From tamasgunda@tigris.klte.hu Fri Mar 7 03:27:42 1997 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.8.3/950822.1) id CAA21311; Fri, 7 Mar 1997 02:43:19 -0500 (EST) Message-Id: <199703070743.CAA21311@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Fri, 07 Mar 1997 08:41:45 EST Comments: Authenticated sender is X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Fri, 7 Mar 1997 08:41:45 +1 Subject: Re: CCL:PDB format Documented? Reply-To: tamasgunda@tigris.klte.hu Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Nicholas C. DeMello wrote > > Folks, > > Can someone point me to documentation in the literature > regarding the PDB file format? I've noticed that > several software products have slightly different > "PDB" output formats for small molecules. I'm > interested in getting more information on what the > standard says... I'm just having trouble finding > where that standard is documented :-) > > Pointers to HTTP sites, journal articles, or other > places where the PDB standard is authoritatively > described would be appreciated. Thanks, > Hi, 2-3 years ago I asked for and got the documentation of PDB files from Brookhaven itself. Try now the url www.pdb.bnl.gov Take into consideration, that although the PDB molfile format itself is a strict one, the informations it contains may be redundant and not all of the possible fields are necessary to include. In other words, the chemical symbols and the coordinates of the atoms are a must, as these define the structure, nearly all the other infos/fields can be neglected. It depends on the creator program, what is included and what not in the file, and on the intelligence of the program using the file, how can it digest the content. For example, the hydrogens and atom connectivities may be included or not, this is usually a choice in the creator program. Whether the user program can add hydrogens and generate connectivities, it is another question. For small molecules (not peptides) the atom structural fields must begin with the token HETATM, and the lines should contain at least the coordinates and the atom symbols. Substructure information may be included or not. The connectivities are contained by the CONECT lines, but it is not necessary to include. The file must be ended with END. Tamas Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From vkitzing@sunny.mpimf-heidelberg.mpg.de Fri Mar 7 05:27:42 1997 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.8.3/950822.1) id EAA21957; Fri, 7 Mar 1997 04:44:52 -0500 (EST) Received: from sunny.mpimf-Heidelberg.mpg.de by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA24923; Fri, 7 Mar 97 10:44:42 +0100 Received: from [149.217.50.47] (mac20) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA05139; Fri, 7 Mar 97 10:42:50 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 7 Mar 1997 10:41:40 +0100 To: , chemistry@www.ccl.net From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:HYDRATED METAL IONS At 15:33 Uhr 06.03.1997, wrote: >I HAVE A COLLEAGUE WORKING ON AN ION CONDUCTING CHANNEL AND IS REQUESTING INFO >ON 'EFFECTIVE' HYDRATED ION SIZE. ANY TAKERS FOR A SUITABLE REFERENCE ? The classical reference is: E. R. Nightingale Jr. (1959). "Phenomenological Theory of Ion Solvation. Effective Radii of Hydrated Ions." Journal of Physical Chemistry [#361] 63(9) 1381-1387. One can also use the result of Adams et al and interpolate: David J. Adams, Terry M. Dwyer and Bertil Hille (1980). "The Permeability of Endplate Channels to Monovalent and Divalent Metal Cations." The Journal of General Physiology 75 493-510. An alternative source for alkali metal ions is: Dikeos Mario Soumpasis, Michel Robert-Nicoud and Thomas M. Jovin (1987). "B-Z DNA conformational transition in 1:1 electrolytes: dependence upon counter-ion size." Letters of the Federation of European Biochemical Societies [#481] 213(2) 341-344. ====================================================================== Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69115 Heidelberg Germanny email: vkitzing@sunny.mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From mebel@linsgi.iams.sinica.edu.tw Fri Mar 7 06:27:41 1997 Received: from linsgi.iams.sinica.edu.tw for mebel@linsgi.iams.sinica.edu.tw by www.ccl.net (8.8.3/950822.1) id FAA22207; Fri, 7 Mar 1997 05:50:27 -0500 (EST) Received: by linsgi.iams.sinica.edu.tw (940816.SGI.8.6.9/930416.SGI.AUTO) id TAA18356; Wed, 7 Mar 2001 19:21:34 -0800 Date: Wed, 7 Mar 2001 19:21:30 -0800 (PST) From: "A. Mebel" To: chemistry@www.ccl.net Subject: HONDO Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: Can someone give me the e-mail address of the HONDO team where I can by a license for this program? Thank you very much in advance. Alexander Mebel From brain@amethyst.Chemie.Uni-Dortmund.de Fri Mar 7 10:27:45 1997 Received: from mail.Germany.EU.net for brain@amethyst.Chemie.Uni-Dortmund.de by www.ccl.net (8.8.3/950822.1) id JAA23850; Fri, 7 Mar 1997 09:30:51 -0500 (EST) Received: by mail.Germany.EU.net with SMTP (5.59+:34/EUnetD-2.6.1.i) via EUnet id PAA11220; Fri, 7 Mar 1997 15:30:50 +0100 Received: by amethyst.Chemie.Uni-Dortmund.de (AIX 3.2/UCB 5.64/OCB-loki-1.0-31011995) id AA12556; Fri, 7 Mar 1997 15:28:54 +0100 From: brain@amethyst.Chemie.Uni-Dortmund.de (Christoph Schwittek) Message-Id: <9703071428.AA12556@amethyst.Chemie.Uni-Dortmund.de> Subject: electrochemistry To: chemistry@www.ccl.net Date: Fri, 7 Mar 1997 15:28:54 +0100 (NFT) X-Mailer: ELM [version 2.4 PL2] Content-Type: text A more practical question: What time does it take for a molecule to be reduced by a catode in solution? How is this time related to the typical timescale of diffusion and to the time the electronic relaxation of the filled orbitals? (Is the latter important at all, what is the timescale?) Can anybody help me? C.Schwittek From rew@qc.ag-berlin.mpg.de Fri Mar 7 11:27:54 1997 Received: from oberon.qc.ag-berlin.mpg.de for rew@qc.ag-berlin.mpg.de by www.ccl.net (8.8.3/950822.1) id LAA25281; Fri, 7 Mar 1997 11:11:46 -0500 (EST) Received: by oberon.qc.ag-berlin.mpg.de (AIX 3.2/UCB 5.64/4.03) id AA15713; Fri, 7 Mar 1997 17:11:46 +0100 From: rew@qc.ag-berlin.mpg.de (Rene Windiks) Message-Id: <9703071611.AA15713@oberon.qc.ag-berlin.mpg.de> Subject: Symmetry in DSOLID To: chemistry@www.ccl.net Date: Fri, 7 Mar 1997 17:11:45 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear all, since short time I using DSolid (DMOL for periodic structures) to calculate crystals with large unit cells. The structures have symmetry. So it should be better exploiting symmetry. In the manual is written, that DSolid treats crystalline systems as having P1 symmetry. I asked the author of this program, B. Delley, and he answered that the program is able exploiting symmetry, but not by default. Unfortunately, he did not tell me how. Does somebody know, how one takes symmetry into consideration in DSolid ? Has this something to do with the SYMDEC file? Is it similar as in DMOL? Best wishes, Rene Windiks -- ____________________________________________ Chemical Institute Quantum Chemistry Working Group Humboldt University Berlin Leader: Prof. J. Sauer * Rene Windiks Jaegerstr. 10/11 D-10117 Berlin Germany Tel. +49-30-20192-306 Fax. +49-30-20192-302 e-mail: rew@qc.ag-berlin.mpg.de ____________________________________________ From daizadeh@indigo.ucdavis.edu Fri Mar 7 11:33:18 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id LAA25331; Fri, 7 Mar 1997 11:16:39 -0500 (EST) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id IAA22371; Fri, 7 Mar 1997 08:22:28 -0800 From: "Iraj Daizadeh" Message-Id: <9703070822.ZM22369@indigo.ucdavis.edu> Date: Fri, 7 Mar 1997 08:22:15 -0800 In-Reply-To: "nick.c" "CCL:PDB format Documented?" (Mar 6, 4:07pm) References: X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Re: CCL:PDB format Documented? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. The following url reference facilitated my understanding of the PDB format: http://www.pdb.bnl.gov/Format.doc/formatdoc.html#RTFToC56 Good Luck. Iraj Daizadeh Department of Chemistry University of California Davis, CA 95616 P.S. This file existed circa. 07/95 hopefully it's still there. On Mar 6, 4:07pm, nick.c wrote: > Subject: CCL:PDB format Documented? > > > Folks, > > Can someone point me to documentation in the literature > regarding the PDB file format? I've noticed that > several software products have slightly different > "PDB" output formats for small molecules. I'm > interested in getting more information on what the > standard says... I'm just having trouble finding > where that standard is documented :-) > > Pointers to HTTP sites, journal articles, or other > places where the PDB standard is authoritatively > described would be appreciated. Thanks, > > > > > > ____Nicholas C. DeMello, Ph.D.________________________________________ > > Online at MacTech Magazine, the Journal of Macintosh Programming > http://www.MacTech.com/ > _/ _/ _/ _/_/_/ _/ _/ > Chemistry: Nick@chem.UCLA.edu _/_/ _/ _/ _/ _/ _/_/_/ > MacTech: Online@MacTech.com _/ _/_/ _/ _/ _/ _/ > http://www.chem.ucla.edu/~nick/ _/ _/ _/_/_/ _/ _/ > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: online@mactech.com > -- Original Sender From: Address: online@mactech.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html >-- End of excerpt from nick.c From youngd2@mallard.duc.auburn.edu Fri Mar 7 11:36:40 1997 Received: from mallard.duc.auburn.edu for youngd2@mallard.duc.auburn.edu by www.ccl.net (8.8.3/950822.1) id LAA25324; Fri, 7 Mar 1997 11:16:12 -0500 (EST) Received: from wood.mail.auburn.edu by mallard.duc.auburn.edu (SMI-8.6/SMI-SVR4) id KAA23191; Fri, 7 Mar 1997 10:16:10 -0600 Received: by wood.mail.auburn.edu (SMI-8.6/SMI-SVR4) id KAA03874; Fri, 7 Mar 1997 10:16:10 -0600 Date: Fri, 7 Mar 1997 10:16:10 -0600 From: youngd2@mail.auburn.edu Message-Id: <199703071616.KAA03874@wood.mail.auburn.edu> To: CHEMISTRY@www.ccl.net Subject: Chem Topic: Excited States Hello all, I have written the following short essay for my users and am posting it here for your enjoyment and comments. Please let me know if I missed any important techniques. My compilation of chemical topics can be accessed via the web at URL http://www.auburn.edu/~youngd2/topics/contents.html Dave Young youngd2@mail.auburn.edu --------------------------------------------------------------------------- Calculating Electronic Excited States David Young Division of University Computing 144 Parker Hall Auburn University Auburn, AL 36849 INTRODUCTION This is an introduction to the techniques used for the calculation of electronic excited states of molecules (sometimes called eximers). Specifically, these are methods for obtaining wave functions for the excited states of a molecule from which energies and other molecular properties (such as dipole moments) can be calculated. These calculations are an important tool for the analysis of spectroscopy, reaction mechanisms and other excited state phenomena. These same techniques may also be necessary to find the ground state wave function. Determining the ground state electron configuration can be particularly difficult for compounds with very low energy excited states. This document is concerned only with ab initio calculations. These are calculations in which only the theory of quantum mechanics is applied with no experimental data used in the calculation. Some of these techniques are also applicable to certain classes of semiempirical calculations. This write up is not intended to be a detailed description. It is meant to be a short introduction with a discussion of strengths and weaknesses of various methods. This should also serve as a check list of available methods when faced with computational difficulties. References are provided for more detailed discussions information. SPIN STATES Ab initio programs attempt to compute the lowest energy state of a specified multiplicity. Thus calculations for different spin states will give a lowest energy state and a few of the excited states. This is most often done to determine singlet - triplet gaps in organic molecules. CIS A single excitation configuration interaction (CIS) calculation is probably the most common way to get excited state energies. This is because it is one of the easiest calculations to perform. A configuration interaction calculation uses molecular orbitals that have been optimized typically with a Hartree-Fock (HF) calculation. Generalized Valence Bond (GVB) and multi-configuration self consistent field (MCSCF) calculations can also be used as a starting point for a configuration interaction calculation. A CIS calculation starts with this initial set of orbitals and moves one electron to one of the virtual orbitals from the original calculation. This gives a description of one of the excited states of the molecule, but does not change the quality of the description of the ground state as double excitation CIs do. This gives a wave function of somewhat lesser quality than the original calculation since the orbitals have been optimized for the ground state. Often this results in the ground state energy being a bit low relative to the other states. A CIS calculation is not extremely accurate. However, it has the advantage of being able to compute many excited state energies easily. INITIAL GUESS If the initial guess for a calculation is very close to an excited state wave function, the calculation may converge to that excited state. This is typically done by doing an initial calculation then using it's wave function with some of the orbitals switched as the initial guess for another calculation. The advantage of this method is that the orbitals have been optimized for the excited state. The disadvantage is that there is no guarantee that it will work. If there is no energy barrier between the initial guess and the ground state wave function, the entire calculation will converge back to the ground state. The convergence path may take the calculation to an undesired state in any case. A second disadvantage of this technique applies if the state is the same symmetry as a lower energy state. There is no guarantee that the state obtained is completely orthogonal to the ground state. This means that the wave function obtained may be some mix of the lower energy state and a higher energy state. In practice, this type of calculation only converges to a higher state if a fairly reasonable description of the excited state wave function is obtained. Mixing tends to be a significant concern if the orbital energies are very close together or the system is very sensitive to correlation effects. BLOCK DIAGONAL HAMILTONIANS Most ab initio calculations use symmetry adapted molecular orbitals. Under this scheme, the Hamiltonian matrix is block diagonal meaning that every molecular orbital will behave according to the symmetry of one of the irreducible representations of the point group. No orbitals will be described by a mixing of different irreducible representations. Some programs such as COLUMBUS, DMOL and GAMESS actually set up a separate matrix for each irriducible representation and solve them separately. Such programs give the user the option of defining how many electrons are of each irreducible representation. This defines the symmetry of the wave function. In this case the resulting wave function is the lowest energy wave function of a particular symmetry. This is a very good way to get excited states which differ in symmetry from the ground state and are the lowest energy state within that symmetry. HIGHER ROOTS OF A CI For configuration interaction calculations of double excitations or higher, it is possible to solve the CI super-matrix for the second root, third root, fourth root, etc. This is a very reliable way to get a high quality wave function for the first few excited states. For higher excited states, CPU times become very large since more iterations are generally needed to converge the CI calculation. NEGLECTING A BASIS FUNCTION Some programs, such as COLUMBUS, allow a calculation to be done with some orbitals completely neglected from the calculation. For example, in a transition metal compound you could work with four d functions so that the calculation would have no way to occupy the function that was left out. This is a reliable way to get an excited state wave function even when it is not the lowest energy wave function of that symmetry. However it might take a bit of work to construct the input file depending upon the individual program. IMPOSING ORTHOGONALITY - DFT TECHNIQUES Traditionally, excited states have not been one of the strong points of density functional theory. This is due to the difficulty in ensuring orthogonality to the ground state wave function when no wave functions are being used in the calculation. The easiest excited states to find using density functional theory techniques are those which are the lowest state of a given symmetry thus using a ground state calculation. A promising techniques is one which uses a variational bound for the average of the first M states of a molecule. A few other options have been examined. However, there is not yet a large enough volume of work applying DFT to excited states to predict the reliability of any of these techniques. IMPOSING ORTHOGONALITY - QMC TECHNIQUES Quantum Monte Carlo (QMC) methods are computations which use a statistical integration to calculate integrals which could not be evaluated analytically. These calculations can be extremely accurate, but often at the expense of enormous CPU times. There are a number of methods for getting excited state energies >from QMC calculations. These methods will only be mentioned here and are explained more fully in the text by Hammond, Lester and Reynolds referenced at the end of this document. Computations done in imaginary time can yield an excited state energy by a transformation of the energy decay curve. If an accurate description of the ground state is already available, an excited state description can be obtained by forcing the wave function to be orthogonal to the ground state wave function. Diffusion and Green's function QMC calculations are often done using a fixed node approximation. Within this scheme, the nodal surfaces used define the state that is obtained as well as ensuring an antisymmetric wave function. Matrix QMC procedures similar to configuration interaction treatments have been devised in an attempt to calculate many states concurrently. These methods are not yet well developed as evidenced by oscillatory behavior in the excited state energies. FURTHER INFORMATION There are many books on the principles of quantum mechanics and every physical chemistry text has an introductory treatment. The work which I am listing here is a two volume set with each chapter broken into a basic and advanced sections making it excellent for both intermediate and advanced users. C. Cohen-Tannoudji, B. Diu, F. Laloe "Quantum Mechanics Volumes I & II" Wiley-Interscience (1977) For an introduction to quantum chemistry see D. A. McQuarrie "Quantum Chemistry" University Science Books (1983) A graduate level text on quantum chemistry is I. N. Levine "Quantum Chemistry" Prentice Hall (1991) For quantum Monte Carlo methods, order the following book using ISBN 981-02-0322-5 because the title is listed incorrectly in 'Books in Print'. B. L. Hammond, W. A. Lester, Jr., P. J. Reynolds "Monte Carlo Methods in Ab Initio Quantum Chemistry" World Scientific (1994) For density functional theory see R. G. Parr, W. Yang "Density-Functional Theory of Atoms and Molecules" Oxford (1989) There is a comprehensive listing of all available molecular modeling software and structural databanks, free or not, in appendix 2 of "Reviews in Computational Chemistry Volume 6" Ed. K. B. Lipkowitz and D. B. Boyd, VCH (1995) --------------------------------------------------------------------------- From tvd@msi.com Fri Mar 7 14:27:46 1997 Received: from bioc1.msi.com for tvd@msi.com by www.ccl.net (8.8.3/950822.1) id NAA26455; Fri, 7 Mar 1997 13:50:54 -0500 (EST) Received: from iris69.msi.com by bioc1.msi.com (5.64/0.0) id AA14320; Fri, 7 Mar 97 10:50:24 -0800 Received: by iris69.msi.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@www.ccl.net id KAA15447; Fri, 7 Mar 1997 10:50:28 -0800 Date: Fri, 7 Mar 1997 10:50:28 -0800 From: tvd@msi.com (Ton van Daelen) Message-Id: <199703071850.KAA15447@iris69.msi.com> To: CHEMISTRY@www.ccl.net Subject: ACS seminar on Cerius2 software developer's kit To all software developers out there... Molecular Simulations is organizing a seminar on the Cerius2 Software Developer's Kit. The seminar is free of charge, but please sign up soon as space is limited. With best regards - Ton van Daelen ---------------------------------------------- Cerius2 Software Developer's Kit Seminar ACS San Fransisco Rm 276, Moscone Convention Center 9:00am-11:00am, April 14, 1997 During the ACS meeting in San Francisco MSI is organizing a seminar on the Cerius2 software developer's toolkit (C2.SDK). C2.SDK allows you to plug your own chemistry applications into MSI's Cerius2 modeling environment. You can link in existing software or develop entirely new applications. You concentrate on the scientific side of your program and C2.SDK takes care of the molecular graphics, window management, and data visualization. C2.SDK is used to develop scientific applications that solve research problems in fields including polymer science, rational drug design, combinatorial chemistry, catalysis, chemical reactions, and protein chemistry. The C2.SDK toolkit consists of a rich API set dealing with all aspects of interfacing chemistry codes, including GUI design, structure visualization, graphing, and volumetric display. Applications can be written in FORTRAN, C, or C++. The seminar will also discuss imminent SDK extensions that allow you to run applications through the internet, or an intranet, from a web browser interface on your desktop computer (PC, or MAC). In addition, we will demonstrate the use of C2.Tcl, the scripting language for the Cerius2 interface, for simple customization of routine modeling operations. C2.Tcl is based on the standard tcl scripting language, it lets you put together a simple application with its own graphical user interface in a matter of minutes. C2.Tcl aids in all aspects of molecular modeling, in particular in drug design and protein analysis. For more information about C2.SDK and C2.Tcl: http://www.msi.com/support/sdk/ The seminar is offered free of charge. Because space is limited, attendance is by registration only. The deadline for advanced registration is April 7. You can sign up at the following URL: http://www.acs.org/meetings/sanfran/exhwksp.html Ton van Daelen Product Manager Software Developer's Kit __o E: tvd@msi.com _`\<,_ Molecular Simulations P: -1-619-546-5329 (*)/ (*) 9685 Scranton Road F: -1-619-458-0136 /\/\/\/\/\/\ San Diego, CA 92121 W: http://www.msi.com Check out What's New in SDK on the SDK web pages at http://www.msi.com/support/sdk/ From ccl@www.ccl.net Thu Mar 6 05:44:12 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id FAA13143; Thu, 6 Mar 1997 05:25:34 -0500 (EST) Received: from chemik.chem.univ.gda.pl for czarek@rutyl.chem.univ.gda.pl by bedrock.ccl.net (8.8.3/950822.1) id FAA21651; Thu, 6 Mar 1997 05:25:17 -0500 (EST) Received: from rutyl.chem.univ.gda.pl by chemik.chem.univ.gda.pl with SMTP (1.37.109.4/16.2) id AA08037; Thu, 6 Mar 97 11:22:36 GMT Received: by rutyl.chem.univ.gda.pl (4.1/1.2-Univ. of Gdansk Chemistry) id AA06949; Thu, 6 Mar 97 11:15:40 +0100 Date: Thu, 6 Mar 1997 11:15:39 +0100 (MET) From: Cezary Czaplewski Subject: Re: CCL: G94 on LINUX To: R29CLOSE@ETSU.ETSU-TN.EDU Cc: chemistry@ccl.net In-Reply-To: <199702281901.OAA24055@bedrock.ccl.net> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 28 Feb 1997 R29CLOSE@ETSU.ETSU-TN.EDU wrote: > > It seems that I have a faulty memory chip. My computer, a Gateway > P6 has 64 Mbytes of new memory. The machine says all is ok on boot- > up. But I have random problems with the C-compiler quitting. > So maybe there is a memory problem. Gaussian suggested removing > or switching memory. Now it appear I can compile the program > with only 2x16 Mbytes of memory. There is also a possibility that memory is not completely bad but just too slow. I had similar problems - compilation of large code crashing with Signal 11. I have changed just one parameter in chipset features setup - "DRAM Write CAS Width" from 2T to 3T and now everything is OK. Cezary Czaplewski Faculty of Chemistry University of Gdansk From l504@cacr.ioc.ac.ru Thu Mar 6 18:27:40 1997 Received: from netserv2.free.net for l504@cacr.ioc.ac.ru by www.ccl.net (8.8.3/950822.1) id RAA17741; Thu, 6 Mar 1997 17:48:28 -0500 (EST) Received: from cacr.ioc.ac.ru by netserv2.free.net (8.6.12.C2.1/8s) with ESMTP id BAA08327 for ; Fri, 7 Mar 1997 01:48:17 +0300 Received: from [193.233.3.9] by cacr.ioc.ac.ru (8.6.12.C1/7s) with SMTP id BAA22327 for ; Fri, 7 Mar 1997 01:48:16 +0300 From: "Sergey Nogaev" Date: Fri, 7 Mar 97 02:48:59 +0400 Message-Id: <10142.l504@cacr.ioc.ac.ru> X-POPmail-Charset: IBM 8-Bit To: chemistry@www.ccl.net Subject: Studies on ozone Dear Collegues, We have just started the studies on ozone interaction with different molecules, mainly F- and Cl-containing, using quantum chemical methods. This is in connection with stratospheric ozone depletion problem. I would be happy if somebody share his/her experience in this field. Any references on this subject are appreciated. Sincerely, Sergey Nogaev, Institute of Chemical Physics, Russia. From wagenert@Mailer.Uni-Marburg.DE Fri Mar 7 05:34:02 1997 Received: from Mailer.Uni-Marburg.DE for wagenert@Mailer.Uni-Marburg.DE by www.ccl.net (8.8.3/950822.1) id FAA22056; Fri, 7 Mar 1997 05:21:52 -0500 (EST) Received: from localhost by Mailer.Uni-Marburg.DE (AIX 4.1/UCB 5.64/25.11.96) id AA20626; Fri, 7 Mar 1997 11:21:51 +0100 Date: Fri, 7 Mar 1997 11:21:51 +0100 (CET) From: Thomas Wagener X-Sender: wagenert@pprz03.HRZ.Uni-Marburg.DE To: Computational Chemistry List Subject: Fixing Electronic Configuration in Atoms Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, since I would like to add an polarization f-funtion to an ECP basis set of palladium I am trying to get the DFT atomic energies for the 1S, 3D and 3F configuration. The singlet state is no trouble at all as well as the 3D state which comes out automatically if I force the multiplicity to be a triplet but I am not able to fix the electronic configuration to the 3F configuration. Any attempt with guess=alter has failed so far though the program claims to switch the correct orbitals. So, is there any way to force Gaussian to optimize a fixed electronic configuration? TIA Thomas - "You are wrong! 2+2=5.8354! Please adjust your equipment accordingly." The Computer (your friend) ***************************************************************************** * Thomas Wagener * Tel: ++49-(0)6421-285561 * * FB Chemie * * * Phillips-Universitaet Marburg * Email: wagenert@mailer.uni-marburg.de * * * * * 35032 Marburg * * * Germany * * ***************************************************************************** From BISETTYK@wpogate.mlsultan.ac.za Fri Mar 7 06:37:37 1997 Received: from Raven.und.ac.za for BISETTYK@wpogate.mlsultan.ac.za by www.ccl.net (8.8.3/950822.1) id GAA22254; Fri, 7 Mar 1997 06:00:35 -0500 (EST) Received: from wpogate.mlsultan.ac.za (wpogate.mlsultan.ac.za [196.13.102.11]) by Raven.und.ac.za (8.8.3/8.7.3) with SMTP id NAA15556 for ; Fri, 7 Mar 1997 13:00:06 +0200 (SAT) From: "KRISHNA BISETTY" To: chemistry@www.ccl.net Date: Fri, 07 Mar 1997 12:45:00 +200 Subject: Request-Modeling Biopolymers X-Gateway: iGate, (WP Office) vers 4.04c - 1009 MIME-Version: 1.0 Message-Id: <331FF21D.04B3.0000@wpogate.mlsultan.ac.za> Content-Type: TEXT/PLAIN; Charset=US-ASCII Content-Transfer-Encoding: 7BIT Dear Netters, I am carrying out computational studies on some small peptide molecules as test cases in terms of reproducibility, and presently using the PC version of HyperChem. However, I would be grateful if someone could please recommend other suitable packages for both molecular mechanics and semi-empirical applications. We are investigating CHARMM and the pc version of Spartan. Any hints??? Thanking you in advance. Best wishes, --------------------------------------------------------------------------------------------- Vincent Bisetty Department of Chemistry ML Sultan Technikon Durban South Africa BisettyK@wpo.MLSULTAN. ac.za ------------------------------------------------------------------------------------------------- From info@chemcomp.com Fri Mar 7 16:27:50 1997 Received: from bobino.sefmedia.com for info@chemcomp.com by www.ccl.net (8.8.3/950822.1) id QAA27754; Fri, 7 Mar 1997 16:16:25 -0500 (EST) Received: from annex5-decarie-ppp-67.accent.net (annex5-decarie-ppp-67.accent.net [205.236.55.213]) by bobino.sefmedia.com (NTMail 3.02.10) with ESMTP id la001883 for ; Fri, 7 Mar 1997 16:15:49 -0500 Message-ID: <3320AFB3.194A@chemcomp.com> Date: Fri, 07 Mar 1997 16:15:47 -0800 From: General Information Organization: Chemical Computing Group Inc. X-Mailer: Mozilla 2.02E-KIT (Win95; U; 16bit) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: hayden@chemcomp.com Subject: New Computational Chemistry Software X-URL: http://www.ccl.net/ccl/welcome.html#2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Chemical Computing Group, Inc. has posted a text on the CCL Commercial Software List announcing the release of it's new Molecular Operating Environment (MOE). We encourage you to read about the latest advance in computational chemistry software by visiting: gopher://www.ccl.net/11/software/info-on-software/ or by visiting our website: http://www.chemcomp.com Thank you, Bill Hayden Vice President CHEMICAL COMPUTING GROUP, INC. From cmartin@curie.syr.edu Fri Mar 7 16:36:02 1997 Received: from curie.syr.edu for cmartin@curie.syr.edu by www.ccl.net (8.8.3/950822.1) id QAA27817; Fri, 7 Mar 1997 16:22:38 -0500 (EST) Received: by curie.syr.edu (950413.SGI.8.6.12/940406.SGI.AUTO) id PAA13353; Fri, 7 Mar 1997 15:48:05 -0800 Date: Fri, 7 Mar 1997 15:48:05 -0800 Message-Id: <199703072348.PAA13353@curie.syr.edu> From: Charles Martin To: youngd2@mail.auburn.edu Cc: CHEMISTRY@www.ccl.net Subject: CCL:Chem Topic: Excited States In-Reply-To: <199703071616.KAA03874@wood.mail.auburn.edu> References: <199703071616.KAA03874@wood.mail.auburn.edu> > > I have written the following short essay for my users and am > posting it here for your enjoyment and comments. Please let me know > if I missed any important techniques. > What about many-body theories? These include effective operator theory, many-body green's functions, etc. Chuck Martin -- ======================================================== || Charles H. Martin || || 2-004 Center for Science and Technology || || W. M. Keck Center for Molecular Electronics || || Department of Chemistry || || Syracuse University || || Syracuse, NY 13244 || -------------------------------------------------------- || cmartin@cat.syr.edu || || cmartin@rainbow.uchicago.edu || || CELL (315) 415-2093 || || OFFICE (315) 443-3754 || || LAB (315) 443-5928 || || FAX (315) 443-4070 || ======================================================== From csg.admin@amgen.com Fri Mar 7 16:40:14 1997 Received: from castle-smtp.amgen.com for csg.admin@amgen.com by www.ccl.net (8.8.3/950822.1) id PAA27494; Fri, 7 Mar 1997 15:38:45 -0500 (EST) Received: by castle-smtp.amgen.com; id MAA13806; Fri, 7 Mar 1997 12:25:01 -0800 Received: from www-int.amgen.com(138.133.10.135) by castle-smtp.amgen.com via smap (V3.1) id xma013800; Fri, 7 Mar 97 12:24:49 -0800 Received: from iago.amgen.com (iago [138.133.10.249]) by www-int.amgen.com (8.8.5/8.8.5) with SMTP id MAA00093 for ; Fri, 7 Mar 1997 12:24:48 -0800 (PST) Received: from amgen.com (amgengate) by iago.amgen.com (5.x/SMI-SVR4) id AA18154; Fri, 7 Mar 1997 12:24:42 -0800 Message-Id: Date: 7 Mar 1997 13:21:54 -0800 From: "csg admin" Subject: CCL-ACS seminar on Cerius2 To: CHEMISTRY@www.ccl.net X-Mailer: Mail*Link SMTP-QM 4.0.0 Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; Name="Message Body" Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by www-int.amgen.com id MAA00093 Mail*Link=AE SMTP CCL:ACS seminar on Cerius2 software devel= oper's kit To all software developers out there... Molecular Simulations is organizing a seminar on the=20 Cerius2 Software Developer's Kit. The seminar is free=20 of charge, but please sign up soon as space is limited. With best regards - Ton van Daelen ---------------------------------------------- Cerius2 Software Developer's Kit Seminar ACS San Fransisco Rm 276, Moscone Convention Center 9:00am-11:00am, April 14, 1997 During the ACS meeting in San Francisco MSI is organizing a seminar on the Cerius2 software developer's toolkit (C2.SDK). C2.SDK allows you to plug your own chemistry applications into MSI's Cerius2 modeling environment. You can link in existing software or develop entirely new applications. You concentrate on the scientific side of your program and C2.SDK takes care of the molecular graphics, window management, and data visualization. C2.SDK is used to develop scientific applications that solve research problems in fields including polymer science, rational drug design, combinatorial chemistry, catalysis, chemical reactions, and protein chemistry. The C2.SDK toolkit consists of a rich API set dealing with all aspects of interfacing chemistry codes, including GUI design, structure visualization, graphing, and volumetric display. Applications can be written in FORTRAN, C, or C++. The seminar will also discuss imminent SDK extensions that allow you to run applications through the internet, or an intranet, from a web browser interface on your desktop computer (PC, or MAC). In addition, we will demonstrate the use of C2.Tcl, the scripting language for the Cerius2 interface, for simple customization of routine modeling operations. C2.Tcl is based on the standard tcl scripting language, it lets you put together a simple application with its own graphical user interface in a matter of minutes. C2.Tcl aids in all aspects of molecular modeling, in particular in drug design and protein analysis. For more information about C2.SDK and C2.Tcl: http://www.msi.com/support/sdk/ The seminar is offered free of charge. Because space is limited, attendance is by registration only. The deadline for advanced registration is April 7. You can sign up at the following URL: http://www.acs.org/meetings/sanfran/exhwksp.html Ton van Daelen Product Manager Software Developer's Kit =20 __o E: tvd@msi.com _`\<,_ Molecular Simulations P: -1-619-546-5329 (*)/ (*) 9685 Scranton Road F: -1-619-458-0136 /\/\/\/\/\/\ San Diego, CA 92121 W: http://www.msi.com Check out What's New in SDK on the SDK web pages at http://www.msi.com/su= pport/sdk/ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: tvd@msi.com -- Original Sender From: Address: tvd@msi.com CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordin= ator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net= 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html=20 ------------------ RFC822 Header Follows ------------------ Received: by amgen.com with ADMIN;7 Mar 1997 11:58:57 -0800 Received: from www-int.amgen.com by dorothy.amgen.com via ESMTP (940816.S= GI.8.6.9/921111.SGI) id LAA28094; Fri, 7 Mar 1997 11:43:54 -0800 Received: from castle-smtp.amgen.com (castle-smtp [138.133.19.51]) by www-int.amgen.com (8.8.5/8.8.5) with SMTP id LAA27579; Fri, 7 Mar 1997 11:43:53 -0800 (PST) Received: by castle-smtp.amgen.com; id LAA12209; Fri, 7 Mar 1997 11:43:52= -0800 Received: from www.ccl.net(128.146.36.5) by castle-smtp.amgen.com= via smap (V3.1) id xma012203; Fri, 7 Mar 97 11:43:43 -0800 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.8.3/950822.1) id OAA26680; Fri, 7 Mar 1997 14:= 31:51 -0500 (EST) X-Authentication-Warning: www.ccl.net: mail set sender to chemist= ry-request@www.ccl.net using -f Received: from bioc1.msi.com for tvd@msi.com by www.ccl.net (8.8.3/950822.1) id NAA26455; Fri, 7 Mar 1997 13:= 50:54 -0500 (EST) Received: from iris69.msi.com by bioc1.msi.com (5.64/0.0) id AA14320; Fri, 7 Mar 97 10:50:24 -0800 Received: by iris69.msi.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@www.ccl.net id KAA15447; Fri, 7 Mar 1997 10:50:28 -0800 Date: Fri, 7 Mar 1997 10:50:28 -0800 From: tvd@msi.com (Ton van Daelen) Message-Id: <199703071850.KAA15447@iris69.msi.com> To: CHEMISTRY@www.ccl.net Subject: CCL:ACS seminar on Cerius2 software developer's kit Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk From bruce@cosy.utmb.edu Fri Mar 7 18:27:49 1997 Received: from cosy.utmb.edu for bruce@cosy.utmb.edu by www.ccl.net (8.8.3/950822.1) id RAA28457; Fri, 7 Mar 1997 17:47:09 -0500 (EST) Received: by cosy.utmb.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id QAA07916; Fri, 7 Mar 1997 16:47:47 -0600 From: "Bruce A. Luxon" Message-Id: <9703071647.ZM7914@cosy.utmb.edu> Date: Fri, 7 Mar 1997 16:47:39 -0600 Organization: Sealy Center for Structural Biology Reply-To: bruce@nmr.utmb.edu X-Phone: (409) 747-6802 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net, str-nmr@net.bio.NET Subject: NMR SOFTWARE UPDATE: MORASS 2.3 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii NMR SOFTWARE ANNOUNCEMENT: MORASS 2.3 is now available for downloading with improved handling of proteins, RNA and DNA over previous versions. MORASS - Multiple Overhauser Relaxation AnalysiS and Simulation - uses a full hybrid matrix eigenvalue/eigenvector solution to the Bloch equations to derive cross-relaxation rates and interproton distances for determining the NMR solution structures of DNA/RNA and proteins. MORASS is available free for academic use from the research laboratories of Prof. David Gorenstein. Distribution is available from: http://www.nmr.utmb.edu/ provides downloading & information via the WWW. nmr.utmb.edu in /pub/morass for standard ftp anonymous protocol. For more information contact: Bruce Luxon bruce@nmr.utmb.edu -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * Sealy Center for Structural Biology U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From matteo@pauli.mbi.ucla.edu Fri Mar 7 21:27:51 1997 Received: from MVS.OAC.UCLA.EDU for matteo@pauli.mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id VAA29411; Fri, 7 Mar 1997 21:19:38 -0500 (EST) Received: from ewald.mbi.ucla.edu by MVS.OAC.UCLA.EDU (IBM MVS SMTP V2R2.1) with TCP; Fri, 07 Mar 97 18:19:50 PST Received: from galileo.mbi.ucla.edu by ewald.mbi.ucla.edu; (5.65/1.1.8.2/29Nov95-1114AM) id AA24545; Fri, 7 Mar 1997 18:19:38 -0800 Received: from localhost by galileo.mbi.ucla.edu (5.65v3.2/1.1.10.5/17Oct96-1150PM) id AA03131; Fri, 7 Mar 1997 18:19:52 -0800 Sender: matteo@galileo.mbi.ucla.edu Message-Id: <3320CCC3.41C6@pauli.mbi.ucla.edu> Date: Fri, 07 Mar 1997 18:19:47 -0800 From: Matteo Pellegrini X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: circular dichroism (CD) calculations Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear netters, Would anyone tell me which package is able to calculate CD related properties (rotatory strength) for peptides? Sincerely Matteo Pellegrini matteo@galileo.mbi.ucla.edu