From owner-hyperchem@hyper.com Tue Jul 4 14:35:17 1995 Date: Mon, 3 Jul 1995 12:37:23 +0300 (IDT) From: Daniel Kost To: Joel Polowin Cc: hyperchem@www Subject: Optimizations Here is another one: We are trying to calculate various pi-pi molecular complexes. We don't think force fields would respond to this kind of interaction, so we use AM1 and PM3. Trouble is, optimizations do not converge to the same geometry. They are substantially dependent on initial geometry. Any idea why? Daniel Kost ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jul 4 14:40:42 1995 From: "Claus Scheuer-Larsen" Organization: Odense University To: hyperchem@hyper.com Date: Mon, 3 Jul 1995 16:32:36 GMT-1 Subject: DNA : RNA Hello Hyperchemists! I have a minor problem, and hopefully some of you will be able to help me. I want to build a DNA strand complementary to a RNA strand, like dT5 : rA5 using the database of nucleic acids. I will compare DNA towards RNA, both modified and unmodified. Thanks Claus Scheuer-Larsen 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 Tue Jul 4 14:49:50 1995 Date: Mon, 3 Jul 1995 12:10:16 +0300 (IDT) From: Daniel Kost To: Joel Polowin Cc: hyperchem@www Subject: linear translation in Hyperchem Dear Hyperchemers, I have been unable to selectively translate one molecule away from another by a certain distance in the X-Y axes. "Selection" of one molecule (out of two) and moving the selected molecule, say, 5A in the Y-dirction results in motion in both X and Y, and it is irreproducible in the sense that when one attempts to reverse the operation by moving the same molecule in the same axis by the same value with negative sign - it goes to a totally different location than the original. By the way, this does not happen with Z-translation, nor when BOTH molecules are translated simultaneously. Can anyone provide an explanation and/or solution to the problem? Daniel Kost Department of Chemistry Ben Gurion University Beer Sheva, Israel ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jul 4 14:49:51 1995 From: CSL@chem.ou.dk To: hyperchem@hyper.com Organization: Odense University Date: 4 Jul 95 11:28:49 GMT-1 Subject: DNA towards RNA Hello hyperchemists! I just mailed this message, but got it back, so if any of you receive the same questions twice, please ignore this! My problem is as follows: Is it possible to build a DNA/RNA duplex in hyperchem using the database of nucleic acids - that means DNA hybridized with RNA. I want a dT5 hybridized with rA5 and then do energy minimization using Amber / MM+. If any one knows how to do this, please let me know. Claus Scheuer-Larsen 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 Tue Jul 4 16:15:47 1995 Date: Tue, 4 Jul 95 12:59:30 -0400 From: polowin (Joel Polowin) To: bouyer@ext.jussieu.fr (Frederic BOUYER) Subject: Re: MNDO/d softwares and sparkles Cc: chemistry@osc.edu, hyperchem@www > Date: Fri, 30 Jun 1995 08:58:01 +0100 > From: bouyer@ext.jussieu.fr (Frederic BOUYER) > Subject: MNDO/d softwares and sparkles > 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) HyperChem has Na parameters for the CNDO/INDO and ZINDO/1 methods. We'd be interested in pointers to published parameters for other methods. 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" to hyperchem-request@hyper.com ________________________________________________________________________ From chemistry-request@osc.edu Tue Jul 4 18:30:06 1995 Date: Tue, 4 Jul 95 12:59:30 -0400 From: polowin (Joel Polowin) To: bouyer@ext.jussieu.fr (Frederic BOUYER) Subject: CCL:MNDO/d softwares and sparkles Cc: chemistry@osc.edu, hyperchem@www Sender: Computational Chemistry List Errors-To: ccl@osc.edu > Date: Fri, 30 Jun 1995 08:58:01 +0100 > From: bouyer@ext.jussieu.fr (Frederic BOUYER) > Subject: MNDO/d softwares and sparkles > 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) HyperChem has Na parameters for the CNDO/INDO and ZINDO/1 methods. We'd be interested in pointers to published parameters for other methods. 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" to hyperchem-request@hyper.com -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: owner-chemistry@osc.edu -- Original Sender From: Address: polowin@hyper.hyper.com CHEMISTRY@osc.edu -- everyone | CHEMISTRY-REQUEST@osc.edu -- coordinator MAILSERV@osc.edu: HELP CHEMISTRY | Gopher: infomeister.osc.edu 73 Anon. ftp infomeister.osc.edu | CHEMISTRY-SEARCH@osc.edu -- archive search http://www.osc.edu/chemistry.html | for info send: HELP SEARCH to MAILSERV ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jul 4 19:07:44 1995 Date: Tue, 4 Jul 95 16:33:04 -0400 From: polowin (Joel Polowin) To: hyperchem@www Subject: Re: DNA towards RNA > From: CSL@chem.ou.dk > Date: 4 Jul 95 11:28:49 GMT-1 > Subject: DNA towards RNA > > Is it possible to build a DNA/RNA duplex in hyperchem using the > database of nucleic acids - that means DNA hybridized with RNA. > I want a dT5 hybridized with rA5 and then do energy minimization > using Amber / MM+. I was hoping that it might be possible to do this by modifying the CHEM.TPL file. When a residue tag is prefixed by a '-', it indicates that that residue is to be used for construction of a second strand or a backwards strand. I was hoping that by moving those flags for the complementary RNA residues to the appropriate DNA residues, the second strand would be built of DNA. It didn't work; apparently the information about complementary nucleotides is built into HyperChem (there's no way to specify complements for user-defined residues), and HyperChem builds with the residues that it finds under the regular flags and not the complements. Perhaps this is something that we should change. You could still work this way, but you would need to have two different template files and two copies of HyperChem running. In one file you would change the RU entry to contain DT and the RC entry to contain DC, and in the other you would change the RA entry to contain DA and the RG entry to contain DG. You would use the first to add rA and rG residues, and the complementary strand would be built of DNA; you would switch to the second for the other residues. This, needless to say, would be cumbersome. It would be fairly simple to write an Excel macro or a Visual Basic program that would read along an RNA strand, one residue at a time, and mutate each residue to the appropriate DNA residue. This is probably the best solution. 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 Tue Jul 4 20:01:38 1995 Date: Tue, 4 Jul 95 16:41:26 -0400 From: polowin (Joel Polowin) To: Daniel Kost Subject: Re: Optimizations Cc: hyperchem@www > From: Daniel Kost > To: Joel Polowin > > We are trying to calculate various pi-pi molecular complexes. We don't > think force fields would respond to this kind of interaction, so we use > AM1 and PM3. Trouble is, optimizations do not converge to the same > geometry. They are substantially dependent on initial geometry. Molecular mechanics force fields include non-bonded interactions, but these probably don't model these kinds of pi-pi interactions very well. Any kind of optimization can be highly dependent on initial geometry if there are lots of local minima available for the system to settle into, and it seems to me that this kind of system is a good candidate: many local minima, relatively weak attractive forces. Since I don't know what kind of system you are modelling, it's hard for me to judge. Is this the kind of problem you are facing? 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 Tue Jul 4 20:17:04 1995 Date: Tue, 4 Jul 95 17:39:01 -0400 From: polowin (Joel Polowin) To: Daniel Kost Subject: Re: linear translation in Hyperchem Cc: hyperchem@www > Date: Mon, 3 Jul 1995 12:10:16 +0300 (IDT) > From: Daniel Kost > > I have been unable to selectively translate one molecule away from > another by a certain distance in the X-Y axes. "Selection" of one molecule > (out of two) and moving the selected molecule, say, 5A in the Y-dirction > results in motion in both X and Y, and it is irreproducible in the sense > that when one attempts to reverse the operation by moving the same > molecule in the same axis by the same value with negative sign - it goes > to a totally different location than the original. > By the way, this does not happen with Z-translation, nor when BOTH > molecules are translated simultaneously. > Can anyone provide an explanation and/or solution to the problem? The basic problem is that the "translate-selection" script command, and the equivalent menu operation, are not "translate selection by x,y,z increments" but "translate selection to x,y,z coordinates". The selection is moved to the coordinates that you specify in Molecular Coordinate space. (Since a single system is usually centred on Z=0, you don't have a comparable problem with Z translation.) We could probably use a "translate-by" in addition to the "translate-to" command. That goes on the wish-list. Possible work-arounds: (1) An Excel macro or Visual Basic program that goes through the selected atoms and increments their coordinates as you want; or (2) save the file, and edit the coordinates of those atoms. You could also add an extra atom to the molecule; set translate-whole- molecules off; translate the extra atom to 0,0,0; set translate-whole- molecules on; translate the extra atom by the coordinates corresponding to the desired increment; delete the extra atom. Easier than any of these, I think, is to set the default value for translation using the icon or keyboard (under File/Preferences/Tools) to the desired amount, and then use the Shift, Control, and arrow keys to do that incremental translation. 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 Tue Jul 4 22:49:07 1995 From: "Matthew E. Harbowy" Subject: Optimizations To: hyperchem@hyper.com Date: Tue, 4 Jul 1995 20:32:05 -0400 (EDT) >Here is another one: >We are trying to calculate various pi-pi molecular complexes. We don't >think force fields would respond to this kind of interaction, so we use >AM1 and PM3. Trouble is, optimizations do not converge to the same >geometry. They are substantially dependent on initial geometry. >Any idea why? >Daniel Kost The choice of semiempirical techniques to study pi-pi complexes seems to be a poor one. Without a good treatment of electron correlation, you're never going to get a decent result. That doesn't explain your problems with optimization however. The reason you keep getting a different geometry is not because you are starting from different geometries, necessarily, but because you are trying to minimize a geometry on a next-to-flat potential energy surface. You need to set your gradient optimization very, very, tight to get a good minimization for your molecules, but for the computational cost, why bother? What do you really want to learn? Perhaps a rough picture of the HOMO or LUMO orbitals of each separate molecule might tell you more for less. matt -- o-cha@cnj.digex.net | matthew.harbowy@tjlus.sprint.com | "I'm the bear that went harbowy@aol.com | over the mountain." http://www.cnj.digex.net/~o-cha | ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jul 5 08:39:58 1995 From: heelisp@delta.newi.ac.uk Date: Wed, 5 Jul 1995 09:33:48 +0100 To: hyperchem@hyper.com Subject: spectral calculations Dear Hyperchemists, I have been using Hyperchem to calculate the UV/Vis spectra of a cofactor in an enzyme (from a PDB file). If I delete all the residues except the cofactor (i.e. cofactor alone) I get a certain result, whereas if I carry out the calculation with all the residues present but only the cofactor selected, I get a 50nm shift. Chemically I have no problem with this, as it is just what I am expecting for the molecule. The cofactor is a charged heterocycle and there is a negative carboxyl almost within Van der Waals contact. My question is, how does Hyperchem carry out the calculation (Zindo) on only the selected molecule but take into account the surrounding molecule. I cannot think of a way to do this with say MOPAC, as a molecule is either put inot the Z matrix or it isn't. As far as I know there is no way to ask it to use orbitals of the target molecule, but just take into account the electro statics of another molecule. All comments would be welcome. Paul Heelis North East Wales Institue , UK Heelisp@newi.ac.uk ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jul 5 16:17:20 1995 Date: Wed, 5 Jul 95 13:16:39 -0400 From: polowin (Joel Polowin) To: heelisp@delta.newi.ac.uk Subject: Re: spectral calculations Cc: hyperchem@hyper.com > From: heelisp@delta.newi.ac.uk > Date: Wed, 5 Jul 1995 09:33:48 +0100 > > My question is, how does Hyperchem carry out the calculation (Zindo) > on only the selected molecule but take into account the surrounding > molecule. I cannot think of a way to do this with say MOPAC, as > a molecule is either put inot the Z matrix or it isn't. As far as I > know there is no way to ask it to use orbitals of the target > molecule, but just take into account the electro statics of another > molecule. This is described in the _Computational Chemistry_ manual -- briefly pn pages 215-219, and in more detail in the following sections for each of the semi-empirical methods. The general heading is "Mixed Model". I have no idea whether or not other software packages can do this. 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 Mon Jul 10 14:35:25 1995 Date: Mon, 10 Jul 1995 15:58:19 +0200 To: hyperchem@hyper.com From: ki@twi.ch (Markus Koenig) Subject: Hardware : Hyperchem-Dongle Gentlemems We use HyperChem from Hypercube with a 5 license network-dongle from Rainbow Technologies Inc. at Irvine CA. We have Windows for Workgroup 3.11 PC's, all the same. Now I will make one WfW 3.11 PC as a Dongle-Server. The problem I have is: I have only a DOS-File NSRVDN.EXE to make the Server, no Windows-File. (It runs, but it's not pretty) This File only works with the NetBeui-Protocol, not with Microsoft's TCP/IP 3.11a, but the NetBeui-Protocol is not available everywhere, TCP/IP is. Is there a File witch runs under Windows (something like NSRVDN.386)? And how can I use the TCP/IP-Protocol? yours sincerely Markus Koenig Markus E. Koenig Laegernstrasse 2 8304 Wallisellen Tel 052 2677 441 Fax 052 2677 231 ki@twi.ch ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jul 18 18:14:30 1995 Date: Tue, 18 Jul 1995 18:58:38 +0100 To: hyperchem@HYPER.COM From: ujordis@pop.tuwien.ac.at (DR. ULRICH JORDIS) Subject: HyperChem Release 4.5 diskette problems I just received (invoice # 1779) the update release 4.5 but found, that the content of floppy disk labelled disk 2 is in fact an exact copy of disk #1 and I therefor cannot install the software update. In order to avoid the costs of sending a new disk I suggest that you send a zipped version of disk#2 via Internet, e.g. as an attachment to email of via FTP file transfer. I have here a server running where you could deposit the file via FTP transfer: the address is 128.130.138.14, user=anonymous, password=your email account number: this should be an open directory! ........................................................................... 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 Jul 19 04:00:22 1995 From: "Rob Ledger, School Pharmacy, x7241" Organization: University of Otago To: hyperchem@hyper.com Date: Wed, 19 Jul 1995 15:53:10 GMT+1200 Subject: Power PCs Will Hyperchem run on Macintosh Power PCs? We have been running Hyperchem on IBM computers for several years. We now want to expand to a network version but our institution is predominantly Mac or oriented. With the advent of the Mac Power PC we see an oportunity to introduce molecular graphics to all our undergraduate students, second, third and final year students. Dr Rob Ledger CChem FRSC FNZIC School of Pharmacy University of Otago DUNEDIN, New Zealand Voice +(64)3 497 7241 (office) +(64)3 454 4393 (home) Fax +(64)3 479 7034 e-mail rledger@gandalf.otago.ac.nz snail mail PO Box 913, Dunedin ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jul 19 14:44:39 1995 Date: Wed, 19 Jul 95 10:02:04 -0400 From: polowin (Joel Polowin) To: hyperchem@www Subject: Re: Power PCs > From: "Rob Ledger, School Pharmacy, x7241" > Date: Wed, 19 Jul 1995 15:53:10 GMT+1200 > Subject: Power PCs > > Will Hyperchem run on Macintosh Power PCs? We have been running > Hyperchem on IBM computers for several years. We now want to expand > to a network version but our institution is predominantly Mac or > oriented. With the advent of the Mac Power PC we see an oportunity to > introduce molecular graphics to all our undergraduate students, > second, third and final year students. There is no MacIntosh version of HyperChem at this time and the Windows version will not run under SoftWindows on PowerMacs because SoftWindows does not yet support Windows in 386 Enhanced mode. (According to _Byte_, April 1995, pg. 166, an improved version of SoftWindows is on the way.) We've been considering a Mac version for over 6 years. So far our estimated porting costs outweigh our estimates of increased revenue, but there are some automated porting tools on the horizon which may change the equation. We've recently been talking with Apple about getting their help with the port. This is still categorized as "something we want to do but we're not promising it and certainly not scheduling it yet." We've also heard about a new 486 board that can be plugged into a PowerMac and which lets it run regular DOS software. Our software *should* run under Windows on this -- if it's also set up with PC-style ports that our hardware lock can be plugged into. But this hasn't been tested. So far, the only 486 boards that we've heard about don't have PC-style parallel ports. If you know of one that does, we'd love to hear about it. For HyperChem to work under the improved SoftWindows may present similar problems. 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 Wed Jul 19 20:15:20 1995 Date: Wed, 19 Jul 1995 15:32:02 -0400 To: hyperchem@hyper.com From: l_wester@lvc.edu (Lance M. Westerhoff) Subject: PowerMacs >> From: "Rob Ledger, School Pharmacy, x7241" >> Date: Wed, 19 Jul 1995 15:53:10 GMT+1200 >> Subject: Power PCs >> >> Will Hyperchem run on Macintosh Power PCs? We have been running >> Hyperchem on IBM computers for several years. We now want to expand >> to a network version but our institution is predominantly Mac or >> oriented. With the advent of the Mac Power PC we see an oportunity to >> introduce molecular graphics to all our undergraduate students, >> second, third and final year students. > >There is no MacIntosh version of HyperChem at this time and the Windows >version will not run under SoftWindows on PowerMacs because SoftWindows >does not yet support Windows in 386 Enhanced mode. (According to _Byte_, >April 1995, pg. 166, an improved version of SoftWindows is on the way.) > >We've been considering a Mac version for over 6 years. So far our estimated >porting costs outweigh our estimates of increased revenue, but there are >some automated porting tools on the horizon which may change the equation. >We've recently been talking with Apple about getting their help with the >port. This is still categorized as "something we want to do but we're >not promising it and certainly not scheduling it yet." > >We've also heard about a new 486 board that can be plugged into a PowerMac >and which lets it run regular DOS software. Our software *should* run >under Windows on this -- if it's also set up with PC-style ports that >our hardware lock can be plugged into. But this hasn't been tested. >So far, the only 486 boards that we've heard about don't have PC-style >parallel ports. If you know of one that does, we'd love to hear about it. >For HyperChem to work under the improved SoftWindows may present similar >problems. > >Regards, >Joel It's unfortunate that Hyperchem isn't to be ported. We recently built a large molecular modeling lab, and had to opt for another modeling company because we bought all Powermacs. Our science building is preeminently Mac and since the PowerPC processor competes quite well with (and in some cases even better then) the Pentium, we figured Powermac is a better choice for our particular establishment. --just another vote in support of a Powermac port as soon as possible. I wouldn't hold you breath for HyperChem working with Softwindows. Joel is right, unless Hyperchem changes the hardware-lock, Hyperchem still wouldn't work with Softwindows - Macs aren't equipped with PC-style parallel ports. -Lance _________________________ Lance M. Westerhoff Biochemistry/Applied Computer Science at Lebanon Valley College of Pennsylvania Can be reached at: Cornell University Section of Plant Biology 228 Plant Science Building Ithaca, NY 14853-5908 United States of America Phone: (607)255-2234 (Office) (607)272-2775 (Personal) Fax: (607)255-5407 Internet: lmw6@cornell.edu l_wester@lvc.edu lancew@aol.com ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jul 20 14:59:54 1995 From: "Dr. Steven Desjardins" Organization: Washington & Lee University To: hyperchem@hyper.com Date: Thu, 20 Jul 1995 08:56:24 EDT Subject: PowerMacs Just to include my two cents. We have a mixed environment (Pentiums, PowerMacs, and SGI's) and run about six copies of HyperChem, which we use mainly for course work. Our three synthetic chemists (two organic, one inorganic) all use Macs, however. When they need a calculation they ask me, despite the fact that they could easily learn how to run hyperchem. They just don't want to deal with non-Macs. C&E News recently had an article on molecular modelling which stated this problem in a wider arena; bench chemists simply don't want to learn advanced OS's (Like Unix) in order to run MM packages. I think that Macs have a greater influence in chemistry than they do elsewhere, mainly because of good drawing packages like ChemDraw. In particular, I think that the Mac is often the system of choice for synthetic chemists. It is important to realize that if another MM package dominates the Mac world, it will probably be ported to Windows, so that even if HyperChem is a better product it could be supplanted. Note that this is a friendly comment from a HyperChem fan. in ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jul 24 20:06:27 1995 From: imcvey@Phoenix.kent.edu (McVey Iain ) Subject: mm+ aqueous geometries? To: hyperchem@hyper.com Date: Mon, 24 Jul 1995 15:30:18 -0400 (EDT) Content-Length: 732 Hello Hyperchemists, I would like to predict aqueous geometries of larger molecules using MM+ and so for the sake of expediency I would like to use the settings in the MM+ dialog box to mimic the presencess of wter rather than using a periodic box. So my question is: Is swithced or shifted cutoffs better for this and what would be "good" values to use for the inner and outer cutoffs? AND Is this method going to produce reasonable results or should I bite the bullet and do these optimizations in a box of water. Thanks in advance for all your replies and of course I'll send out a summary if anyone is interested. Iain McVey Graduate student Kent State University imcvey@phoenix.kent.edu or imcvey@en.com ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jul 26 22:47:13 1995 Date: Wed, 26 Jul 1995 23:25:01 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: Semi-empirical parameters for metal ions To: support@hyper.com Cc: hyperchem@hyper.com Hi, I am interested in estimating enthalpies of formation of the complexes formed between metal ions and calixarenes (a class of macrocycle). Some of the semi- empirical methods in HyperChem have parameters for Na for example. Will these parameters be suitable for Na+? Regards, Paddy Paddy Kane School of Chemical Sciences Dublin City University Ireland e.mail 94970459@vax1.dcu.ie ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jul 27 02:59:39 1995 Date: Wed, 26 Jul 95 23:24:57 -0400 From: polowin (Joel Polowin) To: Paddy Kane <94970459@vax1.dcu.ie> Subject: Re: Semi-empirical parameters for metal ions Cc: hyperchem@www > Date: Wed, 26 Jul 1995 23:25:01 +0000 (GMT) > From: Paddy Kane <94970459@vax1.dcu.ie> > Subject: Semi-empirical parameters for metal ions > > I am interested in estimating enthalpies of formation of the complexes formed > between metal ions and calixarenes (a class of macrocycle). Some of the semi- > empirical methods in HyperChem have parameters for Na for example. Will these > parameters be suitable for Na+? As you may have noticed, all of the semi-empirical methods assign charges to each atom based on total system charges; you cannot assign specific charges arbitrarily to atoms. 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 Jul 27 12:33:39 1995 From: "MORTEN LANGGaaRD - BIOKEM" Organization: Roskilde Universitetscenter To: hyperchem@hyper.com Date: Thu, 27 Jul 1995 11:32:24 +0100 Subject: Ab initio performance Dear HyperChem users! Here is some notes on "ab initio" performance in HyperChem. I received my HyperChem 4.5 upgrade for a few weeks ago and was very curious to see how well the new ab initio part is implemented. As usual with HyperChem I find that the user interface is almost perfect for the non specialist user - everything you really want is there - just a click away. Applause, applause! To check the new Gauss engine, I decide to run some simple tests on a little well known molecule - Ethanol. For comparison I ran the same test with the original Gaussian 92 for Windows program from Gaussian, Inc. The results listed below, are all started from the same input structure (AM1 optimized gnorm=0.1). Termination condition was set to gnorm=0.1 in HyperChem and the default "tight" in G92W. It is not straight forward to compare these two criteria, but I guess that they are very close, since HyperChem's gnorm=0.1 will be satisfied after just a few cycles on a G92W optimized structure (this will always be necessary due to rounded figures). The computer used for these calculation is a AMD DX4-100MHz with 32Mb ram, 256kb cache, and a reasonable fast Western Digital 730Mb HD. Geometry optimization of ethanol: HyperChem, STO-3G, direct SCF, 32 min. HyperChem, STO-3G, non-direct SCF, 16 min. G92W, STO-3G, direct SCF, 6 min. 35 sec. HyperChem, 3-21G, direct SCF, 1 H. 30 min. HyperChem, 3-21G, non-direct SCF, 45 min. G92W, 3-21G, direct SCF, 8 min. 33 sec. G92W, 3-21G, non-direct SCF, 10 min. 21 sec. HyperChem, 6-31G*, non-direct SCF, 4 H. 33 min. G92W, 6-31G*, direct SCF, 1 H. 12 min. Comments: As it follows from these figures, it is exactly twice as expensive to run direct SCF with HyperChem - this is strange! With G92W it doesn't really matter and my experience is, that the direct method often is the fastest. There is not mush logic in this and as the G92W manual says "you have to try". By using the direct method you don't have to worry about disk space. Why is HyperChem about 4-6 times slower than G92W? Well, I don't know - maybe I do something wrong! But I have tried the following changes from the default settings: Raffenetti integral format - No effect at all! (G92W uses these as default) Buffer size increased to 10000 - no effect! (G92W uses 8192 words for these calculations) A general change I have made is to use INDO MO initial guess instead of the default Core Hamiltonian (INDO is also used by G92W). My short experience is that the Core Hamiltonian often fails totally and causes corrupted structures (try it on Ethanol and you may see the end of this molecule - whooh). Any explanation? INDO guess's are fast and seem to work every time. By default G92W has "Two-electron integral symmetry turned on" (keyword SYMM) which might speed up the calculation. The symmetry can be turned off by the keyword NOSYMM, but this only causes slightly longer computational times (about 5%). I don't know what HyperChem use regarding these "two electron" symmetries. Is it so bad that the Gauss.exe code simply is slow or is there some good explanation for these figures? Do we have to wait for release 5 (and Win9?)? After all, I still think it is a great event to see ab initio in HyperChem. Best regards, Morten =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Morten Langgaard Department of Chemistry Phone: +45 46757711 Roskilde University (RUC) Fax: +45 46757721 POB 260, DK-4000 Roskilde, Denmark e-mail: ML@mmf.ruc.dk ________________________________________________________________________ From owner-hyperchem@hyper.com Fri Jul 28 15:22:06 1995 Date: Fri, 28 Jul 1995 11:50:18 +0100 To: hyperchem@hyper.com From: tadrury@liverpool.ac.uk (Adam Drury) Subject: HyperChem Version 2.0 Dear All, Does anyone have, or know how I can get hold of a copy of HyperChem Version 2.0 ? I have a particular reason for wanting that version. Many thanks Adam Drury ------------------------------------------------------------------------ Adam Drury Chemistry Courseware Consortium C/O CTI Chemistry Department of Chemistry University of Liverpool P.O. Box 147 Liverpool L69 3BX ENGLAND Tel : 0151-794-3523 Fax : 0151-794-3586 E-mail : tadrury@liverpool.ac.uk ________________________________________________________________________ From owner-hyperchem@hyper.com Fri Jul 28 15:53:51 1995 Date: Fri, 28 Jul 1995 08:23:15 -0700 To: hyperchem@www From: hrmatthews@ucdavis.edu (Harry R. Matthews) Subject: hardware lock That ***!***!*** hardware lock "bit" me again. Sometimes it works; sometimes it doesn't. My department was going to buy several licences for HyperChem but I advised against it and we have gone with another program because of this stupid lock. Does anyone else have problems with their hardware lock? Any solutions? Harry R. Matthews Professor of Biological Chemistry email hrmatthews@ucdavis.edu WWW home page http://ocsbcm01.ucdavis.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Fri Jul 28 21:06:29 1995 Date: Fri, 28 Jul 1995 13:17:04 -0700 To: hyperchem@www From: hrmatthews@ucdavis.edu (Harry R. Matthews) Subject: Re: hardware lock I hadn't heard that HyperChem required a dedicated printer port. Can you suggest where I might buy a $15 printer port? Surely just the installation will cost more than that? >Are you running NT on the Pentium? I suggest that on the Ambra, you buy >another printer port ($15.00) and run the printer off that port and leave >the hardware lock on lpt1. Also you should check to see that the printer >port on the Ambra is not setup for ECP (advanced printer port mode). > > Harry R. Matthews Professor of Biological Chemistry email hrmatthews@ucdavis.edu WWW home page http://ocsbcm01.ucdavis.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jul 31 13:02:14 1995 Date: Mon, 31 Jul 1995 04:27:45 -0400 (EDT) From: "William T. Winter" To: "Harry R. Matthews" Cc: hyperchem@www Subject: Re: hardware lock On Fri, 28 Jul 1995, Harry R. Matthews wrote: > That ***!***!*** hardware lock "bit" me again. Sometimes it works; sometimes > it doesn't. My department was going to buy several licences for HyperChem > but I advised against it and we have gone with another program because of > this stupid lock. > We have two locks and have found them fully interchangeable with code running on several machines ranging from lap top to 486 DX2/66 to pentium90 and have not encountered any problems to date. We do advise users to lightly screw them in especially if a printer cable is to be attached. They are a nuisance but work reliably in our hands. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Prof. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 URL http://www-chem.esf.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jul 31 17:06:29 1995 Date: Mon, 31 Jul 95 12:21:09 -0400 From: polowin (Joel Polowin) To: hrmatthews@ucdavis.edu (Harry R. Matthews) Subject: Re: hardware lock Cc: hyperchem@www > Date: Fri, 28 Jul 1995 17:32:11 -0700 > From: hrmatthews@ucdavis.edu (Harry R. Matthews) > Subject: Re: hardware lock > > The replacement hardware lock that I bought was about a year ago. My message > produced some responses from others who have had problems as well. Since the > problem is intermittent, it is not obvious how to diagnose it. I can say > that I have never had a printing problem using the parallel port and, apart > from the power supply that failed in the first week, the computer has been > reliable. This afternoon, HyperChem is working again. > > The computer is an Ambra P90, about a year old. It has a Pentium, 90 MHz, > processor and 32 Mb of RAM. There is about 600 Mb of free hard disk space. > The Rainbow lock is in the single parallel port and a Laserjet III is > connected on top of the lock. The operating system is Windows NT 3.50 > Workstation. The computer has cards for sound, SCSI, Ethernet and video > (Matrox MGA II). It has good physical security. I do occasionally haul it to > a classroom, but I haven't noted any correlation between these movements and > the failure of HyperChem. Once started, HyperChem runs fine. But what are the symptoms of the problem? Is it that, once in a while, HyperChem can't seem to connect with the lock, and so fails to start? You say you're running under NT; so you must be running the port driver in order for HyperChem to communicate with the lock. Is it possible that one of the other software packages is shutting down the port driver, either temporarily or permanently? In the lab that I used to work in, I noticed that the screen-saver software that was supposed to be running all the time would occasionally be terminated. We never did find out if this was through interference by other software, or by accident on the part of the many people who used the system. The port driver will fail if it's not configured properly, though the correct configuration should not change except through hardware alterations -- as far as I know. 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.