From owner-chemistry@ccl.net Tue Nov 29 05:15:00 2005 From: "Szabolcs Csepregi scsepregi^^^chemaxon.com" To: CCL Subject: CCL: seek software about "rule 5" Message-Id: <-30100-051129051342-1125-FTT/jzTaM4V1Jhu/A8Neyw,server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 29 Nov 2005 11:12:59 +0100 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [scsepregi**chemaxon.com] Hi Steven, Have a look at Evaluator from ChemAxon. A sample web application using Lipinski's Rule of Five filtering can be found at: http://www.chemaxon.com/jchem/examples/jsp1_x/index.jsp. Open the NCI database table and go to the query page. You will see some example filters there; you can modify them or write your own ones. That sample application uses the Java-based Evaluator software for calculating the Chemical Terms expressions on the fly, but Evaluator can also be used with files from command line, and you can build it in your own application using the API. Evaluator doc: http://www.chemaxon.com/jchem/doc/user/Evaluator.html (ChemAxon offers FREE academic licenses) Gyorgy Gyorgy Pirok CTO ChemAxon Ltd. 1037 Budapest Maramaros koz 3/A Tel: +36 (1) 453-2661 Fax: +36 (1) 453-2659 -- Szabolcs Csepregi, PhD Cheminformatics Scientist, ChemAxon Ltd. http://www.chemaxon.com Skype: szabolcs.csepregi Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 From owner-chemistry@ccl.net Tue Nov 29 07:05:00 2005 From: "Ben Sattelle ben.sattelle]~[postgrad.manchester.ac.uk" To: CCL Subject: CCL:G: Convergence of ruthenium nitrosyl complexes Message-Id: <-30101-051129063210-27897-0JmAIz969NwWaNOyo3GRzw*|*server.ccl.net> X-Original-From: Ben Sattelle Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format="flowed" Date: Tue, 29 Nov 2005 10:20:40 +0000 MIME-Version: 1.0 Sent to CCL by: Ben Sattelle [ben.sattelle__postgrad.manchester.ac.uk] find good tips here -> http://www.ccl.net/cca/documents/dyoung/topics-orig/converge.html the book, Computational Chemistry: A Practical Guide ... is useful, ben. >> I have some problems of convergence in gaussian opt >> calculations for >> Ruthenium nitrosyl complexes. The problem began when >> I change a chlorine >> atoms in the sphere of coordination of ruthenium by >> nitrosyl molecules >> (NO). When I try to optimize the geometry of the >> complex (charge=+3 and >> multiplicity=1) by LanL2DZ or 3-21G* basis I always >> found that the >> criteria of convergence is not met??? >> The error is the following: >> >> Restarting incremental Fock formation. >> Restarting incremental Fock formation. >> Restarting incremental Fock formation. >> >>>>>>>>>> Convergence criterion not met. >> SCF Done: E(RHF) = -6991.67598454 A.U. after >> 65 cycles >> Convg = 0.3086E-04 -V/T >> = 2.0035 >> S**2 = 0.0000 >> Convergence failure -- run terminated. >> Error termination via Lnk1e in //g98/l502.exe. >> >> thanks >> bye From owner-chemistry@ccl.net Tue Nov 29 07:39:00 2005 From: "=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= FB153746:-:ATIL.CEA.FR" To: CCL Subject: CCL:G: Trouble with Gaussian03 Message-Id: <-30102-051129072150-14316-j6jGbi4IRXakbS2fcikGlA{:}server.ccl.net> X-Original-From: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 29 Nov 2005 13:21:45 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= [FB153746+*+ATIL.CEA.FR] Dear CCL users, Gaussian03 has been compiled on two same machines, but in one case it is runing, on the other case, we have a trouble, see below. (machines: Xeon, RedHat9, with ifort, icc and mkl) Many thanks to let me know what to do in that case. I am looking forward to hearing from you. Regards, Frederic PS: a df -k command let us know that there is of course enough space on the disk. ____________________________________________________________________________ ________ ****************************************** Gaussian 03: IA32L-G03RevC.02 12-Jun-2004 29-Nov-2005 ****************************************** Erroneous write during file extend. write -1 instead of 4096 Probably out of disk space. Erroneous write during file extend. write -1 instead of 4096 Probably out of disk space. Write error in NtrExt1 Write error in NtrExt1: Bad address forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source Unknown 003371F1 Unknown Unknown Unknown Unknown 007E6B12 Unknown Unknown Unknown Unknown 007E5327 Unknown Unknown Unknown Unknown 00B935B0 Unknown Unknown Unknown Unknown 00B94102 Unknown Unknown Unknown Unknown 00A124E2 Unknown Unknown Unknown Unknown 00AFF886 Unknown Unknown Unknown l1.exe 0805CADA Unknown Unknown Unknown l1.exe 08114F4C Unknown Unknown Unknown From owner-chemistry@ccl.net Tue Nov 29 08:25:00 2005 From: "Paul Fleurat-Lessard Paul.Fleurat-Lessard\a/ens-lyon.fr" To: CCL Subject: CCL: Trouble with Gaussian03 Message-Id: <-30103-051129082305-23594-E9O266xzYOANkHnwB4ppQg]_[server.ccl.net> X-Original-From: Paul Fleurat-Lessard Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 29 Nov 2005 14:22:58 +0100 MIME-Version: 1.0 Sent to CCL by: Paul Fleurat-Lessard [Paul.Fleurat-Lessard-x-ens-lyon.fr] Dera Frederic, I don't know if this is still valid with a Xeon processor, but with ifort I ran into the problem of 2Gb limit for file size with ifort. It might be that your job demands more than 2Gb... try to split the rwf files. Regards, paul. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard]=[ens-lyon.fr Laboratoire de Chimie Ecole Normale Supérieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allée d'Italie Fax: + 33 (0)4 72 72 88 60 69364 Lyon Cedex 07 From owner-chemistry@ccl.net Tue Nov 29 09:27:00 2005 From: "Daniel Norberg daniel.norberg~!~kvac.uu.se" To: CCL Subject: CCL:G: Constrained optimization scan in Gaussian03 Message-Id: <-30104-051129052023-2935-ISmGu4jlZYbxv+m8EApnPg!=!server.ccl.net> X-Original-From: "Daniel Norberg" Sent to CCL by: "Daniel Norberg" [daniel.norberg(0)kvac.uu.se] Hello everyone, I have a question regarding constrained optimization scans in Gaussian03 using the opt=modredundant keyword for requesting the scan. The scan I am performing have two angular constraints. The scan parameter is a distance which I decrease by an increment of -0.1 Angstrom/optimization step. All other geometrical degrees of freedom are optimized in every optimization step. The calculation proceeds fine for about 10 optimization steps (i.e. ca 1.0 Angstrom), each optimization step ending with the message "Optimization completed". However at a particular point the scan stops with the following error message: New curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in /usr/g03/l103.exe at Tue Nov 29 02:01:27 2005. Job cpu time: 0 days 6 hours 15 minutes 52.8 seconds. File lengths (MBytes): RWF= 21 Int= 0 D2E= 0 Chk= 8 Scr= 1 Based on the second line in the error message above it seems that it has to do with the angular constraints which I have imposed to the optimizations. Can anyone help me to interpret this error, and perhaps suggest what I could try to do in order to cicumvent this problem. Thanks in advance! Daniel, PhD-student From owner-chemistry@ccl.net Tue Nov 29 10:46:00 2005 From: "Derosa-Latech pderosa%a%latech.edu" To: CCL Subject: CCL:G: Trouble with Gaussian03 Message-Id: <-30105-051129094133-28878-aWrnx/gsYWYGuGjGFRmmFQ,,server.ccl.net> X-Original-From: "Derosa-Latech" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 29 Nov 2005 08:41:24 -0600 MIME-Version: 1.0 Sent to CCL by: "Derosa-Latech" [pderosa===latech.edu] What exactly is your problem?, it does not run at all, it runs but failed, other? Also, how similar are your computers? I learned that Xeon, RedHat9 does not univocally define your system ----- Original Message ----- > From: "BOUYER Frédéric 153746 FB153746:-:ATIL.CEA.FR" To: "Derosa, Pedro " Sent: Tuesday, November 29, 2005 6:50 AM Subject: CCL:G: Trouble with Gaussian03 > Sent to CCL by: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= > [FB153746+*+ATIL.CEA.FR] > Dear CCL users, > > Gaussian03 has been compiled on two same machines, but in one case it is > runing, on the other case, we have a trouble, see below. > (machines: Xeon, RedHat9, with ifort, icc and mkl) > > Many thanks to let me know what to do in that case. I am looking forward > to > hearing from you. > > Regards, > > Frederic > > PS: a df -k command let us know that there is of course enough space on > the > disk. > ____________________________________________________________________________ > ________ > > ****************************************** > Gaussian 03: IA32L-G03RevC.02 12-Jun-2004 > 29-Nov-2005 > ****************************************** > Erroneous write during file extend. write -1 instead of 4096 > Probably out of disk space. > Erroneous write during file extend. write -1 instead of 4096 > Probably out of disk space. > Write error in NtrExt1 > Write error in NtrExt1: Bad address > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > Unknown 003371F1 Unknown Unknown Unknown > Unknown 007E6B12 Unknown Unknown Unknown > Unknown 007E5327 Unknown Unknown Unknown > Unknown 00B935B0 Unknown Unknown Unknown > Unknown 00B94102 Unknown Unknown Unknown > Unknown 00A124E2 Unknown Unknown Unknown > Unknown 00AFF886 Unknown Unknown Unknown > l1.exe 0805CADA Unknown Unknown Unknown > l1.exe 08114F4C Unknown Unknown Unknown> > > > From owner-chemistry@ccl.net Tue Nov 29 12:13:00 2005 From: "Andrew D. Fant fant|*|pobox.com" To: CCL Subject: CCL: Small Molecule Modeling/Chemoinformatics R&D in New York City and environs [probaby OT] Message-Id: <-30106-051129121017-22346-te7fFhUSIj947bS90MeKBQ++server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 29 Nov 2005 12:10:01 -0500 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant_._pobox.com] My apologies if this is off-topic, but the list seemed like the best place to start asking questions. Can anyone recommend places in New York City and its near environs where people are doing serious R&D work with small molecule modeling and/or chemoinformatics? Rahway and such are probably a little further afield than the scope of this search. I am not particularly concerned about industry vs. academia. If people would rather contact me off-line in private email, that would be fine as well. Thanks in advance, Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant(~)pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Tue Nov 29 13:22:01 2005 From: "Joaquin Barroso Flores joaco_barroso^-^yahoo.com" To: CCL Subject: CCL:G: Constrained optimization scan in Gaussian03 Message-Id: <-30107-051129124805-6436-jJeaYDk1EF2KHbBnoRYBSw++server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-999580885-1133282881=:91609" Date: Tue, 29 Nov 2005 10:48:01 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso*yahoo.com] --0-999580885-1133282881=:91609 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Try to visualize the path of the scan using the animation feature in molekel (I am not sure if Molden might be useful too). Maybe then you might observe if there is something wrong with the geometry at the final step and rethink your input Good luck! "Daniel Norberg daniel.norberg~!~kvac.uu.se" escribió: Sent to CCL by: "Daniel Norberg" [daniel.norberg(0)kvac.uu.se] Hello everyone, I have a question regarding constrained optimization scans in Gaussian03 using the opt=modredundant keyword for requesting the scan. The scan I am performing have two angular constraints. The scan parameter is a distance which I decrease by an increment of -0.1 Angstrom/optimization step. All other geometrical degrees of freedom are optimized in every optimization step. The calculation proceeds fine for about 10 optimization steps (i.e. ca 1.0 Angstrom), each optimization step ending with the message "Optimization completed". However at a particular point the scan stops with the following error message: New curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in /usr/g03/l103.exe at Tue Nov 29 02:01:27 2005. Job cpu time: 0 days 6 hours 15 minutes 52.8 seconds. File lengths (MBytes): RWF= 21 Int= 0 D2E= 0 Chk= 8 Scr= 1 Based on the second line in the error message above it seems that it has to do with the angular constraints which I have imposed to the optimizations. Can anyone help me to interpret this error, and perhaps suggest what I could try to do in order to cicumvent this problem. Thanks in advance! Daniel, PhD-student********************************************************** Q. Joaquín Barroso Flores Instituto de Química UNAM Correo Alterno: joaquin_barroso.++.correo.unam.mx ********************************************************** --------------------------------- Do You Yahoo!? La mejor conexión a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx --0-999580885-1133282881=:91609 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Try to visualize the path of the scan using the animation feature in molekel (I am not sure if Molden might be useful too). Maybe then you might observe if there is something wrong with the geometry at the final step and rethink your input
 
Good luck!

"Daniel Norberg daniel.norberg~!~kvac.uu.se" <owner-chemistry.++.ccl.net> escribió:
Sent to CCL by: "Daniel Norberg" [daniel.norberg(0)kvac.uu.se]
Hello everyone,

I have a question regarding constrained optimization scans in Gaussian03 using the opt=modredundant keyword for requesting the scan.

The scan I am performing have two angular constraints. The scan parameter is a distance which I decrease by an increment of -0.1 Angstrom/optimization step. All other geometrical degrees of freedom are optimized in every optimization step. The calculation proceeds fine for about 10 optimization steps (i.e. ca 1.0 Angstrom), each optimization step ending with the message "Optimization completed". However at a particular point the scan stops with the following error message:

New curvilinear step not converged.
Error imposing constraints
Error termination via Lnk1e in /usr/g03/l103.exe at Tue Nov 29 02:01:27 2005.
Job cpu time: 0 days 6 hours 15 minutes 52.8 seconds.
File lengths (MBytes): RWF= 21 Int= 0 D2E= 0 Chk= 8 Scr= 1

Based on the second line in the error message above it seems that it has to do with the angular constraints which I have imposed to the optimizations.

Can anyone help me to interpret this error, and perhaps suggest what I could try to do in order to cicumvent this problem.

Thanks in advance!

Daniel, PhD-student



**********************************************************
Q. Joaquín Barroso Flores

Instituto de Química UNAM
Correo Alterno: joaquin_barroso.++.correo.unam.mx
**********************************************************

Do You Yahoo!? La mejor conexión a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx --0-999580885-1133282881=:91609-- From owner-chemistry@ccl.net Tue Nov 29 13:56:01 2005 From: "Frauke Graeter frauke.graeter]![mpi-bpc.mpg.de" To: CCL Subject: CCL: EMBO course "Proteins: structure, dynamics, energetics" Shanghai Message-Id: <-30108-051129121411-22911-qc6mGLtWiVMCN/s3fG5ieA .. server.ccl.net> X-Original-From: "Frauke Graeter" Sent to CCL by: "Frauke Graeter" [frauke.graeter===mpi-bpc.mpg.de] Dear all, Are you interested in protein (un)folding, protein non-native states and protein structure predictions by simulations? Then apply to the EMBO course "Proteins: Structure, Dynamics, and Energetics" at the Partner-Institute for Computational Biology (PICB) in Shanghai, China, from 10/05/06 to 17/05/06. Teachers: Protein free energy landscapese Vijay Pande, Stanford (confirmed) Chris Dobson and Michele Vendrusculo, University of Oxford (confirmed) Amadeo Caflish, University of Zuerich (confirmed) N.N. (Baker lab), University of Washington Structural Genomics/Proteomics William R. Atchley, North Carolina State University, Raleigh (confirmed) Luis Serrano, EMBL, Heidelberg (confirmed) Enforced protein unfolding/unbinding Jane Clarke, University of Cambridge (confirmed) Helmut Grubmueller, MPI for Biophysical Society, Goettingen (confirmed) For details see www.mpibpc.mpg.de/embo06 Applications are to be sent directly to Yechun Xu: yechun.xu[at]weizmann.ac.il Best regards, Frauke Graeter Andreas Dress From owner-chemistry@ccl.net Tue Nov 29 14:31:01 2005 From: "Close, David M. CLOSED:mail.etsu.edu" To: CCL Subject: CCL:G: Trouble with Gaussian03 Message-Id: <-30109-051129100228-1521-xQ7EbTtdeIdi7SQo6OFY8w++server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 29 Nov 2005 09:00:19 -0500 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED#,#mail.etsu.edu] While your diagnostics may show enough memory, the problem is likely that Gaussian is configured to write files only up to 2 Gbytes. Your program may be requesting more than this space for scratch files. The Gaussian manual shows how to break up the read-write files into 2 Gbyte blocks, using %rwf=a,1800mb,b,1800mb,c, etc. -----Original Message----- > From: owner-chemistry]=[ccl.net [mailto:owner-chemistry]=[ccl.net] Sent: Tuesday, November 29, 2005 7:45 AM To: Close, David M. Subject: CCL:G: Trouble with Gaussian03 Sent to CCL by: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= [FB153746+*+ATIL.CEA.FR] Dear CCL users, Gaussian03 has been compiled on two same machines, but in one case it is runing, on the other case, we have a trouble, see below. (machines: Xeon, RedHat9, with ifort, icc and mkl) Many thanks to let me know what to do in that case. I am looking forward to hearing from you. Regards, Frederic PS: a df -k command let us know that there is of course enough space on the disk. ________________________________________________________________________ ____ ________ ****************************************** Gaussian 03: IA32L-G03RevC.02 12-Jun-2004 29-Nov-2005 ****************************************** Erroneous write during file extend. write -1 instead of 4096 Probably out of disk space. Erroneous write during file extend. write -1 instead of 4096 Probably out of disk space. Write error in NtrExt1 Write error in NtrExt1: Bad address forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source Unknown 003371F1 Unknown Unknown Unknown Unknown 007E6B12 Unknown Unknown Unknown Unknown 007E5327 Unknown Unknown Unknown Unknown 00B935B0 Unknown Unknown Unknown Unknown 00B94102 Unknown Unknown Unknown Unknown 00A124E2 Unknown Unknown Unknown Unknown 00AFF886 Unknown Unknown Unknown l1.exe 0805CADA Unknown Unknown Unknown l1.exe 08114F4C Unknown Unknown Unknownhttp://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 Tue Nov 29 19:03:00 2005 From: "Sengen Sun sengensun(~)yahoo.com" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-30110-051129170328-694-IJU5tTo3Ph5S+qd0mwNyPw(!)server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 29 Nov 2005 13:03:20 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun/a\yahoo.com] My apologies if I am a bad guy again. But in contrast to the recent discussions by Wayne Steinmetz and Ulrike Salzner, Roald Hoffmann recently said: “Photoelectron spectroscopy has provided me with experimental proof of the ways orbitals interact.” (See: http://acswebcontent.acs.org/chemistry/autumn_2005.pdf) My questions are: 1. Is it possible that a Nobel Laureate is always more correct than other ordinary scientists? 2. Has science been evolving to such an era of complexity that human will never be able to resolve right and wrong about opposite philisophical views on the nature? In the other words, will there be such a day that science is made correct first unconditionally when a contradiction arises? Based on my experience of discussions on CCL, many graduate students and young scholars on this list are interested in this kind of questions. Thanks in advance for any comments on these issues. Sengen ------------------------------- > From: "Wayne Steinmetz" > Date: Fri, 11 Nov 2005 11:02:20 -0800 > Subject: CCL: question on molecular orbitals in CO > and NO > > > You have asked a host of questions around one theme, > qualitative MO > theory. > > An excellent summary of experimental data can be > found > in P. Krupenie, > The Band spectrum of Carbon Monoxide. This was > published by the US > Government Printing Office as NSRDS-NBS 5. The > government periodicals > desk at the UCLA library may help you track down > this > document. > Krupenie also published a critical review of > spectroscopic data for N2 > and O2 in the Journal of Physical Chemical Reference > Data. > > What is your audience for the qualitative use of MO > theory? I have been > convinced that MO theory provides a good reason for > bringing back the > index (Index censorum librorum). The index was not > established as an > absolute prohibition to reading materials but as a > warning. Only those > who are mature enough to understand the materials > should be exposed to > it. When I teach General Chemistry, I ask the > students to burn the > section on the MO treatment of diatomic molecules. > It > is usually a > swindle. I do use MO theory in the examination of > the > properties of > transition-metal complexes. In this case, crystal > field theory is a > swindle and VB doesn't explain much. > > I do use MO theory to discuss H2 as the treatment > provides insights into > the nature of bonding. Period. I found that the > extension to > homonuclear and heteronuclear diatomic molecules to > be > counterproductive. One has to be well versed in > quantum mechanics to > use MO theory correctly. Alexander Pope was right > in > stating "A little > knowledge is a dangerous thing; drink deeplyu or not > at all of the > Pyrean (sic) spring". > > In the right context, qualitative MO theory can be > used as a framework > for interpreting experimental data. The simplistic > approach in most > textbooks cannot be used in most cases to predict > the > results. Given > the low cost of programs such as Spartan that are > based on good physics, > why should we bother with the old, flawed approaches > at all? In this > case, the availability of good software should > change > the way we teach! > > Molecular orbitals are a means to an end. They are > not observables. > The electron density and the total energy are > measurable. This is one > of the reasons why DFT is so successful. I have > found > that the spacing > between the orbital energies and in some cases the > order depend > critically on the basis set. Hence, if very > sophisticated methods yield > different results for these intermediate pieces, why > should we encumber > students with them? > > I would be pleased to continue this discussion if > you wish. > > Wayne E. Steinmetz > Carnegie Professor of Chemistry > Woodbadge Course Director > Chemistry Department > Pomona College > 645 North College Avenue > Claremont, California 91711-6338 > USA > phone: 1-909-621-8447 > FAX: 1-909-707-7726 > Email: wsteinmetz .. pomona.edu > WWW: pages.pomona.edu/~wsteinmetz > > > > > > ---------------- > From: Ulrike Salzner > > Date: Fri, 11 Nov 2005 17:54:15 +0200 > Subject: CCL: question on molecular orbitals in CO > and NO > > > I was thinking about this a lot. I am still puzzled. > The first year > textbooks give the orbital diagram usually without > reference. I did HF > calculations, and as it was stated in the other > mails, > the order of > sigma and pi for N2 is different. Interestingly, > with > DFT sigma and pi > orbitals change place. But DFT orbitals are quite > controversial. > Experiment measures the order of states not of > orbitals, and correlated > methods reproduce the correct ordering of states but > they do not produce > molecular orbitals either. So where do those orbital > interaction > diagrams come from in the first place? Have > experimental states been > mapped onto matching MOs? It would be great if > someone > could provide a > reference regarding this mattter. > > Thanks, > Ulrike > > Ulrike Salzner > Associate Professor > Department of Chemistry > Bilkent University > 06800 Bilkent, Ankara > Turkey > > > > > > > __________________________________ > Yahoo! Music Unlimited > Access over 1 million songs. Try it free. > http://music.yahoo.com/unlimited/ > __________________________________ Yahoo! Music Unlimited Access over 1 million songs. Try it free. http://music.yahoo.com/unlimited/ From owner-chemistry@ccl.net Tue Nov 29 19:38:02 2005 From: "shireen alfalah shireenalfalah::hotmail.com" To: CCL Subject: CCL:G: transition state optmization Message-Id: <-30111-051129150617-17329-11RZJJerPUbYnNTGkiYBTw*server.ccl.net> X-Original-From: "shireen alfalah" Sent to CCL by: "shireen alfalah" [shireenalfalah__hotmail.com] Dear CCL users, i have been trying to submit a transition state search using Gaussian 03. The calculation stopped after some time and I can not know what is wrong. The end of the log file looks like: ............................................... Leave Link 716 at Tue Nov 29 20:46:35 2005, MaxMem= 6291456 cpu: 0.0 (Enter /usr/license/gaussian/g03/l9999.exe) YOU CAN LEAD A BOY TO COLLEGE.... BUT YOU CANNOT MAKE HIM THINK.... ELBERT HUBBARD Error termination request processed by link 9999. Error termination via Lnk1e in /usr/license/gaussian/g03/l9999.exe at Tue Nov 29 20:46:35 2005. Job cpu time: 0 days 0 hours 12 minutes 17.8 seconds. File lengths (MBytes): RWF= 14 Int= 0 D2E= 0 Chk= 6 Scr= 1 ** Address Error ** ........................................................ HAve any oe faced such a problem? May you help me in understnding what is going wrong with these calculations and how can I solve this problem? My input file look like: %chk=tsl_qst2 P HF/6-31G* OPT=(QST2,calcall,maxcyc=90) FREQ NOSYM Thanks in advance. Best regards, Shireen From owner-chemistry@ccl.net Tue Nov 29 20:13:00 2005 From: "Bob Johnson robertjo%%physics.upenn.edu" To: CCL Subject: CCL: Langevin Dynamics Message-Id: <-30112-051129171043-1200-2ArmIxMqLF0rLFlhs6YDNA:server.ccl.net> X-Original-From: Bob Johnson Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 29 Nov 2005 15:33:43 -0500 MIME-Version: 1.0 Sent to CCL by: Bob Johnson [robertjo _ physics.upenn.edu] Hello everyone, I am simulating a single stranded DNA molecule adsorbing to a carbon nanotube. I've conducted simulations with various amounts of water ranging from complete hydration to complete vacuum. I have also looked at how the DNA conformation about the nanotube changes upon removing water. It seems that the water effectively screens the DNA base-tube interactions. Removing the water allows the DNA to form a tighter conformation about the nanotube. Since, ultimately, I am interested in the DNA conformation about the nanotube in vacuo, would using Langevin dynamics for the adsorption process be useful? Thanks, Bob Johnson robertjo%x%physics.upenn.edu From owner-chemistry@ccl.net Tue Nov 29 20:48:00 2005 From: "Chunyi Sung juneyi1/./yahoo.com.tw" To: CCL Subject: CCL: BSSE for n-mers Message-Id: <-30113-051129150038-12168-U+SVJjY7jCqa4B1UKx5tBw|-|server.ccl.net> X-Original-From: "Chunyi Sung" Sent to CCL by: "Chunyi Sung" [juneyi1(0)yahoo.com.tw] Hi, I want to apply BSSE for two cases 1. AB+C---> AB_C 2 A..B+C--->A..B_C where C is a surface, AB and A..B adsorb(physical)on surface C. A..B is dissociated form of AB. In case one, I treated AB and C as two fragments to get BSSE. I'm not sure for case two, should I treat A..B and C as two fragmentas, or I should treat A, B, and C as three fragments? Thanks From owner-chemistry@ccl.net Tue Nov 29 21:48:00 2005 From: "Rick Venable rvenable|*|pollux.cber.nih.gov" To: CCL Subject: CCL: Langevin Dynamics Message-Id: <-30114-051129213805-15312-8mhwW3QmsZAdOCMVRPU8hg+*+server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 29 Nov 2005 21:35:59 -0500 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable*|*pollux.cber.nih.gov] On Tue, 29 Nov 2005, Bob Johnson robertjo%%physics.upenn.edu wrote: > Hello everyone, I am simulating a single stranded DNA molecule > adsorbing to a carbon nanotube. I've conducted simulations with > various amounts of water ranging from complete hydration to complete > vacuum. I have also looked at how the DNA conformation about the > nanotube changes upon removing water. It seems that the water > effectively screens the DNA base-tube interactions. Removing the water > allows the DNA to form a tighter conformation about the nanotube. > > Since, ultimately, I am interested in the DNA conformation about the > nanotube in vacuo, would using Langevin dynamics for the adsorption > process be useful? Thanks, > > Bob Johnson Yes and no; Langevin dynamics models solvent collisions, so the choice of a collision frequency affects the amount of damping. The use of underdamped systems (low collision frequency, 2/ps) has been shown to allow more torsional transitions per timestep than vacuum MD or Langevin dynamics at larger collision frequencies. This allows sampling more conformations in a given simulation. See: Loncharich RJ, Brooks BR, Pastor RW. Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide. Biopolymers. 1992 May;32(5):523-35. However, there's still the issue of electrostatics; an implicit solvent method may be needed to help get the correct DNA:nanotube binding constant. There's also the issue of screening the phosphates > from each other; an increased dielectric is one approach. ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable AT nih*gov ALT email: rvenable AT speakeasy*org -------------------------------------