From owner-chemistry@ccl.net Fri Sep 4 06:30:00 2009 From: "Tobias Kraemer tobiask:_:chem.gla.ac.uk" To: CCL Subject: CCL:G: Problem with saving NBOs in NBO5.G Message-Id: <-40163-090904055336-16864-OaGWYa/oN2V+ngBrcEu8uA+*+server.ccl.net> X-Original-From: Tobias Kraemer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 04 Sep 2009 09:30:01 +0100 MIME-Version: 1.0 Sent to CCL by: Tobias Kraemer [tobiask]![chem.gla.ac.uk] Dear CCLers.... I started using the NBO analysis tool (NBO5.G with G03), and came across a rather confusing problem. Although I searched the list archive, I couldn't find any discussion related to this topic, but I might have just overlooked it accidentally. However, I think this can be easily answered. When trying to save the NBOs to the checkpoint file for later visualization with Chemcraft, using the SAVENBOS keyword, it just doesn't work. With the NBO3.1 version, this procedure didn't cause any trouble, and the following lines were printed at the end of the file, after the NBO output. Sorting of NBOs: 8 7 4 6 5 1 3 2 9 26 Sorting of NBOs: 23 27 28 25 24 16 15 14 10 22 Sorting of NBOs: 21 11 12 17 13 18 19 20 Reordering of NBOs for storage: 8 7 4 6 5 1 3 2 9 26 Reordering of NBOs for storage: 23 27 28 25 24 16 15 14 10 22 Reordering of NBOs for storage: 21 11 12 17 13 18 19 20 Labels of output orbitals: CR CR BD BD BD BD BD BD LP BD* BD* BD* BD* BD* BD* RY* RY* RY* RY* RY* Labels of output orbitals: RY* RY* RY* RY* RY* RY* RY* RY* In the NBO5.G, these lines are missing, indicating, that no NBOs were actually reordered and stored. Indeed, after reading the orbitals into the log file, the visualisation of these orbitals reveals their 'normal ' shape, not NBO-type. Again, with NBO3.1 this can be done without problems. So now I wonder, if I ignored something here, or if this is a known issue? Here is my input for a simple example: %NProc=2 %chk=CH3NH2_NBO.chk %mem=1024MB # rhf/3-21g gfprint gfinput IOP(6/7=3) pop(FULL,NBOREAD,SAVENBOS) GUESS=(READ) GEOM=CHECK Methylamine...RHF/3-21G//Pople-Gordon standard geometry 0 1 $NBO $END Any suggestions are much appreciated, also any links to existing discussions about this topic. Thanks Tobi -- ____________________________________ dipl.-chem. tobias kraemer westCHEM, department of chemistry university of glasgow joseph black building university avenue glasgow G12 8QQ scotland, uk |phone| +44 (0)141 330 8121 |email| tobiask|-|chem.gla.ac.uk ____________________________________ From owner-chemistry@ccl.net Fri Sep 4 09:05:01 2009 From: "Abhinav Kumar abhinavmarshal-x-gmail.com" To: CCL Subject: CCL:G: Weak interaction energy calculations Message-Id: <-40164-090904051457-12845-pi+kybF2yvAt3t2xXt8MVA(~)server.ccl.net> X-Original-From: "Abhinav Kumar" Date: Fri, 4 Sep 2009 05:14:51 -0400 Sent to CCL by: "Abhinav Kumar" [abhinavmarshal_+_gmail.com] I want to calculate energies for Hg..S and Hg..N interactions in my molecules using G03W package. For this I used the term counterpoise=2 for assining two molecules in the XYZ coordinate and optimizing geometry. But I want to freeze some atoms (especially Hg, N and S) and leaving rest of the atoms in variable phase. I don't how to do this? Abhinav Kumar abhinavmarshal(0)gmail.com Department of Chemistry Faculty of Science Lucknow University Lucknow 226 007 India From owner-chemistry@ccl.net Fri Sep 4 09:41:00 2009 From: "Juan Beltran beltranj[A]averell.umh.ac.be" To: CCL Subject: CCL:G: How Gausssum obtains the absorption coefficient from Gaussian? Message-Id: <-40165-090904082840-27476-DkToLcB/I+VVYZFo9dqjsA(~)server.ccl.net> X-Original-From: "Juan Beltran" Date: Fri, 4 Sep 2009 08:28:37 -0400 Sent to CCL by: "Juan Beltran" [beltranj#,#averell.umh.ac.be] Dear CCL community, I am using Gaussian03 to TDDFT calculate the absorption spectra of some metal transition complexes. I plot such simulated spectra with Gausssum which provides the absorption coefficient, besides the oscillator strength, versus the wavelength of the excitation state. I am particularly interested to know which expression is used by Gausssum to obtain the absorption coefficient from the parameters that can be read from a Gaussian calculation. Thank you and best regards, Juan From owner-chemistry@ccl.net Fri Sep 4 10:14:00 2009 From: "Abhinav Kumar abhinavmarshal]|[gmail.com" To: CCL Subject: CCL: Composition of Molecular orbital Message-Id: <-40166-090904093738-30082-SKFtHg0cfiMWpM46Yk+oGw#server.ccl.net> X-Original-From: "Abhinav Kumar" Date: Fri, 4 Sep 2009 09:37:34 -0400 Sent to CCL by: "Abhinav Kumar" [abhinavmarshal{=}gmail.com] How I can asses the exact composition of molecular orbital in a TD-DFT calculation. Abhinav Kumar abhinavmarshal++gmail.com Department of Chemistry Faculty of Science Lucknow University Lucknow 226 007 India From owner-chemistry@ccl.net Fri Sep 4 10:54:01 2009 From: "Serge Gorelsky gorelsky..gmail.com" To: CCL Subject: CCL: Composition of Molecular orbital Message-Id: <-40167-090904103053-11464-T08lkNJdpyCC7L2T68jD7A(_)server.ccl.net> X-Original-From: Serge Gorelsky Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8 Date: Fri, 4 Sep 2009 10:30:38 -0400 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky_+_gmail.com] Please check the AOMix manual (http://www.sg-chem.net/aomix/AOMix-manual.pdf) - it provides the description about how to assess compositions of molecular orbitals. S.G. On Fri, Sep 4, 2009 at 9:37 AM, Abhinav Kumar abhinavmarshal]|[gmail.com wrote: > > Sent to CCL by: "Abhinav =C2=A0Kumar" [abhinavmarshal{=3D}gmail.com] > How I can asses the exact composition of molecular orbital in a TD-DFT ca= lculation. > > Abhinav Kumar > abhinavmarshal|a|gmail.com > Department of Chemistry > Faculty of Science > Lucknow University > Lucknow 226 007 > India > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/chemistry/sub_unsub.shtml> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt> > > --=20 Best regards, Serge Gorelsky From owner-chemistry@ccl.net Fri Sep 4 11:27:00 2009 From: "Naser Eltaher Eltayeb nasertaha90_-_yahoo.co.uk" To: CCL Subject: CCL: NMR error Message-Id: <-40168-090904103900-17590-7jq+J5JjBhj9qQY+IcucEw^server.ccl.net> X-Original-From: "Naser Eltaher Eltayeb" Date: Fri, 4 Sep 2009 10:38:56 -0400 Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90 * yahoo.co.uk] Dear All I run NMR calculations using DFT, the calculations finnished normally, without any errors. But I tried to open the output file using Gaussview to visullize the spectrum I got error. below the message of error: "CConnectionGLOG::Parse_GLOG() Failure reading NMR data Last line read = 2037" Anyone encounter this error before? Naser From owner-chemistry@ccl.net Fri Sep 4 16:17:00 2009 From: "Henry Martinez hmartine]_[gmail.com" To: CCL Subject: CCL:G: Transition state calculation Message-Id: <-40169-090904161543-26686-q7C/zwcO/cNcAK+VuC6ggA:-:server.ccl.net> X-Original-From: "Henry Martinez" Date: Fri, 4 Sep 2009 16:15:40 -0400 Sent to CCL by: "Henry Martinez" [hmartine**gmail.com] I am trying to calculate what seems to be a very simple Transition state calculation, but I always get the same error, can anybody tell me a good way to calculate transition states in general. Thanks this is what I a doing # opt=(calcall,ts) freq geom=connectivity This is what I always get Error termination request processed by link 9999. Error termination via Lnk1e in c:\program files\g03w\l9999.exe at Sun Aug 23 18:38:45 2009. thanks a lot From owner-chemistry@ccl.net Fri Sep 4 18:37:01 2009 From: "veronica ferraresi veroferraresi[]gmail.com" To: CCL Subject: CCL:G: Transition state calculation Message-Id: <-40170-090904183526-15537-8oeRABVyR67Lym2/yE0SqA:+:server.ccl.net> X-Original-From: veronica ferraresi Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 4 Sep 2009 19:35:11 -0300 MIME-Version: 1.0 Sent to CCL by: veronica ferraresi [veroferraresi++gmail.com] It might be that you need to increase the SCF cycles SCF(maxcyc=3D1000) Ver=F3nica. 2009/9/4 Henry Martinez hmartine]_[gmail.com : > > Sent to CCL by: "Henry Martinez" [hmartine**gmail.com] > I am trying to calculate what seems to be a very simple Transition state = calculation, but I always get the same error, can anybody tell me a good wa= y to calculate transition states in general. > Thanks > > this is what I a doing > # opt=3D(calcall,ts) freq geom=3Dconnectivity > > This is what I always get > > Error termination request processed by link 9999. > Error termination via Lnk1e in c:\program files\g03w\l9999.exe at Sun Au= g 23 18:38:45 2009. > > > thanks a lot > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > From owner-chemistry@ccl.net Fri Sep 4 19:28:00 2009 From: "Ron Salesky rsalesky.:.unm.edu" To: CCL Subject: CCL: VMD SWCNT .psf generation question Message-Id: <-40171-090904171304-23472-pYhTgfGoItD5b5LZiOwvhQ _ server.ccl.net> X-Original-From: "Ron Salesky" Date: Fri, 4 Sep 2009 17:13:00 -0400 Sent to CCL by: "Ron Salesky" [rsalesky|-|unm.edu] Hello, I've generated a SWCNT .pdb coordinate file using the VMD nanotube generator plug-in. Auto generating the .psf file runs into problems because the residue name in the .pdb file is "CNT". Does anyone have a recommendation for a residue name that is appropriate for a C bonded as a SWCNT (rolled up graphene) configuration? Thanks! Ron From owner-chemistry@ccl.net Fri Sep 4 21:56:00 2009 From: "Morad El-Hendawy m80elhendawy%%yahoo.com" To: CCL Subject: CCL:G: Transition state calculation Message-Id: <-40172-090904212729-15775-pHZjM1MD3nrg5jtt5OusFg[]server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-460955360-1252112428=:48856" Date: Fri, 4 Sep 2009 18:00:28 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy[-]yahoo.com] --0-460955360-1252112428=:48856 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sir, This problem is due to error in termination the final steps of optimization= . There are two solutions for your problem: 1- Take the xyz coordinate from the standard orientation from output file t= hen put it in molecular specification then run your calculation. Or 2- Another way, restart your calculation from check point file and add thes= e keywords: GDIIS, NOEIGEN, XQC. My regards=20 ***************************************************************************= ***********************Morad M. El-Hendawy, IRELAND ***************************************************************************= ***********************=A0If you want a happy life, do four things:=A01- Co= ntemplate and be thankful, 2- The past is gone forever, 3- Today all that you have, 4- Leave the future alone untill it come.=A0*******************************= ***************************************************************************= ********* =A0 --- On Sat, 9/5/09, veronica ferraresi veroferraresi[]gmail.com wrote: > From: veronica ferraresi veroferraresi[]gmail.com Subject: CCL:G: Transition state calculation To: "El-Hendawy, Morad Metwally " Date: Saturday, September 5, 2009, 12:35 AM Sent to CCL by: veronica ferraresi [veroferraresi++gmail.com] It might be that you need to increase the SCF cycles SCF(maxcyc=3D1000) Ver=F3nica. 2009/9/4 Henry Martinez hmartine]_[gmail.com : > > Sent to CCL by: "Henry=A0 Martinez" [hmartine**gmail.com] > I am trying to calculate what seems to be a very simple Transition state = calculation, but I always get the same error, can anybody tell me a good wa= y to calculate transition states in general. > Thanks > > this is what I a doing > # opt=3D(calcall,ts) freq geom=3Dconnectivity > > This is what I always get > >=A0 Error termination request processed by link 9999. >=A0 Error termination via Lnk1e in c:\program files\g03w\l9999.exe at Sun = Aug 23 18:38:45 2009. > > > thanks a lot > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0=A0 =A0 =A0=A0 =A0 =A0=0A=0A=0A --0-460955360-1252112428=:48856 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Sir,
This problem is due to error in = termination the final steps of optimization. There are two solutions for yo= ur problem:
1- Take the xyz coordinate from the standard orientation fro= m output file then put it in molecular specification then run your calculat= ion.
Or
2- Another way, restart your calculation from check point fil= e and add these keywords: GDIIS, NOEIGEN, XQC.
My regards

<= strong>****************= ***************************************************************************= *******
Morad M. El-Hendawy,
IRELAND
**********************************************************= ****************************************
=  If you want a happy life, do four things:
 
1- Contemplate and be thankful= ,
2- The past is gone forever,
3- Today all tha= t you have,
4- Leave the future alone untill it come. 
********************= ***************************************************************************= ********************

 =


--- On S= at, 9/5/09, veronica ferraresi veroferraresi[]gmail.com <owner-chemis= try/./ccl.net> wrote:

From: veroni= ca ferraresi veroferraresi[]gmail.com <owner-chemistry/./ccl.net>
Subject: CCL:G= : Transition state calculation
To: "El-Hendawy, Morad Metwally "= <m80elhendawy/./yahoo.com>
Date: Saturday, September 5, 2009, 12:35= AM


Sent to CCL by: veronica ferraresi = [veroferraresi++gmail.com]
It might be that you need to increase the SCF= cycles
SCF(maxcyc=3D1000)
Ver=F3nica.

2009/9/4 Henry Martinez= hmartine]_[gmail.com <owner-chemistry#%#ccl.net>:
>
> Se= nt to CCL by: "Henry  Martinez" [hmartine**gmail.com]
> I am try= ing to calculate what seems to be a very simple Transition state calculatio= n, but I always get the same error, can anybody tell me a good way to calcu= late transition states in general.
> Thanks
>
> this is w= hat I a doing
> # opt=3D(calcall,ts) freq geom=3Dconnectivity
>=
> This is what I always get
>
>  Error termination request processed by link 9999.
>  Error termination via Lnk1e = in c:\program files\g03w\l9999.exe at Sun Aug 23 18:38:45 2009.
>
= >
> thanks a lot
>
>
>
> -=3D This is auto= matically added to each message by the mailing script =3D->
>
&= gt;



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