From owner-chemistry@ccl.net Sun Nov 14 06:09:01 2010 From: "Yvonne Martin yvonnecmartin]=[gmail.com" To: CCL Subject: CCL: Randomization Message-Id: <-43161-101113105438-24866-GLcPSipGKx7OypmaUPsMYQ-.-server.ccl.net> X-Original-From: Yvonne Martin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 13 Nov 2010 09:54:27 -0600 MIME-Version: 1.0 Sent to CCL by: Yvonne Martin [yvonnecmartin===gmail.com] To do such a validation, separate the value to be predicted (Y) from the others, generate the same number of random numbers next to each of these Y values, sort these according to the value of the random number, and reassemble the dataset with the Y values to be predicted now dissociated from the others. Repeat this scrambling 100 or so times to see if your true model is superior to these random models. Yvonne Martin On Wednesday, November 10, 2010, Jon Heinz goeeoe*|*hotmail.com wrote: > > Sent to CCL by: "Jon  Heinz" [goeeoe!A!hotmail.com] > Hello, > > I am trying to validate my QSAR models and I have read about Y- randomisation method. I do not understand what this technique means OR why it is important to carry it out. Are there any other suitable validation studies I can perform on my models, apart from cross validation? > > thank you > Jon Heinz > goeeoe[]hotmail.com > Portsmouth UK>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Sun Nov 14 12:48:00 2010 From: "Kavi Sona kavisona7{}gmail.com" To: CCL Subject: CCL:G: Douglas-Kroll-Hess calculation Message-Id: <-43162-101114123357-7840-7ybO2v8PY+5DtRaY50pQDQ(_)server.ccl.net> X-Original-From: "Kavi Sona" Date: Sun, 14 Nov 2010 12:33:56 -0500 Sent to CCL by: "Kavi Sona" [kavisona7[]gmail.com] Hi everybody, I am trying to do Douglas-Kroll-Hess calculation using G09. I wonder, I could not able to find an example in the online Gaussian manual. If anybody can provide me an example input file, that would be very helpful to me. Many thanks, Kavi From owner-chemistry@ccl.net Sun Nov 14 13:23:00 2010 From: "William F. Coleman wcoleman^-^wellesley.edu" To: CCL Subject: CCL: Error using SaveNBOs in Gaussian for NBO Calculations Message-Id: <-43163-101114082814-9053-y74AjLoSK1YhPTmF+gDonA!A!server.ccl.net> X-Original-From: "William F. Coleman" Content-Type: multipart/alternative; boundary="--=_--21b1b4aa.21b1b3d1.c9059461" Date: Sun, 14 Nov 2010 08:28:01 -0500 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman*wellesley.edu] This is a multi-part message in MIME format. ----=_--21b1b4aa.21b1b3d1.c9059461 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit "CCL Subscribers" writes: >I have not had any success visualizing NBOs from only the .log file. I'd >appreciate any further guidance you could provide. One way to do this is in the latest version of the open-source visualizer JMol - directions for doing this are at http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.0-documentation-2.pdf Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html http://www.flicksstuff.com/photos/pictures.html new galleries 9/4/2010 Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html ----=_--21b1b4aa.21b1b3d1.c9059461 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>
"CCL Subscribers" <chemistry=40ccl.net> writes:
I have not had any success visualizing NBOs from only the .log fil= e.  I'd appreciate any further guidance you could provide.

One way to do this is in the latest v= ersion of the open-source visualizer JMol - directions for doing this are a= t

Cheers,

Flick

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481


Editor, JCE WebWare and JCE Featured = Molecules


----=_--21b1b4aa.21b1b3d1.c9059461-- From owner-chemistry@ccl.net Sun Nov 14 13:58:01 2010 From: "Wojciech Kolodziejczyk dziecial\a/icnanotox.org" To: CCL Subject: CCL:G: Douglas-Kroll-Hess calculation Message-Id: <-43164-101114133712-26342-zwxlylMK3b9sGGL1b1pDJA%a%server.ccl.net> X-Original-From: Wojciech Kolodziejczyk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 14 Nov 2010 19:36:59 +0100 MIME-Version: 1.0 Sent to CCL by: Wojciech Kolodziejczyk [dziecial++icnanotox.org] Kavi, here you have example for DKH calculations for water. You can use DKH keyword as you want (in integral sction). How to use DKH keywords you can find here http://www.gaussian.com/g_tech/g_ur/k_integral.htm. Of course don't forget about relativistic basis set. %chk=water.chk %mem=1024MB %nproc=1 # opt hf/3-21g integral=dkh Title Card Required 0 1 O H 1 B1 H 1 B2 2 A1 B1 0.96000000 B2 0.96000000 A1 109.50000006 2010/11/14 Kavi Sona kavisona7{}gmail.com : > > Sent to CCL by: "Kavi  Sona" [kavisona7[]gmail.com] > Hi everybody, > > I am trying to do Douglas-Kroll-Hess calculation using G09. I wonder, I could not able to find an example in the online Gaussian manual. If anybody can provide me an example input file, that would be very helpful to me. > > Many thanks, > Kavi>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Sun Nov 14 16:52:00 2010 From: "Hamdy El Sheshtawy h.elsheshtawy~~jacobs-university.de" To: CCL Subject: CCL:G: solvent effect Message-Id: <-43165-101114165015-14875-hWftBNX52aXUfe5SnR2MIQ^-^server.ccl.net> X-Original-From: Hamdy El Sheshtawy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes Date: Sun, 14 Nov 2010 22:50:03 +0100 MIME-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Hamdy El Sheshtawy [h.elsheshtawy:jacobs-university.de] Dear all, I am doing calculations on solvent effect on some radicals. I am using G03, but I am not sure which parameter to use in the comparison. I did optimization in the gas phase , then Freq. calculations on the same structure in the gas phase as well. Then I repeated the same calculations in case of Benzene and acetonitrile with PCM model. The frequency output file: Sum of electronic and zero-point Energies= -655.872244 Sum of electronic and thermal Energies= -655.857444 Sum of electronic and thermal Enthalpies= -655.856499 Sum of electronic and thermal Free Energies= -655.917806 But I am not sure which parameter to use, is it the Free Energies= -655.917806, or......... Please, I need someone to make it clear for me. Thank you in advance Hamdy From owner-chemistry@ccl.net Sun Nov 14 18:08:00 2010 From: "Zork Zou zorkzou%%gmail.com" To: CCL Subject: CCL:G: Douglas-Kroll-Hess calculation Message-Id: <-43166-101114180608-9894-6ty23C/ez9ysQ4yY9zRPgw]|[server.ccl.net> X-Original-From: Zork Zou Content-Type: multipart/alternative; boundary=485b397dd555d67add04950b5da3 Date: Sun, 14 Nov 2010 17:05:58 -0600 MIME-Version: 1.0 Sent to CCL by: Zork Zou [zorkzou%a%gmail.com] --485b397dd555d67add04950b5da3 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi Kavi, There are two ways to perform DKH2 calculations using G03 or G09. 1. DKH2 with point nuclei model, as done in most of the other quantum chemistry programs (Molpro, Molcas, Gamess) # B3LYP (or HF, CCSD, CASSCF, ...) Gen Integral=3DDKH2 IOP(3/93=3D1) {title} {charge}, {multiplicity} {coordinates} {basis sets} Basis sets: Many people have pointed out that the non-relativistic basis sets can result in wrong DKH calculations, so you have to use DKH2 contracted basis sets. However, the DKH2 contracted basis sets are not included in Gaussian's basis set library, but you can obtain them from EMSL= . Go to https://bse.pnl.gov/bse/portal, and find ANO-RCC or (aug-)cc-p(wC)VnZ-DK. You can also re-contract non-relativistic basis sets with DKH2, or use non-contracted basis sets. 2. DKH2 with finite nuclear model The finite nuclear model is default in Gaussian=92s DKH, so you should dele= te IOP(3/93=3D1) or specify IOP(3/93=3D2). Since there are no public DKH2 contracted basis sets with finite nuclear model (maybe they are included in the basis set library of the ORCA program= , but I'm not sure), you have to re-contract non-relativistic basis sets with DKH2 and finite nuclear model, or use non-contracted basis sets. On Sun, Nov 14, 2010 at 11:33 AM, Kavi Sona kavisona7{}gmail.com < owner-chemistry-.-ccl.net> wrote: > > Sent to CCL by: "Kavi Sona" [kavisona7[]gmail.com] > Hi everybody, > > I am trying to do Douglas-Kroll-Hess calculation using G09. I wonder, I > could not able to find an example in the online Gaussian manual. If anybo= dy > can provide me an example input file, that would be very helpful to me. > > Many thanks, > Kavi > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --485b397dd555d67add04950b5da3 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable

<= font face=3D"Times New Roman" size=3D"3">=A0

<= font size=3D"3">Hi Kavi,

<= font face=3D"Times New Roman" size=3D"3">=A0

There are two=A0ways to pe= rform DKH2 calculations using G03 or G09.

<= font face=3D"Times New Roman" size=3D"3">=A0

<= font size=3D"3">1. DKH2 with point nuclei mo= del, as done in most of the other quantum chemistry programs (Molpro, Molca= s, Gamess)

<= font face=3D"Times New Roman" size=3D"3">=A0

<= font size=3D"3"># B3LYP (or HF, CCSD, CASSCF= , ...) Gen Integral=3DDKH2 IOP(3/93=3D1)

<= font face=3D"Times New Roman" size=3D"3">=A0

<= font size=3D"3">{title}=

<= font face=3D"Times New Roman" size=3D"3">=A0

<= font size=3D"3">{charge}, {multiplicity}

<= font size=3D"3">{coordinates}<= /span>

<= font face=3D"Times New Roman" size=3D"3">=A0

<= font size=3D"3">{basis sets}

<= font face=3D"Times New Roman" size=3D"3">=A0

<= font size=3D"3">Basis sets: Many people have= pointed out that the non-relativistic basis sets can result in wrong DKH c= alculations, so you have to use DKH2 contracted basis sets. However, the DK= H2 contracted basis sets are not included in Gaussian's basis set libra= ry, but you can obtain them from EMSL. Go to https://bse.pnl.gov/bse/portal, and find ANO-RCC or (aug-)= cc-p(wC)VnZ-DK.

<= font face=3D"Times New Roman" size=3D"3">=A0

<= font size=3D"3">You can also re-contract non= -relativistic basis sets with DKH2, or use non-contracted basis sets.

<= font face=3D"Times New Roman" size=3D"3">=A0

<= font size=3D"3">2. DKH2 with finite nuclear = model

<= font size=3D"3">The finite nuclear model is = default=A0in Gaussian=92s DKH, so you should delete IOP(3/93=3D1) or specif= y IOP(3/93=3D2).

<= font face=3D"Times New Roman" size=3D"3">=A0

<= font face=3D"Times New Roman" size=3D"3">Since there are no public DKH2 con= tracted basis sets with finite nuclear model (maybe they are included in th= e basis set library of the ORCA program, but I'm not sure), you have to= re-contract non-relativistic basis sets with DKH2 and finite nuclear model= , or use non-contracted basis sets.



On Sun, Nov 14, 2010 at 11:33 AM, Kavi Sona kavi= sona7{}gmail.com <owner-chemistry-.-ccl.net> wrote:

Sent to CCL by: "Kavi = =A0Sona" [kavisona7[]g= mail.com]
Hi everybody,

I am trying to do Douglas-Kroll-Hess calculation using= G09. I wonder, I could not able to find an example in the online Gaussian = manual. If anybody can provide me an example input file, that would be very= helpful to me.

Many thanks,
Kavi



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