From chemistry-request@server.ccl.net Fri Dec 18 03:07:18 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA05011 for ; Fri, 18 Dec 1998 03:07:18 -0500 Received: from mail.matav.hu (mail.matav.hu [145.236.224.244]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA23876 Fri, 18 Dec 1998 03:04:12 -0500 (EST) Received: (qmail 9204 invoked from network); 18 Dec 1998 09:03:51 +0100 Received: from line-209-172.dial.matav.net (HELO inhale) (145.236.209.172) by mail.matav.hu with SMTP; 18 Dec 1998 09:03:51 +0100 Message-ID: <009001be2a5c$dc35e530$6b92e0c1@inhale.inhaledomain> From: "Ferenc Csizmadia" To: Subject: Re: CCL:SUMMARY: Looking for an utility to generate unique SMILES Date: Fri, 18 Dec 1998 08:58:27 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" 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 ChemAxon's Marvin Sketcher Java applet can be used to generate unique SMILES from graphic input or MDL Molfile. All you need is a Java capable browser (e.g. Netscape or IE) to run it. The applet is available at http://www.chemaxon.com/marvin. It can also be downloaded to the users' site. Ferenc Csizmadia ~~~~~~ Ferenc Csizmadia, Ph.D. ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T:+3620 9570988 mailto:fcsiz@chemaxon.com -----Original Message----- From: Christoph.Helma@univie.ac.at To: chemistry@www.ccl.net Cc: dalke@bioreason.com Date: Thursday, December 17, 1998 4:58 PM Subject: CCL:SUMMARY: Looking for an utility to generate unique SMILES >Some weeks ago I was asking for a tool for the generation of unique >SMILES under Linux. A source for the SMILES uniquetizer is available >from > > outreach@superior.dul.epa.gov > >I was able to compile it without problems, but did not have time >enough to test it thoroughly. > >On a SGI it is possible to use the Daylight toolkit or TSAR (Oxford >Molecular) to generate unique SMILES. > > >Christoph Helma > >---- >Christoph Helma christoph.helma@univie.ac.at >Institut fuer http://helma.cancer.univie.ac.at/ >Tumorbiologie-Krebsforschung >Borschkegasse 8a tel +43-1-4277-65147 >A-1090 Wien, Austria fax +43-1-4277-9651 > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: chemistry-request@www.ccl.net >-- Original Sender From: Address: Christoph.Helma@univie.ac.at >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From chemistry-request@server.ccl.net Fri Dec 18 06:33:30 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA05176 for ; Fri, 18 Dec 1998 06:33:30 -0500 Received: from pp2.shef.ac.uk (pp2.shef.ac.uk [143.167.1.32]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA24737 Fri, 18 Dec 1998 06:30:14 -0500 (EST) Received: from [143.167.103.254] (helo=ramsley.shef.ac.uk) by pp2.shef.ac.uk with esmtp (Exim 2.02 #5) id 0zqy6h-0006d1-00; Fri, 18 Dec 1998 11:30:07 +0000 Received: from RAMSLEY/MAILQUEUE by ramsley.shef.ac.uk (Mercury 1.44); 18 Dec 98 11:30:07 +0000 Received: from MAILQUEUE by RAMSLEY (Mercury 1.43); 18 Dec 98 11:30:00 +0000 From: "David B.Turner" Organization: Sheffield University To: chemistry@www.ccl.net Date: Fri, 18 Dec 1998 11:29:50 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:Enhancing CoMFA CC: bclark@tripos.com, trevor@tripos.com Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Message-ID: <4B2E38B7D69@ramsley.shef.ac.uk> Dear all To add to the previous message from Bob Clark: I agree with everything he has to say about CoMFA grid resolution / sampling-related effects. I didn't realise that Arthur Wang was suggesting that you take the orientation with the highest q2; this is clearly the wrong thing to do. I have myself performed some extensive analyses of the effects on q2, r2 and test predictive r2 (pr2) of aggregate-body reorientation within the 3D-grid. I have done this at both 1 Ang and 2 Ang for two datasets. The results, from >1,000 different orientations, are (in brief): Melatonin receptor ligands (Sicsic et al, JMC, 1997, 40, 739) 1 Ang 2 Ang q2 0.67 - 0.76 Mean 0.72 0.58 - 0.81 Mean 0.69 r2 0.85 - 0.97 Mean 0.93 0.72 - 0.97 Mean 0.87 pr2 0.66 - 0.80 Mean 0.73 0.43 - 0.88 Mean 0.70 Steroids (from original CoMFA paper but corrected by Wagener et al, JAmChemSoc, 1995, 117. 7769 ): (Fluorine-containing compound omitted from prediction set) 1 Ang 2 Ang q2 0.85 - 0.88 Mean 0.86 0.76 - 0.90 Mean 0.85 r2 0.93 - 0.94 Mean 0.93 0.88 - 0.96 Mean 0.93 pr2 0.81 - 0.86 Mean 0.84 0.63 - 0.91 Mean 0.83 In all cases there is almost zero-correlation (r) between q2 and test set pr2 which clearly demonstrates the problem with taking the orientation with the maximum q2 (although this doesn't really need demonstrating...) The steroid results are pretty stable (low variance) at 1 Ang while the melatonin scores are less so. I haven't looked at the variation in prediction for individual compounds - I have the data however. The 2 Ang results (see also Cho and Tropsha CV-R2 GRS) suggest that many published PLS results are pretty meaningless**. My results for test set pr2 show this even more strongly than with q2. Overall, the probability of getting a model significantly different from the mean ("true"?) model is quite low at 1 Ang but you _don't know_ where in the distribution your initial model is unless you do some kind of reorientation testing ... I think this will be the case whether or not Sybyl "ORIENT BEST_VIEW" is used. The steroid results will appear in a paper about EVA (in press JCAMD, Trevor Heritage and Allan Ferguson are co-athors). The melatonin results have been submitted as part of a paper about the application of a GA to selecting localised Gaussian kernel widths in an EVA analysis. Surely, the most straightforward means of improving model-reliability is to use the smallest grid-spacing possible / reasonable with the resources available. The use of SAMPLS makes this feasible for 1 Ang. resolution and less (depending on the number and size of compounds, of course). Once the q2 resulting from a particular resolution approximates to that of the mean/mode/median q2 from many analyses at, say, 2A resolution then one can say that you may have a reliable model that can be used for test set prediction. On a slightly different subject why doesn't Tripos make general (rather than HQSAR-only) use of SAMPLS to perform fitted analyses and test predictions? It's very easy to implement. Regards David Turner ** This is ignoring: dataset design aspects which is another kettle of fish, the type of CV to use and its relationship to dataset design or lack of etc ... Experimental errors for bioactivity data are also apparently generally ignored so the precision of some estimates may be unwarranted ... Dr David B. Turner Dept. of Information Studies University of Sheffield, Sheffield S10 2TN UK Tel.: 0114 2222 650 Fax.: 0114 2780 300 E-mail: D.Turner@sheffield.ac.uk From chemistry-request@server.ccl.net Fri Dec 18 09:08:39 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA05230 for ; Fri, 18 Dec 1998 09:08:23 -0500 Received: from scsx01.sc.ehu.es (root@scsx01.sc.ehu.es [158.227.150.40]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA25490 Fri, 18 Dec 1998 09:05:11 -0500 (EST) Received: from scox01.sc.ehu.es (scox01.sc.ehu.es [158.227.150.10]) by scsx01.sc.ehu.es (8.8.4/8.7.3) with ESMTP id PAA00410 for ; Fri, 18 Dec 1998 15:04:48 +0100 (MET) Status: N Received: from sq.ehu.es (pobmelat@sqpx94.sq.ehu.es [158.227.108.94]) by scox01.sc.ehu.es (8.8.5/8.7.3) with ESMTP id PAA12949 for ; Fri, 18 Dec 1998 15:04:47 +0100 (MET) Sender: pobmelat@sc.ehu.es Message-ID: <367A621A.8936EC87@sq.ehu.es> Date: Fri, 18 Dec 1998 15:09:30 +0100 From: Txema Mercero Reply-To: pobmelat@sq.ehu.es Organization: E.H.U. X-Mailer: Mozilla 4.04 [en] (X11; I; Linux 2.0.34 i586) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: NBO 4.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi There, Does anybody know where could we get the NBO 4.0 version? Thank you all! Txema Mercero Euskal Herriko Unibertsitatea From chemistry-request@server.ccl.net Fri Dec 18 10:16:47 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA05291 for ; Fri, 18 Dec 1998 10:16:47 -0500 Received: from majuelo.sdi.uam.es (majuelo.sdi.uam.es [150.244.9.25]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA26704 Fri, 18 Dec 1998 10:12:52 -0500 (EST) Received: from roble.sdi.uam.es (roble.sdi.uam.es [150.244.9.71]) by majuelo.sdi.uam.es (8.8.5/8.8.5) with SMTP id QAA24974 for ; Fri, 18 Dec 1998 16:11:36 +0100 (MET) Received: from brihuega ([150.244.37.59]) by roble.sdi.uam.es with SMTP for chemistry@www.ccl.net; Fri, 18 Dec 1998 16:11:37 +0100 Message-Id: <1.5.4.16.19981218150714.1dcf5216@bosque.sdi.uam.es> X-Sender: depaz@bosque.sdi.uam.es X-Mailer: Windows Eudora Light Version 1.5.4 (16) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 18 Dec 1998 16:07:14 +0100 To: chemistry@www.ccl.net From: Dr Jose Luis Garcia de Paz Subject: Summary:CIS and solvent calculation Hi all, Thank you to all who respond. It looks like there is not any ab initio package able to perform CIS and SCFR calculations. But there are some semiempirical ones: VAMP ARGUSLAB ZINDO Regards Jose _____________ Dr. Jose Luis Garcia de Paz |_ / Departamento de Quimica Fisica | | Facultad de Ciencias, C-XIV-602 | 0 / Universidad Autonoma de Madrid < | Telephon: +34-91-397.4957 or 4263 Ctra de Colmenar Km. 15 |_ ___/ Fax: +34-91-397.4512 E-28049 Madrid (SPAIN) \/ E-mail: alt E-mail: http://www.uam.es/qfa/depaz.html http://www.adi.uam.es/~depaz From chemistry-request@server.ccl.net Fri Dec 18 17:04:15 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA06125 for ; Fri, 18 Dec 1998 17:04:15 -0500 Received: from ganimedes.overnet.com.ar (ns1.overnet.com.ar [200.10.96.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA29902 Fri, 18 Dec 1998 17:01:01 -0500 (EST) Received: from carpincho.overnet.com.ar (carpincho.overnet.com.ar [200.10.96.19]) by ganimedes.overnet.com.ar (8.8.7/8.8.3) with ESMTP id TAA13017 for ; Fri, 18 Dec 1998 19:12:00 -0300 Received: from nppp238.overnet.com.ar (nppp238.overnet.com.ar [200.16.162.251]) by carpincho.overnet.com.ar (8.8.8/8.8.5) with SMTP id TAA09577 for ; Fri, 18 Dec 1998 19:11:30 -0300 Message-Id: <3.0.6.16.19981218185912.334f627c@pop.overnet.com.ar> X-Sender: dfa953uo@pop.overnet.com.ar X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (16) Date: Fri, 18 Dec 1998 18:59:12 To: chemistry@www.ccl.net From: "Dr. Daniel Glossman" Subject: bonding analysis Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear netters: How should one interpret the numbers coming from a Mulliken bonding analysis in G94? Thanks in advance Dr. Daniel Glossman glossman@overnet.com.ar From chemistry-request@server.ccl.net Fri Dec 18 17:32:29 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA06170 for ; Fri, 18 Dec 1998 17:32:29 -0500 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA00031 Fri, 18 Dec 1998 17:29:14 -0500 (EST) Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.14]) by ccshst09.cs.uoguelph.ca (8.8.6/8.8.6) with SMTP id RAA14954 for ; Fri, 18 Dec 1998 17:29:15 -0500 (EST) Date: Fri, 18 Dec 1998 17:29:15 -0500 (EST) From: Ruth Tanner X-Sender: rtanner@ccshst01 To: chemistry@www.ccl.net Subject: Linux vs Windows 95 vs Windows NT In-Reply-To: <3.0.6.16.19981218185912.334f627c@pop.overnet.com.ar> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am debating which platform to use on my PC when (if) we get a new PC that will be dedicated for running Gaussian98. I would like to know what the benefits are to using a Unix platform on a PC over using a Windows-based platform (and vice versa). I would also like to know from people who have had experience installing Gaussian98 on PCs whether they prefer Linux, Windows 95/98 or Windows NT and for what reasons. thanks :) Ruth ----------------------------------------------------------------------------- Ruth Tanner rtanner@uoguelph.ca Masters Student in Physical Chemistry Chemistry Department B.Sc. Chemical Physics (Co-op) Minor in English Literature University of Guelph http://www.uoguelph.ca/~rtanner/ ---------------------------------------------------------------------------- "The only way to atone for being occasionally a little over-dressed is by being always absolutely over-educated." Oscar Wilde ============================================================================