From chemistry-request@server.ccl.net Thu May 18 11:05:08 2000 Received: from tech.chem.ethz.ch (ltcmail.ethz.ch [129.132.124.253]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA15604 for ; Thu, 18 May 2000 11:05:07 -0400 Received: from tech.chem.ethz.ch (baiker8.ethz.ch [129.132.125.8]) by tech.chem.ethz.ch (8.8.8/8.8.8) with ESMTP id RAA27075 for ; Thu, 18 May 2000 17:04:50 +0200 (CEST) Message-ID: <392407A4.E49305C9@tech.chem.ethz.ch> Date: Thu, 18 May 2000 17:09:24 +0200 From: angelo vargas Organization: ETHZ X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: gaussian98 Z-matrix optimization Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit hallo everybody does anybody know how to force G98 to print out the partially optimized parameters during a Z-matrix geometry optimization, for every optimization step, and not only at the end of the converged optimization? ....just trying to save a Z-matrix Angelo -- _______________________________________________________________________ Angelo Vargas Laboratory of Technical Chemistry Department of Chemical Engineering and Industrial Chemistry Swiss Federal Institute of Technology (ETHZ) ETH Zentrum, Universitätsstr. 6 Telefon: 0041/1/632 31 54, Room CNB B98.3 CH-8092 Zürich - Switzerland Fax: 0041/1/632 11 63 E-mail: vargas@tech.chem.ethz.ch http://mercury.ethz.ch/HOMEPAGE/members/vargas/vargas.html ________________________________________________________________________ From chemistry-request@server.ccl.net Thu May 18 17:07:29 2000 Received: from lrz.uni-muenchen.de (root@lsanca1-ar99-078-042.biz.dsl.gtei.net [4.3.78.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA17045 for ; Thu, 18 May 2000 17:07:29 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id OAA13330; Thu, 18 May 2000 14:05:19 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14628.23311.497499.642018@lrz.uni-muenchen.de> Date: Thu, 18 May 2000 14:05:19 -0700 (PDT) To: Subject: "MULTIMODE"; a code to obtain accurate rovibrational energy levels for many-mode molecules X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid From: Joel Bowman Sender: molecular-dynamics-news-request@mailbase.ac.uk To: molecular-dynamics-news@mailbase.ac.uk Subject: no subject (file transmission) Date: Thu, 18 May 2000 11:25:16 -0400 (EDT) Program announcement "MULTIMODE"; a code to obtain accurate rovibrational energy levels for many-mode molecules by: S. Carter, 39, Grove Hill, Caversham, Reading RG4 8PS, UK J.M. Bowman, Department of Chemistry, Emory University, Atlanta GA 30322, USA and contributions from N.C. Handy, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK "MULTIMODE" is a near-variational procedure for the calculation of rovibrational energies of polatomic molecules, adsorbates and clusters. The method is based on the Watson normal coordinate hamiltonian for non-linear molecules, and proceeds via vibrational SCF and rovibrational CI steps. The complete hamiltonian is used at all times, but approximations are made in order to integrate the potential and coriolis terms. These terms are included as N-mode expansions in the normal coordinates, but are truncated at the 4-mode terms. It has been demonstrated that higher terms are insignificant compared with the inaccuracies in the potential itself. The method has been thoroughly tested for a variety of triatomic and tetraatomic molecules and, in particular, against exact variational results for H2CS (6 modes, ref. 1) and more recently it has been applied to CH4 (9 modes, ref. 2). In both cases, excellent convergence has been achieved for all of the low-lying vibrational levels. "MULTIMODE" can be used in less accurate calculations, for example at the SCF level alone, or in SCF-CI calculations, where specified numbers of vibrational (non-orthogonal) SCF functions are used in a vibrational CI basis. These methods also allow for an adiabatic rotation scheme, which gives reasonable values for rotational constants, in particular. "MULTIMODE" is currently being extended to include the Watson hamiltonian for linear molecules, and also to include the Miller-Adams-Handy Reaction Path hamiltonian in order to describe a single large-amplitude coordinate, for example the torsion in H2O2. This will widen the scope of molecules that can be handled. information: www.emory.edu/CHEMISTRY/faculty/bowman/multimode enquiries: s.carter@reading.ac.uk References ---------- 1. S. Carter, J.M. Bowman and N.C.Handy; Theor. Chem. Accts., 100, 191 (1998) 2. S. Carter and J.M. Bowman; J. Phys. Chem. 104, 2443 (2000) From chemistry-request@server.ccl.net Thu May 18 23:55:09 2000 Received: from mail9.wlv.netzero.net (mail9.wlv.netzero.net [209.247.163.66]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA18329 for ; Thu, 18 May 2000 23:55:09 -0400 Received: (qmail 17981 invoked by uid 0); 19 May 2000 03:54:47 -0000 Received: from pppa33-resalelafayettein1-1r7229.saturn.bbn.com (HELO pavilion) (4.54.202.62) by mail9.wlv.netzero.net with SMTP; 19 May 2000 03:54:47 -0000 Message-ID: <001001bfc142$515cc5e0$0200a8c0@pavilion> From: "jfbaker" To: Cc: "Mary O'Sullivan" Subject: AutoDock / amino-aromatic H-bonds Date: Thu, 18 May 2000 22:28:33 -0500 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 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear CCL subscribers, We've been using AutoDock 3.0 to do enzyme-ligand docking simulations with compounds which contain aromatic substituants (such as 3-phenylpropyl groups). We suspect that weak "amino-aromatic" and "aromatic-aromatic" hydrogen-bonds are important in the binding of these compounds to the active site of our enzyme. Since the pi-faces of aromatic substituants in the ligand aren't directly associated with an individual atom, it's difficult to see how AutoDock can be made to understand the location and directionality between them and hydrogen-N(sp2) donors in the active site. Has anyone figured out a way to get AutoDock to include these types of non-classical hydrogen-bonds in it's H-bond calculations? Thanks very much for any help you can provide us with... Sincerely, Jerry Baker jfbaker@netzero.net _____________________________________________ NetZero - Defenders of the Free World Click here for FREE Internet Access and Email http://www.netzero.net/download/index.html From chemistry-request@server.ccl.net Fri May 19 06:28:25 2000 Received: from classic.chem.msu.su (classic.chem.msu.su [158.250.32.143]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA20228 for ; Fri, 19 May 2000 06:26:56 -0400 From: gran@classic.chem.msu.su Received: from localhost ( [127.0.0.1] ) by classic.chem.msu.su (Hethmon Brothers Smtpd) ; Fri, 19 May 2000 14:22:28 MSK-3MSD-4,3,5,0,7200,10,5,0,10800 Message-Id: <200004191422.2825342.7@classic.chem.msu.su> Date: Fri, 19 May 2000 14:22:24 +0400 To: CHEMISTRY@ccl.net Cc: gamess-users@Glue.umd.edu, qcnt@onelist.com Subject: the PC GAMESS version 6.0 X-Mailer: MR/2 Internet Cruiser Edition for OS/2 v1.60 b60 (Unregistered) Dear GAMESS users, We are glad to announce the new public release of the PC GAMESS, v. 6.0, which is based on the newer official GAMESS sources. There are multiple enhancements, functional extensions, and performance improvements incorporated into this latest PC GAMESS distribution as compared with previous public PC GAMESS version 5.4 (the full list of changes and new features will be available from the PC GAMESS home site at MSU within several weeks). A few examples of the new features are as follows: We offer the full set of Pentium/Pentium Pro/Pentium II/Pentium III- optimized native Linux SMP-aware PC GAMESS ELF binaries as a part of the PC GAMESS distribution. New Pentium Pro/Pentium II/Pentium III-optimized OS/2-based SMP & JFS - aware binaries are now available. Large files are supported via transparent file splitting on all 32-bit file systems imposing 2 or 4 GB limit on the maximum file size. For further information, see the URLs: http://classic.chem.msu.su/gran/gamess/index.html http://quantum-2.chem.msu.ru/gran/gamess/index.html Yours Sincerely, Alex Granovsky, Laboratory of Chemical Cybernetics, Moscow State University, Moscow, Russia. From chemistry-request@server.ccl.net Fri May 19 04:55:33 2000 Received: from tech.chem.ethz.ch (ltcmail.ethz.ch [129.132.124.253]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA19893 for ; Fri, 19 May 2000 04:55:33 -0400 Received: from tech.chem.ethz.ch (baiker8.ethz.ch [129.132.125.8]) by tech.chem.ethz.ch (8.8.8/8.8.8) with ESMTP id KAA01494 for ; Fri, 19 May 2000 10:55:23 +0200 (CEST) Message-ID: <39250290.58D97B9C@tech.chem.ethz.ch> Date: Fri, 19 May 2000 11:00:00 +0200 From: angelo vargas Organization: ETHZ X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: another prob.with gaussian Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit hallo everybody. I have a problem with the use of the option MaxCycle in Gaussian. if I want to do a simple optimization #P HF/STO-3G Opt=Z-matrix gfinput IOP(6/7=3) everything works until I include MaxCycle=5 then the computation stops due to a syntax error in the route section. Does anybody know of incompatibilities with the keywords I used? Ever had similar troubles? thanks in anticipation angelo -- _______________________________________________________________________ Angelo Vargas Laboratory of Technical Chemistry Department of Chemical Engineering and Industrial Chemistry Swiss Federal Institute of Technology (ETHZ) ETH Zentrum, Universitätsstr. 6 Telefon: 0041/1/632 31 54, Room CNB B98.3 CH-8092 Zürich - Switzerland Fax: 0041/1/632 11 63 E-mail: vargas@tech.chem.ethz.ch http://mercury.ethz.ch/HOMEPAGE/members/vargas/vargas.html ________________________________________________________________________ From chemistry-request@server.ccl.net Fri May 19 07:37:53 2000 Received: from patronimo.umh.ac.be (patronimo.umh.ac.be [193.190.192.79]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA21403 for ; Fri, 19 May 2000 07:37:52 -0400 Received: (from Anusooya@localhost) by patronimo.umh.ac.be (8.8.5/8.7) id NAA24068; Fri, 19 May 2000 13:37:33 +0200 Date: Fri, 19 May 2000 13:37:33 +0200 (DFT) From: Anusooya To: Giulio Vistoli cc: CCL Subject: UNSUBSCRIBE In-Reply-To: <014001bfa852$39ca3100$204f959f@farma.unimi.it.farma.unimi.it> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ************************************************************************* Y. Anusooya Service de Chimie des Materiaux Nouveaux et Centre de Recherche en Electronique et Photonique Moleculaires Universite Mons-Hainaut 20, Place du Parc B7000 MONS, BELGIUM fax: +32 65 37 33 66 +32 65 37 30 54 TEL: +32 65 37 33 59 ************************************************************************* From chemistry-request@server.ccl.net Fri May 19 08:53:55 2000 Received: from mail4.nycap.rr.com (mail4-1.nyroc.rr.com [24.92.33.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA21775 for ; Fri, 19 May 2000 08:53:55 -0400 Received: from ruc7980.nycap.rr.com ([24.161.16.113]) by mail4.nycap.rr.com (Post.Office MTA v3.5.3 release 223 ID# 0-59787U250000L250000S0V35) with SMTP id com for ; Fri, 19 May 2000 08:56:46 -0400 From: "Rolf Claessen" To: Subject: partition function for organometallic complexes (solid and liquid) Date: Fri, 19 May 2000 08:52:55 -0400 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 In-Reply-To: <200004191422.2825342.7@classic.chem.msu.su> X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Colleagues, I am pretty new to the recent applications of statistical thermodynamics, so excuse my simple question. Could anyone point me to some references or ideas, how to construct a partition function for organometallic complexes in solid and gas form? The complexes are generally 1,3-diketonates and contain transition metals like copper or cobalt. How do I model intermolecular interactions? Maybe interesting: The bond character in these complexes is nearly covalent, not ionic. Regards, Rolf Claessen _______ Rolf U Claessen Chem. Dept. SUNY Albany Albany NY 12222 518 - 442 - 4887 rc7980@cnsvax.albany.edu From chemistry-request@server.ccl.net Fri May 19 10:32:49 2000 Received: from yeager5.chem.tamu.edu (yeager5.chem.tamu.edu [165.91.176.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA22669 for ; Fri, 19 May 2000 10:32:48 -0400 Received: (from noj@localhost) by yeager5.chem.tamu.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) id QAA28983; Fri, 19 May 2000 16:33:06 +0200 (MDT) Date: Fri, 19 May 2000 16:33:06 +0200 (MDT) Message-Id: <200005191433.QAA28983@yeager5.chem.tamu.edu> From: noj malcolm To: vargas@tech.chem.ethz.ch CC: chemistry@ccl.net In-reply-to: <392407A4.E49305C9@tech.chem.ethz.ch> (message from angelo vargas on Thu, 18 May 2000 17:09:24 +0200) Subject: Re: CCL:gaussian98 Z-matrix optimization Reply-To: noj@yeager5.chem.tamu.edu X-Beard: Beard v5.3 X-Child: Bethany Angelo, If you use #p at the start of your route card this info should be printed out. noj -- -------------------------------------------------------------------------- Dr. N.O.J. Malcolm e-mail:noj@yeager5.chem.tamu.edu Department of Chemistry Texas A&M University College Station TX 77843 U.S.A -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri May 19 10:41:32 2000 Received: from yeager5.chem.tamu.edu (yeager5.chem.tamu.edu [165.91.176.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA22778 for ; Fri, 19 May 2000 10:41:32 -0400 Received: (from noj@localhost) by yeager5.chem.tamu.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) id QAA29006; Fri, 19 May 2000 16:41:50 +0200 (MDT) Date: Fri, 19 May 2000 16:41:50 +0200 (MDT) Message-Id: <200005191441.QAA29006@yeager5.chem.tamu.edu> From: noj malcolm To: vargas@tech.chem.ethz.ch CC: chemistry@ccl.net In-reply-to: <39250290.58D97B9C@tech.chem.ethz.ch> (message from angelo vargas on Fri, 19 May 2000 11:00:00 +0200) Subject: Re: CCL:another prob.with gaussian Reply-To: noj@yeager5.chem.tamu.edu X-Beard: Beard v5.3 X-Child: Bethany Angelo, Assuming that its my mail-reader that is adding 3D's to your route card, are youtrying to limit the number of scf cycles or optimisation cycles? These can be controlled via the scfcyc and optcyc directives respectively. noj -- -------------------------------------------------------------------------- Dr. N.O.J. Malcolm e-mail:noj@yeager5.chem.tamu.edu Department of Chemistry Texas A&M University College Station TX 77843 U.S.A -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri May 19 12:47:25 2000 Received: from mail.science.siu.edu (mail.science.siu.edu [131.230.107.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA23510 for ; Fri, 19 May 2000 12:47:21 -0400 Received: from tapas (131.230.99.83) by mail.science.siu.edu with SMTP (Eudora Internet Mail Server 2.2.2); Fri, 19 May 2000 11:47:07 -0500 Message-ID: <003801bfc1b1$a3db65a0$5363e683@thchem.siu.edu> From: "Tapas Kar" To: "angelo vargas" , References: <39250290.58D97B9C@tech.chem.ethz.ch> Subject: Re: CCL:another prob.with gaussian Date: Fri, 19 May 2000 11:45:28 -0500 To increase SCF cycle (default is 65 in general), use scfcyc=n or iop(5/7=n) where n is the number of scf iteration steps. For geom optimization use, optcyc=n ---------------------------------------------------- Tapas Kar Department of Chemistry 1245 Lincoln Dr. # 146F Southern Illinois University Carbondale, IL 62901-4409 Tel: 618-453-6485(Off)/6433(Lab) Fax: 618-453-6408 email: tapaskar@siu.edu tapas@risky3.thchem.siu.edu ----- Original Message ----- From: angelo vargas To: Sent: Friday, May 19, 2000 4:00 AM Subject: CCL:another prob.with gaussian > hallo everybody. > I have a problem with the use of the option MaxCycle in Gaussian. > > if I want to do a simple optimization > > > #P HF/STO-3G Opt=Z-matrix gfinput IOP(6/7=3) > > everything works until I include MaxCycle=5 > > then the computation stops due to a syntax error in the route section. > Does anybody know of incompatibilities with the keywords I used? Ever had similar troubles? > thanks in anticipation > > angelo > -- > _______________________________________________________________________ > Angelo Vargas > Laboratory of Technical Chemistry > Department of Chemical Engineering and Industrial Chemistry > Swiss Federal Institute of Technology (ETHZ) > ETH Zentrum, Universitätsstr. 6 Telefon: 0041/1/632 31 54, Room CNB B98.3 > CH-8092 Zürich - Switzerland Fax: 0041/1/632 11 63 > E-mail: vargas@tech.chem.ethz.ch > http://mercury.ethz.ch/HOMEPAGE/members/vargas/vargas.html > ________________________________________________________________________ From chemistry-request@server.ccl.net Fri May 19 15:37:59 2000 Received: from Kitten.mcs.net (Kitten.mcs.com [192.160.127.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA24304 for ; Fri, 19 May 2000 15:37:58 -0400 Received: from oemcomputer (P57-Chi-Dial-17.pool.mcs.net [205.253.228.57]) by Kitten.mcs.net (8.9.3/8.9.3) with SMTP id OAA75207 for ; Fri, 19 May 2000 14:37:58 -0500 (CDT) (envelope-from rone@mcs.net) Message-ID: <00c201bfc1c8$bb05c240$c4e0fdcd@oemcomputer> From: "Rebecca Rone" To: Subject: Fw: CCL:HEME parameters Date: Fri, 19 May 2000 14:30:03 -0500 Dear Rachelle, At one time in QUANTA we had worked out all of the porphyrin related groups. As I recall it was necessary to explicitly detemine the correct single, double, and resonant bonds as shown in either Metzler or similar textbooks. You use the Chemnote facility for this. You may need to let the initial geometry relax a little to get a flattened ring system. Just use several cycles of minimization. At the time that we completed that parameter project there were no "missing parameters". If you have trouble call the MSI support line again. Dr. Rebecca Rone Rone Biotechnology Consulting -----Original Message----- From: Bienstock.Rachelle To: 'CHEMISTRY@ccl.net' Date: Tuesday, May 16, 2000 4:36 PM Subject: CCL:HEME parameters > >Hi, > >Does anyone know if there are readily available force field parameters for >hemes? I searched the ccl archives and saw reference to AMBER parameters >that were ftp-able from David Case at Scripps, however, when I went to the >ftp site and looked in the pub directory, the AMBER heme parameters were no >longer there. In the 970 MSI distribution, there is a cvff_heme.frc file in >the irix6m3/bioxym_lib directory, however, I have been cautioned by Jodi >Shaulsky, Senior Scientist Scientific Support MSI, not to use these >parameters as they are not "validated" and there are missing "parameters". > >Any recommendations appreciated and will be summarized for the list. >Thanks, Rachelle > >Dr. Rachelle J. Bienstock >Molecular Modeling and Structural Biochemistry >NIH >NIEHS / ITSS >P.O. Box 12233 MD F0-01 >Research Triangle Park, NC 27709 >Telephone: (919) 541-3397 >E-mail: biensto1@niehs.nih.gov >Office: Room F091 > >