Yahoo! India Answers: Share what you know. Learn something new Click here
Catch all the FIFA World Cup 2006 action on Yahoo! India Click here --0-1770479829-1151413342=:57951-- From owner-chemistry@ccl.net Tue Jun 27 23:35:00 2006 From: "Tapas Kar tapaskar#%#cc.usu.edu" To: CCL Subject: CCL:G: Gaussian individual basis set Message-Id: <-32038-060627163041-13822-HGhDA9FU0WDpUE+4hnELzg__server.ccl.net> X-Original-From: "Tapas Kar" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 27 Jun 2006 13:54:52 -0600 MIME-Version: 1.0 Sent to CCL by: "Tapas Kar" [tapaskar[#]cc.usu.edu] Hello, I used the protocol using different basis for functionalized carbon nanotubes using gen keyward of Gaussianxx. I used the term SLDB "same level different basis" for this technique and it looks better than ONIOM or QM:MM for delocalized systems, as pi-network is preserved. Here are the refs: CPL 423 (2006) 126 and CPL 392 (2004) 176. Thanks Tapas -----Original Message----- > From: owner-chemistry[]ccl.net [mailto:owner-chemistry[]ccl.net] Sent: Tuesday, June 27, 2006 1:43 PM To: Kar, Tapas Subject: CCL:G: Gaussian individual basis set Sent to CCL by: Kaliappan Muthukumar [muthukumar2k3()yahoo.com] --0-1770479829-1151413342=:57951 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Orlin, More obviously, I hope ONIUM method could help you in G03. Here you could assign various basis set for various atoms along with gen keyword. Visit http://www.gaussian.com/g_ur/k_oniom.htm for details. Hope this helps you. Regards, Muthu "Orlin Blajiev blajiev=-=vub.ac.be" wrote: Sent to CCL by: Orlin Blajiev [blajiev_+_vub.ac.be] Hi, Thank you for the answer. I was wondering is not it possible to have an individual basis set assingment for Ag in particular or for each atom in the structure. It is a possibility in the case of GAMESS, for example. There every atom can be given its own basis set. Therefore, 6-31 can be used for light ones and lesser for the transition metals. Orlin kefalidi(a)chem.auth.gr wrote: > Sent to CCL by: kefalidi-*-chem.auth.gr > Hi Orlin, > > The basis set you asked for the Ag atom is not available because Ag is > a second > row transition metal. For information about all the basis set that you can use > for the Ag atom or any other atom, you can visit the site > http://www.emsl.pnl.gov/forms/basisform.html > > Christos > > Quoting "Orlin Blajiev blajiev_-_vub.ac.be" : > > >> Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be] >> Hi, >> >> I will appreciate some help with the following question. I have the >> following input for Gaussian-how can I ask for a individual basis set >> for Ag as 6-31 is not available for it. >> >> %chk=clBHA.chk >> %mem=20000000 >> # opt freq b3lyp/6-31g(d) formcheck output=wfn >> >> XX clBHAN311.log >> >> 0 1 >> O 1.03535 -1.04284 0.02249 >> C 0.41990 0.04621 0.23888 >> C -1.06633 0.06016 0.14887 >> C -1.75191 -1.11823 0.41903 >> C -3.13397 -1.16168 0.35358 >> C -3.82195 -0.01875 0.00104 >> C -3.16803 1.15775 -0.29437 >> C -1.78409 1.19172 -0.22084 >> N 1.03103 1.15471 0.56393 >> H 0.53306 1.97165 0.81387 >> O 2.41620 1.28733 0.63971 >> Ag 3.35043 -0.74343 0.20642 >> H -1.19437 -1.99336 0.67135 >> H -3.66278 -2.06484 0.56731 >> Cl -5.62080 -0.06847 -0.08841 >> H -3.71992 2.02505 -0.58447 >> H -1.27777 2.09764 -0.48124 >> -- Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl .net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtMr. Kaliappan Muthukumar, Computational Modelling Group, Tyndall National Institute, University College Cork, Lee Maltings, Prospect Row, Cork, Ireland Phone : ++ 353 21 4904201 Mobile : 00 353 851616568 E- Mail : muthukumar2k3 : yahoo.com, kmkumar : tyndall.ie Website : http://www.tyndall.ie/research/computational-modelling-group/members.html --------------------------------- Yahoo! India Answers: Share what you know. Learn something new Click here Catch all the FIFA World Cup 2006 action on Yahoo! India Click here --0-1770479829-1151413342=:57951 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear Orlin,
 
More obviously, I hope ONIUM method could help you in G03. Here you could assign various basis set for various atoms along with gen keyword.
 
 
Hope this helps you.
 
Regards,
Muthu

"Orlin Blajiev blajiev=-=vub.ac.be" <owner-chemistry : ccl.net> wrote:
Sent to CCL by: Orlin Blajiev [blajiev_+_vub.ac.be]
Hi,

Thank you for the answer. I was wondering is not it possible to have an
individual basis set assingment for Ag in particular or for each atom
in the structure. It is a possibility in the case of GAMESS, for
example. There every atom can be given its own basis set. Therefore,
6-31 can be used for light ones and lesser for the transition metals.

Orlin





kefalidi(a)chem.auth.gr wrote:
> Sent to CCL by: kefalidi-*-chem.auth.gr
> Hi Orlin,
>
> The basis set you asked for the Ag atom is not available because Ag is
> a second
> row transition metal. For information about all the basis set that you can use
> for the Ag atom or any other atom, you can visit the site
> http://www.emsl.pnl.gov/forms/basisform.html
>
> Christos
>
> Quoting "Orlin Blajiev blajiev_-_vub.ac.be" :
>
>
>> Sent to CCL by: Orlin Blajiev [blajiev- -vub.ac.be]
>> Hi,
>>
>> I will appreciate some help with the following question. I have the
>> following input for Gaussian-how can I ask for a individual basis set
>> for Ag as 6-31 is not available for it.
>>
>> %chk=clBHA.chk
>> %mem=20000000
>> # opt freq b3lyp/6-31g(d) formcheck output=wfn
>>
>> XX clBHAN311.log
>>
>> 0 1
>> O 1.03535 -1.04284 0.02249
>> C 0.41990 0.04621 0.23888
>> C -1.06633 0.06016 0.14887
>> C -1.75191 -1.11823 0.41903
>> C -3.13397 -1.16168 0.35358
>> C -3.82195 -0.01875 0.00104
>> C -3.16803 1.15775 -0.29437
>> C -1.78409 1.19172 -0.22084
>> N 1.03103 1.15471 0.56393
>> H 0.53306 1.97165 0.81387
>> O 2.41620 1.28733 0.63971
>> Ag 3.35043 -0.74343 0.20642
>> H -1.19437 -1.99336 0.67135
>> H -3.66278 -2.06484 0.56731
>> Cl -5.62080 -0.06847 -0.08841
>> H -3.71992 2.02505 -0.58447
>> H -1.27777 2.09764 -0.48124
>>


--
Orlin Blajiev
Department of Metallurgy, Electrochemistry and Materials Science
Faculty of Applied Science
Vrije Universiteit Brussel
Pleinlaan 2, B-1050 Brussels
Belgium

http://www.vub.ac.be/META/

tel.: 32-(0)2-6293538
fax : 32-(0)2-6293200


http://www.ccl.net/cgi-bin /ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_mess age
http://www.ccl.net/chemistry/sub_unsub.shtml
http://www.ccl.net/spammers.txt





Mr. Kaliappan Muthukumar,
Computational Modelling Group,
Tyndall National Institute,
University College Cork,
Lee Maltings, Prospect Row,
Cork, Ireland
 
Phone    : ++  353 21 4904201 Mobile : 00 353 851616568

Yahoo! India Answers: Share what you know. Learn something new Click here
Catch all the FIFA World Cup 2006 action on Yahoo! India Click here --0-1770479829-1151413342=:57951--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt