From owner-hyperchem@hyper.com Fri Jun 2 07:35:57 1995 Date: Fri, 2 Jun 1995 09:26:24 +0100 To: chemistry@osc.edu From: bouyer@ext.jussieu.fr (Frederic BOUYER) Subject: Thermochemistry and Point Group Cc: hyperchem@hyper.com Hello Netters, Is anyone aware of thermochemistry based on structural and vibrational HF or DFT calculations to determine thermochemical functions? My problem is the following : I have two molecules (of the same stoechiometry) of which structural and energetic differences are very (around 5 10-5 Ha, DMol BLYP functional) very small. Only the point group is different, one is C3v, the other Cs. The rotational contribution on thermochemical functions is not the same, because of the symmetry number (3 or 1, depending on the point group) and the consequence is drastic on the free enthalpy of formation ! (about 12 kJ/mol, and around 3 for the order of magnitude on the reaction constant at 1300K) I don't know how to decide which symmetry I am to take into account (5 10-5 Ha is too small) (-by vibrational calculations only ? If I can get frequencies at this level of accuracy-). I have verified these thermo-quantities with a simple run with Gamess, and I have the same difference (12 kJ/mol) on the free enthalpie of reaction (with the same structures). Why is there a so big difference between these thermo-quantities for these two symmetries? I expected that thermochemical functions would be continuous vs. the structure. Any comments, suggestions ? Frederic Bouyer Lab.Electrochimie-ENSCP-Paris-France bouyer@ext.jussieu.fr http://alcyone.enscp.jussieu.fr/ http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/FB/ ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jun 8 08:56:37 1995 From: "Claus Scheuer-Larsen" Organization: Odense University To: hyperchem@hyper.com Date: Thu, 8 Jun 1995 10:01:43 GMT-1 Subject: minimization in DNA Hello Hyperchemists! I'm new in hyperchem, and I have some questions concerning this program. I'm working with the synthesis of modified nucleosides and oligonucleotides and would therefore like to hear other hyperchemists experience with DNA minimization. 1) Is is possible to e.g. minimize a pentamer of unmodified DNA, and compare the structure with a modified one ? (e.g. simple modifications in one sugar residue). 2) What force field is the best to use, and with what parameters? If you have some comments or solutions / experience with this kind of problems, please contact me. My adress is CSL@CHEM.OU.DK ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ You have received E-mail from: Claus Scheuer-Larsen Kemisk institut, Odense Universitet Campusvej 55, DK-5230 Odense M , Denmark Phone: 66158696, ext. 2524 Private: 4016517 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jun 12 14:24:16 1995 From: "John West" Date: Mon, 12 Jun 95 07:07:05 EDT To: hyperchem@hyper.com Subject: HyperChem on Solaris 2.4 or Wabi 2.0 Hyperchemists: Has anyone tried to run Hyperchem under Solaris 2.0 or Wabi 2.0 ? Send your replies directly to me and I will summarize. west west@qtp.ufl.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jun 12 15:02:49 1995 Date: Mon, 12 Jun 95 16:08:07 +0100 From: "Ronald Wiegers" Subject: Ribbon Color and/or Width To: hyperchem@hyper.com Hi, Please let me know whether it is possible to modify the color and/or the width of the "ribbon", since for studying larger proteins, the ribbon is too wide and too brightly colored. In the manuals I cannot find any clue. ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jun 12 17:46:33 1995 Date: Mon, 12 Jun 95 12:47:42 -0400 From: polowin (Joel Polowin) To: hyperchem@www Subject: Re: Ribbon Color and/or Width Cc: ronw@gpa.fuji-ef.nl > Date: Mon, 12 Jun 95 16:08:07 +0100 > From: "Ronald Wiegers" > Subject: Ribbon Color and/or Width > > Please let me know whether it is possible to modify the > color and/or the width of the "ribbon", since for studying > larger proteins, the ribbon is too wide and too brightly > colored. In the manuals I cannot find any clue. At the moment, there is no easy way to change these features of the SGI HyperChem "ribbon" display. I'll add it to the wish-list for Release 4.5 for SGI, which will be shipping by the end of July. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jun 12 18:55:28 1995 Date: Mon, 12 Jun 95 14:50:34 -0400 From: polowin (Joel Polowin) To: "Claus Scheuer-Larsen" Subject: Re: minimization in DNA Cc: hyperchem@www > From: "Claus Scheuer-Larsen" > Date: Thu, 8 Jun 1995 10:01:43 GMT-1 > Subject: minimization in DNA > > I'm working with the synthesis of modified nucleosides and > oligonucleotides and would therefore like to hear other hyperchemists > experience with DNA minimization. > > 1) Is is possible to e.g. minimize a pentamer of unmodified DNA, and > compare the structure with a modified one ? (e.g. simple modifications > in one sugar residue). Yes. (Though after you modify a residue manually, you can no longer use the MUTATE function on that residue.) You can even create your own modified nucleosides and add them to the standard template list so that you can work with them with the Databases dialogue boxes. > 2) What force field is the best to use, and with what parameters? This is likely to depend very strongly on what you want to do with your structures, and how you are modifying them from the regular ones. The OPLS, BIO+, and AMBER force fields were optimized for biological macromolecules, but have some limitations in their parameters. The MM+ force field is more general and can handle a much greater variety of structures. If you make some kinds of modifications to known structures, you will not be able to model them with one or more of OPLS, BIO+, and AMBER unless you define new parameters. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jun 12 19:24:16 1995 Date: Mon, 12 Jun 95 14:50:34 -0400 From: polowin (Joel Polowin) To: "Claus Scheuer-Larsen" Subject: Re: minimization in DNA Cc: hyperchem@www > From: "Claus Scheuer-Larsen" > Date: Thu, 8 Jun 1995 10:01:43 GMT-1 > Subject: minimization in DNA > > I'm working with the synthesis of modified nucleosides and > oligonucleotides and would therefore like to hear other hyperchemists > experience with DNA minimization. > > 1) Is is possible to e.g. minimize a pentamer of unmodified DNA, and > compare the structure with a modified one ? (e.g. simple modifications > in one sugar residue). Yes. (Though after you modify a residue manually, you can no longer use the MUTATE function on that residue.) You can even create your own modified nucleosides and add them to the standard template list so that you can work with them with the Databases dialogue boxes. > 2) What force field is the best to use, and with what parameters? This is likely to depend very strongly on what you want to do with your structures, and how you are modifying them from the regular ones. The OPLS, BIO+, and AMBER force fields were optimized for biological macromolecules, but have some limitations in their parameters. The MM+ force field is more general and can handle a much greater variety of structures. If you make some kinds of modifications to known structures, you will not be able to model them with one or more of OPLS, BIO+, and AMBER unless you define new parameters. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ ________________________________________________________________________ From owner-hyperchem Fri Jun 16 16:44:12 1995 Return-Path: mcaffery@keller.clarke.edu Date: Fri, 16 Jun 1995 15:48:34 -0500 (CDT) From: "S. Mary Lou Caffery" To: hyperchem@hyper.com Subject: returning arrays to excel I would like help in writing a line in an Excel macro that returns the values of an array from Hyperchem to Excel. Example: I would like the alpha-scf-eigenvector list returned to Excel Currently I have a line similar to the one in your sample macro (page 350 in Reference guide) = FORMULAARRAY(REQUEST(Channel, "alpha-scf-eigenvector"),"rc[5]') My macro works but all of the items end up in the same cell. I haven't been able to find the place in the Excel manual that might help get the values into individual cells - preferably in the same row but in columns 5 through 10. Any suggestions would be helpful. If you have any other example EXCEL Macros you could share it would be helpful! Thanks Mary L. Caffery, Ph.D. Department of Chemistry Clarke College 1550 Clarke Drive Dubuque, IA 52001-3198 EMAIL: mcaffery@keller.clarke.edu VOICE: 319-588-6363 FAX: 319-588-6789 ________________________________________________________________________ From owner-hyperchem Sun Jun 18 14:41:03 1995 Return-Path: graham@sentex.net Date: Sun, 18 Jun 1995 14:48:54 -0400 To: "S. Mary Lou Caffery" , hyperchem@hyper.com From: graham@sentex.net (Graham Hurst) Subject: Re: returning arrays to excel On 6/16/95, S. Mary Lou Caffery wrote: >I would like help in writing a line in an Excel macro that returns the >values of an array from Hyperchem to Excel. >Example: I would like the alpha-scf-eigenvector list returned to Excel >Currently I have a line similar to the one in your sample macro (page >350 in Reference guide) > > = FORMULAARRAY(REQUEST(Channel, "alpha-scf-eigenvector"),"rc[5]') > >My macro works but all of the items end up in the same cell. I haven't been >able to find the place in the Excel manual that might help get the values >into individual cells - preferably in the same row but in columns 5 >through 10. Any suggestions would be helpful. In Excel 5, the Text to Columns command under the Data menu does the trick. Recording this as an Excel 4 macro gives the TEXT.TO.COLUMNS command. Recording this as a VBA macro uses Selection.TextToColumns. In both cases there are a bunch of arguments that can be specified. I vaguely recall that the command was called PARSE in earlier versions of Excel (and "parsing" is a good keyword to search the online help with for related information). Hope this helps, Graham ------- Graham Hurst, PhD or Cambridge, Ontario, Canada ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jun 19 10:54:41 1995 From: "Gregor Fels" Organization: Universitaet-GH Paderborn FB13 To: hyperchem@hyper.com Date: Mon, 19 Jun 1995 11:48:26 GST Subject: comparison of AM1-energies Dear HyperChemists, how do I compare relative energies from AM1-geometrical optimizations? e.g. cis- and trans-(2)-butene yields: 1. with molecular mechanics methods (MM+) for cis (2)-Butene: Energy=1.556775 for trans (2)-Butene: Energy=0.132888 This is o.k. as comparison of these numbers would be meaningful. 2. with semiempirical methods (AM1): for cis (2)-Butene: Total Energy = -14349.7152696 (kcal/mol) Total Energy = -22.867270305 (a.u.) for trans (2)-Butene: Total Energy = -14350.8569853 (kcal/mol) Total Energy = -22.869089709 (a.u.) In this case however a comparison of numbers (from a log-file) does not seem to be meaningful as you have a small difference of two large numbers. Is there any other way to deal with AM1-enegetical differences of isomeric structures? G. Fels Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 0049-5251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jun 19 17:33:21 1995 From: "Gregor Fels" Organization: Universitaet-GH Paderborn FB13 To: hyperchem@hyper.com Date: Mon, 19 Jun 1995 19:15:41 GST Subject: Excel-Macros Dear HyperChemists, some time ago there was an announcement for an Excel-Macro that generates 3-D energy-surfaces from HyperChem structures (varying torsion angles and/or bond length). Could somebody point me to where I can download this from? Regards Gregor Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 0049-5251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jun 19 21:39:51 1995 Date: Mon, 19 Jun 95 17:48:46 -0400 From: polowin (Joel Polowin) To: "Gregor Fels" Subject: Re: comparison of AM1-energies Cc: hyperchem > From: "Gregor Fels" > Date: Mon, 19 Jun 1995 11:48:26 GST > Subject: comparison of AM1-energies > > e.g. cis- and trans-(2)-butene yields: > 1. with molecular mechanics methods (MM+) > for cis (2)-Butene: Energy=1.556775 > for trans (2)-Butene: Energy=0.132888 > This is o.k. as comparison of these numbers would be meaningful. > 2. with semiempirical methods (AM1): > for cis (2)-Butene: Total Energy = -14349.7152696 (kcal/mol) > Total Energy = -22.867270305 (a.u.) > for trans (2)-Butene: Total Energy = -14350.8569853 (kcal/mol) > Total Energy = -22.869089709 (a.u.) > > In this case however a comparison of numbers (from a log-file) does > not seem to be meaningful as you have a small difference of two large > numbers. You *do* have a small difference of two large numbers, but you have plenty of digits of precision, and the results are reasonable. From MM+, you got an energy difference of 1.42 kcal/mol, and from AM1 you got a difference of 1.14 kcal/mol. This appears to be reasonable agreement between the two radically differnet methods. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jun 20 16:45:19 1995 Date: Tue, 20 Jun 95 11:33:20 -0400 From: polowin (Joel Polowin) To: GF@chemie.uni-paderborn.de, info@thstech.com Subject: Re: Excel-Macros Cc: hyperchem@www > From: "Gregor Fels" > Date: Mon, 19 Jun 1995 19:15:41 GST > > Dear HyperChemists, > some time ago there was an announcement for an Excel-Macro that > generates 3-D energy-surfaces from HyperChem structures (varying > torsion angles and/or bond length). Could somebody point me to where > I can download this from? I've just put this PHIPSI macro, and two other macros, up on our WWW server, http://www.hyper.com, under Utilities/Macros. They're also available by ftp from ftp.hyper.com, in /pub/macros; the file names are phipsi.xlm, ribosebb.xlm, and nh2selec.xlm . We're sorry about the delay in construction of our home page; we've been a bit busy getting HyperChem Release 4.5 out of the nest. It's shipping now. >From: info@thstech.com (Schmelz Technologie-Dienstleistungen) >Date: 20 Jun 1995 08:47:00 +0200 > >In Germany however (working with a german Excel version) this >macro needs 'reprocessing'. I think we've got it somewhere ... >But I'm not shure whether it can be redistributed without the package >(Hello Hypercube ? Tell me !) Yes, this macro can be redistributed; copyright notices and so forth must of course be left intact! In what way does the macro need to be changed? I would have expected that when it was read into a non-English version of Excel, the tokens would be expanded into their other-language instructions but that text strings and functionality would not be changed. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jun 20 18:55:56 1995 Date: Tue, 20 Jun 1995 14:15:48 -0500 (CDT) From: "S. Mary Lou Caffery" To: hyperchem@hyper.com Subject: chemplus trouble I was using ChemPlus to write some Scripts and have had a problem ... I had a "General Protection Error..." while running one of my scripts. After restarting Windows and Chemplus I got a message "ChemPlus Failed to attach itself to the Hyperchem Window" I tried reloading Chemplus from the original disks but continue to get the same error.... Where do I go from here? Mary L. Caffery, Ph.D. Department of Chemistry Clarke College 1550 Clarke Drive Dubuque, IA 52001-3198 EMAIL: mcaffery@keller.clarke.edu VOICE: 319-588-6363 FAX: 319-588-6789 ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jun 21 00:38:40 1995 From: MOCALC@emuvax.emich.edu Date: Tue, 20 Jun 1995 21:24:06 -0400 (EDT) To: hyperchem@hyper.com Subject: installation problem Dear Hyperchem users, I am having difficulties running Hyperchem Release 4. The first time I installed to program everything worked perfectly. However, when I needed to reinstall the program on a new computer, the program no longer worked. I tried to install the program again on the first computer, but I was not successful this time. The tool icons seem to work properly. But when I attempt to use the menu bar, the message, "attempting to acquire a license to run Hyperchem", appears. Then a warning dialog box appears with the message, "No available licenses. Try again later." Another unusual thing I noticed is that when I install Hyperchem from the four floppies to my computer's hard drive, the dialog box for the fourth floppy only shows that 72% of the data was transferred. The installation then seems to complete normally. I have also checked the win.ini files. The information that was supposed to be there was not. I entered it, and then saved it. Unfortunately, this did not work either. Each computer was a Dell with a 75 MHz Pentium processor. I have Windows 3.1, DOS 5.0, and the hardware lock installed snugly to the parallel port. I believe that I have followed the installation procedures in the Hyperchem manual correctly. If you have any suggestions, I would greatly appreciate it if you would pass them along to me. I really enjoyed the program while it was working, and I am anxious to try it again!!! Thank you, John Goldsmith ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jun 21 16:40:29 1995 Date: Wed, 21 Jun 95 11:46:18 -0400 From: polowin (Joel Polowin) To: hyperchem@hyper.com Subject: HyperChem list administrivia Sorry for taking up bandwidth, but this in the interest of saving later trouble... In response to a recent wave of messages requesting unsubscriptions from this list that have been sent to everybody, I would like to remind everyone that these administrative messages should be sent to hyperchem-request@hyper.com and NOT to hyperchem@hyper.com, which sends them to everyone, who generally don't care to see them. Specifically, someone who wishes to unsubscribe should send the message unsubscribe hyperchem to hyperchem-request@hyper.com . To subscribe or unsubscribe an address other than the one you're sending the message from, send a message of the form subscribe hyperchem youracct@your.other.org and it will go to the list administrator (i.e., me) to be processed. Thanks. Regards, ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 Jun 21 21:22:13 1995 Date: Wed, 21 Jun 95 17:46:51 -0400 From: polowin (Joel Polowin) To: "John West" Subject: Re: HyperChem on Solaris 2.4 or Wabi 2.0 Cc: hyperchem@www > From: "John West" > Date: Mon, 12 Jun 95 07:07:05 EDT > Subject: HyperChem on Solaris 2.4 or Wabi 2.0 > > Has anyone tried to run Hyperchem under Solaris 2.0 or Wabi 2.0 ? > Send your replies directly to me and I will summarize. I've heard back from Rainbow Technologies, who manufacture the hardware locks. I was told that they do not currently have any support for any sort of Wabi. A request-for-development will be filed, but we shouldn't expect anything at all soon. We've been having reasonably good results in running HyperChem and ChemPlus under beta-test versions of Windows 95 -- on some machines. So far, the critical factor seems to be whether or not Win95 was installed over a previous installation of Windows; if so, a whole lot of errors show up which give the appearance of the sort of DDE errors that we've seen caused by the language and comma/decimal-point settings in Windows. (The problem only *appears* to be DDE-related; it actually involves incompatible library functions.) When Win95 is installed without a previous Windows installation, things seem to work properly. We'd appreciate any relevant comments from users. At least one of the 486 boards for PowerMacs does not provide support of a parallel port, and so will not let HyperChem run for lack of a place to connect the hardware lock. If anyone knows of one of these boards that *does* run a parallel port, again, we'd really like to hear about it. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 Jun 22 17:56:57 1995 Date: Thu, 22 Jun 95 13:17:01 -0400 From: polowin (Joel Polowin) To: Wolfgang=Ziche@rz.hu-berlin.de Subject: re: Re: Excel-Macros Cc: hyperchem@www > From Wolfgang=Ziche@rz.hu-berlin.de Thu Jun 22 08:29:00 1995 > Date: Thu, 22 Jun 95 13:31:40 MDT > Subject: re: Re: Excel-Macros > > Hello HyperChemers, > > The EXCEL macro PhiPsi (I had it from ChemPlus package) is really fine for > visualizing hypersurfaces. However, as already noticed it needs some manual > rewriting for "foreign" EXCEL versions. The German version 4.0 does not > translate the "r" and "c" for row and column. These have to be replaced by > "Z" and "S". Interesting. Thanks for telling us! It appears that the problem is that these are entered as text strings, and so are not translated. I will note this problem on the bug list, though I am not sure what we can do about this problem. > In line 169 I detected a bug (my version of PhiPsi) that causes > trouble only when "revert to exact angles" is checked: it reads " vl > Optim.ok" and should be "vlOptim.flag". That seems odd. It may be another translation artifact. In this macro on my machine, cell A168 contains the text 'vIOptim.ok', in italics. Cell B168 contains '= REQUEST(Channel,"optim-converged")' and has the name 'vIOptim.ok' applied to it. Then the instruction in B169 references that result by name. To get the result that you describe, it seems to me that the name for cell B168 would have to have been changed to 'vlOptim.flag'. Is this correct? Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 Sat Jun 24 23:38:44 1995 From: "John West" Date: Sat, 24 Jun 95 20:38:42 EDT To: hyperchem@hyper.com Subject: Summary of HyperChem on Solaris Hello HyperChemists: I posted the following question to the list two weeks ago: Has anyone tried to run HyperChem under Solaris 2.4 or Wabi 2.0? The replies that I recieved are presented below. Many thanks to Joel Polowin and Jim Newhouse for their helpful replies. John West ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From: polowin@hyper.hyper.com (Joel Polowin) > > Has anyone tried to run HyperChem under Solaris 2.4 or Wabi2.0 ? I've just spoken with someone at Rainbow Technologies, the makers of the locks and management software. They don't yet have a port driver for those systems, though I was assured a couple of months ago that they'd see what they could do. The fellow I was speaking with suggested that our software might work without a special driver, but I've had no reports of anyone doing so successfully. I'm still waiting to hear back from the fellow I was dealing with before who is (I hope) more aware of our particular problem. I left a message for him a few hours ago. ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Return-Path: From: newhojs@duc.auburn.edu (James S Newhouse) Hi, this is Jim Newhouse, an analyst on the Alabama Supercomputer Network located at Auburn University. I have visualization workstations located in various departments at Auburn. One is a SparcStation 10 in Pharmacy that runs Solaris 2.4 and Wabi 2.0 (I administer the machine for them and put up all software). Since I am a physical chemist, I thought it would be convenient for them to be able to use HyperChem on the workstation, so I attempted putting their copy up, but the hardware lock is of course the problem. I've talked with the HyperCube people, exchanging email. The hardware lock technology is obtained from Rainbow, and they haven't addressed a patch for accessing the lock on the Sun (as they have under Windows NT; a feature I use on my Pentium at home). Until Rainbow gets around to it, it won't be available. I have heard of boards designed to read the hardware lock encoding (and thus defeat its purpose), but I haven't heard of one for the Sun (and my conscience would probably bother me anyway :-) I have been introducing the pharmacists (and biochemists) to rational drug design using an inexpensive suite of programs--Connolly's MS, DelPhi, DOCK (from the Kuntz group at UCSF), Midas Plus, and Amber (which we run on our C90). The HyperChem is useful in manipulating the Protein Data Bank files (which need repairs often). The Amber trajectories are visualized with viewers like MOIL-View8 (which has NTSC video capabilities) and Scarecrow on an Indigo 2 with Extreme Graphics (another of the visualization machines, located in Chemistry). Jim *************************************************************************** Dr. James S. Newhouse 144 Parker Hall Research Scientist/Analyst Auburn University on Alabama Supercomputer Network Auburn, Alabama 36849 for Nichols Research Corporation Phone: (205) 844-4512 e-mail: newhojs@mail.auburn.edu on ASN: asnjsn01@asnmail.asc.edu *************************************************************************** +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >From polowin@hyper.hyper.com Wed Jun 21 22:54 EDT 1995 Subject: Re: HyperChem on Solaris 2.4 or Wabi 2.0 I've heard back from Rainbow Technologies, who manufacture the hardware locks. I was told that they do not currently have any support for any sort of Wabi. A request-for-development will be filed, but we shouldn't expect anything at all soon. We've been having reasonably good results in running HyperChem and ChemPlus under beta-test versions of Windows 95 -- on some machines. So far, the critical factor seems to be whether or not Win95 was installed over a previous installation of Windows; if so, a whole lot of errors show up which give the appearance of the sort of DDE errors that we've seen caused by the language and comma/decimal-point settings in Windows. (The problem only *appears* to be DDE-related; it actually involves incompatible library functions.) When Win95 is installed without a previous Windows installation, things seem to work properly. We'd appreciate any relevant comments from users. At least one of the 486 boards for PowerMacs does not provide support of a parallel port, and so will not let HyperChem run for lack of a place to connect the hardware lock. If anyone knows of one of these boards that *does* run a parallel port, again, we'd really like to hear about it. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jun 26 16:19:16 1995 To: hyperchem@hyper.com From: chen@pop.tuwien.ac.at (Qing-Qi Chen) Date: Mon, 26 Jun 1995 14:54:57 +0000 Dear Hyperchemers, I am an M.D. with little background on hardcore Chemistry, just starting to use Hyperchem as a tool to predict shapes of antigenic oligopeptides. I would like to know about basic literature on molecular modeling/molecular dynamics of oligopeptides concerning both the parameters used (algorithm, time and temperature of run, dielectric constant, minimization in water, etc) that I can find in books or published papers. Gratefully, Edecio Cunha-Neto, M.D., Ph.D. Lab of Transplantation Immunology Faculty of Medicine, Universidade de Sao Paulo, Brazil ........................................................................... Univ. Doz. Dr. Ulrich Jordis Dr. Ulrich Jordis, Associate Professor Institut fuer Organische Chemie Institute of Organic Chemistry Technische Universitaet Wien TU Vienna Getreidemarkt 9/154 Getreidemarkt 9/154 A-1060 Wien / Oesterreich A-1060 Vienna / Austria Tel: +43 (1) 58801.5013 Handy: +43 663 086962 Fax: +43 (1) 586 6931 ........................................................................... ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jun 28 20:44:11 1995 Date: Wed, 28 Jun 95 15:36:43 -0400 From: polowin (Joel Polowin) To: hyperchem@www Subject: Non-English Excel users We've got a test version of the PHIPSI macro for Excel that should work properly in non-English versions of the spreadsheet. It works around the problems caused by the spreadsheet expecting strings other than the English "true"/"false", and rows and columns designated by "R" and "C". The file is available by ftp from ftp.hyper.com, /pub/macros/phipsia.xlm, or from our WWW server, http://www.hyper.com in the Software Archives under Macros. If you use a non-English version of Excel, please try out this updated macro and let me know if it does the job. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@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 Fri Jun 30 07:34:43 1995 Date: Fri, 30 Jun 1995 08:58:01 +0100 To: chemistry@osc.edu From: bouyer@ext.jussieu.fr (Frederic BOUYER) Subject: MNDO/d softwares and sparkles Cc: hyperchem@hyper.com Hello everybody, 1 - Is there MNDO/d softwares in the public domain (possibly commercial programs) ? 2 - My problem is that counter-cations, like Na, ..., are taken into account like sparkles; their charge is +1, ... . Is there a semi-empirical program, or new parameters of Mopac, or new hamiltonians, that treat correctly counter-cations? (except Hartree-Fock or DFT programs) Thank you in advance for responding. Frederic Bouyer Lab. Electrochimie et Chimie Analytique ENSCP-CNRS, Paris, France bouyer@ext.jussieu.fr http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/FB/