From shen@athena.cs.uga.edu Mon May 10 19:53:40 1993 Date: Mon, 10 May 93 23:53:40 EDT From: Mingzuo Shen Message-Id: <9305110353.AA24926@athena.cs.uga.edu> To: chemistry@ccl.net Subject: "tools" --- how do I love thee!!! Hi all, At this very moment, only if I could have these "tools" related to high symmetry: * given a set of cartesian coordinates and a schonflies symmetry symbol, a tool to symmetrize the coordinates according to the specified symmetry. * given a set of cartesian coordinates and energy gradients, a tool to update the cartesian coordinates according to a symmetry (leading to a local minimum, or some higher order stationary points). To repeat: I have programs to calculate gradients. potential problem: my program may use different ordering from your favorite program(s). * given an equilibrium geometry (cartesian coordinates) and a symmetry, a tool to generate a set of displacements (cartesian OK, internal better). My program(s) will then calculate gradients at these displacements. THEN the same tool will take these displacements and gradients and calculate energy second derivatives (finite diff approximations). Any symmetry must be OK (not just abelian groups). * given a set of cartesian coordinates, a tool which tells me its highest point group (to within a user-specified threshold). I am aware that many "programs" already have these capabilities (such as Hondo from M. Dupuis and friends, and Turbomole from R. Ahlrichs and students). But they are not "tools" as described by Dr. Ron Shepard --- not tools in the Unix spirit. and these programs are written in Fortran and do not take command-line arguments. Is it just me, or do some people also feel kind of strange when huge systems such as Hondo, Cadpac, etc., only have one, *one*, executable around? There are well known systems which are more modular, such as Columbus and Turbomole, and H. F. Schaefer's group code (called Psi). Mingzuo Shen From aono-pro@tansei.cc.u-tokyo.ac.jp Tue May 11 03:07:11 1993 Date: Tue, 11 May 93 15:29:46 JST From: Aono-pro Message-Id: <9305110629.AA02642@tansei1.tansei.cc.u-tokyo.ac.jp> To: CHEMISTRY@ccl.net Subject: Charges Hi netters, Concerning on Margaret Wong's comment, I'd also like to ask about charges. When a molecu is isolated, the chrage distribution is given by ab-initio calculation. But when the molecule is weakly adsorbed to a solid surface, the charge distribution must be diiferent from them that are isolated. Could anyone give comments if there are any programs which can deal molecules on the surface? Thanks in advance. Hitoshi Nejoh aono-pro@tansei.cc.u-tokyo.ac.jp From rwoods@biop.ox.ac.uk Tue May 11 11:03:52 1993 Date: Tue, 11 May 1993 10:03:52 +0100 From: rwoods@biop.ox.ac.uk To: chemistry@ccl.net Message-Id: <0096C56C.0A2A90E0.24030@biop.ox.ac.uk> Subject: ESP-Charges ("actual vs. exptl.") Dear netters, In response to Margaret Wong's question regarding the "validity" of ab initio charges, I think it is a good time to remind everyone who uses these charges in molecular modelling, etc. that there is no such thing as a net atomic charge. Regardless of the method by which they are "generated", they simply provide a convenient model with which to interpret reactivities, model coulombic interactions (hydrogen bonds etc), or generate dipole moments. Of course the electrons are not "localized" so the whole idea is a very artificial BUT useful concept. Rob Woods Robert J. Woods, Ph.D. Glycobiology Institute University of Oxford South Parks Road Oxford, OX1 3QU From jas@medinah.atc.ucarb.com Tue May 11 03:54:47 1993 Message-Id: <9305111251.AA25243@medinah.atc.ucarb.com> Date: Tue, 11 May 1993 08:54:47 -0500 To: chemistry@ccl.net From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: Re: Z-matrix to Cartesian Transformation > >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 > I would like to see QCPE made available on the Internet as an anonymous FTP site and accessible via Gopher (and perhaps even mirrored at OSC). I think there would be a lot more contributions of this nature to QCPE if it were more accessible. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH ...................................................................... Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From fredvc@esvax.dnet.dupont.com Tue May 11 06:57:21 1993 Date: Tue, 11 May 93 10:57:21 -0400 Message-Id: <9305111457.AA03445@esds01.es.dupont.com> From: fredvc@esvax.dnet.dupont.com To: chem@ccl.net Subject: CHARGES, DIPOLE MOMENTS. ETC To reinforce Rob Woods reminder, net atomic charges for a molecule are a fiction. What is real are the moments (dipole, quadrupole, octopole, etc.) of the charge distribution. The concepts of net atomic charges, bond dipoles, etc, have evolved as DEVICES for dealing with moments, particularly dipole moments. What a dipole moment really measures, however, is the *non-coincidence* of the centers of +ve & -ve charge in a molecule. When one considers the total charge on a molecule this separation is actually quite small (~1.0e-02 Angstroms). From the standard definition of a dipole moment (Z*e) * l We have calculated the following "l" values; Molecule Dip. Mom. "l" ======== ======== ======== HCL (Z = 18) 1.08 D 0.0125 Ang. CH2=O (Z = 16) 2.34 0.0304 CH3-CN (Z = 22) 3.90 0.0368 p-nitroanisole 5.26 0.0137 (Z = 80) From edvard@atf1.fagmed.uit.no Tue May 11 18:11:17 1993 Date: Tue, 11 May 93 17:11:17 +0100 From: edvard@atf1.fagmed.uit.no (Oyvind Edvardsen Computer Graphics Lab. IMB Univ. Tromsoe) Message-Id: <9305111611.AA14165@atf1.fagmed.uit.no> To: CHEMISTRY@ccl.net Subject: Re: "tools" --- how do I love thee!!! Hello, The idea of "tools" in general and "chemistry tools" to be more specific, is good. As have been mentioned by others the strength of unix is the ability to tie together several "tools" by pipes. Each tool performs a small (?) task, and does it well. This leads to one of the crucial points here: -a "tool" needs to be quite flexible and robust => thinking and programming may require quite some energy Another crucial point is the file format(s) of the things you feed into the "tools". The first "tools" to create could possibly be general (?) "tools" for converting file formats to some standard formats used by the workhorse "tools". Maybe we're close to the reason(s) why one is writing "packages" instead of "tools": -lower generality => easier to implement -each "package" its own file format => the file format solicits the "package" This is not meant as critizism of "packages" and the folks behind them! Not at all!! Since I feel the idea of "tools" is very interesting and has the potential of providing added productivity to research laboratories, it may be worth analyzing why there are so many "packages" and so few "(chemistry) tools". I have written a number of utilities that we use in our laboratory, but they are definitely not general enough nor robust enough to be "tools". Many of those utilities are specially tailored for AMBER and MIDAS. However, they save lots of efforts needed to do some routine and tedious everyday tasks => increased productivity and less frustration (and less errors?). I really value the unix tools, which I often use in nifty (?) shell scripts to perform some kind of file manipulation. Being able to do so with other kinds of tools would definitely be nice. -oed. From DSMITH@uoft02.utoledo.edu Tue May 11 07:53:24 1993 Date: Tue, 11 May 1993 12:53:24 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: QCPE on Internet To: chemistry@ccl.net Message-Id: <01GY1SSPEZ2U0075JG@UOFT02.UTOLEDO.EDU> The question of accessing QCPE programs via internet has arisen before. The problem is (correct me if I misstate this, Richard) that QCPE is not supported by sources other than income derived from the sale of programs, bulletins, etc. So, if it free and unlimited access were provided via internet, there would soon be nothing to access. Richard Counts has done an excellent job over many years running, maintaining and expanding QCPE. He deserves a big round of thanks. 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 DSMITH@uoft02.utoledo.edu Tue May 11 08:04:20 1993 Date: Tue, 11 May 1993 13:04:20 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: stereoviewing in molecular modeling - summary To: chemistry@ccl.net, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Message-Id: <01GY1T65IWK60075JG@UOFT02.UTOLEDO.EDU> A few weeks ago I posted a series of questions to the net concerning the need and use of stereo viewing, 3D, and virtual reality for molecular modeling. I have put all of the responses (31) into a file called 3d.mail, which is available via anonymous ftp. Here is how you get these files using ftp: ftp FTP.UTOLEDO.EDU (or 131.183.1.1) login: anonymous password: your_e-mail_address (please !). ftp> cd [.CHEMISTRY] ftp> ls -l (to get the listing of all files which are there). ftp> get file_you_want (in this case 3d.mail) ftp> quit. 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 vaisman@gibbs.oit.unc.edu Tue May 11 18:12:44 1993 Date: Tue, 11 May 1993 13:11:44 +0501 (EDT) From: Iosif Vaisman Subject: Re: charges To: Margaret Wong Message-Id: On Tue, 11 May 1993, Margaret Wong wrote: > ... > What is the physical evidence, apart from dipole > moment and high resolution X-ray crystallography, existing > for calculated charges vs. actual charges? > Effective atomic charge could be determined using X-ray photoelectron and Auger transition energies (V.I.Nefedov et al., J.Electron Spectr. Relat. Phenom., 1988, 46, 381) or, in case of electron-donating atoms in molecules of liquid solvents, comparing the rates of quadrupole relaxation of the nuclei of [7]Li+ cation in mixtures of these solvents (A.I.Mishustin, Russ.J.Phys.Chem.[Zh.Fiz.Khim.], 1983, 57, 11, 1665). > > Margaret Wong > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Iosif Vaisman Laboratory for Molecular Modeling School of Pharmacy University of North Carolina Chapel Hill, NC 27599-7360 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From DSMITH@uoft02.utoledo.edu Tue May 11 08:10:58 1993 Date: Tue, 11 May 1993 13:10:58 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: use of color in molecular modeling To: chemistry@ccl.net, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Message-Id: <01GY1TCEULO00075JG@UOFT02.UTOLEDO.EDU> In response to my recent question on stereo viewing, I was asked about the use of color in molecular modeling. So.... I have a general question for anyone out there who wishing to open a dialog about the use of color in molecular modeling. Please send responses directly to me and I will summarize for the net. I use color all the time in my modeling - I find that in addition to simple uses such as identifying atoms or residues by type or charge or hydrophobicity, mapping properties onto surfaces is quite useful. Use of color rather than or in addition to grids or translucent surfaces is also advantageous. And color is certainly cheap on today's hardware and software. Would any one else like to comment on why color is or is not important, useful, advantageous, indespensible, etc.? In addition to opinions, I would like to hear success stories where the use of color has enhanced the chemistry or helped to solve a problem which was insoluble without it or would have taken a longer time or would have resulted in a lower quality answer. 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 --- 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 jp_lafemina@ccmail.pnl.gov Tue May 11 03:01:00 1993 Date: Tue, 11 May 93 11:01 PST From: John P Lafemina Subject: Point Charges and M&M's To: chemistry@ccl.net Message-Id: <3A8BEFC7B9FF200134@pnlg.pnl.gov> Bravo! to Robert Woods for reminding us that point charges are an artificial, albeit useful, construct and have less physical reality than M&M's. The question of whether point charges are "good" or not depends entirely upon what criteria one establishes for defining "good". After all, given a charge distribution, one can come up with a enormous number of ways in which to divide the distribution so that almost any charge can be obtained for any given atomic center. All of these possibilities are equally "good" in the sense that, when put together in that special way, the original charge distribution is reconstituted. Unless one has some independent measure of the effect of the charge distribution on some physical property, which can then be reproduced by a point charge model, it is difficult for me to believe that any one of these point charge models is "better" than any other. John P. LaFemina Staff Scientist Materials and Interfaces Molecular Science Research Center Pacific Northwest Laboratory d3c876@pnlg.pnl.gov "Sometimes you get shown the light in the strangest of places if you look at it right" From avs@iris95.biosym.com Tue May 11 05:20:59 1993 Message-Id: <9305111920.AA23197@iris95.biosym.com> To: edvard@fagmed.uit.no Subject: Re: "tools" --- how do I love thee!!! Date: Tue, 11 May 93 12:20:59 -0700 From: avs@iris95.biosym.com The AI Chemistry Group at the University of Arizona (Prof. Dan Dolata, Pat Walters, Ajay Shah, Rawn Shah) is about to release the program Babel which interconverts among 10 different file in the public domain (in a few weeks). I presented a paper of the underlying data structure of the program at the ASTM Symposium on Chemical Data Standards in Atlanta GA. last week. We are hoping that ASTM will adopt the underlying molecular data structure (UMS) as a standard for the representation of molecules, thus streamlining the data conversion process. Please do not send us e-mail, we will send out all the details along with the paper, documentation and programmers' guide to adding the reader/writer routines. At present, we plan to put the program at anon ftp site and possibly deposit it in QCPE. Ajay Shah ajay@mercury.aichem.arizona.edu avs@biosym.com From jwm07@cas.org Tue May 11 11:02:37 1993 Date: Tue, 11 May 93 15:02:37 EDT From: jwm07@cas.org (John W. Macko (jwm07-3952)) Message-Id: <9305111502.AA4294@cas.org> Subject: 3D search alpha testers needed - CAS To: CHEMISTRY@ccl.net .nf ******************************************************************************** CHEMICAL ABSTRACTS SERVICE ******************************************************************************** CAS is currently testing a prototype of a single conformer 3D search system on the CAS REGISTRY file. This search system is the first phase in an ongoing project to investigate a variety of search techniques for use on the more than 12 million substances in the REGISTRY file. Future projects may include 2D-3D and molecular property based similarity search, 3D conformation searching, clustering, ranking and alternative search paradigms in the REGISTRY file. We are looking for additional (about 10) alpha testers of this and future systems and features. The ultimate goal is to design, develop and implement full-scale production systems that we will offer to the general chemistry community. Who we are looking for: Computational Chemists, Molecular Modelers, Medicinal Chemists, Researchers, etc with interest and knowledge in 3D database building, searching etc. We are looking for individuals from commercial and academic organizations. We are not looking for software vendors. You should have some kind of working knowledge of Sybyl (6.0 or 5.5) and access to it. It is preferable that you have the ability to ftp/telnet over the i'net without much trouble. There are alternatives, but basically - files will be sent back and forth between CAS and yourself and the easier this is for you the better. What we want from you: Time & patience. We need your time to play with our systems, test them, use them and tell us what you think we should do, change, improve etc. We will give you access to the system and all that we ask is that you evaluate it, and give us feedback. There is some training involved. We'll deal with this on an individual basis with each tester, but it may require some minor local traveling on your part. Other than this, there should be no cost to you. The current prototype provides single conformer searching of about 600,000 substances from the Registry file. Since this is a prototype, support is bare bones. This is where your patience will be required. We will also need you to sign a simple non-disclosure agreement. There a lot of details that may be best shared with only those that are interested. So, if you are interested and would like more information, please respond to me directly by sending an email to or call: John W. Macko New Product Development Chemical Abstracts Service jwm07@cas.org 1-800-848-6538 ext 3952 (Please do not respond to the mailer) From steven@cell.BIH.Harvard.Edu Tue May 11 11:45:35 1993 Date: Tue, 11 May 93 15:45:35 EDT From: steven@cell.BIH.Harvard.Edu (Steven Blechner) Message-Id: <9305111945.AA00822@cell.bih.harvard.edu> To: chemistry@ccl.net Subject: Sun Workstations... I know that Silicon Graphics Workstations appear to be the platform of choice for the quantum chemistry and visualization groups, but can someone please respond as to what has been ported and is available for the Sun Workstation community ? -steven From rs0thp@RohmHaas.Com Wed May 12 49:43:26 1993 From: rs0thp@RohmHaas.Com (Dr. Tom Pierce) Message-Id: <9305111920.AA11606@monte.br.RohmHaas.Com> Subject: Re: Z-matrix to Cartesian Transformation To: chemistry@ccl.net Date: Tue, 11 May 1993 15:20:26 +22305823 (EDT) > > > Ron Shepard previously said: > >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 .... > >In general, I would like to see more tools developed and shared. > >shepard@tcg.anl.gov > And Jack Smith replied:> > I would like to see QCPE made available on the Internet as an anonymous > FTP site and accessible via Gopher (and perhaps even mirrored at OSC). I > think there would be a lot more contributions of this nature to QCPE if it > were more accessible. QCPE 'could' be made available if it was somehow funded. It currently is supported to a large degree (in my persoanl opinion) by the membership fee( $10.00) and by distribution charges for software. If we *paid* for QCPE internet membership (say $100-$500 a year) then perhaps QCPE could afford to offer internet access to programs on a susbscription basis, ie my address of 136.141.228.2 would be allowed to login to the QCPE gopher or ftp site... if I had subscribed... QCPE contribution to computational chemistry has been very useful, but it was to a large degree created by the funding mechanisms of grants and fees. Something similar would have to be created before I expect to see QCPE available on the Internet. -- Sincerely, Thomas Pierce, Internet Address: THPierce@RohmHaas.Com Observation - Network Computing is Computer Slavery. Official Disclaimer:"The opinions expressed are those of the writer and not the Rohm and Haas Company." From tudor@wucmd.wustl.edu Tue May 11 10:24:46 1993 Date: Tue, 11 May 93 15:24:46 -0500 From: tudor@wucmd.wustl.edu (Tudor Oprea) Message-Id: <9305112024.AA26562@wucmd> To: CHEMISTRY@ccl.net Subject: dipole moments While I agree with fredvc@esvax.dnet.dupont.com that net charges are pure fiction, and about the implicit definition of the dipole moment as the "*non-coincidence* of the centers of +ve & -ve charge in a molecule", I find it rather hard to believe that the definition dpm=q*l can be rewritten as a "standard definition (Z*e) * l". This would lead to fictitious lengths in the dipole (as it does in the given examples), as huge charges are used. It is rather improbable that such charges come to effect, nor that the dipole of the molecule is so short. The (perhaps personal) interpretation of electric dpm is that the +ve and -ve are the centers of charge - which should be distributed in space along the longest axis of the molecule, at a length l which sould be defined as the distance (in the long axis) between the farthest atoms minus the covalent radii of these atoms (thus to ensure that the dipole is enveloped in the molecule). Hence, charge should not be the arithmetic mean of Z's involved, but should be inferred (if needed) from 'dpm/l' - where the length is approximately defined above. Thus, the rewritten examples should be: Molecule Dip. Mom. lenght charge (e) HCl 1.08 1.008 0.321 CH2O 2.34 1.720 2.578 CH3CN 3.90 3.O16 2.508 p-nitroanisol 5.26 7.272 0.0128 Please note that lengths are merely for illustrative purposes, and that I did not consider rotamers for the 4th case. Structures were merely constructed in Sybyl (no fancy calculations involved). Any comments and discussions are welcome. Tudor Ionel Oprea Research Associate Wash U Center for Molecular Design tudor@wucmd.wustl.edu From mail Tue May 11 14:04:29 1993 From: hyper!slee (Thomas Slee) Message-Id: <9305111813.AA29975@hyper.hyper.com> Subject: Re: charges To: chemistry@ccl.net Date: Tue, 11 May 1993 14:13:18 -0400 There have already been several responses to Margaret Wong's question concerning the validity of "atomic charges" as produced by various methods. So here's my two cents' worth. The question can only be answered once "actual charges" are defined, of course. Many people mean "charges that reproduce the electrostatic field produced by the total charge density as well as possible", and if this is what you want then there is only an empirical answer. The most widely used method is to fit the charges to the electrostatic potential at a sampling of points; the results depend, of course, on the points chosen. This electrostatic fitting procedure has long been advocated in the force field area by Peter Kollman, and you may wish to look at articles by him and coworkers, e.g., J. Comp. Chem. 1984, v5, 129, for their approach from ab initio calculations (and with many references to earlier work along the same lines) or J Comp Chem 1990, v11, 431 for a comparison of ab initio and semi-empirical charges arrived at by the fitting method. Another approach is to take a serious look at whether one can define "atoms" within molecules. By far the most consistent and in-depth look at this question is the work of Richard F. W. Bader and coworkers over the last many years (interest declared: I was one of the coworkers) which addresses the question in general terms, not simply with respect to charges but also other atomic properties (energies, for instance). Bader has a recent book that covers most of the work: "Theory of Atoms in Molecules" >from Oxford University Press. The charges derived from this "atoms in molecules" approach do turn out to be consistent with chemical expectation as long as you remember that the atoms can also have substantial dipole moments, being unspherical. Thus, using these atomic charges alone will not in general give a good respresentation of the electrostatic field. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 From tudor@wucmd.wustl.edu Tue May 11 11:08:30 1993 Date: Tue, 11 May 93 16:08:30 -0500 From: tudor@wucmd.wustl.edu (Tudor Oprea) Message-Id: <9305112108.AA27063@wucmd> To: CHEMISTRY@ccl.net Subject: erratum @ dipole moment Due to bugs in the code, in the _just_sent_ message (Murphy has his ways!), the charges are plain WRONG, so please note the corrected table Molecule Dip. Mom. lenght charge (e) HCl 1.08 1.008 0.223 CH2O 2.34 1.720 0.288 CH3CN 3.90 3.O16 0.269 p-nitroanisol 5.26 7.272 0.151 Sorry for any nuisance (including my own embarassment!). Tudor Ionel Oprea Research Associate Wash U Center for Molecular Design tudor@wucmd.wustl.edu From U09872@UICVM.bitnet Tue May 11 11:50:13 1993 Message-Id: <199305112156.AA10487@oscsunb.ccl.net> Date: Tue, 11 May 1993 16:50:13 CDT From: "Bob Goldstein 6-6664" To: chemistry@ccl.net Subject: Re: CHARGES, DIPOLE MOMENTS. ETC > To reinforce Rob Woods reminder, net atomic charges for a molecule are > a fiction. What is real are the moments (dipole, quadrupole, octopole, etc.) > of the charge distribution. The concepts of net atomic charges, bond dipoles, The use of the word "real" is interesting. In fact, only the lowest non-vanishing multipole moment is independent of choice of coordinate origin. What really is real is the electric potential near the molecule. When two molecules interact electrostatically, ignoring for the moment any charge rearrangements due to the "other" molecule, the apportionment of interaction energy into dipole-dipole, dipole-quadrupole, etc terms depends on the origins, (execpt for the lowest order term), but of course the energy itself is independent of origin. Bob Goldstein From klemm@msc.edu Tue May 11 12:36:18 1993 From: klemm@msc.edu (Stefan Klemm) Message-Id: <9305112236.AA15662@uh.msc.edu> Subject: XMol Version 1.3.1 To: chemistry@ccl.net Date: Tue, 11 May 93 17:36:18 CDT XMOL 1.3.1 DISTRIBUTED Minnesota Supercomputer Center, Inc. (MSCI) is pleased to announce the availability of XMol Version 1.3.1. Version 1.3.1 is a minor release incorporating several user-requested fixes and enhancements. Unlike previous versions, Version 1.3.1 has no built-in expiration date. XMol is based on the X Window System and uses OSF/Motif 1.1 for the display and analysis of molecular data. Data from several common file formats can be read and written. Formats currently supported include: Alchemy, CHEMLAB-II, Gaussian, MOLSIM, MOPAC, PDB, and MSCI's XYZ format. XMol can also be used to convert data between some of these formats. Version 1.3.1 does not provide model building or model editing capabilities. XMol includes a number of capabilities and features some of which are: support for color or monochrome displays interactive, mouse-driven rotation of models precise, keyboard-driven rotation of models animation of multiple-step data files the ability to attach 3-D vectors to atoms measurement of distances, angles, and dihedral angles context-sensitive help Encapsulated PostScript output Version 1.3.1 has a number of new features, as well as improved ones, that make it easier for you to use the package: default input and output formats can now be specified on the command line or in the X-resource file input file names can now be specified on the command line standard Motif selection boxes are now used for reading and saving files XMol is available for DECstation, Silicon Graphics IRIS-4D, SPARCstation, and Sun-3 architectures. We are currently assessing the prospect of an RS/6000 version of XMol. MSCI is making this release of XMol publicly available to anyone through internet ftp access. HOW TO GET XMOL VERSION 1.3.1 Make a directory to contain the XMol files, and 'cd' into that directory. Perform an 'ftp' to 'ftp.msc.edu'. Enter 'anonymous' as username. Enter your e-mail address as password (eg., user@school.edu). Enter the following commands at the ftp prompt: cd pub/xmol binary mget README xmol.tar xmol.arch ---- quit ...where "arch" is the architecture type of your machine: mips, sgi, sun3, or sun4. Un-package the distribution with the command 'tar xvf xmol.tar'. Run 'sh INSTALL' to get XMol up and running. CITING XMOL When citing XMol version 1.3.1 in published works, please use the following citation: XMol, version 1.3.1, Minnesota Supercomputer Center, Inc., Minneapolis MN, 1993. SUPPORT AND DISCLAIMER XMol version 1.3.1 (the "Software") is provided by MSCI "AS IS". MSCI does not provide maintenance, improvements, or support of any kind. The aforementioned not withstanding, we welcome your comments, suggestions, and problem reports and ask that you email those to us at the following email address: xmol@msc.edu. MSCI MAKES NO WARRANTIES OR REPRESENTATIONS, EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, AS TO ANY ELEMENT OF THE XMol SOFTWARE OR ANY SUPPORT PROVIDED IN CONNECTION WITH THIS SOFTWARE. In no event shall MSCI be responsible for any damages, including but not limited to consequential damages, arising from or relating to any use of the Software or related support. NEW OR DIFFERENT SOFTWARE MSCI has developed and makes available to its users of Computer Services new or different releases of this Software, which incorporate all or part of this Software. Access to such new or different Software requires the execution of a Computing Services Agreement and the purchase of computing services. COPYRIGHT (c) Copyright 1990, 1991, 1992, 1993 Research Equipment, Inc., dba Minnesota Supercomputer Center, Inc. You may make copies of the Software only for your archival purposes: however, you must reproduce and include the copyright notice and restricted rights legend on all backup copies. This Software is copyrighted. You may not distribute, sell, rent, license or otherwise provide copies of the Software to any other person or organization; electronic transmission of the Software to another computer is not permitted. No reverse engineering or decompiling of the Software is authorized or permitted. No rights to modify or make derivative works of the Software are granted. RESTRICTED RIGHTS Use, duplication, or disclosure of the Software and its documentation by the Government is subject to restrictions as set forth in subdivision {(c) (1) (ii)} of the Rights in Technical Data and Computer Software clause at DFARS 52.227-7013, and in the case of Government units or agencies other than the Department of Defense, the restrictions set forth in the clause at FAR 52.227.19 (c) (2) or, in the case of NASA, in the clause at 18-52.227 86(d) of the NASA Supplement to the FAR. TRADEMARKS Alchemy is a trademark of Tripos Associates, Inc. CHEMLAB-II is a product of Chemlab, Inc. DECstation is a trademark of Digital Equipment Co. GAUSSIAN 88,90, etc. are products of GAUSSIAN, Inc. IRIS is a trademark of Silicon Graphics, Inc. MOLSIM is a product of the Chem21 Group at the University of Illinois. MOPAC is a product of the Frank J. Seiler Research Laboratory at the USAF Academy. Motif is a trademark of Open Software Foundation. PDB is a product of Brookhaven National Lab. PostScript is a trademark of Adobe Systems, Inc. RS/6000 is a trademark of IBM corporation. Sun-3 and SPARCstation are trademarks of Sun Microsystems. X Window System is a trademark of the Massachusetts Institute of Technology. From ukreis@sfu.ca Tue May 11 09:20:52 1993 Date: Tue, 11 May 93 16:20:52 -0700 From: ukreis@sfu.ca Message-Id: <9305112320.AA12563@beaufort.sfu.ca> To: CHEMISTRY@ccl.net Subject: Hydrogen bonds to Cl acceptor ? Dear netters, I'm looking for information about hydrogen bonds to a chlorine atom as acceptor, i.e. O-H ... Cl. What about their stability, how strong is their influence ...? Anybody out there done some calculations/experimentals on that ? Any comments or hints to literature welcome. I'll summarize for the list. Cheers, Uwe ------------------------------------------------------------------------------ - - -> Dr.-Ing. Uwe C. Kreis - -> Department of Chemistry Tel. (Int) 604 291 5650 <- -> Simon Fraser University FAX: (Int) 604 291 3765 <- -> Burnaby, B.C. V5A 1S6 E-Mail: uwe_kreis@sfu.ca <- -> Canada E-Mail: ukreis@sfu.ca <- - - ------------------------------------------------------------------------------ From dave@carbon.chem.csiro.au Wed May 12 05:10:19 1993 Message-Id: <199305120010.AA06444@shark.mel.dit.csiro.au> Date: Wed, 12 May 93 10:10:19 EST From: (Dr.) Dave Winkler Subject: Net access to self funding databases & archives To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net Dear Netters, There are queries from time to time along the lines of..."why can't we get free ftp access to QCPE?" or "can you search the Cambridge Crystallographic Database via the Internet". The reason why these things cannot be done is that the organizations maintaining these archives or databases rely on income from purchases of software/databases to continue operating. I've often wondered whether it might be possible to devise a secure way of allowing this type of access via the net by means of encrypted files, special access keys or, more obviously special temporary accounts with passwords. Could some way could be developed where, say QCPE programs, could be available on a public ftp archive in a 'locked' form with unlocking instructions provided once the credit card transaction has been processed? As the director of the Australian Affiliated Centre for Cambridge Database I know from personal experience what a hassle it is to ship tapes, disks, manuals etc all over the world and distribute them within a country. Electronic distribution would be much simpler if the money side of things could be solved. In a less than perfect world I guess this would still lead to net bandwidth problems if someone tried to ftp Gaussian in one lump! Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From h8714031@hkuxa.hku.hk Tue May 11 23:50:16 1993 From: h8714031@hkuxa.hku.hk (Mok Kam Wah) Message-Id: <9305120345.AA27078@hkuxb.hku.hk> Subject: Question on GAMESS To: chemistry@ccl.net (Computational Chemistry) Date: Wed, 12 May 93 11:45:55 WST Dear Netters, I am using GAMESS (USA version) to perform some CI/MCSCSF calculations. Sometimes the program terminate and said inaccurate integral during the integral transformation. What is the problem if I set the 'Threshold cutoff for keeping transfered two electron integrals'to a larger value so that it treat the 'inaccurate integral' as zero? The default setting is 10e-9 for the threshold while I might need 10e-7. Is 10e-7 too large, what will I loss? Accuracy in the wavefunctrion? Besides, I am interested in Spin Orbit calculation for transition metal. Does anybody know any tublated Effective Nuclear Charge for transition metal and other main group element so that I can use in my SOC calculations? Or how can I calculated the Zeff? These maybe a simple question but please be patient to answer me! K.W.Mok -- K.W.Mok E-Mail: h8714031@hkuxa.hku.hk Dept. of Chem., University of Hong Kong.