From owner-hyperchem@hyper.com Mon Oct 2 10:03:35 1995 Date: Mon, 2 Oct 1995 9:16:08 UTC+0100 From: "Jose G. de la Campa" Subject: windows 95 To: hyperchem@hyper.com We have been using windows 95 for the last 4 months (beta versions) and had several problems of DDE between Hyperchem and Chemplus (the same problems you can find if you do not set the language correctly in Windows 3.1) As we read the same history about the problems with the previous versions of Windows 3.1, we reformated the hard disk and installed it again, without previous versions, but nothing improved and the problems were the same. However, now we have installed the commercial final version of Windows 95 and, if you use English as language, everything is all right and there is no problems, at least in our case. Best Regards Jose G. de la Campa Instituto de Ciencia y Tecnologia de Polimeros (C.S.I.C.) Madrid, Spain ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Oct 2 14:18:34 1995 From: "Deon Steyn" Organization: UOFS To: hyperchem@hyper.com Date: Mon, 2 Oct 1995 16:13:11 GMT2 Subject: Selective printing to log file? Can anybody help? I am in the process of developing molecular machenics force field parameters for a group of metal complexes. For this I need to print only the "stretch and bend info" to the relevant log-file during a single point calculation after the geometries for each of sixteen complexes are obtained by geometry optimizations utilizing the developed force field. The problem is that it takes a while to write sixteen log files containing ALL the info and it seems that there is no difference between what you get when you set the MolecularMechanicsPrintLevel to 1,2, or 3 in the CHEM.ini file. What I thus want is a way to print ONLY stretch and bend info to the log file. Is it possible? It feels to me as if the hard disk is taking too much of as hammering when info is written to it for half an hour non-stop! I will have to do this plenty of times! May be this is OK? I will appreciate any comments including anything on my sympathetic feeling toward my hard disk! Regards Deon Steyn (Ph.D) Department of Chemistry University of the Orange Free State South-Africa ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Oct 4 00:52:53 1995 Date: Tue, 3 Oct 95 14:18:08 -0400 From: polowin (Joel Polowin) To: hyperchem@www Subject: Re: Selective printing to log file? > From: "Deon Steyn" > Date: Mon, 2 Oct 1995 16:13:11 GMT2 > I am in the process of developing molecular machenics force field > parameters for a group of metal complexes. For this I need to > print only the "stretch and bend info" to the relevant log-file > during a single point calculation after the geometries for > each of sixteen complexes are obtained by geometry > optimizations utilizing the developed force field. The problem > is that it takes a while to write sixteen log files containing > ALL the info and it seems that there is no difference between > what you get when you set the MolecularMechanicsPrintLevel to > 1,2, or 3 in the CHEM.ini file. Those settings determine whether or not dipole data and van der Waals energy information are included in the log; they don't affect the amount of information about the stretch, bend, and other energy contributions which is saved in the file. > What I thus want is a way to print ONLY stretch and bend > info to the log file. Is it possible? It feels to me as if the > hard disk is taking too much of as hammering when info is > written to it for half an hour non-stop! I will have to do > this plenty of times! May be this is OK? There isn't a way to specify that a detailed list of *some* energy factors but not others should be saved. All that I can think of off-hand is to set up a RAMDRIVE on your system, and save the log file to that "disk" and "directory" in RAM. Then you can cut out the unwanted parts of the log file before you save it to a real disk. Obviously, this requires that you have enough RAM that you can afford to tie up at least as much of it as the size of the log file you need to save. The most convenient way to process a large file to keep only selected parts, if you know the format of the file, is to use a text utility of some kind. The program AWK can be used to print all lines of an input file that lie between lines containing specified search terms -- for example, to look for lines containing "Bond lengths" and "Van der Waals" and print all the lines between them. Several shareware/freeware versions of AWK are available from a variety of sources -- for example, by ftp from the SimTel archive (machine: ftp.coast.net; directory: SimTel/msdos/awk), or with a WWW browser (ftp://ftp.coast.net/SimTel/msdos/awk). To do keyword searches on large text files, a variety of other utilities are available. My favourite (because I wrote it) is also available from the SimTel archive (directory: SimTel/msdos/textutil; file: filtr30.zip; by WWW browser, ftp://ftp.coast.net/msdos/textutil/filtr30.zip). 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 Oct 5 21:57:04 1995 Date: Thu, 5 Oct 95 12:24:51 -0400 From: polowin (Joel Polowin) To: hyperchem@www Subject: Network HyperChem & PowerMacs People run HyperChem on a variety of network configurations, and usually I get to hear only about the setups that cause trouble. When someone calls to ask if some peculiar configuration will work, I often can't give a definite answer. The following may be of some general interest. The most critical reason that HyperChem can't be run on a PowerMac, even with the 486 boards that are now available, is that the PowerMac doesn't have a parallel port that the hardware lock can be attached to. I was just asked if it was possible to use the network version of HyperChem, with the lock on a PC elsewhere on the network, and with HyperChem running under Windows on a 486 board in a PowerMac. It looks like it *should* work, but we don't know, and we don't have the hardware to find out. Have any of you tried something like this, and if so, what results have you got? 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 Oct 7 11:38:43 1995 From: Journal of Molecular Modeling Subject: Acceptance of the J.Mol.Model. WWW-homepage To: hyperchem@www Date: Sat, 7 Oct 95 14:05:40 MET THANKS ! The Journal of Molecular Modeling has gained a very wide acceptance. We did count a total of 150,000 visits to the Journal of Molecular Modeling WWW-homepage in the first 39 weeks of operation and a peak of almost 12,500 visits in one week. We are currently running at a steady 8,000 visits per week, which suggests that people are using the Journal of Molecular Modeling abstracts actively. Once again, thanks for your support. Best wishes Tim Clark If you have a good paper looking for a home - don't forget us. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ Journal of Molecular Modeling ^ Tel: [+49](0)9131 / 85-2948 ^ ^ Computer-Chemie-Centrum ^ [+49](0)9131 / 85-6567 ^ ^ Universitaet Erlangen-Nuernberg ^ ^ ^ Naegelsbachstrasse 25 ^ Fax: [+49](0)9131 / 85-6565 ^ ^ D-91052 Erlangen ^ ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ email: jmolmod@organik.uni-erlangen.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ URL: http://www.organik.uni-erlangen.de/info/JMOLMOD/jmolinfo.html ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Oct 10 18:08:22 1995 Date: Tue, 10 Oct 1995 14:56:24 -0500 (EST) From: "David W. Ewing (216) 397-4241" Subject: printer/plotter To: hyperchem@hyper.com Fellow HyperChemists: I have $500 - $1000 to spend on a printer (does anyone still make a "printer/plotter"?). What have other users found that works well in outputing structures, orbitals, etc. from HyperChem. Just a decent color laser printer? My first HyperChem station has a plotter, but I wanted the second station to have a more versatile output device. Thanks! Dave Ewing John Carroll University ewing@jcvaxa.jcu.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Oct 10 22:51:43 1995 Date: Tue, 10 Oct 1995 15:53:02 -0700 (PDT) From: Scott Kellogg To: "David W. Ewing (216) 397-4241" Cc: hyperchem@hyper.com Subject: Re: printer/plotter My vote is for the Primera Pro color printer. It only works with Windows but that's most software currently. It does both thermal wax and dye sublimation (paper or transparency). The dye sublimations are incredible and look just like color photographic prints. Print costs range from $0.50 to $2.50, while the printer is around $1,100-$1,200. I don't know of any color lasers that cheap yet. For quick and dirty color printing I use an inexpensive HP inkjet (540/560). On Tue, 10 Oct 1995, David W. Ewing (216) 397-4241 wrote: > Fellow HyperChemists: > > I have $500 - $1000 to spend on a printer (does anyone still > make a "printer/plotter"?). What have other users found that works well in > outputing structures, orbitals, etc. from HyperChem. Just a decent color > laser printer? My first HyperChem station has a plotter, but I wanted the > second station to have a more versatile output device. > > Thanks! > > Dave Ewing > John Carroll University > ewing@jcvaxa.jcu.edu > > ________________________________________________________________________ From polowin Wed Oct 11 22:11:42 1995 Date: Wed, 11 Oct 95 10:11:59 -0400 From: polowin (Joel Polowin) To: "David W. Ewing (216) 397-4241" Subject: Re: printer/plotter Cc: hyperchem@www > Date: Tue, 10 Oct 1995 14:56:24 -0500 (EST) > From: "David W. Ewing (216) 397-4241" > > I have $500 - $1000 to spend on a printer (does anyone still > make a "printer/plotter"?). What have other users found that works well in > outputing structures, orbitals, etc. from HyperChem. Just a decent color > laser printer? My first HyperChem station has a plotter, but I wanted the > second station to have a more versatile output device. Well, I should offer a warning that HyperChem doesn't like to send "Spheres" rendered pictures to the current versions of the device drivers for HP660C and HP850C printers. It appears that HyperChem generally starts to print a picture by sending a message to the printer driver -- something like "what kind of printer are you?" or "can you draw this kind of picture element?" It is interpreting the response from those drivers to mean that they are for something like a pen plotter. I don't know yet if HyperChem is asking the wrong question, or misunderstanding the answer -- or if the drivers are replying incorrectly. Sticks, dots, and disks are all fine with those printers -- anything but spheres. ChemPlus works properly with those printers, in all modes as far as I know. There are no problems if a picture is saved as a bitmap or metafile, imported to other software, and printed from there. And I suspect that if one used a driver for a different HP colour printer and sent the output to one of these printers, everything would be fine. In general, any printer supported by a Windows printer driver *should* be fine. We have an order in for an HP660 so that we can try to solve the problem, but it hasn't arrived yet. 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 Wed Oct 11 22:20:26 1995 Date: Wed, 11 Oct 95 10:11:59 -0400 From: polowin (Joel Polowin) To: "David W. Ewing (216) 397-4241" Subject: Re: printer/plotter Cc: hyperchem@www > Date: Tue, 10 Oct 1995 14:56:24 -0500 (EST) > From: "David W. Ewing (216) 397-4241" > > I have $500 - $1000 to spend on a printer (does anyone still > make a "printer/plotter"?). What have other users found that works well in > outputing structures, orbitals, etc. from HyperChem. Just a decent color > laser printer? My first HyperChem station has a plotter, but I wanted the > second station to have a more versatile output device. Well, I should offer a warning that HyperChem doesn't like to send "Spheres" rendered pictures to the current versions of the device drivers for HP660C and HP850C printers. It appears that HyperChem generally starts to print a picture by sending a message to the printer driver -- something like "what kind of printer are you?" or "can you draw this kind of picture element?" It is interpreting the response from those drivers to mean that they are for something like a pen plotter. I don't know yet if HyperChem is asking the wrong question, or misunderstanding the answer -- or if the drivers are replying incorrectly. Sticks, dots, and disks are all fine with those printers -- anything but spheres. ChemPlus works properly with those printers, in all modes as far as I know. There are no problems if a picture is saved as a bitmap or metafile, imported to other software, and printed from there. And I suspect that if one used a driver for a different HP colour printer and sent the output to one of these printers, everything would be fine. In general, any printer supported by a Windows printer driver *should* be fine. We have an order in for an HP660 so that we can try to solve the problem, but it hasn't arrived yet. 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 Oct 12 18:53:50 1995 Date: Thu, 12 Oct 1995 13:20:48 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: Gibbs Free Energy To: hyperchem@hyper.com, support@hyper.com Cc: chemistry@infomeister.osc.edu Hi, I am a user of HyperChem and I am interested in calculating Gibb's free energy of formation of complexes formed between calixarenes and neutral guests such as toluene. In the past somebody mentioned that while HyperChem cannot do this directly, a macro in excel could be written. What exactly should I get the macro to do? Secondly, while I know that the energies obtained in a molecular mechanics calculation have no absolute meaning, would the difference in energies of two optimised conformations of the same complex have any meaning? If so, what kind of energy are we talking about? Thirdly, is it possible to determine the contribution to each of the above energies made by the different types of interaction (van der Waals, pi-pi) between the host and the guest? Kind Regards, Paddy. Paddy Kane Dublin City University 94970459@vax1.dcu.ie ________________________________________________________________________ From owner-hyperchem@hyper.com Fri Oct 13 19:04:01 1995 Date: Fri, 13 Oct 95 15:43:30 -0400 From: polowin (Joel Polowin) To: Paddy Kane <94970459@vax1.dcu.ie> Subject: Re: Gibbs Free Energy Cc: hyperchem@www > Date: Thu, 12 Oct 1995 13:20:48 +0000 (GMT) > From: Paddy Kane <94970459@vax1.dcu.ie> > > I am a user of HyperChem and I am interested in calculating Gibb's free > energy of formation of complexes formed between calixarenes and neutral > guests such as toluene. > > In the past somebody mentioned that while HyperChem cannot do this directly, > a macro in excel could be written. What exactly should I get the macro to do? None of the methods in HyperChem calculate Gibbs free energies. > Secondly, while I know that the energies obtained in a molecular mechanics > calculation have no absolute meaning, would the difference in energies of > two optimised conformations of the same complex have any meaning? If so, what > kind of energy are we talking about? Yes. The energy differences are the differences in the contributions to the total energy: bond stretches, angle distortions, van der Waals interactions, etc. See _Computational Chemistry_; or open a log file and do a single- point MM+ calculation with the MechanicsPrintLevel set to a high value. > Thirdly, is it possible to determine the contribution to each of the above > energies made by the different types of interaction (van der Waals, pi-pi) > between the host and the guest? Van der Waals, yes -- again, you can get this information from a log file, as above. Pi-pi interactions, no, since those aren't computed by MM methods. 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 Tue Oct 17 17:32:08 1995 Date: Tue, 17 Oct 1995 11:26:44 -0500 (EST) From: Phil Bays To: hyperchem@hyper.com Subject: SGI version My vendors tell me that the SGI version of HyperChem has yet to be released. Is that true, and if so what is the projected release date? Phil Bays Department of Chemistry Saint Mary's College Notre Dame IN 46556 pbays@saintmarys.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Oct 17 21:03:01 1995 Date: Tue, 17 Oct 95 17:45:13 -0400 From: polowin (Joel Polowin) To: Phil Bays Subject: Re: SGI version Cc: hyperchem@www > Date: Tue, 17 Oct 1995 11:26:44 -0500 (EST) > From: Phil Bays > > My vendors tell me that the SGI version of HyperChem has yet to be > released. Is that true, and if so what is the projected release date? We just got the boxes back from the manufacturer yesterday; the shipments started going out to the dealers today. There are sighs of relief all 'round. We expect that CD-ROMs with the demo version will be back in a few days. Expected price, US$10. This is a full working version of the software, but the license is limited to only 30 days; the CD includes the tutorial book _Getting Started_ in PostScript format. We're also working on making the demo software available for download. I will put more information onto this mailing list (and onto our WWW page) when it is available. 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 Wed Oct 18 15:02:12 1995 From: "W. Wasikiewicz, POLAND, WUofT" Organization: Wydzial Chemiczny To: hyperchem@hyper.com Date: Wed, 18 Oct 1995 13:54:17 CET Subject: modelling of complexes Hi netters, I'm relatively new in the molecular modelling and interested in modelling of kation complexes of crown ethers and related compounds. Is it possible to do this with Hyper Chem, and how to "prepare" the complex for the calculations? Regards, Wojciech Wasikiewicz------------------- Wojciech Wasikiewicz Department of Chemistry Technical University of Warsaw e-mail: wojtal@ch.pw.edu.pl ----------------------------------------------- ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Oct 18 16:19:14 1995 Date: Wed, 18 Oct 1995 08:51:17 -0500 To: hyperchem@hyper.com From: lee@drugs.bsd.uchicago.edu (lee shekter) Subject: SGI version... Does the SGI version have the capability of being run on under X-windows from a remote machine (the way Insight from Biosym does using the "Axxess" module), or does one have to have access to an SGI terminal? Also, have limits for the size of the periodic box been increased over the PC version? Thanks. Lee R. Shekter Dept. of Pharmacology & Physiol. 947 E. 58th St., The University of Chicago Chicago IL 60637 ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Oct 18 18:36:32 1995 From: Massimo Trotta Subject: references on nmr/molecular dynamics To: hyperchem@hyper.com Date: Wed, 18 Oct 1995 17:47:35 +0100 (MET) Cc: west@qtp.ufl.edu A while ago I posted a message on nmr and molecular dynamics. Recently I found the following article that is right to the point: Engelse, Penhoat and Perez Molecular relaxation of sucrose in aqueous solution:how a nanosecond molecular dynamics simulation helps to reconcile nmr data J. Phys. Chem. 1995, vol.99, pagg 13334-13351 enjoy massimo -- !==============================================================! ! Massimo Trotta ! ! Centro Studi Chimico Fisici sull'Interazione Luce Materia ! ! c/o Dept. of Chemistry ! ! V. Orabona, 4 I-70126 Italy ! ! e-mail: csilmt12@area.ba.cnr.it ! !==============================================================! ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Oct 19 00:28:13 1995 Date: Wed, 18 Oct 1995 18:02:20 -0700 (PDT) From: Gang Sun To: hyperchem@hyper.com Subject: problems I purchased hyperchem V4.5 recently. Unfortunately it is not working. The problem is that the software can not find the lock key. I changed the lock to another computer, it was working. So the problem is from my computer. This computer is a Gateway 2000 P5-120 loaded with windows for workgroups. I called the technical support from hypercube. They only told me to change the parallel port mode to bidirectional. I did it, but it is still not working. Any suggestion will be greatly appreciated. Gary ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Oct 19 17:15:41 1995 Date: Thu, 19 Oct 95 11:57:36 -0400 From: polowin (Joel Polowin) To: Gang Sun Subject: Re: problems Cc: hyperchem@www > Date: Wed, 18 Oct 1995 18:02:20 -0700 (PDT) > From: Gang Sun > > I purchased hyperchem V4.5 recently. Unfortunately it is not working. The > problem is that the software can not find the lock key. I changed the > lock to another computer, it was working. So the problem is from my > computer. This computer is a Gateway 2000 P5-120 loaded with windows for > workgroups. I called the technical support from hypercube. They only told > me to change the parallel port mode to bidirectional. I did it, but it is > still not working. It should also be pointed out that you have an unusual hardware configuration to allow for a modem connection, and that a printer connected to that parallel port does work properly -- this indicates that the port is working at least partly correctly. Did it make a difference for the lock whether the printer was attached or not? If you have a controller card (multi-IO card) with a WINBOND W83757F chip, "noise" from the chip may block recognition of the lock. This is an old problem; I don't know if any manufacturers are still using this chip. As I mentioned to you, a few systems, because of their particular configurations, simply will not recognise the lock on the regular parallel port. According to my information, we have *never* had a report that the addition of a separate, dedicated AT-type parallel port has failed to solve the problem. One of these additional ports is generally not expensive (US$20-25) but does require a free expansion slot in the computer. 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 polowin Thu Oct 19 17:17:57 1995 Date: Thu, 19 Oct 95 11:57:36 -0400 From: polowin (Joel Polowin) To: Gang Sun Subject: Re: problems Cc: hyperchem@www > Date: Wed, 18 Oct 1995 18:02:20 -0700 (PDT) > From: Gang Sun > > I purchased hyperchem V4.5 recently. Unfortunately it is not working. The > problem is that the software can not find the lock key. I changed the > lock to another computer, it was working. So the problem is from my > computer. This computer is a Gateway 2000 P5-120 loaded with windows for > workgroups. I called the technical support from hypercube. They only told > me to change the parallel port mode to bidirectional. I did it, but it is > still not working. It should also be pointed out that you have an unusual hardware configuration to allow for a modem connection, and that a printer connected to that parallel port does work properly -- this indicates that the port is working at least partly correctly. Did it make a difference for the lock whether the printer was attached or not? If you have a controller card (multi-IO card) with a WINBOND W83757F chip, "noise" from the chip may block recognition of the lock. This is an old problem; I don't know if any manufacturers are still using this chip. As I mentioned to you, a few systems, because of their particular configurations, simply will not recognise the lock on the regular parallel port. According to my information, we have *never* had a report that the addition of a separate, dedicated AT-type parallel port has failed to solve the problem. One of these additional ports is generally not expensive (US$20-25) but does require a free expansion slot in the computer. 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 Oct 19 17:18:08 1995 Date: Thu, 19 Oct 95 11:24:19 -0400 From: polowin (Joel Polowin) To: "W. Wasikiewicz, POLAND, WUofT" Subject: Re: modelling of complexes Cc: hyperchem@www > From: "W. Wasikiewicz, POLAND, WUofT" > Date: Wed, 18 Oct 1995 13:54:17 CET > > I'm relatively new in the molecular modelling and interested in modelling of > kation complexes of crown ethers and related compounds. Is it > possible to do this with Hyper Chem, and how to "prepare" the > complex for the calculations? You may be able to model these compounds with molecular mechanics. You would need to assign charges to the atoms and to use atomic charges instead of bond dipoles in the modelling. Since the force fields were not optimized for these kinds of compounds, it is likely that you would need to modify the parameters, or even to define new atom types, to get good results. You are more likely to get good results with semi-empirical calculations, if parameters for the cations you wish to model are available and if the molecular systems are small enough to be managed by your computer. The charts on pages 188-189 of the Reference manual show the elements that the various semi-empirical methods can work with. In general it is possible to reduce a semi-empirical problem's size by doing calculations on only part of a structure at once, but this may not give good results for some systems. These partial calculations work best when a structure has well-defined divisions or regions which do not interact with each other very much. 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 polowin Thu Oct 19 17:20:25 1995 Date: Thu, 19 Oct 95 11:24:19 -0400 From: polowin (Joel Polowin) To: "W. Wasikiewicz, POLAND, WUofT" Subject: Re: modelling of complexes Cc: hyperchem@www > From: "W. Wasikiewicz, POLAND, WUofT" > Date: Wed, 18 Oct 1995 13:54:17 CET > > I'm relatively new in the molecular modelling and interested in modelling of > kation complexes of crown ethers and related compounds. Is it > possible to do this with Hyper Chem, and how to "prepare" the > complex for the calculations? You may be able to model these compounds with molecular mechanics. You would need to assign charges to the atoms and to use atomic charges instead of bond dipoles in the modelling. Since the force fields were not optimized for these kinds of compounds, it is likely that you would need to modify the parameters, or even to define new atom types, to get good results. You are more likely to get good results with semi-empirical calculations, if parameters for the cations you wish to model are available and if the molecular systems are small enough to be managed by your computer. The charts on pages 188-189 of the Reference manual show the elements that the various semi-empirical methods can work with. In general it is possible to reduce a semi-empirical problem's size by doing calculations on only part of a structure at once, but this may not give good results for some systems. These partial calculations work best when a structure has well-defined divisions or regions which do not interact with each other very much. 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 Oct 19 19:05:10 1995 Date: Thu, 19 Oct 95 11:44:01 -0400 From: polowin (Joel Polowin) To: lee@drugs.bsd.uchicago.edu (lee shekter) Subject: Re: SGI version... Cc: hyperchem@www > Date: Wed, 18 Oct 1995 08:51:17 -0500 > From: lee@drugs.bsd.uchicago.edu (lee shekter) > > Does the SGI version have the capability of being run on under X-windows > from a remote machine (the way Insight from Biosym does using the "Axxess" > module), or does one have to have access to an SGI terminal? Also, have > limits for the size of the periodic box been increased over the PC version? Unfortunately, the front end of the SGI package uses the SGI graphics language; it can't run over X-windows. It is possible to operate the package remotely by doing a remote login, and redirecting the display to the local SGI system. The limits for the automatically-generated periodic box full of water molecules are the same as in the Windows version; unravelling that limitation from the code was of lower priority than getting other things to work properly. It's in the wish list for future versions. It is still possible to save a structure in .HIN format, and edit the 'box' line manually to change the box size arbitrarily. 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 polowin Thu Oct 19 20:15:09 1995 Date: Thu, 19 Oct 95 11:44:01 -0400 From: polowin (Joel Polowin) To: lee@drugs.bsd.uchicago.edu (lee shekter) Subject: Re: SGI version... Cc: hyperchem@www > Date: Wed, 18 Oct 1995 08:51:17 -0500 > From: lee@drugs.bsd.uchicago.edu (lee shekter) > > Does the SGI version have the capability of being run on under X-windows > from a remote machine (the way Insight from Biosym does using the "Axxess" > module), or does one have to have access to an SGI terminal? Also, have > limits for the size of the periodic box been increased over the PC version? Unfortunately, the front end of the SGI package uses the SGI graphics language; it can't run over X-windows. It is possible to operate the package remotely by doing a remote login, and redirecting the display to the local SGI system. The limits for the automatically-generated periodic box full of water molecules are the same as in the Windows version; unravelling that limitation from the code was of lower priority than getting other things to work properly. It's in the wish list for future versions. It is still possible to save a structure in .HIN format, and edit the 'box' line manually to change the box size arbitrarily. 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 Oct 19 21:27:16 1995 Date: 19 Oct 95 16:57:14 EDT From: Heinz Hofmann <100411.2306@compuserve.com> To: HyperChem E-mail list Subject: New HyperChem Add-On now available Dear HyperChemers: This is to inform you that MOMEC, a new HyperChem add-on especially designed for transition metal chemists, is now available. MOMEC is a molecular mechanics system that has been developed for strain energy minimisation of metal complexes and operates under Microsoft Windows in conjugation with HyperChem. MOMEC offers: - Graphical input and output through HyperChem. - A choice of either conjugate gradients or full matrix Newton Raphson refinement or a combination of the two methods. - True constraints of internal coordinates. - Selective inclusion of 1,3-interactions. - Modeling of coordination geometries by either intraligand repulsion, electrostatic interactions, ligand field based electronic functions or a combination of various methods. - An existing extensive force field for metal complexes. - An editor for force field parameters and data files. - Ready extension to new systems. - Run of batch jobs. - Additional modules are available for applications in conjunction with MOMEC and/or HyperChem include Jahn-Teller, Energy and Conversion. For further information, please contact Science direct Dr. Heinz Hofmann Im grossen Garten 1B D-63110 Rodgau Germany Phone +49-6106-826001 Facsimile +49-6106-29124 Internet: 100411.2306@compuserve.com ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Oct 23 15:03:54 1995 Date: Mon, 23 Oct 1995 14:46:37 -0500 (EST) From: "YARD.DOC. TEREZA VARNALI" To: hyperchem@hyper.com Subject: Co complex with Sn Dear Hyperchem Users, I am interested to run a structure which is a Cobalt complex and also incorporates a Sn atom. I want to run semiempirical calcs. Co parameters are available in ZINDO and Sn parameters are available in PM3 methods. How does one carry calcs for a structure with both Sn and Co? Furthermore I want to do a transition state location too. Can anybody help me out with this problem? Thanks ... Tereza Varnali Bogazici University Chemistry Department 80815 Bebek Istanbul, Turkey fax:90 212 2872467 ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Oct 23 19:04:09 1995 From: CHEGSCHN@ACS.EKU.EDU id <01HWS42ML0X0000NUR@ACS.EKU.EDU>; Mon, 23 Oct 1995 13:08:33 -0400 (EDT) Date: Mon, 23 Oct 1995 13:08:33 -0400 (EDT) Subject: Re: problems To: polowin Cc: hyperchem@www polowin@hyper.hyper.com 19-OCT-1995 writes: > >> Date: Wed, 18 Oct 1995 18:02:20 -0700 (PDT) >> From: Gang Sun >> >> I purchased hyperchem V4.5 recently. Unfortunately it is not working. The >> problem is that the software can not find the lock key. I changed the >> lock to another computer, it was working. So the problem is from my >> computer. This computer is a Gateway 2000 P5-120 loaded with windows for >> workgroups. I called the technical support from hypercube. They only told >> me to change the parallel port mode to bidirectional. I did it, but it is >> still not working. > >It should also be pointed out that you have an unusual hardware configuration >to allow for a modem connection, and that a printer connected to that >parallel port does work properly -- this indicates that the port is working >at least partly correctly. > >Did it make a difference for the lock whether the printer was attached or not? > >If you have a controller card (multi-IO card) with a WINBOND W83757F chip, >"noise" from the chip may block recognition of the lock. This is an old >problem; I don't know if any manufacturers are still using this chip. > >As I mentioned to you, a few systems, because of their particular >configurations, simply will not recognise the lock on the regular parallel >port. According to my information, we have *never* had a report that the >addition of a separate, dedicated AT-type parallel port has failed to solve >the problem. One of these additional ports is generally not expensive >(US$20-25) but does require a free expansion slot in the computer. > >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. > > Hey all, I've had the same problem with a Gateway 2000 P5-100. In my case, all is well IF (and only if) I print something through the printer port before booting up Hyperchem 4.5. That's it. I start the computme other trivial ditty, and voila! Go figure. I don't remember if I have to do that after loading windows. If anyone has a solution that doesn't waste a piece of paper, I'd like to know about it. Alan ======================================================================== G. Alan Schick Phone: (606) 622-2338 Dept. of Chemistry Fax: Same (when it's turned on) Eastern Kentucky University e-mail: chegschn@acs.eku.edu Richmond, KY 40475-3124 ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Oct 23 22:03:44 1995 From: Mike Taylor To: hyperchem@hyper.com Date: Mon, 23 Oct 1995 16:37:49 +0000 Subject: atom number limits for QSAR properties Hello, I am trying to calculate molecular surface areas and molecular volumes for moderately sized molecules, using ChemPlus v1.0a under Windows 3.1. Using alkane chains as test molecules, the calculation fails with the helpful message: "QSAR Properties Error Error in DoCalculation No Resume Abort Retry Ignore" when the number of carbons in the chain increases from 500 to 1000. Does anyone know the reason: is this a DDE limitation again? Is there a way round the problem? Would this work better if I upgraded to ChemPlus v1.5? Thanks for your advice, Mike Taylor. Mike Taylor (m.taylor@pra.org.uk) Paint Research Association PRA 8 Waldegrave Road TEDDINGTON TW11 8LD UK Tel: +44 (181) 977 4427 Fax: +44 (181) 943 4705 ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Oct 24 08:08:42 1995 Date: Tue, 24 Oct 1995 08:50:00 -0500 (EST) From: "YARD.DOC. TEREZA VARNALI" To: hyperchem@hyper.com Subject: Co complex with Sn Dear Hyperchem Users, I am interested to run a structure which is a Cobalt complex and also incorporates a Sn atom. I want to run semiempirical calcs. Co parameters are available in ZINDO and Sn parameters are available in PM3 methods. How does one carry calcs for a structure with both Sn and Co? Furthermore I want to do a transition state location too. Can anybody help me out with this problem? Thanks ... Tereza Varnali Bogazici University Chemistry Department 80815 Bebek Istanbul, Turkey fax:90 212 2872467 ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Oct 24 14:35:20 1995 Date: Tue, 24 Oct 1995 10:59:15 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: semi-empirical methods To: hyperchem@hyper.com, support@hyper.com Cc: chemistry@infomeister.osc.edu Hi, I am a HyperChem user and I wish to estimate the enthalpy of formation of complexes formed between calixarenes and metal ions. I optimised the geometry of both the ligand and complex using molecular mechanics. I then carried out semi-empirical single point calculations to determine the enthalpies of formation of the ligand and the complex using the ZINDO/1 method ( because this is the only semi-empirical method in Hyperchem which has parameters for calcium and magnesium). This gave values of -45 000 kcal/mol approximtely. The magnitude of these values is very high and so I carried calculations on simpler molecules. The results for these simpler systems are given below Calculation of heat of formation of benzoic acid delta Hf/(kcal/mol) AM1 -54.1467462 PM3 -53.6776001 ZINDO/1 -3117.2768454 ZINDO/S -5062.7571910 Calculation of heat of formation of cyclopentanone delta Hf/(kcal/mol) AM1 -52.5334612 PM3 -53.1513803 ZINDO/1 -2586.4691313 ZINDO/S -4012.5111479 I have three questions: 1) The HyperChem Computational Chemistry manual quotes values of -70.1 kcal/mol and -46.0 kcal/mol for the enthalpy of formation of benzoic acid and cyclopentanone respectively. So how accurate can we expect Hyperchem's semiempirical methods to be? 2) Why are the ZINDO/1 and ZINDO/S methods giving me such apparently incorrect values? 3) Another question (apparently unrelated to the first two questions) is why the following message appeared in my log file for calcium but not for magnesium in the ZINDO/1 calculations on the calixarene complexes: WARNING message received from node=0: Atom 221 with atomic number 20 the value of bonding parameter of s orbital is less than or equal to zero, please check your parameter file zindo1_1.abp. Regards, Paddy Paddy Kane Dublin City University 94970459@vax1.dcu.ie ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Oct 25 18:51:40 1995 Date: Wed, 25 Oct 95 14:05:26 -0400 From: polowin (Joel Polowin) To: CHEGSCHN@acs.eku.edu Subject: Re: problems Cc: hyperchem@hyper.com > From: CHEGSCHN@ACS.EKU.EDU > Date: Mon, 23 Oct 1995 13:08:33 -0400 (EDT) > Hey all, I've had the same problem with a Gateway 2000 P5-100. In my > case, all is well IF (and only if) I print something through the printer > port before booting up Hyperchem 4.5. That's it. I start the computme > other trivial ditty, and voila! Go figure. That's really strange. I don't know why it would do that. Gang Sun found that adding a new dedicated parallel port to his Gateway Pentium solved the problem. I think that I need to add another note to our file on parallel port problems, to mention the Gateway systems. 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 Wed Oct 25 19:19:21 1995 Date: Wed, 25 Oct 95 13:57:34 -0400 From: polowin (Joel Polowin) To: "YARD.DOC. TEREZA VARNALI" Subject: Re: Co complex with Sn Cc: hyperchem@hyper.com > Date: Mon, 23 Oct 1995 14:46:37 -0500 (EST) > From: "YARD.DOC. TEREZA VARNALI" > > I am interested to run a structure which is a Cobalt complex and also > incorporates a Sn atom. I want to run semiempirical calcs. Co parameters > are available in ZINDO and Sn parameters are available in PM3 methods. > How does one carry calcs for a structure with both Sn and Co? > Furthermore I want to do a transition state location too. > Can anybody help me out with this problem? PM3 is fundamentally unable to do calculations with Co, but ZINDO is (in principle) able to work on Sn; however, we do not provide parameters for Sn for the ZINDO methods since (as far as we know) such parameters have not been published. If you add your own parameters to the files, you can do these calculations. You may be able to obtain "unofficial" parameters by asking on the Computational Chemistry mailing list (subscribe by sending a request to CHEMISTRY-REQUEST@ccl.osc.edu). If you do find something, please let us know! If the two atoms are far apart and therefore not interacting much, you might be able to trick HyperChem into running the calculations. You could, for example, change the Co to some other element, select the Sn part of the structure, and do a PM3 calculation on the selected part; then restore the Co, change the Sn to something else, select the Co part of the structure, and run ZINDO/1 on the selected part. HyperChem does not have a mechanism for finding transition states -- not yet, at least. One can find transition states by using external software, such as Microsoft Excel or Visual Basic, to control HyperChem, applying structural restraints. One can perform optimizations at the HF level with HyperChem; this includes transition states, if one applies structural restraints to a system to hold it at the transition state. In other words, HyperChem can perform calculations on transition states; it just doesn't have a simple way of finding them. 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 Wed Oct 25 22:09:58 1995 Date: Wed, 25 Oct 1995 18:09:47 -0700 From: tmmec@fcindy5.NCIFCRF.GOV (tmmec) To: HYPERCHEM@HYPER.COM Subject: TMMeC - Call for Papers Dear Colleagues, The Molecular Modeling e-Conference (TMMeC), a new mechanism for the publication of scientific papers which blends together the benefits of a Scientific Meeting, a printed paper and a multimedia publication, is making through this means its first CALL-FOR-PAPERS. Organized primarily in the Internet, the TMMeC displays the multimedia works of participating authors in three mirror sites, located in USA, Europe and Latin-America. The electronic addresses of these sites are http://bilbo.edu.uy/agora http://uqbar.ncifcrf.gov/agora http://stark.udg.es/agora The conference takes advantage of the posibilities of the WWW and the Chemical Mime Types by providing the authors with unmatched freedom for the communication of their ideas. In TMMeC the readers will have the opportunity to comment about the ideas of other authors, adding their own comments to a special section of each paper. Thus, the usual verbal exchange produced in normal scientific meetings is preserved, with the advantage that even those scientists not involved in the discussions can benefit from the conclusions. The open discussion of the papers would also serve as a means to ensure the highest quality of material is exposed in the e-Conference. The products of the e-Conference are permanent in time. Not only the whole multimedia version of the papers will be produced in CD-ROM but also a printed copy of the work will be produced, if the authors wish so, by choosing for this purpose one of the journals that have agreed to be associated with us in this venture. One of the main characteristics of this conference is that we are not limiting it to works published in English. In fact, it will bring the opportunity to scientist of Latin expression to obtain accelerated publications in their native languages. This characteristic will also be used to give support to the Congresses of Theoretical Chemists of Latin Expression and their Association, just formed in Spain. A second unique characteristic is that we will be publishing not only contributed papers, but Current Reviews of interest to the Theoretical Chemistry and Molecular Modeling community. Differently from their printed analogs, Current Reviews, only present in the e-Conference, will be continuously updated. Even at the same moment that a new contribution is produced in the field. This can be accomplished using the automatic facilities that only an electronic publication may offer. These reviews promise to be a highest impact publication as they would become a necesary entry point for anyone looking for up to day information in any of the subjects covered in them. All these exciting projects and others are fully described in the editorial pages of the conference and we will be extremely pleased if you visit TMMeC. You will find there a more detailed description about the scope of our ideas. We apologize for any duplications of this letter that may reach your mail-box. This first and only Call for Papers is being send to several especialized mail lists, thus duplications may occur. With our best regards, Oscar N. Ventura (oscar@bilbo.edu.uy) Raul E. Cachau (cachau@ncifcrf.gov) Miquel Duran (quel@stark.udg.es) ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Oct 26 17:56:36 1995 Date: Thu, 26 Oct 1995 17:12:27 +0100 From: "S.C.Rogers" To: hyperchem@hyper.com Subject: Windows95 and HyperChem Hi, I guess you're fed up with this subject, but I've tried installing HyperChem and ChemPlus on 2 different P120 PC's now and still can't get DDE to work. I'm sure the last trial was as clean as we could make it - we installed Win95 from Dos having wiped the disk previously! The error message always refers to the atomic number with a query value error. We have the programs working perfectly on a Windows 3.11 P133 machine. It will be a real pain to take the PC's we want to use back down to Windows 3.11 as we have configured a lot of LAN stuff and other programs. Please, is there any progress on the Win95 problem? Steve Rogers ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Oct 26 17:57:17 1995 Date: Thu, 26 Oct 95 11:04:44 -0400 From: polowin (Joel Polowin) To: hyperchem@hyper.com Subject: HyperChem 4.5 for SGI Everyone on this list is, I expect, already a user of HyperChem. Still, it's worth letting you in on the formal announcement. We are pleased to announce the release of HyperChem 4.5 for Silicon Graphics workstations. It's out, and it's shipping. The demo version of the software is available from the Computational Chemistry archives at ccl.osc.edu, in the directory /pub/chemistry/software/SGI/HyperChem-demo . So is the tutorial book _Getting Started_, in PostScript format. With a web browser, you can download the files with: ftp://ccl.osc.edu/pub/chemistry/software/SGI/HyperChem-demo The demo software is the complete working package but the license is limited to one month of use. We are also selling the demo software on CD-ROM for US$10. (The files are also available from our own server, ftp.hyper.com, in the /pub/demo/sgi directory. So that the files could be downloaded successfully, we had to split them into 1-MB pieces which must then be recombined on your system. Instructions are available in the file README in that directory. Depending on the load on our server, it will probably be faster for most users to obtain the files from the ccl.osc.edu site.) Details about the new software version follow. 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. ---------- Running on Silicon Graphics computers, HyperChem is an affordable tool that makes computer simulation more accessible to researchers and to educators. HyperChem can provide valuable insight into molecular structure, flexibity, and properties. You can compute heats of formation, ionization potentials, electron affinities, dipole moments, as well as UV-visible and IR spectra. HyperChem integrates easily with scientific and business productivity software and chemical databases. As usual, Hypercube supplies documentation which not only shows users how to operate the software, but also provides a solid introduction to the theory of ab initio calculations. This makes HyperChem an extremely useful educational tool. Model Bulding and Visualization * Building molecules with HyperChem is simple: you choose an element from a periodic table, and click and drag with the mouse to sketch a structure. * HyperChem's model builder turns rough sketches straight into 3D structures. It can even handle fused rings and highly coordinated metal complexes. * Peptides and nucleic acids can be built from amino acid and nucleotide residue libraries. * Molecular structures can be imported from several file formats: Brookhaven PDB, Tripos MOL2 (.ML2), MOPAC Z-Matrix, and crystallographic cartesian coordinates. * 3D grid data can be imported from Gaussian 92 or Gaussian 94 to generate chemical structures with associated electronic surfaces. Data can be displayed as "wire frames" or solids. * Rendering choices include sticks, disks and CPK spheres. Stereo viewing is available, and protein backbones can be viewed as ribbons. * Extensive selection and highlighting capabilities make it easy to focus on areas of interest in complex molecules. * Mouse control of stereochemistry, rotation around bonds, and "rubber banding" of bonds makes manipulation of structures easy. * Residue mutation in peptides and nucleic acids is straightforward. * Almost all functions can be run through HyperChem's scripting language, or under external control from other software. Data values can be easily retrieved from HyperChem back to external software. Computational Chemistry * HyperChem integrates molecular mechanics, and ab initio and semi- empirical quantum mechanics (molecular orbital) calculations into a single package. * Choose from a large number of supplied ab initio basis sets, or define your own through a simple text-file format. Assign different basis sets to atoms selected with the mouse; interactively assign a primitive s, p, sp, d, or spd shell to that atom. Treat a selected set of atoms as "ghost nuclei", such that their basis functions are used but their nuclear interactions are neglected. Single-point correlation energy calculations at the MP2 level can be performed. * Choose from nine semi-empirical methods, all the way from Extended Huckel to AM1 or PM3. * Choose from four mechanics force fields, MM+ for general purpose modeling or one of three specialized biomolecule force fields. * Single point calculations, geometry optimizations, and molecular dynamics simulations are available with almost all methods, including ab initio. * Build in restraints to your optimizations or dynamics runs. * Compute and view IR spectra, and show animations of the vibrational modes. With this release, HyperChem can include isotope effects in its calculations. * Compute UV spectra with ZINDO/S, developed specifically for the purpose. * Display orbital energy levels, and contour plots and isosurfaces of the orbitals themselves. HyperChem Release 4.5 for SGI is available on the following distribution media: CD-ROM, 4mm DAT tape, 1/4" tape cartridge. HyperChem is a registered trademark of Hypercube, Inc. SGI is a trademark of Silicon Graphics Inc. All other brand and product names are trademarks of their respective holders. A demo version of HyperChem Release 4.5 for SGI is available on CD for US$10. It includes a tutorial book in PostScript format, and the software is the same as the standard version except that its license is valid for only 30 days. Until December 31st, 1995, the price for HyperChem Release 4.5 for SGI is US$2,595 commercial, US$1,295 academic. The cost to upgrade from Release 2 for SGI is US$595 commercial, US$295 academic. As of January 1st, 1996, prices will return to their regular levels: US$2,995 commercial, US$1,495 academic. The cost to upgrade from Release 2 for SGI will be US$995 commercial, US$495 academic. Site licenses and other upgrades are possible; please contact us. Upgrade orders must be accompanied by the first page of the _Getting Started_ or _New Features_ manual with the serial number, end user name, address, and phone number listed on it. For More Information... HyperChem is a product of Hypercube, Inc., specialists in scientific software. Hypercube can be reached at: Hypercube, Inc. 419 Phillip Street Waterloo, Ontario Canada, N2L 3X2 Tel: (800) 960-1871 (from USA or Canada) (519) 725-4040 Fax: (519) 725-5193 E-mail: info@hyper.com ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Oct 26 19:11:11 1995 Date: Thu, 26 Oct 95 11:58:37 -0400 From: polowin (Joel Polowin) To: Paddy Kane <94970459@vax1.dcu.ie> Subject: Re: CCL:semi-empirical methods Cc: CHEMISTRY@infomeister.osc.edu, hyperchem@hyper.com > Date: Tue, 24 Oct 1995 10:59:15 +0000 (GMT) > From: Paddy Kane <94970459@vax1.dcu.ie> > Calculation of heat of formation of benzoic acid > delta Hf/(kcal/mol) > AM1 -54.1467462 > PM3 -53.6776001 > ZINDO/1 -3117.2768454 > ZINDO/S -5062.7571910 > > Calculation of heat of formation of cyclopentanone > delta Hf/(kcal/mol) > AM1 -52.5334612 > PM3 -53.1513803 > ZINDO/1 -2586.4691313 > ZINDO/S -4012.5111479 > > 1) The HyperChem Computational Chemistry manual quotes values of > -70.1 kcal/mol and -46.0 kcal/mol for the enthalpy of formation of benzoic > acid and cyclopentanone respectively. So how accurate can we expect > Hyperchem's semiempirical methods to be? As has been stated here before, several times and recently -- we can expect HyperChem's calculations to be *exactly* as accurate as the same calculations performed by other software. We use published methods with standard parameters; we have not had any reports of our results differing from the results of others' calculations that did not turn out to be because of differences in the options selected or in the structure being calculated. My calculations with HyperChem for benzoic acid gave heats of formation of -68.1 kcal/mol for AM1, -66.4 kcal/mol for PM3, and -3147.6 kcal/mol for ZINDO/1. ZINDO/S did not converge. The AM1 and PM3 results are consistent with literature values for those calculations. (See J.J. Stewart, _J. Computer-Aided Mol. Design_ *4*, 1-105 (1990).) The ZINDO methods do not reproduce heats of formation well. My results for cyclopentanone are: -55.5 kcal/mol for AM1, -55.3 kcal/mol for PM3, -2608.3 for ZINDO/1, and no convergence for ZINDO/S. The Stewart article gives -36.1 kcal/mol as the heat of formation calculated with AM1 with MOPAC, but our repetition of that calculation with AM1 with MOPAC gives -55.3 kcal/mol. This appears to be an error in the article (and in our manual, which quotes results from the article). > 2) Why are the ZINDO/1 and ZINDO/S methods giving me such apparently > incorrect values? The ZINDO methods weren't parameterized by fitting to experimental heats of formation. ZINDO/S was optimized to give good electronic transition (UV/visible) results. > 3) Another question (apparently unrelated to the first two questions) is > why the following message appeared in my log file for calcium but not for > magnesium in the ZINDO/1 calculations on the calixarene complexes: > WARNING message received from node=0: > Atom 221 with atomic number 20 the value of bonding parameter of s orbital > is less than or equal to zero, please check your parameter file zindo1_1.abp. The s and p bonding parameters for Ca are actually negative, unlike those parameters for all of the other atoms. Usually, for those parameters to be negative would indicate an error in the parameter set, so HyperChem is warning you of a possible problem. In this case, you should ignore the warning and continue the calculation. 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 Thu Oct 26 19:53:41 1995 Date: Thu, 26 Oct 1995 19:00:45 GMT To: hyperchem@hyper.com From: Vernon Anderson Subject: SGI hyperchem Are there any comparisons of calculational efficiency for the same calculation on a PC versus the same calculation on the SGI. Clearly the calculation times depend on the individual systems, but it would be informative to see how much the performance is enhanced on the SGI, especially for the quantum chemical calculations or molecular dynamics runs. Thanks ************************************************************* Vernon Anderson Department of Biochemistry Case Western Reserve University 10900 Euclid Ave., Cleveland, OH 44106-4935 Phone: 216-368-2599 FAX: 216-368-4544 ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Oct 26 20:17:59 1995 Date: Thu, 26 Oct 95 13:46:11 -0400 From: polowin (Joel Polowin) To: m.taylor@pra.org.uk Subject: Re: atom number limits for QSAR properties Cc: hyperchem@hyper.com > From: Mike Taylor > Date: Mon, 23 Oct 1995 16:37:49 +0000 > > Using alkane chains as test molecules, the calculation fails with the > helpful message: > > "QSAR Properties Error > Error in DoCalculation > No Resume > Abort Retry Ignore" > > when the number of carbons in the chain increases from 500 to 1000. > > Does anyone know the reason: is this a DDE limitation again? Is there a > way round the problem? Would this work better if I upgraded to ChemPlus v1.5? It looks like a DDE thing. The first error message that I get is "DDE Error: Timeout while waiting for DDE response", followed by the message that you report above. When I try this with a 750-C alkane, I can get the system from HyperChem to the QSAR Properties module if I don't have much else running, but not if I have a few other programs running at the same time. This is with ChemPlus 1.5; the version doesn't seem to make a difference. The simple work-around is to save the structure as a .HIN file, and then read it with the QSAR Properties module's File/Open command. 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 Oct 27 15:59:25 1995 Date: Fri, 27 Oct 95 09:45:59 -0400 From: polowin (Joel Polowin) To: Vernon Anderson Subject: Re: SGI hyperchem Cc: hyperchem@hyper.com > Date: Thu, 26 Oct 1995 19:00:45 GMT > From: Vernon Anderson > > Are there any comparisons of calculational efficiency for the same > calculation on a PC versus the > same calculation on the SGI. Clearly the calculation times depend on the > individual systems, but it would be informative > to see how much the performance is enhanced on the SGI, especially for the > quantum chemical calculations or molecular dynamics runs. Thanks My predecessor did this kind of benchmarking for a variety of systems. I'll append the results below. The quick summary is that a Pentium is comparable in power to one of the workstations after one takes into account differences in processor speed, etc. 386- and 486-based PCs are noticeably inferior to Pentiums for this kind of work because they lack some of the Pentium's mathematical functions. ----- MNDO energy and gradient for C60, converged to 1e-2, without DIIS: Computer Time (s) Rel. speed 486DX 50 MHz 375 1 Pentium 90 MHz 87.6 4.28 DECpc AXP 150 MHz 59.8 6.27 SGI Indy R4000SC 100 Mhz 77.8 4.82 IBM RS/6000-250 66 MHz 51.8 7.24 DEC 3000 200 MHz (I think) 42.4 8.84 The first two numbers are for full HyperChem (user interface and calculation module) running on the same processor under Windows 3.11. The third is for full HyperChem running under Windows NT. The last three are for the computation module running on the unix computer with the HyperChem user interface running on a 486. All times are wall clock times for start to finish observed on the PC. All times are for HyperChem R4. The 486DX 50 MHz is a clone with 128k secondary cache and 20Mb RAM. The Pentium 90 MHz is a Dell Dimension XPS 90 with 256k secondary cache and 16Mb RAM. The SGI Indy 100MHz is an R4000SC with 1Mb secondary cache and 64Mb RAM. I don't know the cache/memory configurations of the IBM or DEC. All times were measured with a hand held stopwatch when machines were "quiet" (no other users) but not in single user mode. The maximal optimization switches that produced working code (-O2 for the RISCs I believe) were set for all compilations, and the source code was identical. ----- 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 Oct 27 20:56:17 1995 Date: Fri, 27 Oct 95 18:13:27 -0400 From: polowin (Joel Polowin) To: "S.C.Rogers" Subject: Re: Windows95 and HyperChem Cc: hyperchem@hyper.com > Date: Thu, 26 Oct 1995 17:12:27 +0100 > From: "S.C.Rogers" > > I guess you're fed up with this subject, but I've tried installing HyperChem > and ChemPlus on 2 different P120 PC's now and still can't get DDE to work. > I'm sure the last trial was as clean as we could make it - we installed Win95 > from Dos having wiped the disk previously! The error message always refers > to the atomic number with a query value error. We have the programs working > perfectly on a Windows 3.11 P133 machine. > > It will be a real pain to take the PC's we want to use back down to Windows 3.11 > as we have configured a lot of LAN stuff and other programs. Please, is there > any progress on the Win95 problem? <*sigh*> Nothing new, I'm afraid. I assume that that's an "unknown variable" error? All that I can think of to ask you to check is that your settings should have periods used as decimal markers and commas as thousands markers. (This has been confirmed as a requirement for running under Win'95, as it is under Windows.) If you're not already using a language setting of U.S. English, you might try that to see if it helps. We don't *know* if other language settings cause trouble with Win'95, as they did with Windows (Danish, Swedish, and Spanish (but not "Spanish (Modern)"), specifically), but I wouldn't be at all surprised if they did. 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 Mon Oct 30 13:52:35 1995 Date: Mon, 30 Oct 1995 12:55:06 +0100 (MET) From: Jaroslaw Chojnacki 23-59 To: hyperchem@hyper.com Subject: Details in *.log file ? This is perhaps a simple question, maybe a FAQ? I am doing some conformational analysis by running a script. I want to put selected torsion angles, bonds, charges on atoms etc. of one conformer to the log file and start calculation on another conformation. I tried to select the desired items, but nothing go to the log file, although I could read it in the screen bottom line. 1. How to do that in the most simple way? One more not related question. 2. Is that possible to obtain LCAO coefficients for given wavefunction under hyperchem? Jaroslaw Chojnacki Technical University of Gdansk Department of Chemical Technology jarekch@chem.pg.gda.pl ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Oct 30 17:06:59 1995 Date: Mon, 30 Oct 95 11:38:11 -0500 From: Stephen Little To: hyperchem@hyper.com Subject: hyperchem sgi demo and hyperchem sgi 4.5 Hello, Is there any potential problem in installing the demo for Hyperchem 4.5 for the SGI if the full version of Hyperchem 4.5 for SGI will be installed at a later date. Are there any files that need to be removed. Will the hyperchem_elmadmin become confused, etc. Your reassurance on the one issue will be appreciated. Stephen Little sbl@linus.herl.epa.gov ********************************************************************* * * * Stephen Little sbl@linus.herl.epa.gov * * Research Chemist * * U.S. Environmental Protection Agency * * HERL/ECD/CMB MD-68 * * Research Triangle Park, NC 27711 919-541-0963 * * * *Disclaimer: Mention of trade names or products does not constitute * *endorsement by the United States Environmental Protection Agency. * ********************************************************************* ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Oct 30 20:22:54 1995 Date: Mon, 30 Oct 95 17:30:52 -0500 From: polowin (Joel Polowin) To: Stephen Little Subject: Re: hyperchem sgi demo and hyperchem sgi 4.5 Cc: hyperchem@hyper.com > Date: Mon, 30 Oct 95 11:38:11 -0500 > From: Stephen Little > > Is there any potential problem in installing the demo for Hyperchem 4.5 > for the SGI if the full version of Hyperchem 4.5 for SGI will be installed > at a later date. Are there any files that need to be removed. Will the > hyperchem_elmadmin become confused, etc. Your reassurance on the one > issue will be appreciated. The two versions use the same file names; installing one will completely get rid of the other. One must re-run the license manager setup, as given in the installation instructions, since the demo license will be invalid for the regular software, but we have had no problems here in installing successive demo and regular versions during the process of testing the software. 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 Tue Oct 31 15:41:15 1995 From: "Bruno Fong-Ponne" Date: Tue, 31 Oct 1995 16:04:27 +0100 To: hyperchem@hyper.com Subject: HyperChem4.5 DEMO Cc: polowin Hi, When I 'm trying to save a molecule my HyperChem4.5 DEMO shutdown and give on the Xwindow : > [2] + Segmentation fault hyperchem (core dumped). How can I solve this problem ???? -- Bruno Fong-Ponne LCOPS - bat 305 Universite Claude Bernard tel (+33) 72 43 11 39 43 BD du 11 novembre 1918 fax (+33) 72 43 81 36 F-69622 Villeurbanne e-mail bruno@copssg.univ-lyon1.fr ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Oct 31 17:36:50 1995 Date: Tue, 31 Oct 95 11:44:58 -0500 From: polowin (Joel Polowin) To: Jaroslaw Chojnacki 23-59 Subject: Re: Details in *.log file ? Cc: hyperchem@hyper.com > Date: Mon, 30 Oct 1995 12:55:06 +0100 (MET) > From: Jaroslaw Chojnacki 23-59 > > I am doing some conformational analysis by running a script. I want to put > selected torsion angles, bonds, charges on atoms etc. of one conformer to > the log file and start calculation on another conformation. I tried to > select the desired items, but nothing go to the log file, although I > could read it in the screen bottom line. > 1. How to do that in the most simple way? The script commands 'omsgs-to-file' and 'append-omsgs-to-file' can be used to send output messages to a file (instead of to the screen, as usual). The second of these would be more suitable for what you want here, since it can append messages to the log file instead of erasing the log file. Then the command 'query-value', which usually displays variables on the screen, will send its output to the file. And one of our users discovered that the command 'status-message', which is usually used to display information on the status line at the bottom of the window, can act as a variable itself, holding the last status-line message that was displayed. So if you have a log file test.log, and have run the script command append-omsgs-to-file test.log and have performed some HyperChem operation that has resulted in a message sent to the status line -- for example, selecting an angle -- then the command query-value status-line will append that status-line message to the file. Other 'query-value' instructions will likewise send information to the file until the command omsgs-not-to-file is executed, after which the messages will again be displayed on the screen. > One more not related question. > 2. Is that possible to obtain LCAO coefficients for given wavefunction > under hyperchem? Unless I'm misunderstanding what you're asking for, those coefficients are the values in the eigenvector table that you can find in the log file after you run a quantum mechanics calculation. 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 Tue Oct 31 19:21:48 1995 Date: Tue, 31 Oct 95 14:54:58 -0500 From: polowin (Joel Polowin) To: "Bruno Fong-Ponne" Subject: Re: HyperChem4.5 DEMO Cc: hyperchem@hyper.com > From: "Bruno Fong-Ponne" > Date: Tue, 31 Oct 1995 16:04:27 +0100 > > When I 'm trying to save a molecule my HyperChem4.5 DEMO shutdown and give on > the Xwindow : > > > [2] + Segmentation fault hyperchem (core dumped). This is something that we haven't seen. What format were you saving the file in, and what kind of structure was it? Would you please execute the command hinv which will give information about your system, and tell me more about your system? You had trouble with the installation, as well; you managed to get it to work with the IRIX 5.3 installation utility but I don't know which version of 'inst' *didn't* work for you. 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.