From chemistry-request@server.ccl.net Tue Aug 13 12:58:52 2002 Received: from haney.hbond.com ([207.137.2.252]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7DGwol01008 for ; Tue, 13 Aug 2002 12:58:51 -0400 Received: (from haney@localhost) by haney.hbond.com (8.9.3/8.9.3) id KAA01775; Tue, 13 Aug 2002 10:00:53 -0700 From: "Dr. David N. Haney" Message-Id: <200208131700.KAA01775@haney.hbond.com> Subject: Molecular Descriptors for Mac OS-X To: CHEMISTRY@ccl.net Date: Tue, 13 Aug 2002 10:00:22 -0700 (PDT) X-Mailer: ELM [version 2.5 PL5] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL QSAR/QSPR experts: eduSoft, LC Announces New Versions of Descriptor Software: Molconn-Z ### Molconn-Z STANDALONE ### Now for Mac OS-X -over 300 MOLECULAR DESCRIPTORS: the standard for DESCRIPTOR analysis -easy-to-use command interface common to all platforms -three standard input formats, easy to read or filter output format -has been tested with large complex databases like NCI ### Molconn-Z DEVELOPERS' TOOLKIT ### Now for Mac OS-X -includes Molconn-Z Standalone functionality plus some source code -greater flexibility for input/ouput, on-the-fly computations, SQL get/put -integrate with in-house tools or re-package for clients -DATABASE+MOLCONN-Z+STATISTICS --> New Leads Molconn-Z has been found by dozens of companies to be an excellent tool for QSAR/QSPR and predicting properties such as biological activity, polymer properties, toxicity, solubility, partition coefficients, and logP. Molconn-Z is now available for UNIX/LINUX, Windows, Mac OS-X. website http://www.edusoft-lc.com/molconn/ FREE TRIAL AVAILABLE -- ######### David N. Haney, Ph.D. ######### # Haney Associates Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney@hbond.com # ################# ##################### From chemistry-request@server.ccl.net Thu Sep 5 05:06:42 2002 Received: from web12801.mail.yahoo.com ([216.136.174.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g8596g318779 for ; Thu, 5 Sep 2002 05:06:42 -0400 Message-ID: <20020905090641.58479.qmail@web12801.mail.yahoo.com> Received: from [61.9.73.250] by web12801.mail.yahoo.com via HTTP; Thu, 05 Sep 2002 02:06:41 PDT Date: Thu, 5 Sep 2002 02:06:41 -0700 (PDT) From: amor san juan Subject: autodock testing To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all, Does anyone did correlation analysis between predicted and experimental binding energy? Using the AutoDock data predicted energy of binding, how were you able to convert it into predicted IC50. Kindly state the formula to be used in this case. Sincerely, Amor __________________________________________________ Do You Yahoo!? Yahoo! Finance - Get real-time stock quotes http://finance.yahoo.com From chemistry-request@server.ccl.net Thu Sep 5 07:52:18 2002 Received: from mhub2.bbsrc.ac.uk ([149.155.202.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g85BqH322041 for ; Thu, 5 Sep 2002 07:52:17 -0400 Received: from exrout.cc.bbsrc.ac.uk ([149.155.100.88]) by mhub2.bbsrc.ac.uk with esmtp (Exim 3.36 #3) id 17mv7O-0004IC-04 for chemistry@ccl.net; Thu, 05 Sep 2002 12:48:14 +0100 Received: from bits-exch1.bits.bbsrc.ac.uk ([149.155.108.13]) by exrout.cc.bbsrc.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id SJ424YAF; Thu, 5 Sep 2002 12:48:49 +0100 Received: by bits-exch1.bits.bbsrc.ac.uk with Internet Mail Service (5.5.2653.19) id ; Thu, 5 Sep 2002 12:48:49 +0100 Message-ID: <41773CEF2B8FD411920200508BDCDC12BE1488@bits-exch1.bits.bbsrc.ac.uk> From: "michael hanlon (BITS)" To: "'chemistry@ccl.net'" Subject: setting up Autodock Date: Thu, 5 Sep 2002 12:48:48 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-ECS-MailScanner-BBSRC: Found to be clean I'm on an Alpha with CTU5.1 and want to set up Autodock. There is an executable for the Alpha called alpha.OSF1_4.0. whiuch the website says you can just copy to a directory. I've done that but how do I start it. Any help with setting up much appreciated. Mike From chemistry-request@server.ccl.net Thu Sep 5 22:05:00 2002 Received: from mail.staff.site.ntu.edu.au ([138.80.69.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8624t315537 for ; Thu, 5 Sep 2002 22:05:00 -0400 Received: from mail.staff.site.ntu.edu.au ([138.80.49.23]) by mail.staff.site.ntu.edu.au with Microsoft SMTPSVC(5.0.2195.5329); Fri, 6 Sep 2002 11:34:51 +0930 Received: by mail.staff.site.ntu.edu.au (sSMTP sendmail emulation); Fri, 6 Sep 2002 11:34:21 +0930 Date: Fri, 6 Sep 2002 11:34:21 +0930 From: Brian Salter-Duke To: Comp Chem List Subject: Summary: Localised Kohn-Sham orbitals Message-ID: <20020906020421.GB636@BSALTERDUKE1> Mail-Followup-To: Comp Chem List Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.99i X-OriginalArrivalTime: 06 Sep 2002 02:04:52.0952 (UTC) FILETIME=[C9FC3D80:01C25549] My original question was:- Is the Kohn-Sham DFT energy and electron density (as generated for example by Gaussian98 using BLYP or other functionals) invariant to a unitary transformation of the Kohn-Sham orbitals to localised orbitals by any or all of the standard methods, in the same way that the Hartree-Fock wavefunction is invariant to unitary transformations of the Hartree-Fock orbitals? I will summarise if this turns out to be an interesting question. I had two replies:- ------------------------------------------------------------------------- Huub van Dam E-mail: h.j.j.vandam@dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD replied:- Hi Brian, I think the answer must be yes, DFT is invariant for unitary transformations among orbitals with the same occupation. The reason is quite simple: Call the orbitals Y and their occupation numbers n. Because the Kohn-Sham density matrix is diagonal (single determinant approximation) the density P is given by P = sum_i n_i Y_i^* Y_i Using the fact that mixing two generate eigenfunctions results in yet again an eigenfunction with the same eigenvalue, I can mix all occupied orbitals among each other by an unitary transformation and get an equally valid density matrix. The occupation numbers remain the same, and the new orbitals will be eigenfunctions of this density matrix. Therefore I can apply the same expression to get the density which will be the same as before. Finally as the energy is a functional of the density it follows that if the density is the same the energy has to be the same as well. Perhaps there is a more compact explaination but I think this covers most aspects. Good luck, Huub ------------------------------------------------------------------------- Douglas J. Fox Technical Support Gaussian, Inc. help@gaussian.com replied:- Brian, My gut answer was yes, the same machinery is used in both cases and all the MO integrals are retained so the most common semi-empirical problems are avoided. My experimental side ran the following, %Chk=lw2tBL #p B3LYP/6-311G** Cyclic Water Dimer RBLYP/6-311G** Optimisation 0 1 O -0.441888678 -3.645331531 -0.949088929 H -0.784006389 -3.840454337 -1.851910976 H 0.537637876 -3.616431553 -1.071306833 O 1.570274523 -1.575840084 -0.777018993 H 1.907288823 -1.418001616 0.134591502 H 0.594354979 -1.678408943 -0.656798044 --link1-- %Chk=lw2tBL # B3LYP/6-311G** Guess=(Read,Local,Save,Only) Geom=AllCheck --link1-- %Chk=lw2tBL #p B3LYP/6-311G** Guess=(Read) Geom=AllCheck which takes two cycles in the last run. The energy matches to 8 significant figures which is all I expect for single point accuracy. It takes two cycles because the coefficients change substantially even if the density and energy are invariant. ------------------------------------------------------------------------- Doug's reply did not quite convince me, but after reruning his example with changes I was convinced. Adding "scf=tight" gives the energy matching exactly to the digits printed. It also means that the 3rd step converges in one cycle not two. Adding pop=full to steps 1 and 3 shows that the density is identical at all three steps while the orbitals, being localised, are different at step 2 from steps 1 and 3. Replacing B3LYP with RHF gives the exact same pattern as expected. So I am convinced that the answer to my question is "Yes". Thanks to both Huub and Doug for replying. Brian. -- Brian Salter-Duke (Brian Duke) b_duke@octa4.net.au Honorary Fellow in Chemistry, NT University, Darwin, NT 0909, Australia. Post: Box 1028, Humpty Doo, NT 0836, Australia. Phone 08-89881600. Fax 08-89881302. http://www.octa4.net.au/linden/brian/ From chemistry-request@server.ccl.net Thu Sep 5 14:23:49 2002 Received: from xsmtp.ethz.ch ([129.132.97.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g85INm327711 for ; Thu, 5 Sep 2002 14:23:48 -0400 Received: from xfe1.d.ethz.ch ([129.132.97.23] RDNS failed) by xsmtp.ethz.ch with Microsoft SMTPSVC(5.0.2195.4905); Thu, 5 Sep 2002 20:23:48 +0200 Received: from laplinux ([129.132.118.154]) by xfe1.d.ethz.ch with Microsoft SMTPSVC(5.0.2195.4905); Thu, 5 Sep 2002 20:23:48 +0200 Content-Type: text/plain; charset="iso-8859-15" From: Alessandro Contini Organization: Istituto di Chimica Organica To: chemistry@ccl.net Subject: Water in Autodock Date: Thu, 5 Sep 2002 20:24:13 +0200 X-Mailer: KMail [version 1.4] MIME-Version: 1.0 Message-Id: <200209052024.13331.alessandro.contini@unimi.it> X-OriginalArrivalTime: 05 Sep 2002 18:23:48.0241 (UTC) FILETIME=[60885810:01C25509] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g85INn327712 Hi CClers, does anybody iknows if it's possible and how consider water during docking runs? I'll appreciate much any hint about it. Thanks Alessandro -- Alessandro Contini Istituto di Chimica Organica, Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm