From uunet.ca!triton.unm.edu!jborn@hyper.hyper.com Thu Jun 2 19:09:03 1994 From: triton.unm.edu!jborn@hyper.hyper.com Subject: Windows NT To: hyperchem@hyper.com Date: Thu, 2 Jun 1994 17:32:47 -0400 Does Hyperchem run under Windows NT? J. L. Born jborn@triton.unm.edu ________________________________________________________________________ From uunet.ca!risc1.chimorg.unifi.it!chimichi@hyper.hyper.com Fri Jun 3 16:40:45 1994 Date: Fri, 3 Jun 1994 11:47:00 -0400 From: "stefano chimichi" Sender: risc1.chimorg.unifi.it!chimichi@hyper.hyper.com To: hyperchem@hyper.com Subject: hypernmr Hello Netters, I'd like to know if somebody is using the hyperNMR software (hoping the list is appropriate for the question!) Thanks for answers (I'll post the results to the list) Cheers Stefano ---------------------------------------------------------------------- Prof. Stefano Chimichi Phone: 39+55+2757631 Organic Chemistry Dept. Fax: 39+55+2476964 Via Gino Capponi, 9 I-50121 FIRENZE - Italy ---------------------------------------------------------------------- ________________________________________________________________________ From uunet.ca!spectre.uunet.ca!cellbio.wustl.edu!paul@hyper.hyper.com Fri Jun 3 20:16:31 1994 Date: Fri, 3 Jun 1994 13:26:53 -0400 To: hyperchem@uunet.ca From: cellbio.wustl.edu!paul@hyper.hyper.com (Paul Schlesinger) Subject: Have just aquired OS2 for windows and was wondering if anyone has run Hyperchem 4 under it with success? thank you ________________________________________________________________________ From uunet.ca!zui.unizh.ch!toukie@hyper.hyper.com Sat Jun 4 16:11:16 1994 From: zui.unizh.ch!toukie@hyper.hyper.com (Hr Dr. S. Shapiro) Subject: Modelling hydrophobic interactions, isotope effects, &c. To: hyperchem@HYPER.COM Date: Sat, 4 Jun 1994 16:11:58 -0400 Cc: toukie@zui.unizh.ch Dear Sirs/Madames: A couple of questions about HyperChem 3.0 and MOPAC 6.0, if you don't mind: (i) I am interested in examining the interactions between biological mem- n branes and hydrophobic weak acids in order to better understand why some of these acids are toxic towards cells and others are not. The molecular model- ling software I have at my disposal are HyperChem 3.0 and MOPAC 6.0. Can any- one suggest how these programmes might be used to esamine prospective interac- tions between biomembranes and small molecular weight compounds? Would anyone care to recommend _other_ programmes which can be used to accomplish this? Of course, literature references and citations are always welcome. (ii) I am interested in comparing certain predicted molecular properties for some small molecular weight compounds and their corresponding deuterio- and tritio- derivatives. Firstly, I would like to know if it is possible to draw or otherwise construct deuterio- and/or tritio-substituted molecules using HyperChem 3.0? I couldn't find any information about this specifically in the user's manuals (I am willing to concede that I may have overlooked this infor- mation), so I had to construct the Z-matrix manually. When I fed the perhydro- and the corresponding perdeuterio- and pertritio- compounds into MOPAC 6.0 under the constraints t=72000 am1 uhf nointer ef precise the output for all three compounds was absolutely identical EXCEPT FOR THE MOLECULAR WEIGHTS (which were correct). Is AM1 to insensitive to the subtle physicochemical differences between isotopically-substituted molecules so as to be unable to determine energetic and other differences between them (aside from differences in molecular weight)? (iii) Using HyperChem 3.0, is it possible to obtain a picture such as those n shown in Figs. 3, 4, and 5 (but for AM1 and PM3 calculations) of Esaki, T. Chem. Pharm. Bull. 35(8): 3105-3111 (1987)? If so, please give details on how this may be accomplished. I thank in advance all respondents. Sincerely, S. Shapiro Internet: toukie@zui.unizh.ch ________________________________________________________________________ From hurst@hyper.hyper.com Mon Jun 6 18:31:32 1994 Date: Mon, 6 Jun 1994 14:31:32 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: paul@cellbio.wustl.edu (Paul Schlesinger) Subject: Re: HyperChem under OS/2 Cc: hyper!hyperchem@uunet.ca Paul Schlesinger asks: > Have just aquired OS2 for windows and was wondering if anyone has run > Hyperchem 4 under it with success? > thank you Many users have reported running HyperChem successfully under OS/2 2.1, however I believe that you need to set it up so that all the HyperChem executables run in the same Windows session so that DDE between the front and back ends works optimally. Cheers, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From hurst@hyper.hyper.com Mon Jun 6 19:41:48 1994 Date: Mon, 6 Jun 1994 15:41:48 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: toukie@zui.unizh.ch (Hr Dr. S. Shapiro), hyperchem@HYPER.COM Subject: Re: Modelling hydrophobic interactions, isotope effects, &c. Hr Dr. S. Shapiro asks: > A couple of questions about HyperChem 3.0 and MOPAC 6.0, if you don't > mind: > > (i) I am interested in examining the interactions between biological mem- > branes and hydrophobic weak acids in order to better understand why some of > these acids are toxic towards cells and others are not. The molecular model- > ling software I have at my disposal are HyperChem 3.0 and MOPAC 6.0. Can any- > one suggest how these programmes might be used to esamine prospective interac- > tions between biomembranes and small molecular weight compounds? Would anyone > care to recommend _other_ programmes which can be used to accomplish this? Of > course, literature references and citations are always welcome. In HyperChem you could use one of the molecular mechanics force fields to examine interactions that do not involve bond making or breaking, or you could use a quantum mechanical method in HyperChem to treat the small molecule and perhaps part of the membrane. The latter is referred to as a "mixed model" calculation in HyperChem, because the selected part of the system is treated quantum mechanically and the rest is included as charges in the quantum mechanical calculation. To the best of my knowledge, MOPAC does not offer mixed model calculations and does not have molecular mechanics, so you are restricted to treating the whole system quantum mechanically. Thus you would have to choose a fairly small subset of the membrane for a feasible calculation. By default I think that MOPAC is limited to 50 atoms, though you can recompile it to handle larger systems (HyperChem uses dynamic memory management and so does not require recompilation). By the way, the modelling programs have been sped up in release 4.0 of HyperChem, particularly for semi-empirical calculations. For general information about how to use modelling, the "Practical Applications" part of the HyperChem Computational Chemistry manual (and the New Features guide in the case of Release 3) describe the types of calculations that you can do with HyperChem and their expected accuracy. > (ii) I am interested in comparing certain predicted molecular properties > for some small molecular weight compounds and their corresponding deuterio- > and tritio- derivatives. Firstly, I would like to know if it is possible to > draw or otherwise construct deuterio- and/or tritio-substituted molecules using > HyperChem 3.0? I couldn't find any information about this specifically in the > user's manuals (I am willing to concede that I may have overlooked this infor- > mation), so I had to construct the Z-matrix manually. When I fed the perhydro- > and the corresponding perdeuterio- and pertritio- compounds into MOPAC 6.0 > under the constraints > > t=72000 am1 uhf nointer ef precise > > the output for all three compounds was absolutely identical EXCEPT FOR THE > MOLECULAR WEIGHTS (which were correct). Is AM1 to insensitive to the subtle > physicochemical differences between isotopically-substituted molecules so as > to be unable to determine energetic and other differences between them (aside > from differences in molecular weight)? HyperChem only supports isotopic substitution in molecular mechanics, which can be done by adding new atom types or changing the mass for an existing type. This will affect the results of molecular dynamics calculations that use molecular mechanics. The calculations available in HyperChem, MOPAC, and most other computational chemistry codes, do not use the nuclear mass in calculating potential energies. Nuclear masses are used for vibrations (including zero point energy corrections) and molecular dynamics. Of course NMR calculations (such as those available in HyperNMR) use the nuclear spin of an isotope, and you can do isotopic substitution in HyperNMR. > (iii) Using HyperChem 3.0, is it possible to obtain a picture such as those n > shown in Figs. 3, 4, and 5 (but for AM1 and PM3 calculations) of Esaki, T. > Chem. Pharm. Bull. 35(8): 3105-3111 (1987)? If so, please give details on how > this may be accomplished. I can't advise you without seeing the figures. If you would fax copies of the figures to 1-519-725-5193 I should be able to tell you... Hope this helps, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From uunet.ca!KENTVM.KENT.EDU!IMCVEY@hyper.hyper.com Tue Jun 7 17:37:12 1994 Date: Tue, 7 Jun 1994 13:37:12 -0400 From: Iain McVey Subject: Mobility of Hyper chem generated ML2 files To: hyperchem@HYPER.COM Hello all, We are using Spartan 3.1 to do calculations on some of our larger molecules. To avoid redrawing all the structures I saved the Hyperchem generated structures as .ML2 files, which spartan is supposed to read. BUT when I import the files into Spartan the molecules still have the correct shape but all the carbon atoms are not recognized. Similary when I try to import the .ML2 files into Alchemy3.0 the same problem arises. All the carbon atoms are imported as Du atom types. This is a real big pain because Hyperchem has the best molecules building "facilities" of any of the modeling software I have used, and I would like to build all my molecules with Hyperchem and upload them to the faster computers, rather than struggle with t heir arcane model builders. I hope you can help me ThanX Iain IMCVEY@KENTVM.KENT.EDU ________________________________________________________________________ From hurst@hyper.hyper.com Tue Jun 7 19:56:00 1994 Date: Tue, 7 Jun 1994 15:56:00 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: Iain McVey Subject: Re: Mobility of Hyper chem generated ML2 files Cc: hyper!hyperchem@uunet.ca Iain McVey writes: > We are using Spartan 3.1 to do calculations on some of our larger molecules. > To avoid redrawing all the structures I saved the Hyperchem generated > structures as .ML2 files, which spartan is supposed to read. BUT when > I import the files into Spartan the molecules still have the correct > shape but all the carbon atoms are not recognized. Similary when I try > to import the .ML2 files into Alchemy3.0 the same problem arises. All the > carbon atoms are imported as Du atom types. This is a real big pain because > Hyperchem has the best molecules building "facilities" of any of the > modeling software I have used, and I would like to build all my molecules with > Hyperchem and upload them to the faster computers, rather than struggle with > their arcane model builders. I would suggest try ZMT, PDB or MOL formats instead, or getting a third party format converter (such as Babel). When HyperChem writes MOL2 files, it writes the element correctly, but uses the default atom type (Du) for all atoms. This was a deliberate design compromise, to avoid having to map all of the four HyperChem forcefield type sets (each with completely user definable types!) to the set of types in the current Tripos force field (which could change, though I don't know if a Tripos user can change their definitions or not). At one point we considered making the MOL2 filter read-only because of this, but opted for writing with default types instead. Too bad neither Tripos or Wavefunction offer the ability to assign types based on user-editable rules like HyperChem can. ;-) If you want to be able to use faster computers for HyperChem calculations, you can now purchase UNIX HyperChem backend modules. Instead of having a backend icon pop up on your Windows screen when you start a calculation, HyperChem can seamlessly run the calculation on a UNIX computer. (Your PC must be connected to the UNIX computer with network software that supports Winsock 1.1, as almost all TCP/IP programs for DOS/Windows now do.) The platforms that are currently supported are SGI, IBM RS/6000 and DEC Alpha (running OSF/1). For instance, an MNDO calculation of C60 using a DEC 3000-500 for the backend (and a NEC 486DX/50 for the frontend) runs 18 times faster than on a NEC 486DX/50. The list price is US$ 2000 for either the UNIX molecular mechanics programs or the UNIX semi-empirical programs (i.e. 4K for both) with a 50% government and academic discount. (They also require release 4 of HyperChem.) Hope this helps, Graham P.S. I'm glad you like the way you can build molecules in HyperChem. Can we quote you? ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From uunet.ca!falli.uku.fi!POSO@hyper.hyper.com Wed Jun 8 09:22:42 1994 Date: Wed, 8 Jun 1994 05:22:42 -0400 From: Antti Poso Subject: Re: HyperChem under OS/2 To: hyperchem@uunet.ca Reply-To: messi.uku.fi!poso@hyper.hyper.com > Date: Mon, 6 Jun 1994 14:31:32 -0400 > From: hurst@hyper.hyper.com (Graham Hurst) > To: paul@cellbio.wustl.edu (Paul Schlesinger) > Subject: Re: HyperChem under OS/2 > Cc: hyper!hyperchem@uunet.ca > Paul Schlesinger asks: > > Have just aquired OS2 for windows and was wondering if anyone has run > > Hyperchem 4 under it with success? > > thank you > > Many users have reported running HyperChem successfully under OS/2 2.1, > however I believe that you need to set it up so that all the HyperChem > executables run in the same Windows session so that DDE between the front > and back ends works optimally. This is done automatically by the OS/2 2.1 unless you specify somethin else. However, you should check, that the 386 enchanced compatibility has been selected fot HyperChem (Dos (WinOS/2)-setings). What comes to the speed of the calculations, I have to tell something. With OS/2 2.1 HyperChem (AM1) calculations (if long enough) are faster than under MS-Windows. I don't know why, but the difference is somewhere between 5-40%, depending if you are doing something else at the same time. But still, are there any plans for HyperChem for OS/2? > > Cheers, > > Graham > ------------ > Graham Hurst > Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 > internet: hurst@hyper.com > Antti Poso poso@messi.uku.fi phone: +358-(9)71-162462 Department of Pharmaceutical Chemistry fax: -162456 University of Kuopio Finland pro fide ________________________________________________________________________ From uunet.ca!zygote.hsc.usc.edu!bolger@hyper.hyper.com Wed Jun 8 15:40:11 1994 Date: Wed, 8 Jun 1994 11:40:11 -0400 To: hyperchem@HYPER.COM From: zygote.hsc.usc.edu!bolger@hyper.hyper.com (Michael Bolger) Subject: Upgrade from 3.0 to 4.0 I have been using HyperChem 3.0 for about six months and just joined this list server when I received the HyperChem 4.0 upgrade. What is new about version 4.0 except that it is distributed by HyperCube? I looked for some kind of short document like "What's new in version 4.0" and I checked the program for new features. I don't get it? Please help. ________________________________________________________________________ From hurst@hyper.hyper.com Wed Jun 8 18:18:08 1994 Date: Wed, 8 Jun 1994 14:18:08 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: "Jeffry D. Madura" Subject: Re: A few questions about Hyperchem and Chemplus Cc: hyper!hyperchem@uunet.ca Hi HyperChemists, Jeffry Madura sent me some questions that I thought it would be worthwhile sharing with the HyperChem email group (and Jeffry told me that it's okay with him). > Date: Tue, 7 Jun 1994 17:02:41 -0400 > From: "Jeffry D. Madura" > Subject: A few questions about Hyperchem and Chemplus > To: hurst@hyper.com > > Dear Dr. Hurst, > > I am using Hyperchem 4.0 and Chemplus 1.0a. Now for the questions. Hi Jeffry - I think we have talked or emailed before. I would prefer that you send support questions to support@hyper.com and product information questions to info@hyper.com, so that someone else could answer them if I'm away. > 1. I would like to know if it is possible to generate a stereo view > using Presentations from Chemplus. I tried by turning on the stereo > mode in Hyperchem and grab the coordinates while in presentations > but no go. Do you have any tricks that will allow me to do that. You can do this by generating two separate images and then placing them beside each other in a drawing or paint program. Generate an image for the left eye, copy and paste into the drawing program, rotate the system to the left (in Chem or ChemPlus) to generate the image for the right eye and copy and paste it into the drawing program to the right (for wall-eyed stereo) or left (for cross-eyed) of the previously pasted image. The angle of rotation to use is gven by 2*arctan(d/2r) where d is the interocular distance (the distance between the viewer's eyes) and r is the distance of the object from the viewer. If you rotate the view in Chem and then do a Get View in Molecule Presentations you can set the rotation precisely, but one or two presses on the left arrow key in MP should do the trick. > 2. I have been playing around with the Crystals section and don't quite > understand how it is working. What I am trying to do is input the > three asymmetric atoms of the ice-Ih crystal then create a larger > system. I do successfully get the ice-Ih coordinates input but when I > try to create a 2 x 2 x 2 system the unit cell does not have the > correct number of water molecules. Is there a way to transform the > unique asymmetric coordinates to all of the coordinates in the unit cell? Um, I'm not sure that I understand the problem. If you want to define 2 x 2 x 2 unit cells to be a new, single unit cell, do a Put to HyperChem followed by a Get. You would then have to type in the new unit cell dimensions (i.e. twice the previous values). > 3. Is there a way to display the electrostatic potential as a 3D surface? Not with ChemPlus, though it is on the wishlist... > 4. Is there a way to coax Hyperchem to run a periodic box of atoms. For > example I would like to have Hyperchem do a molecular dynamics > simulation on a box of argon atoms. Yes. One way is to add a box line to the HIN file, but since you have ChemPlus I'd use the Crystal Builder and check the option to put the system in a periodic box. HyperChem will then use periodic boundary conditions for molecular mechanics calculations. > Other than the difficulties list above I really like the program. Keep > up the good work. The students also like using the program. Thanks! > Regards, > > jeffry > > Jeffry D. Madura > Department of Chemistry > University of South Alabama > Mobile, AL 36688 > > Phone: (205) 460-7430 > FAX: (205) 460-7359 > > e-mail: madura@moe.chem.usouthal.edu Hope this helps, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From hurst@hyper.hyper.com Wed Jun 8 19:20:16 1994 Date: Wed, 8 Jun 1994 15:20:16 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: poso@messi.uku.fi Subject: Re: HyperChem under OS/2 Cc: hyperchem@hyper.hyper.com > Date: Wed, 8 Jun 1994 05:22:42 -0400 > From: Antti Poso > Subject: Re: HyperChem under OS/2 > > > Date: Mon, 6 Jun 1994 14:31:32 -0400 > > From: hurst@hyper.hyper.com (Graham Hurst) > > To: paul@cellbio.wustl.edu (Paul Schlesinger) > > Subject: Re: HyperChem under OS/2 > > Cc: hyper!hyperchem@uunet.ca > > > Paul Schlesinger asks: > > > Have just aquired OS2 for windows and was wondering if anyone has run > > > Hyperchem 4 under it with success? > > > thank you > > > > Many users have reported running HyperChem successfully under OS/2 2.1, > > however I believe that you need to set it up so that all the HyperChem > > executables run in the same Windows session so that DDE between the front > > and back ends works optimally. > > This is done automatically by the OS/2 2.1 unless you specify > somethin else. However, you should check, that the 386 enchanced > compatibility has been selected fot HyperChem (Dos > (WinOS/2)-setings). Thanks - I know we need 386 Enhanced, but could not remember if it was the default in Win0S/2. > What comes to the speed of the calculations, I have to tell > something. With OS/2 2.1 HyperChem (AM1) calculations (if long > enough) are faster than under MS-Windows. I don't know why, but the > difference is somewhere between 5-40%, depending if you are doing > something else at the same time. Interesting but not surprising if I have correctly understood that calculations *slow down less* compared to the slow down in Windows when you start doing something else at the same time. The backends are 32-bit and the only time spent in Windows system code is periodic message handling to allow cooperative multitasking. For an AM1 calculation on Windows with nothing else running (except ProgMan, a profiler and the HyperChem front end) less than 10% of the time is spent outside of HyperNDO. Thus I would expect the speed would be the same for OS/2 and Windows when nothing else is running. What you are seeing is that whatever other program you are using doesn't cooperatively multitask very well, and needs pre-emptive multitasking to make it behave! > But still, are there any plans for HyperChem for OS/2? It is one of the platforms on our wishlist, but I can't tell you where it is on the list... Without wishing to start yet another OS/2 vs. Windows debate, I have to say that in a way IBM shot itself in the foot by making OS/2 run Windows so well. Personally I think that OS/2 is technically superior to Win16, but when a Win16 app runs well on OS/2, the cost of porting from GDI to PM so far outweighs likely increased sales revenue (in my opinion). Now if IBM wants to fund a port, the equation changes... We have ported to Win32 (i.e. NT) and have demonstrated this running on DEC alphas at a couple of shows. FYI on a 150 MHz Alpha PC, semi-empirical calculations run 12 times faster than a 486DX/50. > Antti Poso poso@messi.uku.fi phone: +358-(9)71-162462 > Department of Pharmaceutical Chemistry fax: -162456 > University of Kuopio > Finland > pro fide Thanks again for clarify the required OS/2 2.1 settings for running HyperChem. Cheers, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From hurst@hyper.hyper.com Wed Jun 8 19:24:19 1994 Date: Wed, 8 Jun 1994 15:24:19 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: bolger@zygote.hsc.usc.edu (Michael Bolger), hyperchem@HYPER.COM Subject: Re: Upgrade from 3.0 to 4.0 Michael Bolger asks: > I have been using HyperChem 3.0 for about six months and just joined > this list server when I received the HyperChem 4.0 upgrade. What is new > about version 4.0 except that it is distributed by HyperCube? I looked for > some kind of short document like "What's new in version 4.0" and I checked > the program for new features. I don't get it? Please help. Look at the file readme.txt or the README section of the online help. Hope this helps, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From uunet.ca!netcom.com!uscience@hyper.hyper.com Thu Jun 9 18:20:15 1994 Date: Thu, 9 Jun 1994 14:20:15 -0400 From: Jack Breithart Subject: Molecular Images and Stereo viewing. To: HyperChem Dear Hyperchem Users, There has been a few postings lately about stereo viewing and making presentation quality images. I'd like to inform the group of a program available that works extremely well with HyperChem called Molecular Images Software. We hope this information is useful to this group. Molecular Images Software, was designed from the ground up for Windows-not a DOS or UNIX port; to achieve faster protein viewing and superior molecular graphics. The program involves three inter-linked modules that can also be used with your present molecular modeling software or molecular presentation software. Showcase ray-tracer gives you high quality graphics with correct shading, coloring, reflection and transparency. You can make ray- traced animation's and 'photo realistic' images Transfer these graphic images into Windows based text and presentation programs. Import bitmap files for stunning presentations. Images can be used as wallpaper, printed or exported for uses such as making slides. Math co-processor required. Molw, protein molecular graphics, quickly render your molecules or secondary structure in ribbons,CA link tubular, CPK, ball-and-stick, H-bond display, van der Waals dot surface, with extensive coloring and selecting options. Go To a particular residue, mutate, rotate, translate, torsion bond and analyze nearest neighbor atoms, distance, and torsion angles. You can even do least-squares superposition of two structures. Load as many models as memory permits. Available with Molw is a reflective stereographic viewers ($59.00) that makes for easy 'real-time' side-by-side stereo viewing for the "stereo- impaired". PSearch, allows you to link images with data; using the browse command you can search the directories of the PDB files for keywords, including the PDB CD-Rom from the Brookhaven National LaboratoryProtein Data Bank. How can I obtain this program? The program costs under $200 Academic ($295.00 Commercial, and special multi-site academic pricing available) A demo version of Molw and several Showcase bitmap images are available. We look forward to hearing from you. Thank you Molecular Images Software US Science P.O. Box 6689 San Diego, CA 92106 (619) 223-4687 Fax (619) 523-1949 Telephone uscience@netcom.com ________________________________________________________________________ From uunet.ca!MERLE.ACNS.NWU.EDU!akazala@hyper.hyper.com Thu Jun 9 19:58:53 1994 From: MERLE.ACNS.NWU.EDU!akazala@hyper.hyper.com Subject: transition metals To: hyperchem@HYPER.COM (hyperchem) Date: Thu, 9 Jun 1994 15:58:53 -0400 Hi, I have recently purchased version four of Hyperchem. On the whole, I am quite pleased with its performance, but I have a few questions. I am trying to do molecular mechanics on systems which contain a heavy atom, such as rhenium, as well as large organic ligands. I know that the AMBER force field is better for the organic part of the molecule, but there are no stretching parameters for the transition metal. How have people with Hyperchem solved similar problems? Where are the necessary parameters obtained from? I also am aware that it is possible to minimize part of the molecule semi-empirically, while minimizing the other part with molecular mechanics. Will this give a reasonable answer to geometry changes for the organic ligand? Thank you. Amy Kazala ________________________________________________________________________ From uunet.ca!kean.ucs.mun.ca!MSCHRIVER@hyper.hyper.com Fri Jun 10 16:22:24 1994 Date: Fri, 10 Jun 1994 12:22:24 -0400 From: "Schriver,M;Chemistry;" Subject: Bare Wires Version To: hyperchem@hyper.com Cc: mschriver@kean.ucs.mun.ca HyperChemists, This may be a duplicate posting, we seem to be having computer troubles. I use HyperChem in a fourth year course where I use it to show how MO calc'ns are used in Main Group chemistry. I currently have HyperChem 3 [+ ChemPlus] running on a 486 PC and am pretty happy except that I have to lug the whole system into the clasroom for demonstrations. I would like to load the program onto my laptop [386 + math, 2 meg memory, 16 MHz] but when I do the poor thing has a nervous breakdown. Is there anyway to reduce the Hyperchem program to just the graphical package running AM1 calcns? Is there anyway to reduce the memory requirements so that my laptop will run calcns on small moelcules (n < 10 atoms) and not cause the computer to go catatonic? Just asking. If any of you code-jockeys have an answer please give step-by-step instructions in words of one syllable, remember I'm a phosphorus chemist. Thanks for any replies mel %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Dr. Mel Schriver, Assist. Prof., %% What does the Lord ask of us? % % Memorial University, St. John's, %%%%%% To act justly % % Newfoundland, Canada, A1B 3X7 %% To love mercy % % Ph.: (709)-737-8744 %% To walk humbly with your God % % EML: mschriver@kean.ucs.mun.ca %% Micah 6:8 % ________________________________________________________________________ From uunet.ca!moe.chem.usouthal.edu!madura@hyper.hyper.com Fri Jun 10 22:32:45 1994 Date: Fri, 10 Jun 1994 18:32:45 -0400 From: "Jeffry D. Madura" Subject: Displaying G9X vibrational modes with HyperChem To: hyperchem@HYPER.COM Dear HyperChem Users, Does anyone have a way to convert the results of a G9X frequency calculation into a format that can be displayed using HyperChem? We can display the G9X frequency results using winvib but would like to do so using HyperChem. Thanks Regards, Jeffry D. Madura Department of Chemistry University of South Alabama Mobile, AL 36688 Phone: (205) 460-7430 FAX: (205) 460-7359 e-mail: madura@moe.chem.usouthal.edu ________________________________________________________________________ From hurst@hyper.hyper.com Mon Jun 13 15:03:19 1994 Date: Mon, 13 Jun 1994 11:03:19 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: akazala@merle.acns.nwu.edu, hyperchem@HYPER.COM (hyperchem) Subject: Re: transition metals Amy Kazala writes: > I have recently purchased version four of Hyperchem. On the whole, I am quite > pleased with its performance, but I have a few questions. I am trying to do > molecular mechanics on systems which contain a heavy atom, such as rhenium, as > well as large organic ligands. I know that the AMBER force field is better > for the organic part of the molecule, but there are no stretching parameters > for the transition metal. How have people with Hyperchem solved similar > problems? Where are the necessary parameters obtained from? I also am aware > that it is possible to minimize part of the molecule semi-empirically, while > minimizing the other part with molecular mechanics. Will this give a > reasonable answer to geometry changes for the organic ligand? Thank you. This isn't a solution but perhaps will give you some things to try... If your metal is drawn as being bonded to the ligands you will probably also need bending and torsion parameters as well as the stretching parameters. One approach that is often used for metals or highly coordinated atoms in molecular mechanics is to ignore bends and torsions but include 1-3 non-bonding interactions. This is what is done with the MM+ force field in HyperChem. You can do something similar with the AMBER force field in HyperChem by drawing the ligand as not being bonded and adding restraining forces where each bond was. This is tedious to set up, but the restraints are saved in the HIN file. You will still have to come up with parameters for the "bonds" (implemented by restraints), but you can experiment with values interactively or via automated scripts (perhaps from Excel). A possible drawback of this approach is that "1-2" non-bonded interactions are also included. Hope this helps, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From hurst@hyper.hyper.com Mon Jun 13 20:21:59 1994 Date: Mon, 13 Jun 1994 16:21:59 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: "Schriver,M;Chemistry;" , hyperchem@hyper.com Subject: Re: Bare Wires Version Mel Schriver asks: > I use HyperChem in a fourth year course where I use it to show how MO > calc'ns are used in Main Group chemistry. I currently have HyperChem 3 > [+ ChemPlus] running on a 486 PC and am pretty happy except that I have > to lug the whole system into the clasroom for demonstrations. I would > like to load the program onto my laptop [386 + math, 2 meg memory, 16 MHz] > but when I do the poor thing has a nervous breakdown. Is there anyway to > reduce the Hyperchem program to just the graphical package running AM1 > calcns? Is there anyway to reduce the memory requirements so that my > laptop will run calcns on small moelcules (n < 10 atoms) and not cause > the computer to go catatonic? Just asking. If any of you code-jockeys > have an answer please give step-by-step instructions in words of one > syllable, remember I'm a phosphorus chemist. If you could get your hands on a copy of release 2 it might work okay with 2 MB, as long as you don't want to do IR or UV calcs or show the orbital energy levels. (Most of the bloat in nod.exe size from rel 2 to 3 came from adding ZINOD methods and extending the integral routines to go up to Xe.) If you could live with EHT instead of AM1, it needs much less memory. Also ChemPlus can save 3D orbitals and does not need HyperChem to run (just launch it from Program Manager). Hope this helps, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From hurst@hyper.hyper.com Tue Jun 14 13:43:16 1994 Date: Tue, 14 Jun 1994 09:43:16 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: "Jeffry D. Madura" , hyperchem@HYPER.COM Subject: Re: Displaying G9X vibrational modes with HyperChem Jeffry D. Madura asks: > Does anyone have a way to convert the results of a G9X frequency > calculation into a format that can be displayed using HyperChem? We can > display the G9X frequency results using winvib but would like to do so > using HyperChem. Thanks Gaussian 92 for Windows can create a HyperChem script file directly for displaying normal modes in HyperChem, but I don't know if the same capability is offered with Gaussian for other platforms. Cheers, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com ________________________________________________________________________ From MSCHRIVER@kean.ucs.mun.ca Tue Jun 14 10:38:16 1994 Date: Tue, 14 Jun 1994 06:38:16 -0400 From: "Schriver,M;Chemistry;" Subject: Bare Wires Version (Answers) To: hyperchem@HYPER.COM Cc: mschriver@kean.ucs.mun.ca Thanks for the answers that I received concerning wether I could strip down HyperChem to run on less memory. The answer seems to be no, but I could do the calculations and them _show_ the results using just the ChemPlus module. I will give that a try. The other suggestion was that I use HyperChem II. Which I find amusing because I had to put a bullet through my copy of HyperChem II to up- grade to HyperChem III. Any chance the boys at HyperChem be willing to send me a copy of the program II diskettes coded to my hardware lock? Just one other comment. The last time I posted to this users group it snowed email messages for three days but they were all generated by computers telling me that they couldn't deliver the message. Any chance the HyperChem people could clean-up their mailing list? I like email as much as the next person but this is ridiculous. mel %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Dr. Mel Schriver, Assist. Prof., %% What does the Lord ask of us? % % Memorial University, St. John's, %%%%%% To act justly % % Newfoundland, Canada, A1B 3X7 %% To love mercy % % Ph.: (709)-737-8744 %% To walk humbly with your God % % EML: mschriver@kean.ucs.mun.ca %% Micah 6:8 % ________________________________________________________________________ From GF@chemie.uni-paderborn.de Wed Jun 15 17:50:43 1994 From: "Gregor Fels" To: hyperchem@HYPER.COM Date: Wed, 15 Jun 1994 13:50:43 -0400 Subject: Using HyperChem to predict reactions Priority: normal Dear netters, could somebody perhaps give me an advice on how to use HyperChem to predict the outcome of an reaction,e.g.: a) take an unsymmetrically substituted Alkene [say (CH3)2C=CH2] and let it react with BH3. Can HyperChem indeed show, that the Boron binds to the less substituted Carbon? or b) take a Ru-complex with 6 coordinations, 4 of which are taken by organic residues while the remaining 2 are binding Cl (i.e. RuR4Cl2). Can HyperChem predict wether or not the two remaining chlorines can also be substituted by some spacefilling organic residues? Gregor Gregor Fels gf@chemie.uni-paderborn.de ________________________________________________________________________ From mcaffery@keller.clarke.edu Thu Jun 16 13:41:06 1994 Date: Thu, 16 Jun 1994 09:41:06 -0400 From: "S. Mary Lou Caffery" Subject: VSEPR and Hyperchem To: hyperchem@HYPER.COM Has anyone worked on parameterizing mmp for the molecules typically included in general chemistry text VSEPR theory sections? If so would you be willing to share the parameters? ________________________________________________________________________ From mcaffery@keller.clarke.edu Fri Jun 17 15:45:50 1994 Date: Fri, 17 Jun 1994 11:45:50 -0400 From: "S. Mary Lou Caffery" Sender: "S. Mary Lou Caffery" Reply-To: "S. Mary Lou Caffery" Subject: lone pair mass in mmp To: hyperchem@HYPER.COM Why is the mass of the lone pair set at 3.000 in the file mmptype.txt? Is this a misprint or is it required for your implementation...I believe Allinger's value was 0.0. I have define a new type S6 to deal with octahedral sulfur. I defined the connectivity as follows: connected to (R)(R)(R)(R)(R)R? =S6. so I could make compounds with halogens, lone pairs etc. It works fine for six halogens but as soon as I put a lone pair on, and "BUILD" the type reverts to S+. I have defined some parameters for S6....stretch, bends and vanderwaals. ________________________________________________________________________ From hurst@hyper.hyper.com Fri Jun 17 19:49:36 1994 Date: Fri, 17 Jun 1994 15:49:36 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: hyperchem@HYPER.COM, "S. Mary Lou Caffery" Subject: Re: lone pair mass in mmp S. Mary Lou Caffery asks: > Why is the mass of the lone pair set at 3.000 in the file mmptype.txt? > Is this a misprint or is it required for your implementation...I believe > Allinger's value was 0.0. I think the mass was "borrowed" from AMBER. It was changed from zero because low masses can cause molecular dynamics to blow up (I don't think the MM2 program can do MD so it doesn't face this problem). If you use a value lower than 1e-10, the program substitutes 1e-10 (to avoid dividing by zero in molecular mechanics). > I have define a new type S6 to deal with octahedral sulfur. I defined > the connectivity as follows: connected to (R)(R)(R)(R)(R)R? > =S6. > so I could make compounds with halogens, lone pairs etc. It works fine > for six halogens but as soon as I put a lone pair on, and "BUILD" the > type reverts to S+. I have defined some parameters for S6....stretch, > bends and vanderwaals. The documentation describing R is in error. "R" excludes H and Lp, so you need additional rules where "Lp" replaces "R". For example: connected to (R)(R)(R)(R)(R)Lp? =S6. ; Handles one Lp. connected to (R)(R)(R)(R)(Lp)Lp? =S6. ; Handles two Lp's. Hope this helps, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com ________________________________________________________________________ From mcaffery@keller.clarke.edu Mon Jun 20 17:41:12 1994 Date: Mon, 20 Jun 1994 13:41:12 -0400 From: "S. Mary Lou Caffery" Subject: VSEPR and Hyperchem To: hyperchem@HYPER.COM Has anyone tried to do mmp calculations on molecules which are typically found in general chemistry books dealing with VSEPR? If anyone has parameters to share I would be grateful! ________________________________________________________________________ From helaja@cc.helsinki.fi Tue Jun 21 13:47:47 1994 Date: Tue, 21 Jun 1994 09:47:47 -0400 From: Juho P Helaja To: hyperchem@HYPER.COM Subject: application variables from exel Grid search ? I have tried to build a gridsearch using exel macro, but I met a problem how to use variables in constrain-bond-torsion(VARIABLE). I wonder if I'm toARIABLE). Am I in totally wrong trails? I gratefully take better soluttake gratefully better solutions if there exist! Cheers Juho helaja@introni.helsinki.fi