From owner-chemistry@ccl.net Wed Nov 2 07:36:00 2005 From: "qftjesus[-]usc.es" To: CCL Subject: CCL:G: Error with Gaussian03. PickT4: no shell combinations can fit! Message-Id: <-29862-051102054044-6590-yc3kdNZmuIAUo7L7frxFSw!A!server.ccl.net> X-Original-From: qftjesus~~usc.es Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 02 Nov 2005 10:48:20 +0100 MIME-Version: 1.0 Sent to CCL by: qftjesus|*|usc.es Dear Netters, I am trying to run calculations with several halide containing molecules with gaussian 03. I have no problem when fluoride or chloride are present but, when I try to use bromide the calculation charshes with the following error: JobTyp=1 Pass 1: I= 1 to 12 NPSUse= 1 ParTrn=F ParDer=F DoDerP=F. PickT4: no shell combinations can fit! NKLS2p= 257 NKLS2= 257 MaxCom= 247 Error termination via Lnk1e in /home/g03/l906.exe at Thu Oct 27 23:51:09 2005. I wonder how I can solve this problem. Regards From owner-chemistry@ccl.net Wed Nov 2 09:25:00 2005 From: "Antoine FORTUNE Antoine.Fortune*ujf-grenoble.fr" To: CCL Subject: CCL: COMFA =?ISO-8859-1?Q?q=B2_SUMMARY?= Message-Id: <-29863-051102091927-12485-9dZB5o6gFumWSAKmOOw6cA*_*server.ccl.net> X-Original-From: Antoine FORTUNE Content-Type: multipart/mixed; boundary="------------070007080702030009050909" Date: Wed, 02 Nov 2005 15:04:52 +0100 MIME-Version: 1.0 Sent to CCL by: Antoine FORTUNE [Antoine.Fortune\a/ujf-grenoble.fr] This is a multi-part message in MIME format. --------------070007080702030009050909 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Many thank's to all who help me and the CCL. Here is a summery of the answers I got. "q-sq" is the same as "crossvalidated r-sq". When you do a comfa run with crossvalidation (choose the leave-one-out radio button in the setup dialog box), the r-sq reported in the summary output is the crossvalidated r-sq. You have to do a second run with the proper number of components and without crossvalidation to get the conventional r-sq. Steve Bowlus Seascape Learning, LLC (Tripos distributor) Sent to CCL by: "Barbault Florent" [florent.barbault(a)paris7.jussieu.fr] When you do a cross-validation the r² in SYBYL represent the q². So you have to do a cross-validation analysis first, and if it is correct a non-cross-validation analysis. Best regards >Sent to CCL by: Prashanth Athri [athriprashanth!=!yahoo.com] > >Hi, > >On the Partial Least Squares Analysis dialog box: > >1. Click on the SAMPLS button and set the number of > >components to a value higher than what you would > >expect the dimensionality of your data to be. Then > >click on "Run PLS". > >2. A dialog informing you about SAMPLS pops up- click > >OK. > >3. On the terminal window, you will eventually see > >crossvalidated r-squared [alias q-squared]. The number > >of components you will choose for the final run will > >be the one for which the q-squared is the highest. > >Hope this helps. > >-Prashanth > > --- "Antoine FORTUNE > Antoine.Fortune^_^ujf-grenoble.fr" > wrote: > >>Sent to CCL by: Antoine FORTUNE [Antoine.Fortune- >>-ujf-grenoble.fr] >>Hi all, >>I'm working with sybyl MSS to do comfa study. As I >>run a PLS, sybyl >>gives r² value in the report. Where / how can i get >>the q² value ? It's >>not in the report log. >>Thank's >> >>Antoine >> >> --------------070007080702030009050909 Content-Type: text/x-vcard; charset=utf-8; name="Antoine.Fortune.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Antoine.Fortune.vcf" begin:vcard fn;quoted-printable:Antoine Fortun=C3=A9 n;quoted-printable:Fortun=C3=A9;Antoine org:UFR Pharmacie - Universite Grenoble 1;Departement de Pharmacochimie Moleculaire adr:38240;;5 avenue de Verdun ;MEYLAN;;;FRANCE email;internet:Antoine.Fortune(_)ujf-grenoble.fr title:Ingenieur Modelisation Moleculaire tel;work:+33 4 76 04 10 38 x-mozilla-html:TRUE url:http://dpm.ujf-grenoble.Fr version:2.1 end:vcard --------------070007080702030009050909-- From owner-chemistry@ccl.net Wed Nov 2 10:42:00 2005 From: "Cory Pye cpye]=[crux.smu.ca" To: CCL Subject: CCL:G: Error with Gaussian03. PickT4: no shell combinations can fit! Message-Id: <-29864-051102094952-26561-r6000VgAEz+2AFqTn6jIpg . server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 2 Nov 2005 10:49:43 -0400 (AST) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye/a\crux.smu.ca] Hello, It sounds like a problem I had when I tried to do an MP2/6-31+G* calculation on ZnBr4 2- once. Try doubling the amount of memory (%mem=XXXMb), then quadrupling, etc.. until it works. Don't specify more memory than you have physically available however. Also check that your default memory specification is reasonable. I always specify %mem because I think the default when I compiled G98 was 4 Mw (32 Mb) which is small compared to today's machines. -Cory On Wed, 2 Nov 2005, qftjesus[-]usc.es wrote: > > Sent to CCL by: qftjesus|*|usc.es > > > Dear Netters, > > I am trying to run calculations with several halide containing molecules with > gaussian 03. I have no problem when fluoride or chloride are present but, when > I try to use bromide the calculation charshes with the following error: > > JobTyp=1 Pass 1: I= 1 to 12 NPSUse= 1 ParTrn=F ParDer=F DoDerP=F. > PickT4: no shell combinations can fit! > NKLS2p= 257 NKLS2= 257 MaxCom= 247 > Error termination via Lnk1e in /home/g03/l906.exe at Thu Oct 27 23:51:09 2005. > > > I wonder how I can solve this problem. > > Regards ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye/a\crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Wed Nov 2 16:53:00 2005 From: "jmmckel~~attglobal.net" To: CCL Subject: CCL: XYZ grad to internal gradients Message-Id: <-29865-051102193527-25115-DhvkCYMZPYuc+pChcLNVDw+/-server.ccl.net> X-Original-From: jmmckel!A!attglobal.net Date: Wed, 02 Nov 2005 15:46:18 +0000 Sent to CCL by: jmmckel-$-attglobal.net Hello.. I have a set of cartesian coordinates and the corresponding cartesian gradients, and the connectivities for each atom in a Z-matrix form. Can someone point me to a routine or two that can be adapted to convert the cartesian gradients into internal gradients? Many thanks, John McKelvey From owner-chemistry@ccl.net Wed Nov 2 17:28:00 2005 From: "Lisa Subissati lsubissati(_)chemcomp.com" To: CCL Subject: CCL: Call for Applicants: Excellence Award Message-Id: <-29866-051101105333-1234-ONy0kkO/oLyKBxBsU+uX9A+/-server.ccl.net> X-Original-From: "Lisa Subissati" Content-Transfer-Encoding: quoted-printable Date: Mon, 31 Oct 2005 11:32:35 -0500 MIME-Version: 1.0 Sent to CCL by: "Lisa Subissati" [lsubissati===chemcomp.com] =20 =20 Excellence Award Chemical Computing Group and the ACS Division of Computers in Chemistry, invite applications for the 2006 CCG Excellence Award. These awards will = be presented to five (5) individuals who have exhibited outstanding work = and dedication in the field of Computational Chemistry.=09 The winners will each receive $1,150, a certificate, and the opportunity = to present a poster of their award-winning work during the ACS Spring = National Meeting to be held in Atlanta, Georgia, 26-30 March, 2006. =20 Futhermore, winners will be honoured with a one-year software license = (from CCG) for the most recent version of MOE (Molecular Operating = Environment) for their academic research group. =09 For the 2006 Awards, applications should be sent to:=09 Dr. Andrew Good Bristol Myers Squibb Rte. 206 & Provinceline Rd. Princeton, NJ 08543 Email: Andrew.Good[#]bms.com=20 =20 Also, an abstract must be submitted through the: ACS OASYS - Online Abstract Submittal System: http://oasys.acs.org/acs/231nm/comp/papers/index.cgi The deadline is 15 November 2005.=09 =09 Instructions for Submissions: =09 . Applicants must be graduate students in good standing, who must present their work within the COMP program, either in oral or poster format=09 . Applications will be welcomed for all candidates from North, Central or South America (European students can apply for a similar = award through the Molecular Graphics and Modeling Society)=09 . Applications should consist of:=09 =09 . . . an extended (2-page) abstract of a poster or presentation a letter of support from the research advisor a two-page CV, and a personal statement=09 =09 =09 For further information on the Chemical Computing Group Excellence = Awards, please contact: Lisa Subissati, Chemical Computing Group. Email: lsubissati[#]chemcomp.com =09 =09 =09 =09 =09 =09 =09 =09 =09 =09 =09 =09 =09