From owner-chemistry@ccl.net Fri Dec 14 04:10:01 2007 From: "andras.borosy_-_givaudan.com" To: CCL Subject: CCL: solvent models in MOPAC Message-Id: <-35848-071213151139-1213-HBLL7+//jZ2YwdhvhA0L0A : server.ccl.net> X-Original-From: andras.borosy^givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 0062B1EBC12573B0_=" Date: Thu, 13 Dec 2007 18:58:00 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy#givaudan.com This is a multipart message in MIME format. --=_alternative 0062B1EBC12573B0_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, Might conformer generation be improved (both HF and geometry) in MOPAC by = adding a solvent model like Tomasi: http://cc-ipcp.icp.ac.ru/mopac93.pdf Or anything else? Regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com --=_alternative 0062B1EBC12573B0_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

Might  conformer generation be improved (both HF and geometry) in MOPAC  by adding a solvent model like Tomasi:

http://cc-ipcp.icp.ac.ru/mopac93.pdf=

Or anything else?

Regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com
--=_alternative 0062B1EBC12573B0_=-- From owner-chemistry@ccl.net Fri Dec 14 06:06:01 2007 From: "Herbert Fruchtl herbert.fruchtl~~st-andrews.ac.uk" To: CCL Subject: CCL: origin of ab initio Message-Id: <-35849-071214043900-30169-em5pTxP4vAx7vF19ejgd+A * server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 14 Dec 2007 09:38:20 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl[]st-andrews.ac.uk] This discussion is as exciting and useless as C/Fortran or vi/emacs, but since it has started, here are my two pence worth of why using a basis set doesn't break the "ab initio" definition, by way of an analogy. We know how to get to a more complete basis set. We just can't afford to go all the way. So we choose one, and possibly a second (better) one to check how close we are. We know how to do Full CI. Can't afford that either. So we stick with some limited number of excitations, and possibly do a few test calculations with a better method to check. So, if we call HF, MP2 and CCSD ab initio, we can as well call minimal basis, vdz and vtz ab initio. There is no systematic way to make B3LYP (in the complete basis set limit) more accurate, and this is why DFT isn't ab initio. Herbert John McKelvey jmmckel:+:gmail.com wrote: > Kirk, > > Your comment is correct with respect to construction of basis sets; > however in any of the ZDO schemes, or other more elegant schemes, the > choice of basis set, the choice of post-SCF treatment, or the choice of > a DFT functional [or its construction] to get results that best > reproduce experiment is routinely done and is either semi-empirical or > purely empirical. Which term suits the best, I do not know. IMHO, > "Everybody adjusts something to get the best answer." > > Regards, > > John McKelvey > > On Dec 12, 2007 6:59 PM, Kirk Peterson kipeters-*-wsu.edu > > wrote: > > > Sent to CCL by: Kirk Peterson [kipeters-$-wsu.edu ] > > As a sidebar to this discussion, I have to strongly disagree that > basis set parameters, exponents or contraction coefficients, > use empirical data in their construction. All commonly used basis > sets, even the Pople-style sets, are generated by optimizing > exponents and contraction coefficients to minimize (ab initio) > energies of atoms and sometimes molecules. Some of the Pople-style > basis sets utilize scale factors to apply to atom-optimized exponents, > but these were based on (ab initio) molecular calculations > and not experimental data. > > regards, > > -Kirk > > On Dec 12, 2007, at 8:21 AM, Rene Fournier renef+*+yorku.ca wrote: > > > > > Sent to CCL by: Rene Fournier [renef\a/yorku.ca] > > David Craig and Robert Parr first used "ab initio" in quantum > > chemistry, > > see > > http://www.quantum-chemistry-history.com/Parr1.htm > > Near the middle of that page, Parr recounts: > > > > " Craig and I published this paper on "configuration interaction in > > benzene", where we took the pi-system and did essentially a complete > > configuration interaction calculation on it. > > > > That has some trivial historical interest in that it was there that > > the > > word, the term ab initio was introduced. Craig and Ross had computed > > everything from the start in London and I had personally computed > > everything from start in Pittsburgh. Then we compared our answers > > when we > > were finished- This involved computing of all the integrals as > best as > > they could be done and selecting the configurations to mix for the > > ground > > and exited states because there were electronic states that were of > > experimental interest and we checked our answers one against each > > other > > when we were finished. And what the paper says is, that these > > calculations > > were done ab initio by Craig and Ross and by me, independently. And > > Mulliken later said that this was the introduction of the term ab > > initio > > into quantum chemistry. In the short review that you have, I talk > > about > > this and reproduce a picture of a letter from Craig to me where he > > uses > > the term ab initio in a different context. So ab initio was > > introduced in > > the quantum chemistry by Craig in a letter to me and I put it > into the > > manuscript. That's where ab initio came from. " > > > > > > Funny thing is Parr later became a champion of Density Functional > > Theory > > and for many years (70's, 80's) DFT practitioners were often > > criticized > > for doing calculations that were not "ab initio". I think views have > > changed now; "first-principles" was introduced probably to say > > "mostly > > not empirical" but without the implications "ab initio" had acquired > > over > > the years. The term "ab initio calculation", as it's commonly used, > > very rarely refers to a calculation "devoid of empiricism", for > > example > > the choice of basis set parameters is almost always empirical, > > see discussion on > > > http://www.ccl.net/chemistry/resources/messages/2001/11/28.002-dir/index.html > > > > Rene Fournier Office: 303 Petrie > > Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 > > 4700 Keele Street, Toronto FAX: (416)-736-5936 > > Ontario, CANADA M3J 1P3 e-mail: renef*_* yorku.ca > > > > > > > On Wed, 12 Dec 2007, Christoph Etzlstorfer christoph.etzlstorfer . > > jku.at wrote: > > > >> There is a story about that in Michael J.S. Dewars biography "A > >> semiempirical life", American Chemical Society, 1992, p. 129. > >> > >> Best regards > >> > >> Christoph > >> > >> > >> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ > >> chemistry.gatech.edu : > >> > >>> > >>> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . > chemistry.gatech.edu ] > >>> Dear CCLers; > >>> I would appreciate it if anyone could tell me who used the term of > >>> "ab initio > >>> calculations" first. > >>> Thank you very much for your kind attention. > >>> > >>> Best wishes, > >>> > >>> Tommy > >>> > >>> > >>> -- > >>> Tommy Ohyun Kwon, Ph.D > >>> School of Chemistry and Biochemistry > >>> Georgia Institute of Technology > >>> Atlanta Georgia, 30332 > >>> Email: ohyun.kwon]*[chemistry.gatech.edu > > >>> > >>> > >>> > >>> -= This is automatically added to each message by the mailing > >>> script =- > >>> To recover the email address of the author of the message, please > >>> change> Conferences: http://server.ccl.net/chemistry/announcements/ > >>> conferences/ > >>> > >>> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > >>> search)> > >>> > >> > >> #################################################### > >> www.etzlstorfer.com > > >> *********************************************************** > >> Dr. Christoph Etzlstorfer Phone: *43-732-2468-8750 > >> Universitaet Linz Fax: *43-732-2468-8747 > >> A-4040 Linz E-mail: christoph.etzlstorfer,+,jku.at > > >> Austria http://www.orc.uni-linz.ac.at > >> #################################################### > >> > >> > >> > >> > >> > > > > > > > > -= This is automatically added to each message by the mailing script > > =- > > To recover the email address of the author of the message, please > > change> Conferences: http://server.ccl.net/chemistry/announcements/ > > conferences/ > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > > > > > > > > > > E-mail to subscribers: CHEMISTRY],[ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net > or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Fri Dec 14 06:55:00 2007 From: "Andreas Klamt klamt^cosmologic.de" To: CCL Subject: CCL: solvent models in MOPAC Message-Id: <-35850-071214064921-31825-10fdlFQ+i4b0B7bW1+QFKQ(~)server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 14 Dec 2007 12:49:07 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt**cosmologic.de] Dear Andras, I am not absolutely sure, which kind of improvement you are looking for. = We at COSMOlogic are doing our conformational searches for low-energy=20 conformations in gas-phase and solution since long based on AM1-gasphase = and AM1/COSMO in a locally modified version of MOPAC7. Altogether we do=20 it in a sophisitcated procedure called COSMOconf , involving an initial = molecular perception for relevant flexible bonds, potential=20 intramolecular H-bonds, ... followed by multiple AM1/MOPAC runs with=20 constraints (which are enabled in our version) and subsequent=20 constraint-released optimizations, geometry clustering, AM1/COSMO runs=20 for the lowest energy cluster representatives, and final selection of=20 the lowest energy gasphase and COSMO conformations. On top of that,=20 COSMOconf can further reduce the conformations by sigma profile=20 similarity, it can submit DFT/COSMO jobs for the low-lying MOPAC=20 conformations, and several things more. We have just released COSMOconf as a product. For a test installation=20 please contact us. Andreas andras.borosy_-_givaudan.com schrieb: > > Dear Colleagues, > > Might conformer generation be improved (both HF and geometry) in=20 > MOPAC by adding a solvent model like Tomasi: > > http://cc-ipcp.icp.ac.ru/mopac93.pdf > > Or anything else? > > Regards, > > Dr. Andr=E1s P=E9ter Borosy > Scientific Modelling Expert > Fragrance Research > Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendor= f=20 > - Switzerland > T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com=20 --=20 -------------------------------------------------------------------------= ---- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt|-|cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------= ---- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------= ---- From owner-chemistry@ccl.net Fri Dec 14 07:41:01 2007 From: "Ken W. Browne kbrowne-#-technologynetworks.net" To: CCL Subject: CCL: Virtual Discovery Conference, 23-24 Jan, Palm Springs, CA Message-Id: <-35851-071214071459-26385-VGJTCyeh4OrfszRPSnIOFQ^^^server.ccl.net> X-Original-From: "Ken W. Browne" Date: Fri, 14 Dec 2007 07:14:55 -0500 Sent to CCL by: "Ken W. Browne" [kbrowne * technologynetworks.net] The agenda for this conference is now online: https://selectbiosciences.com/conferences/VD2008/ It is co-located with "Advances in Protein Crystallography" so lots of opportunities for cross-pollination! Academics can register for just $499 and pre-docs $ 250 If you prefer a brochure there is a pdf here : https://selectbiosciences.com/conferences/files/Agendas2008/VD_APC_USA.pdf Hope to see you here! Best Wishes, Ken P.S. We are also planning a European version of this event in June and are currently accepting abstracts: http://www.selectbiosciences.com/conferences/VDE2008/ From owner-chemistry@ccl.net Fri Dec 14 08:15:00 2007 From: "John McKelvey jmmckel:-:gmail.com" To: CCL Subject: CCL: origin of ab initio Message-Id: <-35852-071214074205-9279-+P4Oqizu0q6mxmCLSFWyBQ(-)server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_766_2677250.1197636112260" Date: Fri, 14 Dec 2007 07:41:52 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel!A!gmail.com] ------=_Part_766_2677250.1197636112260 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Herbert's comments made me smile because I once started a Fortran/C discussion on the CCL list. Both the Fortran/C and this "ab initio" discussion [initiated accidentally with tongue in cheek remark] have brought forth some very useful information. There are always newcomers to computational chemistry who hopefully can benefit from these discussions. The accessibility of more and more computational programs and codes, particularly at little or no cost, and the seemingly ever increasing price performance of desktop and laptop PC's brings more and more people into the computational domain, and not all of these have the same background. These discussions are helpful to the less experienced, and and probably to some of us who have been around for a long time. Frankly, I still enjoy sitting in a library rereading some of the very earliest volumes of Theoretica Chimica Acta from the '60s, not unlike musicians who often go back to doing scales to limber up and refresh the mind and body. There is a lot to be learned at the pi-only PPP level. Cheers to all!! John McKelvey On Dec 14, 2007 4:38 AM, Herbert Fruchtl herbert.fruchtl~~st-andrews.ac.uk < owner-chemistry(0)ccl.net> wrote: > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl[]st-andrews.ac.uk] > This discussion is as exciting and useless as C/Fortran or vi/emacs, but > since it has started, here are my two pence worth of why using a basis > set doesn't break the "ab initio" definition, by way of an analogy. > > We know how to get to a more complete basis set. We just can't afford to > go all the way. So we choose one, and possibly a second (better) one to > check how close we are. > > We know how to do Full CI. Can't afford that either. So we stick with > some limited number of excitations, and possibly do a few test > calculations with a better method to check. > > So, if we call HF, MP2 and CCSD ab initio, we can as well call minimal > basis, vdz and vtz ab initio. There is no systematic way to make B3LYP > (in the complete basis set limit) more accurate, and this is why DFT > isn't ab initio. > > Herbert > > John McKelvey jmmckel:+:gmail.com wrote: > > Kirk, > > > > Your comment is correct with respect to construction of basis sets; > > however in any of the ZDO schemes, or other more elegant schemes, the > > choice of basis set, the choice of post-SCF treatment, or the choice of > > a DFT functional [or its construction] to get results that best > > reproduce experiment is routinely done and is either semi-empirical or > > purely empirical. Which term suits the best, I do not know. IMHO, > > "Everybody adjusts something to get the best answer." > > > > Regards, > > > > John McKelvey > > > > On Dec 12, 2007 6:59 PM, Kirk Peterson kipeters-*-wsu.edu > > > > wrote: > > > > > > Sent to CCL by: Kirk Peterson [kipeters-$-wsu.edu ] > > > > As a sidebar to this discussion, I have to strongly disagree that > > basis set parameters, exponents or contraction coefficients, > > use empirical data in their construction. All commonly used basis > > sets, even the Pople-style sets, are generated by optimizing > > exponents and contraction coefficients to minimize (ab initio) > > energies of atoms and sometimes molecules. Some of the Pople-style > > basis sets utilize scale factors to apply to atom-optimized > exponents, > > but these were based on (ab initio) molecular calculations > > and not experimental data. > > > > regards, > > > > -Kirk > > > > On Dec 12, 2007, at 8:21 AM, Rene Fournier renef+*+yorku.ca wrote: > > > > > > > > Sent to CCL by: Rene Fournier [renef\a/yorku.ca] > > > David Craig and Robert Parr first used "ab initio" in quantum > > > chemistry, > > > see > > > http://www.quantum-chemistry-history.com/Parr1.htm > > > Near the middle of that page, Parr recounts: > > > > > > " Craig and I published this paper on "configuration interaction > in > > > benzene", where we took the pi-system and did essentially a > complete > > > configuration interaction calculation on it. > > > > > > That has some trivial historical interest in that it was there > that > > > the > > > word, the term ab initio was introduced. Craig and Ross had > computed > > > everything from the start in London and I had personally computed > > > everything from start in Pittsburgh. Then we compared our answers > > > when we > > > were finished- This involved computing of all the integrals as > > best as > > > they could be done and selecting the configurations to mix for > the > > > ground > > > and exited states because there were electronic states that were > of > > > experimental interest and we checked our answers one against each > > > other > > > when we were finished. And what the paper says is, that these > > > calculations > > > were done ab initio by Craig and Ross and by me, independently. > And > > > Mulliken later said that this was the introduction of the term ab > > > initio > > > into quantum chemistry. In the short review that you have, I talk > > > about > > > this and reproduce a picture of a letter from Craig to me where > he > > > uses > > > the term ab initio in a different context. So ab initio was > > > introduced in > > > the quantum chemistry by Craig in a letter to me and I put it > > into the > > > manuscript. That's where ab initio came from. " > > > > > > > > > Funny thing is Parr later became a champion of Density Functional > > > Theory > > > and for many years (70's, 80's) DFT practitioners were often > > > criticized > > > for doing calculations that were not "ab initio". I think views > have > > > changed now; "first-principles" was introduced probably to say > > > "mostly > > > not empirical" but without the implications "ab initio" had > acquired > > > over > > > the years. The term "ab initio calculation", as it's commonly > used, > > > very rarely refers to a calculation "devoid of empiricism", for > > > example > > > the choice of basis set parameters is almost always empirical, > > > see discussion on > > > > > > http://www.ccl.net/chemistry/resources/messages/2001/11/28.002-dir/index.html > > > > > > Rene Fournier Office: 303 Petrie > > > Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 > > > 4700 Keele Street, Toronto FAX: (416)-736-5936 > > > Ontario, CANADA M3J 1P3 e-mail: renef*_* yorku.ca > > > > > > > > > > > On Wed, 12 Dec 2007, Christoph Etzlstorfer christoph.etzlstorfer. > > > jku.at wrote: > > > > > >> There is a story about that in Michael J.S. Dewars biography "A > > >> semiempirical life", American Chemical Society, 1992, p. 129. > > >> > > >> Best regards > > >> > > >> Christoph > > >> > > >> > > >> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ > > >> chemistry.gatech.edu : > > >> > > >>> > > >>> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . > > chemistry.gatech.edu ] > > >>> Dear CCLers; > > >>> I would appreciate it if anyone could tell me who used the term > of > > >>> "ab initio > > >>> calculations" first. > > >>> Thank you very much for your kind attention. > > >>> > > >>> Best wishes, > > >>> > > >>> Tommy > > >>> > > >>> > > >>> -- > > >>> Tommy Ohyun Kwon, Ph.D > > >>> School of Chemistry and Biochemistry > > >>> Georgia Institute of Technology > > >>> Atlanta Georgia, 30332 > > >>> Email: ohyun.kwon]*[chemistry.gatech.edu > > > > >>> > > >>> > > >>> > > >>> -= This is automatically added to each message by the mailing > > >>> script =- > > >>> To recover the email address of the author of the message, > please > > >>> change> Conferences: > http://server.ccl.net/chemistry/announcements/ > > >>> conferences/ > > >>> > > >>> Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: > > >>> search)> > > >>> > > >> > > >> #################################################### > > >> www.etzlstorfer.com > > > > >> *********************************************************** > > >> Dr. Christoph Etzlstorfer Phone: *43-732-2468-8750 > > >> Universitaet Linz Fax: *43-732-2468-8747 > > >> A-4040 Linz E-mail: christoph.etzlstorfer,+,jku.at > > > > >> Austria http://www.orc.uni-linz.ac.at > > >> #################################################### > > >> > > >> > > >> > > >> > > >> > > > > > > > > > > > > -= This is automatically added to each message by the mailing > script > > > =- > > > To recover the email address of the author of the message, please > > > change> Conferences: > http://server.ccl.net/chemistry/announcements/ > > > conferences/ > > > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > > search)> > > > > > > > > > > > > > > > > > > > > > E-mail to subscribers: CHEMISTRY],[ccl.net > > or use:> > > E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net > > or use> > Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > > > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > > > > > > > -- > Herbert Fruchtl > EaStCHEM Fellow > School of Chemistry > University of St Andrews> > > ------=_Part_766_2677250.1197636112260 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Herbert's comments made me smile because I once started a Fortran/C discussion on the CCL list.  Both the Fortran/C and this "ab initio"  discussion  [initiated accidentally with tongue in cheek remark] have brought forth some very useful information.  There are always newcomers to computational chemistry who hopefully can benefit from these discussions. 

The accessibility of more and more computational programs and codes, particularly at little or no cost, and the seemingly ever increasing price performance of desktop and laptop PC's brings more and more people into the computational domain, and not all of these have the same background.  These discussions are helpful to the less experienced, and  and probably to some of us who have been around for a long time. 

Frankly, I still enjoy sitting in a library rereading  some of the very earliest volumes of Theoretica Chimica Acta from the '60s, not unlike musicians who often go back to doing scales to limber up and refresh the mind and body.  There is a lot to be learned at the pi-only PPP level.

Cheers to all!!

John McKelvey 

On Dec 14, 2007 4:38 AM, Herbert Fruchtl herbert.fruchtl~~st-andrews.ac.uk <owner-chemistry(0)ccl.net > wrote:

Sent to CCL by: Herbert Fruchtl [herbert.fruchtl[]st- andrews.ac.uk]
This discussion is as exciting and useless as C/Fortran or vi/emacs, but
since it has started, here are my two pence worth of why using a basis
set doesn't break the "ab initio" definition, by way of an analogy.

We know how to get to a more complete basis set. We just can't afford to
go all the way. So we choose one, and possibly a second (better) one to
check how close we are.

We know how to do Full CI. Can't afford that either. So we stick with
some limited number of excitations, and possibly do a few test
calculations with a better method to check.

So, if we call HF, MP2 and CCSD ab initio, we can as well call minimal
basis, vdz and vtz ab initio. There is no systematic way to make B3LYP
(in the complete basis set limit) more accurate, and this is why DFT
isn't ab initio.

  Herbert

John McKelvey jmmckel:+:gmail.com wrote:
> Kirk,
>
> Your comment is correct with respect to construction of basis sets;
> however in any of the ZDO schemes, or other more elegant schemes, the
> choice of basis set, the choice of post-SCF treatment, or the choice of
> a DFT functional [or its construction] to get results that best
> reproduce experiment is routinely done and is either semi-empirical or
> purely empirical.  Which term suits the best, I do not know.  IMHO,
> "Everybody adjusts something to get the best answer."
>
> Regards,
>
> John McKelvey
>
> On Dec 12, 2007 6:59 PM, Kirk Peterson kipeters-*- wsu.edu
> <http://wsu.edu> <owner-chemistry],[ccl.net
> <mailto:owner-chemistry ],[ccl.net>> wrote:
>
>
>     Sent to CCL by: Kirk Peterson [kipeters-$-wsu.edu < http://wsu.edu>]
>
>     As a sidebar to this discussion, I have to strongly disagree that
>     basis set parameters, exponents or contraction coefficients,
>     use empirical data in their construction.  All commonly used basis
>     sets, even the Pople-style sets, are generated by optimizing
>     exponents and contraction coefficients to minimize (ab initio)
>     energies of atoms and sometimes molecules.  Some of the Pople-style
>     basis sets utilize scale factors to apply to atom-optimized exponents,
>     but these were based on (ab initio) molecular calculations
>     and not experimental data.
>
>     regards,
>
>     -Kirk
>
>     On Dec 12, 2007, at 8:21 AM, Rene Fournier renef+*+yorku.ca wrote:
>
>      >
>      > Sent to CCL by: Rene Fournier [renef\a/yorku.ca]
>      > David Craig and Robert Parr first used "ab initio" in quantum
>      > chemistry,
>      > see
>      > http://www.quantum-chemistry-history.com/Parr1.htm
>      > Near the middle of that page, Parr recounts:
>      >
>      > " Craig and I published this paper on "configuration interaction in
>      > benzene", where we took the pi-system and did essentially a complete
>      > configuration interaction calculation on it.
>      >
>      > That has some trivial historical interest in that it was there that
>      > the
>      > word, the term ab initio was introduced. Craig and Ross had computed
>      > everything from the start in London and I had personally computed
>      > everything from start in Pittsburgh. Then we compared our answers
>      > when we
>      > were finished- This involved computing of all the integrals as
>     best as
>      > they could be done and selecting the configurations to mix for the
>      > ground
>      > and exited states because there were electronic states that were of
>      > experimental interest and we checked our answers one against each
>      > other
>      > when we were finished. And what the paper says is, that these
>      > calculations
>      > were done ab initio by Craig and Ross and by me, independently. And
>      > Mulliken later said that this was the introduction of the term ab
>      > initio
>      > into quantum chemistry. In the short review that you have, I talk
>      > about
>      > this and reproduce a picture of a letter from Craig to me where he
>      > uses
>      > the term ab initio in a different context. So ab initio was
>      > introduced in
>      > the quantum chemistry by Craig in a letter to me and I put it
>     into the
>      > manuscript. That's where ab initio came from.  "
>      >
>      >
>      > Funny thing is Parr later became a champion of Density Functional
>      > Theory
>      > and for many years (70's, 80's) DFT practitioners were often
>      > criticized
>      > for doing calculations that were not "ab initio".  I think views have
>      > changed now;  "first-principles" was introduced probably to say
>      > "mostly
>      > not empirical" but without the implications "ab initio" had acquired
>      > over
>      > the years.  The term "ab initio calculation", as it's commonly used,
>      > very rarely refers to a calculation "devoid of empiricism", for
>      > example
>      > the choice of basis set parameters is almost always empirical,
>      > see discussion on
>      >
>     http://www.ccl.net/chemistry/resources/messages/2001/11/28.002-dir/index.html
>      >
>      >  Rene Fournier                   Office:  303 Petrie
>      >  Chemistry Dpt, York University  Phone: (416) 736 2100 Ext. 30687
>      >  4700 Keele Street,  Toronto     FAX:   (416)-736-5936
>      >  Ontario, CANADA   M3J 1P3       e-mail: renef*_* yorku.ca
>     <http://yorku.ca>
>      >
>      >
>      > On Wed, 12 Dec 2007, Christoph Etzlstorfer christoph.etzlstorfer .
>      > jku.at <http://jku.at > wrote:
>      >
>      >> There is a story about that in Michael J.S. Dewars biography "A
>      >> semiempirical life", American Chemical Society, 1992, p. 129.
>      >>
>      >> Best regards
>      >>
>      >> Christoph
>      >>
>      >>
>      >> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _
>      >> chemistry.gatech.edu <http://chemistry.gatech.edu>:
>      >>
>      >>>
>      >>> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon .
>     chemistry.gatech.edu < http://chemistry.gatech.edu>]
>      >>> Dear CCLers;
>      >>> I would appreciate it if anyone could tell me who used the term of
>      >>> "ab initio
>      >>> calculations" first.
>      >>> Thank you very much for your kind attention.
>      >>>
>      >>> Best wishes,
>      >>>
>      >>> Tommy
>      >>>
>      >>>
>      >>> --
>      >>> Tommy Ohyun Kwon, Ph.D
>      >>> School of Chemistry and Biochemistry
>      >>> Georgia Institute of Technology
>      >>> Atlanta Georgia, 30332
>      >>> Email: ohyun.kwon]*[chemistry.gatech.edu
>     < http://chemistry.gatech.edu>
>      >>>
>      >>>
>      >>>
>      >>> -= This is automatically added to each message by the mailing
>      >>> script =-
>      >>> To recover the email address of the author of the message, please
>      >>> change> Conferences: http://server.ccl.net/chemistry/announcements/
>      >>> conferences/
>      >>>
>      >>> Search Messages: http://www.ccl.net/htdig  (login: ccl, Password:
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>      >>
>      >> ####################################################
>      >>                                   www.etzlstorfer.com
>     <http://www.etzlstorfer.com>
>      >> ***********************************************************
>      >> Dr. Christoph Etzlstorfer       Phone:  *43-732-2468-8750
>      >> Universitaet Linz              Fax:    *43-732-2468-8747
>      >> A-4040 Linz               E-mail: christoph.etzlstorfer,+,jku.at
>     < http://jku.at>
>      >> Austria                   http://www.orc.uni-linz.ac.at
>      >> ####################################################
>      >>
>      >>
>      >>
>      >>
>      >>
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------=_Part_766_2677250.1197636112260-- From owner-chemistry@ccl.net Fri Dec 14 08:51:01 2007 From: "Roland Schaap rolandschaap(0)gmail.com" To: CCL Subject: CCL:G: Problems with the massage command in Gaussian 03 Message-Id: <-35853-071213082615-25597-v6lGafrV6RatJ+nivftnTA|server.ccl.net> X-Original-From: "Roland Schaap" Date: Thu, 13 Dec 2007 08:26:11 -0500 Sent to CCL by: "Roland Schaap" [rolandschaap . gmail.com] Hello, I have been running several jobs in Gaussian 03 using the massage command. All seemed to be doing fine untill one job ended in a very strange fashion, without showing an error message. The job was removed from the queu on the cluster therefore I assume it is terminated. Displayed below is the output which shows the basis sets etc. The job concerns the BSSE calculations on a 4-methylimidazole and a porphirine ring containing a magnesium, to which the imidazole is oriented (to slightly shorten the message I left out the beginning of the output). Any help or suggestions would be appreciated! ****************************************** Gaussian 03: AM64L-G03RevD.01 13-Oct-2005 8-Dec-2007 ****************************************** %NoSave %Chk=L173_B851_Cryst_BSSE1.chk %Mem=1024MB ---------------------------------------------------------------------- # BLYP/6-311++G(d,p) SCF=Tight Population=minimal density=current Mass age ---------------------------------------------------------------------- 1/30=1,38=1/1; 2/15=1,17=6,18=5,40=1/2; 3/5=4,6=6,7=1111,10=10,11=2,16=1,25=1,30=1,74=402/1,2,3; 4//1; 5/5=2,32=2,38=5/2; 6/7=2,8=2,9=2,10=2,22=-1,28=1/1; 99/5=1,9=1/99; ---------------------------------------------------------------------- BSSE Calculations on crystal structure LHis-173 coordinated to BChl-85 1, both wi ---------------------------------------------------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C 19.271 92.374 42.96 N 19.809 93.421 42.247 C 20.991 93.721 42.753 N 21.23 92.907 43.769 C 20.159 92.051 43.933 C 20.059 91.094 45.084 C 20.377 89.632 44.735 N 20.056 88.778 45.88 C 21.865 89.465 44.431 O 22.287 89.506 43.273 O 22.6928 89.27111 45.4868 Mg 19.235 94.878 40.16 N 21.263 94.917 39.705 C 21.9 93.952 39.002 C 23.258 94.272 38.815 C 23.503 95.572 39.472 C 22.189 95.883 40.023 C 21.269 92.818 38.522 C 19.957 92.396 38.574 N 18.92 93.077 39.166 C 17.735 92.338 38.931 C 18.013 91.07 38.146 C 19.486 91.139 37.961 C 16.494 92.825 39.396 C 16.303 94.009 40.131 C 14.965 94.304 40.5 C 14.184 93.246 39.963 C 15.074 92.25 39.222 N 17.235 94.935 40.538 C 16.53 95.894 41.219 C 15.17 95.588 41.254 C 17.061 97.027 41.782 C 18.371 97.411 41.751 C 18.845 98.678 42.354 C 20.332 98.694 42.065 C 20.543 97.41 41.296 N 19.393 96.689 41.14 C 18.127 99.892 41.643 C 18.879 101.217 41.51199 C 21.742 97.011 40.78099 C 21.179 98.712 43.33899 C 14.003 96.39 41.909 C 14.711 90.811 39.666 O 15.402 90.186 40.472 O 12.94 93.216 40.106 C 20.047 89.979 38.812 C 17.283 91.22 36.791 C 17.38 90.066 35.811 C 16.074 89.294 35.728 O 15.335 89.236 36.704 C 24.782 96.428 39.567 O 24.738 97.512 40.179 C 24.16 93.274 37.992 C 26.079 95.931 38.869 O 15.774 88.727 34.635 O 13.649 90.365 39.092 C 13.077 89.066 39.294 H 22.03636 92.98081 44.39635 H 20.26402 87.80184 45.64661 H 19.06072 88.87033 46.10625 H 19.77938 89.3494 43.85072 H 20.838 91.40784 45.80511 H 19.05227 91.1556 45.52526 H 18.31263 91.89481 42.77678 H 21.65525 94.50401 42.39571 H 23.60579 89.18329 45.12267 H 21.93726 92.12544 38.00359 H 22.54572 97.71577 40.99707 H 16.36618 97.6884 42.30767 H 17.68927 90.12512 38.61237 H 19.78599 91.0863 36.89885 H 19.63443 89.02342 38.44797 H 19.76052 90.12578 39.86784 H 21.14608 89.95979 38.72909 H 17.82765 92.03547 36.2898 H 16.22038 91.4621 36.9703 H 18.1649 89.37541 36.171 H 17.64241 90.45404 34.81101 H 14.9079 88.26986 34.7293 H 23.7521 93.16543 36.96922 H 24.1691 92.29113 38.4895 H 25.1847 93.66595 37.93759 H 25.89722 95.828 37.78844 H 26.3696 94.95626 39.28675 H 26.89071 96.66063 39.03823 H 20.63998 99.60071 41.51489 H 18.63088 98.75716 43.4368 H 22.24661 98.62902 43.07184 H 20.89393 97.86285 43.98091 H 21.0079 99.65762 43.88166 H 17.31342 100.14124 42.34716 H 17.76386 99.57451 40.64792 H 19.80386 101.05897 40.92952 H 19.13702 101.59442 42.51575 H 18.24002 101.95319 40.99555 H 13.94421 97.39449 41.45186 H 14.1876 96.4894 42.9943 H 13.063 95.862 41.747 H 14.94568 92.13178 38.1348 H 12.81024 88.94419 40.35099 H 13.80869 88.29496 39.0094 H 12.17464 88.96204 38.67326 Symmetry turned off by external request. Stoichiometry C41H45MgN7O8 Framework group C1[X(C41H45MgN7O8)] Deg. of freedom 300 Full point group C1 Z-Matrix orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 19.271000 92.374001 42.960000 2 7 0 19.808999 93.421001 42.247000 3 6 0 20.990999 93.721001 42.753000 4 7 0 21.230001 92.907001 43.769000 5 6 0 20.159001 92.051001 43.933000 6 6 0 20.059001 91.094001 45.084000 7 6 0 20.377000 89.632001 44.734999 8 7 0 20.056001 88.778001 45.879998 9 6 0 21.865000 89.465001 44.430999 10 8 0 22.287000 89.506001 43.272999 11 8 0 22.692801 89.271109 45.486803 12 12 0 19.234999 94.878001 40.160000 13 7 0 21.262999 94.917001 39.704999 14 6 0 21.899999 93.952001 39.001999 15 6 0 23.257999 94.272002 38.814998 16 6 0 23.502999 95.572002 39.471997 17 6 0 22.188999 95.883001 40.022999 18 6 0 21.268999 92.818001 38.521999 19 6 0 19.957000 92.396001 38.574000 20 7 0 18.920000 93.077000 39.166000 21 6 0 17.735000 92.338000 38.931000 22 6 0 18.012999 91.070000 38.146000 23 6 0 19.485999 91.139001 37.961000 24 6 0 16.494000 92.825000 39.396000 25 6 0 16.303000 94.009001 40.131000 26 6 0 14.965000 94.304001 40.500001 27 6 0 14.184000 93.246001 39.963001 28 6 0 15.074000 92.250000 39.222001 29 7 0 17.235000 94.935001 40.537999 30 6 0 16.529999 95.894001 41.218999 31 6 0 15.169999 95.588001 41.254000 32 6 0 17.061000 97.027001 41.781999 33 6 0 18.371000 97.411001 41.750998 34 6 0 18.845001 98.678001 42.353998 35 6 0 20.332001 98.694000 42.064995 36 6 0 20.543000 97.410000 41.295996 37 7 0 19.393000 96.689000 41.139998 38 6 0 18.127001 99.892001 41.642998 39 6 0 18.879001 101.217000 41.511995 40 6 0 21.741998 97.011001 40.780995 41 6 0 21.179003 98.712001 43.338995 42 6 0 14.002999 96.390001 41.908999 43 6 0 14.711000 90.811001 39.666002 44 8 0 15.402000 90.186001 40.472001 45 8 0 12.940000 93.216001 40.106001 46 6 0 20.046999 89.979001 38.811999 47 6 0 17.282999 91.220000 36.791000 48 6 0 17.379999 90.066000 35.811000 49 6 0 16.073998 89.294001 35.728000 50 8 0 15.334998 89.236001 36.704000 51 6 0 24.781998 96.428002 39.566996 52 8 0 24.737999 97.512002 40.178996 53 6 0 24.159999 93.274002 37.991997 54 6 0 26.078998 95.931002 38.868997 55 8 0 15.773998 88.727000 34.635000 56 8 0 13.648999 90.365001 39.092002 57 6 0 13.076999 89.066000 39.294002 58 1 0 22.036365 92.980806 44.396346 59 1 0 20.264019 87.801838 45.646613 60 1 0 19.060718 88.870326 46.106245 61 1 0 19.779380 89.349398 43.850724 62 1 0 20.838005 91.407837 45.805111 63 1 0 19.052273 91.155596 45.525263 64 1 0 18.312631 91.894815 42.776782 65 1 0 21.655253 94.504015 42.395712 66 1 0 23.605791 89.183286 45.122674 67 1 0 21.937258 92.125442 38.003592 68 1 0 22.545715 97.715768 40.997069 69 1 0 16.366180 97.688397 42.307672 70 1 0 17.689271 90.125120 38.612370 71 1 0 19.785994 91.086298 36.898852 72 1 0 19.634432 89.023422 38.447970 73 1 0 19.760517 90.125785 39.867837 74 1 0 21.146080 89.959790 38.729087 75 1 0 17.827653 92.035466 36.289797 76 1 0 16.220378 91.462103 36.970298 77 1 0 18.164896 89.375412 36.171000 78 1 0 17.642407 90.454039 34.811010 79 1 0 14.907896 88.269862 34.729299 80 1 0 23.752104 93.165433 36.969222 81 1 0 24.169100 92.291131 38.489500 82 1 0 25.184703 93.665949 37.937587 83 1 0 25.897221 95.827995 37.788439 84 1 0 26.369598 94.956258 39.286750 85 1 0 26.890708 96.660629 39.038230 86 1 0 20.639979 99.600714 41.514887 87 1 0 18.630877 98.757156 43.436798 88 1 0 22.246608 98.629020 43.071840 89 1 0 20.893933 97.862851 43.980912 90 1 0 21.007902 99.657617 43.881661 91 1 0 17.313421 100.141242 42.347155 92 1 0 17.763863 99.574508 40.647920 93 1 0 19.803863 101.058973 40.929524 94 1 0 19.137023 101.594420 42.515747 95 1 0 18.240023 101.953192 40.995547 96 1 0 13.944210 97.394490 41.451860 97 1 0 14.187603 96.489402 42.994300 98 1 0 13.062999 95.862000 41.746999 99 1 0 14.945676 92.131782 38.134799 100 1 0 12.810237 88.944195 40.350985 101 1 0 13.808685 88.294955 39.009401 102 1 0 12.174645 88.962037 38.673256 --------------------------------------------------------------------- Rotational constants (GHZ): 0.0482690 0.0340364 0.0299106 Standard basis: 6-311++G(d,p) (5D, 7F) The nuclear charge for atom 1 has been changed to Z= 0 0.000000 The nuclear charge for atom 2 has been changed to Z= 0 0.000000 The nuclear charge for atom 3 has been changed to Z= 0 0.000000 The nuclear charge for atom 4 has been changed to Z= 0 0.000000 The nuclear charge for atom 5 has been changed to Z= 0 0.000000 The nuclear charge for atom 6 has been changed to Z= 0 0.000000 The nuclear charge for atom 7 has been changed to Z= 0 0.000000 The nuclear charge for atom 8 has been changed to Z= 0 0.000000 The nuclear charge for atom 9 has been changed to Z= 0 0.000000 The nuclear charge for atom 10 has been changed to Z= 0 0.000000 The nuclear charge for atom 11 has been changed to Z= 0 0.000000 The nuclear charge for atom 58 has been changed to Z= 0 0.000000 The nuclear charge for atom 59 has been changed to Z= 0 0.000000 The nuclear charge for atom 60 has been changed to Z= 0 0.000000 The nuclear charge for atom 61 has been changed to Z= 0 0.000000 The nuclear charge for atom 62 has been changed to Z= 0 0.000000 The nuclear charge for atom 63 has been changed to Z= 0 0.000000 The nuclear charge for atom 64 has been changed to Z= 0 0.000000 The nuclear charge for atom 65 has been changed to Z= 0 0.000000 The nuclear charge for atom 66 has been changed to Z= 0 0.000000 Integral buffers will be 131072 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned off. 1577 basis functions, 2471 primitive gaussians, 1634 cartesian basis functions 167 alpha electrons 167 beta electrons nuclear repulsion energy 5908.7664887872 Hartrees. NAtoms= 102 NActive= 102 NUniq= 102 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=T Big=T One-electron integrals computed using PRISM. NBasis= 1577 RedAO= T NBF= 1577 NBsUse= 1557 1.00D-06 NBFU= 1557 Harris functional with IExCor= 402 diagonalized for initial guess. ExpMin= 1.46D-02 ExpMax= 4.39D+04 ExpMxC= 1.51D+03 IAcc=3 IRadAn= 5 AccDes= 0.00D+00 HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 5 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 Warning: off-atom basis functions, so minimal bfn integration tests in XC quadrature. Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. Spurious integrated density or basis function: NE= 334 NElCor= 0 El error=8.92D+01 rel=2.67D-01 Tolerance=1.00D-03 Shell 61 absolute error=3.51D+02 Tolerance=no limit Shell 61 signed error=3.51D+02 Tolerance=no limit PGFIO-F-235/formatted write/unit=6/edit descriptor does not match item type. File name = stdout formatted, sequential access record = 9 In source file caldsu.f, at line number 952 From owner-chemistry@ccl.net Fri Dec 14 10:01:00 2007 From: "Close, David M. CLOSED]^[mail.etsu.edu" To: CCL Subject: CCL:G: Problems with the massage command in Gaussian 03 Message-Id: <-35854-071214095840-4980-Fcrn4YvvyZS02VcC5ujycQ[#]server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 14 Dec 2007 09:58:00 -0500 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED__mail.etsu.edu] Roland: You are lucky that there is information on the nature of this error. Many jobs simply terminate without giving any details. Your output says there is an error writing information on line 952 of file caldsu.f. Do you have the FORTRAN code for your copy of Gaussian? If so, you could look at the write command (that's what unit=3D6 means) and see that that the program is trying to write something that disagrees with a certain FORMAT in the program. Fortran is very fussy about all this. Formated writes have to be exactly as described in the FORMAT statement. This is of course old fashion, most new code is unformatted, but there is still lots formatted inputs/outputs imbedded in modern code. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+*+ccl.net [mailto:owner-chemistry+*+ccl.net]=20 Sent: Thursday, December 13, 2007 8:26 AM To: Close, David M. Subject: CCL:G: Problems with the massage command in Gaussian 03 Sent to CCL by: "Roland Schaap" [rolandschaap . gmail.com] Hello, I have been running several jobs in Gaussian 03 using the massage command. All seemed to be doing fine untill one job ended in a very strange fashion, without showing an error message. The job was removed > from the queu on the cluster therefore I assume it is terminated. Displayed below is the output which shows the basis sets etc. The job concerns the BSSE calculations on a 4-methylimidazole and a porphirine ring containing a magnesium, to which the imidazole is oriented (to slightly shorten the message I left out the beginning of the output). Any help or suggestions would be appreciated! ****************************************** Gaussian 03: AM64L-G03RevD.01 13-Oct-2005 8-Dec-2007=20 ****************************************** %NoSave %Chk=3DL173_B851_Cryst_BSSE1.chk %Mem=3D1024MB ---------------------------------------------------------------------- # BLYP/6-311++G(d,p) SCF=3DTight Population=3Dminimal density=3Dcurrent = Mass age ---------------------------------------------------------------------- 1/30=3D1,38=3D1/1; 2/15=3D1,17=3D6,18=3D5,40=3D1/2; = 3/5=3D4,6=3D6,7=3D1111,10=3D10,11=3D2,16=3D1,25=3D1,30=3D1,74=3D402/1,2,3= ; 4//1; 5/5=3D2,32=3D2,38=3D5/2; 6/7=3D2,8=3D2,9=3D2,10=3D2,22=3D-1,28=3D1/1; 99/5=3D1,9=3D1/99; ---------------------------------------------------------------------- BSSE Calculations on crystal structure LHis-173 coordinated to BChl-85 1, both wi ---------------------------------------------------------------------- Symbolic Z-matrix: Charge =3D 0 Multiplicity =3D 1 C 19.271 92.374 42.96=20 N 19.809 93.421 42.247=20 C 20.991 93.721 42.753=20 N 21.23 92.907 43.769=20 C 20.159 92.051 43.933=20 C 20.059 91.094 45.084=20 C 20.377 89.632 44.735=20 N 20.056 88.778 45.88=20 C 21.865 89.465 44.431=20 O 22.287 89.506 43.273=20 O 22.6928 89.27111 45.4868=20 Mg 19.235 94.878 40.16=20 N 21.263 94.917 39.705=20 C 21.9 93.952 39.002=20 C 23.258 94.272 38.815=20 C 23.503 95.572 39.472=20 C 22.189 95.883 40.023=20 C 21.269 92.818 38.522=20 C 19.957 92.396 38.574=20 N 18.92 93.077 39.166=20 C 17.735 92.338 38.931=20 C 18.013 91.07 38.146=20 C 19.486 91.139 37.961=20 C 16.494 92.825 39.396=20 C 16.303 94.009 40.131=20 C 14.965 94.304 40.5=20 C 14.184 93.246 39.963=20 C 15.074 92.25 39.222=20 N 17.235 94.935 40.538=20 C 16.53 95.894 41.219=20 C 15.17 95.588 41.254=20 C 17.061 97.027 41.782=20 C 18.371 97.411 41.751=20 C 18.845 98.678 42.354=20 C 20.332 98.694 42.065=20 C 20.543 97.41 41.296=20 N 19.393 96.689 41.14=20 C 18.127 99.892 41.643=20 C 18.879 101.217 41.51199=20 C 21.742 97.011 40.78099=20 C 21.179 98.712 43.33899=20 C 14.003 96.39 41.909=20 C 14.711 90.811 39.666=20 O 15.402 90.186 40.472=20 O 12.94 93.216 40.106=20 C 20.047 89.979 38.812=20 C 17.283 91.22 36.791=20 C 17.38 90.066 35.811=20 C 16.074 89.294 35.728=20 O 15.335 89.236 36.704=20 C 24.782 96.428 39.567=20 O 24.738 97.512 40.179=20 C 24.16 93.274 37.992=20 C 26.079 95.931 38.869=20 O 15.774 88.727 34.635=20 O 13.649 90.365 39.092=20 C 13.077 89.066 39.294=20 H 22.03636 92.98081 44.39635=20 H 20.26402 87.80184 45.64661=20 H 19.06072 88.87033 46.10625=20 H 19.77938 89.3494 43.85072=20 H 20.838 91.40784 45.80511=20 H 19.05227 91.1556 45.52526=20 H 18.31263 91.89481 42.77678=20 H 21.65525 94.50401 42.39571=20 H 23.60579 89.18329 45.12267=20 H 21.93726 92.12544 38.00359=20 H 22.54572 97.71577 40.99707=20 H 16.36618 97.6884 42.30767=20 H 17.68927 90.12512 38.61237=20 H 19.78599 91.0863 36.89885=20 H 19.63443 89.02342 38.44797=20 H 19.76052 90.12578 39.86784=20 H 21.14608 89.95979 38.72909=20 H 17.82765 92.03547 36.2898=20 H 16.22038 91.4621 36.9703=20 H 18.1649 89.37541 36.171=20 H 17.64241 90.45404 34.81101=20 H 14.9079 88.26986 34.7293=20 H 23.7521 93.16543 36.96922=20 H 24.1691 92.29113 38.4895=20 H 25.1847 93.66595 37.93759=20 H 25.89722 95.828 37.78844=20 H 26.3696 94.95626 39.28675=20 H 26.89071 96.66063 39.03823=20 H 20.63998 99.60071 41.51489=20 H 18.63088 98.75716 43.4368=20 H 22.24661 98.62902 43.07184=20 H 20.89393 97.86285 43.98091=20 H 21.0079 99.65762 43.88166=20 H 17.31342 100.14124 42.34716=20 H 17.76386 99.57451 40.64792=20 H 19.80386 101.05897 40.92952=20 H 19.13702 101.59442 42.51575=20 H 18.24002 101.95319 40.99555=20 H 13.94421 97.39449 41.45186=20 H 14.1876 96.4894 42.9943=20 H 13.063 95.862 41.747=20 H 14.94568 92.13178 38.1348=20 H 12.81024 88.94419 40.35099=20 H 13.80869 88.29496 39.0094=20 H 12.17464 88.96204 38.67326=20 =20 Symmetry turned off by external request. Stoichiometry C41H45MgN7O8 Framework group C1[X(C41H45MgN7O8)] Deg. of freedom 300 Full point group C1 Z-Matrix orientation: =20 --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 19.271000 92.374001 42.960000 2 7 0 19.808999 93.421001 42.247000 3 6 0 20.990999 93.721001 42.753000 4 7 0 21.230001 92.907001 43.769000 5 6 0 20.159001 92.051001 43.933000 6 6 0 20.059001 91.094001 45.084000 7 6 0 20.377000 89.632001 44.734999 8 7 0 20.056001 88.778001 45.879998 9 6 0 21.865000 89.465001 44.430999 10 8 0 22.287000 89.506001 43.272999 11 8 0 22.692801 89.271109 45.486803 12 12 0 19.234999 94.878001 40.160000 13 7 0 21.262999 94.917001 39.704999 14 6 0 21.899999 93.952001 39.001999 15 6 0 23.257999 94.272002 38.814998 16 6 0 23.502999 95.572002 39.471997 17 6 0 22.188999 95.883001 40.022999 18 6 0 21.268999 92.818001 38.521999 19 6 0 19.957000 92.396001 38.574000 20 7 0 18.920000 93.077000 39.166000 21 6 0 17.735000 92.338000 38.931000 22 6 0 18.012999 91.070000 38.146000 23 6 0 19.485999 91.139001 37.961000 24 6 0 16.494000 92.825000 39.396000 25 6 0 16.303000 94.009001 40.131000 26 6 0 14.965000 94.304001 40.500001 27 6 0 14.184000 93.246001 39.963001 28 6 0 15.074000 92.250000 39.222001 29 7 0 17.235000 94.935001 40.537999 30 6 0 16.529999 95.894001 41.218999 31 6 0 15.169999 95.588001 41.254000 32 6 0 17.061000 97.027001 41.781999 33 6 0 18.371000 97.411001 41.750998 34 6 0 18.845001 98.678001 42.353998 35 6 0 20.332001 98.694000 42.064995 36 6 0 20.543000 97.410000 41.295996 37 7 0 19.393000 96.689000 41.139998 38 6 0 18.127001 99.892001 41.642998 39 6 0 18.879001 101.217000 41.511995 40 6 0 21.741998 97.011001 40.780995 41 6 0 21.179003 98.712001 43.338995 42 6 0 14.002999 96.390001 41.908999 43 6 0 14.711000 90.811001 39.666002 44 8 0 15.402000 90.186001 40.472001 45 8 0 12.940000 93.216001 40.106001 46 6 0 20.046999 89.979001 38.811999 47 6 0 17.282999 91.220000 36.791000 48 6 0 17.379999 90.066000 35.811000 49 6 0 16.073998 89.294001 35.728000 50 8 0 15.334998 89.236001 36.704000 51 6 0 24.781998 96.428002 39.566996 52 8 0 24.737999 97.512002 40.178996 53 6 0 24.159999 93.274002 37.991997 54 6 0 26.078998 95.931002 38.868997 55 8 0 15.773998 88.727000 34.635000 56 8 0 13.648999 90.365001 39.092002 57 6 0 13.076999 89.066000 39.294002 58 1 0 22.036365 92.980806 44.396346 59 1 0 20.264019 87.801838 45.646613 60 1 0 19.060718 88.870326 46.106245 61 1 0 19.779380 89.349398 43.850724 62 1 0 20.838005 91.407837 45.805111 63 1 0 19.052273 91.155596 45.525263 64 1 0 18.312631 91.894815 42.776782 65 1 0 21.655253 94.504015 42.395712 66 1 0 23.605791 89.183286 45.122674 67 1 0 21.937258 92.125442 38.003592 68 1 0 22.545715 97.715768 40.997069 69 1 0 16.366180 97.688397 42.307672 70 1 0 17.689271 90.125120 38.612370 71 1 0 19.785994 91.086298 36.898852 72 1 0 19.634432 89.023422 38.447970 73 1 0 19.760517 90.125785 39.867837 74 1 0 21.146080 89.959790 38.729087 75 1 0 17.827653 92.035466 36.289797 76 1 0 16.220378 91.462103 36.970298 77 1 0 18.164896 89.375412 36.171000 78 1 0 17.642407 90.454039 34.811010 79 1 0 14.907896 88.269862 34.729299 80 1 0 23.752104 93.165433 36.969222 81 1 0 24.169100 92.291131 38.489500 82 1 0 25.184703 93.665949 37.937587 83 1 0 25.897221 95.827995 37.788439 84 1 0 26.369598 94.956258 39.286750 85 1 0 26.890708 96.660629 39.038230 86 1 0 20.639979 99.600714 41.514887 87 1 0 18.630877 98.757156 43.436798 88 1 0 22.246608 98.629020 43.071840 89 1 0 20.893933 97.862851 43.980912 90 1 0 21.007902 99.657617 43.881661 91 1 0 17.313421 100.141242 42.347155 92 1 0 17.763863 99.574508 40.647920 93 1 0 19.803863 101.058973 40.929524 94 1 0 19.137023 101.594420 42.515747 95 1 0 18.240023 101.953192 40.995547 96 1 0 13.944210 97.394490 41.451860 97 1 0 14.187603 96.489402 42.994300 98 1 0 13.062999 95.862000 41.746999 99 1 0 14.945676 92.131782 38.134799 100 1 0 12.810237 88.944195 40.350985 101 1 0 13.808685 88.294955 39.009401 102 1 0 12.174645 88.962037 38.673256 --------------------------------------------------------------------- Rotational constants (GHZ): 0.0482690 0.0340364 0.0299106 Standard basis: 6-311++G(d,p) (5D, 7F) The nuclear charge for atom 1 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 2 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 3 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 4 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 5 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 6 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 7 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 8 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 9 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 10 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 11 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 58 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 59 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 60 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 61 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 62 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 63 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 64 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 65 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 66 has been changed to Z=3D 0 0.000000 Integral buffers will be 131072 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned off. 1577 basis functions, 2471 primitive gaussians, 1634 cartesian basis functions 167 alpha electrons 167 beta electrons nuclear repulsion energy 5908.7664887872 Hartrees. NAtoms=3D 102 NActive=3D 102 NUniq=3D 102 SFac=3D 7.50D-01 NAtFMM=3D = 80 NAOKFM=3DT Big=3DT One-electron integrals computed using PRISM. NBasis=3D 1577 RedAO=3D T NBF=3D 1577 NBsUse=3D 1557 1.00D-06 NBFU=3D 1557 Harris functional with IExCor=3D 402 diagonalized for initial guess. ExpMin=3D 1.46D-02 ExpMax=3D 4.39D+04 ExpMxC=3D 1.51D+03 IAcc=3D3 = IRadAn=3D 5 AccDes=3D 0.00D+00 HarFok: IExCor=3D 402 AccDes=3D 0.00D+00 IRadAn=3D 5 IDoV=3D1 ScaDFX=3D 1.000000 1.000000 1.000000 1.000000 Warning: off-atom basis functions, so minimal bfn integration tests in XC quadrature. Requested convergence on RMS density matrix=3D1.00D-08 within 128 = cycles. Requested convergence on MAX density matrix=3D1.00D-06. Requested convergence on energy=3D1.00D-06. No special actions if energy rises. Spurious integrated density or basis function: NE=3D 334 NElCor=3D 0 El error=3D8.92D+01 rel=3D2.67D-01 = Tolerance=3D1.00D-03 Shell 61 absolute error=3D3.51D+02 Tolerance=3Dno = limit Shell 61 signed error=3D3.51D+02 Tolerance=3Dno = limit PGFIO-F-235/formatted write/unit=3D6/edit descriptor does not match item type. File name =3D stdout formatted, sequential access record =3D 9 In source file caldsu.f, at line number 952 -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Dec 14 11:38:00 2007 From: "Pedro Salvador pedro.salvador^-^udg.edu" To: CCL Subject: CCL:G: Problems with the massage command in Gaussian 03 Message-Id: <-35855-071214113426-3591-gOj10RHV9tZ2TWi9MXu0wA_+_server.ccl.net> X-Original-From: Pedro Salvador Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 14 Dec 2007 17:34:00 +0100 MIME-Version: 1.0 Sent to CCL by: Pedro Salvador [pedro.salvador\a/udg.edu] Hi, the use of massage is not recommended. Use "-bq" instead for the atoms you wish to massage (see Counterpoise keyword). The key error message you got is "Spurious integrated density or basis function:" This is quite typical in ghost orbital calculations. Better use also guess=core. Hope it helps Pedro Roland Schaap rolandschaap(0)gmail.com wrote: >Sent to CCL by: "Roland Schaap" [rolandschaap . gmail.com] > >Hello, >I have been running several jobs in Gaussian 03 using the massage command. All seemed to be doing fine untill one job ended in a very strange fashion, without showing an error message. The job was removed from the queu on the cluster therefore I assume it is terminated. Displayed below is the output which shows the basis sets etc. The job concerns the BSSE calculations on a 4-methylimidazole and a porphirine ring containing a magnesium, to which the imidazole is oriented (to slightly shorten the message I left out the beginning of the output). Any help or suggestions would be appreciated! > > > ****************************************** > Gaussian 03: AM64L-G03RevD.01 13-Oct-2005 > 8-Dec-2007 > ****************************************** > %NoSave > %Chk=L173_B851_Cryst_BSSE1.chk > %Mem=1024MB > ---------------------------------------------------------------------- > # BLYP/6-311++G(d,p) SCF=Tight Population=minimal density=current Mass > age > ---------------------------------------------------------------------- > 1/30=1,38=1/1; > 2/15=1,17=6,18=5,40=1/2; > 3/5=4,6=6,7=1111,10=10,11=2,16=1,25=1,30=1,74=402/1,2,3; > 4//1; > 5/5=2,32=2,38=5/2; > 6/7=2,8=2,9=2,10=2,22=-1,28=1/1; > 99/5=1,9=1/99; > ---------------------------------------------------------------------- > BSSE Calculations on crystal structure LHis-173 coordinated to BChl-85 > 1, both wi > ---------------------------------------------------------------------- > Symbolic Z-matrix: > Charge = 0 Multiplicity = 1 > C 19.271 92.374 42.96 > N 19.809 93.421 42.247 > C 20.991 93.721 42.753 > N 21.23 92.907 43.769 > C 20.159 92.051 43.933 > C 20.059 91.094 45.084 > C 20.377 89.632 44.735 > N 20.056 88.778 45.88 > C 21.865 89.465 44.431 > O 22.287 89.506 43.273 > O 22.6928 89.27111 45.4868 > Mg 19.235 94.878 40.16 > N 21.263 94.917 39.705 > C 21.9 93.952 39.002 > C 23.258 94.272 38.815 > C 23.503 95.572 39.472 > C 22.189 95.883 40.023 > C 21.269 92.818 38.522 > C 19.957 92.396 38.574 > N 18.92 93.077 39.166 > C 17.735 92.338 38.931 > C 18.013 91.07 38.146 > C 19.486 91.139 37.961 > C 16.494 92.825 39.396 > C 16.303 94.009 40.131 > C 14.965 94.304 40.5 > C 14.184 93.246 39.963 > C 15.074 92.25 39.222 > N 17.235 94.935 40.538 > C 16.53 95.894 41.219 > C 15.17 95.588 41.254 > C 17.061 97.027 41.782 > C 18.371 97.411 41.751 > C 18.845 98.678 42.354 > C 20.332 98.694 42.065 > C 20.543 97.41 41.296 > N 19.393 96.689 41.14 > C 18.127 99.892 41.643 > C 18.879 101.217 41.51199 > C 21.742 97.011 40.78099 > C 21.179 98.712 43.33899 > C 14.003 96.39 41.909 > C 14.711 90.811 39.666 > O 15.402 90.186 40.472 > O 12.94 93.216 40.106 > C 20.047 89.979 38.812 > C 17.283 91.22 36.791 > C 17.38 90.066 35.811 > C 16.074 89.294 35.728 > O 15.335 89.236 36.704 > C 24.782 96.428 39.567 > O 24.738 97.512 40.179 > C 24.16 93.274 37.992 > C 26.079 95.931 38.869 > O 15.774 88.727 34.635 > O 13.649 90.365 39.092 > C 13.077 89.066 39.294 > H 22.03636 92.98081 44.39635 > H 20.26402 87.80184 45.64661 > H 19.06072 88.87033 46.10625 > H 19.77938 89.3494 43.85072 > H 20.838 91.40784 45.80511 > H 19.05227 91.1556 45.52526 > H 18.31263 91.89481 42.77678 > H 21.65525 94.50401 42.39571 > H 23.60579 89.18329 45.12267 > H 21.93726 92.12544 38.00359 > H 22.54572 97.71577 40.99707 > H 16.36618 97.6884 42.30767 > H 17.68927 90.12512 38.61237 > H 19.78599 91.0863 36.89885 > H 19.63443 89.02342 38.44797 > H 19.76052 90.12578 39.86784 > H 21.14608 89.95979 38.72909 > H 17.82765 92.03547 36.2898 > H 16.22038 91.4621 36.9703 > H 18.1649 89.37541 36.171 > H 17.64241 90.45404 34.81101 > H 14.9079 88.26986 34.7293 > H 23.7521 93.16543 36.96922 > H 24.1691 92.29113 38.4895 > H 25.1847 93.66595 37.93759 > H 25.89722 95.828 37.78844 > H 26.3696 94.95626 39.28675 > H 26.89071 96.66063 39.03823 > H 20.63998 99.60071 41.51489 > H 18.63088 98.75716 43.4368 > H 22.24661 98.62902 43.07184 > H 20.89393 97.86285 43.98091 > H 21.0079 99.65762 43.88166 > H 17.31342 100.14124 42.34716 > H 17.76386 99.57451 40.64792 > H 19.80386 101.05897 40.92952 > H 19.13702 101.59442 42.51575 > H 18.24002 101.95319 40.99555 > H 13.94421 97.39449 41.45186 > H 14.1876 96.4894 42.9943 > H 13.063 95.862 41.747 > H 14.94568 92.13178 38.1348 > H 12.81024 88.94419 40.35099 > H 13.80869 88.29496 39.0094 > H 12.17464 88.96204 38.67326 > > Symmetry turned off by external request. > Stoichiometry C41H45MgN7O8 > Framework group C1[X(C41H45MgN7O8)] > Deg. of freedom 300 > Full point group C1 > Z-Matrix orientation: > --------------------------------------------------------------------- > Center Atomic Atomic Coordinates (Angstroms) > Number Number Type X Y Z > --------------------------------------------------------------------- > 1 6 0 19.271000 92.374001 42.960000 > 2 7 0 19.808999 93.421001 42.247000 > 3 6 0 20.990999 93.721001 42.753000 > 4 7 0 21.230001 92.907001 43.769000 > 5 6 0 20.159001 92.051001 43.933000 > 6 6 0 20.059001 91.094001 45.084000 > 7 6 0 20.377000 89.632001 44.734999 > 8 7 0 20.056001 88.778001 45.879998 > 9 6 0 21.865000 89.465001 44.430999 > 10 8 0 22.287000 89.506001 43.272999 > 11 8 0 22.692801 89.271109 45.486803 > 12 12 0 19.234999 94.878001 40.160000 > 13 7 0 21.262999 94.917001 39.704999 > 14 6 0 21.899999 93.952001 39.001999 > 15 6 0 23.257999 94.272002 38.814998 > 16 6 0 23.502999 95.572002 39.471997 > 17 6 0 22.188999 95.883001 40.022999 > 18 6 0 21.268999 92.818001 38.521999 > 19 6 0 19.957000 92.396001 38.574000 > 20 7 0 18.920000 93.077000 39.166000 > 21 6 0 17.735000 92.338000 38.931000 > 22 6 0 18.012999 91.070000 38.146000 > 23 6 0 19.485999 91.139001 37.961000 > 24 6 0 16.494000 92.825000 39.396000 > 25 6 0 16.303000 94.009001 40.131000 > 26 6 0 14.965000 94.304001 40.500001 > 27 6 0 14.184000 93.246001 39.963001 > 28 6 0 15.074000 92.250000 39.222001 > 29 7 0 17.235000 94.935001 40.537999 > 30 6 0 16.529999 95.894001 41.218999 > 31 6 0 15.169999 95.588001 41.254000 > 32 6 0 17.061000 97.027001 41.781999 > 33 6 0 18.371000 97.411001 41.750998 > 34 6 0 18.845001 98.678001 42.353998 > 35 6 0 20.332001 98.694000 42.064995 > 36 6 0 20.543000 97.410000 41.295996 > 37 7 0 19.393000 96.689000 41.139998 > 38 6 0 18.127001 99.892001 41.642998 > 39 6 0 18.879001 101.217000 41.511995 > 40 6 0 21.741998 97.011001 40.780995 > 41 6 0 21.179003 98.712001 43.338995 > 42 6 0 14.002999 96.390001 41.908999 > 43 6 0 14.711000 90.811001 39.666002 > 44 8 0 15.402000 90.186001 40.472001 > 45 8 0 12.940000 93.216001 40.106001 > 46 6 0 20.046999 89.979001 38.811999 > 47 6 0 17.282999 91.220000 36.791000 > 48 6 0 17.379999 90.066000 35.811000 > 49 6 0 16.073998 89.294001 35.728000 > 50 8 0 15.334998 89.236001 36.704000 > 51 6 0 24.781998 96.428002 39.566996 > 52 8 0 24.737999 97.512002 40.178996 > 53 6 0 24.159999 93.274002 37.991997 > 54 6 0 26.078998 95.931002 38.868997 > 55 8 0 15.773998 88.727000 34.635000 > 56 8 0 13.648999 90.365001 39.092002 > 57 6 0 13.076999 89.066000 39.294002 > 58 1 0 22.036365 92.980806 44.396346 > 59 1 0 20.264019 87.801838 45.646613 > 60 1 0 19.060718 88.870326 46.106245 > 61 1 0 19.779380 89.349398 43.850724 > 62 1 0 20.838005 91.407837 45.805111 > 63 1 0 19.052273 91.155596 45.525263 > 64 1 0 18.312631 91.894815 42.776782 > 65 1 0 21.655253 94.504015 42.395712 > 66 1 0 23.605791 89.183286 45.122674 > 67 1 0 21.937258 92.125442 38.003592 > 68 1 0 22.545715 97.715768 40.997069 > 69 1 0 16.366180 97.688397 42.307672 > 70 1 0 17.689271 90.125120 38.612370 > 71 1 0 19.785994 91.086298 36.898852 > 72 1 0 19.634432 89.023422 38.447970 > 73 1 0 19.760517 90.125785 39.867837 > 74 1 0 21.146080 89.959790 38.729087 > 75 1 0 17.827653 92.035466 36.289797 > 76 1 0 16.220378 91.462103 36.970298 > 77 1 0 18.164896 89.375412 36.171000 > 78 1 0 17.642407 90.454039 34.811010 > 79 1 0 14.907896 88.269862 34.729299 > 80 1 0 23.752104 93.165433 36.969222 > 81 1 0 24.169100 92.291131 38.489500 > 82 1 0 25.184703 93.665949 37.937587 > 83 1 0 25.897221 95.827995 37.788439 > 84 1 0 26.369598 94.956258 39.286750 > 85 1 0 26.890708 96.660629 39.038230 > 86 1 0 20.639979 99.600714 41.514887 > 87 1 0 18.630877 98.757156 43.436798 > 88 1 0 22.246608 98.629020 43.071840 > 89 1 0 20.893933 97.862851 43.980912 > 90 1 0 21.007902 99.657617 43.881661 > 91 1 0 17.313421 100.141242 42.347155 > 92 1 0 17.763863 99.574508 40.647920 > 93 1 0 19.803863 101.058973 40.929524 > 94 1 0 19.137023 101.594420 42.515747 > 95 1 0 18.240023 101.953192 40.995547 > 96 1 0 13.944210 97.394490 41.451860 > 97 1 0 14.187603 96.489402 42.994300 > 98 1 0 13.062999 95.862000 41.746999 > 99 1 0 14.945676 92.131782 38.134799 > 100 1 0 12.810237 88.944195 40.350985 > 101 1 0 13.808685 88.294955 39.009401 > 102 1 0 12.174645 88.962037 38.673256 > --------------------------------------------------------------------- > Rotational constants (GHZ): 0.0482690 0.0340364 0.0299106 > Standard basis: 6-311++G(d,p) (5D, 7F) > The nuclear charge for atom 1 has been changed to Z= 0 0.000000 > The nuclear charge for atom 2 has been changed to Z= 0 0.000000 > The nuclear charge for atom 3 has been changed to Z= 0 0.000000 > The nuclear charge for atom 4 has been changed to Z= 0 0.000000 > The nuclear charge for atom 5 has been changed to Z= 0 0.000000 > The nuclear charge for atom 6 has been changed to Z= 0 0.000000 > The nuclear charge for atom 7 has been changed to Z= 0 0.000000 > The nuclear charge for atom 8 has been changed to Z= 0 0.000000 > The nuclear charge for atom 9 has been changed to Z= 0 0.000000 > The nuclear charge for atom 10 has been changed to Z= 0 0.000000 > The nuclear charge for atom 11 has been changed to Z= 0 0.000000 > The nuclear charge for atom 58 has been changed to Z= 0 0.000000 > The nuclear charge for atom 59 has been changed to Z= 0 0.000000 > The nuclear charge for atom 60 has been changed to Z= 0 0.000000 > The nuclear charge for atom 61 has been changed to Z= 0 0.000000 > The nuclear charge for atom 62 has been changed to Z= 0 0.000000 > The nuclear charge for atom 63 has been changed to Z= 0 0.000000 > The nuclear charge for atom 64 has been changed to Z= 0 0.000000 > The nuclear charge for atom 65 has been changed to Z= 0 0.000000 > The nuclear charge for atom 66 has been changed to Z= 0 0.000000 > Integral buffers will be 131072 words long. > Raffenetti 2 integral format. > Two-electron integral symmetry is turned off. > 1577 basis functions, 2471 primitive gaussians, 1634 cartesian basis functions > 167 alpha electrons 167 beta electrons > nuclear repulsion energy 5908.7664887872 Hartrees. > NAtoms= 102 NActive= 102 NUniq= 102 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=T Big=T > One-electron integrals computed using PRISM. > NBasis= 1577 RedAO= T NBF= 1577 > NBsUse= 1557 1.00D-06 NBFU= 1557 > Harris functional with IExCor= 402 diagonalized for initial guess. > ExpMin= 1.46D-02 ExpMax= 4.39D+04 ExpMxC= 1.51D+03 IAcc=3 IRadAn= 5 AccDes= 0.00D+00 > HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 5 IDoV=1 > ScaDFX= 1.000000 1.000000 1.000000 1.000000 > Warning: off-atom basis functions, so minimal bfn integration tests in XC quadrature. > Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. > Requested convergence on MAX density matrix=1.00D-06. > Requested convergence on energy=1.00D-06. > No special actions if energy rises. > Spurious integrated density or basis function: > NE= 334 NElCor= 0 El error=8.92D+01 rel=2.67D-01 Tolerance=1.00D-03 > Shell 61 absolute error=3.51D+02 Tolerance=no limit > Shell 61 signed error=3.51D+02 Tolerance=no limit >PGFIO-F-235/formatted write/unit=6/edit descriptor does not match item type. > File name = stdout formatted, sequential access record = 9 > In source file caldsu.f, at line number 952> > > > From owner-chemistry@ccl.net Fri Dec 14 16:36:01 2007 From: "Petr Toman ccl###linus.imcm.cas.cz" To: CCL Subject: CCL: moplo 2.0 Message-Id: <-35856-071214160633-20250-fwbd616JxCCIVBSj8pwLhQ^server.ccl.net> X-Original-From: Petr Toman Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 14 Dec 2007 21:26:07 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Petr Toman [ccl a linus.imcm.cas.cz] Hello, I wonder if molecule viewer and editor moplo 2.0 can run under Windows XP and how is it possible to obtain this program. Autor of this program should be Georg Thiele. Or could somebody advise me another similar program? Any help would be appreciated. Best regards, Petr Toman From owner-chemistry@ccl.net Fri Dec 14 17:12:00 2007 From: "Brian Austin baustin%a%berkeley.edu" To: CCL Subject: CCL: forum for programming questions Message-Id: <-35857-071214145935-14447-TJ5F6Br6qVu805SV1QHAZQ:-:server.ccl.net> X-Original-From: "Brian Austin" Date: Fri, 14 Dec 2007 14:59:31 -0500 Sent to CCL by: "Brian Austin" [baustin+/-berkeley.edu] Hi CCL'ers, Sometimes in my work, I encounter a programming question that surely has a well known answer, but does not seem to be addressed by any easily-found FAQ's. For example, it can take days to figure out how to do something simple like redirect stdout. Who do you turn to? Can anyone reccommend a good forum for asking these questions? Do you know of an open-source chat room? Thanks -Brian From owner-chemistry@ccl.net Fri Dec 14 19:25:00 2007 From: "Roman D. Gorbunov rgorbuno/a\aecom.yu.edu" To: CCL Subject: CCL:G: Overtone Frequency Calculations in Gaussian Message-Id: <-35858-071214192320-31940-Su6PSnpgL+44fomx1Q5LfQ!A!server.ccl.net> X-Original-From: "Roman D. Gorbunov" Date: Fri, 14 Dec 2007 19:23:16 -0500 Sent to CCL by: "Roman D. Gorbunov" [rgorbuno]=[aecom.yu.edu] Dear CCL Subscribers, I need to calculate overtone anharmonicities with the Gaussian. Trying to do that I have included the following keywords into my input file: #B3LYP/6-31+G(d) GFINPUT IOP(7/33=1) Freq=(HPModes,Anharmonic) And i cannot get the "Normal Termination". The calculations stop with the following message: -------------------------------------------------------------- **** Warning!!: The largest alpha MO coefficient is 0.71988579D+02 Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 17 centers at a time, making 1 passes doing MaxLOS=2. FoFDir/FoFCou used for L=0 through L=2. Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. Store integrals in memory, NReq= 148451441. There are 51 degrees of freedom in the 1st order CPHF. 48 vectors were produced by pass 0. AX will form 48 AO Fock derivatives at one time. 48 vectors were produced by pass 1. -------------------------------------------------------------- It should be mentioned that the problem is related with the "Anharmonic" keyword (since without it I get the "Normal Termination"). Could you pleas help with this problem? Roman From owner-chemistry@ccl.net Fri Dec 14 20:28:01 2007 From: "Rajarshi Guha rguha _ indiana.edu" To: CCL Subject: CCL: forum for programming questions Message-Id: <-35859-071214195112-11857-ey6VUXEDFuv++f3z4s6diQ_+_server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 14 Dec 2007 19:15:33 -0500 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha[]indiana.edu] On Dec 14, 2007, at 2:59 PM, Brian Austin baustin%a%berkeley.edu wrote: > > Sent to CCL by: "Brian Austin" [baustin+/-berkeley.edu] > Hi CCL'ers, > > Sometimes in my work, I encounter a programming question that > surely has a well known answer, but does not seem to be addressed > by any easily-found FAQ's. For example, it can take days to figure > out how to do something simple like redirect stdout. Who do you > turn to? Can anyone reccommend a good forum for asking these > questions? Do you know of an open-source chat room? The comp.lang.* Usenet groups are a good source of help ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- I put up my thumb... and it blotted out the planet Earth. -- Neil Armstrong From owner-chemistry@ccl.net Fri Dec 14 22:32:00 2007 From: "Joe Leonard jleonard42[a]gmail.com" To: CCL Subject: CCL: Summary re: conformational analysis tools Message-Id: <-35860-071214212118-20957-ISmGu4jlZYbxv+m8EApnPg*o*server.ccl.net> X-Original-From: Joe Leonard Content-Type: multipart/alternative; boundary=Apple-Mail-4-331035172 Date: Fri, 14 Dec 2007 20:19:27 -0500 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Joe Leonard [jleonard42-.-gmail.com] --Apple-Mail-4-331035172 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Folks, as you recall, I was interested in open-source conformational analysis codes as prototypes for pre- and post-processing in a GUI. There were a number of good suggestions, and I thought I'd summarize: The open-source alternatives were Tinker and Open Babel tools. The former is a nice package, but probably more complex that I'm interested in. The latter seems to have generator and minimizer routines that bear looking into. Several commercial packages were suggested: Vconf from Verachem, Omega from OpenEye and Marvin from ChemAxon. There are other commercial alternatives out there, but they're not what I need. I'm not sure where smi23d comes in, but I recall several postings about it over the last few months and will check up on it at some point. As always, any advice from the CCL readers is welcome! Joe Leonard jleonard42_._gmail.com P.S. I want to wish everybody the best for this holiday season, and may '08 be a good year for you! -- "That's a paradox. Could blow a hole in the space-time continuum the size of... Well, actually the exact size of Belgium. That's a bit undramatic, isn't it... Belgium?" --Apple-Mail-4-331035172 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Folks, as you recall, I was interested in open-source conformational = analysis codes as prototypes for pre- and post-processing in a GUI. = =A0There were a number of good suggestions, and I thought I'd = summarize:

The = open-source alternatives were Tinker and Open Babel tools. =A0The former = is a nice package, but probably more complex that I'm interested in. = =A0The latter seems to have generator and minimizer routines that bear = looking into.

Several commercial = packages were suggested: Vconf from Verachem, Omega from OpenEye and = Marvin from ChemAxon. =A0There are other commercial alternatives out = there, but they're not what I need.

I'm not sure where smi23d = comes in, but I recall several postings about it over the last few = months and will check up on it at some point. =A0As always, any advice = > from the CCL readers is welcome!

Joe Leonard
P.S. I want to wish = everybody the best for this holiday season, and may '08 be a good year = for you!

=

= --Apple-Mail-4-331035172--