From owner-chemistry@ccl.net Fri Sep 21 08:27:00 2012 From: "MOREAU Yohann 224609 yohann.moreau:_:cea.fr" To: CCL Subject: CCL:G: Torsion angles Message-Id: <-47644-120921034906-23513-TDTFEWJpvWhwVS5fwrWTdQ^server.ccl.net> X-Original-From: MOREAU Yohann 224609 Content-Language: fr-FR Content-Type: multipart/alternative; boundary="_000_CC81E4B73426yohannmoreauceafr_" Date: Fri, 21 Sep 2012 07:48:55 +0000 MIME-Version: 1.0 Sent to CCL by: MOREAU Yohann 224609 [yohann.moreau : cea.fr] --_000_CC81E4B73426yohannmoreauceafr_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear Sergio, By default, in Gaussian, optimizations are done in redundant internal coord= inates. If you check your output file, you'll find at the beginning and at = the end of the optimization the set of redundant internal coordinates. To extract these data, you can use a simple shell command, such as : grep "! D" file.log | awk=91{print $3, " ", $4}' Which will output the dihedral parameters (at least those used by the optim= izer) at the beginning and at the end of the optimization. You can redirect this to another grep filter to find the torsional angle yo= u're looking for : grep "! D" file.log | awk=91{print $3, " ", $4}' | grep "1,2,4,5" Which outputs the dihedral value between atoms 1, 2, 4 & 5 at the beginning= and at the end of the calculation. I'm pretty certain that more "elegant" ways to do it exist but this has wor= ked on my output files. Anyway, nothing guarantees that the specific torsion angle you're looking f= or is actually being used by the optimizer and then listed. I hope this will help you. YM -- Yohann Moreau Ma=EEtre de Conf=E9rence, Universit=E9 Joseph Fourier iRTSV/CBM/MCT, CEA Grenoble 17 avenue des Martyrs 38 054 Grenoble Cedex 09 Tel. : (33) 4 38 78 29 62 Fax : (33) 4 38 78 54 87 De : "Sergio Manzetti sergio.manzetti[-]gmx.com" > R=E9pondre =E0 : CCL Subscribers > Date : jeudi 20 septembre 2012 18:01 =C0 : MOREAU Yohann 224609 > Objet : CCL:G: Torsion angles Dear CCLrs can you recommend a program that can easily report the torsion a= ngles of given atoms in a Gaussian output file? Thanks Best wishes Sergio --_000_CC81E4B73426yohannmoreauceafr_ Content-Type: text/html; charset="Windows-1252" Content-ID: Content-Transfer-Encoding: quoted-printable
Dear Sergio, 

By default, in Gaussian, optimizations are done in redundant internal = coordinates. If you check your output file, you'll find at the beginning an= d at the end of the optimization the set of redundant internal coordinates.=
To extract these data, you can use a simple shell command, such  = as : 

 grep "! D" file.log | awk=91{print $3, " ", = $4}' 

Which will output the dihedral parameters (at least those used by the = optimizer) at the beginning and at the end of the optimization. 
You can redirect this to another grep filter to find the torsional ang= le you're looking for : 

 grep "! D" file.log | awk=91{print $3, " ", = $4}' | grep "1,2,4,5" 

Which outputs the dihedral value between atoms 1, 2, 4 & 5 at the = beginning and at the end of  the calculation.

I'm pretty certain that more "elegant" ways to do it exist b= ut this has worked on my output files.
Anyway, nothing guarantees that the specific torsion angle you're look= ing for is actually being used by the optimizer and then listed.

I hope this will help you.

YM

-- 

Yohann Moreau

Ma=EEtre de Conf=E9rence, Universit=E9 Joseph Fourier
iRTSV/CBM/MCT, CEA Grenoble
17 avenue des Martyrs
38 054 Grenoble Cedex 09
Tel. : (33) 4 38 78 29 62
Fax : (33) 4 38 78 54 87

De : "Sergio Manzetti ser= gio.manzetti[-]gmx.com" <owner-chemistry a ccl.net>
R=E9pondre =E0 : CCL Subscribe= rs <chemistry a ccl.net>
Date : jeudi 20 septembre 2012= 18:01
=C0 : MOREAU Yohann 224609 <= ;yohann.moreau a cea.fr>
Objet : CCL:G: Torsion angles<= br>

Dea= r CCLrs can you recommend a program that can easily report the torsion angl= es of given atoms in a Gaussian output file?

Thanks

Best wishes

Sergio
 --_000_CC81E4B73426yohannmoreauceafr_-- From owner-chemistry@ccl.net Fri Sep 21 11:34:00 2012 From: "Sergio Manzetti sergio.manzetti a gmx.com" To: CCL Subject: CCL:G: Torsion angles Message-Id: <-47645-120921093930-10704-XswqJo+J/F4+mtafuIxkGQ]*[server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary167031348233463392016" Date: Fri, 21 Sep 2012 15:17:43 +0200 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti#,#gmx.com] --========GMXBoundary167031348233463392016 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Thanks Yohann, I found that ChemCraft has a very nice module to make this look nice graphically and quite easy. Otherwise, Gaussivew does also this, however without representing the planes of the dihedrals. Sergio ----- Original Message ----- > From: MOREAU Yohann 224609 yohann.moreau:_:cea.fr Sent: 09/21/12 09:48 AM To: Manzetti, Sergio Subject: CCL:G: Torsion angles Dear Sergio, By default, in Gaussian, optimizations are done in redundant internal coordinates. If you check your output file, you'll find at the beginning and at the end of the optimization the set of redundant internal coordinates. To extract these data, you can use a simple shell command, such as : grep "! D" file.log | awk‘{print $3, " ", $4}' Which will output the dihedral parameters (at least those used by the optimizer) at the beginning and at the end of the optimization. You can redirect this to another grep filter to find the torsional angle you're looking for : grep "! D" file.log | awk‘{print $3, " ", $4}' | grep "1,2,4,5" Which outputs the dihedral value between atoms 1, 2, 4 & 5 at the beginning and at the end of the calculation. I'm pretty certain that more "elegant" ways to do it exist but this has worked on my output files. Anyway, nothing guarantees that the specific torsion angle you're looking for is actually being used by the optimizer and then listed. I hope this will help you. YM -- Yohann Moreau Maître de Conférence, Université Joseph Fourier iRTSV/CBM/MCT, CEA Grenoble 17 avenue des Martyrs 38 054 Grenoble Cedex 09 Tel. : (33) 4 38 78 29 62 Fax : (33) 4 38 78 54 87 De : "Sergio Manzetti sergio.manzetti[-]gmx.com" < owner-chemistry*%7C*ccl.net > Répondre à : CCL Subscribers < chemistry*%7C*ccl.net > Date : jeudi 20 septembre 2012 18:01 À : MOREAU Yohann 224609 < yohann.moreau*%7C*cea.fr > Objet : CCL:G: Torsion angles Dear CCLrs can you recommend a program that can easily report the torsion angles of given atoms in a Gaussian output file? Thanks Best wishes Sergio --========GMXBoundary167031348233463392016 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Thanks Y= ohann, I found that ChemCraft has a very nice module to make this look nice= graphically and quite easy. Otherwise, Gaussivew does also this, however w= ithout representing the planes of the dihedrals.
=20
=20 Sergio
=20
=20

=20 =C2=A0

=20
=20

=20 ----- = Original Message -----

=20

=20 From: = MOREAU Yohann 224609 yohann.moreau:_:cea.fr

=20

=20 Sent: = 09/21/12 09:48 AM

=20

=20 To: Ma= nzetti, Sergio

=20

=20 Subjec= t: CCL:G: Torsion angles

=20
=20
=20
=20
=20
=20 Dear Sergio, 
=20
=20 =C2=A0
=20
=20 By default, in Gaussian, optimizations are done in redundant internal = coordinates. If you check your output file, you'll find at the beginning an= d at the end of the optimization the set of redundant internal coordinates.=
=20
=20 To extract these data, you can use a simple shell command, such  = as : 
=20
=20 =C2=A0
=20
=20  grep "! D" file.log | awk=E2=80=98{print $3, " ", $4}' =20
=20
=20
=20 =C2=A0
=20
=20 Which will output the dihedral parameters (at least those used by th= e optimizer) at the beginning and at the end of the optimization. =20
=20 You can redirect this to another grep filter to find the torsional a= ngle you're looking for : 
=20
=20 =C2=A0
=20
=20  grep "! D" file.log | awk=E2=80=98{print $3, " ", $4}' | grep = "1,2,4,5" 
=20
=20 =C2=A0
=20
=20 Which outputs the dihedral value between atoms 1, 2, 4 & 5 at th= e beginning and at the end of  the calculation.
=20
=20 =C2=A0
=20
=20 I'm pretty certain that more "elegant" ways to do it exist but this = has worked on my output files.
=20
=20 Anyway, nothing guarantees that the specific torsion angle you're lo= oking for is actually being used by the optimizer and then listed.
=20
=20 =C2=A0
=20
=20 I hope this will help you.
=20
=20 =C2=A0
=20
=20 YM
=20
=20 =C2=A0
=20
=20 -- 
=20
=20 =C2=A0
=20
=20
=20
=20 Yohann Moreau
=20
=20 =C2=A0
=20
=20 Ma=C3=AEtre de Conf=C3=A9rence, Universit=C3=A9 Joseph Fourier
= =20
=20 iRTSV/CBM/MCT, CEA Grenoble
=20
=20 17 avenue des Martyrs
=20
=20 38 054 Grenoble Cedex 09
=20
=20 Tel. : (33) 4 38 78 29 62
=20
=20 Fax : (33) 4 38 78 54 87
=20
=20
=20
=20
=20
=20 =C2=A0
=20
=20 De&nb= sp;: "Sergio Manzetti sergio.manzetti[-]gmx.com" <owner-chemistry*|*ccl.net>
=20 R=C3=A9pondre =C3=A0 : CCL = Subscribers <chemistry*|*ccl.ne= t>
=20 Date : jeudi 20 septembre 2= 012 18:01
=20 =C3=80 : MOREAU Yohann 2246= 09 <yohann.moreau*|*cea.fr>
=20 Objet : CCL:G: Torsion angl= es
=20
=20
=20 =C2=A0
=20
=20
=20 <= span style=3D"font-size:12px">Dear CCLrs can you recommend a program that c= an easily report the torsion angles of given atoms in a Gaussian output fil= e?
=20
=20 Thanks
=20
=20 Best wishes
=20
=20 Sergio
=20
=20
=20
=20

=20 =C2=A0

=20
=20 --========GMXBoundary167031348233463392016-- From owner-chemistry@ccl.net Fri Sep 21 12:15:00 2012 From: "Sergio Manzetti sergio.manzetti^^gmx.com" To: CCL Subject: CCL: Symmetry Message-Id: <-47646-120921121334-3008-quXDoKIT0lD9i1OBw+XIBg*server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary167001348243995166740" Date: Fri, 21 Sep 2012 18:13:14 +0200 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti/./gmx.com] --========GMXBoundary167001348243995166740 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Dear CCLrs, it is evident that molecular symmetry is not straight forward for complex molecules. Are there any computational methods to determine the symmetry of an input structure, and its subgroups? Sergio --========GMXBoundary167001348243995166740 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear CCL= rs, it is evident that molecular symmetry is not straight forward for compl= ex molecules. Are there any computational methods to determine the symmetry= of an input structure, and its subgroups?
=20
=20 Sergio --========GMXBoundary167001348243995166740-- From owner-chemistry@ccl.net Fri Sep 21 15:49:00 2012 From: "Nuno A. G. Bandeira nuno.bandeira##ist.utl.pt" To: CCL Subject: CCL: Symmetry Message-Id: <-47647-120921134049-24947-LG2uZ+oloYuemD+nOkdUNg_+_server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Type: multipart/alternative; boundary="------------070502090506080908030008" Date: Fri, 21 Sep 2012 18:40:38 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira|a|ist.utl.pt] --------------070502090506080908030008 Content-Type: text/plain; charset="UTF-8"; format=flowed Content-Transfer-Encoding: 8bit On 21/09/2012 17:13, Sergio Manzetti sergio.manzetti^^gmx.com wrote: > Dear CCLrs, it is evident that molecular symmetry is not straight > forward for complex molecules. Are there any computational methods to > determine the symmetry of an input structure, and its subgroups? > Chemcraft can do it in a very illustrative way. The "Computational methods" are present in physical and inorganic chemistry textbooks in dichotomous trees. If you have lego to model your molecule it helps. What's harder is to symmetrize molecules which the aforesaid program can do as well as others like ADFview or Gaussview. -- Nuno A. G. Bandeira, AMRSC C8 - Centro de Química e Bioquímica FCUL, Campo Grande Lisbon 1749-016 PORTUGAL http://www.researcherid.com/rid/B-6399-2012 http://pt.linkedin.com/pub/nuno-a-g-bandeira/47/55a/2aa -- --------------070502090506080908030008 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: 8bit
On 21/09/2012 17:13, Sergio Manzetti sergio.manzetti^^gmx.com wrote:
Dear CCLrs, it is evident that molecular symmetry is not straight forward for complex molecules. Are there any computational methods to determine the symmetry of an input structure, and its subgroups?


Chemcraft can do it in a very illustrative way.

The "Computational methods" are present in physical and inorganic chemistry textbooks in dichotomous trees. If you have lego to model your molecule it helps.

What's harder is to symmetrize molecules which the aforesaid program can do as well as others like ADFview or Gaussview.


-- 
Nuno A. G. Bandeira, AMRSC  
C8 - Centro de Química e Bioquímica
FCUL, Campo Grande 
Lisbon 1749-016 
PORTUGAL
http://www.researcherid.com/rid/B-6399-2012
http://pt.linkedin.com/pub/nuno-a-g-bandeira/47/55a/2aa
--
--------------070502090506080908030008-- From owner-chemistry@ccl.net Fri Sep 21 16:24:00 2012 From: "David A Mannock dmannock{=}ualberta.ca" To: CCL Subject: CCL:G: Torsion angles Message-Id: <-47648-120921151850-4355-OAAuWJa7i64P8XImzL1jkA~~server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=bcaec55557188a0cc904ca3b1ba4 Date: Fri, 21 Sep 2012 13:18:40 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock-x-ualberta.ca] --bcaec55557188a0cc904ca3b1ba4 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Yohann, is there a way to specifiy all the atoms in a molecule or specific atom types, eg carbon? Also, would this print to a specified filename or a specific type that should be named in the line or is the "file.log" specific to each molecular calculation? Thanks, David On Fri, Sep 21, 2012 at 1:48 AM, MOREAU Yohann 224609 yohann.moreau:_:cea.f= r wrote: > Dear Sergio, > > By default, in Gaussian, optimizations are done in redundant internal > coordinates. If you check your output file, you'll find at the beginning > and at the end of the optimization the set of redundant internal > coordinates. > To extract these data, you can use a simple shell command, such as : > > grep "! D" file.log | awk=91{print $3, " ", $4}' > > Which will output the dihedral parameters (at least those used by the > optimizer) at the beginning and at the end of the optimization. > You can redirect this to another grep filter to find the torsional angle > you're looking for : > > grep "! D" file.log | awk=91{print $3, " ", $4}' | grep "1,2,4,5" > > Which outputs the dihedral value between atoms 1, 2, 4 & 5 at the > beginning and at the end of the calculation. > > I'm pretty certain that more "elegant" ways to do it exist but this has > worked on my output files. > Anyway, nothing guarantees that the specific torsion angle you're looking > for is actually being used by the optimizer and then listed. > > I hope this will help you. > > YM > > -- > > Yohann Moreau > > Ma=EEtre de Conf=E9rence, Universit=E9 Joseph Fourier > iRTSV/CBM/MCT, CEA Grenoble > 17 avenue des Martyrs > 38 054 Grenoble Cedex 09 > Tel. : (33) 4 38 78 29 62 > Fax : (33) 4 38 78 54 87 > > De : "Sergio Manzetti sergio.manzetti[-]gmx.com" < > owner-chemistry*|*ccl.net> > R=E9pondre =E0 : CCL Subscribers > Date : jeudi 20 septembre 2012 18:01 > =C0 : MOREAU Yohann 224609 > Objet : CCL:G: Torsion angles > > Dear CCLrs can you recommend a program that can easily report the > torsion angles of given atoms in a Gaussian output file? > > Thanks > > Best wishes > > Sergio > --bcaec55557188a0cc904ca3b1ba4 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Yohann, is there a way to specifiy all the atoms in a molecule or specific = atom types, eg carbon? Also, would this print to a specified filename or a = specific type that should be named in the line or is the "file.log&quo= t; specific to each molecular calculation? Thanks, David

On Fri, Sep 21, 2012 at 1:48 AM, MOREAU Yoha= nn 224609 yohann.moreau:_:cea.fr <owne= r-chemistry a ccl.net> wrote:
Dear Sergio,=A0

By default, in Gaussian, optimizations are done in redundant internal = coordinates. If you check your output file, you'll find at the beginnin= g and at the end of the optimization the set of redundant internal coordina= tes.
To extract these data, you can use a simple shell command, such =A0as = :=A0

=A0grep "! D" file.log | awk=91{print $3, " ", $4}= '=A0

Which will output the dihedral parameters (at least those used by the = optimizer) at the beginning and at the end of the optimization.=A0
You can redirect this to another grep filter to find the torsional ang= le you're looking for :=A0

=A0grep "! D" file.log | awk=91{print $3, " ", $4}= ' | grep "1,2,4,5"=A0

Which outputs the dihedral value between atoms 1, 2, 4 & 5 at the = beginning and at the end of =A0the calculation.

I'm pretty certain that more "elegant" ways to do it exi= st but this has worked on my output files.
Anyway, nothing guarantees that the specific torsion angle you're = looking for is actually being used by the optimizer and then listed.

I hope this will help you.

YM

--=A0

Yohann Moreau

Ma=EEtre de Conf=E9rence, Universit=E9 Joseph Fourier
iRTSV/CBM/MCT,=A0CEA Grenoble
17 avenue des Martyrs
38 054 Grenoble Cedex 09
Tel. : (33) 4 38 78 29 62
Fax : (33) 4 38 78 54 87

De=A0: "Sergio Manzetti sergio= .manzetti[-]gmx.com" = <owner-= chemistry*|*ccl.net>
R=E9pondre =E0=A0: CCL Subscribers = <chemistry*|*= ccl.net>
Date=A0: jeudi 20 septembre 2012 18= :01
=C0=A0: MOREAU Yohann 224609 <yohann.moreau*|= *cea.fr>
Objet=A0: CCL:G: Torsion angles

Dea= r CCLrs can you recommend a program that can easily report the torsion angl= es of given atoms in a Gaussian output file?

Thanks

Best wishes

Sergio

--bcaec55557188a0cc904ca3b1ba4-- From owner-chemistry@ccl.net Fri Sep 21 16:58:00 2012 From: "Shahar Keinan skeinan^-^gmail.com" To: CCL Subject: CCL: Problems with orbital plots in ArgusLab Message-Id: <-47649-120921165154-10530-0OndwV1A6wBeciWErhdswA,server.ccl.net> X-Original-From: "Shahar Keinan" Date: Fri, 21 Sep 2012 16:51:53 -0400 Sent to CCL by: "Shahar Keinan" [skeinan{=}gmail.com] Dear all, I am trying to use ArgusLab to calculate and display orbitals of molecules containing d orbitals with the INDO/s semi-emprical Hamiltonian. For example [Fe(OH2)6]2+. The energy (and spectra) calculations are ok, but when I try to plot the orbitals I get this error message: "ERROR: GetAtomicParam called by BuildBasis : atomic number 26 has no NSHELLS" Is there anybody with previous experience with that? Is this something the code can do? Thank you in advance, Shahar Keinan --------------------------------------------------- Shahar Keinan, Ph.D. Theory Staff Scientist, UNC EFRC skeinan[]unc.edu (919)-357-5319