From richard@technology.com Sun May 9 18:47:09 1993 Date: Sun, 9 May 93 23:47:09 CDT From: richard@technology.com (Richard Murphy) Message-Id: <9305100447.AA20880@technology.com> To: chemic-l%taunivm.bitnet@ricevm1.rice.edu, chemistry@ccl.net, Subject: help needed Date: May 6, 1993 To: Distribution From: Walter F. Huebner Southwest Research Institute Subject: Chemical Kinetics Data Part of the Research Initiative Program in Advanced Modeling and Simulation (RIP-AMS), involves solving coupled differential equations for chemical kinetics. For this purpose we are assembling a database for reaction rate coefficients of interest to the various programs at the Institute. I am requesting your help in assessing the availability of rate coefficients that you or your colleagues may be using or would like to use. At this time I would appreciate it if you would answer a few questions and return the memo to me. Please feel free to make copies of this memo and distribute it to your colleagues who may be interested in this topic, but did not receive this memo. 1. Name: 2. Company: 3. Telephone number: 3.a E-mail: 4. Chemical kinetics application: 5. Are the rate coefficients you use a. in Arrhenius form: A~(T/To)B~exp(-C/T)? b. in another form? (Please specify): 6. Does your database contain references for the source of the coefficients? 7. What is the maximum number of reactants (including catalysts) in a reaction? 8. What is the maximum number of products (including catalysts) in a reaction? 9. Please attach a very short sample printout of your database (we just want to know the FORTRAN format). From chp1aa@surrey.ac.uk Mon May 10 09:07:18 1993 From: Mr Andrew D Allen Message-Id: <9305100923.AA25284@central.surrey.ac.uk> Subject: Force Field Summary To: chemistry@ccl.net Date: Mon, 10 May 93 10:23:33 BST First of all a big thanx to all who replied, As I see it there are many different ways in which a force field can be generated, many ways in which the individual energy terms can be calculated. Also each different force field will have slightly different paramenters for the ideal bond angles, distances, polarisabilities, etc, and all this adds up to them giving different absolute energies. Things to be wary of:- 1. The atom types from one force field are correctly converted to the atom types of another force field before doing a comparison. 2. Check that the charges used in the different force fields are similar. Or maybe use charges generated from another standard (for sake of argument MOPAC or G92). 3. When comparing the energies don't use the absolute values as the comparison use the differences between structures as a comparison. 4. There are several force fields that are generally accepted for certain applications. MM(P, P2) for small molecules, AMBER, for proteins and nucleic acids. Thanx once again to all who replied, I was aware of most of the above, but was a little concerned at just how different the final total energies could be. ANDY. From vasz@bif.creighton.edu Mon May 10 03:59:08 1993 Date: Mon, 10 May 93 08:59:08 -0500 From: vasz@bif.creighton.edu (Sandor Lovas) Message-Id: <9305101359.AA05234@bif.creighton.edu> To: CHEMISTRY@ccl.net Subject: Re:IBMPCs Dear Netters, The best solution for PC's is to use OS/2 2.0 or 2.1 operation system. It does not make difference what sort of computer is beeing used, however as I know, IBM ships its computer with OS/2 2.0. OS/2 is very powerful, DOS and windows are better, than the original one. Many times I found that programs made for Windows 3.x running better under OS/2. I use this system since the beta version of OS/2 2.0 was available and I am very satisfied with it. I can run my own computational chemistry programs very well. Sincerely, Sandor Lovas, vasz@bif.creighton.edu From Barbara_Graham@MSI.COM Fri May 10 10:09:40 1993 Message-Id: <9305101407.AA28780@schizoid.msi.com> Date: 10 May 1993 10:09:40 +0000 From: "Barbara Graham" Subject: Re: Conflicting energies for To: Pat_Bolis@msi.com, CHEMISTRY@ccl.net Mail*Link(r) SMTP RE>Conflicting energies for Pat--Pls send comp + entangled. I completed the address.--BFG ******************************* * David Maxwell * * Dept. of Chemistry * * Yale University * *New Haven, CT 06511 ******************************* --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net CHEMISTRY-SEARCH@ccl.net --- search the archives, read help.search file first --- From chm6@midway.uchicago.edu Mon May 10 06:21:57 1993 Date: Mon, 10 May 93 11:21:57 CDT From: "charles h martin" Message-Id: <9305101621.AA04061@midway.uchicago.edu> To: CHEMISTRY@ccl.net Subject: Zindo Dear Netters, First, I would like to thank everyone who responded to my query regarding source code for converting cartesian coordinates to Z-matrix format. I can summarize the responses if anyone is interetsed. Second, I would like to obtain ZINDO. Is this available via ftp? Is there a charge? Thanks Chuck Martin Univ of Chicago chm6@quads.uchicago.edu (312) 702-3457 From NCARRASC@USACHVM1.usach.cl Mon May 10 14:08:52 1993 Message-Id: <199305101728.AA05525@oscsunb.ccl.net> Date: Mon, 10 May 93 13:19:14 SEC From: NCARRASC@USACHVM1.usach.cl To: chemistry@ccl.net Subject: CASE PROGRAM Dear Netters: There is a computer program by Gilles Klopman called CASE, this program is about QSAR. I am really very interested in getting information in how could get this program, in case it were available through some academic network. Does anyone know or have information abot CASE?. Does anyone know or have any other alternative programmes for evaluating structure-activity. Thanks in advance A Chilean's friend Claudio From VERCAU@BNANDP11.bitnet Mon May 10 15:35:25 1993 Message-Id: <199305101717.AA05299@oscsunb.ccl.net> Date: Mon, 10 May 93 15:34:25 +01 From: "Daniel P. Vercauteren" Subject: C60 meeting in Namur, Belgium To: chemistry@ccl.net ************************************************************************ * * * Educative Session in Large Scale Computation for Quantum * * Physics and Chemistry * * * * Programme Gouvernemental en Technologie de l'Information * * Calcul de Puissance en Chimie et Physique Quantiques * * * * Facultes Universitaires Notre-Dame de la Paix, Namur, Belgium * * Namur Scientific Computing Facility Center * * J.-M. Andre and J.-P. Vigneron * * * ************************************************************************ Sixth SCF Users Group Meeting COMPUTED PROPERTIES OF CARBON-BASED MATERIALS Auditorium CH3, FUNDP, Dept of Chemistry, 2, rue Grafe, B-5000, Namur, Belgium MAY 17 - 19, 1993 Monday, May 17th ---------------- Morning: General-Introductory H.W. Kroto (Brighton): Materials Science Studies of Fullerenes M.S. Dresselhaus (Boston): Planar and Curved Layers of Carbons Afternoon: J.I. Aihara (Shizuoka): Polycyclic Aromatics and Fullerenes J.H. Weaver (Minneapolis): Electronic Properties of the Alkali and Alkaline Ear th Fullerites: Success and Limitations of Band Calculations G. Meijer (Nijmegen): C60 and C70 Single Crystals Followed by installation of posters. Tuesday, May 18th ----------------- Morning: Selected Observational Facts G. Gensterblum (Namur): Electron Spectroscopies of Fullerite Films S. Amelinckx (Antwerp): Carbons under the Electron Microscope Poster Session. Afternoon: Electronic Properties of Monolayer Fullerenes S.G. Louie (Berkeley): Electron Excitation Energies in C60 Fullerites A. Rosen (Chalmers): Optical Properties of Fullerenes O.F. Sankey (Tempe): Electronic Structure of Giant Fullerenes X. Gonze (Louvain-la-Neuve): Negatively-curved Carbon Network Wednesday, May 19th ------------------- Morning: Electrons and Phonons A.A. Lucas (Namur): Elementary Excitations in Fullerite Films J.L. Martins (Lisboa): Electron-phonon Interaction in Fullerites O. Gunnarsson (Stuttgart): Electronic Structure of Doped Fullerites M. Lannoo (Lille): Superconductivity in Doped Fullerites Afternoon: Structural Properties J.R. Chelikowsky (Minneapolis): Modeling the formation of fullerenes S.B. Fahy (Ann Arbor): Monte Carlo Study of Diamond and Graphite J.C. Charlier (Louvain-la-Neuve): Multilayered Carbon Tubules K. Michel (Antwerp): Phase Transitions in C60 Fullerites For further information, please contact: - Prof. J.-M. Andre, Facultes Universitaires Notre-Dame de la Paix (FUNDP), Laboratoire de Chimie Theorique Appliquee (CTA), 61, rue de Bruxelles, B-5000 Namur, Belgium Tel.: +32 (81) 724553, Fax: +32 (81) 724530 E-mail: ANDRE at SCF.FUNDP.AC.BE - Prof. J.-P. Vigneron, Facultes Universitaires Notre-Dame de la Paix (FUNDP), Laboratoire de Physique du Solide (LPS), 61, rue de Bruxelles, B-5000 Namur, Belgium Tel.: +32 (81) 724711, Fax: +32 (81) 230391 E-mail: VIGNERON at SCF.FUNDP.AC.BE - Prof. D.P. Vercauteren, Facultes Universitaires Notre-Dame de la Paix (FUNDP), Laboratoire de Physico Chimie Informatique (PCI), 61, rue de Bruxelles, B-5000 Namur, Belgium Tel.: +32 (81) 724534, Fax: +32 (81) 724530 E-mail: VERCAU at SCF.FUNDP.AC.BE For registration, please send forms to: - Dr. M.-Cl. Andre, Facultes Universitaires Notre-Dame de la Paix (FUNDP), Laboratoire de Chimie Theorique Appliquee (CTA), 61, rue de Bruxelles, B-5000 Namur, Belgium Tel.: +32 (81) 724553, Fax: +32 (81) 724530 E-mail: MCANDRE at SCF.FUNDP.AC.BE Registration Form for 6th SCF Meeting ===================================== May 17-19,1993, Auditorium CH3 Last name: ............................................................ First name: ........................................................... Title: ................................................................ Address: .............................................................. .............................................................. .............................................................. .............................................................. Telephone: ............................................................ Fax: .................................................................. Telex: ................................................................ E-mail: ............................................................... Acknowledge-To: From mail Mon May 10 13:58:38 1993 Date: Mon, 10 May 1993 14:02:19 -0400 From: hyper!hurst (Graham Hurst) Message-Id: <9305101802.AA25498@hyper.hyper.com> To: chemistry@ccl.net Subject: Re: Conflicting energies from MM2 and MM+ Andrew D Allen wrote: > I have recently been using the MM2 force field on MSI's Biograf >(Ver 2.20) getting minimised energies in the 100 - 120 Kcal ballpark. Our >department here in Surrey, recently obtained Hyperchem, so to back up the >work I have done I run a similiar conjugate energy minimisation on some of >my molecules taken from Biograf in a Brookhaven format. The resulting energies >after minimisation were around 40 - 50 Kcals. In some cases nearly a third of >the energy obtained from Biograf. > Intrigued? I was. Checking further I had a colleague run a similiar >calculation on the same molecules using the CHRAMM force field and the energies >came out around 40 - 50 Kcals. > > Question: Is the MM2 force field in Biograf wrong? > > Question: Has anyone else experienced widely different energies using >different force - fields. As Dora Schnur and David Maxwell have pointed out, absolute energies from different force fields should not be compared. However since HyperChem's MM+ and (I assume) Biograf's MM2 are based on Allinger's MM2 force field, one might expect agreement for the total energy and its components under the following conditions: 1. Same molecular systems (including geometry) 2. Same parameters 3. Same force-field options If all these conditions are satisfied, then the force-field equations have been modified or something is wrong (software, hardware...). Let's assume #1 is true. As Dora Schnur points out, #2 is a likely culprit. HyperChem's MM+ uses MM2(91) parameters, supplied directly from Norman Allinger, if available. If those are not available and the user has not added ones, HyperChem uses parameters from a Dreiding-style default scheme (and tells the user it did so on the status line and in a log file). Thus Andrew Allen should check whether HyperChem is using default parameters, and what parameters BioGraf uses. (HyperChem's default scheme is fully specified in the 300 pg Computational Chemistry manual that comes with the program.) Another possible source of the discrepancy is #3. HyperChem uses the same electrostatic treatment as MM2 by default, namely bond dipoles, while some other "MM2" implementations only allow the use of point charges (which is an option in HyperChem 3). I feel compelled to hop on a soapbox and reply directly to something Dora Schnur wrote: > As to whether on of the force fields is actually "wrong", I would reccommend > actually running Allinger's MM2, preferable MMP2(91). He has often received > complaints about MM2 that turned out to in fact be complaints about someone > else's personal implementation based on his publications. It has been a source > of distress over the years. Yes - it is distressful to not be able to reproduce Prof. Allinger's MM2 results based on his publications! As he has told me himself, his MM2 program is the *only* complete specification of the MM2 force field, so one can't independently reproduce MM2 results from published science! Of course one can reproduce his MM2 force field if one has direct (or indirect) access to the source code for his MM2 program. Unfortunately the newest public domain version (available from QCPE) is MM2(1977)! I don't mean to single out Lou Allinger - he has been helpful and open to us about the unpublished details of MM2. However the problem of incomplete specification of force fields, through oversight or deliberate omission, is widespread. I know this problem has been discussed here and elsewhere many times. I support the idea of a force-field archive and encourage journal referees and authors to insist that molecular mechanics results not be published unless the force field is (or has been) published in full. Of course the acid test of whether a force field has been fully published or not is to be able to read the published description of the functional form and parameters, implement it, and get the same answers. I wouldn't expect everyone to do this, but I have for several force fields and in all cases had to get at least some further details from the authors. As well as equations and parameters, one requires such oft unpublished details as charges, how types are assigned, where to use improper torsions, etc. Now to protect myself (at least somewhat!): The opinions expressed above are my own. MM2 is a registered trademark of Professor Norman L. Allinger. Cheers, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com From mail Mon May 10 16:44:10 1993 Date: Mon, 10 May 1993 16:09:06 -0400 From: hyper!hurst (Graham Hurst) Message-Id: <9305102009.AA26019@hyper.hyper.com> To: chemistry@ccl.net Subject: Re:IBMPCs In response to Ken Fountain's request for comparison of Gateway vs. IBM 486 PC's for HyperChem and Gaussian 92W, Sandor Lovas writes: > The best solution for PC's is to use OS/2 2.0 or 2.1 operation system. It > does not make difference what sort of computer is beeing used, however as > I know, IBM ships its computer with OS/2 2.0. OS/2 is very powerful, DOS > and windows are better, than the original one. I don't want to start another Windows vs. OS/2 flamefest, but Ken Fountain was asking about a PC for HyperChem and Gaussian 92W (an excellent combination IMHO!) and these *won't* run with OS/2 2.0, since they are 32 bit apps that require enhanced mode. OS/2 2.1 is supposed to fix this, but it is still in Beta so I don't think that you can actually buy it. IBM is also due to release it's DOS 6 soon, and that should be fine for Windows 3.1 but I doubt that IBM would bundle Windows (even though they are licensed to sell it)! I gather IBM is offering fantastic prices to educational institutions these days, which could sway the decision that way, but I noticed in the latest PC Magazine that Gateway now throws in CD-ROM drives with many 486's. Brookhaven's Protein Data Bank is now on CD-ROM and is readable by HyperChem, with ribbon rendering new for Rel 3, so this might be quite desirable if the machines are to be used for teaching biochemistry! Gateway also uses local bus ATI Ultra Pro which is a very fast display (which matters for HyperChem, but I doubt G92W needs much graphics speed) though the magazines now find the similarly-priced Diamond Viper local bus video card to be faster. IBM's XGA 2 may have comparable video speed (I don't know) but costs a lot. IBM's micro channel bus is sophisticated and fast, but peripherals are expensive and harder to find. Gateway, like many clones now, counters this by using a fast local bus (VL-Bus standard) for video and disk and a slow ISA bus for cheap and plentiful peripherals. Just my $0.02... Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com From longo@qtp.ufl.edu Mon May 10 12:17:06 1993 Date: Mon, 10 May 93 16:17:06 EDT From: longo@qtp.ufl.edu Message-Id: <9305102017.AA15738@crunch.qtp.ufl.edu> To: chemistry@ccl.net Subject: Subscribe Hi, I'd like to subscribe to the chemistry news group. longo@qtp.ufl.edu Thanks, Ricardo -------------------------------------------------------- Ricardo Luiz Longo longo@qtp.ufl.edu Quantum Theory Project University of Florida Tels: (904) 392-7184 Williamson Hall (904) 392-1594 Gainesville, FL - 32611-2085 USA Fax: (904) 392-8722 -------------------------------------------------------- From shepard@dirac.tcg.anl.gov Mon May 10 12:03:46 1993 Date: Mon, 10 May 93 17:03:46 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9305102203.AA10590@dirac.tcg.anl.gov> To: CHEMISTRY@ccl.net Subject: Z-matrix to Cartesian Transformation [...] > First, I would like to thank everyone who responded to >my query regarding source code for converting cartesian coordinates >to Z-matrix format. I can summarize the responses if anyone is interetsed. [...] > Thanks > Chuck Martin > Univ of Chicago > chm6@quads.uchicago.edu > (312) 702-3457 Yes I would like to see a summary. By the way, this brings up an issue that might be worth discussing in general. Namely, is there a demand for chemistry "tools" rather than chemistry "programs"? The difference is that a tool does only one thing, perhaps with some options, whereas a program is more monolithic. A tool is meant to be used in conjunction with other tools and programs to accomplish tasks. On unix machines, tools can be written using stdin and stdout so that they can be ganged together in various ways and used in pipes in shell commands. In general, I would like to see more tools developed and shared. In particular regarding Z-matrix to Cartesian conversions, I would like to have a tool that does this, and the reverse, along with analytic transformation of derivatives (first and second especially). This is not trivial, and it is undesirable for this effort to be wasted within a single program when this functionality is needed so frequently. Ron Shepard shepard@tcg.anl.gov From mgw@stan.xx.swin.OZ.AU Tue May 11 06:09:50 1993 From: mgw@stan.xx.swin.OZ.AU (Margaret Wong) Message-Id: <9305110109.AA12335@stan.xx.swin.OZ.AU> Subject: charges To: CHEMISTRY@ccl.net Date: Tue, 11 May 93 11:09:50 EST Hi Chemnetters Lately there has been lots about the validity of charges by various methods and all eventually correlate their results to ab-initio calculated charges. This still doesn't answer how valid ab-initio charges actually are. What is the physical evidence, apart from dipole moment and high resolution X-ray crystallography, existing for calculated charges vs. actual charges? Margaret Wong