From chemistry-request@server.ccl.net Tue Sep 18 07:03:39 2001 Received: from arrhenius.che.chalmers.se ([129.16.90.200]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8IB3c330667 for ; Tue, 18 Sep 2001 07:03:39 -0400 Received: from arrhenius.che.chalmers.se (arrhenius.che.chalmers.se [129.16.90.200]) by arrhenius.che.chalmers.se (8.9.3/8.9.3) with ESMTP id NAA4082333; Tue, 18 Sep 2001 13:04:20 +0200 (MDT) Date: Tue, 18 Sep 2001 13:04:20 +0200 From: Harald Svedung X-X-Sender: To: Wei Zhuang cc: Subject: Re: CCL:torsional parameters in MM2/MM3 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Sometimes, for symmetry reasons, one of the terms will be enough to describe the angular dependence of the potential energy. :-) /Harald Harald Svedung (Ph.Lic.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone:+46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden. www.che.chalmers.se/~svedung/welcome.html On Mon, 17 Sep 2001, Wei Zhuang wrote: > Hi,all: > the formula of calculating torsional energy in MM3 is like: > > E=(k'/2)(1+cosA)+(k"/2)(1-cos2A)+(k'''/2)(1+cos3A). > > so I need 3 parameters:k',k",k''',but in the oringinal papers, when they > talked about the types including O and S, they only gave one > parameter,could anybody tell me why?thanks. > > regards > > wei zhuang > > e-mail:weiz@mail.rochester.edu > office phone:716-2750387 > > > > -= 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 chemistry-request@server.ccl.net Tue Sep 18 08:00:16 2001 Received: from mailserver.unimi.it ([159.149.10.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8IC0G331628 for ; Tue, 18 Sep 2001 08:00:16 -0400 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id OAA19600 for ; Tue, 18 Sep 2001 14:00:13 +0200 (MET DST) Message-ID: <008001c14039$b22ea740$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: "CCL" Subject: Announcing VEGA 1.3.0 Standard & OpenGL Editions Date: Tue, 18 Sep 2001 14:01:44 +0200 Organization: Ist. Chimica Farmaceutica 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 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear CCLers, we are glad to announce that the final 1.3.0 release of VEGA package is now ready for free download on our web server (http://users.unimi.it/~ddl). VEGA was developed to create a bridge between most of the molecular software packages, like Quanta/CHARMm, Insight II, MoPac, BioDock, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules. The most important features implemented in VEGA are: - Several file formats supported for input and output. - Multiple files load for assemblies creation. - Atomic charge attribution. - Force field attribution. - Calculation of molecular surfaces. - Calculation of ligand-receptor interaction energy. - Evaluation of logP and lipole. - Dynamic trajectory analysis. - Molecule solvatation. Available OpenGL packages: - VEGA Win32 1.3.0 OpenGL Edition. Available standard packages: - VEGA AmigaOS 1.3.0 - VEGA Linux x86 (1.3.0) - VEGA Silicon Graphics IRIX 6.x (1.3.0) The VEGA OpenGL version allows to visualize 3D molecular structures in several draw mode (wireframe, CPK solid & wireframe, Van der Waals solid & wireframe) using an high optimized graphical engine. The VEGA OpenGL can calculate and display any type of molecular surface: Van der Waals, surface accessible to solvent (SAS), molecular electrostatic potential (MEP), hydropathicity surface (ILM), molecular lypophilicity surface (MLP), etc. Each surface can be colored in several modes (by atom, by molecule, by property, custom). The most significant features are: **** 3D Graphics **** - Strong hardware acceleration (depending on your graphic card). - 3D molecule view (wireframe, CPK wireframe, CPK solid, VdW wireframe, VdW solid). - 3D surface view with most coloring methods (property, atom type and custom). - 3D object manipulation. - Lighting (available with hardware acceleration only). - Smooth animations. - Color properties. - Labels (atom name, element, atom type, atom number and atomic charge). - Mouse control for rotations, translations, scale operations and animations. **** Graphic User Interface **** - All VEGA functions are available trough menu and/or requesters. - Extended menu with accelerators. - Context menu. - Buttons, radio buttons, combo boxes, list boxes, check boxes and sliders. - Copy & Paste operations. - Integrated Html help. **** Calculation Tools **** - Analysis of molecular dynamics trajectory files. - Graphic interface for BioDock 3.0. - Graphic interface for MoPac 6 (included in the package). - Molecular properties. **** Extra Tools **** - Integrated Mini Text Editor. - Integrated Graph Editor. - Task manager. **** External Tools **** - File decompressor (WinDD). - SendVegaCmd console command for batch file creation. **** Other **** - Communication port for batch file scripting (see SendVegaCmd utility). - Full language localization (locale.dll). - Pentium optimized code for maximum performances. - Demo. The VEGA OpenGL package was developed for Windows 9x/ME/NT/2000 only and in the future can be available for other operating systems with OpenGL API support. New features in the 1.3.0 standard and OpenGL releases: - Data De/Compressor Engine updated: now you can pack the output with BZip2, GZip, PowerPacker (Amiga only) and Z-Compress. - ILM (Molecular Hydropathicity Index) surface calculation. - Polar surface area calculation (PSA). - HyperChem HIN loader. - Added charge and force field check in CVFF energy evaluation. - Connectivity routine rewritten and more fast. - Surface routines totally rewritten for load/save operations. - DCD analyzer can load both CRD or MSF packet files. - Water remove option (-w) in trajectory analysis. - Fix: gromos loader/saver. - Fix: multiple PDBF loading. - Fix: routine for ring search. - Fix: CHARMm force field template. - Fix: a little bug in msf loader. - Fix: Mopac loader more compatible. - Fix: solvent layer calculation. - Linux: first official release. - Unix: fixed water detection routine. - Win32: fixed program path detection. - Win32: fixed CTRL+C execution halting. - Win32: setup program for easy insallation. - Win32: WinDD Data Decompressor software included in the package. Thank you for your attention. Giulio Vistoli & Alessandro Pedretti -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-58357522 Fax +39-02-58357565 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Tue Sep 18 06:46:15 2001 Received: from mel.ruc.dk ([130.225.220.27]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8IAkE330320 for ; Tue, 18 Sep 2001 06:46:15 -0400 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id MAA29552 for ; Tue, 18 Sep 2001 12:46:14 +0200 (MET DST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id MAA15117 for ; Tue, 18 Sep 2001 12:22:49 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 18 Sep 01 12:46:13 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 18 Sep 01 12:46:11 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@ccl.net Date: Tue, 18 Sep 2001 12:45:58 +0100 Subject: CCL:Alternant hydrocarbons: "Pairing Symmetry" X-Confirm-Reading-To: "Jens Spanget-Larsen" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <1C01B97B4047@virgil.ruc.dk> CCL:Alternant hydrocarbons ... Just some additional comments: One very interesting aspect of the electronic structure of alternant hydrocarbons is the orbital and state pairing symmetry predicted by simplified model Hamiltonians (e.g., HMO and PPP). This symmetry has important consequences for the predicted electronic transitions for this class of compounds. For example, only dipole transitions between so-called plus and minus states are allowed by the pairing symmetry, and a mirror image relationsship is predicted for the spectra of paired cations and anions. There is strong experimental evidence for the presence of effective orbital and state pairing in alternant hydrocarbons, particularly in benzenoid PAHs, and there can be no doubt that the pairing theorem offers a unique insight into their electronic structure. However, perfect pairing symmetry is an abstract, purely mathematical concept, based an idealized model assumptions. In fact, the pairing properties predicted by a variety of popular quantum chemical procedures are highly sensitive to calculational details. For example, the degeneracies required by the pairing theorem are not even approximated by the CNDO/S method of Del Bene and Jaffe. It seems that a remarkable coincidence, an "accidental cancelation of terms", is responsible for the presence of near-perfect pairing symmetry in benzenoid hydrocarbons.*) Yours, Jens >--< *) J. Spanget-Larsen: "The alternant hydrocarbon pairing theorem and all-valence electrons theory. ..", Theor. Chem. Acc. 98, 137-153 (1997). =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Cell-Phone: +45 2320 6246 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Tue Sep 18 09:23:19 2001 Received: from electra.cc.umanitoba.ca (root@[130.179.16.23]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8IDNJ300492 for ; Tue, 18 Sep 2001 09:23:19 -0400 Received: from hultin (hultin.chem.umanitoba.ca [130.179.48.60]) by electra.cc.umanitoba.ca (8.9.0/8.9.0) with SMTP id IAA05515 for ; Tue, 18 Sep 2001 08:23:17 -0500 (CDT) From: "Phil Hultin" To: Subject: MM2 Parameters for Phosphonates Date: Tue, 18 Sep 2001 08:23:18 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Does anyone out there have an MM2 parameter set appropriate for the phosphonate group, that I could add to the basic MM2 parameters that come with CSC Chem3D? I don't really have the facilities to work out the necessary parameters myself either computationally or experimentally, just at the moment, and Dr. Allinger didn't look at phosphonates back when MM2 was devised. Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin@cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ From chemistry-request@server.ccl.net Tue Sep 18 10:29:59 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8IETo301813 for ; Tue, 18 Sep 2001 10:29:55 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 15jLsZ-0002w3-00; Tue, 18 Sep 2001 16:29:39 +0200 Received: from vejas.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id QAA25088; Tue, 18 Sep 2001 16:57:52 +0200 (GMT) Date: Wed, 19 Sep 2001 04:29:05 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <6128180275.20010919042905@vaidila.vdu.lt> To: Vemparala Satyavani CC: chemistry@ccl.net Subject: CCL: software for docking 2 or more ligands ????? In-reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, CCL'ers, Could anybody point me to software capable produce docking with two and more ligands ? Best wishes to all of you Arturas Z. From chemistry-request@server.ccl.net Tue Sep 18 14:51:14 2001 Received: from mail1.ats.rochester.edu (IDENT:998@[128.151.224.31]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8IIpE306666 for ; Tue, 18 Sep 2001 14:51:14 -0400 Received: from localhost (weiz@localhost) by mail1.ats.rochester.edu (8.11.6/8.11.6) with ESMTP id f8IIq3L2183914 for ; Tue, 18 Sep 2001 14:52:03 -0400 (EDT) Date: Tue, 18 Sep 2001 14:52:03 -0400 From: Wei Zhuang X-Sender: weiz@mail1.ats.rochester.edu To: chemistry@ccl.net Subject: solvent effect in MM3 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi,all: in my opinion,MM3 didn't deal with the matters in solvent. I must say something stupid.:). could anybody tell me is there any paper from professor Allinger's group that talk about this topic.thanks wei zhuang e-mail:weiz@mail.rochester.edu office phone:716-2750387 From chemistry-request@server.ccl.net Tue Sep 18 21:20:53 2001 Received: from be-research.ucsd.edu ([132.239.236.13]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8J1Kq315877 for ; Tue, 18 Sep 2001 21:20:52 -0400 Received: from be-research.ucsd.edu (ile.ucsd.edu [132.239.25.142]) by be-research.ucsd.edu (8.11.1/8.11.1) with ESMTP id f8J1Kp611647 for ; Tue, 18 Sep 2001 18:20:52 -0700 (PDT) Sender: dsteiger@bioeng.ucsd.edu Message-ID: <3BA7E441.990C2398@be-research.ucsd.edu> Date: Tue, 18 Sep 2001 17:18:09 -0700 From: DS X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.5-15 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Lennard-Jones values for ions. Content-Type: text/plain; charset=x-user-defined Content-Transfer-Encoding: 7bit Does anybody know if there is any way of relating the Lennard-Jones values between the positive and negative ions of a given atom? Or a more fundamental question, am I correct in assuming that positive and negative ions of the same atom will have different values? Thanks, Don From chemistry-request@server.ccl.net Tue Sep 18 21:28:19 2001 Received: from mx03.gis.net ([208.218.130.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8J1SI316188 for ; Tue, 18 Sep 2001 21:28:19 -0400 Received: from [216.243.61.52] (host52.216.243.61.gis.net [216.243.61.52] (may be forged)) by mx03.gis.net (8.9.3+Sun/8.8.8+pyrd) with ESMTP id VAA04627; Tue, 18 Sep 2001 21:28:12 -0400 (EDT) X-Sender: jsb@198.112.109.4 Message-Id: In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 18 Sep 2001 21:34:31 -0400 To: "Phil Hultin" From: Jonathan Brecher Subject: Re: CCL:MM2 Parameters for Phosphonates Cc: chemistry@ccl.net >Does anyone out there have an MM2 parameter set appropriate for the >phosphonate group, that I could add to the basic MM2 parameters that come >with CSC Chem3D? I don't really have the facilities to work out the >necessary parameters myself either computationally or experimentally, just >at the moment, and Dr. Allinger didn't look at phosphonates back when MM2 >was devised. If you're really using software named "CSC Chem3D", it's a minimum of six years old and the only thing that surprises me is that you were able to get it to function at all. I don't know of any particular problems modeling phosphonates with MM2 using the latest version of CS Chem3D. There may even be a way to get things to work using your ancient version, I simply don't know. You should contact support@cambridgesoft.com with specifics of your problem, plus serial number, operating system details, sample files, etc, etc. Jonathan Brecher CambridgeSoft Corporation jsb@cambridgesoft.com