From jkl@ccl.net Thu Sep 7 00:58:51 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id AAA07427; Thu, 7 Sep 1995 00:47:14 -0400 Received: from nogakubu.agr.kyushu-u.ac.jp for ahirasim@agr.kyushu-u.ac.jp by bedrock.ccl.net (8.6.10/950822.1) id AAA03320; Thu, 7 Sep 1995 00:47:08 -0400 Received: from [133.5.200.49] (pestic3.ach.agr.kyushu-u.ac.jp [133.5.200.49]) by nogakubu.agr.kyushu-u.ac.jp (8.6.9+2.4W/3.4Wbeta3) with SMTP id NAA26566 for ; Thu, 7 Sep 1995 13:48:05 +0900 Message-Id: <199509070448.NAA26566@nogakubu.agr.kyushu-u.ac.jp> Date: Thu, 7 Sep 1995 13:47:03 +0900 To: chemistry@ccl.net From: ahirasim@agr.kyushu-u.ac.jp (Akinori Hirashima) X-Sender: ahirasim@nogakubu.agr.kyushu-u.ac.jp Subject: CCL:Cambridge Crystallographic Data Centre MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Netters: Anybody who needs to access data base such as Cambridge Crystallographic Data Centre, please visit the following www site. http://csdvx2.ccdc.cam.ac.uk/ Thanks. ==================================== 平島　明法 (Akinori Hirashima)　　　　　　　　　　　　　　 九州大学農学部農芸化学科　　　 〒812-81　福岡市東区箱崎6-10-1　　　　　　　　　 Department of Agricultural Chemistry Kyushu University Fukuoka 812-81, Japan Phone: (+81)92 - 641 - 1101 ext. 6205　 Fax: (+81)92 - 632 - 1960 E-Mail: ahirasim@agr.kyushu-u.ac.jp ===================================== From kris@bionmr1.rug.ac.be Thu Sep 7 02:58:52 1995 Received: from mserv.rug.ac.be for kris@bionmr1.rug.ac.be by www.ccl.net (8.6.10/950822.1) id CAA08321; Thu, 7 Sep 1995 02:55:56 -0400 Received: from bionmr1.rug.ac.be by mserv.rug.ac.be with SMTP id AA09488 (5.67b/IDA-1.5 for <@mserv.rug.ac.be:chemistry@www.ccl.net>); Thu, 7 Sep 1995 08:55:53 +0200 Received: by bionmr1.rug.ac.be (950215.SGI.8.6.10/931108.SGI.AUTO.ANONFTP) id IAA09901; Thu, 7 Sep 1995 08:56:02 +0200 Date: Thu, 7 Sep 1995 08:55:59 +0200 (MDT) From: Kris Boulez Subject: Re: CCL:CCL:Java chemistry applets? To: wdi@eros.ccc.uni-erlangen.de Cc: chemistry@www.ccl.net In-Reply-To: <9509061940.ZM1277@schiele> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 6 Sep 1995, Wolf-Dietrich Ihlenfeldt wrote: > > On Sep 6, 10:06, Hinsen Konrad wrote: > > Subject: CCL:Java chemistry applets? > > [ part about Java deleted ] > > [ part about Python deleted ] > > > [ part about E (prononounced awe) deleted ] > [ part about tcl/tk deleted ] To add one more language : Perl. It's used in the big majority off CGI scripts on the WWW and is a great general programming language. There is a beta-version of safe-perl and work is underway for a perl/tk browser. For a comparison of perl versus the abovementioned languages look at ftp://ftp.perl.com/pub/perl/versus/ This is just to show that there are more (and much more widely used) languages around. So I think the suggestion of Henry Rzepa to use a stand-alone program (Rasmol is great software and free) for molecular visualisation is the way to go. Kris, ---- Kris Boulez (Kris.Boulez@rug.ac.be) Biomolecular NMR unit University of Ghent, Belgium From jkl@ccl.net Thu Sep 7 05:43:54 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA09635; Thu, 7 Sep 1995 05:41:24 -0400 Received: from shiva.jussieu.fr for bouyer@ext.jussieu.fr by bedrock.ccl.net (8.6.10/950822.1) id FAA04741; Thu, 7 Sep 1995 05:41:17 -0400 Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.6.10/jtpda-5.1) with ESMTP id LAA15160 for ; Thu, 7 Sep 1995 11:41:17 +0200 Received: from [134.157.11.12] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Thu, 7 Sep 1995 11:41:13 +0200 X-Sender: bouyer@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 7 Sep 1995 11:47:31 +0100 To: chemistry@ccl.net From: bouyer@ext.jussieu.fr (Frederic BOUYER) Subject: Harris functional Hi everybody, I was wondering what is the Harris functional, in the DFT context, and what are the main differences with the functionals used in programs (DGauss, deMon, DMol, ADF, ...). Any comments would be appreciated and/or a summary. Thank you in advance. Frederic Bouyer ____________________________________________________________________ Frederic BOUYER Laboratoire d'Electrochimie et de Chimie Analytique Equipe "Reactivite en Milieux Ioniques Liquides" (G. PICARD) ENSCP 11, rue Pierre et Marie Curie 75231 PARIS Cedex 05 FRANCE Tel : (33)-1-43-54-53-84 ou (33)-1-44-27-67-51 ou (33)-1-44-27-66-94 Fax : (33)-1-44-27-67-50 E-mail : bouyer@ext.jussieu.fr http://alcyone.enscp.jussieu.fr/ created, in progress ... http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/FB/ From csron@wicc.weizmann.ac.il Thu Sep 7 06:28:55 1995 Received: from wishful.weizmann.ac.il for csron@wicc.weizmann.ac.il by www.ccl.net (8.6.10/950822.1) id GAA09872; Thu, 7 Sep 1995 06:22:12 -0400 Received: from wizard.weizmann.ac.il (wizard-gate.weizmann.ac.il [132.76.63.23]) by wishful.weizmann.ac.il (8.6.5/8.6.5) with ESMTP id MAA111450 for ; Thu, 7 Sep 1995 12:22:53 +0300 From: Ron Edgar Received: from localhost (csron@localhost) by wizard.weizmann.ac.il (8.6.5/8.6.5) id MAA73591 for chemistry@www.ccl.net; Thu, 7 Sep 1995 12:22:07 +0300 Message-Id: <199509070922.MAA73591@wizard.weizmann.ac.il> Subject: summary - algorithms for basic molecule manip.. To: chemistry@www.ccl.net Date: Thu, 7 Sep 1995 12:22:06 +0300 (WET) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 5213 First I would like to thank all who replied, in retrospect, my question was too general and I guess this held back some people with specific answers to a specific problem. If after reading the replies you think you can add - by all means please do. my original question was: I'm writing a C++ library to deal with atoms/molecules. In the good tradition of trying to avoid re-inventing the wheel I would appreciate any references (or source) to algorithms for basic operations which can be applied to groups of atoms defined in Cartesian OR fractional coordinate systems, e.g. torsion and "bend" angles, rotations along an arbitrary vector, etc. Also I would be interested in means of finding internal molecular symmetries for a given set of coordinates. Please reply directly to me, I will summarize to the group. Thanks, Ron ------------------------------------------------------------------- Message 6/14 From Leslie Glasser Organization: CHEMISTRY - WITS UNIVERSITY To: Ron Edgar Date: Tue, 5 Sep 1995 12:13:43 GMT + 2:00 Dear Ron: You will find the vector algebra for some of the operations in which you might be interested in my article "Molecular Geometry and Substituent Ganeration: a MathCAD Program", Comp. Chem., 17(1), 107-8 (1993). Leslie ============================================================== (Prof.) Leslie Glasser Dept. of Chemistry E-mail: glasser@aurum.chem.wits.ac.za Univ. of Witwatersrand Tel: Intl + 27 11 716-2070 P. O. WITS 2050 Fax: Intl + 27 11 339-7967 South Africa Home Pages: University http://sunsite.wits.ac.za Chemistry http://www.chem.wits.ac.za ====================================================================== Message 4/14 From Craig Taverner X-Sender: craig@zaphod.gh.wits.ac.za I have a C (ANSI) program I'm been writing for some time, that contains calculations that may be of some use: It is called "steric", and is primarily for organometalic chemistry. It is for the calculation of linear cone angles (Tolman), solid angles, angles of overlap and molecular volumes (rough fast Monte Carlo) for steric interactions in ligands and molecules. Code that may be of interest: . bond search using vdW radii . group search using recursive bond trace for individual molecules and seperate ligands bonded to central metal atom. . fractional to cartesian transform . some vector manipulations of data (basic and specific). . fully dynamically allocated linked lists to describe all molecular features (seperate molecules, atoms and bonds). . various others I cannot think of now. If you're interested, I'll be glad to try and provide some code. My program has been written to be easily expanded with new functions, but I'm not sure that that will make it easy to provide the current code in a general library format. Unfortunately I never got to learn C++ to facilitate that sort of feature. Cheers, Craig "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa ----------------------------------------------------------------- Message 3/14 From Matt Stahl Date: Tue, 5 Sep 1995 11:25:58 -0700 (MST) Ron, You may want to check out: Computers & Chemistry. 18(4):371-376, 1994 This paper contains an algorithm for automatic point group determination. I have various and sundry routines for internal->cartesian conversion, bond angle, and torsion angle adjustments (rotation about a bond). I can give you sources, but they need to be linked with the BABEL library. Actually, babel may also be a good place to look for vector and matrix routines. If you are interested in playing with the code i have (crude, uncommented C) let me know. matt ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Matthew Stahl, Ph.D. | Department of Chemistry | I'd rather be right half of the University of Arizona | time than half right all the Tucson, AZ 85721 | time. matt@synthesis.chem.arizona.edu | -Malcom S. Forbes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Message 2/14 From Hinsen Konrad Sep 6, 95 10:13:09 am -0400 Date: Wed, 6 Sep 1995 10:13:09 -0400 I have written some C++ code that takes internal coordinate specifications (e.g. a Z matrix, but also more flexible forms) and turns them into Cartesian coordinates. I never had the time to finish this properly; it works, but error checking is minimal. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From ferenc@rchsg8.chemie.uni-regensburg.de Thu Sep 7 09:45:13 1995 Received: from comsun.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.10/950822.1) id JAA12172; Thu, 7 Sep 1995 09:40:12 -0400 Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA12051 (5.65c/IDA-1.4.4 for ); Thu, 7 Sep 1995 15:39:42 +0200 Received: by rchsg8.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for CHEMISTRY@www.ccl.net) id AA01245; Thu, 7 Sep 95 15:38:37 +0200 Date: Thu, 7 Sep 95 15:38:37 +0200 From: Ferenc.Molnar@chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9509071338.AA01245@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@www.ccl.net Subject: normal modes summary Dear Netters: Some days ago I posted the following question: > I have a (maybe trivial) question concerning the calculation > of normal modes in MOPAC. > > The diagonalization of the force matrix (in mass weighted > coordinates) leaves you with a set of eigenvalues and normal > coordinates. > > The eigenvalue number k correspond to (w_k)^2, where the w_ks > are the vibrational frequencies, this means: > > (w_k)^2=K_k/M_k > > K_k: force constant of the kth normal mode > M_k: reduced mass of the k_th normal mode > > Now my question is, if (w_k)^2 determines only the ratio > of K_k and M_k, then how are the reduced masses, reported > in the "vibrational analysis" section of the MOPAC output > file, calculated? Is there a convention, which "fraction" of > (w_k)^2 to use for K_k and which for M_k? Some people asked me for a summary, so here it is. It consist only of one message. I want to thank Jimmy Stewart very much for his reply. It really answered the question! > The reduced mass is like atomic charges, in that it is not an observable, > however, for specific systems - mainly homonuclear diatomics - the reduced > mass does have meaning. The reduced mass definition used in MOPAC can be > understood as follows: > > Each vibration can be modelled by a mass, M_k, at the end of a spring of > force constant K_k, attached to an infinite mass. > > Inf | K_k M_k > Mass | > |^^^^^^^^^^^^^^^^^^O > | > | > > The contribution to the mass is proportional to the amount each atom > contributes to the normal mode, and is proportional to the fraction of > the atomic mass contributed by each atom. > > Put in more formal terms, the contribution of each atom to the effective mass > of a vibration is proportional to the product of the intensity on that > atom times the mass-weighted intensity. > > rho = sum_A = sum_A (c_A_x**2+c_A_y**2+c_A_z**2)**2*M_A > > where c_A are the coefficients of the normal modes. > > > > Consider H2: c_1 = 0.7071*H_1+0.7071*H_2 > > rho_1 = 0.7071**4*1 + 0.7071**4*1 =0.5 > > Consider M-H, M being an atom of very large mass, say 1000: > > c_1 = 0.0316*M+0.9995*H > > rho_1 = 0.0316**4*1000 + 0.9995**4*1 = 0.9990 > > [0.0316 ~ sqrt(1/1000); 0.9995 ~sqrt(1-1/1000)] > > Consider N2: c_1 = 0.7071*N_1+0.7071*N_2 > > rho_1 = 0.7071**4*14+0.7071**4*14 = 7.0 > > > Jimmy Stewart Best Regards, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- Those who do not archive the past are condemned to retype it! -- Garfinkel & Spafford, Practical Unix Security --------------------------------------------------------------------------- From MARSHALL@cas.unt.edu Thu Sep 7 09:58:58 1995 Received: from mercury.unt.edu for MARSHALL@cas.unt.edu by www.ccl.net (8.6.10/950822.1) id JAA12694; Thu, 7 Sep 1995 09:56:01 -0400 Received: from cas.unt.edu by mercury.unt.edu with SMTP id AA05928 (5.65c/IDA-1.4.4 for ); Thu, 7 Sep 1995 08:56:00 -0500 Received: from CAS/SpoolDir by cas.unt.edu (Mercury 1.21); 7 Sep 95 08:56:00 CST6CDT Received: from SpoolDir by CAS (Mercury 1.21); 6 Sep 95 15:46:39 CST6CDT From: "Dr. P. Marshall (Chemistry ext 2294)" Organization: University of North Texas To: chemistry@www.ccl.net Date: Wed, 6 Sep 1995 15:46:31 CST6CDT Subject: QM code for spin-orbit coupling? Priority: normal X-Mailer: Pegasus Mail for Windows (v2.0-WB3) Message-Id: <3ABEC4C4C6C@cas.unt.edu> Dear Netters: I am looking for an easy to use ab initio package capable of computing spin-orbit splittings for halogenated radicals. Any pointers/help will be greatly appreciated (I know what GAMESS can do). If there is sufficient interest, I'll summarize the responses. Thanks in advance, Paul ------------- Paul Marshall marshall@unt.edu Associate Professor University of North Texas Dept. of Chemistry, PO Box 5068, Denton, Texas 76203-0068 tel (817) 565-2294 fax (817) 565-4318 From jkl@ccl.net Thu Sep 7 10:05:44 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA12397; Thu, 7 Sep 1995 09:46:10 -0400 Received: from psizi1.psi.ch for kessi@psizi1.psi.ch by bedrock.ccl.net (8.6.10/950822.1) id JAA06132; Thu, 7 Sep 1995 09:46:07 -0400 Received: by psizi1.psi.ch (AIX 3.2/UCB 5.64/4.03) id AA13552; Thu, 7 Sep 1995 15:47:45 +0200 Date: Thu, 7 Sep 1995 15:47:45 +0200 From: kessi@psizi1.psi.ch (Alain Kessi) Message-Id: <9509071347.AA13552@psizi1.psi.ch> To: chemistry@ccl.net Subject: Re: CCL:Harris functional In-Reply-To: X-Mailer: [XMailTool v3.1.2b] Frederic Bouyer (bouyer@ext.jussieu.fr) wrote: > I was wondering what is the Harris functional, in the DFT context, and what > are the main differences with the functionals used in programs (DGauss, > deMon, DMol, ADF, ...). Any comments would be appreciated and/or a summary. The Harris functional is an alternative formulation to the Kohn-Sham total energy functional. It is therefore not an alternative to the exchange and correlation functionals such as the Perdew and Wang functional, but uses such parametrizations as parts of its total energy expression (just like the Kohn-Sham total energy formulation does). As explained in the DSolid manual, the Harris functional is stationary at the same density as the Kohn-Sham total energy functional and can therefore be used instead for the SCF calculation. It has two advantages as compared to the Kohn-Sham scheme. First, the density does not need to be V-representable. Second, the curvature of the Harris functional about the stationary point is smaller than the curvature of the Kohn-Sham functional, so convergence is faster. Actually, the Harris functional was originally developed for single-shot calculations rather than SCF convergence, and for many purposes, the accuracy after the first iteration may be sufficient. DMol (and its periodic boundary conditions implementation DSolid) uses the Harris functional. -- Alain Kessi (alain.kessi@psi.ch) Paul Scherrer Institut, Zuerich, Switzerland From jkl@ccl.net Thu Sep 7 10:14:03 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA12957; Thu, 7 Sep 1995 10:00:20 -0400 Received: from gauss.uib.es for guillem@gauss.uib.es by bedrock.ccl.net (8.6.10/950822.1) id KAA06300; Thu, 7 Sep 1995 10:00:17 -0400 From: Received: by gauss.uib.es; id AA14466; Thu, 7 Sep 1995 16:00:40 +0100 Message-Id: <9509071500.AA14466@gauss.uib.es> To: chemistry@ccl.net Subject: NBODel Utility on G92 Date: Thu, 07 Sep 95 16:00:40 +0100 X-Mts: smtp Dear Netters, I would like to know how can be done a NBO Fock matrix deletion procedure on G92, particularly by setting some NBO Fock matrix elements to zero and reevaluating the energy. G92 manual refers to NBO separate manual, but unfortunately I have no access to that one. Which methodology do I have to follow? An example G92 input data would be most welcome, as well as any suggestion on the theme. Many thanks for you help, G. Suner ------------------------------------------------------------------------ Dr Guillermo A. Suner; Dep. de Quimica, UNIVERSITAT DE LES ILLES BALEARS E-07071-Palma de Mallorca, SPAIN. E-mail: guillem@gauss.uib.es Tel: + 34 71 173498 Fax: + 34 71 173426 WWW URL: http://www.uib.es/depart/dqu/dquo/suner.html From laidig@pg.com Thu Sep 7 10:29:02 1995 Received: from oldspice.pg.com for laidig@pg.com by www.ccl.net (8.6.10/950822.1) id KAA13484; Thu, 7 Sep 1995 10:14:29 -0400 Received: by oldspice.pg.com (8.6.11/8.6.9) id KAA04445 for <@oldspice.pg.com:CHEMISTRY@www.ccl.net>; Thu, 7 Sep 1995 10:08:30 -0400 Received: from morpheus by pandora via ESMTP (950511.SGI.8.6.12.PATCH526/930416.SGI.AUTO) for <@pandora.na.pg.com:CHEMISTRY@www.ccl.net> id KAA08062; Thu, 7 Sep 1995 10:11:53 -0400 Received: by morpheus (950413.SGI.8.6.12/930416.SGI.AUTO) id KAA03405; Thu, 7 Sep 1995 10:11:49 -0400 Date: Thu, 7 Sep 1995 10:11:49 -0400 From: laidig@pg.com (Bill Laidig) Message-Id: <9509071011.ZM3403@morpheus.na.pg.com> In-Reply-To: Ferenc.Molnar@chemie.uni-regensburg.de (Ferenc Molnar) "CCL:M:normal modes summary" (Sep 7, 3:38pm) References: <9509071338.AA01245@rchsg8.chemie.uni-regensburg.de> X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: CHEMISTRY@www.ccl.net Subject: CCL:Information about MEDLA Cc: laidig@morpheus.na.pg.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii All, In a recent C&E News article an approximate electronic structure method called MEDLA by Prof. P.G. Mezey was discussed. I was asked by my boss if this really was the greatest invention since sliced bread as the article implied. Since I am not familar with this method I was wondering if any of you have thoughts on the subject. Also, is this technique similar to Yang's divide-and-conquer approach? I will summarize to the list if I get any responses. Bill -- ****************************************************************************** * "Like jewels in a crown, the precious stones glittered in the queen's * * round metal hat." - Jack Handey * * * * Bill Laidig * * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * * Miami Valley Laboratories laidig@pg.com (preferred) * * P.O. Box 538707 wd_laidig@pg.com * * Cincinnati, OH 45253-8707 laidig@qtp.ufl.edu * ****************************************************************************** From kessi@psizi1.psi.ch Thu Sep 7 11:28:58 1995 Received: from psizi1.psi.ch for kessi@psizi1.psi.ch by www.ccl.net (8.6.10/950822.1) id LAA15957; Thu, 7 Sep 1995 11:26:29 -0400 Received: by psizi1.psi.ch (AIX 3.2/UCB 5.64/4.03) id AA16957; Thu, 7 Sep 1995 17:28:08 +0200 Date: Thu, 7 Sep 1995 17:28:08 +0200 From: kessi@psizi1.psi.ch (Alain Kessi) Message-Id: <9509071528.AA16957@psizi1.psi.ch> To: chemistry@www.ccl.net Subject: [Q] Empty force field for pure electrostatics X-Mailer: [XMailTool v3.1.2b] Hi everybody, After doing a DFT calculation on a molecule, I would like to look at the purely electrostatic effects. Is there an easy way to do this using the Discover software? Since I'm not very familiar with defining my own force fields, could somebody point out to me what parts of the *.frc file I need to change/drop/add so the only interactions which will be taken into account will be the Coulomb interactions between the point charges? In addition, how can I assign the charges to the atoms using Mulliken charges computed in DMol/DSolid? What intermediate file format would I need to create and read into Insight? If I write a car/mdf pair of files and read in the molecule from them, will the charges read from the mdf file be used? I realize that it's overkill to use Discover for the job. Maybe someone can point me to a public domain code for point charge electrostatics (periodic and molecular)? Thanks for any help! Best regards, Alain -- Alain Kessi (alain.kessi@psi.ch) Paul Scherrer Institut, Zuerich, Switzerland From paul@tammy.harvard.edu Thu Sep 7 12:59:03 1995 Received: from tammy.harvard.edu for paul@tammy.harvard.edu by www.ccl.net (8.6.10/950822.1) id MAA17559; Thu, 7 Sep 1995 12:45:58 -0400 Received: by tammy.harvard.edu (5.64/10.0) id AA05488; Thu, 7 Sep 95 12:48:59 -0400 Date: Thu, 7 Sep 95 12:48:59 -0400 From: paul@tammy.harvard.edu (Paul Lyne) Message-Id: <9509071648.AA05488@tammy.harvard.edu> To: chemistry@www.ccl.net Subject: CADPAC Cc: paul@tammy.harvard.edu Hi, Does anybody have a makefile for CADPAC for the HPUX or DECALPHA computers? Thanks in advance, Paul From gotwals@mcnc.org Thu Sep 7 13:59:04 1995 Received: from robin.mcnc.org.mcnc.org for gotwals@mcnc.org by www.ccl.net (8.6.10/950822.1) id NAA18947; Thu, 7 Sep 1995 13:47:42 -0400 Received: from [128.109.178.113] by robin.mcnc.org.mcnc.org (8.6.9/MCNC/8-10-92) id NAA04488; Thu, 7 Sep 1995 13:47:41 -0400 for Date: Thu, 7 Sep 1995 13:47:41 -0400 Message-Id: <199509071747.NAA04488@robin.mcnc.org.mcnc.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: gotwals@mcnc.org (Bob Gotwals) Subject: CCL:Computational Chemistry Web Course The North Carolina Supercomputing Center (NCSC), a part of the non-profit advanced technologies group known as MCNC, located in Research Triangle Park,NC, is pleased to offer an on-line course entitled "Computational Chemistry for Chemistry Educators". This course is intended for secondary, community college and undergraduate educators of chemistry, as well as graduate students who are interested in chemistry education. The course syllabus and registration information can be viewed by setting your World Wide Web browser to this URL: http://www.mcnc.org/HTML/ITD/NCSC/ccsyllabus.html Description of the workshop: The goal of this course is to introduce chemistry educators to computational techniques in quantum chemistry. The course is intended as an enrichment activity, designed to help educators understand the use of high-performance computing tools and their role in chemical research. Educators are not expected to integrate these technologies into their teaching activities, but the course will offer discussions on how this might be accomplished for those educators interested in doing so. Using commercial third-party software (Gaussian94 and MOPAC) resident on the North Carolina Supercomputing Center's Cray Y-MP supercomputer, educators will investigate, using computational tools,techniques, and technologies, a number of chemical properties, such as single-point energies, geometry optimizations, frequency calculations, potential energy surfaces, and thermochemical properties. Participants will also have the opportunity to complete a number of case studies for potential use in the classroom. Prerequisites: Participants must have access to the Internet via the World Wide Web (WWW), preferably using Netscape 1.1. Text-based access (i.e., via lynx) is inadequate. Access assumes electronic mail capabilities. Participants who have Internet connections through America Online or other non-Internet service are advised to ensure good Web connectivity prior to registering. Educators should also have a basic background in quantum chemistry and atomic structure. Completion of a basic course in physical chemistry at the undergraduate level is the appropriate level. A solid mathematics background, particularly in calculus, is helpful but not mandatory. Participants should also have basic computer literacy skills: use of a word processor, basic understanding of the concepts of an operating system, keyboarding skills, etc. A UNIX background is helpful but not required. No programming skills are required. Prospective participants who wish to discuss their qualifications PRIOR to registering are encouraged to do so with the instructor. Workshop Logistics: The course is designed as a self-paced "seminar" series, consisting of 15 sessions. Each week, a new topic and assignment will be posted to the World Wide Web. Students need to complete the reading and assignment, ask questions via electronic mail, and submit their work via email to the course instructor. Students will be able to interact via an email discussion list (listserv). All reading materials and resources are available electronically, although the use of a basic physical chemistry textbook (Atkins is recommended) is strongly advised. Access to the lessons and the supercomputer will begin on October 3, 1995, and will close on February 16, 1996. The course instructor will be available for electronic support during that period. The fee for this activity is $150. Tuition includes access to all Web materials, addition to the class discussion group maililing list, and computing time on the supercomputer. As there is limited enrollment, participants are asked to give considerable consideration to their commitment PRIOR to registering for this activity. The course will require time (roughly four to five hours per week), effort, and intellectual energy. At this point, no grades or continuing education credit is available; however, certificates of completion with an accompanying descriptive letter are provided to all course "graduates". To register for this course, complete the form below and email it to Robert R. Gotwals (gotwals@mcnc.org). There is limited enrollment in this course. Registration is on a first-come, first-serve basis. Please feel free to send questions about this course to gotwals@mcnc.org Tentative Schedule: Session 1: Overview of Computational Chemistry; Overview of the Cray Y-MP and the UNIX operating system Session 2: Logging On; Using Gaussian94 on the Cray supercomputer; creating and submitting G94 input files Session 3: Basis sets and approximations; Input file options; Calculating Single Point Energies Session 4: Single Point Energies. Analyzing output files Session 5: Case Study: Energies of Isomers Session 6: Geometry Optimizations I Session 7: Geometry Optimizations II Session 8: Preparing Geometry Inputs Session 9: Frequency Calculations I Session 10: Frequency Calculations II Session 11: Potential Energy Scans Session 12: Case Study/Teaching Module: Problem Development and Investigation Session 13: Case Study/Teaching Module: Lab Writeup and Instructor Guide Session 14: Overview of other tools for computational chemistry; Classroom integration Session 15: "Final Exam"; Course Wrap-up / Evaluation ****************************************************************** "Computational Chemistry for Chemistry Educators" Registration Form Last Name: First Name: Position: Phone: Curriculum Area: Primary Courses Taught (intro, AP Chem., etc.) School: District( if appropriate): School Address: FAX: E-mail Address: Degree(s): BS [ ] MS [ ] Doctorate [ ] Other [ ] Subject area(s) of degree(s): Years of Teaching Experience: 1-5 [ ] 6-10 [ ] 11-15 [ ] >16 [ ] Years of Technology Experience: 1-5 [ ] 6-10 [ ] 11-15 [ ] Do you own your own computer system? Yes [ ] No [ ] If yes, indicate the hardware platform: Describe the hardware you will use to access the Web lessons: Describe your Web connection (Dialup SLIP or PPP, America Online, etc.) Describe your chemistry, mathematics, and computing background (coursework, workshops, experiences, etc.) Return this registration form to Robert R. Gotwals, Jr.(gotwals@mcnc.org) or by FAX (919) 248-1101. We are unable to process credit card payments. Send tuition check or PO (payable to MCNC) to: Robert R. Gotwals, Jr. Course Instructor -OR- Faye McLean Ellis Course Registrar North Carolina Supercomputing Center 3021 Cornwallis Road Research Triangle Park, NC 27709 From monty@seminole.chem.wisc.edu Thu Sep 7 15:14:04 1995 Received: from dabulls.chem.wisc.edu for monty@seminole.chem.wisc.edu by www.ccl.net (8.6.10/950822.1) id PAA21208; Thu, 7 Sep 1995 15:05:26 -0400 Received: from seminole.chem.wisc.edu. by dabulls.chem.wisc.edu via SMTP (950215.SGI.8.6.10/940406.SGI.AUTO) id OAA20542; Thu, 7 Sep 1995 14:05:07 -0500 Date: Thu, 7 Sep 95 14:05:34 CDT From: "J. Monty Wright" Subject: Re: CCL:G:NBODel Utility on G92 To: CHEMISTRY@www.ccl.net, guillem@gauss.uib.ES CC: weinhold@chem.wisc.edu X-Mailer: LeeMail 2.0.4 Message-Id: I passed G. Suner's question on to Prof. Frank Weinhold, author of NBO, and his reply follows: Q: >I would like to know how can be done a NBO Fock matrix deletion procedure on >G92, particularly by setting some NBO Fock matrix elements to zero and >reevaluating the energy. G92 manual refers to NBO separate manual, but >unfortunately I have no access to that one. Which methodology do I have to >follow? An example G92 input data would be most welcome, as well as any >suggestion on the theme.  A: Gaussian, Inc. should provide a copy of the NBO manual on request. NBO Fock matrix deletions are described in Sec. B.5 There are nine separate deletion types, for deleting everything from entire orbitals to selected blocks of intermolecular matrix elements. A simple example of the syntax for deleting 3 Fock matrix elements is: $DEL DELETE 3 ELEMENTS 1 15 3 19 23 2 $END All $DEL keylists need the POP=NBODel keyword on the route card. FW ********************************************************************* J.M.-Monty- Wright Research Assistant (C.R. Landis Labs) Molecular Modelling and Solution Structure Determination in Support of Rational Catalyst Design From jkl@ccl.net Thu Sep 7 17:29:03 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id RAA24973; Thu, 7 Sep 1995 17:21:56 -0400 Received: from hkusua.hku.hk for h9290218@hkusua.hku.hk by bedrock.ccl.net (8.6.10/950822.1) id RAA10855; Thu, 7 Sep 1995 17:21:48 -0400 Received: by hkusua.hku.hk (5.0/SMI-SVR4) id AA01140; Fri, 8 Sep 1995 02:29:30 +0800 From: h9290218@hkusua.hku.hk (Danny Yau) Message-Id: <9509071829.AA01140@hkusua.hku.hk> Subject: Conference which held in NOV. or Dec. in 1995 To: chemistry@ccl.net Date: Fri, 8 Sep 1995 02:29:30 +0800 (HKT) Cc: h9290218@hkusua.hku.hk (Danny Yau) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 595 Dear Netters, Would anyone know that are there any computational chemistry conferences(included Monte-Carlo simulation, Molecular dynamic, theoretical calculation etc.) will be held in November or December 1995 in U.S.A or Canada? Even some sort of chemistry conference which include the above topic is also welcome. I would be much appreciated if you could provide those information to me. Thanks in advance. Best wishes, -- Danny H.L.Yau email: h9290218@hkursc.hku.hk Department of chemistry, or h9290218@hkuxb.hku.hk The University of Hong Kong. From jkl@ccl.net Thu Sep 7 18:44:03 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA26129; Thu, 7 Sep 1995 18:30:17 -0400 Received: from qmail.fullerton.edu for steve_hardinger@qmail.fullerton.edu by bedrock.ccl.net (8.6.10/950822.1) id SAA11560; Thu, 7 Sep 1995 18:30:13 -0400 Message-ID: Date: 7 Sep 1995 15:31:16 -0800 From: "Steve Hardinger" Subject: Animations and Spartan To: "CCL" X-Mailer: Mail*Link SMTP-QM 3.0.2 Subject: Time: 3:40 PM OFFICE MEMO Animations and Spartan Date: 9/7/95 Hello CClers... I've been working with trying to animate the rotaion of n-butane with Spartan. Everything works very well, but I would like to improve the presentation. I'd like to know (1) can I change the speed at which the frames are presented, and (2) how can I get the view to stay the saem, i.e, always along the c2-c3 bond axis? Any suggestions will be helpful. I'll post a summary if it all works out. Steve Hardinger California State University Fullerton shardinger@fullerton.edu From iiv@mmlds1.pha.unc.edu Thu Sep 7 18:59:04 1995 Received: from mmlds1.pha.unc.edu for iiv@mmlds1.pha.unc.edu by www.ccl.net (8.6.10/950822.1) id SAA26321; Thu, 7 Sep 1995 18:54:02 -0400 Received: by mmlds1.pha.unc.edu (5.57/TAS/11-16-88) id AA11429; Thu, 7 Sep 95 19:02:44 -0400 Date: Thu, 7 Sep 1995 19:02:42 -0400 (EDT) From: Iosif Vaisman To: chemistry@www.ccl.net Cc: Naomi Siew Subject: Re: Side-chain conformation data bank Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I am looking for a bank of side chain conformations. > Can anyone help me with that? > Thank-you very much, > Naomi Siew > siew@vms.huji.ac.il Roland Dunbrack's backbone-dependent rotamer library is available at http://www.cmpharm.ucsf.edu/public/resources.html The backbone-dependent rotamer library and a program for its use provide a fast means of predicting sidechain conformation from backbone phi and psi values. These methods can be used for homology modeling and structure refinement by x-ray and NMR. References: R. L. Dunbrack Jr. and M. Karplus. "Backbone-dependent Rotamer Library for Proteins: Application to Side-chain prediction." J. Mol. Biol. vol. 230, 543-574 (1993). R. L. Dunbrack Jr. and M. Karplus. "Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains." Nature Structural Biology, 1, 334-340 (1994). Iosif Vaisman UNC - Chapel Hill From jkl@ccl.net Thu Sep 7 20:14:04 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id UAA26854; Thu, 7 Sep 1995 20:11:25 -0400 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by bedrock.ccl.net (8.6.10/950822.1) id UAA12066; Thu, 7 Sep 1995 20:11:21 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA14285; Thu, 7 Sep 95 17:11:27 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma014283; Thu Sep 7 17:11:25 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA07591; Thu, 7 Sep 95 17:11:14 -0700 Date: Thu, 7 Sep 95 17:11:14 -0700 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9509080011.AA07591@mazda.wavefun.com> To: steve_hardinger@qmail.fullerton.edu Cc: chemistry@ccl.net In-Reply-To: (steve_hardinger@qmail.fullerton.edu) Subject: Re: CCL:Animations and Spartan Reply-To: hcj@wavefun.com >>>>> "Steve" == Steve Hardinger writes: Steve> I've been working with trying to animate the rotaion of Steve> n-butane with Spartan. Everything works very well, but I Steve> would like to improve the presentation. I'd like to know Steve> (1) can I change the speed at which the frames are Steve> presented, and (2) how can I get the view to stay the saem, Steve> i.e, always along the c2-c3 bond axis? 1) There is no current way to control the speed of the animations. If the animation is too fast (the usual case) you can generate more conformers which will produce a smoother animation, or get a slower machine 8^) Also the addition of surfaces will often slow things down considerably, so there is often a trade off between the rate of animation of the structure alone, and the structure with surfaces. Future versions of Spartan will most likely include some mechanism for controlling the animation rate directly. 2) When animating a series of conformations it is usually desirable to specify the 'NOMOVE' keyword in the setup dialog of the appropriate energy calculation method (mechanics, semi-empirical, or ab initio). Without NOMOVE the optimization methods will re-orient the molecule in an attempt to recognize symmetry within the molecule. It is usually also desirable to specify 'ENFORCE' and 'DUPLCHECK=NONE' in the conformational analysis setup as well. This prevents the particular dihedral of interest from changing as a result of optimization (enforce), and also turns off duplicate checking. Hope this helps! -Harry +-----------------------+------------------+-------------------------+ |Harry C. Johnson IV | ______________ | E-Mail: hcj@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | | |Suite 370 | \ \\/ | "Seems to me its all | |Irvine, CA 92715 | \/ | just chemistry" - RUSH | +-----------------------+------------------+-------------------------+ From jkl@ccl.net Thu Sep 7 20:44:06 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id UAA27036; Thu, 7 Sep 1995 20:35:56 -0400 Received: from logjam.ucc.nau.edu for ZOELLNER@NAUVAX.UCC.NAU.EDU by bedrock.ccl.net (8.6.10/950822.1) id UAA12196; Thu, 7 Sep 1995 20:35:54 -0400 From: Received: from NAUVAX.UCC.NAU.EDU by NAUVAX.UCC.NAU.EDU (PMDF V4.3-10 #2384) id <01HV03Y4GPI8019GFX@NAUVAX.UCC.NAU.EDU>; Thu, 07 Sep 1995 17:35:53 -0700 (MST) Date: Thu, 07 Sep 1995 17:35:53 -0700 (MST) Subject: Cyclodextrin Z matrix or structures To: chemistry@ccl.net Message-id: <01HV03Y4GPIA019GFX@NAUVAX.UCC.NAU.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Greetings to all! A colleague of mine wishes to do some calculations on cyclodextrins. To those who are unfamiliar with these molecules, they are cyclic sugar- containing systems with either six (alpha-cyclodextrin), seven (beta- cyclodextrin), or eight (gamma-cyclodextrin) sugar residues. Thus, my colleague would like to find either atomic coordinates or a workable Z-matrix for these molecules. If anyone out there can assist him, please reply to me, and, while passing along the information to my colleague, I shall post the results to the CCL as well. Thanks in advance for any assistance given! Robert W. Zoellner, Ph.D. Associate Professor of Chemistry zoellner@nauvax.ucc.nau.edu From markm@portal.vpharm.com Thu Sep 7 23:29:07 1995 Received: from portal.vpharm.com for markm@portal.vpharm.com by www.ccl.net (8.6.10/950822.1) id XAA28686; Thu, 7 Sep 1995 23:22:01 -0400 Received: by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA16453; Thu, 7 Sep 1995 23:08:29 -0400 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9509080308.AA16453@portal.vpharm.com> Subject: metabolism sites in aromatic rings To: chemistry@www.ccl.net Date: Thu, 7 Sep 1995 23:08:29 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 505 I know this is a widely-studied field, and I am currently in the midst of collecting references, but I thought it would also be wise to tap the Collective Wisdom of the group on the following topic: What molecular orbital methods have been DEMONSTRATED to do the best job of explaining/predicting/rationalizing the positions on aromatic rings which undergo different types of metabolic events? For example, P450 or xanthine oxidase oxidation, etc. Any help appreciated. / Mark (markm@vpharm.com) From markm@portal.vpharm.com Thu Sep 7 23:40:39 1995 Received: from portal.vpharm.com for markm@portal.vpharm.com by www.ccl.net (8.6.10/950822.1) id XAA28671; Thu, 7 Sep 1995 23:15:23 -0400 Received: by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA16439; Thu, 7 Sep 1995 23:01:50 -0400 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9509080301.AA16439@portal.vpharm.com> Subject: Summary of metal-bound water pKa data To: chemistry@www.ccl.net Date: Thu, 7 Sep 1995 23:01:50 -0500 (EDT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 3807 Here is a summary of the responses to my recent question about the pKa of waters bound to metals in proteins. Thanks to all who contributed! / Mark (markm@vpharm.com) ================================= From: lasse@KVLVAX.kvl.dk (Lars Hemmingsen) concerning your question about pKa's of metalbound water in proteins: For the zinc enzyme horse liver alcohol dehydrogenase I can give you the following values (NAD+/NADH is a coenzyme, which binds close to the metal) LADH-H2O: pKa=9.2, LADH-NAD+-H2O: pKa=7.6, LADH-NADH-H2O: 11.2 (Kvassmann and Pettersson 1980 Eur. J. Biochem., 103, 565-575 and Kvassmann and Pettersson 1987 Eur. J. Biochem., 166, 167-172. and for the same enzyme with the zinc ion exchanged with cadmium: LADH-H2O: pKa=11.0, LADH-NAD+-H2O: pKa=9.2, LADH-NADH-H2O: Not measured (Hemmingsen et al. 1995 Biochemistry, 35, 7145-7153. Furthermore pKa's have been measured, by the group of professor Michael Zeppezauer in Saarbrucken, for the same enzyme with the zinc ion exchanged with cobalt (the references and numbers are in the Biochemistry reference). If you want more pKa-values I would suggest that you contact the poeple in Saarbrucken, Germany (fax: +49 681 302 2097) ================================= >From HMARQUES@AURUM.CHEM.WITS.AC.ZA Thu Aug 17 00:40:22 1995 (Helder Marques) We compared the pKa of H2O bound to a hemepeptide to pKas in hemoproteins in J. Inorg. Biochem, 27, 245-254 (1986) ================================= From: Steve Cabaniss The hydrolysis constant of a metal can be written as an acid dissociation constant, comparable to the Ka for any 'normal' acid. The pKa's can thus be looked up in any standard compendium (i.e., Smith and Martell). I believe the most authoritative review is "Hydrolysis of Cations" by Baes and Mesmer. (Of course, this is all simple aqueous solution chemistry, not the active sites of proteins.) Fe(III) thus 'induces' a water pKa of 2-3. ================================= From: vg857@dewar.pnl.gov (Yajun Zheng) You asked about references concerning pK's of metal-coordinated waters in enzymes. I have several references. The most famous case is Zn metalloenzymes. The pKa for Zn-Water in human carbonic anhydrase II (HCAII) is 7. In alcohol dehydrogenase (ADH) is about 7.6. In SOD the Cu-Water is about 9. The pKa values usually vary depending on active site environments. In xylose isomerase the value is about 7-9 (in this case, the metals are either Mg2+ or Mn2+). There are also other examples such as DNA related enzymes. For ADH, Kvassman, J.; Pettersson, G. Eur. J. Biochem. 1980, 103, 565. also, in Zinc Enzymes; Bertini, I. et al. 1986. For HCAII, See the above book or Zheng and Merz, JACS 1992, 114, 10498. For SOD, I do not have the exact reference, but you could check Joan Valentie papers. For xylose isomerase and DNA related enzymes, there is no exact numbers and most are just guesses. ================================= From: teoulf@garm.teokem.lu.se (Ulf Ryde) For horse liver alcohol dehydrogenase, G. Pettersson, CRC Crit. Rev. Biochem. 21 (1987)349-389 gives an excellent reviev of pKa values of zinc bound water (an other ligands) in different complexes. For carbonic anhydrase, Campbell et al., J. Mol. Biol. 90 (1974) 469-489 reports a pKa between 7 and 8. For carboxypeptidase the situation is more complicated, but Auld et al. Biochem. 31 (1992) 3840 gives a pKa of 9.0 Similarily, for thermolysin, Mock et al., Biochem. J. 302 (1994) 57-68 provides a recent discussion of pKa values. Aquist and Warshel, J. Am. Chem. Soc. 112 (1990) 2860-2868 have a more general discussion about pKa values for metal bound water molecules in different enzymes. =================================