From owner-chemistry@ccl.net Mon Oct 24 01:21:01 2011 From: "Utpal Sarkar utpalchemiitkgp**gmail.com" To: CCL Subject: CCL:G: Wavefunction or electrondensity of molecular rydberg state. Message-Id: <-45723-111024011927-5038-fMM5ZM31vH7bY/eL2tW0qA*o*server.ccl.net> X-Original-From: Utpal Sarkar Content-Type: multipart/alternative; boundary=14dae93a151bbc73d804b004906e Date: Mon, 24 Oct 2011 10:49:21 +0530 MIME-Version: 1.0 Sent to CCL by: Utpal Sarkar [utpalchemiitkgp^gmail.com] --14dae93a151bbc73d804b004906e Content-Type: text/plain; charset=ISO-8859-1 Dear CCL users, I want to know the electron density or wavefunction of the Rydberg State of Hydrogen Molecule (say one electron is in, principle quantum number, n=10 state). Is it possible to do it by any free software or Gaussian 03 and how? Any type of help is greatly acknowledge. best regards Utpal --14dae93a151bbc73d804b004906e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL users,
=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 I wa= nt to know the electron density or wavefunction of the Rydberg State of Hyd= rogen Molecule (say one electron is in, principle quantum number, n=3D10 st= ate). Is it possible to do it by any free software or Gaussian 03 =A0and ho= w?
Any type of help is greatly acknowledge.
best regards
<= div>Utpal --14dae93a151bbc73d804b004906e-- From owner-chemistry@ccl.net Mon Oct 24 02:49:00 2011 From: "i.nick-#-mail.ru" To: CCL Subject: CCL: Wavefunction or electrondensity of molecular rydberg state. Message-Id: <-45724-111024022337-25304-Wb9BgJc06ZG7Ob9JBWct2Q#,#server.ccl.net> X-Original-From: i.nick|*|mail.ru Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 Date: Mon, 24 Oct 2011 10:23:29 +0400 MIME-Version: 1.0 Sent to CCL by: i.nick++mail.ru Re: CCL:G: Wavefunction or electrondensity of molecular = rydberg state. I calculated su= ch states of Bz2Cr and Bz2V, but only for up to n =3D 7, higher states are = mixed and their energies are out of trusted ranges...in principle you need = simple SP calculation, but be aware of choosing corresponding basis/functio= nal 


 Dear CCL users,
                     = ;    I want to know the electron density or wavefunction of the R= ydberg State of Hydrogen Molecule (say one electron is in, principle quantu= m number, n=3D10 state). Is it possible to do it by any free software or Ga= ussian 03  and how?
Any type of help is greatly acknowledge.
best regards
Utpal




-- 
С уважением,
 i                   &nbs= p;      mailto:i.nick a mail.ru From owner-chemistry@ccl.net Mon Oct 24 08:33:01 2011 From: "cina foroutan canyslopus|yahoo.co.uk" To: CCL Subject: CCL:G: AIM for molecular ion Message-Id: <-45725-111024014347-25789-G9De3jDuegmxgWKl6f1fqQ]*[server.ccl.net> X-Original-From: cina foroutan Content-Type: multipart/alternative; boundary="505732852-1579454661-1319435018=:51168" Date: Mon, 24 Oct 2011 06:43:38 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: cina foroutan [canyslopus _ yahoo.co.uk] --505732852-1579454661-1319435018=:51168 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable The most efficient and user-friendly code for QTAIM calculations is AIMAll.= To have a trial version of this code send a mail to Dr. Todd A. Keith and = ask for a trial version.=0AYou can perform the calculations by making a WFN= file or a FCH file. For WFN see the help of Gaussian.=0A=0A=0A=0A_________= _______________________=0AFrom: Johannes Hachmann jh[*]chemistry.harvard.ed= u =0ATo: "Foroutan-Nejad, Cina " =0ASent: Monday, 24 October 2011, 3:25=0ASubject: CCL:G: AIM= for molecular ion=0A=0A=0ASent to CCL by: "Johannes Hachmann" [jh-$-chemis= try.harvard.edu]=0AI made good experience with the 'Bader Charge Analysis' = code (in DOS, i.e.,=0Ayou have to run it in the Win Command prompt): =0A=0A= http://theory.cm.utexas.edu/bader/=0A=0AJust produce a cube from your chk f= ile (make sure that you have a grid which=0Ais dense enough for a converged= AIM analysis!) and you are good to go:=0A=0Aformchk your.chk your.fchk=0Ac= ubegen 0 density your.fchk your.density.cube -3 =0Abader your.density.cube= =0A=0AThat's already it.=0A=0ABest =0A=0AJohannes =0A=0A=0A----------------= -------------------------------=0ADr. Johannes Hachmann=0APostdoctoral Fell= ow=0A=A0=A0=A0 =0AAspuru-Guzik Research Group=0AHarvard University=0ADepart= ment of Chemistry and Chemical Biology=0A12 Oxford St, Rm M104A=0ACambridge= , MA 02138=0AUSA=0AeMail: jh+*+chemistry.harvard.edu =0A-------------------= ----------------------------=0A=0A=0A=0A> -----Original Message-----=0A> Fr= om: owner-chemistry+jh=3D=3Dchemistry.harvard.edu+*+ccl.net=0A> [mailto:own= er-chemistry+jh=3D=3Dchemistry.harvard.edu+*+ccl.net] On Behalf=0A> Of Serg= io Emanuel Galembeck segalemb__usp.br=0A> Sent: Sunday, October 23, 2011 17= :29=0A> To: Hachmann, Johannes =0A> Subject: CCL:G: AIM for molecular ion= =0A> =0A> =0A> Sent to CCL by: Sergio Emanuel Galembeck [segalemb{=3D}usp.b= r]=0A> Dear Dario,=0A> =0A>=A0 =A0 The use of AIM modules in Gaussian is n= ot recommend, in part=0A> because=0A> this option is not maintained. I reco= mmend the use of AIMAll,=0A> because=0A> this is a fast and robust program.= =0A> =0A>=A0 =A0 =A0 =A0 =A0 =A0 =A0 Hope this help,=0A> =0A>=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Sergio=0A> =0A> =0A> Citando "Dario= Fernando Coral ferchocoralg16 .. gmail.com"=0A> = :=0A> =0A> >=0A> > Sent to CCL by: "Dario Fernando Coral" [ferchocoralg16__= gmail.com]=0A> > regards=0A> >=0A> > Does anyone know how to perform AIM ca= lculations in gaussian 09 or=0A> > 03 for a molecular ion?=0A> >=0A> > I ha= ve performed this calculation for the neutral water molecule,=0A> > but whe= n I use AIM command on the furfuryl-aniline molecular ion,=0A> > gaussian 0= 9 has an error in the link L609=0A> >=0A> > The route card I used is as fol= lows: # ub3lyp/631g(d) AIM=3Dcharge=0A> test=0A> >=0A> > thanks in advance>= =0A> >=0A> >=0A> =0A> =0A> =0A> -=3D This is automatically added to each me= ssage by the mailing script=0A> =3D-=0A> To recover the email address of th= e author of the message, please=0A> change> Conferences:=0A> http://server.= ccl.net/chemistry/announcements/conferences/=0A=0A=0A-=3D This is automatic= ally added to each message by the mailing script =3D-=0ATo recover the emai= l address of the author of the message, please change=0Athe strange charact= ers on the top line to the [a] sign. You can also=0Alook up the X-Original-Fr= om: line in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY[a]ccl.net = or use:=0A=A0 =A0 =A0=0A=0A==0A=A0 =A0 =A0 ht= tp://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0A= =0A=A0 =A0 =A0=0A=0ABefore pos= ting, check wait time at: http://www.ccl.net=0A=0AJob: http://www.ccl.net/j= obs =0AConferences: http://server.ccl.net/chemistry/announcements/conferenc= es/=0A=0ASearch Messages: http://www.ccl.net/chemistry/searchccl/index.shtm= l=0A=0A=0A=A0 =A0 =A0==0A=0ARTFI: http://www.ccl.net/chemistry/ab= outccl/instructions/ --505732852-1579454661-1319435018=:51168 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
The most e= fficient and user-friendly code for QTAIM calculations is AIMAll. To have a= trial version of this code send a mail to Dr. Todd A. Keith and ask for a = trial version.
You can perform the calculations by m= aking a WFN file or a FCH file. For WFN see the help of Gaussian.

From: Johan= nes Hachmann jh[*]chemistry.harvard.edu <owner-chemistry[a]ccl.net>
= To: "Foroutan-Nejad, Cina = " <canyslopus[a]yahoo.co.uk>
Sent: Monday, 24 October 2011, 3:25
Subject: CCL:G: AIM for molecular ion


Sent to CCL by: "Johannes Hachmann" [jh-$-chemistry.harvard.ed= u]
I made good experience with the 'Bader Charge Analysis' code (in DOS,= i.e.,
you have to run it in the Win Command prompt):

http://theory.cm.ute= xas.edu/bader/

Just produce a cube from your chk file (make sure= that you have a grid which
is dense enough for a converged AIM analysis= !) and you are good to go:

formchk your.chk your.fchk
cubegen 0 d= ensity your.fchk your.density.cube -3
bader your.density.cube

Th= at's already it.

Best

Johannes


-----------------= ------------------------------
Dr. Johannes Hachmann
Postdoctoral Fel= low
   
Aspuru-Guzik Research Group
Harvard University
Department of Chemistry and Chemical Biology
12 Oxford St= , Rm M104A
Cambridge, MA 02138
USA
eMail: jh+*+chemistry.harvard.e= du
-----------------------------------------------



> = -----Original Message-----
> From: owner-chemistry+jh=3D=3Dchemistry.= harvard.edu+*+ccl.net
> [mailto:owner-chemistry+jh=3D=3Dchemistry.har= vard.edu+*+ccl.net] On Behalf
> Of Sergio Emanuel Galembeck segalemb_= _usp.br
> Sent: Sunday, October 23, 2011 17:29
> To: Hachmann, = Johannes
> Subject: CCL:G: AIM for molecular ion
>
> > Sent to CCL by: Sergio Emanuel Galembeck [segalemb{=3D}usp.br]
&g= t; Dear Dario,
>
>    The use of AIM modules in Gau= ssian is not recommend, in part
> because
> this option is not = maintained. I recommend the use of AIMAll,
> because
> this is = a fast and robust program.
>
>        &nbs= p;     Hope this help,
>
>       =                   Sergio
&= gt;
>
> Citando "Dario Fernando Coral ferchocoralg16 .. gmail= .com"
> <owner-chemistry,,ccl.net>:
>
> >
&g= t; > Sent to CCL by: "Dario Fernando Coral" [ferchocoralg16__gmail.com]<= br>> > regards
> >
> > Does anyone know how to perf= orm AIM calculations in gaussian 09 or
> > 03 for a molecular ion?=
> >
> > I have performed this calculation for the neutra= l water molecule,
> > but when I use AIM command on the furfuryl-a= niline molecular ion,
> > gaussian 09 has an error in the link L60= 9
> >
> > The route card I used is as follows: # ub3lyp/6= 31g(d) AIM=3Dcharge
> test
> >
> > thanks in advanc= e>
> >
> >
>
>
>
> -=3D This is automatically added to each message by the mailing script
> = =3D-
> To recover the email address of the author of the message, ple= ase
> change> Conferences:
> http://server.ccl= .net/chemistry/announcements/conferences/


-=3D This is autom= atically added to each message by the mailing script =3D-
To recover the= email address of the author of the message, please change
the strange c= haracters on the top line to the [a] sign. You can also
look up the X-Orig= inal-From: line in the mail header.

E-mail to subscribers: CHEMISTRY[a]= ccl.net or use:
      http://www.ccl.net/cgi-bin/c= cl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net or use
      <= a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=3D"_blank= ">http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml  &nbs= p;   htt= p://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/che= mistry/aboutccl/instructions/




--505732852-1579454661-1319435018=:51168-- From owner-chemistry@ccl.net Mon Oct 24 11:58:00 2011 From: "Josh Marell mare0051]*[umn.edu" To: CCL Subject: CCL:G: Explicit consideration of x degress of freedom Message-Id: <-45726-111024114506-3763-vVbHBel6tzNtxpHD/CYtqA%%server.ccl.net> X-Original-From: Josh Marell Content-Type: multipart/alternative; boundary=0015174c3728141bff04b00d4e3a Date: Mon, 24 Oct 2011 10:44:36 -0500 MIME-Version: 1.0 Sent to CCL by: Josh Marell [mare0051**umn.edu] --0015174c3728141bff04b00d4e3a Content-Type: text/plain; charset=ISO-8859-1 Hello, I'm trying to calculate energy of a transition state (using frequency analysis) in gaussian 09. I received the warning above "Warning -- explicit consideration of 12 degrees of freedom as vibrations may cause significant error". I followed some ideas on here about forcing geometry optimization with the verytight keyword and also adding the HinderedRotor option in the frequency calculation, but this has not improved the number of degrees of freedom that were found in the warning. I should add that the calculation does find one and only 1 imaginary frequency, and that the vibration does correspond to the desired movement for the reaction, so I am confident that the transition state found is correct. I am only pausing as I have read that the result of the frequency analysis (in terms of thermochemical information) may not be reliable when this warning is produced. I am wondering if anyone has further suggestions for this addressing this warning. Thank you, Josh --0015174c3728141bff04b00d4e3a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,

I'm trying to calculate energy of a transitio= n state (using frequency analysis) in gaussian 09. =A0I received the warnin= g above "Warning -- explicit consideration of 12 degrees of freedom as= =A0vibrations may cause significant error". =A0I followed some ideas o= n here about forcing geometry optimization with the verytight keyword and a= lso adding the HinderedRotor option in the frequency calculation, but this = has not improved the number of degrees of freedom that were found in the wa= rning. =A0I should add that the calculation does find one and only 1 imagin= ary frequency, and that the vibration does correspond to the desired moveme= nt for the reaction, so I am confident that the transition state found is c= orrect.

I am only pausing as I have read that the result of the= frequency analysis (in terms of thermochemical information) may not be rel= iable when this warning is produced. =A0I am wondering if anyone has furthe= r suggestions for this addressing this warning.

Thank you,

Josh
--0015174c3728141bff04b00d4e3a-- From owner-chemistry@ccl.net Mon Oct 24 12:33:00 2011 From: "=?ISO-8859-1?Q?Jo=E3o_Henriques?= jmhenriques!A!fc.ul.pt" To: CCL Subject: CCL:G: Macro or something for Gaussian 03 Message-Id: <-45727-111024111417-31632-R5ZRiuNq85iLInecrOFooA]-[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jo=E3o_Henriques?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 24 Oct 2011 16:14:07 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_Henriques?= [jmhenriques:+:fc.ul.pt] I wouldn't mind sending you a Python program I wrote to extract a comprehensive amount of data from gaussian03/09 logs. It has no integration with Excel though. I store all my data in txt files. Whenever I want to plot data, I just run gnuplot on them... Best regards, On Wed, Oct 19, 2011 at 7:56 PM, Serdar Badoglu sbadoglu##gazi.edu.tr wrote: > > Sent to CCL by: "Serdar  Badoglu" [sbadoglu-$-gazi.edu.tr] > Hi CCL'ers, > > Do any of you have / know an excel macro / a little program to extract > calculated frequencies, infrared intensities, and Raman activities from > Gaussian log file? I don't need the complete spectrum generated, I only need > the mentioned data of vibrational modes. I'm really tired of switching between > windows and reading and typing the data into spreadsheets. > > Regards.>      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> > > -- Joćo Henriques, MSc in Biochemistry Faculty of Science of the University of Lisbon Department of Chemistry and Biochemistry C8 Building, Room 8.5.47 Campo Grande, 1749-016 Lisbon, Portugal E-mail: joao.henriques.32353||gmail.com / jmhenriques||fc.ul.pt http://intheochem.fc.ul.pt/members/joaoh.html From owner-chemistry@ccl.net Mon Oct 24 13:07:00 2011 From: "Arne Dieckmann adieckma*_*googlemail.com" To: CCL Subject: CCL:G: Explicit consideration of x degress of freedom Message-Id: <-45728-111024124628-4276-7+o9sKLPXz9K/f1lOUqILg(-)server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 24 Oct 2011 09:46:11 -0700 Mime-Version: 1.0 (1.0) Sent to CCL by: Arne Dieckmann [adieckma..googlemail.com] Hi Josh, do your frequencies differ before and after translations and rotations have been projected out? Cheers, Arne On Oct 24, 2011, at 8:44 AM, "Josh Marell mare0051]*[umn.edu" wrote: > Hello, > > I'm trying to calculate energy of a transition state (using frequency analysis) in gaussian 09. I received the warning above "Warning -- explicit consideration of 12 degrees of freedom as vibrations may cause significant error". I followed some ideas on here about forcing geometry optimization with the verytight keyword and also adding the HinderedRotor option in the frequency calculation, but this has not improved the number of degrees of freedom that were found in the warning. I should add that the calculation does find one and only 1 imaginary frequency, and that the vibration does correspond to the desired movement for the reaction, so I am confident that the transition state found is correct. > > I am only pausing as I have read that the result of the frequency analysis (in terms of thermochemical information) may not be reliable when this warning is produced. I am wondering if anyone has further suggestions for this addressing this warning. > > Thank you, > > Josh From owner-chemistry@ccl.net Mon Oct 24 14:04:01 2011 From: "Y. Yuan echemistry(!)yahoo.com" To: CCL Subject: CCL: Chrawler (Chemistry Chrawler) 1.1 Release Message-Id: <-45729-111024121044-23868-aP8Iw+DjZD9F2uvTkO85xQ^server.ccl.net> X-Original-From: "Y. Yuan" Content-Type: multipart/alternative; boundary="-1118611504-2112114931-1319472615=:79147" Date: Mon, 24 Oct 2011 09:10:15 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Y. 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---1118611504-2112114931-1319472615=:79147-- From owner-chemistry@ccl.net Mon Oct 24 15:25:00 2011 From: "Josh Marell mare0051*_*umn.edu" To: CCL Subject: CCL:G: Explicit consideration of x degress of freedom Message-Id: <-45730-111024152124-28968-juMlpXkC/uJypV7EFcwjGg!A!server.ccl.net> X-Original-From: Josh Marell Content-Type: multipart/alternative; boundary=00151750e35cde88ad04b0105203 Date: Mon, 24 Oct 2011 14:20:43 -0500 MIME-Version: 1.0 Sent to CCL by: Josh Marell [mare0051|umn.edu] --00151750e35cde88ad04b0105203 Content-Type: text/plain; charset=ISO-8859-1 Hi Arne, I just checked the frequencies and it still finds the same number of frequencies, and they match very closely (standard deviation of only 0.16 across 60 frequencies). Thanks, Josh On Mon, Oct 24, 2011 at 11:46 AM, Arne Dieckmann adieckma*_*googlemail.com < owner-chemistry-.-ccl.net> wrote: > > Sent to CCL by: Arne Dieckmann [adieckma..googlemail.com] > Hi Josh, > > do your frequencies differ before and after translations and rotations have > been projected out? > > Cheers, > Arne > > On Oct 24, 2011, at 8:44 AM, "Josh Marell mare0051]*[umn.edu" > wrote: > > > Hello, > > > > I'm trying to calculate energy of a transition state (using frequency > analysis) in gaussian 09. I received the warning above "Warning -- explicit > consideration of 12 degrees of freedom as vibrations may cause significant > error". I followed some ideas on here about forcing geometry optimization > with the verytight keyword and also adding the HinderedRotor option in the > frequency calculation, but this has not improved the number of degrees of > freedom that were found in the warning. I should add that the calculation > does find one and only 1 imaginary frequency, and that the vibration does > correspond to the desired movement for the reaction, so I am confident that > the transition state found is correct. > > > > I am only pausing as I have read that the result of the frequency > analysis (in terms of thermochemical information) may not be reliable when > this warning is produced. I am wondering if anyone has further suggestions > for this addressing this warning. > > > > Thank you, > > > > Josh> > > --00151750e35cde88ad04b0105203 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Arne,

I just checked the frequencies and it still fin= ds the same number of frequencies, and they match very closely (standard de= viation of only 0.16 across 60 frequencies). =A0

Thanks,

Josh

On Mon, Oct 24, 2011 at 11:46 AM, Arne Dieckmann adieckma*= _*googlemail.com &l= t;owner-chemistry-.-ccl.net>= ; wrote:

Sent to CCL by: Arne Dieckmann [adieckma..googlemail.com]
Hi Josh,

do your frequencies differ before and after translations and rotations have= been projected out?

Cheers,
Arne

On Oct 24, 2011, at 8:44 AM, "Josh Marell mare0051]*[umn.edu" <owner-chemistry~~ccl.net> wrote:

> Hello,
>
> I'm trying to calculate energy of a transition state (using freque= ncy analysis) in gaussian 09. =A0I received the warning above "Warning= -- explicit consideration of 12 degrees of freedom as vibrations may cause= significant error". =A0I followed some ideas on here about forcing ge= ometry optimization with the verytight keyword and also adding the Hindered= Rotor option in the frequency calculation, but this has not improved the nu= mber of degrees of freedom that were found in the warning. =A0I should add = that the calculation does find one and only 1 imaginary frequency, and that= the vibration does correspond to the desired movement for the reaction, so= I am confident that the transition state found is correct.
>
> I am only pausing as I have read that the result of the frequency anal= ysis (in terms of thermochemical information) may not be reliable when this= warning is produced. =A0I am wondering if anyone has further suggestions f= or this addressing this warning.
>
> Thank you,
>
> Josh



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--00151750e35cde88ad04b0105203-- From owner-chemistry@ccl.net Mon Oct 24 16:33:00 2011 From: "Arne Dieckmann adieckma~!~googlemail.com" To: CCL Subject: CCL:G: Explicit consideration of x degress of freedom Message-Id: <-45731-111024163151-21457-SgOtoplVBBcb3k/rwMjEJg#%#server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 24 Oct 2011 13:31:40 -0700 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Arne Dieckmann [adieckma|,|googlemail.com] Hi Josh, what do you mean by "same number of frequencies"? You should compare the largest frequencies listed with the "Low frequencies" keyword and those appearing later in the output file. Cheers, Arne On Oct 24, 2011, at 12:20 PM, Josh Marell mare0051*_*umn.edu wrote: > Hi Arne, > > I just checked the frequencies and it still finds the same number of frequencies, and they match very closely (standard deviation of only 0.16 across 60 frequencies). > > Thanks, > > Josh > > On Mon, Oct 24, 2011 at 11:46 AM, Arne Dieckmann adieckma*_*googlemail.com wrote: > > Sent to CCL by: Arne Dieckmann [adieckma..googlemail.com] > Hi Josh, > > do your frequencies differ before and after translations and rotations have been projected out? > > Cheers, > Arne > > On Oct 24, 2011, at 8:44 AM, "Josh Marell mare0051]*[umn.edu" wrote: > > > Hello, > > > > I'm trying to calculate energy of a transition state (using frequency analysis) in gaussian 09. I received the warning above "Warning -- explicit consideration of 12 degrees of freedom as vibrations may cause significant error". I followed some ideas on here about forcing geometry optimization with the verytight keyword and also adding the HinderedRotor option in the frequency calculation, but this has not improved the number of degrees of freedom that were found in the warning. I should add that the calculation does find one and only 1 imaginary frequency, and that the vibration does correspond to the desired movement for the reaction, so I am confident that the transition state found is correct. > > > > I am only pausing as I have read that the result of the frequency analysis (in terms of thermochemical information) may not be reliable when this warning is produced. I am wondering if anyone has further suggestions for this addressing this warning. > > > > Thank you, > > > > Josh> > > > E-mail to subscribers: CHEMISTRY.=-=.ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST.=-=.ccl.net or use> > > From owner-chemistry@ccl.net Mon Oct 24 17:08:00 2011 From: "A. Anglea a.anglea90 _ yahoo.com" To: CCL Subject: CCL:G: MOPAC input file Message-Id: <-45732-111024170552-14220-FK1JmAGTDAVrfjSZdHY0Ow##server.ccl.net> X-Original-From: "A. Anglea" Date: Mon, 24 Oct 2011 17:05:48 -0400 Sent to CCL by: "A. Anglea" [a.anglea90{:}yahoo.com] Hi all I am a new user of MOPAC program. For mopac, can I used the z matrix input file as following ********* AM1 1SCF Water Water single point O H 1 B1 H 1 B2 2 A1 B1 0.96000000 B2 0.96000000 A1 109.50000019 1 3 1.0 2 1.0 2 3 ********* I got the Gaussian input file and modified it. Or it has to be converted using openbabel. Cheers From owner-chemistry@ccl.net Mon Oct 24 17:43:00 2011 From: "Edward Holland hollandej-x-Cardiff.ac.uk" To: CCL Subject: CCL:G: Macro or something for Gaussian 03 Message-Id: <-45733-111024153227-21426-f8yH8uBjqutyLPJAUkMwsA]=[server.ccl.net> X-Original-From: Edward Holland Content-Type: multipart/signed; boundary="Apple-Mail=_98B718DB-F3DF-47DE-B4CE-10F683DC84C3"; protocol="application/pgp-signature"; micalg=pgp-sha1 Date: Mon, 24 Oct 2011 20:32:10 +0100 Mime-Version: 1.0 (Apple Message framework v1244.3) Sent to CCL by: Edward Holland [hollandej]_[Cardiff.ac.uk] --Apple-Mail=_98B718DB-F3DF-47DE-B4CE-10F683DC84C3 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Would it be possible to publish this on-line somewhere? I'm currently in = the progress of writing similar python scripts and it seems foolish = to duplicate efforts! Yours Ed Holland On 24 Oct 2011, at 16:14, Jo=E3o Henriques jmhenriques!A!fc.ul.pt wrote: >=20 > Sent to CCL by: =3D?ISO-8859-1?Q?Jo=3DE3o_Henriques?=3D = [jmhenriques:+:fc.ul.pt] > I wouldn't mind sending you a Python program I wrote to extract a > comprehensive amount of data from gaussian03/09 logs. It has no > integration with Excel though. I store all my data in txt files. > Whenever I want to plot data, I just run gnuplot on them... >=20 > Best regards, >=20 > On Wed, Oct 19, 2011 at 7:56 PM, Serdar Badoglu sbadoglu##gazi.edu.tr > wrote: >>=20 >> Sent to CCL by: "Serdar Badoglu" [sbadoglu-$-gazi.edu.tr] >> Hi CCL'ers, >>=20 >> Do any of you have / know an excel macro / a little program to = extract >> calculated frequencies, infrared intensities, and Raman activities = > from >> Gaussian log file? I don't need the complete spectrum generated, I = only need >> the mentioned data of vibrational modes. I'm really tired of = switching between >> windows and reading and typing the data into spreadsheets. >>=20 >> Regards.> => => => >>=20 >>=20 >=20 >=20 >=20 > --=20 > Jo=E3o Henriques, MSc in Biochemistry > Faculty of Science of the University of Lisbon > Department of Chemistry and Biochemistry > C8 Building, Room 8.5.47 > Campo Grande, 1749-016 Lisbon, Portugal > E-mail: joao.henriques.32353{}gmail.com / jmhenriques{}fc.ul.pt > http://intheochem.fc.ul.pt/members/joaoh.html >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail=_98B718DB-F3DF-47DE-B4CE-10F683DC84C3 Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename=signature.asc Content-Type: application/pgp-signature; name=signature.asc Content-Description: Message signed with OpenPGP using GPGMail -----BEGIN PGP SIGNATURE----- iQEcBAEBAgAGBQJOpb08AAoJEEJc9s8gBQly+owIANJKCYw2vnL0OnW4EjFR6vUs xxNCXISqY1GjnUXXKFDSs2lhLkoEVKNPav5wiCgtHPJo59yH7D/UcqOTfBBrO1Ml XVDU0Tdop86Qfj0YCxYA+PsLX++8RRI3yxcW/WmtV455f/LW3TxACnY1Uchj9zjy JXr8ftmYnIIpLIWWFV+35jv3SpYWA8DmAMbS//Svejgk6uNWzvOmyMuMkbEUYB5T FtSbLJ9Gl5hMybTbPSURhu0QcTKr3k8faUephEZ4ZU+varVDC/iN8tq27ggJqfY8 Y6PzMPezOkgvU3SxR6HfUCfj/J+ddBwdkR+1gtfXvpUHrFRv5AI0FPN47bjgTBU= =VwrM -----END PGP SIGNATURE----- --Apple-Mail=_98B718DB-F3DF-47DE-B4CE-10F683DC84C3-- From owner-chemistry@ccl.net Mon Oct 24 20:02:00 2011 From: "Geoffrey Hutchison geoffh{=}pitt.edu" To: CCL Subject: CCL: Macro or something for Gaussian 03 Message-Id: <-45734-111024195451-14927-wZ0ZLq3Wx7kQi8adX3wzPQ_._server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=iso-8859-1 Date: Mon, 24 Oct 2011 19:54:45 -0400 MIME-version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Geoffrey Hutchison [geoffh[]pitt.edu] > Would it be possible to publish this on-line somewhere? I'm currently in the progress of writing similar python scripts and it seems foolish to duplicate efforts! There are already a wide variety of such scripts. I suggest python users look at GaussSum and cclib: http://gausssum.sf.net/ http://cclib.sf.net/ They work to extract data in a wide range of comp-chem packages. Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh-x-pitt.edu web: http://hutchison.chem.pitt.edu/