Hi Amir,

I have seen two=A0refere= nces=A0for this problem\fix, it=A0requires=A0you to fix the .fchk file text= and the to convert it back to .chk:

1, old CCL post:=A0http:= //server.ccl.net/cgi-bin/ccl/message-new?2012+07+18+005

2. In Dr. Joaquin Barroso=A0blog:=A0http://joaquinbarroso.com/links/#comment-2389=

I haven't had a chance to see which one= works, or works better.

Amir

On Wed, Fe= b 27, 2013 at 11:26 PM, Amir Babalhavaeji ababalha!^!chem.utoronto.ca <owner-chemistry]=[ccl.net><= /span> wrote:

Sent to CCL by: "Amir =A0Babalhavaeji" [ababalha_-_chem.utoronto.ca] Hello everyone,

I have run an optimization/frequency job using Gaussian 09 on a remote clus= ter system. In my input file I had included the keyword FormCheck so I coul= d use the formatted checkpoint file on my Personal Computer. Now the job ha= s successfully finished and I have the Test.FChk file. When I try to view t= his file in Gauss View, however, it returns this error:

"CConnectionGFCHKLLParse_GFCHK() Missing or bad data: Alpha Orbital En= ergies Line Number 852"

I am able to open the file as a text and everything looks okay! I also trie= d converting the original chk file to fchk by formchk command, or convertin= g the FChk file to a regular checkpoint by means of "unfchk" util= ity but none of them worked out.

I would appreciate your advice, because I need to visualize orbital surface= s.

Thank you,

------------------------------------------------------
Amirhossein Babalhavaeji

PhD Student
Woolley Lab
Department of Chemistry
University of Toronto
80 St. George Street | Toronto | Ontario M5S 3H6
Canada

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY]=[ccl.n= et or use:
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--=A0

Amir Bernat
http://physwe= b.bgu.ac.il/~bernat/

--f46d044286ca9f9ed604d6c3f681-- From owner-chemistry@ccl.net Thu Feb 28 04:02:00 2013 From: "benoit benoit bonoit_10-,-yahoo.fr" To: CCL Subject: CCL: Ionisation potential/Activation energy Message-Id: <-48338-130228040021-9105-6hgIRLTauDmQzBOHDi/flQ*_*server.ccl.net> X-Original-From: "benoit benoit" Date: Thu, 28 Feb 2013 04:00:20 -0500 Sent to CCL by: "benoit benoit" [bonoit_10 . yahoo.fr] Dear CCLers, I read about the existence of a relationship between activation energy and ionisation potential, I could not understand really this point and i'm not sure if that exists. C'd someone clarify this point, and what's the relationship? Sincerely, Benoit From owner-chemistry@ccl.net Thu Feb 28 05:33:00 2013 From: "Herbert Fruchtl Herbert.Fruchtl(~)st-andrews.ac.uk" To: CCL Subject: CCL:G: Viewing a Formatted Checkpoint File Message-Id: <-48339-130227182303-31222-bc2gnNhguOl/f2xFqn4yQw_._server.ccl.net> X-Original-From: Herbert Fruchtl Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Feb 2013 23:22:38 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [Herbert.Fruchtl:_:st-andrews.ac.uk] This is a bug in Gaussview. It expects as many molecular orbitals as there are basis functions. This is not the case if orbitals have been removed because of near linear dependencies. Try adding the following to your keywords: IOP(3/59=7) This changes the threshold for removing functions from the default of 1^-6 to 1^e-7. If that's not enough, increase the number to 8 or 9. It will take more iterations but is unlikely to cause errors. HF and DFT are fairly insensitive to linear dependency. If you use post-HF correlation methods, things may look different. HTH. Herbert ________________________________________ > From: owner-chemistry+herbert.fruchtl==st-andrews.ac.uk+/-ccl.net [owner-chemistry+herbert.fruchtl==st-andrews.ac.uk+/-ccl.net] on behalf of Amir Babalhavaeji ababalha!^!chem.utoronto.ca [owner-chemistry+/-ccl.net] Sent: 27 February 2013 21:26 To: Herbert Fruchtl Subject: CCL:G: Viewing a Formatted Checkpoint File Sent to CCL by: "Amir Babalhavaeji" [ababalha_-_chem.utoronto.ca] Hello everyone, I have run an optimization/frequency job using Gaussian 09 on a remote cluster system. In my input file I had included the keyword FormCheck so I could use the formatted checkpoint file on my Personal Computer. Now the job has successfully finished and I have the Test.FChk file. When I try to view this file in Gauss View, however, it returns this error: "CConnectionGFCHKLLParse_GFCHK() Missing or bad data: Alpha Orbital Energies Line Number 852" I am able to open the file as a text and everything looks okay! I also tried converting the original chk file to fchk by formchk command, or converting the FChk file to a regular checkpoint by means of "unfchk" utility but none of them worked out. I would appreciate your advice, because I need to visualize orbital surfaces. Thank you, ------------------------------------------------------ Amirhossein Babalhavaeji PhD Student Woolley Lab Department of Chemistry University of Toronto 80 St. George Street | Toronto | Ontario M5S 3H6 Canadahttp://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 Thu Feb 28 07:18:00 2013 From: "Ajita Banthiya ajita.banthiya19:+:gmail.com" To: CCL Subject: CCL:G: Viewing a Formatted Checkpoint File Message-Id: <-48340-130228071350-13283-zBwu9uFTZ/6Mv1OkQ6Z9qw]^[server.ccl.net> X-Original-From: Ajita Banthiya Content-Type: multipart/alternative; boundary=f46d040169754884c904d6c7d2d3 Date: Thu, 28 Feb 2013 17:43:41 +0530 MIME-Version: 1.0 Sent to CCL by: Ajita Banthiya [ajita.banthiya19#,#gmail.com] --f46d040169754884c904d6c7d2d3 Content-Type: text/plain; charset=ISO-8859-1 dear Amir Babalhavaej check this portion of your formchk file..which i have mentioned below.. no of Number of independent functions shold be equal to Number of basis functions. if it is not so then copy the Number of independent functions and pate it in place of no of Basis function ..i hope this will work for you Number of alpha electrons I 149 Number of beta electrons I 149 Number of basis functions I 1033 Number of independent functions I 1033 On Thu, Feb 28, 2013 at 2:56 AM, Amir Babalhavaeji ababalha!^! chem.utoronto.ca wrote: > > Sent to CCL by: "Amir Babalhavaeji" [ababalha_-_chem.utoronto.ca] > Hello everyone, > > I have run an optimization/frequency job using Gaussian 09 on a remote > cluster system. In my input file I had included the keyword FormCheck so I > could use the formatted checkpoint file on my Personal Computer. Now the > job has successfully finished and I have the Test.FChk file. When I try to > view this file in Gauss View, however, it returns this error: > > "CConnectionGFCHKLLParse_GFCHK() Missing or bad data: Alpha Orbital > Energies Line Number 852" > > I am able to open the file as a text and everything looks okay! I also > tried converting the original chk file to fchk by formchk command, or > converting the FChk file to a regular checkpoint by means of "unfchk" > utility but none of them worked out. > > I would appreciate your advice, because I need to visualize orbital > surfaces. > > Thank you, > > ------------------------------------------------------ > Amirhossein Babalhavaeji > > PhD Student > Woolley Lab > Department of Chemistry > University of Toronto > 80 St. George Street | Toronto | Ontario M5S 3H6 > Canada> > > -- Thanks and regards, Ajita Banthiya CSIR-JRF Computataional Chemistry Indian Institute Of Chemical Techonology Hyderabad-500007 --f46d040169754884c904d6c7d2d3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable dear Amir Babalhavaej
check this portion of your formchk file..which i = have mentioned below..=A0 no of=A0 Number of independent=20 functions=A0 shold be equal to Number of basis functions. if it is not so= =20 then copy the Number of independent functions and pate it in place of=A0=20 no of Basis function ..i hope this will work for you

Number of alpha= electrons=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 I=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 149
Number of beta electrons=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 I=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 149
Number of basis functions=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 I=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1033
Number of independent functions=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 I=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 1033

On Thu, = Feb 28, 2013 at 2:56 AM, Amir Babalhavaeji ababalha!^!chem.utoronto.ca <owner-chemistry(0)ccl.net>= wrote:

Sent to CCL by: "Amir =A0Babalhavaeji" [ababalha_-_chem.utoronto.ca] Hello everyone,

I have run an optimization/frequency job using Gaussian 09 on a remote clus= ter system. In my input file I had included the keyword FormCheck so I coul= d use the formatted checkpoint file on my Personal Computer. Now the job ha= s successfully finished and I have the Test.FChk file. When I try to view t= his file in Gauss View, however, it returns this error:

"CConnectionGFCHKLLParse_GFCHK() Missing or bad data: Alpha Orbital En= ergies Line Number 852"

I am able to open the file as a text and everything looks okay! I also trie= d converting the original chk file to fchk by formchk command, or convertin= g the FChk file to a regular checkpoint by means of "unfchk" util= ity but none of them worked out.

I would appreciate your advice, because I need to visualize orbital surface= s.

Thank you,

------------------------------------------------------
Amirhossein Babalhavaeji

PhD Student
Woolley Lab
Department of Chemistry
University of Toronto
80 St. George Street | Toronto | Ontario M5S 3H6
Canada

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY(0)ccl.n= et or use:
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST(0)ccl.net or use
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.shtml

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Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0 h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

--
Thanks and regards,

Ajita Banthiya

CSIR-JRF

Computataional Chemistry

Indian Institute Of C= hemical Techonology=A0

Hyderabad-500007

--f46d040169754884c904d6c7d2d3-- From owner-chemistry@ccl.net Thu Feb 28 07:53:00 2013 From: "Georg Lefkidis lefkidis _ physik.uni-kl.de" To: CCL Subject: CCL:G: WG: G: Viewing a Formatted Checkpoint File Message-Id: <-48341-130228073040-18466-+Cd4xDuZE8wHYfPPmfrvAA!=!server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Language: de Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 28 Feb 2013 13:30:26 +0100 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis^-^physik.uni-kl.de] You can also turn orthogonalization off completely with IOP(3/32=2). I've had the exactly same issue with other programs as well. You can check your fchk file and compare the number of basis functions and the number of independent basis functions. Best regards George -----Urspr�ngliche Nachricht----- Von: owner-chemistry+lefkidis==physik.uni-kl.de|,|ccl.net [mailto:owner-chemistry+lefkidis==physik.uni-kl.de|,|ccl.net] Im Auftrag von Herbert Fruchtl Herbert.Fruchtl(~)st-andrews.ac.uk Gesendet: Donnerstag, 28. Februar 2013 00:23 An: Lefkidis, Georg Betreff: CCL:G: Viewing a Formatted Checkpoint File Sent to CCL by: Herbert Fruchtl [Herbert.Fruchtl:_:st-andrews.ac.uk] This is a bug in Gaussview. It expects as many molecular orbitals as there are basis functions. This is not the case if orbitals have been removed because of near linear dependencies. Try adding the following to your keywords: IOP(3/59=7) This changes the threshold for removing functions from the default of 1^-6 to 1^e-7. If that's not enough, increase the number to 8 or 9. It will take more iterations but is unlikely to cause errors. HF and DFT are fairly insensitive to linear dependency. If you use post-HF correlation methods, things may look different. HTH. Herbert ________________________________________ > From: owner-chemistry+herbert.fruchtl==st-andrews.ac.uk!^!ccl.net > [owner-chemistry+herbert.fruchtl==st-andrews.ac.uk!^!ccl.net] on > behalf of Amir Babalhavaeji ababalha!^!chem.utoronto.ca > [owner-chemistry!^!ccl.net] Sent: 27 February 2013 21:26 To: Herbert Fruchtl Subject: CCL:G: Viewing a Formatted Checkpoint File Sent to CCL by: "Amir Babalhavaeji" [ababalha_-_chem.utoronto.ca] Hello everyone, I have run an optimization/frequency job using Gaussian 09 on a remote cluster system. In my input file I had included the keyword FormCheck so I could use the formatted checkpoint file on my Personal Computer. Now the job has successfully finished and I have the Test.FChk file. When I try to view this file in Gauss View, however, it returns this error: "CConnectionGFCHKLLParse_GFCHK() Missing or bad data: Alpha Orbital Energies Line Number 852" I am able to open the file as a text and everything looks okay! I also tried converting the original chk file to fchk by formchk command, or converting the FChk file to a regular checkpoint by means of "unfchk" utility but none of them worked out. I would appreciate your advice, because I need to visualize orbital surfaces. Thank you, ------------------------------------------------------ Amirhossein Babalhavaeji PhD Student Woolley Lab Department of Chemistry University of Toronto 80 St. George Street | Toronto | Ontario M5S 3H6 Canadahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chem istry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://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 Thu Feb 28 11:30:00 2013 From: "benoit benoit bonoit_10*|*yahoo.fr" To: CCL Subject: CCL:G: G09 single point Message-Id: <-48342-130228112935-15540-M2HCwVEcpP+IeOo9J5DctA\a/server.ccl.net> X-Original-From: "benoit benoit" Date: Thu, 28 Feb 2013 11:29:34 -0500 Sent to CCL by: "benoit benoit" [bonoit_10^-^yahoo.fr] Dear CCLers, I launched a CCSD(T) single point calculation and it stopped after at the link L913. It's the link for the post-scf calculations, that what I read in the Gaussian help. C'd someone tell me what keyword I should add to overcome this problem? Thanks in advance Benoit From owner-chemistry@ccl.net Thu Feb 28 18:22:01 2013 From: "Mehdi Esrafili m_esrafili_+_yahoo.com" To: CCL Subject: CCL:G: G09 single point Message-Id: <-48343-130228182056-13200-EKAO+3Nd3yugQbCOoFA3uw]=[server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="397762125-1230881634-1362093650=:34656" Date: Thu, 28 Feb 2013 15:20:50 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili[*]yahoo.com] --397762125-1230881634-1362093650=:34656 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Benoit;=0AThe error is most likely due to lack of memory. Have you use= d %mem in your input file? CCSD(T) calculations need a lot of memory than u= sual DFT methods.=0ASincerely=0AMehdi=0A=0A=0A=A0=0A=A0=0A-----------------= ---------------------------------------------------------------------------= ----------------------------------=A0=A0=0A`The man who makes no mistakes d= oes not usually make anything.'=0A=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Edward John Ph= elps (1822-1900)=0A--------------------------------------------------------= ---------------------------------------------------------------------- =0AM= ehdi D. Esrafili, Ph.D.=0AAssistant Professor of Physical Chemistry=A0=0ACu= rrent address:=A0Department of Chemistry, =0AFaculty of Basic Sciences,Univ= ersity of=0AMaragheh, Iran. =0AE-mail 1:m_esrafili*yahoo.com=0AE-mail 2: es= rafili*maragheh.ac.ir=0A---------------------------------------------------= ---------------------------------------------------------------------------= =0A=0A=0A________________________________=0A From: Bit benoit bonoit_10*|*= yahoo.fr =0ATo: "Esrafili, Mehdi D " =0ASent: Thursday, February 28, 2013 7:59 PM=0ASubject: C= CL:G: G09 single point=0A =0A=0ASent to CCL by: "benoit=A0 benoit" [bonoit_= 10^-^yahoo.fr]=0ADear CCLers,=0A=0AI launched a CCSD(T) single point calcul= ation and it stopped after at the link L913. It's the link for the post-scf= calculations, that what I read in the Gaussian help.=0AC'd someone tell me= what keyword I should add to overcome this problem?=0A=0AThanks in advance= =0A=0ABenoit=0A=0A=0A=0A-=3D This is automatically added to each message by= the mailing script =3D-=0ATo recover the email address of the author of th= e message, please change=0Athe strange characters on the top line to the * = sign. You can also=0A= =0A=0A=0A=A0 =A0 =A0 http:/= /www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CH= EMISTRY-REQUEST*ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl= /send_ccl_message=0A=0A=0A=A0 =A0 =A0 http://www.ccl= .net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: htt= p://www.ccl.net=0A=0A=0AConferences: http://se= rver.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messages: htt= p://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces f= rom CCL with 5.7.1 error, check:=0A=A0 =A0 =A0 http://www.ccl.net/spammers.= txt=0A=0A--397762125-1230881634-1362093650=:34656 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Benoit;
The= error is most likely due to lack of memory. Have you used %mem in your inp= ut file? CCSD(T) calculations need a lot of memory than usual DFT methods.<= br>Sincerely
Mehdi

------------------------------------------------------------------= ------------------------------------------------------------

`The man who makes no mistakes does not usually make anything.'

&= nbsp; &nbs= p; Edward John Phelps= (1822-1900)

------------------------------------------------------= ------------------------------------------------------------------------ Mehdi D. Esrafili, Ph.D.

Assistant Professor of Physical Chemistr= y
Current address: Department of Chemistry,

F= aculty of Basic Sciences,University of

Maragheh, Iran.

E-m= ail 1: m_esrafili*yahoo.com
E-mail 2: esrafi= li*maragheh.ac.ir

----------------------------------------------------------------------= --------------------------------------------------------

From: Bit benoit bonoit_10*|*yahoo.fr <owner-chemistry= *ccl.net>
To: "Esrafili, Mehdi D " &= lt;m_esrafili*yahoo.com>
Sent= : Thursday, February 28, 2013 7:59 PM
Subject: CCL:G: G09 single point

=0A
Sent to CCL by: "benoit benoit" [bonoit_10^-^yahoo.fr]=
Dear CCLers,

I launched a CCSD(T) single point calculation and i= t stopped after at the link L913. It's the link for the post-scf calculatio= ns, that what I read in the Gaussian help.
C'd someone tell me what keyw= ord I should add to overcome this problem?

Thanks in advance

= Benoit

-=3D This is automatically added to each message by t= he mailing script =3D-
To recover the email address of the author of the= message, please change
the strange characters on the top line to the * = sign. You can also
E-mail to subscribers: CHEMISTRY*ccl.net or use:
= ;

E-mail to a= dministrators: CHEMISTRY-REQUEST*ccl.net or= use
http://www.ccl.net/cgi-bin/ccl/send_ccl_mes= sage
http://www.= ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at= : http://www.ccl.net
Conferences: h= ttp://server.ccl.net/chemistry/announcements/conferences/

Search Mes= sages: http://www.ccl.net/chemistry/searchccl/index.shtml

If your ma= il bounces from CCL with 5.7.1 error, check:
http:/= /www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutcc= l/instructions/

--397762125-1230881634-1362093650=:34656-- From owner-chemistry@ccl.net Thu Feb 28 19:21:00 2013 From: "Devang Sachdev dsachdev[#]nvidia.com" To: CCL Subject: CCL: Learn about AMBER with GPUs from Dr. Ross Walker, AMBER Developer Message-Id: <-48344-130228150802-306-Z9vtNUPuEsbdMkVlln6txg * server.ccl.net> X-Original-From: "Devang Sachdev" Date: Thu, 28 Feb 2013 15:08:01 -0500 Sent to CCL by: "Devang Sachdev" [dsachdev===nvidia.com] Hi Dr. Ross Walker at UCSD and NVIDIA are presenting a webinar on the latest GPU-acceleration technologies available to AMBER users and discusses features, recent updates and future plans. Join us to learn how to obtain the latest accelerated versions of AMBER, which features are supported, the simplicity of it's installation and use, how it performs with latest Kepler GPUs. The webinar is planned for Tuesday, March 5, 2013 9:00 AM - 10:00 AM PST Register here: http://bit.ly/XdvgLS Thanks Devang Sachdev Sr. Product Manager NVIDIA www.linkedin.com/in/devangsachdev