From COMPCHEM%PLWRTU11.BITNET@phem3.acs.ohio-state.edu Tue Oct 19 10:47:20 1993 Date: Tue, 19 Oct 1993 09:47:20 +0100 (CET) From: Andrzej Sokalski Subject: in June 94'nce COMPUTERS IN CHEMISTRY in Wroclaw, Poland To: chemistry@ccl.net Message-Id: <01H4A8WFYBXE8X6XTU@phem3.acs.ohio-state.edu> FIRST ANNOUNCEMENT 3-rd Conference COMPUTERS IN CHEMISTRY '94 (June 23-26, 1994) covering sessions on CHEMOMETRICS IN ANALYTICAL CHEMISTRY COMPUTERS IN CHEMICAL TECHNOLOGY AND CHEMICAL ENGINEERING COMPUTERS IN CHEMICAL EDUCATION MOLECULAR GRAPHICS EXPERT SYSTEMS AND DATABASES and other related topics including Workshop on COMPUTATIONAL METHODS FOR LARGE MOLECULAR SYSTEMS (June 25 - 26 1994) (satellite event of 8th International Congress of Quantum Chemistry in Prag, Czech Republic) Organized by Technical University of Wroclaw University of Wroclaw Location: The conference will be held in Wroclaw, major city in southwestern Poland (Lower Silesia). Wroclaw is connected by direct flights with Warsaw, Frankfurt and Dsseldorf as well as by train and bus transportation with other major European cities. About the conference Previous conferences COMPUTERS IN CHEMISTRY were held in Wroclaw in 1986 and 1988. The conference in 1994 will cover all aspects of computer applications in chemistry and related sciences focusing on review of recent software and hardware developments in this rapidly expanding interdisciplinary field as well as teaching computational chemistry. Student presentations are encouraged. Commercial hardware and software presentations are being planned too. Proceedings : Abstracts of all contributions will be printed in conference materials. Original scientific contributions will be published in special issue of international journal COMPUTERS & CHEMISTRY. The manuscripts should be submitted during first day of the conference at the registration desk. The manuscripts will follow the regular editorial and refereeing procedure. COMPUTERS & CHEMISTRY publishes papers on theoretical and experimental research representing developments in the application of information sciences, particularly computers and computational methods, to diverse problems addressed in all branches of chemistry. Besides research papers also application/software notes or software reviews are acceptable for publication in COMPUTERS & CHEMISTRY ****************************************************************** WORKSHOP ON COMPUTATIONAL METHODS FOR LARGE MOLECULAR SYSTEMS Wroclaw, June 25-26, 1994 part of the 3-rd conference "COMPUTERS IN CHEMISTRY" and Satellite Symposium of 8th International Congress of Quantum Chemistry (possible microbus transportation from Prague to Wroclaw on June 24, 1994) This workshop organized in collaboration with National Institute of Standards and Technology and Center for Advanced Research in Biotechnology in Gaithersburg, MD, USA is devoted to review recent progress in development of quantum chemical methods for modelling large molecular systems. Many chemical processes important for biotechnology or materials science can not be modelled now at molecular level due to the extensive size of molecular systems involved or unsufficient precision of contemporary computational methods. Therefore development of new methods and techniques extending existing boundaries for modeling may open new avenues for rational design of new biocatalysts and new materials with desired properties. Bringing together several leading scientists having important contributions in this field should open the possibility to initiate or expand ongoing collaborations, create future joint projects including academic and commercial sector and introduce graduate students into this rapidly growing field. Planned lectures will cover among others following topics: model potentials and reaction fields, applications of local density functionals in modelling chemical reactions, direct SCF, MP2 methods, molecular frozen fragment approach, treatment of relativistic effects, multicenter multipole expansions, design of optimal catalysts, modeling protein folding etc. Refereed contributions will be published in special issue of international journal COMPUTERS & CHEMISTRY. Preliminary registration form: [ ] I wish to receive the Second Circular [ ] I intend to attend the entire Conference (June 23-26, 1994) [ ] I intend to attend the workshop only (June 25-26, 1994) [ ] I wish to present an oral contribution [ ] I wish to present a poster [ ] I wish to demonstrate a program name of the hardware/software platform......................... [ ] I plan to submit a manuscript for publication in Computers & Chemistry Tentative Title of the Contribution: .................................................................. .................................................................. .................................................................. First name..................... Last Name ..................... Title.......................... Institution............................................... .................................................................. Postal address for correspondence ................................................................. .................................................................. Electronic mail: FAX Telephone Date Please respond until November 30, 1993 to : COMPUTERS IN CHEMISTRY W. Andrzej Sokalski - Conference Secretary Wroclaw Technical University I-30, room 314 A-3 Wyb. Wyspianskiego 27, 50-370 WROCLAW, POLAND e-mail: COMPCHEM@PLWRTU11.BITNET FAX (+48)-(71)-223664 tel. (+48)-(71)-202894, 202457  From Leif.Laaksonen@csc.fi Tue Oct 19 14:28:18 1993 Date: Tue, 19 Oct 1993 12:28:18 +0200 Message-Id: <199310191028.AA25065@csc.fi> To: chemistry@ccl.net From: Leif.Laaksonen@csc.fi Subject: Summary to my request about vDW radii The following is a summary of the responses to my question about the van der Waals radii of the elements. Thank you very much for your help. Original posting: Hi netters, All the molecular modelling packages (and many more) have a list of the van der Waals radii for the different elements. Of course there is no reference in any table. From where are these values collected? Yes I know about the paper by Bondi (JPC 68(1964)441) but there must be more. Thank you for your help. -leif laaksonen ---- Responses: ---- From: carlos@extreme.bio.cornell.edu (Carlos Faerman) "a revision of van der waals atomic radii for molecular crystals N,O,F,S,Cl,Se,Br and I bonded to carbon" Acta Cryst. B41, 274 (1985) and references therein. S.C.Nyburg and C. H. Faerman carlos h. faerman carlos@extreme.bio.cornell.edu ---- From: jle@world.std.com (Joe M Leonard) I've never been able to find a comprehensive list, so I'd appreciate hearing if somebody gives you references for the whole periodic table! Joe Leonard jle@world.std.com ---- From: robyn@scripps.edu (Robyn Stanfield) Hi, I don't know if this will help, but we use atomic radii from a Gelin and Karplus paper for calculating atomic contacts: Gelin, B.R. and Karplus, M. Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment. 1979 Biochemistry, 18:1256-1268. -Robyn Stanfield robyn@scripps.edu ---- From: Alex Tropsha A good recent reference is: Emsley, J. The Elements. Clarendon Press, Oxford, 1989. ---- From: MARTIN%CMDA The Handbook of Chemistry and Physics lists radii. I think also the people from the Cambridge Structural Database also published a list. The problem, of course, is that for molecular mechanics there is a correlation between the softness used for atoms and the radius. If soft atoms are used, then the radius can be bigger. Hence, the radius makes total quantitative sense only in the context of the hardness of the atoms. Probably also the height of the torsions & the strength of the angle bending & bond stretching terms. For our molecular graphics program we liked the looks of somewhat smaller radii such as those used by Scheraga in his earlier versions of ECEP. These radii are smaller because the structures are optimized by torsional rotations only & everything fits better to experiment if "smaller" atoms are used. If you really care, I could dig up the reference to these values. They are >from the 1970's however. Yvonne Martin, Senior Project Leader ---- From: GUSTAVO@nickel.laurentian.ca Hi, This is a follow-up to the question by Leif Laaksonen on the atomic radii. The overall situation on the use of radii is far from uniform: Bondi's radii (A. Bondi, J.Phys.Chem. 68 (1964) 441) and Pauling's radii (L. Pauling, The nature of the Chemical Bond, Cornell, Ithaca, 1960) are used sometimes, although nowadays there's some tendency to use the values given by Gavezzotti (A. Gavezzotti, JACS 105 (1983) 5220). The latest CRC Handbook of Chemistry and Physics will show slightly different values; other quoted source is: J.L. Finney, J. Mol. Biol. 96 (1975) 721. The experimental values depend on the property observed (critical constants, diffusion coefficients, etc) and the model used to interpret them. The same can be said for the radii computed from theory. [For some discussion of this and comparisons with radii derived from electron densities, see J.Comp.Chem. 12 (1991) 1198.] For some metals or unusual elements, the radii are commonly 'made-up', giving just a flat value for most of them. For *qualitative* analyses, these differences may matter little (e.g., when studying only the distribution of electrostatic potential over the van der Waals surface, solvent-accessible surface or the like). Quantitatively, the differences can be important. Thus, it might perhaps be better not to restrict analyses to a single surface but to give results estimated (or averaged) within a reasonable range of values of atomic radii. Hope this helps, G. Arteca ---- From: "Christopher J Cramer-1" For thought: Gustavo A. Arteca recently posted some commentary which I have been thinking a lot about lately, and I'd like to offer my own paraphrase. van der Waals radii are not physical constants, they are parameters. I make this point because I see a lot of modeling done which involves taking the "van der Waals surface" and evaluating some property there. While this particular property may have nothing to do with the physical measurements which were used to develop the vdW radii from some OTHER physical model, nevertheless they are justified as somehow being "better" than parameters which are in fact optimized for EXACTLY the property being studied. My own personal irritation arises when people use Bondi's values, which are derived from X-ray analysis of crystal packing, to create solute cavities in continuum solvation modeling, and seem to regard this as the only God-given legitimate cavity which may be used. Actually optimizing better radii to fit solvation free energies is regarded as somehow "cheating". It makes me wonder what Bondi did to achieve such divine status . . . Perhaps to end on an amusing note, I have always found it fascinating that Gaussian's SCRF model develops a spherical cavity radius by calculating the 0.001 au isodensity surface, scaling the enclosed volume by 1.44, taking the radius which would deliver that volume for a sphere, and then adding 0.5 angstroms. Hey, if Gaussian is willing to be parametric, who am I to say nay? CJC P.S. While my own personal prejudice is showing, naturally I am interested in hearing other's opinions. P.P.S. The Gaussian work is primarily published by Wiberg, Wong, and Frisch, and is quite nice -- no slur is implied or intended. ---- From: hogue@calumet.den.mmc.com (Pat Hogue 1-2183) Dear Netters: Is is logical to think of the van der Waals surface of organic molecules as the analog of the solid state Fermi surface? Pat Hogue ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Telefax: 358 0 4572302 FIN-02101 Espoo | Voice Mail: 358 486257407 FINLAND | Mail: Leif.Laaksonen@csc.fi NOBODY can write a thousand- word essay on what he did during the summer! It's ridiculous! Charlie Brown ------------------------------------------------------------------- From m10!frisch@uunet.UU.NET Tue Oct 19 04:03:55 1993 Message-Id: <9310191204.AA10529@relay1.UU.NET> Date: Tue, 19 Oct 93 08:03:55 EDT From: m10!frisch@uunet.uu.net (Michael Frisch) Subject: Re: Q: 486+unix+g92 works? To: chemistry@ccl.net JKong@ac.dal.ca Dear netters, A friend of mine has a question: Can one install a unix system like linux on a 486 and then run quantum chemistry software like G92? I thought so in principle but I am not sure. Jing A version of Gaussian 92 is available which runs on 486 systems under Microsoft Windows. Contact info@gaussian.com for details. Making the unix workstation version of G92 run under linux is conceivable but would probably be a fair amount of work, which no one has attempted yet. Mike Frisch ------- From young@slater.cem.msu.edu Tue Oct 19 04:24:16 1993 Date: Tue, 19 Oct 93 08:24:16 -0400 From: young@slater.cem.msu.edu (Dave Young) Message-Id: <9310191224.AA03467@slater.cem.msu.edu> To: chemistry@ccl.net Subject: Symmetry in SCF calculations There was a recent question about convergence of SCF calculations in various symmetries. The import reason for using symmetry is that the calculation can be simplified by how it deals with the symmetry of the ORBITALS not the atoms. The first point to note is that different programs will use symmetry in different ways. Some will allow orbitals of different symmetries to mix if that is where the initial guess happens to send the SCF. Other programs (i.e. COLUMBUS) will keep different symmetry orbitals entirely separate if you have defined them that way. If a calculation converges in one symmetry then it will converge in any other applicable symmetry IF THE INITIAL GUESS IS CLOSE ENOUGH. Your best bet for getting a difficult calculation to converge is to use a symmetry that keeps as many of the orbitals in different irreducable representations as possible. These sorts of problems are often seen in transition metals, where there are a number of d orbitals with nearly the same energy. Often if a calculation does converge in a lower symmetry, you will get a very contaminated wave function (mixing of orbitals that should be different symmetries). There was a recent question about convergence of SCF calculations in various symmetries. The import reason for using symmetry is that the calculation can be simplified by how it deals with the symmetry of the ORBITALS not the atoms. The first point to note is that different programs will use symmetry in different ways. Some will allow orbitals of different symmetries to mix if that is where the initial guess happens to send the SCF. Other programs (i.e. COLUMBUS) will keep different symmetry orbitals entirely separate if you have defined them that way. If a calculation converges in one symmetry then it will converge in any other applicable symmetry IF THE INITIAL GUESS IS CLOSE ENOUGH. Your best bet for getting a difficult calculation to converge is to use a symmetry that keeps as many of the orbitals in different irreducable representations as possible. These sorts of problems are often seen in transition metals, where there are a number of d orbitals with nearly the same energy. Often if a calculation does converge in a lower symmetry, you will get a very contaminated wave function (mixing of orbitals that should be different symmetries). Dave Young young@slater.cem.msu.edu youngdc@msucem From bruce@dggpi2.chem.purdue.edu Tue Oct 19 03:56:11 1993 Date: Tue, 19 Oct 93 08:56:11 -0500 From: bruce@dggpi2.chem.purdue.edu (Bruce Luxon) Message-Id: <9310191356.AA00731@dggpi2.chem.purdue.edu> To: CHEMISTRY@ccl.net Subject: MORASS 2D NOE UPDATE PROGRAM UPDATE: MORASS 2.0 NOE CONSTRAINT PACKAGE FOR MIN/MD Several MORASS users had a problem TEX'ing one of the documents (MORASS 1.0 documentation) from our FTP anonymous directory. To remedy this I have also included a PostScript file (morass1.ps) of this document in the distribution. This file is also available by itself for anyone who has the rest of the distribution in our FTP anonymous as pub/morass/morass1.ps. To obtain MORASS 2.0 by ftp anonymous: 1> ftp dggpi2.chem.purdue.edu 2> name: anonymous 3> password: your email address 4> binary 5> cd pub/morass (For the RISC system 6000 version: cd pub/morass/r6000) 6> get morass.tar.Z 7> quit morass.tar.Z contains all the source code, documentation(in LaTex & ps), a unix "help" script and test input files. Use the following unix commands to uncompress and "detar" the files: %> uncompress morass.tar.Z %> tar xvf morass.tar If you have difficulties please feel free to contact me anytime. A short program description follows - contact me for more info. The program MORASS, (Multispin Overhauser Relaxation AnalysiS and Simulation) analyzes 2D NMR NOESY data of nucleic acids and proteins to evaluate cross-relaxation rates (sigma_ij) from which interproton distances are obtained. NOESY derived interproton distances are used to conduct constrained molecular dynamics and molecular mechanics studies on proteins and DNA/RNA. MORASS was written in the labs of Professor David Gorenstein at Purdue University in W. Lafayette, IN. MORASS calculations are carried out by matrix methods involving the relaxation rate matrix specified by the set of simultaneous Bloch equations. MORASS also calculates a NOESY spectrum given a model structure including proton coordinate positions. An important aspect of MORASS is that it has the capability to incrementally merge the experimental NOESY values into the simulated matrix. This has a great deal of value in that it permits the experimental values to be "massaged in" gradually allowing a reasonably continuous transformation of the model structure into the experimentally consistent one. This is particularly important for experimental structures that deviate significantly from model-built ones. These are often some of the most interesting ones in practice for DNA, RNA and Proteins. BRUCE ____________________________________________________________________________ | | | |"You can't always get what you want, | Dr. Bruce A. Luxon | | But if you try sometimes, | Chemistry Department | | You'll get what you need ..." | Purdue University | | | W. Lafayette, IN 47907 | | Mick Jagger | (317)494-5289; Fax (317)494-0239 | | | bruce@dggpi2.chem.purdue.edu | |______________________________________|___________________________________| From windemut@cumbnd.bioc.columbia.edu Mon Oct 18 19:34:54 1993 From: Andreas Windemuth Message-Id: <9310191534.AA00429@cumbnd.bioc.columbia.edu> Date: Mon, 18 Oct 93 23:34:54 -0400 To: chemistry@ccl.net Subject: Re: Q: 486+unix+g92 works? > Can one install a unix system like linux on a 486 and then run > quantum chemistry software like G92? > I thought so in principle but I am not sure. I have a 586-PC from ALR that I run NEXTSTEP on. I have run molecular dynamics at 2-3 times the speed of an SGI 220 GTX. You need either "f2c" or a third party fortran compiler (Absoft sells one for NEXTSTEP) to run chemistry software. I have never had trouble using f2c (which is free) to run fortran code on unix (NeXT) machines. For example, X-plor was successfully compiled this way on a NeXT some time ago. I am very happy with the ALR/NEXTSTEP combination, I get 2/3 the computing power of an SGI Indigo 2 for a small fraction of the price ($6000). And NEXTSTEP is a great general productivity environment. Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Dept. of Biochemistry and Biophysics, BB-221 |630 West 168th St. | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut@cumbne.bioc.columbia.edu +-------------------------------------------------------------------- From DSMITH@uoft02.utoledo.edu Tue Oct 19 12:14:39 1993 Date: Tue, 19 Oct 1993 17:14:39 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: G92 for Windows To: chemistry@ccl.net Message-Id: <01H4AYMINZKY007S4Q@UOFT02.UTOLEDO.EDU> There has been some recent (and past) traffic about Gaussian 92 for Windows on PCs. I have had this for several months now, and should make some comments here. Bottom line -- the product is excellent! I run on a Dell 450DE/2 DGX, which is a 50 MHz speed doubled machine, with 32 MB of RAM and a 1.4 GB hard disk. Approximately 450 MB are set aside for scratch for Gaussian. The windows interface is nice. No molecular graphics, but a nice GUI for job setup and control. It is pretty intuitive, and really does not require that you read the manuals. I use either the AVS Chemistry Viewer or Hyperchem 3.0 for my molecular graphics. G92 runs very efficiently and quickly under Windows -- certainly better and faster than G86 on my old MicroVAX II (now a boat anchor somewhere, I hope). It does not substantially affect Windows and other applications when running in the background, so I can use Word, Excell, even HyperChem graphics without G92 stealing so much time that seconds elapse between my mouse click and an action. The same is not true, for example, of HyperChem running a calculation in the background. G92 for Windows is a fully functional version of the program. I tend to use it to run test jobs and to examine ideas before spending server or Cray time. I have run 6-31+G* optimizations at the RHF and CAS levels on systems as large as 9 and 5 heavy atoms, respectively, and MP2 single points with no complaints. If I was limited in money and resources, I would definitely buy and use G92 for Windows. Doug Douglas A. Smith Assistant Professor of Chemistry and of Medicinal and Biological Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From SHAUN%JASON.DECNET@relay.the.net Sat Oct 19 13:56:06 1993 Date: 19 Oct 1993 19:56:06 -0600 (CST) From: "Shaun D. Black" Subject: Partial specific volumes needed To: chemistry@ccl.net Message-Id: <01H4B4GXQCOY001CBF@nic.the.net> Does anyone know the values for partial specific volumes of heme (protoporphyrin IX), FMN (flavin mononucleotide), and/or FAD (flavin adenine dinucleotide)? I would greatly appreciate any information or leads. I've run out of references and leads! Thanks in advance. Cheers, =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From V098Q3NV@ubvms.cc.buffalo.edu Tue Oct 19 18:54:56 1993 Date: Tue, 19 Oct 1993 22:54:56 -0400 (EDT) From: V098Q3NV@ubvmsb.cc.buffalo.edu Subject: looking for code to find screw axis To: chemistry@ccl.net Message-Id: <01H4BANBDXAQ8WWCZP@ubvms.cc.buffalo.edu> Organization: University at Buffalo Hello Netters! I'm looking for some source code that calculates a screw axis (an axis about which both a rotation and a translation occur) that relates two (chemically identical) species in cartesian space Thanks in advance, John Manchester Roswell Park Cancer Institute / Battelle PNL gg339@jarvis.pnl.gov voice 509/372-4660 fax 509/375-6631