From owner-chemistry@ccl.net Tue Nov 27 01:57:01 2007 From: "akef afaneh akef_afnh#,#yahoo.com" To: CCL Subject: CCL: statistical methods Message-Id: <-35721-071127015624-23095-Lm5wtjObSnVrqOX+nYP6fA!=!server.ccl.net> X-Original-From: akef afaneh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1030799763-1196146571=:12931" Date: Mon, 26 Nov 2007 22:56:11 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: akef afaneh [akef_afnh/a\yahoo.com] --0-1030799763-1196146571=:12931 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Take these two references: 1- Molecular Modeling Principles and Applications; 2nd ed, Andrew R. Leach. 2- (QSAR) Models of Mutagens and Carcinogens Quantitative Structure-Activity Relationship; Edited By Romualdo Benigni "nahren manuel meetnahren:-:yahoo.com" wrote: Hi Nurca, This is a general question. The Adv of MLR is , models can be interpreted. with neural network that is very unlikely. so it all depends what you want the QSAR to be. nahren "ilknurca41#gmail.com" wrote: Sent to CCL by: ilknurca41*o*gmail.com Hi everybody, What do you think about which is the most effective statistical method in drug design using QSAR?(Multiple Lineer Regression, Partial Least Square, Principle Component Analysis, Neural Networks, etc....) Thanks for attention. Kind regards... ilknurca41:-:gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_message http://www.ccl.net/chemistry/s! ub_unsub.shtml--------------------------------- Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. --------------------------------- Get easy, one-click access to your favorites. Make Yahoo! your homepage. --0-1030799763-1196146571=:12931 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Take these two references:
1-     Molecular Modeling Principles and Applications; 2nd ed, Andrew R. Leach.
2-     (QSAR) Models of Mutagens and Carcinogens Quantitative Structure-Activity Relationship; Edited By Romualdo Benigni


"nahren manuel meetnahren:-:yahoo.com" <owner-chemistry^^ccl.net> wrote:
Hi Nurca,
This is a general question. The Adv of MLR is ,  models can be interpreted.
with neural network that is very unlikely.
so it all depends what you want the QSAR to be.
 
nahren

"ilknurca41#gmail.com" <owner-chemistry- -ccl.net> wrote:

Sent to CCL by: ilknurca41*o*gmail.com

Hi everybody,
What do you think about which is the most effective statistical
method in drug design using QSAR?(Multiple Lineer Regression,
Partial Least Square, Principle Component Analysis, Neural Networks,
etc....)

Thanks for attention. Kind regards...

ilknurca41:-:gmail.com


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Get easy, one-click access to your favorites. Make Yahoo! your homepage. --0-1030799763-1196146571=:12931-- From owner-chemistry@ccl.net Tue Nov 27 04:43:01 2007 From: "Shaillay Dogra shaillay**strandls.com" To: CCL Subject: CCL: Data Modeling Challenge Message-Id: <-35722-071127041706-26331-d+ZdTwaTG3lMTXB8NZdTZg#server.ccl.net> X-Original-From: Shaillay Dogra Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 27 Nov 2007 14:44:55 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Shaillay Dogra [shaillay++strandls.com] Hi All, QSAR-World is holding a data modeling competition. For details, visit: http://www.qsarworld.com/ The modeling challenge is on till the 27th of December. Looking forward to your enthusiastic participation! Best regards, Shaillay Dogra Scientific Editor, QSAR-World (http://www.qsarworld.com/) From owner-chemistry@ccl.net Tue Nov 27 05:48:01 2007 From: "Aggelos Avramopoulos aggavramop ~~ yahoo.gr" To: CCL Subject: CCL:G: =?iso-8859-7?q?=C8=DD=EC=E1:=20CCL:G:=20NLO=20hyperpolarizability=20calcu?= =?iso-8859-7?q?lation=20-->=20gamma=20tensors=20(THG)=3F?= Message-Id: <-35723-071125043901-2209-WTQQpNJ4JzBSzJn1pLO+xA-.-server.ccl.net> X-Original-From: Aggelos Avramopoulos Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1856110602-1195979927=:25343" Date: Sun, 25 Nov 2007 08:38:47 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Aggelos Avramopoulos [aggavramop|,|yahoo.gr] --0-1856110602-1195979927=:25343 Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 8bit Hi Anthony You can use alpha or beta results of GAUSSIAN to compute gamma, by implementing a simple numericall differentiation with respect to the field scheme. Thus, by using beta for expample, just use the first derivative of beta as follows g(zzzz) = dB(zzz)/dFz, gzzxx= dB(zzx)/dFx etc. The only question is if gaussian can compute alpha or beta in the presence of the field. If not then you can compute gamma by taking the fourth derivative of the energy with respect of the field. The latter requires the calculation of the following field dependent energies: E(F), E(-F), E(2F), E(2F) and E(0). If you do not find the relevant expression i can post it to you. Aggelos Avramopoulos "Isaac Bersuker bersuker[-]mail.cm.utexas.edu" έγραψε: Sent to CCL by: Isaac Bersuker [bersuker%x%mail.cm.utexas.edu] Dear Anthony De Crisci When calculating first and second hyperpolarizability along with linear hyperpolarizability have a look into I. B. Bersuker and I. Ya. Ogurtsov, Adv. Quant. Chem. 18, 1-84 (1986). Isaac B. Bersuker Institute for Theoretical Chemistry The University of Texas at Austin Chem & Biochem Department 1 University Station A5300 Austin, TX 78712-0165 Phone: (512) 471-4671; Fax: (512) 471-8696 E-mail: bersuker*_*cm.utexas.edu http://www.cm.utexas.edu/directory/isaac_bersuker/ Anthony De Crisci antonio.decrisci+/-utoronto.ca wrote: > Sent to CCL by: "Anthony De Crisci" [antonio.decrisci::utoronto.ca] > Hello All, > > Im investigating nonlinear optical (NLO) properties of single molecules (i.e. first and second hyperpolarizability along with linear hyperpolarizability). I was able to calculate the tensors for mu, alpha and beta using the keywords 'polar' and 'CPHF=ReFreq' with an input wavelength, but im not able to calculate the gamma tensors. Some searches in the archive have had limited hits and they lead to MOPAC and ADF, is Gaussian not able to calculate gamma (or the second hyperpolarizability or third harmonic generation)? Would anybody know how I can calculate the gamma tensors using G03W? > > Thanks in advance. > > Sincerely > Anthony > University of Toronto> > > --http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Χρησιμοποιείτε Yahoo! Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail διαθέτει την καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων http://login.yahoo.com/config/mail?.intl=gr --0-1856110602-1195979927=:25343 Content-Type: text/html; charset=iso-8859-7 Content-Transfer-Encoding: 8bit
Hi Anthony
You can use alpha or beta results of GAUSSIAN to compute gamma, by implementing a simple numericall differentiation with respect to the field scheme. Thus, by using
beta for expample, just use the first derivative of beta as follows
 
g(zzzz) =  dB(zzz)/dFz, gzzxx= dB(zzx)/dFx etc. The only question is
if gaussian can compute alpha or beta in the presence of the field.
If not then you can compute gamma by taking the fourth derivative of the
energy with respect of the field. The latter requires the calculation of the
following field dependent energies: E(F), E(-F), E(2F), E(2F) and E(0).
If you do not find the relevant expression i can post it to you.
Aggelos Avramopoulos

"Isaac Bersuker bersuker[-]mail.cm.utexas.edu" <owner-chemistry%%ccl.net> έγραψε:

Sent to CCL by: Isaac Bersuker [bersuker%x%mail.cm.utexas.edu]
Dear Anthony De Crisci

When calculating first and second hyperpolarizability along with linear
hyperpolarizability have a look into I. B. Bersuker and I. Ya. Ogurtsov,
Adv. Quant. Chem. 18, 1-84 (1986).

Isaac B. Bersuker

Institute for Theoretical Chemistry
The University of Texas at Austin
Chem & Biochem Department
1 University Station A5300
Austin, TX 78712-0165
Phone: (512) 471-4671; Fax: (512) 471-8696
E-mail: bersuker*_*cm.utexas.edu
http://www.cm.utexas.edu/directory/isaac_bersuker/



Anthony De Crisci antonio.decrisci+/-utoronto.ca wrote:
> Sent to CCL by: "Anthony De Crisci" [antonio.decrisci::utoronto.ca]
> Hello All,
>
> Im investigating nonlinear optical (NLO) properties of single molecules (i.e. first and second hyperpolarizability along with linear hyperpolarizability). I was able to calculate the tensors for mu, alpha and beta using the keywords 'polar' and 'CPHF=ReFreq' with an input wavelength, but im not able to calculate the gamma tensors. Some searches in the archive have had limited hits and they lead to MOPAC and ADF, is Gaussian not able to calculate gamma (or the second hyperpolarizability or third harmonic generation)? Would anybody know how I can calculate the gamma tensors using G03W?
>
> Thanks in advance.
>
> Sincerely
> Anthony
> University of Toronto>
>
>

--


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Χρησιμοποιείτε Yahoo!
Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail διαθέτει την καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων
http://login.yahoo.com/config/mail?.intl=gr --0-1856110602-1195979927=:25343-- From owner-chemistry@ccl.net Tue Nov 27 09:20:01 2007 From: "Chupakhin Vladimir chupvl=-=gmail.com" To: CCL Subject: CCL: Data Modeling Challenge Message-Id: <-35724-071127091200-16333-HX2su8UDB0Lv7A0T9JAJIA|-|server.ccl.net> X-Original-From: "Chupakhin Vladimir" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 27 Nov 2007 17:14:43 +0400 MIME-Version: 1.0 Sent to CCL by: "Chupakhin Vladimir" [chupvl:-:gmail.com] Dear Shaillay Dogra, Is naming of the molecules in Training set and test set a part of the competition? Sincerely yours, Chupakhin Vladimir On Nov 27, 2007 1:14 PM, Shaillay Dogra shaillay**strandls.com wrote: > > Sent to CCL by: Shaillay Dogra [shaillay++strandls.com] > Hi All, > > QSAR-World is holding a data modeling competition. > > For details, visit: http://www.qsarworld.com/ > > The modeling challenge is on till the 27th of December. > > Looking forward to your enthusiastic participation! > > Best regards, > Shaillay Dogra > > Scientific Editor, > QSAR-World (http://www.qsarworld.com/)> > > > From owner-chemistry@ccl.net Tue Nov 27 10:49:01 2007 From: "Ridha Khalfa khalfaridha,+,hotmail.com" To: CCL Subject: CCL:G: Question about ONIOM calculation in G03 Message-Id: <-35725-071127104259-15093-FEyjc+/TggjDV3qDFEtT0Q^-^server.ccl.net> X-Original-From: "Ridha Khalfa" Date: Tue, 27 Nov 2007 10:42:56 -0500 Sent to CCL by: "Ridha Khalfa" [khalfaridha,,hotmail.com] Dear all, I am beginner to using ONIOM. I am trying to set an input file (ligand in an enzyme)where DFT in the QM section and UFF in MM section -this is without charges- I am struggling about how to set the connectivity between the QM section and MM section, checked the G03 manual but did not help that much. can any one post an example of an input file showing how it looks like. Regards From owner-chemistry@ccl.net Tue Nov 27 11:47:01 2007 From: "Imran Predhanekar imranpkm^^gmail.com" To: CCL Subject: CCL: Passes in GAMESS Message-Id: <-35726-071127114202-9965-8sdgjAkOmJSYgSgCtUH87g++server.ccl.net> X-Original-From: "Imran Predhanekar" Date: Tue, 27 Nov 2007 11:41:58 -0500 Sent to CCL by: "Imran Predhanekar" [imranpkm]*[gmail.com] Hi I would like to know the meaning of the following in GAMESS single point energy calculation: NUMBER OF PASSES = 64 PASS # 1 TOOK 22.41 SECONDS. PASS # 2 TOOK 24.89 SECONDS....etc regards PKI From owner-chemistry@ccl.net Tue Nov 27 18:00:01 2007 From: "Tom de Greef t.f.a.d.greef : tue.nl" To: CCL Subject: CCL:G: Frequencies PCM Message-Id: <-35727-071127163939-9956-WDkPbahUhko+qyysdXN49g*|*server.ccl.net> X-Original-From: "Tom de Greef" Date: Tue, 27 Nov 2007 16:39:35 -0500 Sent to CCL by: "Tom de Greef" [t.f.a.d.greef/a\tue.nl] Dear all, Sorry about the large amount of questions recently. However, I have two questions left. The first one is: How does Gaussian03 computes the frequencies when u select a solvent model (for example PCM). Does it use the numerical second derivatives or the analtyical second derivatives? Does it make a difference??? Do I have to specify freq=numer when doeing a frequency calculation using PCM? Second question: How do I include nonequilibrium solvent effects on the calculation of infrared frequencies and intensities in gaussian03 See: Nonequilibrium formulation of infrared frequencies and intensities in solution:Analytical evaluation within the polarizable continuum model J. Chem. Phys. -- December 22, 2000 -- Volume 113, Issue 24, pp. 11270-11279. regards, Tom From owner-chemistry@ccl.net Tue Nov 27 23:22:00 2007 From: "Shaillay Dogra shaillay---strandls.com" To: CCL Subject: CCL: Data Modeling Challenge Message-Id: <-35728-071127231951-2319-Yc+P+/ReSp2XbJxlojiQ3w#%#server.ccl.net> X-Original-From: "Shaillay Dogra" Date: Tue, 27 Nov 2007 23:19:47 -0500 Sent to CCL by: "Shaillay Dogra" [shaillay-,-strandls.com] Dear All, I have now replaced the SDFs with new ones that have the molecules labeled as "train_1", "train_2",...; "test_1", "test_2"... The new files are available from the "challenge" page: http://www.qsarworld.com/qsar-challenge.php My sincere apology for any confusion this may have caused and thanks to Chupakhin Vladimir for pointing this out. The actual data and the reference would be duly disclosed once the competition is over. If there any other points of confusion please do let me know. With best regards, Shaillay Dogra Scientific Editor QSAR-World (http://www.qsarworld.com/) editor * qsarworld.com > "Chupakhin Vladimir chupvl=-=gmail.com" wrote: > > Sent to CCL by: "Chupakhin Vladimir" [chupvl:-:gmail.com] > Dear Shaillay Dogra, > > Is naming of the molecules in Training set and test set a part of the > competition? > > Sincerely yours, > Chupakhin Vladimir > > > On Nov 27, 2007 1:14 PM, Shaillay Dogra shaillay**strandls.com > wrote: > > > > Sent to CCL by: Shaillay Dogra [shaillay++strandls.com] > > Hi All, > > > > QSAR-World is holding a data modeling competition. > > > > For details, visit: http://www.qsarworld.com/ > > > > The modeling challenge is on till the 27th of December. > > > > Looking forward to your enthusiastic participation! > > > > Best regards, > > Shaillay Dogra > > > > Scientific Editor, > > QSAR-World (http://www.qsarworld.com/)> > > > > > > > > From owner-chemistry@ccl.net Tue Nov 27 23:57:01 2007 From: "Shaillay Dogra editor()qsarworld.com" To: CCL Subject: CCL: Data Modeling Challenge Message-Id: <-35729-071127231631-2084-35fPAQyuEpBo8i2akzbSsg,+,server.ccl.net> X-Original-From: "Shaillay Dogra" Date: Tue, 27 Nov 2007 23:16:27 -0500 Sent to CCL by: "Shaillay Dogra" [editor_._qsarworld.com] Dear All, I have now replaced the SDFs with new ones that have the molecules labeled as "train_1", "train_2",...; "test_1", "test_2"... The new files are available from the "challenge" page: http://www.qsarworld.com/qsar-challenge.php My sincere apology for any confusion this may have caused and thanks to Chupakhin Vladimir for pointing this out. The actual data and the reference would be duly disclosed once the competition is over. If there any other points of confusion please do let me know. With best regards, Shaillay Dogra Scientific Editor QSAR-World (http://www.qsarworld.com/) > "Chupakhin Vladimir chupvl=-=gmail.com" wrote: > > Sent to CCL by: "Chupakhin Vladimir" [chupvl:-:gmail.com] > Dear Shaillay Dogra, > > Is naming of the molecules in Training set and test set a part of the > competition? > > Sincerely yours, > Chupakhin Vladimir > > > On Nov 27, 2007 1:14 PM, Shaillay Dogra shaillay**strandls.com > wrote: > > > > Sent to CCL by: Shaillay Dogra [shaillay++strandls.com] > > Hi All, > > > > QSAR-World is holding a data modeling competition. > > > > For details, visit: http://www.qsarworld.com/ > > > > The modeling challenge is on till the 27th of December. > > > > Looking forward to your enthusiastic participation! > > > > Best regards, > > Shaillay Dogra > > > > Scientific Editor, > > QSAR-World (http://www.qsarworld.com/)> > > > > > > > >