From owner-hyperchem@hyper.com Mon Feb 3 15:00:31 1997 Date: Mon, 03 Feb 1997 09:44:07 +0100 To: hyperchem@hyper.com From: Kay Kreidler Subject: Localized Orbitals Dear Hyperchem Users! Is it possible, to create/and display localized orbitals with Hyperchem? Thanks for your help. ----------------------------------------------------------------------- From owner-hyperchem@hyper.com Mon Feb 3 19:50:29 1997 Date: Mon, 3 Feb 97 10:31:34 -0500 From: barclay (Victoria Barclay) Subject: new dongle driver Greetings, HyperChemists: Rainbow Technologies, the manufacturer of the hardware locks (dongles) which accompany HyperChem, have just released an update to the driver software for the dongles. The update affects driver software for new locks on Windows 3.1, Windows 95 and Windows NT. According to Rainbow, the new driver software will take care of several problems, among them - the low-power port problems of certain Gateway computers; - problems connected to the high-speed ECP printer port of such printers as the LaserJet 5L series; - failure of driver installation when path name > 30 chars; - NetSentinel NT Service crash for automatic start-up. If you have been experiencing these problems, you may wish to install the new driver software. However, if you are running smoothly, then we recommend a conservative approach. If you do decide to install the new driver software, please keep a backup copy of your old driver folder and documentation in case you need a fall-back position. We are placing the self-extracting archive files of these drivers on our ftp site, in the 'support' directory. To obtain the updated driver, ftp anonymously to ftp.hyper.com, change directory to 'support' and set the transfer type to 'binary'. Then you can get the file appropriate for your system - w95drvr.exe OR - ntdrvr.exe OR - w31drvr.exe When you run the .exe file, it will expand into a ReadMe file and a folder which contains the necessary driver files. We are putting these drivers on our ftp site in 'support' to assist users who have been having lock- and printer-related problems, but a general upgrade of the driver software is not necessary. We would appreciate feedback as to whether these new drivers solve the particular problems you have been experiencing. (Preliminary reports are mixed.) Please drop us a line at support@hyper.com . We will be updating the FAQ-file accordingly in the near future. More detailed information can be obtained from the Readme included in the self-extracting archives, or from Rainbow's web site, http://www.rnbo.com/TECH.HTM Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ------------------------------------------------------------------ Date: Thu, 30 Jan 1997 10:38:03 -0600 (CST) From: "XIE, NING" Subject: Re: MnO4- LUMO Hi, there, The basis set I used is ZINDO/1 and in UHF. I drew the structure and set "constrain bond angle" to tetrahedron angle. Then geometry optimize. Not long after the calculation started, the structure of MnO4- was changed to pyramidal. ning ------------------------------------------------------------------ From owner-hyperchem@hyper.com Tue Feb 4 19:03:44 1997 From: FLYNN_B@sunybroome.edu Date: Tue, 04 Feb 1997 12:02:54 -0500 (EST) Subject: A Puzzle I am a budding,self-taught molecular modeler. Playing around with Hyperchem Release 2 wih my students, we made 1,3,5,7-cyclooctatetrene. To our suprise, we obtained a "boat" structure after model building and geometry optimization. All the standard texts say that this structure is a "tub". Any comments or suggestions gratefully accepted. ------------------------------------------------------------------ From owner-hyperchem@hyper.com Tue Feb 4 20:59:14 1997 From: FLYNN_B@sunybroome.edu Date: Tue, 04 Feb 1997 16:32:53 -0500 (EST) Subject: cyclooctatetrene---again In my exuberance to solve the puzzle, I think I mistakenly claimed to get a "boat " geometry via Hyperchem . I meant to say a chair structure--- actually more like a chaise lounge. Sorry for the confusion. ------------------------------------------------------------------ From owner-hyperchem@hyper.com Tue Feb 4 21:24:10 1997 Date: Tue, 4 Feb 1997 16:39:55 -0500 (EST) From: Steven Clarke Subject: New Driver and Novel VLM Hi We were having a problem with the hardware lock and an appearant conflict with Novell VLMs in Netware 4.0. Does anyone (Victoria?) know if this new driver will fix that conflict? Thanks Steve ************************************************************* * STEVEN CLARKE * ************************************************************* * Graduate Student * E-mail : CLARKES@Chem.Lsa.Umich.Edu * * Dept. of Chemistry * Post : 930 North University Ave * * Univ. of Michigan * : Ann Arbor MI 48109-1055 * ************************************************************* ------------------------------------------------------------------ From owner-hyperchem@hyper.com Wed Feb 5 01:23:46 1997 From: "Graham Wills-Johnson" Date: Wed, 5 Feb 1997 13:18:45 EST-10ESUT Subject: Re: cyclooctatetrene---again > From: FLYNN_B@sunybroome.edu > Date: Tue, 04 Feb 1997 16:32:53 -0500 (EST) > Subject: cyclooctatetrene---again > To: hyperchem@hyper.com > In my exuberance to solve the puzzle, I think I mistakenly claimed to get > a "boat " geometry via Hyperchem . I meant to say a chair structure--- > actually more like a chaise lounge. > Sorry for the confusion. Optimization finds local minima, not global minima. Model build builds the "chaise lounge" form if you draw the original structure with double bonds. MNDO optimization of that starting structure takes you to a lounge conformation with enthalpy of formation +136.83 kcal/mol. If (analogous to procedure with cyclohexane in the Getting Started manual), you define PLANE by selecting a parallel set of double bonds and then reflecting one end of the molecule in that plane, this gives a "tub" initial conformation which MNDO optimizes to "tub" with enthalpy of formation +56.03 kcal/mol. If the original structure you draw is made an "aromatic ring" (double click) before optimization, MNDO optimizes to a flat "aromatic" structure with enthalpy of formation +64.25 kcal/mol. Thus, there are at least three local minima, and which one is found depends on where on the PE surface you begin. If thermal equilibrium is established between these three forms, it is obvious why the textbooks favour the "tub". Graham Wills-Johnson RMIT Melbourne Australia. ------------------------------------------------------------------ From owner-hyperchem@hyper.com Wed Feb 5 22:22:06 1997 Date: Wed, 5 Feb 97 16:28:22 -0500 From: barclay (Victoria Barclay) To: Dirk Dettmering , hyperchem@hyper.com Subject: Re: Hyperchem 5.0/Sybyl Hi Dirk, > I've heard about the new release of hyperchem 5.0 and it's new features. But > on the web pages of Hypercube I couldn't get the information about the > import and export filters supported by hyperchem 5.0 especially concerning > the interchange of data with software packages like sybel running on SGI > workstations. The MOL2 file format is used by Sybyl and other programs from Tripos Associates. It is supported both for File/Open and File/Save in HyperChem 4, 4.5 and 5. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ------------------------------------------------------------------ From owner-hyperchem@hyper.com Thu Feb 6 19:45:38 1997 Date: Thu, 6 Feb 1997 18:51:10 +0100 (MET) From: Sandy Yates Subject: New Version of BABEL HypeChemers, Just to let you know that there is a new version of BABEL v1.16. The authors say thst they have fixed the PDB format column registration/alignment problem which caused difficulties with HyperChem, ie disconnected atoms. Copies for verious platforms can be obtained from Pat Walters Regards, Sandy ------------------------------------------------------------------------ Sandy Yates / Area de Mecanica de Fluidos / Centro Politecnico Superior Maria de Luna, 3 / 50015 ZARAGOZA. SPAIN Phone: Spain (76) 761000 ext 5045. Fax: Spain (76) 761882 Email: sandy@ideafix.cps.unizar.es ------------------------------------------------------------------ From owner-hyperchem@hyper.com Thu Feb 6 21:55:47 1997 Date: Fri, 07 Feb 1997 05:14:01 -0400 To: hyperchem@hyper.com From: "Antonio Conte" Subject: Transition metals complexes Hi There is someone studing transition metals complexes with HyperChem? ------------------------------------------------------------------ From owner-hyperchem@hyper.com Fri Feb 7 21:42:45 1997 Date: Fri, 07 Feb 1997 14:51:35 -0800 From: Pat Walters Subject: Babel 1.6 Thanks to all of you who sent me mail requesting a copy of Babel 1.6. The following files are on joplin.biosci.arizona.edu in pub/Babel babel-1.6.tar.Z - unix sources and Makefile babel16.zip - MS DOS executable, works in Win95 DOS box Please remember to download these files as binary. Have fun, Pat -- W. Patrick Walters, Ph.D. Staff Scientist, Computational Chemistry and Molecular Modeling Vertex Pharmaceuticals, Inc., 130 Waverley St., Cambridge, MA 02139 Voice: (617)577-6000 FAX: (617)577-6400 ------------------------------------------------------------------ From owner-hyperchem@hyper.com Mon Feb 10 11:58:01 1997 Date: Mon, 10 Feb 1997 11:18:08 +0100 (MET) From: "Modelling '97" Subject: Modelling '97 Model(l)ing '97 Model(l)ing '97 is the annual international meeting of the MGMS, which is being organised in cooperation with WATOC for the first time. The meeting will take place from Tuesday, September 2nd to Friday September 5th 1997 at the Institut fuer Organische Chemie and the Computer-Chemie-Centrum of the Universitaet Erlangen-Nuernberg in Erlangen, Germany. All lectures except for those on Wednesday, September 3rd are by invitation. Wednesday's sessions have been reserved for submitted lectures by young scientists (postdocs or non-tenured academic staff), who are invited to submit their contributions as outlined below. Two parallel sessions will emphasise biological/ pharmaceutical methods and applications (Session A) and calculational methodology and non-biological applications (Session B). Conference fees are as follows: MGMS or WATOC members non-members Normal particpant: before 1.6.97 DM 400.- DM 500.- after 1.6.97 DM 550.- DM 650.- Student participants: before 1.6.97 DM 200.- DM 250.- after 1.6.97 DM 275.- DM 325.- Program and registration details are available from: Dr. T. Clark Model(l)ing '97 Computer-Chemie-Centrum Naegelsbachstraae 25 D-91052 Erlangen Germany Email: model97@organik.uni-erlangen.de FAX: +49-(0)9131-856565 URL: http://www.organik.uni-erlangen.de/model97/ ------------------------------------------------------------------ From owner-hyperchem@hyper.com Mon Feb 10 20:15:42 1997 Date: Mon, 10 Feb 1997 12:13:14 -0400 (EDT) From: NORDULF DEBYE Subject: Are you running Hyperchem on a Windows NT LAN? At Towson State, we have used Hyperchem on stand-alone PC's for several years as part of the Intermediate Laboratory curriculum required of our chemistry majors. We are now constructing a 12 workstation LAN using Pentium-based workstations and server. We are intending to connect the LAN together through the University's Ethernet backbone and will probably use Windows NT 4.0 as the operating system. The new set-up is designed to make Hyperchem (and other software) readily available to our freshman and sophomore chemistry students as well as to our upper level majors. We anticipate the LAN growing to about 25 workstations in the next two years. I would appreciate hearing from anyone who is running Hyperchem on a PC-based LAN as I am sure that we could benefit greatly from such experience. Not only are we still debating a bit about the hardware selection (Pentium Pro's? Pentium Pro only for the server? Dual processor server? etc), the operating system (Windows NT 4.0?), but also which versions of Hyperchem might be most useful for the General Chemistry and Organic Chemistry students. Please e-mail me directly if you are willing to share your experience and/or advice and save me from making some drastic mistake as we embark upon this adventure. Tahnks. Nordulf Debye Chemistry Department Towson State University Towson, MD 21204 USA +1 410 830 3046 (voice) +1 410 830 4265 (fax) D7PCA10@toe.towson.edu ------------------------------------------------------------------ From Wolfgang.Roth@zfe.siemens.de Wed Feb 12 09:35:12 1997 To: owner-hyperchem Subject: AW: Two problems with hyperchem Date: Wed, 12 Feb 97 15:14:00 PST Hi, I am working also on the adsorption of molecules on graphite. I was able to build a lattice of a size of more than 1000 C-atoms. There is an attachment with this graphite substrate. Greetings Manfred Groeppel groeppel@organik.uni-erlangen.de [[ GRAPHIT1.HIN : 3597 in GRAPHIT1.HIN ]] ---------- Von: owner-hyperchem[SMTP:owner-hyperchem@hyper.com] Gesendet: Montag, 20. Januar 1997 02:22 An: hyperchem Betreff: Re: Two problems with hyperchem > From: "Forrest Stevens" > Subject: Two problems with hyperchem > > Our research group has been using Hyperchem (release 2) off and on, > and we are now considering upgrading to the current version. > However, there are two problems we have experienced, and we want to > find out if we will also have these problems in the current release. > > 1) We are modeling molecules adsorbed on graphite, so need a graphite > surface to place molecules on. We have tried to model graphite > by building a sheet of aromatic carbon rings, but after > sketching, "add H and model build" causes the sheet to curl and fold > drastically. The following binary file has been uuencoded to ensure successful transmission. Use UUDECODE to extract. begin 600 GRAPHIT1.HIN M.T%UG1E;B!E:6YE("`@#0H[;6]L96MU;&%R92!$ M>6YA;6EK(&=E Subject: Re: Are you running Hyperchem on a Windows NT LAN? CORRECTION Sorry, folks, but my original posting requesting info on Hyperchem/LAN use included an incorrect e-mail address in my signature file. I have received some very helpful responses but am still interested in hearing from additional users of Hyperchem on a Windows-based LAN. My correct e-mail address is: d7pca10@toa.towson.edu ....................................................................... nordulf debye/chemistry/towson state university/towson, md 21252 usa +1 830 3046 (voice) / +1 830 4265 (fax) / d7pca10@toa.towson.edu ....................................................................... -------------------------------------------------------------- From owner-hyperchem@hyper.com Thu Feb 13 09:17:48 1997 From: "Nicolau, Dan" Subject: Transfer of files to HyperChem from Insight Date: Thu, 13 Feb 1997 18:44:57 +1100 HyperChem-ers, For those interested in trasferring files prepared in Insight (from MSI) to HyperChem the only way I could obtain consistent results was: -save Insight files as Mol files; they come with a mol2 extension; -ftp, etc., to your PC; -edit the extension from mol2 to ml2 (as in HyperChem) -open them in HyperChem. All other export options (PDB, etc.) didn't work for charges or connectivity. Hope it helps Dan -------------------------------------------------------------- From owner-hyperchem@hyper.com Thu Feb 13 17:38:31 1997 Date: Thu, 13 Feb 1997 09:39:27 -0600 (CST) From: Ning Xie Subject: hyperchem/Gaussian: why so different Hi, there, When I used hyperchem and Gaussian to calculate the bond length and the energy of ZnCl2, I got quite different results. Here is an example: method Zn--Cl bond length(angstrom) Gaussian Hyperchem PM3 0.7234 2.064 AM1 1.2601 2.0674 Anybody know why? Thank you for your responses. ========================================================================= | XIE, NING Tel: (306)585-5262 (O) | | Chemistry Department (306)585-2184 (H) | | University of Regina E-Mail: xiening@meena.cc.uregina.ca | | Regina, SK or: xiening2@max.cc.uregina.ca | | Canada S4S 0A2 | ========================================================================= -------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Feb 14 10:34:31 1997 Date: Thu, 13 Feb 97 13:41:20 +0300 From: "Ananikov V.P." Subject: Re: hyperchem/Gaussian: why so different Ning Xie wrote: >Hi, there, >When I used hyperchem and Gaussian to calculate the bond length and the >energy of ZnCl2, I got quite different results. Here is an example: > >method Zn--Cl bond length(angstrom) > Gaussian Hyperchem >PM3 0.7234 2.064 >AM1 1.2601 2.0674 > >Anybody know why? > >Thank you for your responses. Check your jobs. It seems something wrong in your Gaussian calcu- lations. Recently I have performed ZnCl2 geometry optimization in GAMESS/US and here is the results: AM1 PM3 MNDO STO-3g 3-21G Zn-Cl,A 2.067 2.064 2.116 1.927 2.193 regards, Ananikov V.P. Valentin P. Ananikov NMR Laboratory N.D. Zelinsky Institute of Organic Chemistry Leninsky Prospect 47 Moscow 117913 Russia e-mail: val@nmr1.ioc.ac.ru Fax (095) 135 5328 Phone (095) 135 9094 -------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Feb 14 10:42:52 1997 Date: Fri, 14 Feb 1997 11:07:11 +0000 From: richardc@chemistry.leeds.ac.uk Subject: (no subject) Using Hyperchem 5.0 with an Excel macro (DDE commands). How can I carry out mm+ geometry optimisations on one (selected) of two molecules then optimise the converged conformation with a semi-empirical type optimisation, without encountering the "recalculate atom types?" pop-up box??. I would like to know if there is a DDE command which can select "OK" when this box appears, or perhaps there is a way of stopping Hyperchem from asking in the first place. Any words of wisdom would be very much appreciated. Somebody please help, Richard Carney (Leeds university; England) -------------------------------------------------------------- From owner-hyperchem@hyper.com Sat Feb 15 00:24:09 1997 Date: Fri, 14 Feb 1997 10:08:14 -0800 From: pastorec@ccmail.orst.edu (Christine Pastorek) Subject: AVI format movies from HyperChem A colleague found the following shareware on the WEB. It will allow you to capture whatever is on your monitor to AVI format movie files for playback anytime. I just tried it out and it seems to work okay. For example, Start HyperCAM, setup a vibrational animation with HyperChem, and select record on HyperCAM. The output goes to a default file that you can rewind, replay, etc. To download it, set your WEB browser to: http://www.hyperionics.com/www/hypercam.htm (Win 95 only). A registered copy is $30. +-+-+-+-+-+-+-+-+-+-+-+--+-+-+-+-+-+-+-+-+-+-+-+--+-+-+-+- Dr. Christine Pastorek voice:(541)737-6732 Gilbert Hall 153 Dept. of Chemistry FAX:(541)737-2062 Oregon State University Corvallis, OR 97331 internet:pastorec@ccmail.orst.edu +-+-+-+-+-+-+-+-+-+-+-+--+-+-+-+-+-+-+-+-+-+-+-+--+-+-+-+- -------------------------------------------------------------- From owner-hyperchem@hyper.com Mon Feb 17 18:52:44 1997 Date: Mon, 17 Feb 97 13:02:58 -0500 From: barclay (Victoria Barclay) Subject: Recalculate? message >Date: Fri, 14 Feb 1997 11:07:11 +0000 >From: richardc@chemistry.leeds.ac.uk > >Using Hyperchem 5.0 with an Excel macro (DDE commands). How can I >carry out mm+ geometry optimisations on one (selected) of two molecules >then optimise the converged conformation with a semi-empirical type >optimisation, without encountering the "recalculate atom types?" pop-up >box??. > I would like to know if there is a DDE command which can select "OK" >when this box appears, or perhaps there is a way of stopping Hyperchem >from asking in the first place. Any words of wisdom would be very much >appreciated. > Hi Richard and HyperChemists, The "Recalculate atom types?" message is intended as a helpful warning message to inform someone who may have inadvertently changed the calculation type. Of course a helpful warning message becomes rather unhelpful in the situation you describe. HyperChem is designed to suppress such messages during the operation of a script or Excel macro by specifying "hide-warnings" or related. (Similar commands may be found on pp. 210-2 of the "Chemist's Developer Kit" manual.) In this case, you could have macro lines which go something like: EXECUTE(Channel,"[hide-warnings(yes)]") EXECUTE(Channel,"[molecular-mechanics-method MM+] [do-optimization]") [...] EXECUTE(Channel,"[hide-warnings(yes)]") EXECUTE(Channel,"[semi-empirical-method CNDO] [do-optimization]") Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. -------------------------------------------------------------- From owner-hyperchem@hyper.com Mon Feb 17 19:13:17 1997 From: "Chemist" Date: Mon, 17 Feb 1997 15:07:45 +0300 (MSK) Subject: Rare earth (lanthanide) metals RARE EARTH (LANTHANIDE) METALS AND ALLOYING MATERIALS ================================================================== Dear sirs! 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The trial parties of materials can be presented under the request of the Buyer. Our contact details as follows: =============================== E-Mail: marlen@fe.msk.ru Address: New Zealand fax (64-9) 377-2821. Cyprus fax +357 (5) 322-729 Russia fax +7 (095) 132-0371, 978-0837, 436-0234 -------------------------------------------------------------- From owner-hyperchem@hyper.com Tue Feb 18 19:33:37 1997 From: D_GARMAN@LVC.EDU Date: Tue, 18 Feb 1997 12:22:13 -0500 (EST) This is in regard to hyperchem on the SGI. Has anyone been able to capture an animation from hyperchem on the SGI and make it into a movie file? Thank you for all your help. Please send any answers to: d_garman@lvc.edu -------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Feb 21 11:56:55 1997 Date: Fri, 21 Feb 1997 09:50:28 +0000 From: Richy C Subject: annoying warnings! Is there any DDE or script commands which can instruct hyperchem 5.0 to refrain from showing the; "recalculate atom types, old types will be lost?" warning box when you switch from semi-empirical calculations to MM+?. I have tried the given commands for warnings in the "chemist's developers kit" page 212, but as yet have had no luck. Yours hopefully, Richard Carney (Leeds Univ) -------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Feb 21 12:06:20 1997 Date: Fri, 21 Feb 1997 11:49:52 +0100 (MET) From: Giulio To: hyperchem@hyper.com Subject: priblems with HyperNMR Dear users, I have a problem regarding HyperNMR I constructed a molecul using Hyperchem and have optimized it using AM1; then I saved the molecule in .HIN format. When I load this molecule into HyperNMR, the geometry looks completely wrong. Do you have suggestions? Thank you very much for your help. Giulio Rastelli Dipartimento di Scienze Farmaceutiche Universita di Modena -------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Feb 21 14:42:32 1997 Date: Fri, 21 Feb 1997 13:57:29 +0100 From: Jerzy Malecki Subject: Reaction field and solvent effects Dear Victoria and HyperChem users, The possibility of taking into account the influence of polarizable environment on structure, energy, dipole moment etc. is of great importance for any conformations and dynamics calculations. As the first approximation can apply the Onsager reaction field. Such a proposal was made by Tapia almost twenty years ago (see e.g. C. Lamborelle and O Tapia, Chem. Phys., vol.42 (1979) p. 25-40 and O. Tapia and B. Silvi, J. Phys. Chem., vol. 84 (1980) p. 2646-2652). Tapia used the self-consistent reaction field theory and the virtual charge model to represent solvent polarization effects on small molecular systems, and on biomolecules as well. Basin on this approach J. Koput (from Institutte of Chemistry, Poznan University, Poland) modified MOPAC 5 packet introducing the correction for the electrostatic energy related to the Onsager reaction field [see: M. Szafran, M. M. Karelson, A. R. Katrizky, J. Koput and M. C. Zerner, J. Comput. Chem., vol. 14 (1993) p.371]. This correction proved to be really important for highly polar conformers immersed in a polarizable medium. Is it possible to introduce this option to the next version of HyperChem ? Jerzy Institute of Molecular Physics Polish Academy of Sciences Smoluchowskiego 17, 60179 PL Poznan, Poland Phone: (4861) 612360 Fax: (4861) 684524 -------------------------------------------------------------- From BEUTLER@DTPAX2.NCIFCRF.GOV Wed Feb 19 16:56:53 1997 Date: Wed, 19 Feb 1997 16:38:33 -0500 From: "John A. Beutler" Subject: Script Question Dear HyperCubists: Is there a simple way to script a series of MD/annealings so that the results are saved to a series of files? I don't see any obvious way to pass filenames or increment a variable within the script language. I'm using version 4. John A. Beutler -------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Feb 21 18:19:49 1997 Date: Fri, 21 Feb 97 12:45:02 -0500 From: barclay (Victoria Barclay) Subject: recalc/mea culpa Hi again Richard and HyperChemists, Last Friday, this question was posted: >Using Hyperchem 5.0 with an Excel macro (DDE commands). How can I >carry out mm+ geometry optimisations on one (selected) of two molecules >then optimise the converged conformation with a semi-empirical type >optimisation, without encountering the "recalculate atom types?" pop-up >box??. > I would like to know if there is a DDE command which can select "OK" >when this box appears, or perhaps there is a way of stopping Hyperchem >from asking in the first place. Any words of wisdom would be very much >appreciated. > And I replied that the solution would be to insert a line in the macro to the effect: EXECUTE(Channel,"[hide-warnings(yes)]") prior to doing the calculations. In principle, this should have worked. However, due to a small bug, it doesn't work, and the problem of the recurrent warning message does not go away. Fortunately our very responsive developers have come up with a patch. We are posting it at our ftp site, ftp.hyper.com, in the "support" directory. Download "chem501b.exe" (remember to set "bin on") and follow the instructions in the README file in the same directory. This patch includes the patches in "chem501a.exe" and supersedes it. In this patch, the "Recalculate atom types" warning will only be issued when the molecular mechanics method is changed by hand. When it is changed via a script, DDE or CDK, the warning will be automatically suppressed. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. -------------------------------------------------------------- From owner-hyperchem@hyper.com Tue Feb 25 20:18:53 1997 Date: Tue, 25 Feb 1997 08:08:26 -0800 (PST) From: Scott Kellogg Subject: NT 4.0 Menu Problems (fwd) ---------- Forwarded message ---------- Date: Wed, 19 Feb 1997 15:32:33 -0800 (PST) From: Scott Kellogg To: polowin@hyper.hyper.com Subject: NT 4.0 Menu Problems I am still having problems with a very slow response if I pick something from a menu. You tried to solve this in early december and I am now just get back to it. Has anything been learned about NT 4.0 or Hyperchem running on NT Workstation while a novell network is up and running that the Workstation is connected to? I have a standalone version of Hyperchem and I think that Hyperchem is going out to the net to look around rather than just looking at the lock. My printer is NOT directly connected to the PC but rather is a printer off of the server. I sure would like this problem fixed as Hyperchem is pretty unusable with this slow speed. Thanks. =================================================================== Scott T. Kellogg, Dept. of Microbiol., Mol. Biol. & Biochem. Univ. of Idaho, Moscow, ID 83844-3052 Internet: skellogg@uidaho.edu Phone: 208-885-6966 Fax: 208-885-6518 -------------------------------------------------------------- From owner-hyperchem@hyper.com Wed Feb 26 16:06:09 1997 Date: Tue, 25 Feb 97 05:42:32 CST From: "Irina K. Vorontsova" Subject: Fixing the geometric parameters Dear Netters, I'm interesting in the following question. Is there any possibility in HYPERCHEM to perform the calculations of the structures with the fixed geometric parameters (bond length, valent and torsion angles) in the framework of the molecular mechanic approach? Please use my direct e-mail account for replay. Thanks a lot in advance. Irina Vorontsova e-mail son@cc.nifhi.ac.ru -------------------------------------------------------------- From owner-hyperchem@hyper.com Wed Feb 26 16:17:23 1997 Date: Wed, 26 Feb 1997 07:55:11 -0600 From: David_DeBerry@radian.com (David DeBerry) Subject: Re: NT 4.0 Menu Problems (fwd) Scott, I had similar problems with Hyperchem 4.0 and NT 4.0 on a novell network. I finally "solved" it by getting an old dot matrix printer out of mothballs and installing it downstream of the dongle. Hyperchem 5.0 was supposed to solve this problem but they do not seem to be able to produce the version for NT which was promised 3 months ago. David ______________________________ Reply Separator _________________________________ Subject: NT 4.0 Menu Problems (fwd) Author: Scott Kellogg at Internet Date: 2/25/97 8:08 AM ---------- Forwarded message ---------- Date: Wed, 19 Feb 1997 15:32:33 -0800 (PST) From: Scott Kellogg To: polowin@hyper.hyper.com Subject: NT 4.0 Menu Problems I am still having problems with a very slow response if I pick something from a menu. You tried to solve this in early december and I am now just get back to it. Has anything been learned about NT 4.0 or Hyperchem running on NT Workstation while a novell network is up and running that the Workstation is connected to? I have a standalone version of Hyperchem and I think that Hyperchem is going out to the net to look around rather than just looking at the lock. My printer is NOT directly connected to the PC but rather is a printer off of the server. I sure would like this problem fixed as Hyperchem is pretty unusable with this slow speed. Thanks. =================================================================== Scott T. Kellogg, Dept. of Microbiol., Mol. Biol. & Biochem. Univ. of Idaho, Moscow, ID 83844-3052 Internet: skellogg@uidaho.edu Phone: 208-885-6966 Fax: 208-885-6518 -------------------------------------------------------------- From owner-hyperchem@hyper.com Wed Feb 26 20:16:40 1997 Date: Wed, 26 Feb 97 15:17:14 -0500 From: barclay (Victoria Barclay) Subject: NT 4.0 Menu Problems Date: Wed, 19 Feb 1997 15:32:33 -0800 (PST) From: Scott Kellogg Subject: NT 4.0 Menu Problems >I am still having problems with a very slow response if I pick something >from a menu. You tried to solve this in early december and I am now just >get back to it. Has anything been learned about NT 4.0 or Hyperchem >running on NT Workstation while a novell network is up and running that >the Workstation is connected to? I have a standalone version of Hyperchem >and I think that Hyperchem is going out to the net to look around rather >than just looking at the lock. My printer is NOT directly connected to >the PC but rather is a printer off of the server. I sure would like this >problem fixed as Hyperchem is pretty unusable with this slow speed. Hi Scott and HyperChemists, Yes, more has been learned about the Windows NT 4.0 situation. There are items on the Microsoft Knowledge Base which discuss a known incompatibility of Windows NT 4.0 with dongle drivers. There is a hot fix which is available from Microsoft. We have placed the details, including paths to the ftp site for the hot fix, on our web page. Go to our web page, www.hyper.com and look at the Support section. There, in the Frequently Asked Questions we have mounted a brand-new FAQ, number 27, which gives you the information. While you are there-- check out FAQ 30, which has links to the latest version of the dongle driver software that I posted a notice about earlier this year. You might also find the latest Novell updates are applicable to your particular version; have a look at http://support.novell.com/home/server/nos/updates.htm Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. -------------------------------------------------------------- From owner-hyperchem@hyper.com Wed Feb 26 21:29:06 1997 Date: Wed, 26 Feb 97 17:13:56 -0500 From: barclay (Victoria Barclay) Subject: Script Question From: "John A. Beutler" Subject: Script Question >Is there a simple way to script a series of MD/annealings so that the >results are saved to a series of files? I don't see any obvious way to >pass filenames or increment a variable within the script language. I'm >using version 4. Hi John and HyperChemists, With HyperChem 4.0, no. The scripting capabilities of HyperChem 4 are only "Type 1"-- no branch or loop structures are possible, and user-defined variables are not allowed. You're pretty much left with straight-line code. Basically what you can do is write a few lines which do what you want once, then duplicate them repeatedly in your text editor and modify each copy of the lines (if necessary). Like: dynamics-restart true open-file mystart.hin do-molecular-dynamics write-file result1.hin do-molecular-dynamics write-file result2.hin and so forth. The capabilities you want--Type 2 scripts-- are now available in HyperChem 5. Besides "old-style" scripts, Version 5.0 also contains the full-featured scripting language Tcl with loops, branches, variables, operators -- everything you need. For those readers who do have HyperChem 5 and want to add control structures to their scripts, please have a look at the "Chemist's Developer Kit" manual. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com -------------------------------------------------------------- From owner-hyperchem@hyper.com Thu Feb 27 17:41:05 1997 Date: Thu, 27 Feb 97 10:35:58 -0500 From: barclay (Victoria Barclay) Subject: downstream of dongle Date: Wed, 26 Feb 1997 07:55:11 -0600 From: David_DeBerry@radian.com (David DeBerry) Subject: Re: NT 4.0 Menu Problems (fwd) > I had similar problems with Hyperchem 4.0 and NT 4.0 on a novell > network. I finally "solved" it by getting an old dot matrix printer > out of mothballs and installing it downstream of the dongle. David, the symptoms you describe--having to place a printer downstream--sound very much like a low-power port problem to us. Have you tried the latest driver software? Rainbow Technologies has released version 5.3 of the drivers; one of the "fixed items" in this release is specifically for low-power ports. We've placed a direct link to the update on our FAQ page; please see question 30. > Hyperchem 5.0 was supposed to solve this problem but they do not seem > to be able to produce the version for NT which was promised 3 months > ago. The version for NT 4.0, HyperChem 5.01, has been shipping since the beginning of this year. The low-power port problem is something that the dongle software must address; the HyperChem program can't tackle the device driver work be it for dongles or printers; it just communicates with the drivers. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. -------------------------------------------------------------- From owner-hyperchem@hyper.com Thu Feb 27 18:17:09 1997 From: Gerardo Burton Subject: Network lock Date: Thu, 27 Feb 1997 13:59:53 -0300 Hello Victoria A couple of months ago I sent this problem to Joel who said he would try = and find out some more info on the license server operation. I would = appreciate if you could take a look at this problem, we are running = HyperChem 5.0 with a network lock (1 license): If the license timeout is set to a shorter time than the calculation = length, the license server will not release the license unless someone = else requests one after the timeout has occurred, Unfortunately this may = happen inadvertently, either because the calculation takes longer than = expected or because the calculation ended but the user was not there to = save the results before the license timed out. In any case, the new user = takes over the license unaware of the situation and leaves the former = calculation running (or waiting) in an unlicensed window. A similar = situation will result if the computer where the license server is = running has a problem and needs to be rebooted. We've tested the = situation and apparently the unlicensed window continues to run and = operate normally, even new calculations may be started without = reengaging the license. However, ocassionally, the unlicensed window = will check for its license and if it has been lost the only option is to = exit and the calculation is lost. Also under normal conditions but with = "heavy network traffic" a window may lose its license (it happened once = so far). In all these cases there is no message to the user informing = that the license has been lost until you try to open a menu and the only = option is to exit without being able to save the results. We couldn't = find a way of forcing HC to reconnect or recheck the license (unless you = exit and restart). Overall the system appears somewhat = unpredictable/unstable. The license timeout has a maximun limit of 60 minutes although Joel gave = me a workaround to this bug by editing the registry and putting a = timeout of up to 65000 minutes. Although this may help it will tie up = the license even after the calculation has ended, and until the first = user closes the window in his machine. Are there any ways of avoiding = these problems? A much safer alternative would be that the calculation be stopped if = the license is lost and allowed to continue once the license is = reestablished, with the option of saving the intermediate result. We = have another program with a similar protection system (Wibu key) which = operates in this way. Regards Gerardo Prof. Gerardo Burton e-mail: burton@qo.fcen.uba.ar Departamento de Quimica Organica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Tel/FAX 54 1 788-6915 -------------------------------------------------------------- From owner-hyperchem@hyper.com Thu Feb 27 18:40:31 1997 Date: Thu, 27 Feb 1997 12:02:11 -0600 From: David_DeBerry@radian.com (David DeBerry) Subject: how to set up a nonaqueous solvent box? Would someone post a few details on how to set up a "nonaqueous" solvent solvation box? I see how to calculate the number of molecules in the instruction manual, but I am not sure how to then "get started," create a box, add 100+ molecules, equilibrate, etc. Using Hyperchem 5.0 Thanks, David david_deberry@radian.com -------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Feb 28 16:20:01 1997 Date: Fri, 28 Feb 1997 08:38:54 -0500 From: underhil@me2.rmc.ca (Ross Underhill) Subject: Re: Script Question >From: "John A. Beutler" >Subject: Script Question > >>Is there a simple way to script a series of MD/annealings so that the >>results are saved to a series of files? I don't see any obvious way to >>pass filenames or increment a variable within the script language. I'm >>using version 4. > >Hi John and HyperChemists, > >With HyperChem 4.0, no. The scripting capabilities of HyperChem 4 Well actually there is a(nother) solution. You could write some of the script within visual basic (either within Excel or stand alone)and use DDE commands to make Hyperchem do as you want. I usually do this because you often want ot change some of the dynamics parameters as well or save some of the results. It owuld be easy to change filenames this way. Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario K7K 5L0 (613) 541-6000 X6175