From chemistry-request@server.ccl.net Wed Jun 16 07:40:10 1999 Received: from org.chem.msu.su (org.chem.msu.su [158.250.32.94]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA10009 for ; Wed, 16 Jun 1999 07:38:50 -0400 Received: from localhost (serge@localhost) by org.chem.msu.su (8.9.3/8.9.3) with SMTP id PAA28645; Wed, 16 Jun 1999 15:29:53 +0400 (MSD) Date: Wed, 16 Jun 1999 15:29:52 +0400 (MSD) From: Serge Pissarev To: Mark Thompson cc: chemistry@ccl.net Subject: Re: CCL:Ring discovery algorithm In-Reply-To: <000901beb765$a10ee380$ae8dd796@biggeek.wrq.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Mark, As for me, the most simple idea, clear and attractive algorithm for cycle search is published in: Th. Hanser, Ph. Jauffet, S. Kaufmann J.Chem.Inf.Comput.Sci. 1996, Vol 36., 1146-1152. but there are some difficulties in using this algorithm. In particular, preliminary side chain cutting of a graph is required, in spite of what they say in the paper (the cause is the phanthom cycles generation from branched substituents with inappropriate atoms enumeration). But the idea of graph collapsing employed is brilliant and very clearly illustrated.. Moreover this algorithm is capable to enumerate all paths between vertices and it seems to be robust and fast (with small limitations mentioned above). The most recent and great overview I know is: Downs et al. J.Chem.Inf.Comput.Sci. 1988, 29, 172-187. Best wishes! Serge A. Pissarev QSAR and Computational Chemistry Group, Chair of Organic Chemistry Chemistry Department of Moscow State University. Email: serge@qsar.chem.msu.su WWW : http://org.chem.msu.su/~serge On Tue, 15 Jun 1999, Mark Thompson wrote: > A few years back, someone described a nice algorithm for discovering rings in molecular > systems. > > If you recall this article, or just the authors, or any useful bit of > information, would you please reply to me? > > Thanks in advance, > > Mark Thompson > mthompson@seanet.com From chemistry-request@server.ccl.net Wed Jun 16 10:10:43 1999 Received: from pp3.shef.ac.uk (pp3.shef.ac.uk [143.167.2.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA11483 for ; Wed, 16 Jun 1999 10:10:41 -0400 From: d.turner@sheffield.ac.uk Received: from pc100182.shef.ac.uk ([143.167.100.182] helo=davets_pc) by pp3.shef.ac.uk with smtp (Exim 2.02 #2) id 10uGGR-0002kC-00; Wed, 16 Jun 1999 15:02:03 +0100 To: amolive@dedalus.lcc.ufmg.br Date: Wed, 16 Jun 1999 15:02:05 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:CoMFA and SOMFA CC: CHEMISTRY@server.ccl.net, Dave.Winkler@molsci.csiro.au, chairman@chem.ox.ac.uk, daniel@bellatrix.pcl.ox.ac.uk Priority: normal In-reply-to: X-mailer: Pegasus Mail for Win32 (v3.01a) Message-Id: Dear all SOMFA, as recommended below, uses an algorithm which is simply _one-component_ (or latent variable) PLS. The SOMFA method is thus somewhat limited since PLS models usually (but not always) use >1 LV for optimum internal (ie q2) and external (ie test set) predictivity. I can list the steps in PLS which show this equivalence if anyone is interested? The other difference to COMFA is that SOMFA uses binary indicator variables instead of Lennard-Jones potentials for the steric "field", although this is not novel in itself. This combined with the one LV limitation means the method is fast of course. However, this speed-up is insignificant (completely irrelevant) when the very rapid SAMPLS algorithm is used. Thus the only advantage I can see is that the software is free and that it runs on a PC ... but any user should be aware of its main limitation. Also, perhaps SOMFA violates the COMFA patent although I don't believe such things should be "patentable" - but that's another issue ... Dave Turner Date sent: Tue, 15 Jun 1999 15:44:07 -0300 (BSC) From: andre mauricio de oliveira To: Lista de discussao Quim Comp Subject: CCL:CoMFA (fwd) > Dear CCL's, > I.m returnig Dr. David A. Winkler's reply on my question about > 3D-QSAR for PC. > > Andre Mauricio de Oliveira > > VOICE +55-031-374-1325 > +55-031-499-5765 > FAX +55-031-499-5700 > > Laboratorio de QSAR e Modelagem Molecular > Nucleo de Estudos em Quimica Medicinal (NEQUIM) > NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim > Departamento de Quimica ICEx > Federal University of Minas Gerais > Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 > Belo Horizonte MG Brazil > > ---------- Forwarded message ---------- > Date: Fri, 11 Jun 1999 11:14:58 +1000 > From: "Dr. Dave Winkler" > To: andre mauricio de oliveira > Subject: Re: CCL:CoMFA > > >Hi all, > > Can anyone point me any PC program to perform CoMFA analysis > >(preferebly free)? > > > CoMFA is a patented technology owned by Tripos Associates > (http://www.tripos.com) and is not available for the PC or for free. > However, Graham Richards at Oxford University Centre for Molecular Sciences > has developed the SoMFA method which approximates CoMFA. It runs on a PC > and is available from his web site at Oxford > (http://bellatrix.pcl.ox.ac.uk). > > 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 > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > Dr David Turner Dept of Information Studies, Sheffield University Sheffield, S10 2TN Tel. 0114 2 222 650 E-mail: D.Turner@sheffield.ac.uk From chemistry-request@server.ccl.net Wed Jun 16 10:41:39 1999 Received: from sunflare.ccs.yorku.ca (2QV3FeY7QeYunb8QKowGp66pus1Phl4T@sunflare.ccs.yorku.ca [130.63.236.128]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA11782 for ; Wed, 16 Jun 1999 10:41:39 -0400 Received: from sunlight.ccs.yorku.ca (m9EP8yCggf61R5fRT0ez29OdyxdNd5lw@sunlight.ccs.yorku.ca [130.63.236.85]) by sunflare.ccs.yorku.ca (8.8.7/8.6.11) with ESMTP id KAA20603 for ; Wed, 16 Jun 1999 10:33:40 -0400 (EDT) Received: from localhost (serge@localhost) by sunlight.ccs.yorku.ca (8.8.7/8.7.6) with ESMTP id KAA17255 for ; Wed, 16 Jun 1999 10:33:37 -0400 (EDT) X-Authentication-Warning: sunlight.ccs.yorku.ca: serge owned process doing -bs Date: Wed, 16 Jun 1999 10:33:37 -0400 (EDT) From: Serge Gorelsky X-Sender: serge@sunlight.ccs.yorku.ca To: CHEMISTRY@ccl.net Subject: gaussian98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear collegues. While running some DTF calculations on ruthenium complexes with Gaussian 98, from time to time I get the warning message like this: **** Warning!!: The smallest alpha delta epsilon is 0.64964185D-02 This message appears after convergence of SCF iterations. My questions are 1. what are alpha delta epsilon here? 2. is this a matter for serious concern? 3. is this problem related to the basis set or is it some convergence problems? Any help would be deeply appreciated. Thank you. ________________________________________________________________ Serge Gorelsky, M. Sc. Department of Chemistry, York University 4700 Keele St., Toronto, Ontario M3J 1P3, Canada ________________________________________________________________ From chemistry-request@server.ccl.net Wed Jun 16 12:17:50 1999 Received: from unet.univie.ac.at (unet.univie.ac.at [131.130.230.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA12939 for ; Wed, 16 Jun 1999 12:17:45 -0400 Received: from brain (unet4-116.univie.ac.at [131.130.233.116]) by unet.univie.ac.at (8.8.8/8.8.7) with ESMTP id SAA34602 for ; Wed, 16 Jun 1999 18:09:47 +0200 Received: from 192.168.0.1 by brain ([192.168.0.1] running VPOP3) with SMTP for ; Wed, 16 Jun 1999 18:06:02 +0200 Message-ID: <001901beb812$21a29da0$0100a8c0@brain> Reply-To: "Alexander Klinsky" From: "Alexander Klinsky" To: Subject: SOMFA2 TF2 Files Problems Date: Wed, 16 Jun 1999 18:06:02 +0200 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 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 X-Server: VPOP3 V1.3.1 - Registered to: Lukundoo [HPA] Dear Colleagues ! We have just begun using SOMFA2 and were unfortunately not able to generate the required tf2 files from our structures which are available as pdb files after superpositioning. We did the following without success: 1. Convert the PDB file to CSSR Format using Babel 1.6 then convert it with the included conversion utility -> Error message: Fractional coordinates not supported 2. Generate a CSSR file using molden 3.5 -> The same error message Does anybody know the detailed structure of the tf2 files or how to generate such files form PDB or anything else. Kind regards, Alexander Klinsky Institute of theoretical chemistry University of Vienna Austria From chemistry-request@server.ccl.net Wed Jun 16 13:26:40 1999 Received: from eeyore.cc.uic.edu (EEYORE.CC.UIC.EDU [128.248.171.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA13565 for ; Wed, 16 Jun 1999 13:26:40 -0400 Received: from uic.edu (SLIP5A-09.DIALIN.UIC.EDU [128.248.28.109]) by eeyore.cc.uic.edu (8.9.3/8.9.3) with ESMTP id MAA14035 for ; Wed, 16 Jun 1999 12:16:55 -0500 (CDT) Message-ID: <3767DC4E.E8F22A37@uic.edu> Date: Wed, 16 Jun 1999 12:18:07 -0500 From: "Jose S. Duca" Reply-To: duca@tigger.cc.uic.edu Organization: Laboratory of Molecular Modeling and Design - College of Pharmacy - University of Illinois at Chicago X-Mailer: Mozilla 4.5 [en]C-DIAL (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: "CHEMISTRY@server.ccl.net" Subject: problems downloading SoMFA Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, Does anybody out there know how to download the SoMFA program? Til now all I got is an error message "the directory /somfa2.zip" cannot be found. Any help is welcomed. Regards, Jose Duca From chemistry-request@server.ccl.net Wed Jun 16 13:22:33 1999 Received: from dasher.wustl.edu (dasher.wustl.edu [128.252.162.151]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA13538 for ; Wed, 16 Jun 1999 13:22:33 -0400 Received: from localhost by dasher.wustl.edu (8.8.8/1.1.22.3/13May99-1258PM) id MAA0000001660; Wed, 16 Jun 1999 12:22:12 -0500 (CDT) From: Jay Ponder Message-Id: <199906161722.MAA0000001660@dasher.wustl.edu> X-Authentication-Warning: dasher.wustl.edu: localhost [127.0.0.1] didn't use HELO protocol Reply-To: ponder@dasher.wustl.edu To: chemistry@ccl.net cc: ponder@dasher.wustl.edu Subject: TINKER 3.7 is now available Date: Wed, 16 Jun 1999 12:22:12 -0500 X-Mts: smtp Dear CCL Subscribers, We are pleased to announce TINKER 3.7, a new version of our molecular modeling package which is now available from the TINKER Home Page web site at http://dasher.wustl.edu/tinker/. Many new features, general improvements and bug fixes are incorporated in the new version. We suggest that all current users of the package update. Below is some general information about the capabilities of TINKER as taken from the web site. Jay Ponder -------- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ -------- TINKER -- Software Tools for Molecular Design Version 3.7 June 1999 Introduction The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER-95, CHARMM22, MM2(91), MM3(99), OPLS-AA and OPLS-UA. Parameter sets for other standard force fields such as ENCAD, MMFF and UFF are in progress, as are our own TINKER polarizable multipole parameters. The TINKER package includes a variety of novel algorithms such as a new distance geometry metrization method that has greater speed and better sampling than standard methods, Elber's reaction path methods, several of our Potential Smoothing and Search (PSS) methods for global optimization, an efficient potential surface scanning procedure, a Cartesian polytensor atomic multipole expansion treatment of electrostatics with explicit polarizability, Eisenberg-McLachlan ASP and MacroModel GB/SA solvation, our own truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, velocity Verlet stochastic dynamics, an improved spherical energy cutoff method, Particle Mesh Ewald summation for partial charges under periodic boundary conditions, a novel reaction field treatment of long range electrostatics, and much more.... Current Release The most recent release, version 3.7, contains the following new features and updates from version 3.6: (1) further improvements to our Potential Smoothing and Search global optimization algorithms, (2) updated parameter sets for the CHARMM, AMBER, OPLS and MM3 force fields, further validation of each of these parameters sets against their actual programs has resulted in some fairly major revisions for CHARMM22 and minor changes to the others, (3) a conformational scanning method, SCAN, for use on smoothed potential surfaces which efficiently explores the full potential surface, (4) a new velocity Verlet stochastic dynamics capability added the TINKER MD program, DYNAMIC, (5) Particle Mesh Ewald summation for partial charge electrostatics with periodic boundary conditions, (6) prebuilt executables for systems with up to 10000 atoms provided for Intel Win9X/NT, Intel Linux and Macintosh, and (7) numerous small changes, additions and fixes, many of them suggested by users of the package. Please note that as with prior new releases, version 3.7 is neither backward nor forward compatible with earlier versions of TINKER. For example, version 3.6 parameter files should not be used with version 3.7 executables and vice versa. Availability This distribution version of TINKER, with full source code, is made available free of charge to anyone who wants it. New major releases of the package with additional features are generally placed on this site each February, June and October. Minor changes and bug fixes are added to the distribution version as we finish testing them. The basic package has been used by the Ponder lab and others at Washington University for several years and should be fairly robust. All we ask is that you notify us of any bugs, features you would like to see implemented, or major code extensions that you add yourself. If you make significant use of the package, please return the enclosed license form. Comments and questions are always welcome and should be sent to ponder@dasher.wustl.edu. We try to respond to all email as time allows. -------- From chemistry-request@server.ccl.net Wed Jun 16 13:47:06 1999 Received: from icarus.cc.uic.edu (ICARUS.CC.UIC.EDU [128.248.121.53]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA13888 for ; Wed, 16 Jun 1999 13:47:06 -0400 Received: from localhost (akulka1@localhost) by icarus.cc.uic.edu (8.8.8/8.8.8) with ESMTP id MAA23358; Wed, 16 Jun 1999 12:38:25 -0500 (CDT) X-Authentication-Warning: icarus.cc.uic.edu: akulka1 owned process doing -bs Date: Wed, 16 Jun 1999 12:38:24 -0500 (CDT) From: Amit Subhash Kulkarni X-Sender: akulka1@icarus.cc.uic.edu To: "Jose S. Duca" cc: "CHEMISTRY@server.ccl.net" Subject: Re: CCL:problems downloading SoMFA In-Reply-To: <3767DC4E.E8F22A37@uic.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Jose, I also tried to download the program but got the same message. I hope that the program is still freeware Cheers Amit On Wed, 16 Jun 1999, Jose S. Duca wrote: > Hi all, > Does anybody out there know how to download the SoMFA program? > Til now all I got is an error message "the directory /somfa2.zip" cannot > be found. > > Any help is welcomed. > > Regards, > Jose Duca > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > * * ********************************** * * * FROM: * * * * * * * * Amit S. Kulkarni * * * * * ********* * * * 903 South Ashland Ave. * ********** * Apt. No. 510 B * * * Chicago, Il 60607 * * * USA * * * * * * * ********** * Tel# 312-829-2341 * * * ********* * Email:akulka1@uic.edu * * * * * *CONCENTRATION IS ESSENCE OF LIFE* * * .....swami vivekananda* * ********************************** * ********* COLLEGE OF PHARMACY MEDICINAL CHEMISTRY DEPARTMENT MOLECULAR MODELLING LABORATORY From chemistry-request@server.ccl.net Wed Jun 16 14:36:03 1999 Received: from unet.univie.ac.at (unet.univie.ac.at [131.130.230.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA14544 for ; Wed, 16 Jun 1999 14:35:55 -0400 Received: from brain (uvo1-132.univie.ac.at [131.130.231.132]) by unet.univie.ac.at (8.8.8/8.8.7) with ESMTP id UAA76980; Wed, 16 Jun 1999 20:25:17 +0200 Received: from 192.168.0.1 by brain ([192.168.0.1] running VPOP3) with SMTP; Wed, 16 Jun 1999 20:20:24 +0200 Message-ID: <001301beb824$e69af140$0100a8c0@brain> Reply-To: "Alexander Klinsky" From: "Alexander Klinsky" To: "Jose S. Duca" , References: <3767DC4E.E8F22A37@uic.edu> Subject: Re: CCL:problems downloading SoMFA Date: Wed, 16 Jun 1999 20:20:18 +0200 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 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 X-Server: VPOP3 V1.3.1 - Registered to: Lukundoo [HPA] > Does anybody out there know how to download the SoMFA program? > Til now all I got is an error message "the directory /somfa2.zip" cannot > be found. Try ftp://fangio.pcl.ox.ac.uk/ftproot/somfa2.zip Cheers Alex Klinsky Institute of Theoretical Chemistry University of Vienna Austria