From owner-chemistry@ccl.net Thu May 27 00:37:00 2010 From: "sina rastegar sina_rastegar1979*_*yahoo.com" To: CCL Subject: CCL:G: nbo analysis Message-Id: <-41997-100527003449-32010-IT5yU+aQlyxYptlx98PlNA=-=server.ccl.net> X-Original-From: "sina rastegar" Date: Thu, 27 May 2010 00:34:48 -0400 Sent to CCL by: "sina rastegar" [sina_rastegar1979,yahoo.com] In nbo analysis I have 9 warnings which shows 9 low occupancy in core orbiyals.after which inversion of nbo labels with bd occurs. WARNING: 1 low occupancy (<0.9990e) core orbital found on B 7 1 low occupancy (<0.9990e) core orbital found on B 8 1 low occupancy (<0.9990e) core orbital found on B10 1 low occupancy (<0.9990e) core orbital found on B12 1 low occupancy (<0.9990e) core orbital found on B16 1 low occupancy (<0.9990e) core orbital found on B17 1 low occupancy (<0.9990e) core orbital found on B19 1 low occupancy (<0.9990e) core orbital found on B20 1 low occupancy (<0.9990e) core orbital found on Na21 --- Apparent excited state configuration --- The following "inverted" NBO labels reflect the actual hybrid overlap: NBO 432 has been relabelled BD NBO 442 has been relabelled BD NBO 450 has been relabelled BD Unable to label the NBOs properly: 64 unstarred orbitals 61 occupied orbitals Error Error termination via Lnk1e in /root/g03/l607.exe at Thu May 27 14:41:42 2010. Job cpu time: 0 days 1 hours 19 minutes 32.4 seconds. File lengths (MBytes): RWF= 209 Int= 0 D2E= 0 Chk= 23 Scr= 1 I would appreciate your suggestions. Also I use GenNBO.5 and I could not find free NBOview or any free orbital viewer software.could anybody introduce a software or a link for free download? with my best regards to ccl.net & all subscribers. From owner-chemistry@ccl.net Thu May 27 02:17:01 2010 From: "Simmie, John john.simmie[a]nuigalway.ie" To: CCL Subject: CCL:G: Reaction rate software Message-Id: <-41998-100526101841-5952-dWCGBnZuHzYd13yVFqurZQ#server.ccl.net> X-Original-From: "Simmie, John" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 May 2010 15:18:36 +0100 MIME-Version: 1.0 Sent to CCL by: "Simmie, John" [john.simmie[a]nuigalway.ie] >>Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis:-:borealisgroup.com] >>Hello >>Can anybody suggest a user freindly program that can caclulate reaction rates from files (products, >>reactants and TS)that have been obtained from Gaussian? >>thanks a lot in advance >>Thomas Gkourmpis Thomas: The answer depends very much what you mean by calculating reaction rates and the complexity or otherwise of your system but in terms of user-friendliness I would recommend CHEMRATE CPS [soft^^^chemrate.com] which does interface quite nicely with Gaussian. Unfortunately although all the requisite information is potentially available in outputs from Gaussian, Gamess, Molpro, etc no-one has designed a "Kinetics" button which when clicked spits out reaction rate data. Emeritus Professor John Simmie::Combustion Chemistry Centre::National University of Ireland, Galway work:+353-91-492451::mobile:+353-87-805-9948 From owner-chemistry@ccl.net Thu May 27 02:51:00 2010 From: "Pascal Muller pascal.jm.muller*gmail.com" To: CCL Subject: CCL: 3D structure generator Message-Id: <-41999-100527022621-9516-BN0hQIvIHpz6NO4f/akd6A^-^server.ccl.net> X-Original-From: Pascal Muller Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 27 May 2010 08:26:15 +0200 MIME-Version: 1.0 Sent to CCL by: Pascal Muller [pascal.jm.muller^_^gmail.com] Hi, > FROG code is planned to be fused into OpenBabel - and that would be nice > indeed. Yes, OpenBabel can now generate 3D coordinates. Option --gen3D. babel --gen3D molec.smi molec.sdf I didn't try it on large scale though. Seems time consuming. Regards, Pascal From owner-chemistry@ccl.net Thu May 27 05:35:00 2010 From: "Thomas Gkourmpis thomas.gkourmpis_+_borealisgroup.com" To: CCL Subject: CCL:G: Reaction Rate Software Message-Id: <-42000-100527053326-24045-vO+RWnsOp0lBm3nJcojs+Q{=}server.ccl.net> X-Original-From: "Thomas Gkourmpis" Date: Thu, 27 May 2010 05:33:24 -0400 Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis ~ borealisgroup.com] Thanks a lot for the answer. I'm trying to make a bit more clear what I am looking for. When I get the results from Gaussian I can calculate without any problem the activation energy, but the pre-exponential factor in the Arrhenius equation is more tricky. In order to get the information I need the partition functions that are stored somewhere in the Gaussian output. That's why I need the program. Alternatively if someone knows how to extract that information manually from the relevant files I'm happy to listen. I hope this makes it a bit more clear now. Thanks a lot in advance Thomas Gkourmpis From owner-chemistry@ccl.net Thu May 27 07:36:00 2010 From: "Reinaldo Pis Diez reinaldo.pisdiez=gmail.com" To: CCL Subject: CCL:G: Reaction Rate Software Message-Id: <-42001-100527073318-14101-vOmPpP6GxNqDAzwcAwuqhw() server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Type: multipart/alternative; boundary=0016e6d77f113f4cfb048791c17a Date: Thu, 27 May 2010 08:33:08 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [reinaldo.pisdiez_+_gmail.com] --0016e6d77f113f4cfb048791c17a Content-Type: text/plain; charset=ISO-8859-1 Dear Thomas, You can find the partition functions at 298 K (and 1 atm) after the list of thermal corrections to the electronic energy and the different contributions to the internal energy, Cv and the entropy in a frequency job output. In any case, you have all the information at hand to write a simple code to calculate them: you need the inertia moment and the normal modes only as the translational and electronic contributions are rather trivial. Hope this helps. Regards, Reinaldo 2010/5/27 Thomas Gkourmpis thomas.gkourmpis_+_borealisgroup.com < owner-chemistry ~~ ccl.net> > > Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis ~ borealisgroup.com] > Thanks a lot for the answer. > > I'm trying to make a bit more clear what I am looking for. When I get the > results from Gaussian I can calculate without any problem the activation > energy, but the pre-exponential factor in the Arrhenius equation is more > tricky. In order to get the information I need the partition functions that > are stored somewhere in the Gaussian output. That's why I need the program. > Alternatively if someone knows how to extract that information manually from > the relevant files I'm happy to listen. > > I hope this makes it a bit more clear now. > > Thanks a lot in advance > > Thomas Gkourmpis> > > --0016e6d77f113f4cfb048791c17a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Thomas,

You can find the partition functions at 298 K (and 1 at= m) after the list of thermal corrections to the electronic energy and the d= ifferent contributions to the internal energy, Cv and the entropy in a freq= uency job output. In any case, you have all the information at hand to writ= e a simple code to calculate them: you need the inertia moment and the norm= al modes only as the translational and electronic contributions are rather = trivial.
Hope this helps.
Regards,

Reinaldo

2010/5/27 Thomas Gkourmpis thomas.gkourmpis_+_borealisgroup.com <owner-chemistry ~~ ccl.net>

Sent to CCL by: "Thomas =A0Gkourmpis" [thomas.gkourmpis ~ borealisgroup.com]
Thanks a lot for the answer.

I'm trying to make a bit more clear what I am looking for. When I get t= he results from Gaussian I can calculate without any problem the activation= energy, but the pre-exponential factor in the Arrhenius equation is more t= ricky. In order to get the information I need the partition functions that = are stored somewhere in the Gaussian output. That's why I need the prog= ram. Alternatively if someone knows how to extract that information manuall= y from the relevant files I'm happy to listen.

I hope this makes it a bit more clear now.

Thanks a lot in advance

Thomas Gkourmpis



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--0016e6d77f113f4cfb048791c17a-- From owner-chemistry@ccl.net Thu May 27 10:07:00 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= uekstrom/./gmail.com" To: CCL Subject: CCL: Different single-point DFT energy between GAMESS and Gaussian Message-Id: <-42002-100527041945-23503-RsUCIPoDAgb6kyAJv6+kWw()server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 27 May 2010 10:19:39 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [uekstrom ~ gmail.com] Dear Piotr, you should be aware that the common grid generation schemes will not allow you to reach arbitrary accuracy. For a single atom you can always improve the results by using a bigger grid, but due to the way the molecular grid is commonly constructed from atomic grids this is not possible for molecules. This is different from a plane wave code where you in principle can reach unlimited precision just by decreasing the grid spacing (and increasing the energy cutoff). I know that there is active research in this area, but I can't immediately find any good references. If you want to exactly reproduce dft energies you need to export the grid from one of your codes and use it in the other code. Then there is only the issue of the parameters in the DFT implementations, but these are usually more reliable. I recently reimplemented a couple of xc functionals, and found relative differences of 1e^-8 between differen= t implementations. Regards, Ulf Ekstr=F6m, VU University Amsterdam From owner-chemistry@ccl.net Thu May 27 10:43:00 2010 From: "Bruno Villoutreix bruno.villoutreix..gmail.com" To: CCL Subject: CCL: 3D structure generator Message-Id: <-42003-100527041605-8369-U7cA5+ALvnw+PwnTYsWxEA[-]server.ccl.net> X-Original-From: Bruno Villoutreix Content-Type: multipart/alternative; boundary=0016367fab6bed8fb904878eff31 Date: Thu, 27 May 2010 10:15:55 +0200 MIME-Version: 1.0 Sent to CCL by: Bruno Villoutreix [bruno.villoutreix]=[gmail.com] --0016367fab6bed8fb904878eff31 Content-Type: text/plain; charset=ISO-8859-1 Hello you now have Frog2 online with DG AMMOS and AMMOS (see last NAR web server), DG ammos and ammos with multiconf dock are also standalone sincerely BO Villoutreix On Thu, May 27, 2010 at 8:26 AM, Pascal Muller pascal.jm.muller*gmail.com < owner-chemistry]*[ccl.net> wrote: > > Sent to CCL by: Pascal Muller [pascal.jm.muller^_^gmail.com] > Hi, > > > FROG code is planned to be fused into OpenBabel - and that would be nice > > indeed. > > Yes, OpenBabel can now generate 3D coordinates. Option --gen3D. > > babel --gen3D molec.smi molec.sdf > > I didn't try it on large scale though. Seems time consuming. > > Regards, > Pascal> > > -- Dr. Bruno Villoutreix Director Inserm-Paris 7 Unit U973 Bioinformatics-Chemoinformatics President of the French Society of Chemoinformatics www.chemoinformatique.fr Bat Lamarck Building - 5eme 35 rue Helene Brion 75013 PARIS Web: www.vls3d.com Web lab: http://www.mti.univ-paris-diderot.fr/ Editor-in-Chief: Advances and Applications in Bioinformatics and Chemistry (Dove Medical Press) email: bruno.villoutreix]*[gmail.com --0016367fab6bed8fb904878eff31 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello
you now have Frog2 online with DG AMMOS and AMMOS (see last NAR we= b server), DG ammos and ammos with multiconf dock are also standalone
s= incerely
BO Villoutreix

On Thu, May 27= , 2010 at 8:26 AM, Pascal Muller pascal.jm.muller*gmail.com <owner-chemistry]*[ccl.net> wrote:

Sent to CCL by: Pascal Muller [pascal.jm.muller^_^gmail.com]
Hi,

> FROG code is planned to be fused into OpenBabel - and that would be ni= ce
> indeed.

Yes, OpenBabel can now generate 3D coordinates. Option --gen3D.

babel --gen3D molec.smi molec.sdf

I didn't try it on large scale though. Seems time consuming.

Regards,
Pascal



--
Dr. Bruno V= illoutreix
Director Inserm-Paris 7 Unit U973
Bioinformatics-Chemoinf= ormatics =A0 =A0 =A0 =A0 =A0 =A0
President of the French Society of Che= moinformatics
www.chemoinformatique.fr =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0
Bat Lamarc= k Building - 5eme =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0
35 rue= Helene Brion =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0
75013 PARIS

Web: www.vls3d.com<= br>Web lab: http://www.mt= i.univ-paris-diderot.fr/
Editor-in-Chief: Advances and Applications = in Bioinformatics and Chemistry
(Dove Medical Press)
email: bruno.villoutreix]*[gmail.com
--0016367fab6bed8fb904878eff31-- From owner-chemistry@ccl.net Thu May 27 11:18:00 2010 From: "pierre tuffery pierre.tuffery*o*univ-paris-diderot.fr" To: CCL Subject: CCL: 3D structure generator Message-Id: <-42004-100527033924-25258-brVKYB9LK4i9T6Vu71IvQQ(~)server.ccl.net> X-Original-From: pierre tuffery Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 27 May 2010 09:39:08 +0200 MIME-Version: 1.0 Sent to CCL by: pierre tuffery [pierre.tuffery*|*univ-paris-diderot.fr] FRog2 is now available at http://bioserv.rpbs.jussieu.fr/Frog2 On 05/26/2010 08:35 PM, Vincent Leroux vincent.leroux]~[loria.fr wrote: > Sent to CCL by: Vincent Leroux [vincent.leroux|a|loria.fr] > > Hi Fabio, > > You might want to read this: > > http://fiehnlab.ucdavis.edu/staff/kind/ChemoInformatics/Concepts/3D-conformer/ > > FROG code is planned to be fused into OpenBabel - and that would be nice > indeed. > Server here: http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog > > If you are from the academia you should ask for a free licence for all > OpenEye software, including Omega. > > Regards, > VL > > > Le 26/05/10 16:06, Fabio Molfetta fabioamsc . ig.com.br a écrit : > >> Sent to CCL by: "Fabio Molfetta" [fabioamsc!^!ig.com.br] >> Are there 3D structure generator programs free of charge to virtual screening? I kwown that Corina and Omega but these programs are not free.> > > > -- My present email address is: pierre.tuffery+*+univ-paris-diderot.fr My present phone: (331) 57 27 83 74 From owner-chemistry@ccl.net Thu May 27 11:52:00 2010 From: "Markus Dittrich dittrich###psc.edu" To: CCL Subject: CCL: Request for Proposals for Biomolecular Simulation Time on Anton Message-Id: <-42005-100527085511-10444-6j/ksTfeBpln1+WK5CRN+Q..server.ccl.net> X-Original-From: "Markus Dittrich" Date: Thu, 27 May 2010 08:55:08 -0400 Sent to CCL by: "Markus Dittrich" [dittrich~~psc.edu] Dear Colleagues, The National Resource for Biomedical Supercomputing (NRBSC) is now soliciting proposals for computer time on Anton, a special-purpose supercomputer for molecular dynamics simulation designed by D. E. Shaw Research (DESRES). A 512-node Anton machine will be made available without cost by DESRES for non-commercial research use by universities and other not-for-profit institutions commencing in late 2010. The machine will be hosted by NRBSC at the Pittsburgh Supercomputing Center, with funding from the National Institute of General Medical Sciences under grant RC2GM093307. To qualify for an allocation on Anton, the principal investigator must be a faculty or staff member at a U.S. academic or non-profit research institution. For more details regarding proposal submission please go to or see the attached Request for Proposals. If you have questions please contact grants|psc.edu. With best regards, NRBS From owner-chemistry@ccl.net Thu May 27 12:27:00 2010 From: "Toon Verstraelen Toon.Verstraelen a UGent.be" To: CCL Subject: CCL:G: Reaction Rate Software Message-Id: <-42006-100527090738-20447-Z5cUNZjth7Sa94RcvyHbYw(-)server.ccl.net> X-Original-From: Toon Verstraelen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 27 May 2010 15:07:29 +0200 MIME-Version: 1.0 Sent to CCL by: Toon Verstraelen [Toon.Verstraelen/a\UGent.be] On 05/27/2010 11:33 AM, Thomas Gkourmpis thomas.gkourmpis_+_borealisgroup.com wrote: > Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis ~ borealisgroup.com] > Thanks a lot for the answer. > > I'm trying to make a bit more clear what I am looking for. When I get the results from Gaussian I can calculate without any problem the activation energy, but the pre-exponential factor in the Arrhenius equation is more tricky. In order to get the information I need the partition functions that are stored somewhere in the Gaussian output. That's why I need the program. Alternatively if someone knows how to extract that information manually from the relevant files I'm happy to listen. Hi Thomas, The reaction barrier with zero point corrections is easy to compute based on numbers from the Gaussian output, but it is not the same as the activation energy. They do correlate well, but they have different definitions and are numerically not the same. Both the activation energy and the pre-exponential factor are obtained from a fit of a line (the Arrhenius law) in the ln(k) versus 1/T plot. TAMkin can do the job. More info here: http://molmod.ugent.be/code/static/doc/sphinx/tamkin/latest/index.html TAMkin is a Python library that can compute kinetic parameters and many other things related to the molecular partition function or the normal mode analysis. It interfaces with Gaussian and several other packages. It is open source, but there is an additional condition in the license that you have to cite the relevant papers when you rely (on parts of) TAMkin for (parts of) your scientific communication. I will post the reference to the general TAMkin paper as soon as it is available online. Here is an example Python script to obtain the kinetic parameters for a bimolecular reaction. The three '*.fchk' files are formatted checkpoint files of frequency jobs of the reactants and the transition state. Comment lines start with a '#' sign. > from tamkin import * # Perform normal mode analysis on the three systems. nma_react1 = NMA(load_molecule_g03fchk("aa.fchk"), ConstrainExt()) nma_react2 = NMA(load_molecule_g03fchk("aarad.fchk"), ConstrainExt()) nma_trans = NMA(load_molecule_g03fchk("paats.fchk"), ConstrainExt()) # Construct the three partition functions. pf_react1 = PartFun(nma_react1, [ExtTrans(), ExtRot()]) pf_react2 = PartFun(nma_react2, [ExtTrans(), ExtRot()]) pf_trans = PartFun(nma_trans, [ExtTrans(), ExtRot()]) # Analyze the chemical reaction. These are the arguments: # 1) a list of reactant partition functions # (one for unimolecular, two for bimolecular, ...) # 2) the transition state partition function # 3) the starting temperature for the fit # 4) the final temperature for the fit # The following are optional arguments: # 6) temp_step: The interval on the temperature grid in Kelvin, 10 is # default # 5) cp: when True, the rates are computed at constant pressure, # otherwise at constant volume (default=True) # 7) tunneling: a tunneling correction object, default is None ra = ReactionAnalysis([pf_react1, pf_react2], pf_trans, 280, 360, 10) # make the Arrhenius plot ra.plot_arrhenius("arrhenius.png") # summary of the analysis ra.write_to_file("reaction.txt") Put all these lines in a file reaction.py and execute it (after TAMkin is installed) as follows on the command line: python reaction.py Have fun! Toon From owner-chemistry@ccl.net Thu May 27 13:25:00 2010 From: "Jamin Krinsky jamink%a%berkeley.edu" To: CCL Subject: CCL:G: nbo analysis Message-Id: <-42007-100527120522-23127-MKOnjLcvikrgO1t75/TkYQ*_*server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=000feaf20b090a520e0487958ee6 Date: Thu, 27 May 2010 09:05:09 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink(a)berkeley.edu] --000feaf20b090a520e0487958ee6 Content-Type: text/plain; charset=ISO-8859-1 Hi Sina, The low core orbital occupancy warnings are common and usually can be ignored, just look sat the core orbital occupations and make sure they are all over 1.999 (in the closed-shell case). In your case NBO may be alerting you that you do not have a stable "wavefunction." After all, you need a good set of MOs to read into NBO or it won't work. I'd do a stability calculation on your structure before the NBO calc to rule that out, before spending too much time investigating the error. Re NBO visualization from gennbo output, I saw the following post recently but have not tried it myself. Credit for this obviously goes to Wenli, but I didn't see a surname on the post. Only 4.3 version of Molekel can plot NBO. Plese use my NBO2Molden program, and then plot NBO using Molden or GabEdit. http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/?C392068e53NOu-7358-1231+00.htm Wenli Regards, Jamin On Wed, May 26, 2010 at 9:34 PM, sina rastegar sina_rastegar1979*_*yahoo.com wrote: > > Sent to CCL by: "sina rastegar" [sina_rastegar1979,yahoo.com] > In nbo analysis I have 9 warnings which shows 9 low occupancy in core > orbiyals.after which inversion of nbo labels with bd occurs. > > WARNING: 1 low occupancy (<0.9990e) core orbital found on B 7 > 1 low occupancy (<0.9990e) core orbital found on B 8 > 1 low occupancy (<0.9990e) core orbital found on B10 > 1 low occupancy (<0.9990e) core orbital found on B12 > 1 low occupancy (<0.9990e) core orbital found on B16 > 1 low occupancy (<0.9990e) core orbital found on B17 > 1 low occupancy (<0.9990e) core orbital found on B19 > 1 low occupancy (<0.9990e) core orbital found on B20 > 1 low occupancy (<0.9990e) core orbital found on Na21 > > --- Apparent excited state configuration --- > The following "inverted" NBO labels reflect the actual hybrid overlap: > > NBO 432 has been relabelled BD > > NBO 442 has been relabelled BD > > NBO 450 has been relabelled BD > > Unable to label the NBOs properly: 64 unstarred orbitals > 61 occupied orbitals > Error > Error termination via Lnk1e in /root/g03/l607.exe at Thu May 27 14:41:42 > 2010. > Job cpu time: 0 days 1 hours 19 minutes 32.4 seconds. > File lengths (MBytes): RWF= 209 Int= 0 D2E= 0 Chk= 23 > Scr= 1 > > I would appreciate your suggestions. > Also I use GenNBO.5 and I could not find free NBOview or any free orbital > viewer software.could anybody introduce a software or a link for free > download? > > with my best regards to ccl.net & all subscribers.> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink _ berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --000feaf20b090a520e0487958ee6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Sina,

The low core orbital occupancy warnings are common and usua= lly can be ignored, just look sat the core orbital occupations and make sur= e they are all over 1.999 (in the closed-shell case). In your case NBO may = be alerting you that you do not have a stable "wavefunction." Aft= er all, you need a good set of MOs to read into NBO or it won't work. I= 'd do a stability calculation on your structure before the NBO calc to = rule that out, before spending too much time investigating the error.

Re NBO visualization from gennbo output, I saw the following post recen= tly but have not tried it myself. Credit for this obviously goes to Wenli, = but I didn't see a surname on the post.

Only=A04.3 version of Molekel can plot NBO.
=A0
Plese use my NBO2Molden program, and then plot NBO using Molden or=20 GabEdit.
=A0
=A0
Wenli

Regards,
Jamin
3D""


On Wed, May 26, 2010 at 9:34 PM, sina rastegar sin= a_rastegar1979*_*yahoo.com <owner-chemistry _ ccl.net> wrote:

Sent to CCL by: "sina =A0rastegar" [sina_rastegar1979,yahoo.com]
In nbo analysis I have 9 warnings which shows 9 low occupancy in core orbiy= als.after which inversion of nbo labels with bd occurs.

WARNING: =A01 low occupancy (<0.9990e) core orbital =A0found on =A0B 7 =A0 =A0 =A0 =A0 =A0 1 low occupancy (<0.9990e) core orbital =A0found on= =A0B 8
=A0 =A0 =A0 =A0 =A0 1 low occupancy (<0.9990e) core orbital =A0found on= =A0B10
=A0 =A0 =A0 =A0 =A0 1 low occupancy (<0.9990e) core orbital =A0found on= =A0B12
=A0 =A0 =A0 =A0 =A0 1 low occupancy (<0.9990e) core orbital =A0found on= =A0B16
=A0 =A0 =A0 =A0 =A0 1 low occupancy (<0.9990e) core orbital =A0found on= =A0B17
=A0 =A0 =A0 =A0 =A0 1 low occupancy (<0.9990e) core orbital =A0found on= =A0B19
=A0 =A0 =A0 =A0 =A0 1 low occupancy (<0.9990e) core orbital =A0found on= =A0B20
=A0 =A0 =A0 =A0 =A0 1 low occupancy (<0.9990e) core orbital =A0found on= Na21

=A0 =A0 =A0 =A0 =A0 --- Apparent excited state configuration ---
=A0The following "inverted" NBO labels reflect the actual hybrid = overlap:

=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 NBO 432 has been relabelled BD

=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 NBO 442 has been relabelled BD

=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 NBO 450 has been relabelled BD

=A0Unable to label the NBOs properly: =A064 unstarred orbitals
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 61= occupied orbitals
=A0Error
=A0Error termination via Lnk1e in /root/g03/l607.exe at Thu May 27 14:41:42= 2010.
=A0Job cpu time: =A00 days =A01 hours 19 minutes 32.4 seconds.
=A0File lengths (MBytes): =A0RWF=3D =A0 =A0209 Int=3D =A0 =A0 =A00 D2E=3D = =A0 =A0 =A00 Chk=3D =A0 =A0 23 Scr=3D =A0 =A0 =A01

I would appreciate your suggestions.
Also I use GenNBO.5 and I could not find free NBOview or any free orbital v= iewer software.could anybody introduce a software or a link for free downlo= ad?

with my best regards to ccl.ne= t & all subscribers.



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jamink _ berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--000feaf20b090a520e0487958ee6-- From owner-chemistry@ccl.net Thu May 27 14:28:00 2010 From: "Alavi, Saman Saman.Alavi() nrc-cnrc.gc.ca" To: CCL Subject: CCL:G: Reaction Rate Software Message-Id: <-42008-100526092458-3493-MQwEw5E67ds5F8ifYeK1aA=server.ccl.net> X-Original-From: "Alavi, Saman" Content-Language: en-CA Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 May 2010 09:20:52 -0400 MIME-Version: 1.0 Sent to CCL by: "Alavi, Saman" [Saman.Alavi]-[nrc-cnrc.gc.ca] Hi Thomas, You may want to try POLYRATE that was developed in the University of Minnes= ota. http://comp.chem.umn.edu/polyrate/ You may need to set certain options in Gaussian runs in order for all the n= ecessary data to be provided for POLYRATE. Saman ________________________________________ > From: owner-chemistry+saman.alavi=3D=3Dnrc.ca() ccl.net [owner-chemistry+sama= n.alavi=3D=3Dnrc.ca() ccl.net] On Behalf Of Thomas Gkourmpis thomas.gkourmpis= ,+,borealisgroup.com [owner-chemistry() ccl.net] Sent: May 26, 2010 8:37 AM To: Alavi, Saman Subject: CCL:G: Reaction Rate Software Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis:-:borealisgroup.com] Hello Can anybody suggest a user freindly program that can caclulate reaction rat= es from files (products, reactants and TS)that have been obtained from Gaus= sian? thanks a lot in advance Thomas Gkourmpis -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt= From owner-chemistry@ccl.net Thu May 27 22:32:00 2010 From: "majiabi majiabi=iccas.ac.cn" To: CCL Subject: CCL: a question about density distribution Message-Id: <-42009-100527212820-23040-jkhM/P79VAYS13fnbA61fA|a|server.ccl.net> X-Original-From: "majiabi" Content-Type: multipart/alternative; boundary="=====003_Dragon722842843486_=====" Date: Fri, 28 May 2010 09:30:17 +0800 Mime-Version: 1.0 Sent to CCL by: "majiabi" [majiabi() iccas.ac.cn] This is a multi-part message in MIME format. --=====003_Dragon722842843486_===== Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear All: Can anyone tell me the difference between "electron density distribution" and "spin density distribution"? Thank you in advance! 2010-05-28 majiabi Institute of Chemistry, Chinese Academy of Sciences Beijing 100190, P.R. CHINA --=====003_Dragon722842843486_===== Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: 7bit
Dear All:
     Can anyone tell me the difference between "electron density distribution" and "spin density distribution"?
 
        Thank you in advance!
 
 
 
2010-05-28
majiabi
Institute of Chemistry, Chinese Academy of Sciences 
Beijing 100190, P.R. CHINA 
 
 --=====003_Dragon722842843486_=====--