From chemistry-request@server.ccl.net Fri Oct 19 11:10:28 2001 Received: from dagger.nd.edu ([129.74.250.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9JFASB28059 for ; Fri, 19 Oct 2001 11:10:28 -0400 Received: from mahler (mahler.chem.nd.edu [129.74.80.173]) by dagger.nd.edu (8.10.2/8.10.2) with SMTP id f9JFASC16722 for ; Fri, 19 Oct 2001 10:10:29 -0500 (EST) Message-ID: <003701c158b0$82a1ba50$ad504a81@mahler> From: "Nicolas Saettel" To: Subject: HONDO scratch files Date: Fri, 19 Oct 2001 10:12:46 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0034_01C15886.99918F80" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_0034_01C15886.99918F80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I have been trying to run HONDO/s calculations but the computer I am = running it on crashes because of a gigantic .FT08 file. I tried to alter = the command MBYTES and THIZE (in $INTGRL) or try a DIRECT=3D1 = calculation (in $CNTRL), but I must not get this right because it does = not change anything. Anyone has any experience with this? Thanks Nicolas SAETTEL http://www.nd.edu/~nsaettel = University of Notre Dame =20 Department of Chemistry and Biochemistry =20 NOTRE DAME, IN 46556 tel: +1 (219) 631-4007=20 ------=_NextPart_000_0034_01C15886.99918F80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
I have been trying to run HONDO/s = calculations but=20 the computer I am running it on crashes because of a gigantic .FT08 = file. I=20 tried to alter the command MBYTES and THIZE (in $INTGRL) or try a = DIRECT=3D1=20 calculation (in $CNTRL), but I must not get this right because it does = not=20 change anything.
Anyone has any experience with = this?
Thanks
      Nicolas=20 SAETTEL           =            =20 http://www.nd.edu/~nsaettel = ;=20
   University of Notre=20 Dame           &nb= sp;    =20
Department of Chemistry and Biochemistry   =20
     NOTRE DAME, IN=20 46556           &n= bsp;       =20 tel: +1 (219) 631-4007
------=_NextPart_000_0034_01C15886.99918F80-- From chemistry-request@server.ccl.net Fri Oct 19 01:06:26 2001 Received: from deakin.edu.au ([128.184.136.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9J56OB13765 for ; Fri, 19 Oct 2001 01:06:25 -0400 Received: from [128.184.88.189] (128-184-88-189.bcs.deakin.edu.au [128.184.88.189]) by deakin.edu.au (8.11.4/8.11.4) with ESMTP id f9J56C811367; Fri, 19 Oct 2001 15:06:12 +1000 (EST) Mime-Version: 1.0 X-Sender: lim@128.184.136.2 (Unverified) Message-Id: In-Reply-To: References: Date: Fri, 19 Oct 2001 13:52:42 +1000 To: CCL From: "Kieran F Lim (Lim Pak Kwan)" Subject: Re: CCL:isolobal vs. isoelectronic Cc: Guosheng Wu , Roy Jensen , "Shobe, Dave" , "'Krzysztof Radacki'" Content-Type: text/plain; charset="us-ascii" ; format="flowed" >On Fri, 19 Oct 2001, Kieran F Lim (Lim Pak Kwan) wrote: > > > My text books state that isoelectronic means same number of electrons. > > USUALLY (not always) this implies same electronic configuration. At 10:21 PM -0500 18/10/01, Guosheng Wu wrote: >If we check the textbooks for general chemistry with more sense of >science, for every 3-4 pages, we may find at least one statement needs to >be corrected. For "isoelectronic", it is just a very empirical word used Too true. Sadly for our community, the textbook that I checked was an advanced treatise on physical chemistry published in 2000, which goes to show there is a lot of confusion about the terms "isoelectronic", "isolobal", etc. (which is where the discussion started.) At 10:21 PM -0500 18/10/01, Guosheng Wu wrote: >(2)IUPAC 1994 > >http://www.chem.qmw.ac.uk/iupac/gtpoc/I.html#34 > >GLOSSARY OF TERMS USED IN PHYSICAL ORGANIC CHEMISTRY >(IUPAC Recommendations 1994) Thanks to Guosheng Wu for pointing out that one of the roles of IUPAC is to bring order out of confusion. At 10:32 AM +1000 19/10/01, Kieran F Lim (Lim Pak Kwan) wrote: >but am very happy to be corrected if wrong. I will be more careful in my usage. Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim ------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Oct 19 07:39:31 2001 Received: from rudjer.irb.hr (root@[161.53.128.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9JBdSB23304 for ; Fri, 19 Oct 2001 07:39:29 -0400 Received: from rudjer.irb.hr (indigo2.irb.hr [161.53.128.24]) by rudjer.irb.hr (8.10.0/8.10.0VS) with ESMTP id f9JBdHv19101 for ; Fri, 19 Oct 2001 13:39:17 +0200 (MET DST) Sender: tomic@rudjer.irb.hr Message-ID: <3BD08F9F.8A72E568@rudjer.irb.hr> Date: Fri, 19 Oct 2001 13:39:59 -0700 From: Sanja Tomic Reply-To: Sanja.Tomic@irb.hr Organization: Institute "Rudjer Boskovic", Zagreb X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: INDOLE with MOPAC Content-Type: multipart/alternative; boundary="------------41303B0AA4F06E7A3040AD53" --------------41303B0AA4F06E7A3040AD53 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLer's, I have problems with optimization of indole ring by MOPAC/PM3 (and similar MOPAC/MNDO) The optimization does not preserve planarity of H bonded to N with the indole ring? Does anybody have some experience with this problem Thanks Sanja -- Dr. Sanja Tomic Institute "Rudjer Boskovic" Bijenicka 54 HR-10000 ZAGREB Croatia --------------41303B0AA4F06E7A3040AD53 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLer's,

I have problems with optimization of indole ring by MOPAC/PM3 (and similar MOPAC/MNDO)
The optimization does not preserve planarity of H bonded to N with the indole ring?
Does anybody  have some experience with this problem

Thanks
Sanja 

-- 
Dr. Sanja Tomic
Institute "Rudjer Boskovic"
Bijenicka 54
HR-10000 ZAGREB
Croatia
  --------------41303B0AA4F06E7A3040AD53-- From chemistry-request@server.ccl.net Fri Oct 19 09:55:41 2001 Received: from mailhub1.shef.ac.uk ([143.167.1.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9JDteB26897 for ; Fri, 19 Oct 2001 09:55:41 -0400 Received: from ramsley.shef.ac.uk ([143.167.103.254]) by mailhub1.shef.ac.uk with esmtp (Exim 3.22 #4) id 15ua7g-000042-00 for chemistry@ccl.net; Fri, 19 Oct 2001 14:55:40 +0100 Received: from RAMSLEY/SpoolDir by ramsley.shef.ac.uk (Mercury 1.48); 19 Oct 01 15:10:10 +0100 Received: from SpoolDir by RAMSLEY (Mercury 1.48); 19 Oct 01 15:10:03 +0100 From: "O.Nicolotti" To: chemistry@ccl.net Date: Fri, 19 Oct 2001 15:09:54 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: QSAR and scarmbling Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12a) Message-Id: Hy everybody, comments on scrambling QSAR data have been reported as follows thanks, Orazio Hy James and thanks a lot for your help. I have been reading your paper you referenced. Basically your results summarised in table 5 seems to confirm my initial feeling that r2 values are not relevant after scrambling data. And in fact your results (linear equation, but the same can be extended to the spline one) coming from G/PLS approach as on MFA as on Descriptor Data showed that the r2 values are still quite high (0.714 and 0.709 respectively) while r2(CV) values drop down (0.129 and 0.266 compared to 0.789 and 0.728 of the corresponding unscrambled data). According to your results, I would say that scrambling is effective only to validate predictive QSAR power which means to look only at r2(CV) values before and after scrambling. Therefore r2, which accounts only for the model fitting is not worth to be investigated in scrambling. If you agree this conclusion I will make a recap for any CCL users. Please let me know Still thanks for your mail. Orazio > > Hi Orazio > > Theres a couple of papers that tackle part of this, they are > referenced in a paper I did on organophosphates (Drew, M.G.B., Lumley, > J.A. and Price, N.R., Predicting ecotoxicology or organophosphorous > insecticies: Successful parameter selection with the genetic function > algorithm., Quant.Struct.Activity Rel. 1999 18 573-583). We found > scrambling a useful technique for validating regression equations when > using approaches like GAs to select the best descriptors (e.g.: > from > CoMFA like analysis). If I remember correctly the original papers (by > Toplis and Edwards ?) looked at the effect of increasing the number of > original variables used to select the regression equation components. > They found that the r2 increased with the number of original starting > variables regardless of the number of descriptors in the final > equation. Thus r2 alone does not indicate whether you have found a > chance regression equation. We found that scrambling the activity > data does give you some indication and r2(CV)s helped. There may be > some other papers we referenced of interest. > > hope this is of some help, > > james > > ************************ > Dr. James A. Lumley > Arrow Therapeutics > Woodmansterne Road > Carshalton Surrey > SM5 4DS > Tel: 0208 652 9618 > Fax: 0208 652 9620 > http://www.arrowt.co.uk > ************************ > > Confidentiality Notice: > The contents of this email from Arrow Therapeutics are confidential to > the ordinary user of the email address to whom it was addressed. > No-one else may copy or forward all or any of it in any form. If you > receive this email in error please reply to the sender so that we can > arrange for proper delivery and then please delete the message > from > your inbox. Thank You. > > > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request@ccl.net]On Behalf Of O.Nicolotti Sent: > Saturday, October 13, 2001 3:09 PM To: chemistry@ccl.net Subject: > CCL:QSAR and scrambling > > > Hy everybody, > I would like to know your opinion about scrambling the activities data > for validating QSAR models. > > Usually, after scrambling affinity data, the classical statistics > parameters (r2 and q2) are supposed to go dramatically down if the > original QSAR models was a reliable model. > > Anyway, if you are dealing with CoMFA, I would expect bad q2 > after scrambling but the r2 could also be still quite high since r2 > tend to be high when the number of descriptors is very large as it is > in the CoMFA grid. In other word while q2 must to go down, r2 values > should not mean anything of relevant for validating the QSAR models. > > Any comment is very welcome. > > Orazio > Orazio Nicolotti, PhD Research Associate Dept. Information Studies University of Sheffield Western Bank Sheffield S10 2TN tel. 0114 222 2657 From chemistry-request@server.ccl.net Fri Oct 19 16:48:21 2001 Received: from popserver.healthtech.com ([140.239.39.130]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9JKmLB03415 for ; Fri, 19 Oct 2001 16:48:21 -0400 Received: by popserver.healthtech.com from localhost (router,SLMail V4.3); Fri, 19 Oct 2001 16:21:16 -0400 for Received: from edelo [140.239.39.147] by popserver.healthtech.com [140.239.39.130] (SLmail 4.3.0.3454) with SMTP id C1D6381F3D5540E4AA8638679AC0B0E9 for ; Fri, 19 Oct 2001 16:21:13 -0400 Message-Id: <4.1.20011019160508.00a91280@140.239.39.130> X-Sender: eoregan@140.239.39.130 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Fri, 19 Oct 2001 16:16:17 -0400 To: chemistry@ccl.net From: "Edel O'Regan" Subject: Chemoinformatics meeting - Call for Speakers Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-SLUIDL: 44D8F2FC-437444D1-AC852584-E7CF415E http://www.chi-intelligentdrug.com/ci/ci.htm Edel O'Regan Ph.D. Conference Producer Cambridge Healthtech Institute FAX: 617-630-1325 Phone: 617-630-1323 email: eoregan@healthtech.com From chemistry-request@server.ccl.net Fri Oct 19 14:45:58 2001 Received: from femail22.sdc1.sfba.home.com ([24.0.95.147]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9JIjvB00635 for ; Fri, 19 Oct 2001 14:45:57 -0400 Received: from C1353359A ([65.4.172.51]) by femail22.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20011019184551.DOXR661.femail22.sdc1.sfba.home.com@C1353359A> for ; Fri, 19 Oct 2001 11:45:51 -0700 Message-ID: <002101c158cd$f22f4a50$33ac0441@sttln1.wa.home.com> Reply-To: "Mark A. Thompson" From: "Mark A. Thompson" To: Subject: Ring perception algorithm Date: Fri, 19 Oct 2001 11:43:29 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001E_01C15893.459983D0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_001E_01C15893.459983D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I would like to hear from anyone who has implemented the ring perception = algorithm of Balducci and Pearlman (1994). I have some interesting = questions and observations to share. Mark Thompson ------------------------------------------- http://www.planaria-software.com ------=_NextPart_000_001E_01C15893.459983D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
I would like to hear from = anyone who has=20 implemented the ring perception algorithm of Balducci and Pearlman = (1994). =20 I have some interesting questions and observations to = share.
 
Mark Thompson
 
-------------------------------------------
 
------=_NextPart_000_001E_01C15893.459983D0-- From chemistry-request@server.ccl.net Fri Oct 19 21:43:24 2001 Received: from hinet.hinet.net ([211.75.218.116]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9K1hNB13769 for ; Fri, 19 Oct 2001 21:43:24 -0400 Message-Id: <200110200143.f9K1hNB13769@server.ccl.net> Received: from 65-45-88-174.customer.algx.net by hinet.hinet.net with SMTP (Microsoft Exchange Internet Mail Service Version 5.0.1458.49) id VG411N49; Sat, 20 Oct 2001 09:43:39 +0800 From: Pride of America To: chemistry@ccl.net Subject: Free American Flag Pin X-Mailer: Mailer Signature Reply-To: info@prideofamerica.com Date: Fri, 19 Oct 2001 18:43:00 -0800 Mime-Version: 1.0 Content-Type: text/html; charset=us-ascii We want all Americans to have a flag pin. Let us send you one for free! For your free pin visit http://prideofamerica.net