From owner-chemistry@ccl.net Mon Jan 3 04:56:01 2011 From: "Jean Jules FIFEN julesfifen]_[gmail.com" To: CCL Subject: CCL:G: .chk to .fchk Message-Id: <-43499-110103045031-10176-5yEiJFSpWRD6xA5X8eka8w{:}server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=0015175cb6f28edfc70498ee149b Date: Mon, 3 Jan 2011 10:50:21 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen]~[gmail.com] --0015175cb6f28edfc70498ee149b Content-Type: text/plain; charset=ISO-8859-1 If you are using windows, run in command windows the command: formchk.exe However, if you are using Linux OS, type in console, formchk. On 1 January 2011 19:19, ABHISHEK SHAHI shahi.abhishek1984,,gmail.com < owner-chemistry!A!ccl.net> wrote: > Dear All, > > I am doing AIM calculation using AIMALL and generation of .wfn file using > "# MP2(full)/aug-cc-pvtz OUTPUT=WFN DENSITY=CURRENT POP=NOAB FORCE NOSYMM" > route section by G03/G09 both. Now problem occurs when i run this .wfn with > AIMALL (AIMQB) having an error message "Invalid traditional wfn file ! > Normalisationhaek fail. Could be due to orientation inconsistency." > I have .chk file of all the system. How can i create .fchk from this .chk > file? This .fchk file will generate .wfn/.wfx file with right orientation by > using AIMQB (as mentioned by Todd A. Keith). So my main problem is "How can > i create .fchk from this .chk file? ". OR any valuable suggetion from your > side ?? > > Thanking a lot. > > Happy New year 2011 > > > With regards; > *ABHISHEK SHAHI* > > *Research Scholar > Inorganic and Physical Chemistry > Indian Institute Of Science > Bangalore-12* > E-mail: shahi()ipc.iisc.ernet.in > shahi.abhishek1984()gmail.com > * > * > -- J. Jules. --0015175cb6f28edfc70498ee149b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
If you are using windows, run in command windows the comma= nd: formchk.exe
However, if you are using Linux OS, type in console, for= mchk.

On 1 January 2011 19:19, ABHISHEK S= HAHI shahi.abhishek1984,,gmail.com <owner-chemistry!A!c= cl.net> wrote:
Dear All,
=A0 I am doing AIM calculation using AIMALL and generation of .wfn file us= ing "# MP2(full)/aug-cc-pvtz OUTPUT=3DWFN DENSITY=3DCURRENT POP=3DNOAB= FORCE NOSYMM" route section by G03/G09 both. Now problem occurs when = i run this .wfn with AIMALL (AIMQB) having an error message "Invalid t= raditional wfn file ! Normalisationhaek fail. Could be due to orientation i= nconsistency."
I have .chk file of all the system. How can i create .fchk from this .chk f= ile? This .fchk file will generate .wfn/.wfx file with right orientation by= using AIMQB (as mentioned by Todd A. Keith). So my main problem is "H= ow can i create .fchk from this .chk file? ". OR any valuable suggetio= n from your side ??

Thanking a lot.

Happy New year 2011


With regards;
=A0ABHISHEK SHAHI

Research Scholar
Bangalore-12
E-mail: =A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <= a style=3D"font-family: arial black,sans-serif;" href=3D"mailto:shahi%28%29= ipc.iisc.ernet.in" target=3D"_blank">shahi()ipc.iisc.ernet.in
=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 shahi.abhishek1984()gmail.com





--
J. Jules.

--0015175cb6f28edfc70498ee149b-- From owner-chemistry@ccl.net Mon Jan 3 10:24:00 2011 From: "mahshid - saberinasab saberinasabmahshid||yahoo.com" To: CCL Subject: CCL: termination error Message-Id: <-43500-110102063134-1597-oKVz50rHkQRry6MDf1ml2g===server.ccl.net> X-Original-From: "mahshid - saberinasab" Date: Sun, 2 Jan 2011 06:31:33 -0500 Sent to CCL by: "mahshid - saberinasab" [saberinasabmahshid#%#yahoo.com] Hi all, I'm doing an optimization at DFT level, applying B3LYP, 6-31G* basis set and specifying the solvent. It was beginning very well but after a while it was stopped by following message: Error termination in NtrErr: NtrErr Called from File --------------------------------------------------------------------------- dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 66048 FType=2 FMxFil=10000 Number 0 Base 20480 End 66048 End1 66048 Wr Pntr 20480 Rd Pntr 20480 Length 45568 Error termination in NtrErr: NtrErr Called from FileIO. ---------------------------------------------------------------------------- In advance, thanks for any assistance. M.saberinasab From owner-chemistry@ccl.net Mon Jan 3 10:59:00 2011 From: "Nathalie Reuter nathalie**cbu.uib.no" To: CCL Subject: CCL: new version of WEBnma (server for normal mode analysis of proteins) Message-Id: <-43501-110103043211-31263-lWH5YcGkJhbc1LcamlUB4A~~server.ccl.net> X-Original-From: "Nathalie Reuter" Date: Mon, 3 Jan 2011 04:32:10 -0500 Sent to CCL by: "Nathalie Reuter" [nathalie],[cbu.uib.no] Dear all, a new version of WEBnma, our web server for normal mode analysis of proteins is now available at http://apps.cbu.uib.no/webnma/home. As for the previous version, the api relies heavily on MMTK (Konrad Hinsen, http://dirac.cnrs-orleans.fr/MMTK/). Among other new functionalities, this totally refactored application includes a JMol applet for the visualization of vibrational modes and vector fields. It also now allows for comparative analysis of normal modes calculated on aligned protein structures. Happy New Year! With best regards, Nathalie Reuter --- Computational Biology Unit & Department of Molecular Biology University of Bergen 5008 Bergen Norway http://reutergroup.cbu.uib.no/ From owner-chemistry@ccl.net Mon Jan 3 12:17:00 2011 From: "Bradley Welch bwelch5^slu.edu" To: CCL Subject: CCL:G: Implementing a nanotube with Gaussian 09 PBC. Message-Id: <-43502-110103121359-12069-hx4LfQuH6hy8o2OB5JKhww##server.ccl.net> X-Original-From: "Bradley Welch" Date: Mon, 3 Jan 2011 12:13:57 -0500 Sent to CCL by: "Bradley Welch" [bwelch5{:}slu.edu] > From anyone's experience, is it possible to actually implement a full nanotube using Gaussian 09's PBC? If so, how would I generate the translation vectors for it? Regards Bradley Welch bwelch5|*|slu.edu Saint Louis University Monsanto Hall 3501 Laclede Avenue Rm 218 From owner-chemistry@ccl.net Mon Jan 3 14:42:00 2011 From: "Manuel Melle Franco manuelmelle||gmail.com" To: CCL Subject: CCL:G: Implementing a nanotube with Gaussian 09 PBC. Message-Id: <-43503-110103134436-11098-GstXppy/RDZG6eYTTOOVbw . server.ccl.net> X-Original-From: Manuel Melle Franco Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 3 Jan 2011 18:44:04 +0000 MIME-Version: 1.0 Sent to CCL by: Manuel Melle Franco [manuelmelle###gmail.com] Dear Bradley well, it is not a big deal if you are familiar with periodic calculations. First you need to know what periodic boundary contions are. Then how they do work in gaussian (gaussview actually helps a lot if you are not familiar with that kind of calculations). You need to know what the unit cell is for your nanotube. Add the displacement vector with the periodic dimension. Put the cartesian in gaussian and then try. I would advice you to experiment first with something small and semiconductor, (10,0) CNT is ideal with that with pure dft calculations, for instance PBE. regards Manuel ____________________________________________________________ Mohandas K. Gandhi often changed his mind publicly.  An aide once asked him how he could so freely contradict this week what he had said just last week.  The great man replied that it was because this week he knew better. ____________________________________________________________ Manuel Melle-Franco, Ph.D. Investigador Auxiliar do Requimte Theoretical and Computational Chemistry Group Chemistry Department Faculty of Sciences University of Porto Rua do Campo Alegre,687 4169-007 Porto Portugal. --------------------------------------------------------- A mind all logic is like a knife all blade. It makes the hand bleed that uses it. Rabindranath Tagore --------------------------------------------------------- On Mon, Jan 3, 2011 at 5:13 PM, Bradley Welch bwelch5^slu.edu wrote: > > Sent to CCL by: "Bradley   Welch" [bwelch5{:}slu.edu] >> From anyone's experience, is it possible to actually implement a full nanotube > using Gaussian 09's PBC? If so, how would I generate the translation vectors > for it? > > Regards > > Bradley Welch > bwelch5*o*slu.edu > Saint Louis University > Monsanto Hall > 3501 Laclede Avenue > Rm 218>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Mon Jan 3 21:48:00 2011 From: "Ritesh Ruhela riteshruhela]_[gmail.com" To: CCL Subject: CCL:G: Error during G09 run Message-Id: <-43504-110103211540-3531-KozQ6m4B28buu3FJHUDn/g!^!server.ccl.net> X-Original-From: "Ritesh Ruhela" Date: Mon, 3 Jan 2011 21:15:39 -0500 Sent to CCL by: "Ritesh Ruhela" [riteshruhela!A!gmail.com] Dear CCL Subscribers, We have encountered a peculiar problem while running Gaussian G09. We are doing optimization and frequency calculation of simple molecules like Butanol. The Job was completed successfully but while going through the log file we find the following errors (1)End of G2Drv Frequency-dependent properties file 721 does not exist. End of G2Drv Frequency-dependent properties file 722 does not exist. IDoAtm=111111111111111 (2)End of Minotr Frequency-dependent properties file 721 does not exist. End of Minotr Frequency-dependent properties file 722 does not exist. (3)Warning -- explicit consideration of 7 degrees of freedom as vibrations may cause significant error We have followed the previous threads of CCL containing discussions on same type of error but could not find the solution Please advice Ritesh Ruhela riteshruhela*gmail.com