From owner-chemistry@ccl.net Wed Jan 26 01:50:00 2011 From: "i.nick- -mail.ru" To: CCL Subject: CCL: optimization of excited states Message-Id: <-43761-110125112146-6662-EWczmJ5prg3hlF3oD9C7tg.@.server.ccl.net> X-Original-From: i.nick#mail.ru Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1251 Date: Tue, 25 Jan 2011 19:21:26 +0300 MIME-Version: 1.0 Sent to CCL by: i.nick(~)mail.ru It seems I find the answer to my question - there are no analytical 2-nd derivatives in TDDFT, so when we put opt=calcall together with td(read, root=N) we get an error. Moreover, if we put freq=numer then, nevertheless, we will see "A SYNTX ERR". Because I have transition metals in some molecules only single "opt" keyword is available. Thanks to all replying. -- Ñ óâàæåíèåì, i mailto:i.nick---mail.ru From owner-chemistry@ccl.net Wed Jan 26 02:24:00 2011 From: "Krishna Govender kk.govender]~[gmail.com" To: CCL Subject: CCL:G: help with freq calculation Message-Id: <-43762-110125092402-28880-BQi/b3kuMDxR9NvKKt1zxA[A]server.ccl.net> X-Original-From: "Krishna Govender" Content-Language: en-za Content-Type: multipart/alternative; boundary="----=_NextPart_000_0004_01CBBCAC.3F97C960" Date: Tue, 25 Jan 2011 16:23:44 +0200 MIME-Version: 1.0 Sent to CCL by: "Krishna Govender" [kk.govender{=}gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_0004_01CBBCAC.3F97C960 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I usually take the final geometry produced in the Gaussian log file and submit it for a frequency calculation. I have often found that this doesn't end up producing errors such as those which you are experiencing when reading in the checkpoint file. > From: owner-chemistry+kk.govender==gmail.com]^[ccl.net [mailto:owner-chemistry+kk.govender==gmail.com]^[ccl.net] On Behalf Of Close, David M. CLOSED-,-mail.etsu.edu Sent: 25 January 2011 03:52 PM To: Govender, Krishna Kuben Subject: CCL:G: help with freq calculation CCL: I have performed a SCRF calculation in Gaussian and would like to have the thermodynamic properties. I tried a frequency calculation on the SCRF calculation using the checkpoint file, with the line #b3lyp/6-31G(d) freq geom=checkpoint. This job started, read the proper geometry, and ran just until it was to start the frequency calculation. The last line printed was Approx Polarizability, then failed with the line FiileIO operation on a non-existent file. How do I get this to work? Regards, Dave Close ------=_NextPart_000_0004_01CBBCAC.3F97C960 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I usually take the = final geometry produced in the Gaussian log file and submit it for a frequency calculation.

I have often found = that this doesn’t end up producing errors such as those which you are = experiencing when reading in the checkpoint file.

 

From:= = owner-chemistry+kk.govender=3D=3Dgmail.com]^[ccl.net [mailto:owner-chemistry+kk.govender=3D=3Dgmail.com]^[ccl.net] On Behalf = Of Close, David M. CLOSED-,-mail.etsu.edu
Sent: 25 January 2011 03:52 PM
To: Govender, Krishna Kuben
Subject: CCL:G: help with freq calculation

 

CCL:

  I have performed a SCRF calculation in = Gaussian and would like to have the thermodynamic properties.  I tried a = frequency calculation on the SCRF calculation using the checkpoint file, with the = line #b3lyp/6-31G(d) freq geom=3Dcheckpoint.  This job started, read the = proper geometry, and ran just until it was to start the frequency = calculation.  The last line printed was Approx Polarizability, then failed with the = line FiileIO operation on a non-existent file.  How do I get this to = work?

  Regards, Dave Close

------=_NextPart_000_0004_01CBBCAC.3F97C960-- From owner-chemistry@ccl.net Wed Jan 26 06:20:00 2011 From: "Mark D mackey mark~!~cresset-group.com" To: CCL Subject: CCL: Peptide coordinate generator Message-Id: <-43763-110126061733-26846-rsHEOiLM8Kroy5ID8Dt9Uw*server.ccl.net> X-Original-From: "Mark D mackey" Date: Wed, 26 Jan 2011 06:17:32 -0500 Sent to CCL by: "Mark D mackey" [mark:+:cresset-group.com] Dear All, Does anyone out there know of a command-line or otherwise scriptable tool to generate 3D peptide structures given sequence, phi, psi, omega and a sidechain conformer library? I've found things like RIBOSOME, but it doesn't have the sidechain conformer sampling bit. Mark. -- Dr Mark Mackey Cresset BMD From owner-chemistry@ccl.net Wed Jan 26 06:55:00 2011 From: "Shirin Seifert shirin.seifert+/-gmail.com" To: CCL Subject: CCL:G: Gaussian Error Message-Id: <-43764-110126062824-20239-Bd2DHL1fOH6k+PZqbdHWNw-.-server.ccl.net> X-Original-From: Shirin Seifert Content-Type: multipart/alternative; boundary=001485f1dc168bda7e049abe2045 Date: Wed, 26 Jan 2011 14:58:07 +0330 MIME-Version: 1.0 Sent to CCL by: Shirin Seifert [shirin.seifert*|*gmail.com] --001485f1dc168bda7e049abe2045 Content-Type: text/plain; charset=ISO-8859-1 hi possibilities are: 1- Not enough physical memory is available or installed. 2- If it is in windows, there is a limitation of 2GB memory with 32 bit applications. hope this helps Best, SS On Tue, Jan 25, 2011 at 10:56 PM, Tijesunimi John Odebode tijesunimi__yahoo.com wrote: > > Sent to CCL by: "Tijesunimi John Odebode" [tijesunimi+*+yahoo.com] > Hello, > > I was wondering if anybody had an answer to my question. I am trying to > visualize the HOMO and LUMO of a compound on MOLDEN of which I ran gaussian > calculations on. I read an article online that says that for MOLDEN to find > all required information in the output file, I need to run a single point > calculation at the desired level of theory including the pop=full and > gfinput keywords. I entered the above in my input file and the following is > my input: > > %chk=Chlorin-1_b3lyp_go > %mem=23000mb > %nprocshared=8 > # b3lyp/6-31G(d) sp scf=tight pop=full gfinput maxdisk=50gb > > b3lyp geometry optimization using Gaussian > Chlorin-sp-1 > > The mem value in the run script is 23500mb and maxdisk=50gb. However, when > I run this job, an error message comes up which says: galloc: cannot > allocate memory. I tried increasing the memory on the run script to 24000mb > but I keep getting the message Requested node configuration unavailable. I > also tried leaving the memory on the run script as 23500mb and reducing the > %mem on the input file to 20000mb; however, I keep getting the same message > saying galloc: cannot allocate memory.' I do not know what the problem is. > Is there a problem with my input file or what else do you think I should do. > I am sorry if I did not do a good job explaining the problem; I am new to > this. Thanks a lot for your anticipated response. > > Tijesunimi Odebode> > > --001485f1dc168bda7e049abe2045 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable hi
possibilities are:

1- Not enough physical memory is available = or installed.
2- If it is in windows, there is a limitation of 2GB memor= y with 32 bit applications.

hope this helps

Best,
SS

On Tue, Jan 25, 2011 at 10:56 PM, Tijesunimi= John Odebode tijesunimi__yahoo.co= m <owne= r-chemistry**ccl.net> wrote:

Sent to CCL by: "Tijesunimi John Odebode" [tijesunimi+*+yahoo.com]
Hello,

I was wondering if anybody had an answer to my question. I am trying to vis= ualize the HOMO and LUMO of a compound on MOLDEN of which I ran gaussian ca= lculations on. I read an article online that says that for MOLDEN to find a= ll required information in the output file, I need to run a single point ca= lculation at the desired level of theory including the pop=3Dfull and gfinp= ut keywords. I entered the above in my input file and the following is my i= nput:

%chk=3DChlorin-1_b3lyp_go
%mem=3D23000mb
%nprocshared=3D8
# b3lyp/6-31G(d) sp scf=3Dtight pop=3Dfull gfinput maxdisk=3D50gb

b3lyp geometry optimization using Gaussian
Chlorin-sp-1

The mem value in the run script is 23500mb and maxdisk=3D50gb. However, whe= n I run this job, an error message comes up which says: galloc: cannot allo= cate memory. I tried increasing the memory on the run script to 24000mb but= I keep getting the message Requested node configuration unavailable. I als= o tried leaving the memory on the run script as 23500mb and reducing the %m= em on the input file to 20000mb; however, I keep getting the same message s= aying galloc: cannot allocate memory.' =A0I do not know what the proble= m is. Is there a problem with my input file or what else do you think I sho= uld do. I am sorry if I did not do a good job explaining the problem; I am = new to this. Thanks a lot for your anticipated response.

Tijesunimi Odebode



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--001485f1dc168bda7e049abe2045-- From owner-chemistry@ccl.net Wed Jan 26 08:14:00 2011 From: "Piotr Nowak piotrnowak^student.uw.edu.pl" To: CCL Subject: CCL:G: Gaussian question Message-Id: <-43765-110126054858-32163-86bvzYRoYhmsXSFpBL7WVQ() server.ccl.net> X-Original-From: Piotr Nowak Content-Type: multipart/alternative; boundary=90e6ba47682b85d988049abd93cb Date: Wed, 26 Jan 2011 11:48:41 +0100 MIME-Version: 1.0 Sent to CCL by: Piotr Nowak [piotrnowak/./student.uw.edu.pl] --90e6ba47682b85d988049abd93cb Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Tijesunimi, First of all, MP2 introduces electron correlation via Rayleigh-Schroedinger perturbation theory using occupied and virtual orbitals and their energies > from Hartree-Fock calculation, so it does not create new orbitals or orbita= l energies. Therefore FMOs from your MP2 calculation are de facto HF orbitals. Second, it is well known that DFT gives different orbital energies than HF (but you cannot say they're worse). For detailed discussion you can check e.g.: Stowasser, R., & Hoffmann, R. (1999). What Do the Kohn-Sham Orbitals and Eigenvalues Mean? Journal of the American Chemical Society, 121(14), 3414-3420.Kar, T., =C1ngy=E1n, J. G., & Sannigrahi, A. B. (2000). Compariso= n of ab Initio Hartree-Fock and Kohn-Sham Orbitals in the Calculation of Atomic Charge, Bond Index, and Valence. The Journal of Physical Chemistry A, 105(3), 9953-9963. Zhang, G., & Musgrave, C. B. (2007). Comparison of DFT methods for molecula= r orbital eigenvalue calculations. The Journal of Physical Chemistry A,111(8)= , 1554-1561. Best regards, Piotr Nowak On Tue, Jan 25, 2011 at 8:42 PM, Tijesunimi John Odebode tijesunimi=3D yahoo.com wrote: > > Sent to CCL by: "Tijesunimi John Odebode" [tijesunimi:-:yahoo.com] > Hello all, > > I was wondering if I could get an answer to this question: > > I did a geometry optimization of a compound using Gaussian(b3lyp/6-31G(d)= ). > I found the HOMO and LUMO energy and calculated the energy gap. I then > decided to do an MP2 single point calculation on the same compound to > determine the HOMO and LUMO energy gap. The energy gap for the single poi= nt > MP2 calculation was 3.49eV more than that for the b3lyp. Is this normal?= Or > do you think there is a problem somewhere? Has anybody carried out such > calculations? Thanks a lot for your anticipated response. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 ****** Piotr Nowak University of Warsaw Department of Chemistry Laboratory of Stereocontrolled Organic Synthesis Pasteura 1, 02-093 Warsaw, Poland ****** --90e6ba47682b85d988049abd93cb Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Tijesunimi,

First of all, MP2 introduces= electron correlation via Rayleigh-Schroedinger perturbation theory using o= ccupied and virtual orbitals and their energies from Hartree-Fock calculati= on, so it does not create new orbitals or orbital energies. Therefore FMOs = > from your MP2 calculation are de facto HF orbitals. 
Second, it is well known that DFT gives different orbital energies than HF = (but you cannot say they're worse). For detailed discussion you can che= ck e.g.: 

Stowasser, R., &= ; Hoffmann, R. (1999). What Do the Kohn−Sham Orbitals and Eigenvalues= Mean? Journal of the American Chemical Society, 121(14), 3414-34= 20.

Kar, T., =C1ngy=E1n, J. G., & Sannigrahi, = A. B. (2000). Comparison of ab Initio Hartree−Fock and Kohn−Sha= m Orbitals in the Calculation of Atomic Charge, Bond Index, and Valence.&nb= sp;The Journal of Physical Chemistry A, 105(3), 9953-9963.

Zhang, G., & Musgrave, C. B. (2007). = Comparison of DFT methods for molecular orbital eigenvalue calculations.&nb= sp;The Journal of Physical Chemistry A,111(8), 1554-1561.

Best regards,
Piotr Nowak

On Tue, Jan 25, 2011 at 8:42= PM, Tijesunimi John Odebode tijesunimi=3Dyaho= o.com <= owner-chemistry*|*ccl.net> wrote:

Sent to CCL by: "Tijesunimi John Odebode" [tijesunimi:-:yahoo.com]
Hello all,

I was wondering if I could get an answer to this question:

I did a geometry optimization of a compound using Gaussian(b3lyp/6-31G(d)).= I found the HOMO and LUMO energy and calculated the energy gap. I then dec= ided to do an MP2 single point calculation on the same compound to determin= e the HOMO and LUMO energy gap. The energy gap for the single point MP2 cal= culation was 3.49eV  more than that for the b3lyp. Is this normal? Or = do you think there is a problem somewhere? Has anybody carried out such cal= culations? Thanks a lot for your anticipated response.



-=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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--
******
Piotr Nowak<= /div>
University of Warsaw
Department of Chemistry
= Laboratory of Stereocontrolled Organic Synthesis
Pasteura 1, 02-0= 93 Warsaw, Poland
******

--90e6ba47682b85d988049abd93cb-- From owner-chemistry@ccl.net Wed Jan 26 08:49:00 2011 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas|-|chem.elte.hu" To: CCL Subject: CCL:G: Error on optimization Message-Id: <-43766-110125191421-11263-EEHYao/OGjctcXuO9i3fkQ _ server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Wed, 26 Jan 2011 01:13:53 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas=chem.elte.hu] Hi Guilherme, I'm somewhat confused, as the job starts well, and also, l1.exe starts and seemingly does its job well. l101.exe should follow but the error occurs. If l101.exe is present and can be started (if you start it, it will fail with some error but if it can start) it means, it should also be able to start as part of Gaussian. Unfortunately, I never met a problem like this before, only on this list but it does not seem to be related. As I have Windows XP on my laptop, tomorrow I'll put G98W back and try a few runs if I can see any kind of error like this. Also, could you let me know the kind of processor in your machine and that the operating system is 32 or 64 bit version. Could you complete anything with Gaussian 98 on this machine? Have you tried G03 or G09? Best wishes, Odon Farkas Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány Péter sétány H-1117 Budapest, Hungary Cellphone: +36-30-2553111 On Tuesday 25 January 2011 16:14:10 Guilherme Luis Cordeiro guilhermecord(0)gmail.com wrote: > Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord^_^gmail.com] > Hi Mr. Farkas, > > I started Gaussian program through g98w executable. There are a couple of > things I want to comment about: > > 1st) a message of error like: > "Error message #2065 > Can't overwrite/remove file C:\G98W\Scratch\gxx-exec.dat" > > 2nd) following the message above comes another like: > "Severe error message #2070 > The processing of the last link ended abnormally. All processing has been > aborted." > > And the full output file is : > > Entering Link 1 = C:\G98W\l1.exe PID= 5844. > > Copyright (c) 1988,1990,1992,1993,1995,1998 Gaussian, Inc. > All Rights Reserved. > > This is part of the Gaussian(R) 98 program. It is based on > the Gaussian 94(TM) system (copyright 1995 Gaussian, Inc.), > the Gaussian 92(TM) system (copyright 1992 Gaussian, Inc.), > the Gaussian 90(TM) system (copyright 1990 Gaussian, Inc.), > the Gaussian 88(TM) system (copyright 1988 Gaussian, Inc.), > the Gaussian 86(TM) system (copyright 1986 Carnegie Mellon > University), and the Gaussian 82(TM) system (copyright 1983 > Carnegie Mellon University). Gaussian is a federally registered > trademark of Gaussian, Inc. > > This software contains proprietary and confidential information, > including trade secrets, belonging to Gaussian, Inc. > > This software is provided under written license and may be > used, copied, transmitted, or stored only in accord with that > written license. > > The following legend is applicable only to US Government > contracts under DFARS: > > RESTRICTED RIGHTS LEGEND > > Use, duplication or disclosure by the US Government is subject > to restrictions as set forth in subparagraph (c)(1)(ii) of the > Rights in Technical Data and Computer Software clause at DFARS > 252.227-7013. > > Gaussian, Inc. > Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA > > The following legend is applicable only to US Government > contracts under FAR: > > RESTRICTED RIGHTS LEGEND > > Use, reproduction and disclosure by the US Government is subject > to restrictions as set forth in subparagraph (c) of the > Commercial Computer Software - Restricted Rights clause at FAR > 52.227-19. > > Gaussian, Inc. > Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA > > > --------------------------------------------------------------- > Warning -- This program may not be used in any manner that > competes with the business of Gaussian, Inc. or will provide > assistance to any competitor of Gaussian, Inc. The licensee > of this program is prohibited from giving any competitor of > Gaussian, Inc. access to this program. By using this program, > the user acknowledges that Gaussian, Inc. is engaged in the > business of creating and licensing software in the field of > computational chemistry and represents and warrants to the > licensee that it is not a competitor of Gaussian, Inc. and that > it will not use this program in any manner prohibited above. > --------------------------------------------------------------- > > > Cite this work as: > Gaussian 98, Revision A.9, > M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, > M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., > R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, > A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, > V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, > S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, > K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, > J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, > B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, > R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, > C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, > B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, > M. Head-Gordon, E. S. Replogle, and J. A. Pople, > Gaussian, Inc., Pittsburgh PA, 1998. > > ********************************************* > Gaussian 98: x86-Win32-G98RevA.9 19-Apr-2000 > 25-Jan-2011 > ********************************************* > %mem=6MW > %nproc=1 > Will use up to 1 processors via shared memory. > %chk=Quer.chk > Default route: MaxDisk=2000MB > --------------------------- > #P RHF/6-31+G(d,p) Opt Test > --------------------------- > 1/18=20,38=1/1,3; > 2/9=110,17=6,18=5,40=1/2; > 3/5=1,6=6,7=111,11=1,25=1,30=1/1,2,3; > 4/7=1/1; > 5/5=2,38=4/2; > 6/7=2,8=2,9=2,10=2,28=1/1; > 7//1,2,3,16; > 1/18=20/3(1); > 99//99; > 2/9=110/2; > 3/5=1,6=6,7=111,11=1,25=1,30=1/1,2,3; > 4/5=5,7=1,16=2/1; > 5/5=2,38=4/2; > 7//1,2,3,16; > 1/18=20/3(-5); > 2/9=110/2; > 6/7=2,8=2,9=2,10=2,19=2,28=1/1; > 99/9=1/99; > Leave Link 1 at Tue Jan 25 12:07:57 2011, MaxMem= 6291456 cpu: 0.0 > open of exec.fil failed. > > Thanks. From owner-chemistry@ccl.net Wed Jan 26 09:24:00 2011 From: "Shirin Seifert shirin.seifert**gmail.com" To: CCL Subject: CCL:G: unexpected job termination Message-Id: <-43767-110126041828-24126-KaY3O9JjCUb0BClTSpjHFw%server.ccl.net> X-Original-From: Shirin Seifert Content-Type: multipart/alternative; boundary=0016e6de03bed3e603049abc4f5e Date: Wed, 26 Jan 2011 12:48:10 +0330 MIME-Version: 1.0 Sent to CCL by: Shirin Seifert [shirin.seifert_+_gmail.com] --0016e6de03bed3e603049abc4f5e Content-Type: text/plain; charset=ISO-8859-1 Hello, Because CASSCF calculations requests several GB's of memory,I am doing casscf calculations with scf=conventional or noincore %nprocshared=8 Will use up to 8 processors via shared memory. %mem=4GB %chk=/home/nanolab/Desktop/project/1245.chk --------------------------------------------------- #p casscf(6,8,nroot=2,stateaverage)/6-31g(d) nosymm scf(conventional) --------------------------------------------------- the job terminates without any message! here is last part in the output file. Symmetry turned off by external request. Stoichiometry C18H32(2+,3) Framework group C2V[SGV(C2H4),X(C16H28)] Deg. of freedom 38 Full point group C2V NOp 4 Rotational constants (GHZ): 0.2038488 0.1034278 0.0700853 Leave Link 202 at Wed Jan 26 11:48:33 2011, MaxMem= 536870912 cpu: 0.0 (Enter /home/nanolab/Desktop//g09/l301.exe) Standard basis: 6-31G(d) (6D, 7F) Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. Integral buffers will be 131072 words long. Regular integral format. Two-electron integral symmetry is turned off. 334 basis functions, 632 primitive gaussians, 334 cartesian basis functions 70 alpha electrons 68 beta electrons nuclear repulsion energy 1088.3652015427 Hartrees. IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 50 NActive= 50 NUniq= 50 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F Leave Link 301 at Wed Jan 26 11:48:34 2011, MaxMem= 536870912 cpu: 0.5 (Enter /home/nanolab/Desktop//g09/l302.exe) NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. One-electron integrals computed using PRISM. The smallest eigenvalue of the overlap matrix is 2.819D-03 NBasis= 334 RedAO= F NBF= 334 NBsUse= 334 1.00D-04 NBFU= 334 Leave Link 302 at Wed Jan 26 11:48:34 2011, MaxMem= 536870912 cpu: 2.9 (Enter /home/nanolab/Desktop//g09/l303.exe) DipDrv: MaxL=1. Leave Link 303 at Wed Jan 26 11:48:34 2011, MaxMem= 536870912 cpu: 0.6 Whats the problem here? Thanks for your suggestions. Regards, SS --0016e6de03bed3e603049abc4f5e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,
Because CASSCF calculations requests several GB's of memory,= I am doing casscf calculations with scf=3Dconventional or noincore

%npr= ocshared=3D8
=A0Will use up to=A0=A0=A0 8 processors via shared memory.
=A0%mem=3D4GB=
=A0%chk=3D/home/nanolab/Desktop/project/1245.chk
=A0----------------= -----------------------------------
=A0#p casscf(6,8,nroot=3D2,stateaver= age)/6-31g(d) nosymm scf(conventional)
=A0---------------------------------------------------
the job terminates without any message!
here is last part in the output= file.

Symmetry turned off by external request.
=A0Stoichiometry= =A0=A0=A0 C18H32(2+,3)
=A0Framework group=A0 C2V[SGV(C2H4),X(C16H28)]
=A0Deg. of freedom=A0=A0= =A0 38
=A0Full point group=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0 C2V=A0=A0=A0=A0 NOp=A0=A0 4
=A0Rotational constants (GHZ):=A0=A0=A0= =A0=A0 0.2038488=A0=A0=A0=A0=A0 0.1034278=A0=A0=A0=A0=A0 0.0700853
=A0Le= ave Link=A0 202 at Wed Jan 26 11:48:33 2011, MaxMem=3D=A0 536870912 cpu:=A0= =A0=A0=A0=A0=A0 0.0
=A0(Enter /home/nanolab/Desktop//g09/l301.exe)
=A0Standard basis: 6-31G(= d) (6D, 7F)
=A0Ernie: Thresh=3D=A0 0.10000D-02 Tol=3D=A0 0.10000D-05 Str= ict=3DF.
=A0Integral buffers will be=A0=A0=A0 131072 words long.
=A0R= egular integral format.
=A0Two-electron integral symmetry is turned off.
=A0=A0 334 basis functi= ons,=A0=A0 632 primitive gaussians,=A0=A0 334 cartesian basis functions
= =A0=A0=A0 70 alpha electrons=A0=A0=A0=A0=A0=A0 68 beta electrons
=A0=A0= =A0=A0=A0=A0 nuclear repulsion energy=A0=A0=A0=A0=A0 1088.3652015427 Hartre= es.
=A0IExCor=3D=A0=A0=A0 0 DFT=3DF Ex=3DHF Corr=3DNone ExCW=3D0 ScaHFX=3D=A0 1= .000000
=A0ScaDFX=3D=A0 1.000000=A0 1.000000=A0 1.000000=A0 1.000000 Sca= lE2=3D=A0 1.000000=A0 1.000000
=A0IRadAn=3D=A0=A0=A0=A0=A0 0 IRanWt=3D= =A0=A0=A0=A0 -1 IRanGd=3D=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0 ICorTp=3D0
= =A0NAtoms=3D=A0=A0 50 NActive=3D=A0=A0 50 NUniq=3D=A0=A0 50 SFac=3D 7.50D-0= 1 NAtFMM=3D=A0=A0 80 NAOKFM=3DF Big=3DF
=A0Leave Link=A0 301 at Wed Jan 26 11:48:34 2011, MaxMem=3D=A0 536870912 cp= u:=A0=A0=A0=A0=A0=A0 0.5
=A0(Enter /home/nanolab/Desktop//g09/l302.exe)<= br>=A0NPDir=3D0 NMtPBC=3D=A0=A0=A0=A0 1 NCelOv=3D=A0=A0=A0=A0 1 NCel=3D=A0= =A0=A0=A0=A0=A0 1 NClECP=3D=A0=A0=A0=A0 1 NCelD=3D=A0=A0=A0=A0=A0 1
=A0= =A0=A0=A0=A0=A0=A0=A0 NCelK=3D=A0=A0=A0=A0=A0 1 NCelE2=3D=A0=A0=A0=A0 1 NCl= Lst=3D=A0=A0=A0=A0 1 CellRange=3D=A0=A0=A0=A0 0.0.
=A0One-electron integrals computed using PRISM.
=A0The smallest eigenval= ue of the overlap matrix is=A0 2.819D-03
=A0NBasis=3D=A0=A0 334 RedAO=3D= F=A0 NBF=3D=A0=A0 334
=A0NBsUse=3D=A0=A0 334 1.00D-04 NBFU=3D=A0=A0 334=
=A0Leave Link=A0 302 at Wed Jan 26 11:48:34 2011, MaxMem=3D=A0 53687091= 2 cpu:=A0=A0=A0=A0=A0=A0 2.9
=A0(Enter /home/nanolab/Desktop//g09/l303.exe)
=A0DipDrv:=A0 MaxL=3D1.=A0Leave Link=A0 303 at Wed Jan 26 11:48:34 2011, MaxMem=3D=A0 536870912 = cpu:=A0=A0=A0=A0=A0=A0 0.6

Whats the problem here?

Thanks for= your suggestions.
Regards,
SS

--0016e6de03bed3e603049abc4f5e-- From owner-chemistry@ccl.net Wed Jan 26 10:41:00 2011 From: "Guilherme Luis Cordeiro guilhermecord!=!gmail.com" To: CCL Subject: CCL: Error on otpmization Message-Id: <-43768-110126103907-22398-54mlKYP989KYFJMbyAjd5w[A]server.ccl.net> X-Original-From: "Guilherme Luis Cordeiro" Date: Wed, 26 Jan 2011 10:38:59 -0500 Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord*gmail.com] Mr. Close, Here it goes my input file. I am still having same problems. %mem=6MW %nproc=1 %chk=Quer.chk #T RHF/6-31+G(d,p) Opt Test Quercetin Optimization 0 1 C C 1 B1 C 2 B2 1 A1 C 3 B3 2 A2 1 D1 C 4 B4 3 A3 2 D2 C 5 B5 4 A4 3 D3 O 1 B6 2 A5 3 D4 H 2 B7 1 A6 6 D5 O 3 B8 2 A7 1 D6 C 4 B9 3 A8 2 D7 O 5 B10 4 A9 3 D8 H 6 B11 5 A10 4 D9 C 10 B12 4 A11 3 D10 C 9 B13 3 A12 2 D11 O 10 B14 4 A13 3 D12 O 13 B15 10 A14 4 D13 C 14 B16 9 A15 3 D14 C 17 B17 14 A16 9 D15 C 18 B18 17 A17 14 D16 C 19 B19 18 A18 17 D17 C 20 B20 19 A19 18 D18 C 17 B21 14 A20 9 D19 H 18 B22 17 A21 14 D20 O 19 B23 18 A22 17 D21 O 20 B24 19 A23 18 D22 H 21 B25 20 A24 19 D23 H 22 B26 17 A25 14 D24 H 1 B27 2 A26 3 D25 H 5 B28 4 A27 3 D26 H 19 B29 18 A28 17 D27 H 20 B30 19 A29 18 D28 H 13 B31 10 A30 4 D29 B1 1.372801 B2 1.422011 B3 1.418868 B4 1.421719 B5 1.373340 B6 1.430000 B7 1.100332 B8 1.422034 B9 1.422083 B10 1.430000 B11 1.099953 B12 1.372861 B13 1.372941 B14 1.430000 B15 1.430000 B16 1.540000 B17 1.395160 B18 1.394712 B19 1.395427 B20 1.394825 B21 1.394829 B22 1.099655 B23 1.430000 B24 1.430000 B25 1.099761 B26 1.099604 B27 1.970203 B28 1.970203 B29 1.970203 B30 1.970203 B31 2.083099 A1 120.509949 A2 119.095898 A3 119.210326 A4 120.455910 A5 120.647682 A6 120.883197 A7 121.700364 A8 119.059634 A9 118.644142 A10 120.645654 A11 120.549051 A12 120.496771 A13 118.591323 A14 120.649172 A15 120.685041 A16 119.997223 A17 120.008632 A18 119.994165 A19 119.993992 A20 120.004320 A21 119.980770 A22 120.012795 A23 119.981142 A24 120.011343 A25 120.007997 A26 93.299763 A27 91.296223 A28 147.360712 A29 147.329037 A30 97.126654 D1 0.017099 D2 -0.009558 D3 -0.004037 D4 179.995156 D5 -179.997141 D6 -179.987545 D7 179.994687 D8 -179.987828 D9 -179.999030 D10 0.001446 D11 -179.999529 D12 179.998375 D13 179.983869 D14 179.998729 D15 -0.038425 D16 -179.972926 D17 -0.056843 D18 0.034114 D19 179.956300 D20 -0.052026 D21 179.961852 D22 -179.996436 D23 -179.999514 D24 -0.005550 D25 179.995156 D26 -179.991131 D27 179.977135 D28 179.950703 D29 179.978543 1 2 1.5 6 1.5 7 1.0 2 3 1.5 8 1.0 3 4 1.5 9 1.5 4 5 1.5 10 1.5 5 6 1.5 11 1.0 6 12 1.0 7 28 1.0 8 9 14 1.5 10 13 1.5 15 1.0 11 29 1.0 12 13 14 1.5 16 1.0 14 17 1.0 15 16 32 1.0 17 18 1.5 22 1.5 18 19 1.5 23 1.0 19 20 1.5 24 1.0 20 21 1.5 25 1.0 21 22 1.5 26 1.0 22 27 1.0 23 24 30 1.0 25 31 1.0 26 27 28 29 30 31 32 From owner-chemistry@ccl.net Wed Jan 26 11:16:00 2011 From: "Close, David M. CLOSED#,#mail.etsu.edu" To: CCL Subject: CCL: Error on otpmization Message-Id: <-43769-110126110736-10136-Mg8pfjGiQCzjNpv+Rkdt/g:_:server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 Jan 2011 16:06:48 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED#mail.etsu.edu] Now I see. You don't want the space between the charge/multiplicity, and the atom coordinates. -----Original Message----- > From: owner-chemistry+closed==etsu.edu,+,ccl.net [mailto:owner-chemistry+closed==etsu.edu,+,ccl.net] On Behalf Of Guilherme Luis Cordeiro guilhermecord!=!gmail.com Sent: Wednesday, January 26, 2011 10:39 AM To: Close, David M. Subject: CCL: Error on otpmization Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord*gmail.com] Mr. Close, Here it goes my input file. I am still having same problems. %mem=6MW %nproc=1 %chk=Quer.chk #T RHF/6-31+G(d,p) Opt Test Quercetin Optimization 0 1 C C 1 B1 C 2 B2 1 A1 C 3 B3 2 A2 1 D1 C 4 B4 3 A3 2 D2 C 5 B5 4 A4 3 D3 O 1 B6 2 A5 3 D4 H 2 B7 1 A6 6 D5 O 3 B8 2 A7 1 D6 C 4 B9 3 A8 2 D7 O 5 B10 4 A9 3 D8 H 6 B11 5 A10 4 D9 C 10 B12 4 A11 3 D10 C 9 B13 3 A12 2 D11 O 10 B14 4 A13 3 D12 O 13 B15 10 A14 4 D13 C 14 B16 9 A15 3 D14 C 17 B17 14 A16 9 D15 C 18 B18 17 A17 14 D16 C 19 B19 18 A18 17 D17 C 20 B20 19 A19 18 D18 C 17 B21 14 A20 9 D19 H 18 B22 17 A21 14 D20 O 19 B23 18 A22 17 D21 O 20 B24 19 A23 18 D22 H 21 B25 20 A24 19 D23 H 22 B26 17 A25 14 D24 H 1 B27 2 A26 3 D25 H 5 B28 4 A27 3 D26 H 19 B29 18 A28 17 D27 H 20 B30 19 A29 18 D28 H 13 B31 10 A30 4 D29 B1 1.372801 B2 1.422011 B3 1.418868 B4 1.421719 B5 1.373340 B6 1.430000 B7 1.100332 B8 1.422034 B9 1.422083 B10 1.430000 B11 1.099953 B12 1.372861 B13 1.372941 B14 1.430000 B15 1.430000 B16 1.540000 B17 1.395160 B18 1.394712 B19 1.395427 B20 1.394825 B21 1.394829 B22 1.099655 B23 1.430000 B24 1.430000 B25 1.099761 B26 1.099604 B27 1.970203 B28 1.970203 B29 1.970203 B30 1.970203 B31 2.083099 A1 120.509949 A2 119.095898 A3 119.210326 A4 120.455910 A5 120.647682 A6 120.883197 A7 121.700364 A8 119.059634 A9 118.644142 A10 120.645654 A11 120.549051 A12 120.496771 A13 118.591323 A14 120.649172 A15 120.685041 A16 119.997223 A17 120.008632 A18 119.994165 A19 119.993992 A20 120.004320 A21 119.980770 A22 120.012795 A23 119.981142 A24 120.011343 A25 120.007997 A26 93.299763 A27 91.296223 A28 147.360712 A29 147.329037 A30 97.126654 D1 0.017099 D2 -0.009558 D3 -0.004037 D4 179.995156 D5 -179.997141 D6 -179.987545 D7 179.994687 D8 -179.987828 D9 -179.999030 D10 0.001446 D11 -179.999529 D12 179.998375 D13 179.983869 D14 179.998729 D15 -0.038425 D16 -179.972926 D17 -0.056843 D18 0.034114 D19 179.956300 D20 -0.052026 D21 179.961852 D22 -179.996436 D23 -179.999514 D24 -0.005550 D25 179.995156 D26 -179.991131 D27 179.977135 D28 179.950703 D29 179.978543 1 2 1.5 6 1.5 7 1.0 2 3 1.5 8 1.0 3 4 1.5 9 1.5 4 5 1.5 10 1.5 5 6 1.5 11 1.0 6 12 1.0 7 28 1.0 8 9 14 1.5 10 13 1.5 15 1.0 11 29 1.0 12 13 14 1.5 16 1.0 14 17 1.0 15 16 32 1.0 17 18 1.5 22 1.5 18 19 1.5 23 1.0 19 20 1.5 24 1.0 20 21 1.5 25 1.0 21 22 1.5 26 1.0 22 27 1.0 23 24 30 1.0 25 31 1.0 26 27 28 29 30 31 32http://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 Wed Jan 26 11:51:00 2011 From: "VITORGE Pierre 094605 Pierre.VITORGE(~)cea.fr" To: CCL Subject: CCL:G: NBO analysis Message-Id: <-43770-110126113324-30763-qGxR1eIxXknqcjiYFGtwRA]-[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: Wed, 26 Jan 2011 17:32:24 +0100 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE-.-cea.fr] Each one has its own rule of thumb. A logical one is to consider the NBO second order perturbation analysis when it finds stabilization by more than the accuracy of the calculation... now what is the accuracy of such quantum calculation? ...!!! I would say when you have more than 10 kcal/mol you might want to consider such interpretation... Do not bother with numbers less than I would say 5 kcal/mol. Note that thermal energy can also be of this order of magnitude... You can also compare the (mono or)bi-electronic MOs used by Gaussian (pop=full) with NBOs and LPs found by the NBO software, to my experience the differences -in energies, characters and visual shapes- between the two sets of bi-electronic MOs is consistent with high energy interactions found by the second order perturbation analysis of the NBO software. -- Pierre Vitorge -----Message d'origine----- De : owner-chemistry+pierre.vitorge==cea.fr(!)ccl.net [mailto:owner-chemistry+pierre.vitorge==cea.fr(!)ccl.net] De la part de P.D.Jarowski(a)surrey.ac.uk Envoyé : mardi 25 janvier 2011 19:49 À : VITORGE Pierre 094605 Objet : CCL:G: NBO analysis Sent to CCL by: [P.D.Jarowski-.-surrey.ac.uk] Hello, I recently did an nbo analysis where I was looking for some donations into sigma star to rationalize some geometric bond elongations. I found the interactions in the second ordere perturbation analysis, but I have no idea how to assess whether or not they are significant. Does anyone know a rule of thumb for this? if the second order perturbations a re only a small percentage of the total energy then what amount of this is significant. I am getting numbers on the order of a few kcal/mol in a sea of interaction of similar magnitude. If you need the file, I could send it. Best, Peter ***Sent via RoadSync® for Android(tm) -----Original Message----- > From: VITORGE Pierre 094605 Pierre.VITORGE-,-cea.fr Sent: Jan 24, 2011 4:56 PM To: Jarowski PD Dr (Physics) Subject: CCL:G: NBO analysis Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE]![cea.fr] Marcin, I am simplifying your NBO output: 1. (1.99952) BD ( 1) C 1 - O 2 ( 28.51%) 0.5339* C 1 s( 24.94%)p 2.99( 74.66%) ( 71.49%) 0.8455* O 2 s( 39.85%)p 1.49( 59.48%) 2. (1.99959) BD ( 2) C 1 - O 2 ( 22.67%) 0.4761* C p86.96( 98.32%) ( 77.33%) 0.8794* O p54.81( 97.77%) 3. (2.00000) BD ( 3) C 1 - O 2 ( 22.41%) 0.4734* C p 1.00( 99.45%) ( 77.59%) 0.8809* O p 1.00( 99.56%) 6. (1.99926) LP ( 1) C 1 s( 76.76%)p 0.30( 23.20%) 7. (1.99335) LP ( 1) O 2 s( 58.46%)p 0.71( 41.47%) to highlight qualitative interpretation: NBOs 1, 2 and 3 are for C-O triple bond NBOs 2 and 3 are virtually 100% from p orbitals they certainly correspond to 2 pi bonds, if you further look elsewhere in the NBO output, you will certainly find that the p orbitals are px and py, since the C-O axis is usually taken as the z geometric axis, for symmetry reason probably one NBO with only px functions, the other NBO with only py functions NBO 1 is built from one C sp hydrid and one O sp hydrid. The p function should now be a pz one: this is the sigma bond. The interpretation of the % of s and p functions need to consider the LPs and the "second order perturbation analysis" of the NBO output, since NBO1 and the LPs are certainly of same symmetry, namely sigma. 6 and 7 are lone pairs (LPs), they certainly are of sigma symmetry as NBO 1, and as NBO 1 built with s and pz functions. For this reason they should not be interpreted independently from NBO 1. Do not hesitate to contact me directly (pierre.vitorge//\\cea.fr) for more details: Using Section Second order perturbation analysis Having a more quantitative interpretation directly from the MOs used by Gaussian (pop=full) -- Pierre Vitorge Directeur de recherche CEA Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, LAMBE, UMR 8587, CEA, Univ Evry, CNRS, Bd. Francois Mitterrand, Bat. Maupertuis, S 02 F-91025 Evry, France tel.01.69.47.01.40 (+33.1.69.47.01.40) http://www.lambe.univ-evry.fr/pvitorge http://www.vitorge.name Saclay : CEA, DEN, DPC, SECR, LSRM, Bat.391 Pe.121 F-91191 Gif-sur-Yvette, France. tel.01.69.08.32.65 (+33.1.69.08.32.65) -----Message d'origine----- De : owner-chemistry+pierre.vitorge==cea.fr() ccl.net [mailto:owner-chemistry+pierre.vitorge==cea.fr() ccl.net] De la part de Marcin Sterniczuk m.sterniczuk,,ichtj.waw.pl Envoyé : lundi 24 janvier 2011 12:46 À : VITORGE Pierre 094605 Objet : CCL:G: NBO analysis Sent to CCL by: "Marcin Sterniczuk" [m.sterniczuk###ichtj.waw.pl] Hello, I have a problem with NBO analysis. How on +CO molecule example recognize hybrydization on carbon. What is hybrydization on orbital with unpaired electrone. One bonding orbital on carbon is sp3, two p and lone electron have orbital sp0,3. I know that sp0,3 we can describe sp. What we can do when some carbon centrum shows absurd like: one orbital sp3, one sp2, one sp and one p. That is a +CO part output from Gaussian 03W. (Occupancy) Bond orbital/ Coefficients/ Hybrids --------------------------------------------------------------------------------- 1. (1.99952) BD ( 1) C 1 - O 2 ( 28.51%) 0.5339* C 1 s( 24.94%)p 2.99( 74.66%)d 0.02( 0.39%) 0.0000 0.4639 -0.1850 0.7795 -0.0509 0.3691 -0.0133 0.0000 0.0000 0.0347 0.0000 0.0000 0.0425 -0.0304 ( 71.49%) 0.8455* O 2 s( 39.85%)p 1.49( 59.48%)d 0.02( 0.67%) 0.0000 0.6298 -0.0434 -0.7688 0.0247 0.0556 0.0059 0.0000 0.0000 0.0144 0.0000 0.0000 0.0697 -0.0403 2. (1.99959) BD ( 2) C 1 - O 2 ( 22.67%) 0.4761* C 1 s( 1.13%)p86.96( 98.32%)d 0.48( 0.55%) 0.0000 -0.0988 0.0394 -0.3676 0.0137 0.9208 -0.0114 0.0000 0.0000 0.0627 0.0000 0.0000 -0.0385 0.0065 ( 77.33%) 0.8794* O 2 s( 1.78%)p54.81( 97.77%)d 0.25( 0.45%) 0.0000 -0.1332 0.0092 -0.0390 -0.0061 0.9880 0.0032 0.0000 0.0000 -0.0656 0.0000 0.0000 0.0116 0.0085 3. (2.00000) BD ( 3) C 1 - O 2 ( 22.41%) 0.4734* C 1 s( 0.00%)p 1.00( 99.45%)d 0.01( 0.55%) 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.9971 -0.0142 0.0000 0.0729 0.0147 0.0000 0.0000 ( 77.59%) 0.8809* O 2 s( 0.00%)p 1.00( 99.56%)d 0.00( 0.44%) 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.9978 0.0045 0.0000 -0.0651 -0.0131 0.0000 0.0000 4. (1.99981) CR ( 1) C 1 s(100.00%) 1.0000 0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 5. (1.99988) CR ( 1) O 2 s(100.00%)p 0.00( 0.00%) 1.0000 -0.0001 0.0000 -0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 6. (1.99926) LP ( 1) C 1 s( 76.76%)p 0.30( 23.20%)d 0.00( 0.03%) -0.0001 0.8757 0.0292 -0.4705 -0.0394 -0.0949 -0.0080 0.0000 0.0000 -0.0060 0.0000 0.0000 -0.0143 0.0089 7. (1.99335) LP ( 1) O 2 s( 58.46%)p 0.71( 41.47%)d 0.00( 0.07%) 0.0002 0.7641 0.0267 0.6311 0.0108 0.1273 0.0022 0.0000 0.0000 -0.0091 0.0000 0.0000 -0.0216 0.0135 8. (0.00673) RY*( 1) C 1 s( 64.49%)p 0.55( 35.30%)d 0.00( 0.21%) 0.0000 0.0883 0.7982 0.1569 0.5609 0.0317 0.1132 0.0000 0.0000 0.0154 0.0000 0.0000 0.0367 -0.0230 9. (0.00005) RY*( 2) C 1 s( 21.74%)p 2.25( 48.95%)d 1.35( 29.31%) 10. (0.00000) RY*( 3) C 1 s( 0.01%)p 1.00( 99.79%)d 0.00( 0.20%) 11. (0.00000) RY*( 4) C 1 s( 0.00%)p 1.00(100.00%)d 0.00( 0.00%) 12. (0.00000) RY*( 5) C 1 s( 1.37%)p 2.07( 2.83%)d70.09( 95.80%) 13. (0.00000) RY*( 6) C 1 s( 0.00%)p 1.00( 0.53%)d99.99( 99.47%) 14. (0.00000) RY*( 7) C 1 s( 0.00%)p 1.00( 0.02%)d99.99( 99.98%) 15. (0.00000) RY*( 8) C 1 s( 6.16%)p 1.75( 10.81%)d13.48( 83.03%) 16. (0.00000) RY*( 9) C 1 s( 3.40%)p 1.80( 6.13%)d26.63( 90.47%) 17. (0.00089) RY*( 1) O 2 s( 8.59%)p 4.64( 39.84%)d 6.00( 51.56%) 0.0000 0.0416 0.2902 -0.0794 -0.6136 -0.0160 -0.1238**************** -0.2411 **************** -0.5732 0.3590 18. (0.00003) RY*( 2) O 2 s( 11.89%)p 3.41( 40.51%)d 4.00( 47.61%) 19. (0.00000) RY*( 3) O 2 s( 0.57%)p99.99( 98.63%)d 1.41( 0.80%) 20. (0.00000) RY*( 4) O 2 s( 0.00%)p 1.00(100.00%)d 0.00( 0.00%) 21. (0.00000) RY*( 5) O 2 s( 0.00%)p 1.00( 0.98%)d99.99( 99.01%) 22. (0.00000) RY*( 6) O 2 s( 0.00%)p 1.00( 0.42%)d99.99( 99.58%) 23. (0.00000) RY*( 7) O 2 s( 0.00%)p 1.00( 0.02%)d99.99( 99.98%) 24. (0.00000) RY*( 8) O 2 s( 78.85%)p 0.27( 21.07%)d 0.00( 0.08%) 25. (0.00000) RY*( 9) O 2 s( 0.00%)p 1.00( 0.26%)d99.99( 99.74%) 26. (0.00041) BD*( 1) C 1 - O 2 ( 71.49%) 0.8455* C 1 s( 24.94%)p 2.99( 74.66%)d 0.02( 0.39%) 0.0000 0.4639 -0.1850 0.7795 -0.0509 0.3691 -0.0133 0.0000 0.0000 0.0347 0.0000 0.0000 0.0425 -0.0304 ( 28.51%) -0.5339* O 2 s( 39.85%)p 1.49( 59.48%)d 0.02( 0.67%) 0.0000 0.6298 -0.0434 -0.7688 0.0247 0.0556 0.0059 0.0000 0.0000 0.0144 0.0000 0.0000 0.0697 -0.0403 27. (0.00048) BD*( 2) C 1 - O 2 ( 77.33%) 0.8794* C 1 s( 1.13%)p86.96( 98.32%)d 0.48( 0.55%) 0.0000 -0.0988 0.0394 -0.3676 0.0137 0.9208 -0.0114 0.0000 0.0000 0.0627 0.0000 0.0000 -0.0385 0.0065 ( 22.67%) -0.4761* O 2 s( 1.78%)p54.81( 97.77%)d 0.25( 0.45%) 0.0000 -0.1332 0.0092 -0.0390 -0.0061 0.9880 0.0032 0.0000 0.0000 -0.0656 0.0000 0.0000 0.0116 0.0085 28. (0.00000) BD*( 3) C 1 - O 2 ( 77.59%) 0.8809* C 1 s( 0.00%)p 1.00( 99.45%)d 0.01( 0.55%) ( 22.41%) -0.4734* O 2 s( 0.00%)p 1.00( 99.56%)d 0.00( 0.44%) Thank youhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/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.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 Wed Jan 26 12:25:00 2011 From: "Anup Thomas anupiict!A!gmail.com" To: CCL Subject: CCL:G: Gaussian question Message-Id: <-43771-110126114039-4849-t2MwsYC8ko5hrjZCXV6JCQ++server.ccl.net> X-Original-From: "Anup Thomas" Date: Wed, 26 Jan 2011 11:40:25 -0500 Sent to CCL by: "Anup Thomas" [anupiict+*+gmail.com] Dear Tijesunimi, I would like to add a few papers which can help you with DFT orbitals and HF orbitals Comparison of Hartree-Fock and Kohn-Sham Determinats as wave functions By Petr Bour Journal of Compuational Chemistry 21 8-16 2000 A Comparative analysis of Hartree-Fock and Kohn-Sham orbital Energies by Peter Politzer and Fakher Abu-Awwad. Theor. Chem. Acc 1998 99 83-87. Design of Low Band Gap Polymers Employing Density Functional Theory - Hybrid Functionals Ameliorate Band Gap Problem By U Salzner et al J. Computational Chemistry 18, 1943-1953 1997. Estimation of the first excitation energy in diradicaloid croconate dyes having absorption in the near infra red (NIR): A DFT and SF-TDDFT study Anup Thomas, Kola Srinivasa, Ch. Prabhakar, K. Bhanuprakash, , and V. Jayathirtha Rao Chem. Phys. Lett. 454 36-41 2008 Regards Anup Thms ============================================================================ On Tue, Jan 25, 2011 at 8:42 PM, Tijesunimi John Odebode tijesunimi=yahoo.com wrote: Sent to CCL by: "Tijesunimi John Odebode" [tijesunimi:-:yahoo.com] Hello all, I was wondering if I could get an answer to this question: I did a geometry optimization of a compound using Gaussian(b3lyp/6-31G(d)). I found the HOMO and LUMO energy and calculated the energy gap. I then decided to do an MP2 single point calculation on the same compound to determine the HOMO and LUMO energy gap. The energy gap for the single point MP2 calculation was 3.49eV more than that for the b3lyp. Is this normal? Or do you think there is a problem somewhere? Has anybody carried out such calculations? Thanks a lot for your anticipated response. ============================================================================ From owner-chemistry@ccl.net Wed Jan 26 14:42:00 2011 From: "Tijesunimi Odebode tijesunimi###yahoo.com" To: CCL Subject: CCL:G: Gaussian question Message-Id: <-43772-110126140440-18084-/JsdoCDMdMO/TMfR4Y82fQ.:.server.ccl.net> X-Original-From: Tijesunimi Odebode Content-Type: multipart/alternative; boundary="0-70936306-1296068617=:33021" Date: Wed, 26 Jan 2011 11:03:37 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Tijesunimi Odebode [tijesunimi * yahoo.com] --0-70936306-1296068617=:33021 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Thanks a lot for your response. This greatly helps. Did not look at it that= way.=0A=0ATijesunimi Odebode=0A=0A=0A=0A=0A_______________________________= _=0AFrom: Piotr Nowak piotrnowak^student.uw.edu.pl =0ATo: "Odebode, Tijesunimi John " =0ASent: = Wed, January 26, 2011 5:48:41 AM=0ASubject: CCL:G: Gaussian question=0A=0A= =0ADear Tijesunimi,=0AFirst of all, MP2 introduces electron correlation via= Rayleigh-Schroedinger =0Aperturbation theory using occupied and virtual or= bitals and their energies from =0AHartree-Fock calculation, so it does not = create new orbitals or orbital =0Aenergies. Therefore FMOs > from your MP2 = calculation are de facto HF orbitals. =0ASecond, it is well known that DFT = gives different orbital energies than HF (but =0Ayou cannot say they're wor= se). For detailed discussion you can check e.g.: =0A=0AStowasser, R., & Hof= fmann, R. (1999). What Do the Kohn=E2=88=92Sham Orbitals and =0AEigenvalues= Mean? Journal of the American Chemical Society, 121(14), 3414-3420.=0AKar,= T., =C3=81ngy=C3=A1n, J. G., & Sannigrahi, A. B. (2000). Comparison of ab = Initio =0AHartree=E2=88=92Fock and Kohn=E2=88=92Sham Orbitals in the Calcul= ation of Atomic Charge, Bond =0AIndex, and Valence. The Journal of Physical= Chemistry A, 105(3), 9953-9963.=0AZhang, G., & Musgrave, C. B. (2007). Com= parison of DFT methods for molecular =0Aorbital eigenvalue calculations. Th= e Journal of Physical Chemistry A,111(8), =0A1554-1561.=0A=0ABest regards,= =0APiotr Nowak=0A=0AOn Tue, Jan 25, 2011 at 8:42 PM, Tijesunimi John Odebod= e tijesunimi=3Dyahoo.com =0A wrote:=0A=0A=0A>Sen= t to CCL by: "Tijesunimi John Odebode" [tijesunimi:-:yahoo.com]=0A>Hello al= l,=0A>=0A>I was wondering if I could get an answer to this question:=0A>=0A= >I did a geometry optimization of a compound using Gaussian(b3lyp/6-31G(d))= . I =0A>found the HOMO and LUMO energy and calculated the energy gap. I the= n decided to =0A>do an MP2 single point calculation on the same compound to= determine the HOMO =0A>and LUMO energy gap. The energy gap for the single = point MP2 calculation was =0A>3.49eV more than that for the b3lyp. Is this= normal? Or do you think there is a =0A>problem somewhere? Has anybody carr= ied out such calculations? Thanks a lot for =0A>your anticipated response.= =0A>=0A>=0A>=0A>-=3D This is automatically added to each message by the mai= ling script =3D-=0A>=0A>E-mail to subscribers: CHEMISTRY[a]ccl.net or use:= =0A=0A>=0A>E-mail to a= dministrators: CHEMISTRY-REQUEST[a]ccl.net or use=0A> http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message=0A>=0A>Subscribe/Unsubscribe:=0A> http:/= /www.ccl.net/chemistry/sub_unsub.shtml=0A>=0A>Before posting, check wait ti= me at: http://www.ccl.net=0A>=0A>Job: http://www.ccl.net/jobs=0A>Conference= s: http://server.ccl.net/chemistry/announcements/conferences/=0A>=0A>Search= Messages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A>=0A> h= ttp://www.ccl.net/spammers.txt=0A>=0A>RTFI: http://www.ccl.net/chemistry/ab= outccl/instructions/=0A>=0A>=0A>=0A=0A=0A-- =0A******=0APiotr Nowak=0AUnive= rsity of Warsaw=0ADepartment of Chemistry=0ALaboratory of Stereocontrolled = Organic Synthesis=0APasteura 1, 02-093 Warsaw, Poland=0A******=0A=0A=0A=0A = --0-70936306-1296068617=:33021 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Thanks a lot for your response. This greatly helps. Did n= ot look at it that way.

Tijesunimi Odebode

From: Piotr Nowak piotrnowak^student.uw.edu.pl &l= t;owner-chemistry(a)ccl.net>
To:<= /span> "Odebode, Tijesunimi John " <tijesunimi(a)yahoo.com>=
Sent: Wed, January 26,= 2011 5:48:41 AM
Subject: CCL:G: Gaussian question

=0A
Dear Tijesunimi,

First of all, MP2 introduces electron correlation via Rayl= eigh-Schroedinger perturbation theory using occupied and virtual orbitals a= nd their energies from Hartree-Fock calculation, so it does not create new = orbitals or orbital energies. Therefore FMOs > from your MP2 calculation= are de facto HF orbitals. 
=0ASecond, it is well known that DFT g= ives different orbital energies than HF (but you cannot say they're worse).= For detailed discussion you can check e.g.: 

=0AStowasser, R., & Hoffmann, R. (1999). What Do the Kohn=E2=88=92Sham O= rbitals and Eigenvalues Mean? Journal of the American Chemical Society= , 121(14), 3414-3420.

=0A

=0AKar, T., =C3=81ngy=C3=A1n, J. G., & Sannigrahi, A. B. = (2000). Comparison of ab Initio Hartree=E2=88=92Fock and Kohn=E2=88=92Sham = Orbitals in the Calculation of Atomic Charge, Bond Index, and Valence. = ;The Journal of Physical Chemistry A, 105(3), 9953-9963.

= =0A
Zhang, G., & Musgrave, C. B. (2007). Co= mparison of DFT methods for molecular orbital eigenvalue calculations. = ;The Journal of Physical Chemistry A,111(8), 1554-1561.
=0A
Best r= egards,
=0A
Piotr Nowak
=

=0A
On Tue, Jan 25, 2011 at 8:42 PM, Tijesunimi John Odebode tijesuni= mi=3Dyahoo.= com <owner-chemistry[a]ccl.net> wrote:
=0A

=0ASent to CCL by: "Tijesunim= i John Odebode" [tijesunimi:-:yahoo.com]
=0AHello all,
=0A
=0AI was wonde= ring if I could get an answer to this question:
=0A
=0AI did a geomet= ry optimization of a compound using Gaussian(b3lyp/6-31G(d)). I found the H= OMO and LUMO energy and calculated the energy gap. I then decided to do an = MP2 single point calculation on the same compound to determine the HOMO and= LUMO energy gap. The energy gap for the single point MP2 calculation was 3= .49eV  more than that for the b3lyp. Is this normal? Or do you think t= here is a problem somewhere? Has anybody carried out such calculations? Tha= nks a lot for your anticipated response.
=0A=0A
=0A
=0A
=0A-=3D= This is automatically added to each message by the mailing script =3D-
= =0A
=0AE-mail to subscribers: CHEM= ISTRY[a]ccl.net or use:
=0A      http://www.= ccl.net/cgi-bin/ccl/send_ccl_message
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=0ABefore posting, check wai= t time at: http://www.ccl.= net
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=0AJob: http://www.ccl.net/jobs
=0AConference= s: http://server.ccl.net/chemistry/announcements/conferences/=
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=0ASearch Messages: http://www.ccl.net/= chemistry/searchccl/index.shtml
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=0A    = ;  http:= //www.ccl.net/spammers.txt
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=0ARTFI: http:= //www.ccl.net/chemistry/aboutccl/instructions/
=0A
=0A
= =0A



--
******
Piotr Now= ak
University of Warsaw
Department of Chemistry
Laboratory of Stereocontrolled Organic Synthesis
Pasteura 1, 0= 2-093 Warsaw, Poland
=0A
******

=0A
=0A
= =0A
=0A=0A=0A=0A=0A=0A=0A=0A --0-70936306-1296068617=:33021-- From owner-chemistry@ccl.net Wed Jan 26 18:00:00 2011 From: "Tijesunimi Odebode tijesunimi*_*yahoo.com" To: CCL Subject: CCL:G: Gaussian Error Message-Id: <-43773-110126140329-17499-zxcczLYp0krpCIk8gIodMg^server.ccl.net> X-Original-From: Tijesunimi Odebode Content-Type: multipart/alternative; boundary="0-350150758-1296068568=:92923" Date: Wed, 26 Jan 2011 11:02:48 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Tijesunimi Odebode [tijesunimi[a]yahoo.com] --0-350150758-1296068568=:92923 Content-Type: text/plain; charset=us-ascii Thanks a lot for your response. That helps. TJ ________________________________ > From: Shirin Seifert shirin.seifert+/-gmail.com To: "Odebode, Tijesunimi John " Sent: Wed, January 26, 2011 6:28:07 AM Subject: CCL:G: Gaussian Error hi possibilities are: 1- Not enough physical memory is available or installed. 2- If it is in windows, there is a limitation of 2GB memory with 32 bit applications. hope this helps Best, SS On Tue, Jan 25, 2011 at 10:56 PM, Tijesunimi John Odebode tijesunimi__yahoo.com wrote: >Sent to CCL by: "Tijesunimi John Odebode" [tijesunimi+*+yahoo.com] >Hello, > >I was wondering if anybody had an answer to my question. I am trying to >visualize the HOMO and LUMO of a compound on MOLDEN of which I ran gaussian >calculations on. I read an article online that says that for MOLDEN to find all >required information in the output file, I need to run a single point >calculation at the desired level of theory including the pop=full and gfinput >keywords. I entered the above in my input file and the following is my input: > >%chk=Chlorin-1_b3lyp_go >%mem=23000mb >%nprocshared=8 ># b3lyp/6-31G(d) sp scf=tight pop=full gfinput maxdisk=50gb > >b3lyp geometry optimization using Gaussian >Chlorin-sp-1 > >The mem value in the run script is 23500mb and maxdisk=50gb. However, when I run >this job, an error message comes up which says: galloc: cannot allocate memory. >I tried increasing the memory on the run script to 24000mb but I keep getting >the message Requested node configuration unavailable. I also tried leaving the >memory on the run script as 23500mb and reducing the %mem on the input file to >20000mb; however, I keep getting the same message saying galloc: cannot allocate >memory.' I do not know what the problem is. Is there a problem with my input >file or what else do you think I should do. I am sorry if I did not do a good >job explaining the problem; I am new to this. Thanks a lot for your anticipated >response. > >Tijesunimi Odebode> >E-mail to subscribers: CHEMISTRY:+:ccl.net or use:> >E-mail to administrators: CHEMISTRY-REQUEST:+:ccl.net or use> > > --0-350150758-1296068568=:92923 Content-Type: text/html; charset=us-ascii
Thanks a lot for your response. That helps.

TJ

From: Shirin Seifert shirin.seifert+/-gmail.com <owner-chemistry .. ccl.net>
To: "Odebode, Tijesunimi John " <tijesunimi .. yahoo.com>
Sent: Wed, January 26, 2011 6:28:07 AM
Subject: CCL:G: Gaussian Error

hi
possibilities are:

1- Not enough physical memory is available or installed.
2- If it is in windows, there is a limitation of 2GB memory with 32 bit applications.

hope this helps

Best,
SS

On Tue, Jan 25, 2011 at 10:56 PM, Tijesunimi John Odebode tijesunimi__yahoo.com <owner-chemistry:+:ccl.net> wrote:

Sent to CCL by: "Tijesunimi John Odebode" [tijesunimi+*+yahoo.com]
Hello,

I was wondering if anybody had an answer to my question. I am trying to visualize the HOMO and LUMO of a compound on MOLDEN of which I ran gaussian calculations on. I read an article online that says that for MOLDEN to find all required information in the output file, I need to run a single point calculation at the desired level of theory including the pop=full and gfinput keywords. I entered the above in my input file and the following is my input:

%chk=Chlorin-1_b3lyp_go
%mem=23000mb
%nprocshared=8
# b3lyp/6-31G(d) sp scf=tight pop=full gfinput maxdisk=50gb

b3lyp geometry optimization using Gaussian
Chlorin-sp-1

The mem value in the run script is 23500mb and maxdisk=50gb. However, when I run this job, an error message comes up which says: galloc: cannot allocate memory. I tried increasing the memory on the run script to 24000mb but I keep getting the message Requested node configuration unavailable. I also tried leaving the memory on the run script as 23500mb and reducing the %mem on the input file to 20000mb; however, I keep getting the same message saying galloc: cannot allocate memory.'  I do not know what the problem is. Is there a problem with my input file or what else do you think I should do. I am sorry if I did not do a good job explaining the problem; I am new to this. Thanks a lot for your anticipated response.

Tijesunimi Odebode



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--0-350150758-1296068568=:92923-- From owner-chemistry@ccl.net Wed Jan 26 18:34:01 2011 From: "Ron Bakus rbakus+*+chem.ucsb.edu" To: CCL Subject: CCL:G: Solving linear dependence in Gaussian with IOp(3/59) Message-Id: <-43774-110126182406-27281-gvYzmRPICXn7A6GVaHdnhA=-=server.ccl.net> X-Original-From: "Ron Bakus" Date: Wed, 26 Jan 2011 18:24:04 -0500 Sent to CCL by: "Ron Bakus" [rbakus() chem.ucsb.edu] I typically work with large pi-conjugated systems and most of the work done requires the use of diffuse functions in the basis set (eg B3LYP/6-31+G(d,p)). Sometimes in these large systems I encounter situations where there is some near linear dependence and a resulting oscillation in the SCF with no converegence. I have tried all the standard tricks (vshift, xqc, changing the initial guess, nodiis, novaracc, starting from lower basis sets and computing force constants, etc) in Gaussian 03 Rev. e01 to resolve this. The only reliable fix I have found is to use IOp(3/59) (threshold for throwing away eigenvectors of S) and change it from the default 6 to some lower number, usually 5 (I can see that this results in an extra 10 or so [out of a 1000] basis sets being culled from the calculation). I was hoping someone could detail some of the consequences and possible pitfalls of changing the default value. Thanks, Ron