I do= n't know how to specify these=A0requirements=A0while giving NMR Input. = Is there somebody to give hand to my problem , it will helpful for me...

Advance thanks

--
SARAVANAN.I
Jr. Sci= entist Chemoinformatics

--000e0cd14b0287353004672c1c6c-- From owner-chemistry@ccl.net Fri Apr 10 09:52:01 2009 From: "Christopher Cramer cramer__umn.edu" To: CCL Subject: CCL:G: User defined functional problem Message-Id: <-39057-090410095022-29189-08zHajW8EAWB20JC7S1kBg:+:server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-1--928796917 Date: Fri, 10 Apr 2009 08:50:07 -0500 Mime-Version: 1.0 (Apple Message framework v930.4) Sent to CCL by: Christopher Cramer [cramer..umn.edu] --Apple-Mail-1--928796917 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit You used the "opt freq" option. When Gaussian launches the second job (the frequency job) it does not necessarily use all the same keywords in that job. You can check by simply looking at the output, which will show what was used. My guess is that your iops failed to be propagated forward. It will be trivial, though, to fix things as your geometry, etc., is still available. Just run the frequency as a separate job with the iops included in the keywords and you should have no trouble. (The other diagnostic, by the way, will be that the energy in the frequency will not agree with that for the last geometry of the optimization, since it is likely using pure BLYP instead of your iop specifications.) Best regards, Chris On Apr 10, 2009, at 6:26 AM, Tobias Kraemer tobiask__chem.gla.ac.uk wrote: > > Sent to CCL by: Tobias Kraemer [tobiask##chem.gla.ac.uk] > Dear CCLs > > I came accross a result obtained with Gaussian03 that I can't > explain. In order to investigate the dependence on HF exchange, I > optimised a copper complex I'm interested in, > using the "user-defined DFT model" keywords as described in the > manual (setting IOps 3/76 to 3/78 with BLYP keyword). Apart from > different values for the HF exchange parameter, > the parameters for the remaining exchange and correlation > functionals were kept constant (B3LYP values were used). > Comparing the result for the user defined functional (20% HF) > calculation, with the result for the same calculation but using the > B3LYP keyword, the former yields > exactly the same optimisation steps with same energies, and exactly > the same final geometry and energy. However, the same calculation > gives 6 negative frequencies (-197i, 196i, 195i, 127i, 93i, 29i > cm-1) for this structure. > In the 'pure' B3LYP optimisation the same structure corresponds to a > true minimum. How can the frequencies be so different although the > calculations are in fact the same (this is actually the example from > the manual). > Am I missing something here?? > > Here are my input files (the defined .chk-files are the same in both > cases, so the initial conditions are the same) > > For user-defined model: > > %NProc=4 > %mem=6000MB > %chk=cu2_N_no2tmemach_BLYP_hf-20.chk > #P UBLYP/gen IOp(3/76=1000002000) IOp(3/77=0720008000) > IOp(3/78=0810010000) opt freq gfprint gfinput pop=full guess=read > geom=check > > HF=20% > > 1 2 > > Cu N O 0 > 6-311+G(2df) > ************** > C H 0 > 6-31G* > ************** > > > For B3LYP keyword > > > %NProc=4 > %mem=6000MB > %chk=cu2_N_no2tmemach_B3LYP.chk > #P UB3LYP/gen opt freq gfprint gfinput pop=full geom=check > > HF=20% with B3LYP > > 1 2 > > Cu N O 0 > 6-311+G(2df) > ************** > C H 0 > 6-31G* > ************** > > Any ideas will be very much appreciated. Thanks. > > Tobias > > -- > ____________________________________ > > 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%x%chem.gla.ac.uk > ____________________________________ > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/sub_unsub.shtml> > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer^umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-1--928796917 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable You used the "opt freq" = option.

When Gaussian launches the second job (the = frequency job) it does not necessarily use all the same keywords in that = job. You can check by simply looking at the output, which will show what = was used. My guess is that your iops failed to be propagated forward. It = will be trivial, though, to fix things as your geometry, etc., is still = available. Just run the frequency as a separate job with the iops = included in the keywords and you should have no trouble. (The other = diagnostic, by the way, will be that the energy in the frequency will = not agree with that for the last geometry of the optimization, since it = is likely using pure BLYP instead of your iop = specifications.)

Best = regards,

Chris

On Apr 10, 2009, at 6:26 AM, Tobias Kraemer tobiask__chem.gla.ac.uk = wrote:

Sent to CCL by: Tobias Kraemer = [tobiask##chem.gla.ac.uk]
Dear CCLs

I came accross a result = obtained with Gaussian03 that I can't explain. In order to investigate = the dependence on HF exchange, I optimised a copper complex I'm = interested in,
using the "user-defined DFT model" keywords as = described in the manual (setting IOps 3/76 to 3/78 with BLYP keyword). = Apart from different values for the HF exchange parameter,
the = parameters for the remaining exchange and correlation functionals were = kept constant (B3LYP values were used).
Comparing the result for the = user defined functional (20% HF) calculation, with the result for the = same calculation but using the B3LYP keyword, the former = yields
exactly the same optimisation steps with same energies, and = exactly the same final geometry and energy. However, the same = calculation gives 6 negative frequencies (-197i, 196i, 195i, 127i, 93i, = 29i cm-1) for this structure.
In the 'pure' B3LYP optimisation the = same structure corresponds to a true minimum. How can the frequencies be = so different although the calculations are in fact the same (this is = actually the example from the manual).
Am I missing something = here??

Here are my input files (the defined .chk-files are the = same in both cases, so the initial conditions are the same)

For = user-defined = model:

%NProc=3D4
%mem=3D6000MB
%chk=3Dcu2_N_no2tmemach_BLYP_= hf-20.chk
#P UBLYP/gen IOp(3/76=3D1000002000) IOp(3/77=3D0720008000) = IOp(3/78=3D0810010000) opt freq gfprint gfinput pop=3Dfull guess=3Dread = geom=3Dcheck

HF=3D20%

1 2

Cu N O =       0
6-311+G(2df)
**************C H =          0
6-31G*
*****= *********

For B3LYP = keyword

%NProc=3D4
%mem=3D6000MB
%chk=3Dcu2_N_no2tmemach_= B3LYP.chk
#P UB3LYP/gen opt freq gfprint gfinput pop=3Dfull = geom=3Dcheck

HF=3D20% with B3LYP

1 2

Cu N O =       0
6-311+G(2df)
**************C H =          0
6-31G*
*****= *********

Any ideas will be very much appreciated. = Thanks.

Tobias

-- =
____________________________________

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%x%chem.gla.ac.uk
____________________________________

-=3D This is automatically added to each message by the 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
look up the X-Original-From: line in the mail = header.

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<= /div>

Christopher J. Cramer

University of = Minnesota

207 Pleasant St. SE

Minneapolis, MN = 55455-0431

Phone: (612) 624-0859 || = FAX: (612) = 626-2006

cramer^umn.edu

http://pollux.chem.umn.edu/~cr= amer

of Computational = Chemistry: Theories and Models, = 2nd Edition")

= --Apple-Mail-1--928796917-- From owner-chemistry@ccl.net Fri Apr 10 12:55:01 2009 From: "Geoff Skillman skillman##eyesopen.com" To: CCL Subject: CCL: Invitation to Participate in SAMPL09 Message-Id: <-39058-090408163129-31968-t2dkCZuhhBM8+vzdYhEGuw/./server.ccl.net> X-Original-From: "Geoff Skillman" Date: Wed, 8 Apr 2009 16:31:25 -0400 Sent to CCL by: "Geoff Skillman" [skillman*_*eyesopen.com] On the heels of the publication of a special issue of J. Phys. Chem. B highlighting the results of SAMPL-1 (http://pubs.acs.org/toc/jpcbfk/113/14), we would like to invite you to participate in SAMPL-09. We expect this year's evaluation to be another great learning experience for those interested in improving solvation models and aqueous-phase simulations. SAMPL is an annual blinded evaluation of computational methods. This year, we are focusing on the prediction of transfer energies and tautomer ratios. We are pleased to have Peter Guthrie, University of Western Ontario, and Peter Taylor, Astra-Zeneca, retired, to curate the transfer energy and tautomer data sets respectively this year. The SAMPL challenge will allow you to make computational predictions on unpublished and obscure data compounds that are unlikely to have been part of any algorithms parameterization set. Further, many of the compounds have been selected to be pharmaceutically relevant, yet accessible to current approaches. This years data sets include compounds from three different categories: unknown, explanatory and investigatory. Unknown compounds have known but not generally available experimental values. Explanatory compounds have unexpected or interesting experimental values included and we hope you will be able to shed light on the physical processes responsible for the unusual values. Finally, the investigatory compounds have no known experimental measurements, yet are of particular theoretical interest. Together we hope each set will provide insights and spur discussions regarding the differing approaches for calculating the relevant physical properties. We will convene the SAMPL workshop in Montreal on June 18th and 19th at McGill University to discuss the computational prediction of physical properties including transfer energies and tautomer ratios. Topics will include this years predictions as well as methodologies, experimental techniques and future prediction challenges. Complete workshop details can be found at the sampl web site. We will do our best to accommodate all SAMPL participants who would like to speak at the workshop. Non-participants interested in presenting should email abstracts to sampl .. eyesopen.com by May 25th. If you are interested, please visit http://sampl.eyesopen.com to sign up and download one or more of the data sets. The transfer energies and tautomer ratios data sets are available now and the deadline for submission is May 18, 2009. Please feel free to extend this invitation to any of your colleagues. Best regards, Matt Geballe, Geoff Skillman & Anthony Nicholls, OpenEye Scientific Software Peter Guthrie, University of Western Ontario Peter Taylor, Astra Zeneca, retired From owner-chemistry@ccl.net Fri Apr 10 14:41:01 2009 From: "Mauricio Esguerra esguerra**rci.rutgers.edu" To: CCL Subject: CCL: Web Version of 3DNA for Analisis, Reconstruction, and Visualization of DNA/RNA Message-Id: <-39059-090410113911-26656-UxPxIym2qY4q1JJ2ImJ25Q*o*server.ccl.net> X-Original-From: Mauricio Esguerra Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 10 Apr 2009 10:36:52 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Mauricio Esguerra [esguerra(~)rci.rutgers.edu] Dear CCL Users, We would like to announce the release of the web interface to 3DNA, w3DNA. You can find w3DNA at: http://w3dna.rutgers.edu The main versatilities of w3DNA are the reconstruction and analysis of naked, or protein complexed Nucleic Acid Structures, whether they are base-paired or single stranded. Please feel free to contact us with any questions. Guohui Zheng ghzheng]![eden.rutgers.edu Wilma K. Olson Group BioMaPS Institute Rutgers, The State University of New Jersey Phone Number: 732-445-4619