From chemistry-request@server.ccl.net Thu Sep 9 01:43:54 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA17532 for ; Thu, 9 Sep 1999 01:43:49 -0400 Received: from basfegw1.basf-ag.de (basfegw1.basf-ag.de [141.6.1.21]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id BAA02000 for ; Thu, 9 Sep 1999 01:39:32 -0400 (EDT) From: hugo.kubinyi@basf-ag.de Received: from basfigw1.fw.basf-ag.de (actually host dmz-igw1) by basfegw1.basf-ag.de with SMTP (XT-PP) with ESMTP; Thu, 9 Sep 1999 07:39:30 +0200 Received: from pluto1.zx.basf-ag.de by basfigw1.fw.basf-ag.de with SMTP (XT-PP); Thu, 9 Sep 1999 07:39:29 +0200 Received: by pluto1.zx.basf-ag.de(Lotus SMTP MTA v4.6.3 (778.2 1-4-1999)) id C12567E7.001EF870 ; Thu, 9 Sep 1999 07:38:16 +0200 X-Lotus-FromDomain: BASF-AG To: CCL , QSAR Society , Roger Lahana Message-ID: Date: Thu, 9 Sep 1999 07:39:21 +0200 Subject: Drug-like inactive molecules Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear Roger, from my point of view, the "most drug-like" inactive molecules should be the molecules listed in the WDI or in similar drug collections. There should be at least one or several biological target/s for every member at which the respective "drug" is inactive. Another good source might be the literature. There are thousands of publications where active, less active and even inactive analogs are listed with their quantitative data. So what? Best regards Hugo From chemistry-request@server.ccl.net Thu Sep 9 07:18:40 1999 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA19677 for ; Thu, 9 Sep 1999 07:18:38 -0400 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de for @dfvgate.lrz-muenchen.de:chemistry@ccl.net; Thu, 9 Sep 1999 13:14:09 +0200 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) for id NAA10306; Thu, 9 Sep 1999 13:14:01 +0200 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <37D79678.6A1ED336@physik.tu-muenchen.de> Date: Thu, 09 Sep 1999 13:14:01 +0200 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Jaguar & Titan Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi alltogether, does anybody have gained experience with the Jaguar and/or Titan program? Do they calculate molecular geometries and frequencies substantially faster than GAUSSIAN 94/98? Any reply will be helpful. Th. Mehnert From chemistry-request@server.ccl.net Thu Sep 9 11:45:31 1999 Received: from zeus.imim.es (zeus.imim.es [193.144.6.111]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA20779 for ; Thu, 9 Sep 1999 11:39:03 -0400 Received: by zeus.imim.es (950413.SGI.8.6.12/950213.SGI.AUTOCF) for chemistry@ccl.net id RAA02340; Thu, 9 Sep 1999 17:35:21 -0700 Date: Thu, 9 Sep 1999 17:35:21 -0700 From: Jordi Villa Message-Id: <199909100035.RAA02340@zeus.imim.es> To: chemistry@ccl.net Subject: GRASP/DELPHI format Dear all, we are interested in a routine to generate GRASP files from a previously calculated property at a grid of points. We have seen in the GRASP web page that the possible file to do this will have the format of a DelPhi binary potential map file. This can be found in http://honiglab.cpmc.columbia.edu/grasp/grasp_contents.html#read However, we have problems in understanding the meaning of some of the variables. Has anybody created such a routine? Jordi Villa From chemistry-request@server.ccl.net Thu Sep 9 13:37:15 1999 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA21236 for ; Thu, 9 Sep 1999 13:37:14 -0400 Received: from red5 (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id KAA03659 for ; Thu, 9 Sep 1999 10:32:53 -0700 (PDT) Message-Id: <4.2.0.58.19990909103818.01608a30@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Thu, 09 Sep 1999 10:40:34 -0700 To: CCL From: Laurence Lavelle Subject: TITAN Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed I would appreciate anyone's experience/comments with Titan and organometallic complexes. Thanks and summary will follow. Laurence """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Department of Chemistry & Biochemistry and Molecular Biology Institute Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Office): (310) 825-2083 Room 3048A Young Hall Fax: (310) 206-4038 Phone (Lab): (310) 206-8270 Room 269B MBI http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" From chemistry-request@server.ccl.net Thu Sep 9 14:01:54 1999 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA21460 for ; Thu, 9 Sep 1999 14:01:53 -0400 Received: from red5 (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id KAA04622 for ; Thu, 9 Sep 1999 10:57:32 -0700 (PDT) Message-Id: <4.2.0.58.19990909110436.015e4350@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Thu, 09 Sep 1999 11:05:13 -0700 To: CCL From: Laurence Lavelle Subject: TITAN Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed I would appreciate anyone's experience/comments with Titan and organometallic complexes. Thanks and summary will follow. Laurence """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Department of Chemistry & Biochemistry and Molecular Biology Institute Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Office): (310) 825-2083 Room 3048A Young Hall Fax: (310) 206-4038 Phone (Lab): (310) 206-8270 Room 269B MBI http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" From chemistry-request@server.ccl.net Thu Sep 9 14:54:07 1999 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA21709 for ; Thu, 9 Sep 1999 14:54:01 -0400 Received: from localhost (qoajnv@localhost) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id UAA21104 for ; Thu, 9 Sep 1999 20:49:26 +0200 (MET DST) Date: Thu, 9 Sep 1999 20:49:26 +0200 (MET DST) From: Armando Juan Navarro Vazquez To: chemistry@ccl.net Subject: Localizing virtual orbitals with gamess Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All Does anybody know how to obtain localized valence and virtual orbitals using the Boys method in GAMESS-US? I could only print the occupied orbitals. Thanks in advance Armando Navarro Departamento de quimica organica Facultade de quimica Universidade de Santiago de Compostela. Spain e-mail:qoajnv@uscmail.usc.es From chemistry-request@server.ccl.net Thu Sep 9 08:53:59 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA20011 for ; Thu, 9 Sep 1999 08:53:59 -0400 Received: from mailhub2.shef.ac.uk (mailhub2.shef.ac.uk [143.167.2.154]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id IAA08896 for ; Thu, 9 Sep 1999 08:49:27 -0400 (EDT) From: d.turner@sheffield.ac.uk Received: from pc100182.shef.ac.uk ([143.167.100.182] helo=davets_pc) by mailhub2.shef.ac.uk with smtp (Exim 3.02 #2) id 11P3dX-0005n1-00; Thu, 09 Sep 1999 13:49:11 +0100 To: "Dr. Dave Winkler" Date: Thu, 9 Sep 1999 13:50:33 +0100 MIME-Version: 1.0 Content-type: text/enriched; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:cross-validation and prediction with PLS CC: chemistry@www.ccl.net, qsar_society@unil.ch, davel@chmqst.demon.co.uk Priority: normal In-reply-to: References: <37D4FCC1.40AF6E5E@stark.udg.es> X-mailer: Pegasus Mail for Win32 (v3.01a) Message-Id: Dear Dr Winkler I have noted your comments with interest. I am very curious about your suggestion that Bayesian NN QSAR methods don't (may not) require validation; that crossvalidation (CV) may not be needed I can understand but NO validation at all? How do you know that your model has any value without some external criterion? Or have I missed something here? I have some more questions/comments:- 7F00,0000,0000> There are a whole raft of problems which arise with cross-validation and testing, Agree. 7F00,0000,0000> for example: > > 1. What is the best way to chose a validation set (or test for that matter) is > leave-one-out, leave-N-out etc? As far as I know one doesn't use CV (LOO/LNO) to choose validation/test sets. What do you mean here? The only thing I can think of is that CV can be used to help identify training set outliers. > 2. Should clustering be used to choose a representative test set and , if so, 7F00,0000,0000> what kind of clustering algorithm and do you cluster on X, Y or X/Y? Are you using the term "clustering" here to cover PCA/PLS score-based experimental design as well as what is more usually called clustering? 7F00,0000,0000> 3. Effort involved in the cross validation process scales as the square of the > number of compounds and the square of the number of independent variables, > which has important implications for large data sets (eg combichem/HTS data) With the SAMPLS algorithm fitted/CV PLS run-times are independent of the number of independent variables (P). (There will be some overhead for calculating the inter-compound covariance matrix). SAMPLS should be used where P>>M (M=No. of compounds). PLS with large numbers of compounds will always be a problem; one's definition of "large" will obviously change as more computational power becomes available ... 7F00,0000,0000> 4. Once a cross validation process has been completed, there are N QSAR > models, all slightly different. Which is the 'best' or 'true' model? What do you mean N models? With PLS, CV is used to establish the number of PLS latent variables (LV) to use in a final all-observations-included analysis the regression coefficients from which predictions can be made. Or is your "N" an LV indicator? I look forward to hearing your comments Regards Dave Turner 7F00,0000,0000> My colleague, Frank Burden (Monash University) and I have used Bayesian > regularized neural nets for QSAR. We find that they overcome virtually all of > the problems with PLS QSAR models as they give the single statistically best > model possible for the data set. In addition there are good theoretical reasons > why they do not require cross validation or test sets. We are investigating this > for QSAR and preliminary results suggest that this is the case. > > We have published some of this work recently: > > [74] New QSAR Methods Applied to Structure-Activity Mapping and > Combinatorial Chemistry, Burden, F.R. and Winkler, D.A. J. Chem. Inf. > Comput. Sci. 39, 236 (1999). > [75] The Computer Simulation of High Throughput Screening of Bioactive > Molecules, F.R. Burden, D.A. Winkler, in Molecular Modelling and Prediction > of Bioactivity (K. Gundertofte and F.S. Jorgensen eds), Plenum Press 1998. > [80] Robust QSAR Models Using Bayesian Regularised Artificial Neural > Networks, Burden, F.R. and Winkler, D.A. J. Med. Chem., 1999; 42(16); 3183- > 3187 (1999). > [81] A QSAR Model for the Acute Toxicity of Substituted Benzenes towards > Tetrahymena Pyriformis using Bayesian Regularized Neural Networks. F R. > Burden* David A. Winkler, Chem. Res. Toxicol., in press. > [82] Robust QSAR Models from Novel Descriptors and Bayesian Regularized > Neural Networks, Winkler, D.A, Burden, F.R. Mol. Simul. 1999 in press. > [87] Do QSAR Models using Bayesian Regularized Artificial Neural Networks > Really Need Validation? Winkler, D.A. and Burden, F.R. J.Chem. Inf. > Comput. Sci in preparation. > > Cheers, > > Dave > > Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au > Senior Principal Research Scientist Voice: 61-3-9545-2477 > CSIRO Molecular Science Fax: 61-3-9545-2446 > Private Bag 10,Clayton South MDC 3169 http://www.csiro.au > Australia http://www.molsci.csiro.au > Dr David Turner Dept of Information Studies, Sheffield University Sheffield, S10 2TN, UK Tel. 0114 2 222 650 E-mail: D.Turner@sheffield.ac.uk Fax: 0114 2 780 300 From chemistry-request@server.ccl.net Thu Sep 9 09:39:49 1999 Received: from hotmail.com (f171.hotmail.com [207.82.251.57]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA20163 for ; Thu, 9 Sep 1999 09:39:48 -0400 Received: (qmail 18124 invoked by uid 0); 9 Sep 1999 13:33:30 -0000 Message-ID: <19990909133330.18123.qmail@hotmail.com> Received: from 203.197.132.143 by www.hotmail.com with HTTP; Thu, 09 Sep 1999 06:33:26 PDT X-Originating-IP: [203.197.132.143] From: "dakshinamoorthy sivanesan" To: CHEMISTRY@ccl.net Subject: request regarding use of MP2/6-31g* MASSAGE SCRF=dipole calculation in G94w pack Date: Thu, 09 Sep 1999 06:33:26 PDT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Dear ccl members While I am doing calculation on solvent effect in cc stacked dimer for counterpoise correction , but I am getting the following problem in the output: --------------------------------- #T mp2/6-31g* MASSAGE scrf=dipole --------------------------------- ----- Title ----- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 Internal co-ordinates for C-C staked dimer ……………………………………………………..follows H -3.58395 1.50943 3.4 H -2.67444 3.0042 3.4 WANTED A FLOATING POINT NUMBER AS INPUT. FOUND AN INTEGER AS INPUT. 1 Nuc 0.0 ? Error termination via Lnk1e in Link 116. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. File lengths (MBytes): RWF= 1 Int= 0 D2E= 0 Chk= 2 Scr= 1 ** may I ask you , kindly please let me know the causes of this problem and how it can be sorted out. I need it immediately. Thanks in advance. Yours D.Sivanesan It is very convenient for me to access the reply from you to the following e-mail ID: peacok15@hotmail.com Address: D.Sivanesan Senior Research Fellow Chemical laboratory Central Leather Research Institute Adyar Madras 600 020. INDIA E-mail: peacok15@hotmail.com Sivaclri@hotmail.com ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From chemistry-request@server.ccl.net Thu Sep 9 10:43:45 1999 Received: from matavnet.hu (matavnet.hu [145.236.224.246]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA20441 for ; Thu, 9 Sep 1999 10:43:44 -0400 Received: (qmail 29709 invoked from network); 9 Sep 1999 16:39:17 +0200 Received: from line-212-133.dial.matav.net (HELO chemaxon.com) (145.236.212.133) by mail.matav.hu with SMTP; 9 Sep 1999 16:39:17 +0200 Message-ID: <37D7C79B.7509BCEF@chemaxon.com> Date: Thu, 09 Sep 1999 16:43:39 +0200 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU Subject: Marvin 2.1 released Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Please excuse multiple postings. Version 2.1 of the Marvin Java applets for drawing and displaying chemical structures in HTML pages is released and can now be tried and downloaded at http://www.chemaxon.com/marvin. A new paper showing features is at http://reprints.net/ecsoc-3/e0002/e0002.htm Marvin is free for free Internet sites. (Intranet and Extranet sites: 50% discount in September.) Among other possibilities, Marvin can now be integrated with JChem, our new Java based system for searching and handling chemical structures on the Web or Intranets (http://www.jchem.com). We are looking for partners (who would like to integrate our products with their software) and distributors. If you need our help in upgrading, please send your web page containing a previous version of Marvin to support@chemaxon.com. New features: MarvinSketch easier branching and chain drawing smarter rotation of selections easy access to many templates: rings, amino acids, polycyclics for developers: easy template customization, template groups are stored in SD files MarvinView 3D rotation colored 3D structures pop-up menu at right-click items for zooming, translation, rotation Hydrogen display options clipboard actions border in molecule tables dialog boxes for error messages improved integration with MarvinSketch molecule cell selection Import/Export automatic file format recognition SMILES and SDF import new export formats: Sybyl mol, CML(experimental) XYZ, POV-Ray GZIPped file import Molfile display and update in separate window (enables easier Molfile export and import) Swing Marvin 2 comes in two flavors: AWT and Swing Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T: +3620 9570988 mailto:fcsiz@chemaxon.com From chemistry-request@server.ccl.net Thu Sep 9 19:09:38 1999 Received: from pub.jlonline.com. ([202.102.24.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA22691 for ; Thu, 9 Sep 1999 19:09:36 -0400 Received: from chungenl ([10.74.65.238]) by pub.jlonline.com. (8.9.1/8.9.1) with SMTP id HAA28838 for ; Fri, 10 Sep 1999 07:02:38 +0800 (CST) Message-ID: <003e01befb17$dcb7b880$98404a0a@chungenl> From: "Chungen Liu" To: Subject: Help me on the selection of density functional and basis sets for transition metal compunds. Date: Fri, 10 Sep 1999 07:05:15 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 I want to do some calculations on the transition metal compounds(in solid state) using DFT scheme. I am troubled by the selection of the density functional and basis sets. If you have any idea, would you please let me share your experience. Thank you in advance. Chungen yhdou@pub.jlonline.com