From autodesk!uoft02.utoledo.edu!DSMITH@fernwood.mpk.ca.us Tue Mar 2 15:49:08 1993 Date: Tue, 02 Mar 1993 12:36:08 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: DEC Alpha workstations/servers To: chemistry@osc.edu Cc: hyperchem@autodesk.com, mmodinfo@uoft02.utoledo.edu Status: RO Are there any commercial software vendors writing for the Alpha, under either OpenVMS or (preferably) OSF/1? Are they/you writing for the graphics workstation and for what level of graphics? Or is anyone writing for the Alpha as a non-graphical server? Please don't respond about public domain or QCPE software - we do that under a grant from DEC and supply the ports to QCPE ourselves. About 30 programs ought to show up soon. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ________________________________________________________________________ From autodesk!UCBEH.SAN.UC.EDU!EBERHAJS@fernwood.mpk.ca.us Tue Mar 2 19:31:00 1993 Date: 02 Mar 1993 16:16:34 -0500 (EST) From: EBERHAJS@UCBEH.SAN.UC.EDU Subject: questions To: hyperchem@autodesk.com Status: RO From: Jeffrey Eberhard Graduate Student Institute of Environmental Health University of Cincinnati Medical Center INTERNET EBERHAJS@UCBEH.SAN.UC.EDU VOICE 513-558-1735 FAX 513-558-4397 I am a new HyperChem user, currently engaged in application of the software to environmental problems. My first task is use of the software to map electron density about a series of substituted azobenzenes, in order to predict reactivity of these compounds in the environment. I have had some success - predicting identified azo bond cleavage products (oxidative or reductive cleavage) based upon electron density about the azo bond. I have two questions (ares of concern): 1. Computing time. I perform the calculations on an 80486 at 50 MHz, when calculating low energy conformation for complicated molecules - azo dyes with several azo bonds and aromatic moities - the computation converges in about 5 hrs using INDO and a solvation shell (H2O) of about twice the molecular volume. Using the same set-up, convergance takes about 150 - 200 hrs Under the same conditions for 4-hydroxyazobenzene (or 3 or 2) convergence takes about 150-200 hrs.. 2. Solvation. When plotting electron density about the optimized hydroxazobenzenes, solvation is very significant. With no water molecules, electron density is as expected (about azo bond and O atom). With 16 water moleculeshigh density seen about azo bond, O atom AND the 3' position. With 64 water molecules, density seen only about the azo bond. HELP ________________________________________________________________________ From autodesk!cc.gettysburg.edu!tschoolc@fernwood.mpk.ca.us Thu Mar 4 18:56:22 1993 Date: Thu, 4 Mar 93 16:54:00 EST Sender: tschoolc@cc.gettysburg.edu To: hyperchem@autodesk.com From: tschoolc@cc.gettysburg.edu Subject: Hyperchem and MoleCVUE Status: RO Autodesk, I am forwarding this question on to you. --tracy >X-POP3-Rcpt: tschoolc@jupiter >Return-Path: >Received: from by cc.gettysburg.edu (4.1/SMI-4.0-DDN-gettysburg-3.1) id AB09628; Thu, 4 Mar 93 16:42:11 EST >Received: from RITVAX.BITNET (REG3334@RITVAX) by charon.cc.gettysburg.edu (PMDF #2975 ) id <01GVEYFZMZ740000F9@charon.cc.gettysburg.edu>; Thu, 4 Mar 1993 16:02:46 EDT >Received: from ritvax.isc.rit.edu by ritvax.isc.rit.edu (PMDF #2327 ) id <01GVEW3KIT8O9I46NY@ritvax.isc.rit.edu>; Thu, 4 Mar 1993 14:33:41 EST >Date: 04 Mar 1993 14:33:40 -0500 (EST) >From: Robert Gilman >Subject: Hyperchem and MoleCVUE >To: tschoolc@cc.gettysburg.edu >Message-Id: <01GVEW3KIT8Q9I46NY@ritvax.isc.rit.edu> >X-Vms-To: IN%"tschoolc@cc.gettysburg.edu" >X-Vms-Cc: REG3334 >Mime-Version: 1.0 >Content-Transfer-Encoding: 7BIT > >Tracy, >I read your description of Hyperchem and the MoleCVUE Consortium on the >Chemed-l with great interest. I am interested in the generation of 3-D >computer structures that I can then convert to overheads for use in my organic >lectures. I have been considering the purchase of Hyperchem from my personal >software budget, but would like to be sure that it is flexible enough for my >needs before I do so. I need to be able to generate structures of my choice and >then convert them to 3-D representations that can be rotated and >printed(preferably in color..on an HP500C). Do you or any of your members have >experience with the generation of structures of this type? If some members of >the Consortium have interest similar to mine, I would be interested in joining >the group. I would welcome any suggestions that you might have. >Sincerely, >Bob Gilman >Professor of Chemistry >Rochester Institute of Technology >Rochester, NY 14623 > > ________________________________________ Tracy A. Schoolcraft Assistant Professor of Chemistry Department of Chemistry Gettysburg College Gettysburg, Pa 17325 INTERNET: tschoolc@cc.gettysburg.edu Phone: (717) 337-6261 ________________________________________________________________________ From autodesk!magnus.acs.ohio-state.edu!wbecktel@netcom.com Mon Mar 8 17:01:54 1993 Date: Mon, 8 Mar 1993 15:12:44 -0600 To: hyperchem@autodesk.com From: wbecktel@magnus.acs.ohio-state.edu Subject: Excel macro/ HyperChem question Status: RO We have been working on an Excel Macro for use with DDE and HyperChem and seem to be having problems convincing either Excel to send or HyperChem to receive a variable in Integer format. Part of the code looks like: =for("atom1",2,1600,3) atom2 = atom1+1 =execute(Channel,"[select-atom(atom1,1)]") (more commands) =execute(Channel,"[select-atom(atom2,1)]") (more commands) =Next() Executing the macro yields the HyperChem error that the first argument of the select-atom command has to be an integer. OK, we set the format of atom1 and atom2 as integer, but that didn't work. We included something like atom2 = INT(atom2) and that didn't work. I am not sure how to proceed as we have tried most of the reasonable fixes. After looking at the Excel manuals, I think what is happening is that Excel is treating atom1 and atom2 as part of a quoted string and not as variables. If anyone has a suggestion as to how to get around this, I would very much appreciate your response. One possibility, not discussed in the HyperChem manual, would be to use a POKE command to send the data. I am not sure of how this would work. Thanks in advance. wayne ---------------------------------------------------------------- Wayne J. Becktel phone: 614-292-6383 Biochemistry 614-292-6911 The Ohio State University fax: 614-292-6773 Columbus, OH. 43210 ________________________________________________________________________ From autodesk!smith.smith.edu!ROSENFELD@netcom.com Mon Mar 8 21:26:08 1993 Date: 08 Mar 1993 20:22:16 -0400 (EDT) From: ROSENFELD@smith.smith.edu Subject: hyperchem startup To: hyperchem@autodesk.com Status: RO I'm using hyperchem on an iris indigo that was recently connected to ethernet. At the same time, an IP address and name was assigned to W my workstation. Since then I have been unable to launch hyperchem. Is there a simple fix? ________________________________________________________________________ From hyper!slee@autodesk.com Tue Mar 9 09:49:42 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: hyperchem startup To: autodesk!ROSENFELD%smith.smith.edu@netcom.com Date: Tue, 9 Mar 93 9:30:59 EST Cc: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Status: RO > > I'm using hyperchem on an iris indigo that was recently connected to > ethernet. At the same time, an IP address and name was assigned to W > my workstation. Since then I have been unable to launch hyperchem. > Is there a simple fix? > Somebody from Autodesk will be in touch with you directly about this problem. I believe it will be straightforward to resolve. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From autodesk!gw.wmich.edu!harmon@netcom.com Tue Mar 9 10:37:59 1993 Date: Tue, 9 Mar 1993 09:43:42 -0500 From: harmon@gw.wmich.edu To: hyperchem@autodesk.com Cc: HARMON@gw.wmich.edu Subject: Use of Hyperchem in Solving Environmental Problems Status: RO Hyperchem Users: Dave Ware was telling me that someone at the University of Cincinnati was using Hyperchem in their environmental research program. I was wondering how Hyperchem was incorporated into this type of research. Bob Harmon Harmon@gw.wmich.edu. ________________________________________________________________________ From autodesk!gw.wmich.edu!harmon@netcom.com Tue Mar 9 17:48:42 1993 Date: Tue, 9 Mar 1993 16:25:47 -0500 From: harmon@gw.wmich.edu To: hyperchem@autodesk.com Cc: HARMON@gw.wmich.edu Subject: hyperchem Status: RO Dear Hyperchemickers: I am interested in application to environmental problems. Would appreciate a word from anyone who is using Hyperchem in such a research environment. bob harmon Harmon@gw.wmich.edu ________________________________________________________________________ From autodesk!hyper!slee@hyper Wed Mar 10 18:03:33 1993 From: autodesk!hyper!slee@hyper.uucp (Thomas Slee) Subject: Re: Excel macro/ HyperChem question To: hyperloo@autodesk.uucp (hyperloo@autodesk.com) Date: Wed, 10 Mar 1993 15:42:29 -0500 Status: RO Wayne Becktel writes: > > We have been working on an Excel Macro for use with DDE and > HyperChem and seem to be having problems convincing either Excel to send or > HyperChem to receive a variable in Integer format. Part of the code looks > like: > > (abbreviated) > =execute(Channel,"[select-atom(atom1,1)]") > > Executing the macro yields the HyperChem error that the first > argument of the select-atom command has to be an integer. I am far from an Excel expert, but I think your diagnosis is correct: Excel thinks atom1 is a part of a quoted string. The arguments sent back and forth by DDE always have to be strings, but I guess HyperChem is hearing "atom1" rather than a string with its value, "1". I managed to get it working by breaking up the string around the atom1 and sending it as a concatenated string. This is done by replacing =execute(Channel,"[select-atom(atom2,1)]") by =execute(Channel,"[select-atom(" &atom2& ",1)]") In amongst the masses of parentheses, you can see the structure of the argument is "[select-atom(" - a string & - concatenate atom2 - value of atom1. & - concatenate ",1)]" - completion of the string. This seemed to work okay. By the way, HyperChem doesn't take poke commands. > Thanks in advance. > > wayne > > > > ---------------------------------------------------------------- > > Wayne J. Becktel phone: 614-292-6383 > Biochemistry 614-292-6911 > The Ohio State University fax: 614-292-6773 > Columbus, OH. 43210 > -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From gw.wmich.edu!harmon@netcom.com Sun Mar 14 20:04:40 1993 Date: Sun, 14 Mar 93 18:51:47 -0500 To: autodesk!hyperchem@netcom.com Cc: HARMON@gw.wmich.edu Subject: USE OF HYPERCHEM IN TEACHING Status: RO TO FELLOW HYPERCHEM USERS: I WOULD BE INTERESTED IN HEARING ABOUT ANYONE WHO HAS USED HYPERCHEM IN AN UNDERGRADUATE SITUATION. BOB HARMON DEPT. OF CHEM. WESTERN MICHIGAN UNIVERSITY KALAMAZOO, MI 49008 INTERNET: "HARMON@GW.WMICH.EDU" ________________________________________________________________________ From autodesk!cell.BIH.Harvard.Edu!steven@netcom.com Tue Mar 16 09:35:52 1993 Date: Tue, 16 Mar 93 07:54:48 EST From: steven@cell.BIH.Harvard.Edu (Steven Blechner) To: hyperchem@autodesk.com Subject: free-energy perturb... Status: RO Dear group: I am interested in free-energy perturbation studies of site directed mutagens of a group of known (x-tallized) proteins. Has anyone done this using Hyperchem ?? Is it possible ?? Any help would be appreciated. If mailed directly to me, I will summarize... -steve blechner ________________________________________________________________________ From autodesk!tammy.harvard.edu!friedman@netcom.com Tue Mar 23 21:20:15 1993 Date: Tue, 23 Mar 93 20:40:18 -0500 From: friedman@tammy.harvard.edu (Dawn Friedman) To: hyperchem@autodesk.com Subject: electrostatic potentials Cc: friedman@tammy.harvard.edu Status: RO How does one calculate (and map?) electrostatic potentials in HyperChem? Thanks, Dawn Friedman ________________________________________________________________________ From hyper!slee@autodesk.com Wed Mar 24 10:54:15 1993 From: hyper!slee@autodesk.com (Thomas Slee) Subject: Re: electrostatic potentials To: autodesk!hyperchem@netcom.com (HyperChem e-mail group) Date: Wed, 24 Mar 93 9:29:50 EST Cc: friedman@tammy.harvard.edu Status: RO Dawn Friedman asks: > > How does one calculate (and map?) electrostatic potentials in HyperChem? > Electrostatic potentials are computed from any semi-empirical single-point calculation. Detailes of formulae etc. are given in the Computational Chemistry handbook, Theory and Methods section, p. 86. You simply carry out a single point calculation with the Electrostatic Potential radio button clicked on. In the Windows version you will get a contour plot, in the SGI version you can choose from a contour plot or a 3D isosurface. A tricky point with the electrostatic potential plot is that the default contour settings don't give good results. The electrostatic potential is calculated on a grid of points (which you specify), and the default scheme is to place the lowest contour at the minimum value, the highest contour at the maximum, and equally space them in between. This results in the plots being swamped by the huge, but physically uninteresting, values near the nuclei. I would recommend resetting the Increment in the single point dialog box to something around 0.05: this shows the regions of negative electrostatic potential (potential sites of electrophilic attack) clearly. Tom Slee Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From autodesk!uoft02.utoledo.edu!DSMITH@netcom.com Thu Mar 25 18:27:01 1993 Date: Thu, 25 Mar 1993 09:59:01 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: SC&A Conference speakers - thanks To: chemistry@osc.edu, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Status: RO Thank you to all who responded to my recent posting requesting speakers for the Scientific Computing and Automation Conference in October. I have received more than enough responses and have filled all of the remaining slots. If you have not heard from me directly, then you have not been included in the choices (I think I got back to everyone with a personal message, though). I am looking forward to a great conference and a wonderful Molecular Modeling and Computational Chemistry track. I will post details in the near future. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ________________________________________________________________________ From autodesk!TC.Cornell.EDU!jeanne@netcom.com Mon Mar 29 14:01:12 1993 Date: Mon, 29 Mar 1993 12:57:12 -0500 From: "Jeanne C. Miller" To: amber@cgl.ucsf.edu, charmm-bbs-sysop@emperor.harvard.edu, chemistry@osc.edu, dibug@comp.bioz.unibas.ch, gromos@igc.ethz.ch, hyperchem@autodesk.com, mmodinfo@uoft02.utoledo.edu, spasms-users@cgl.ucsf.edu, sybylreq@quant.chem.rpi.edu Subject: KSR Symposium Announcement Cc: donna@TC.Cornell.EDU, jeanne@TC.Cornell.EDU, richard@TC.Cornell.EDU Status: RO ========= SYMPOSIUM ========= Simulation of Polypeptide and Protein Structure May 3-4, 1993 A symposium to discuss research progress in the Theory CenterUs Parallel Processing Resource for Biomedical Scientists, as well as recent advances in computational chemistry and polypeptide modeling. ======== LOCATION ======== Sheraton Inn and Conference Center One Sheraton Drive Ithaca, New York 14850 ================== PRELIMINARY AGENDA ================== Malvin H. Kalos Director, Cornell Theory Center Welcome & Overview of the Parallel Processing Resource for Biomedical Scientists David Shalloway Biochemistry, Cornell University Effective Energy Simulating Annealing for Molecular Structure Prediction Harold Scheraga Chemistry, Cornell University The Multiple-minima Problem in Protein Folding Peter Kollman University of California/San Francisco Molecular Dynamics and Free Energy Calculations of Protein George Nemethy Biomathematical Sciences/Mt. Sinai Medical Center The Structure and Assembly of Collagen Daniel Ripoll/Richard Gillilan Cornell Theory Center Simulation and Visualization of Acetylcholinesterase Electrostatics Klaus Schulten Physics, University of Illinois Urbana-Champaign Large Scale Simulations of Protein-Membrane Systems John Brady Food Science, Cornell University Molecular Dynamics Simulations of Carbohydrates Andrew McCammon Chemistry, University of Houston Computer-aided Molecular Design Chani Pangali Kendall Square Research Corporation Computational Chemistry on the KSR1 Jan Hermans Professor, Biophysics University of North Carolina/Chapel Hill Molecular Dynamics Studies of Peptide Conformational Equilibrium Dr. Dzung Nguyen, Ph.d Scientist, Biosym Technologies, Inc. Molecular Dynamics Study of the Structure and Dynamics of Proteins in a Crystalline Lonic Environment ============== POSTER SESSION ============== To apply for a poster session and/or video theatre presentation, please send abstract of research to cal@tc.cornell.edu by March 30, 1993. ======== WORKSHOP ======== In conjunction with the symposium, the Theory Center will conduct, during May 5-7, a training workshop on using the KSR1 parallel computer. A fee will be charged for the training workshop. Registration available separately. ============== ACCOMMODATIONS ============== Two local hotels have set aside rooms for the nights of May 3-4. Please make your reservations directly with the hotel and mention that you are coming for the Simulation of Polypeptide and Protein Structure symposium. Reservations must be made by April 12 to assure room availability. Sheraton Inn One Sheraton Drive Ithaca, NY 14850 607-257-2000 or 1-800-257-6992 607-257-3998 (fax) Rates start at $62 Holiday Inn 2310 North Triphammer Road Ithaca, NY 14850 607-257-3100 or 1-800-465-4329 607-257-4425 (fax) Rates start at $60 ================= REGISTRATION FORM ================= Return this part only, by April 5: Symposium on Simulation of Polypeptide and Protein Structure May 3-4, 1993 Sheraton Inn and Conference Center, Ithaca, NY Name: __ Title: __ Organization: __ Address: __ City/State/Zip/Country: __ Phone/Fax: __ Email: __ Special dietary requirements: Kosher__ Vegetarian__ Other ________________________________________ Return completed form to: (deadline April 5, 1993) Donna Smith, Conference Coordinator 422 Theory Center Cornell University Ithaca, NY 14853 607-254-8686; 607-254-8888 (fax) donna@tc.cornell.edu