From owner-chemistry@ccl.net Fri Mar 13 04:00:00 2009 From: "Johannes Hachmann jh388 a cornell.edu" To: CCL Subject: CCL:G: (correction) Energy change upon swapping two orbitals in Gaussian 98 Message-Id: <-38830-090313034801-13547-uUtQ0sDhHdMOb7NI6DtZKA * server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 13 Mar 2009 03:47:44 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh388/a\cornell.edu] Dear Yutao, it's hard to say what exactly is going on without a closer look, but if the calc doesn't take too long, try something like # UBLYP/6-31g(d) POP=FULL GFPRINT GFOLDPRINT SYMM=LOOSE GUESS=READ INT=ULTRAFINE STABLE=OPT That will take care of potential threshold and instability issues and you can compare the result to your swap result. Did you use GUESS=MIX in your very first calc? If not, a high symmetry guess might have led you to an instability. I am however a bit surprised that a swap within the occupied orbs helped... Best Johannes --------------------------------------------------------------- Johannes Hachmann Chan Research Group 140D Baker Laboratory Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853-1301 USA --------------------------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh388==cornell.edu#,#ccl.net > [mailto:owner-chemistry+jh388==cornell.edu#,#ccl.net] On Behalf > Of Yutao Yue yutao.yue:-:gmail.com > Sent: Thursday, March 12, 2009 3:16 PM > To: Hachmann, Johannes > Subject: CCL:G: (correction) Energy change upon swapping two > orbitals in Gaussian 98 > > Thank you very much Johannes, I did swap the two highest > OCCUPIED beta orbitals. I was also doubting that the original > solution was not stable. I compared the solutions before and > after swapping, the MO compositions are almost identical for > frontier orbitals, and only some minor differences for some > deeper orbitals. Plus, the S2 values, the NBO charges and > spins of some characteristic atoms (metal, etc) are almost > exactly the same, up to quite a few digits. > > On the other hand, although with highly similar MO > compositions, the MO energy themselves are fairly different > through all MOs including the deepest, e.g., the difference > for a single MO is on the order of 0.01 a.u.. > > By the way, I used the default SCF convergence level (which > is equivalent to conver=4). But I guess that's far from > introducing errors of this magnitude right? > > I wonder is it possible that Gaussian does something > artificial (and arbitrary? because in one case energy went up > and the other case it went down) to the MO energies, once the > initial guess swapping is introduced? > > Regards, > Yutao > > > On Thu, Mar 12, 2009 at 12:50 PM, Johannes Hachmann > jh388~!~cornell.edu wrote: > > > > Sent to CCL by: "Johannes Hachmann" [jh388]*[cornell.edu] > Dear Yutao, > > sounds to me like you might have landed on an > electronic instability the > first time. SCF for (transition-)metal compounds can be > very hard to > converge. Try STABLE=OPT starting from your original > calc without the > orbital swap and see whether that lowers the energy (in > that case, your swap > has introduced some mixing/symmetry breaking and led to > a more stable > state). You can check the S2 value of your two results > to see, whether your > state has changed. You might also want to check your > SCF convergence > threshold and DFT grid (although it should not make a > difference of 20mH). > > Generally, swapping the highest two HOMOs should not > change the energy at > all, but maybe you ment the HOMO-LUMO pair? A vanishing > HOMO-LUMO gap > indicates a system with nondynamic correlation, and you > might not want to > use a single reference method like DFT in the first place. > > Hope that helps. Best > > Johannes > > --------------------------------------------------------------- > Johannes Hachmann > > Chan Research Group > 140D Baker Laboratory > Department of Chemistry and Chemical Biology > Cornell University > Ithaca, NY 14853-1301 > USA > --------------------------------------------------------------- > > > > > > -----Original Message----- > > From: owner-chemistry+jh388==cornell.edu-.-ccl.net > > [mailto:owner-chemistry+jh388 > ==cornell.edu-.-ccl.net] On Behalf > > Of Yutao Yue Yutao.Yue#,#gmail.com > > Sent: Thursday, March 12, 2009 10:55 AM > > To: Hachmann, Johannes > > Subject: CCL:G: (correction) Energy change upon swapping two > > orbitals in Gaussian 98 > > > > > > Sent to CCL by: "Yutao Yue" [Yutao.Yue- -gmail.com] (sorry > > the energy changes are 0.02 a.u., NOT 0.2 a.u.) > > > > Dear All, > > > > I have a successful G98 single point calculation > > (UBLYP/6-31G*) on a metal-containing system of around 70 > > atoms. I use the result MOs as initial guess, but swapped the > > two highest occupied beta orbitals (which are supposed to be > > highly competing with each other) upon reading in the initial > > guess, to do another G98 single point calculation on the same > > system. I then arrived at a solution that, the frontier > > orbitals are almost identical to the original solution > > including the ordering of the beta orbitals, while the single > > point energy is 0.02 a.u. lower! > > > > Similar calculations was done with UBPW91/6-31G*, and again > > the orbitals go back to original ordering, but the single > > point energy is 0.02 a.u. higher now! > > > > Anybody have any idea about those energy changes? > > > > Thanks a lot and wish everybody a nice day! > > > > -Yutao Yue > > > > > > > > -= This is automatically added to each message by the mailing > > script =- To recover the email address of the author of the > > message, please change the strange characters on the top line > > to the -.- sign. You can also look up the > X-Original-From: line > > > in the mail header.> Conferences: > > > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > > -= This is automatically added to each message by the > mailing script =- > > > > 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/chemistry/searchccl/index.shtml> > > > > > From owner-chemistry@ccl.net Fri Mar 13 06:09:01 2009 From: "mi yang agri_chemist]![yahoo.com" To: CCL Subject: CCL: Real NBO charge Message-Id: <-38831-090313052811-27632-NH0LBnK5uxEEXkmyJeBTqg- -server.ccl.net> X-Original-From: "mi yang" Date: Fri, 13 Mar 2009 05:28:07 -0400 Sent to CCL by: "mi yang" [agri_chemist(~)yahoo.com] Dear CCL users I want to confirm one concept. I have optimized and the performed an NBO analysis on an open shell complex by using key word {pop=nboread gfinput iop(6/7=3)}. In the output file there are three values of NBO charges (moving from start to end) each is different from the first one. Although Gauss View reads the first one but I am wondering which would be the right value i.e. first, second or the third one.? Any comment would be highly appreciated.. From owner-chemistry@ccl.net Fri Mar 13 08:12:00 2009 From: "Tatsiana Kirys nushki^^mail.ru" To: CCL Subject: CCL: compare two multivariate distributions Message-Id: <-38832-090313071123-26140-5D/tWg1vrepnJbkv8NqSgw]=[server.ccl.net> X-Original-From: "Tatsiana Kirys" Date: Fri, 13 Mar 2009 07:11:19 -0400 Sent to CCL by: "Tatsiana Kirys" [nushki#mail.ru] Dear All, i need to find whether two multivariate distributions are the same. There are 2 samplings of a n-variate x=(x_1, x_2, ..., x_n) (where n=1,2,3,4,5), and x_i, x_j are not independent. First sampling consists of 16 000 points, second 2000. We want to test whether the samplings are from the same distribution. many thanks Tatsiana Kirys Ph.D. student UIIP NAS of Belarus From owner-chemistry@ccl.net Fri Mar 13 09:32:01 2009 From: "Karine Costuas kcostuas^^univ-rennes1.fr" To: CCL Subject: CCL:G: NBO 3.1 in gaussian : d-elements Message-Id: <-38833-090313092645-29726-6iwh+f173ZkDPSgDAFHvvQ_._server.ccl.net> X-Original-From: "Karine Costuas" Date: Fri, 13 Mar 2009 09:26:41 -0400 Sent to CCL by: "Karine Costuas" [kcostuas^-^univ-rennes1.fr] Dear CCLers, We recently bought the GENNBO 5.0. We are currently studying a problem of reactivity in Fe containing complexes with Gaussian. We were surprized to have really different NBO analysis between the NBO 3.1 included in Gaussian 03, and the NBO 5.0 (post-treatment of the file47 obtained with archive keyword). Here are the atomic charges we obtained for two characteristic atoms: Gaussian 03 E.01 (B3LYP, LANL2DZ + pol) NBO 3.1: Fe -1.010, C -0.218 NBO 5.0: Fe -0.167, C -0.158 Gaussian 03 E.01 (B3LYP, AHLRICHS DZ all electrons) (same atoms, same geometry) NBO 3.1: Fe -0.648, C -0.182 NBO 5.0: Fe +0.414, C -0.38 We are facing the same problems for ruthenium systems. I must confess I have difficulties to understand what's going on. Does anyone know if NBO 3.1 takes correctly into accound d orbitals. Moreover, does anyone already face such a change in charges just by modifying the atomic basis set? Thanks in advance, sincerely, Karine Costuas CNRS researcher, University of Rennes 1 France (research in danger here!) From owner-chemistry@ccl.net Fri Mar 13 10:07:01 2009 From: "Wendy Warr wendy]_[warr.com" To: CCL Subject: CCL: Computational chemistry - arm chair scientists Message-Id: <-38834-090313093515-14051-M4AHrSdxgMvcRhYtj2BaMw:-:server.ccl.net> X-Original-From: "Wendy Warr" Date: Fri, 13 Mar 2009 09:35:11 -0400 Sent to CCL by: "Wendy Warr" [wendy:+:warr.com] There is a lot of truth in what Michel Petitjean had to say. Subscribers to this list might like to read about the status and definition of cheminformatics in my article at http://www.qsarworld.com/cheminformatics-education.php If you reply to the list about this, please copy your message to me at wendy!A!warr.com since I am not a regular reader. Wendy Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./fax +44 (0)1477 533837 wendy!A!warr.com http://www.warr.com From owner-chemistry@ccl.net Fri Mar 13 11:56:00 2009 From: "Nuno A. G. Bandeira nuno.bandeira[A]ist.utl.pt" To: CCL Subject: CCL:G: NBO 3.1 in gaussian : d-elements Message-Id: <-38835-090313114346-5597-HUq3QXMh9NW7QOz4W67wCQ-,-server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Type: multipart/mixed; boundary="=======AVGMAIL-49BA7F210000=======" Date: Fri, 13 Mar 2009 15:43:29 +0000 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira-$-ist.utl.pt] --=======AVGMAIL-49BA7F210000======= Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Karine Costuas kcostuas^^univ-rennes1.fr wrote: > Sent to CCL by: "Karine Costuas" [kcostuas^-^univ-rennes1.fr] > We recently bought the GENNBO 5.0. We are currently studying a problem of reactivity in Fe containing complexes with Gaussian. We were surprized to have really different NBO analysis between the NBO 3.1 included in Gaussian 03, and the NBO 5.0 (post-treatment of the file47 obtained with archive keyword). > > Here are the atomic charges we obtained for two characteristic atoms: > > Gaussian 03 E.01 (B3LYP, LANL2DZ + pol) > NBO 3.1: Fe -1.010, C -0.218 > NBO 5.0: Fe -0.167, C -0.158 > > Gaussian 03 E.01 (B3LYP, AHLRICHS DZ all electrons) (same atoms, same geometry) > NBO 3.1: Fe -0.648, C -0.182 > NBO 5.0: Fe +0.414, C -0.38 > Dear Karine, While NPA charges should chemically make more sense than Mulliken charges they are still just one more way of dividing the charge between atoms. The answer to your question is yes, NBO 3.1 has been used successfully with d elements. In fact most people that use Gaussian only use the 3.1 version. 5.0 is an upgrade which should (in principle at least) provide more reliable results. I notice that you did not use polarisation functions in the second run which may harm the proper description of the density matrix. Add at least one d function for every p element and one f for iron, or better still use a TZVP basis set for iron. Regards, Nuno -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student |,| IST,Lisbon -- --=======AVGMAIL-49BA7F210000======= Content-Type: multipart/alternative; boundary="=======AVGMAIL-49BA7F210000=======" --=======AVGMAIL-49BA7F210000======= Content-Type: text/plain; x-avg=cert; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Content-Description: "AVG certification" No virus found in this outgoing message. Checked by AVG - www.avg.com Version: 8.0.237 / Virus Database: 270.11.13/1999 - Release Date: 03/13/09 0= 5:59:00 --=======AVGMAIL-49BA7F210000=======-- --=======AVGMAIL-49BA7F210000=======-- From owner-chemistry@ccl.net Fri Mar 13 12:31:01 2009 From: "Sergio Mares-Samano sergio.mares-samano###postgrad.manchester.ac.uk" To: CCL Subject: CCL: QSAR software Message-Id: <-38836-090313073514-29640-11sWUjOLKIwfb47/2t4nGQ=-=server.ccl.net> X-Original-From: Sergio Mares-Samano Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 13 Mar 2009 11:01:04 +0000 MIME-Version: 1.0 Sent to CCL by: Sergio Mares-Samano [sergio.mares-samano^_^postgrad.manchester.ac.uk] Dear All, I'm looking for QSAR software other than the most popular currently available e.g Tripos. I would be very grateful if someone is able to provide me with some options. I am particularly interested in free/open source software. Thank you very much in advance. Sergio Mares-Samano The University of Manchester Manchester United Kingdom From owner-chemistry@ccl.net Fri Mar 13 13:12:00 2009 From: "Dipl.-Ing. Thomas Mitterfellner thomas.mitterfellner,tugraz.at" To: CCL Subject: CCL: Turbomole 5.8: Generating localized orbitals Message-Id: <-38837-090313114137-5423-y39BanZ7RKvz3T38LgOKrQ]*[server.ccl.net> X-Original-From: "Dipl.-Ing. Thomas Mitterfellner" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Fri, 13 Mar 2009 16:07:19 +0100 MIME-Version: 1.0 Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" [thomas.mitterfellner..tugraz.at] Hello! I am trying to generate localized orbitals for plotting in gOpenMol with Turbomole 5.8. However, the documentation is rather unclear on how to prepare the input file, whether to use the (unsupported) moloch program or the dscf program, how to choose the orbitals to be plotted etc. Could anyone give me a sample input file (or rather the keywords needed) to perform the localization of mos? Thank you, Thomas From owner-chemistry@ccl.net Fri Mar 13 13:40:01 2009 From: "Kalju Kahn kalju^chem.ucsb.edu" To: CCL Subject: CCL:G: compare two multivariate distributions Message-Id: <-38838-090313124145-25480-uUtQ0sDhHdMOb7NI6DtZKA_+_server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 13 Mar 2009 09:41:26 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju]|[chem.ucsb.edu] Tatsiana, I think it is appropriate to analyze your two multivariate data (n=5) sets as two sets of five uni-variate distributions and ask for each of the five variables if the samplings are from the same distribution or nor. Samplings are likely from the same distribution if their moments are the same within the confidence level you specify. The first four moments are: 1) Mean; use Student's t-test (e.g. Welch's formula if you do not know that variances are the same) 2) Variance; use the F-test for this 3) Skewness; one usually just tests that the skewness is zero, i.e. that the distribution is normal. I believe the t-test and F-test assume zero skewness. The standard error of skewness is Sqrt(6/Npoints), so for Gaussian distribution skewness should be zero within 2*Sqrt(6/Npoints) 4) Kurtosis or peakedness; again one usually tests that the distribution is Gaussian for the same reason as for skewness. Notice that the Gaussian distribution has kurtosis of 3. The standard error of kurtosis is Sqrt(24/N), so for Gaussian distribution kurtosis should be 3 within 2*Sqrt(24/N). You can use statistical or general math software (e.g. Mathematica) to easily calculate the skewness and kurtosis of your ten uni-variate distributions; if all these are normal perform the F-test, then proceed with the appropriate t-test. If the distributions are not normal, you need to look up more advanced tests to compare variances and means. P.S. That could be considered "computational chemistry", right :) Kalju > > Sent to CCL by: "Tatsiana Kirys" [nushki#mail.ru] > Dear All, > > i need to find whether two multivariate distributions are the same. > > There are 2 samplings of a n-variate x=(x_1, x_2, ..., x_n) (where > n=1,2,3,4,5), > and x_i, x_j are not independent. > First sampling consists of 16 000 points, second 2000. > We want to test whether the samplings are from the same distribution. > > > many thanks > Tatsiana Kirys > Ph.D. student > UIIP NAS of Belarus > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Fri Mar 13 15:12:01 2009 From: "Niels Johan Christensen njc%a%life.ku.dk" To: CCL Subject: CCL: QSAR software Message-Id: <-38839-090313143432-22112-hqU1GQ/Hoz+7RZoplGdmDQ|server.ccl.net> X-Original-From: "Niels Johan Christensen" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 13 Mar 2009 18:33:44 +0100 Mime-Version: 1.0 Sent to CCL by: "Niels Johan Christensen" [njc]^[life.ku.dk] Dear Sergio. I am sure you will be able to find a fair bit of opensource/freeware programs for the calculation of various molecular descriptors if you spend some time searching the web. The choice of descriptors depends on the problem you wish to investigate. It may be a good start to look at the fairly large collection of descriptors provided by this descriptor calculator GUI (from the CDK toolkit): http://rguha.net/code/java/cdkdesc.html To the best of my knowledge, there is no open-source COMFA like software out there. After the calculation of descriptors, you´ll need some kind of regression software to establish a relationship between the calculated descriptors and the activity/property of interest. SciLab is a free matlab clone, and a great kind of environment for working with multivariate problems (among other things). Check out the toolboxes as well - you´ll find PLS/PCR regression, ANN, and whatnot: http://www.scilab.org/contrib/index_contrib.php?page=download&category=MODELING%20AND%20CONTROL%20TOOLS Best, Niels >>> "Sergio Mares-Samano sergio.mares-samano###postgrad.manchester.ac.uk" 03/13/09 12:01 PM >>> Sent to CCL by: Sergio Mares-Samano [sergio.mares-samano^_^postgrad.manchester.ac.uk] Dear All, I'm looking for QSAR software other than the most popular currently available e.g Tripos. I would be very grateful if someone is able to provide me with some options. I am particularly interested in free/open source software. Thank you very much in advance. Sergio Mares-Samano The University of Manchester Manchester United Kingdomhttp://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 Fri Mar 13 15:51:01 2009 From: "Michel Petitjean petitjean.chiral++gmail.com" To: CCL Subject: CCL: compare two multivariate distributions Message-Id: <-38840-090313151550-29024-rNabDCjNpjqL7SYZZ8JKWQ]=[server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 13 Mar 2009 20:15:37 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral###gmail.com] Tatsiana, You have two samples assumed to come from a common parent multivariate distribution in R5 and you would like to test this hypothesis. If you know the parent distribution, you may test if the first sample is issued from it and then if the second sample if issued from it. But probably you do not know the parent distribution. In this case you need to find in the literature a distribution-free test for this situation. I'm not expert in this area, so I suggest that you formulate your question in the sci.stat.math newsgroup, in which you should get the adequate information. Best regards, Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean(-)cea.fr, petitjean.chiral(-)gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.html ------------------------------------------------------------------------------------------ Sent to CCL by: "Tatsiana Kirys" [nushki#mail.ru] Dear All, i need to find whether two multivariate distributions are the same. There are 2 samplings of a n-variate x=(x_1, x_2, ..., x_n) (where n=1,2,3,4,5), and x_i, x_j are not independent. First sampling consists of 16 000 points, second 2000. We want to test whether the samplings are from the same distribution. many thanks Tatsiana Kirys Ph.D. student UIIP NAS of Belarus From owner-chemistry@ccl.net Fri Mar 13 16:26:01 2009 From: "Mikko Vainio mikko.vainio_+_abo.fi" To: CCL Subject: CCL: QSAR software Message-Id: <-38841-090313154713-11912-vHw37uiVNlpHiuGnaViDIA#%#server.ccl.net> X-Original-From: Mikko Vainio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 13 Mar 2009 21:03:47 +0200 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mikko.vainio===abo.fi] Dear Sergio, McQSAR is a somewhat experimental but free tool for QSAR model generation and validation: http://web.abo.fi/~mivainio/mcqsar/ It uses a genetic algorithm to derive linear and/or nonlinear models on pre-computed sets of descriptors. Regards, Mikko Vainio Sergio Mares-Samano sergio.mares-samano###postgrad.manchester.ac.uk wrote: > > Sent to CCL by: Sergio Mares-Samano > [sergio.mares-samano^_^postgrad.manchester.ac.uk] > Dear All, > > I'm looking for QSAR software other than the most popular currently > available e.g Tripos. I would be very grateful if someone is able to > provide me with some options. I am particularly interested in free/open > source software. > > Thank you very much in advance. > > Sergio Mares-Samano > The University of Manchester > Manchester > United Kingdom > > From owner-chemistry@ccl.net Fri Mar 13 17:02:00 2009 From: "Tom Stockfisch t.stockfisch|,|cox.net" To: CCL Subject: CCL: QSAR software Message-Id: <-38842-090313145611-26164-nqkkuvMI1L6HN5S86lO+2Q.:.server.ccl.net> X-Original-From: Tom Stockfisch Content-Type: multipart/alternative; boundary=Apple-Mail-3-960894767 Date: Fri, 13 Mar 2009 10:42:12 -0700 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Tom Stockfisch [t.stockfisch*|*cox.net] --Apple-Mail-3-960894767 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi Sergio - Are you looking for 3D QSAR (like COMFA) or 2D QSAR? Are you looking for statistical prediction model creation methods (like neural nets, decision trees, PLS) or descriptor calculations? Tom Tom Stockfisch t.stockfisch~!~cox.net http://www.tstockfisch.com On Mar 13, 2009, at 4:01 AM, Sergio Mares-Samano sergio.mares- samano###postgrad.manchester.ac.uk wrote: > > Sent to CCL by: Sergio Mares-Samano [sergio.mares- > samano^_^postgrad.manchester.ac.uk] > Dear All, > > I'm looking for QSAR software other than the most popular currently > available e.g Tripos. I would be very grateful if someone is able > to provide me with some options. I am particularly interested in > free/open source software. > > Thank you very much in advance. > > Sergio Mares-Samano > The University of Manchester > Manchester > United Kingdom > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/ > sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/> > --Apple-Mail-3-960894767 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hi Sergio -

Are you looking for 3D QSAR (like COMFA) = or 2D QSAR?
Are you looking for statistical prediction model = creation methods (like neural nets, decision trees, PLS) or descriptor = calculations?

Tom

Tom = Stockfisch
http://www.tstockfisch.com

On Mar 13, 2009, at 4:01 AM, = Sergio Mares-Samano sergio.mares-samano###postgrad.manchester.ac.uk = wrote:


Sent to CCL by: Sergio Mares-Samano = [sergio.mares-samano^_^postgrad.manchester.ac.uk]
Dear All,

I'm looking for QSAR software = other than the most popular currently available e.g Tripos. I would be = very grateful if someone is able to provide me with some options. I am = particularly interested in free/open source software.

Thank = you very much in advance.

Sergio Mares-Samano
The University of Manchester
Manchester
United = Kingdom



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= --Apple-Mail-3-960894767-- From owner-chemistry@ccl.net Fri Mar 13 17:36:01 2009 From: "David Mannock dmannock*o*ualberta.ca" To: CCL Subject: CCL: Computational Chemistry - Arm chair Scientists !!! Message-Id: <-38843-090313054638-29347-p6aXGvYBHq/1KgFeroNVtA^^^server.ccl.net> X-Original-From: David Mannock Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Fri, 13 Mar 2009 02:55:51 -0600 Mime-Version: 1.0 Sent to CCL by: David Mannock [dmannock**ualberta.ca] Michelle, There have always been trends and rankings in science and as someone who started my academic life as a biologist, changed to lipid biophysics, then organic chemistry and now am trying to learn computational chemistry techniques, I think that this emergence of computers in chemistry is a phase. eventually the computer chemists will come to the same conclusion as the experimentalists, which is "rubbish in, rubbish out". Sometimes computational chemists forget that it is frequently possible to perform experiments on the systems on which they work and so generate real numbers. This is where the combined approach, preferably done by experts in each area, yields useful progress, whereas the never ending search for the perfect force field is like searching for the ever elusive Yeti/Sasquatch! Excuse the humour! I'm English and I can't help it! Dave At 02:24 AM 3/12/2009, you wrote: >Sent to CCL by: Michel Petitjean [petitjean.chiral%a%gmail.com] >Dear All, > >Here (France), only experimental chemistry is recognized. Tasks >requiring computers are often considered as low level secondary tasks, >easy to do (or to be done by some student). Proof: the ten years old >son of the experimentalist plays on the net all the day, so computer >tasks are easy to do (however it may be boring the experimentalist). >The true researchers are the experimentalists, and the other ones must >serve the experimentalists because they are not true researchers. Only >one exception: the quantum chemists (called here "theoretical >chemists") constitute a well recognized community, of which many >members consider themselves as superior to any other chemist, probably >due to the stupid ranking math > physics > chemistry > biology > >social sciences and all the rest (quantum chemistry thus appears >closer to physics than the rest of chemistry). A consequence is that >chem/info people not falling in the quantum chemistry field are >ignored, and by no way >are considered: difficulties to get funds, evaluation of activity done >by quantum chemists who do not care, etc. > >By the way, please let me know where I can read the definition of the >following fields: >computational chemistry, theoretical chemistry, mathematical >chemistry, quantum chemistry, cheminformatics, chemometrics, >structural bioinformatics, molecular modeling. >Particularly, I would be interested to know how cheminformatics is >defined, and in what it differs from the other fields enumerated >above. > >Finally, in-silico chemists play and do not work. Proof: they have >time to read and to write posts in the CCL forum while the >experimentalists really work. > >Thanks. > >Michel Petitjean, >DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, >91191 Gif-sur-Yvette Cedex, France. >Phone: +331 6908 4006 / Fax: +331 6908 4007 >E-mail: michel.petitjean^cea.fr, petitjean.chiral^gmail.com >http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html > >Sent to CCL by: "Soumya Samineni" [soumya_samineni|*|rediffmail.com] >Dear all, > With the ever increasing computational power, there has been an >enormous growth in the theoretical/computational chemistry ( >personally i feel the word "Theoretical Chemistry" has been abused by >considering it as an alternative word for "Computational chemsitry" by >people practising computational chemistry). while people doing >computational chemistry are also growing like mushrooms and the volume >of pages occupied by it has also exploded, the number of people doing >the theoretical chemistry (analytical) is dwindling with time. > Any ways: It would be nice to hear comments from the leading (and >novice) experts of computational and theoretical chemistry regarding >the general feeling of the experimental community (who consider that >they toil pretty hard physically for every bit of the sentence they >write .. ) that we are "Arm chair scientists", who like to quench our >thirst for science sitting before a computer all through the day and >gulping loads of liquids !! > >I hope a small debate would make things more clear. > >regards >SoumyaDr David Mannock 339 Med Sci Bldg, Dept of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7 Canada Tel: 1-780-492-2412 FAX: 1-780-492-0886 From owner-chemistry@ccl.net Fri Mar 13 18:16:00 2009 From: "Sergio Emanuel Galembeck segalemb{=}usp.br" To: CCL Subject: CCL: Real NBO charge Message-Id: <-38844-090313141135-11837-BxcFXkHlxfRv3ltCuBHs6g _ server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 13 Mar 2009 14:11:21 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb]*[usp.br] Dear Mi Yang, When you use unrestricted methods, NBO treats alpha and beta orbitals in a separated way. As, the first set of charges are the total charges (alpha + beta), the second for alpha electrons and the third for beta electrons. Hope this help you, Sergio Emanuel Galembeck Citando "mi yang agri_chemist]![yahoo.com" : > > Sent to CCL by: "mi yang" [agri_chemist(~)yahoo.com] > Dear CCL users I want to confirm one concept. > > I have optimized and the performed an NBO analysis on an open shell =20 > complex by using key word {pop=3Dnboread gfinput iop(6/7=3D3)}. > > In the output file there are three values of NBO charges (moving =20 > from start to end) each is different from the first one. Although =20 > Gauss View reads the first one but I am wondering which would be the =20 > right value i.e. first, second or the third one.? Any comment would =20 > be highly appreciated.. > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > From owner-chemistry@ccl.net Fri Mar 13 18:45:00 2009 From: "kamel kamel_mansouri-.-yahoo.fr" To: CCL Subject: CCL: QSAR software Message-Id: <-38845-090313172116-18325-eDAy5arUVRUdMo0s1jdFiw[*]server.ccl.net> X-Original-From: kamel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 13 Mar 2009 21:25:17 +0100 MIME-Version: 1.0 Sent to CCL by: kamel [kamel_mansouri:-:yahoo.fr] you can try weka, that's a free java package for data mining. developed at waikato university, new zeeland. http://www.cs.waikato.ac.nz/ml/weka/ Niels Johan Christensen njc%a%life.ku.dk a écrit : > Sent to CCL by: "Niels Johan Christensen" [njc]^[life.ku.dk] > Dear Sergio. > > I am sure you will be able to find a fair bit of opensource/freeware > programs for the calculation of various molecular descriptors if you > spend some time searching the web. The choice of descriptors depends on > the problem you wish to investigate. It may be a good start to look at > the fairly large collection of descriptors provided by this descriptor > calculator GUI (from the CDK toolkit): > > http://rguha.net/code/java/cdkdesc.html > > To the best of my knowledge, there is no open-source COMFA like software > out there. > > After the calculation of descriptors, you´ll need some kind of > regression software to establish a relationship between the calculated > descriptors and the activity/property of interest. SciLab is a free > matlab clone, and a great kind of environment for working with > multivariate problems (among other things). Check out the toolboxes as > well - you´ll find PLS/PCR regression, ANN, and whatnot: > > http://www.scilab.org/contrib/index_contrib.php?page=download&category=MODELING%20AND%20CONTROL%20TOOLS > > Best, > Niels > > > > >>>> "Sergio Mares-Samano >>>> > sergio.mares-samano###postgrad.manchester.ac.uk" > 03/13/09 12:01 PM >>> > > Sent to CCL by: Sergio Mares-Samano > [sergio.mares-samano^_^postgrad.manchester.ac.uk] > Dear All, > > I'm looking for QSAR software other than the most popular currently > available e.g Tripos. I would be very grateful if someone is able to > provide me with some options. I am particularly interested in free/open > source software. > > Thank you very much in advance. > > Sergio Mares-Samano > The University of Manchester > Manchester > United Kingdomhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > > ___________________________________________________________________________ Yahoo! Mail réinvente le mail ! Découvrez le nouveau Yahoo! Mail et son interface révolutionnaire. http://fr.mail.yahoo.com From owner-chemistry@ccl.net Fri Mar 13 19:20:01 2009 From: "Guenter Grethe ggrethe\a/comcast.net" To: CCL Subject: CCL: Last Call - Abstract Submission for CINF-FIZ Scholarships Message-Id: <-38846-090313190011-27373-vT9UqPQ0dFwthJqJeFZvaw(a)server.ccl.net> X-Original-From: "Guenter Grethe" Date: Fri, 13 Mar 2009 19:00:07 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe|*|comcast.net] 2009 CINF Scholarship for Scientific Excellence Sponsored by FIZ Chemie Berlin The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by FIZ Chemie Berlin is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Three scholarships valued at $1,000 each will be given out at the 238th ACS National Meeting in Washington, DC, August 16 20, 2009. Applicants have to be enrolled at a certified college or university. They have to present a poster during a poster session at the National Meeting. Abstracts for the posters have to be submitted electronically through OASYS before March 20, 2009. Please, go to http://oasys.acs.org/acs/238nm/cinf/papers/index.cgi and look for the CINF Scholarship" session. To enter your abstract, just follow the instructions. If you encounter any problems, please contact the Chair of the selection committee, Guenter Grethe at ggrethe[]comcast.net. At the time you are submitting your short abstract, you have to inform the Chair that you are applying for a scholarship. Additionally, a 2,000-word long abstract describing the work to be presented has to be sent in electronic form to the Chair of the selection committee by June 15, 2009. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced at the meeting. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked Winner of the CINF-FIZ Chemie Berlin Academic Scientific Excellence at the poster session. Guenter Grethe From owner-chemistry@ccl.net Fri Mar 13 20:55:00 2009 From: "James J. P. Stewart MrMOPAC() att.net" To: CCL Subject: CCL: Computational Chemistry - Arm chair Scientists !!! Message-Id: <-38847-090313205127-14801-v3iabS/6xtj6//Kasl0B9Q[]server.ccl.net> X-Original-From: "James J. P. Stewart" Date: Fri, 13 Mar 2009 20:51:23 -0400 Sent to CCL by: "James J. P. Stewart" [MrMOPAC]-[att.net] David Mannock said, "Sometimes computational chemists forget that it is frequently possible to perform experiments on the systems on which they work and so generate real numbers." While true in most cases, the converse is also true sometimes. To illustrate: The NIST WebBook represents one of the finest collections of thermochemical data extant. During the development of PM6, a few instances were found in the WebBook where reference heats of formation were simply not credible, and using semiempirical methods I generated what I considered to be more accurate values. On being informed of this, NIST updated the WebBook to add or replace the experimental values with the theoretically predicted values. For a list of these species, see: http://webbook.nist.gov/cgi/cbook.cgi?Source=2004STE6-10&Units=SI&Mask=1 The point is that although experimentalists generate real numbers, on rare occasions the numbers in compendia such as the WebBook might be of questionable accuracy. This may be due to any one of several reasons, for example the experimental work might involve questionable steps, the arithmetic involved in converting from experimental measurement to heat of formation might be faulty, the formula used might be incorrect, there might be typographic errors in the journal article, or the printed heat of formation might be in error by a sign. Examples of all of these errors were found on reviewing the original literature written by experimentalists. Simple computational chemistry calculations, requiring only a few seconds each, revealed the potential errors. That the reported data were inaccurate was confirmed by examining the original articles and identifying the error. As a semiempiricalist, I am acutely aware of the great debt we owe to the experimental community for generating reference data, but to suggest that collections of experimental data should be regarded as infallibly accurate and that computational results should be regarded cum granus salis is simple unwarrented. Jimmy ( .. .. ) .-----------------oOOo----(_)----oOOo--------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: MrMOPAC*OpenMOPAC.net | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | http://openmopac.net/ | | USA | SKYPE: Jimmy.Stewart2 GMT 1500 - 0200| | .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo.| | .-----------------------\ (----( )---------------------------------------. \_) ) / (_/