From owner-hyperchem@hyper.com Mon Jun 3 16:27:17 1996 From: Journal of Molecular Modeling Subject: J.Mol.Model. invites you to contribute a paper To: hyperchem@www Date: Mon, 3 Jun 1996 16:03:20 +0200 (MET) Journal of Molecular Modeling The advanced way of publishing Call for Papers The Journal of Molecular Modeling invites you to contribute your papers. The Journal of Molecular Modeling is the first fully electronic journal in chemistry. It is the perfect medium for presenting results of scientific research produced on the computer, offering the unique possibility of applying all the daily tools of computational chemistry to the world of scientific publishing to benefit authors and readers. The aim of the Editor and the Publisher is to produce a high quality chemistry journal that takes advantage of modern electronic communication techniques. Thus the journal offers many advantages important to the active scientist in the field: * unprecedentedly short publication times; * fully peer reviewed; fully citable (ISSN; CAS; ISI); * no page charges; full color; * no extra costs for sophisticated presentation materials; * possibility of incorporating videos, program demos, VRML-scenes etc.; * publication of fully hyperlinked texts in PDF format; * generally accessible graphical abstracts of accepted papers on several WWW-sites; * widespread visibility of your research in the Internet. The journal is made accessible through FTP- and WWW-servers to subscribers with individual papers being accessible for at least two years. (URL: http://science.springer.de) The server mode of publication, however, does not mean that we do not provide for the longevity of the published material, which will be guaranteed by issuing CD-ROMs and print archive editions. The Journal of Molecular Modeling publishes all quality science that passes the critical review of experts in the field and falls within the scope of the journal coverage, including: * computer aided molecular design * visualization, classification and handling of chemical data * rational drug design, de novo ligand design and receptor modeling * computational enhanced desktop tools for life sciences * protein and peptide modeling * molecular mechanics/dynamics simulation of polymers and biopolymers * prediction of biological activities (QSAR) and physico-chemical properties (QSPR) * genetic algorithms and neural nets * catalyst modeling The editorial office of the Journal of Molecular Modeling is located at the Computer-Chemie-Centrum of the Institut fuer Organische Chemie, Friedrich-Alexander-Universitaet Erlangen-Nuernberg. As the Editor-in-Chief I encourage all scientists to submit their contributions making use of full color graphics and/or other sophisticated presentation techniques. I look forward to welcome you as a new author of this exciting journal. Best wishes, Dr. Tim Clark (editor-in-chief) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ Journal of Molecular Modeling ^ Tel: [+49](0)9131 / 85-2948 ^ ^ Editorial Office ^ ^ ^ 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 ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ http://www.organik.uni-erlangen.de ^ http://science.springer.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jun 5 17:28:36 1996 Date: Wed, 5 Jun 1996 17:27:46 +0100 (BST) From: Michael Hodgson To: hyperchem@hyper.com Subject: Solvating Systems + Periodic Boxes Hi, I am currently trying to carry out a simulation on a DNA decomer with counter ions, and explicit water molecules, using periodic boundery conditions. When solvating the system with a small box of water I have no trouble and the simulation runs well. However when trying to use a bigger box I get a error message telling me that two atoms are in the same position. By gradually increasing the size of the solvent box I have established that the clash occurs in the Y direction between 38 and 40 A. Has anyone else experianced this trouble and is there any way of getting hyperchem to tell me exactly where the problem is so that I can delete one of the water molecules. It is impossible to isolate the clash by just looking... I've tried. On a similar subject... why is it that hyperchems max solvent box is set to 56A cubed ? I only require this volume, but a longer box would be useful as this would allow me to use longer cutoffs. Thanks, ,----- Michael Hodgson < mkh100@unix.york.ac.uk > ,----- | __/ | __/ l_F-< A_A_A,-mmmmm--=_ =---<==r==- l_F-< L \ _ _H_H_H_,-------|..|-,_,--| L \ r-i ) I I=L|==L<_ >L|: : : :|..|>|_<>:II r-i ) I \ " / H H H `-------|_ |-' `--' \ " / `---' U U U `---' (http://www.york.ac.uk/~mkh100) "I say we should listen to the customers and give them what they want." "What they want is better products for free." --Scott Adams _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jun 6 14:55:04 1996 Date: Thu, 06 Jun 1996 16:14:53 +0100 (MET) From: Giorgio Contini Subject: question X-Sender: CONTINIG@IASI.RM.CNR.IT To: hyperchem@hyper.com Dear, I am doing some vibrational calculation with ab initio methods on aromatic, small-size molecules. My question is about the RMS gradient: the values calculated at the end of the geometry optimization and just before beginning the vibrational analysis are very different. The details of the procedure adopted are as follows: - I choose the basis set (now I am using the 4-21 G*), and set the SCF convergence limit at 10-5. - I run the geometry optimization (Polak-Ribiere algorithm), with a RMS gradient of, for example, 10-3. After convergence, the RMS gradient is obviously less than this value. - then I run the vibrational analysis of the optimized structure; before calculating the constant matrix, HyperChem recalculate the gradient, but the obtained value is more than one order of magnitude higher of the previous calculated value (in this example, about 10-2). If I perform the single point calculation of the gradient, the result (about 10-2) is again higher than the convergence value. How does differ the gradient calculation in the two cases? Why are the results so different? Thank you Giorgio Contini _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jun 6 16:25:06 1996 Date: Thu, 6 Jun 96 11:00:02 -0400 From: polowin (Joel Polowin) To: Michael Hodgson , hyperchem@hyper.com Subject: Re: Solvating Systems + Periodic Boxes > Date: Wed, 5 Jun 1996 17:27:46 +0100 (BST) > From: Michael Hodgson > > I am currently trying to carry out a simulation on a DNA decomer > with counter ions, and explicit water molecules, using periodic boundery > conditions. When solvating the system with a small box of water I have > no trouble and the simulation runs well. However when trying to use a > bigger box I get a error message telling me that two atoms are in the > same position. By gradually increasing the size of the solvent box I have > established that the clash occurs in the Y direction between 38 and 40 A. > Has anyone else experianced this trouble and is there any way of getting > hyperchem to tell me exactly where the problem is so that I can delete > one of the water molecules. It is impossible to isolate the clash by > just looking... I've tried. I have seen this problem reported once before, though I have never been able to reproduce it myself. (Would you please send me a copy of the structure which gives this result when it is solvated, along with the box dimensions?) It appears that the routine which adds the water molecules causes two of them to overlap, or causes the periodic image of one to overlap with another, or something like that. I can think of a couple of ways of isolating the problem. One would be to re-orient the viewpoint to look along the Y axis, then use the clipping tool to show only the 38--40 A slice which appears to contain the problem. By setting the Selection level to Molecules, and using rectangular area selection, you can select a few of the visible molecules at once. When you find the overlapping molecules, the status line will report that you have just selected N molecules even though you see only N-1 molecules selected. The overlapping pair would be among that set. Another possibility would be to copy all of the "atom" lines from the HIN file to another file, and then to sort them by their coordinates to find duplicates. This sort of thing could be done with a spreadsheet or with a variety of UNIX tools, but I think that it would require some utilities beyond those which are included with just DOS and Windows. (The DOS SORT utility is limited to files under 64 kB, and the "atom" lines from a structure this large would be beyond that.) Copying these lines from the original file can be done by text utilities such as "grep" or my "filter" utility -- look in the SimTel software archive (oak.oakland.edu) and its mirror sites in the directories under SimTel/msdos/textutil . > On a similar subject... why is it that hyperchems max solvent box is set > to 56A cubed ? I only require this volume, but a longer box would be > useful as this would allow me to use longer cutoffs. At the time that the program was first released, a solvent box 56 A cubed was already improbably large for calculating with the computers of the day... but computers have become more powerful. The removal of that fixed limit is in the development wish list. And you can still use a larger box even with the current versions of HyperChem, by saving the structure in a HIN file and then using a text editor to change the "box" line near the beginning of the file. (See Appendix D in the Reference Manual.) You would still need to add the extra water molecules manually to fill the box -- for example, by selecting a bunch of water molecules, copying them, unselecting, pasting, and then using the translation tools with the right mouse button to move the duplicated molecules to about the right positions. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jun 6 19:55:22 1996 Date: Thu, 6 Jun 96 16:57 MET DST To: hyperchem@hyper.com Subject: NEW : TUTORIALS IN COMPUTATIONAL CHEMISTRY USING HYPERCHEM X-Sender: 0924191216-0001@t-online.de (Dr. Heinz Hofmann) From: Science_direct@t-online.de (Heinz Hofmann) Attention : Everybody interested in Computational Chemistry Available as of June 1996 : The first of a series of tutorials in computational chemistry, edited by Dr. Tim Clark, author of the leading " Handbook of Computational Chemistry" and editor of the "Journal of Molecular Modeling". This first tutorial covers semiempirical molecular orbital theory and is targeted at students, educators and experimental chemists; blending theory and practical applications; showing examples based on widely used modeling programs. Initially available in English, Japanese, German and French versions will be available later in 1996. The initial introductory price will be US$ 49 per tutorial, ( US$ 39 in electronic form ) with a total price of US$ 250 for the whole set comprising six tutorials covering semiempirical MO theory, force fields, ab initio MO theory, spectroscopy, QSAR, and application examples in computational chemistry. For more information and list of content/example chapter, please contact http://www.sciencelearn.com *********************************************************** Science direct Dr. Heinz Hofmann Phone : +49-(0)9241-91216 Sandrangen 3 Fax : +49-(0)9241-91217 D-91257 Pegnitz E-mail : Science_direct@t-online.de *********************************************************** _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Jun 7 15:30:12 1996 Date: Fri, 7 Jun 96 11:51:31 -0400 From: polowin (Joel Polowin) To: Giorgio Contini , hyperchem@hyper.com Subject: Re: question > Date: Thu, 06 Jun 1996 16:14:53 +0100 (MET) > From: Giorgio Contini > > - I choose the basis set (now I am using the 4-21 G*), and set the SCF > convergence limit at 10-5. > - I run the geometry optimization (Polak-Ribiere algorithm), with a RMS > gradient of, for example, 10-3. After convergence, the RMS gradient is > obviously less than this value. > - then I run the vibrational analysis of the optimized structure; before > calculating the constant matrix, HyperChem recalculate the gradient, but the > obtained value is more than one order of magnitude higher of the previous > calculated value (in this example, about 10-2). I asked our quantum-mechanics expert. He told me that the effect is due to the 16-bit precision used to store the atomic coordinates in the main program. The computational module uses 32-bit precision in its calculations, including the optimisation and the gradient calculations, but when it returns the atomic coordinates, the main program stores them with only about 7 decimal places of precision. When the single-point calculation is started, the coordinates are sent back to the computational module. The difference due to the rounding is enough to cause that very small change in the gradient. > If I perform the single point calculation of the gradient, the result (about > 10-2) is again higher than the convergence value. The vibrational calculation begins with a single-point calculation; you should see the same energies and gradients from both. (Turning the SCF convergence accelerator on or off can also have a slight effect on the gradient 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 Sat Jun 8 01:27:52 1996 X-Sender: graham@mail.sentex.net Date: Fri, 07 Jun 1996 23:30:24 -0400 To: hyperchem@hyper.com From: Graham Hurst Subject: Re: question At 11:51 AM 6/7/96 -0400, Joel Polowin wrote: >I asked our quantum-mechanics expert. He told me that the effect is due >to the 16-bit precision used to store the atomic coordinates in the main >program. The computational module uses 32-bit precision in its calculations, >including the optimisation and the gradient calculations, but when it >returns the atomic coordinates, the main program stores them with only >about 7 decimal places of precision. Joel meant 32-bit (single precision) in the front end and 64-bit (double precision) in the back end. Hi to all my old friends on this list! If you want to see what I've been working on since I left Hypercube check out: http://www.powersoft.com/products/internet/optima.html Cheers, Graham P.S. Welcome back to Canada Neil! ------- Graham Hurst, PhD or Cambridge, Ontario, Canada _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jun 10 19:43:37 1996 Date: Mon, 10 Jun 1996 16:22:13 -0400 X-Sender: vuckovic@hyper.com To: hyperchem@www From: Dragan Vuckovic Subject: HyperChem User Group-II Announcement --=====================_834448331==_ The First World HyperChem User Group Meeting - Second Announcement The Second Announcement for HyperChem User Group Meeting (September 8-11, Clevelands House, Minett, Muskoka, Ontario, Canada) has been mailed. Interested persons should contact me or visit our home page (http://www.hyper.com under the New section) for more information and the final registration form. --=====================_834448331==_ ********************************************************************* * Dr. Dragan Lj. Vuckovic phone: (519) 725-4040 * * International Marketing Manager fax: (519) 725-5193 * * Hypercube, Inc. e-mail: vuckovic@hyper.com * * 419 Phillip Street URL: http://www.hyper.com * * Waterloo, Ontario Info: info@hyper.com * * Canada, N2L 3X2 * ********************************************************************* --=====================_834448331==_-- _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jun 13 15:46:44 1996 Date: Thu, 13 Jun 1996 14:15:16 MET+02 From: "A.J.M.DRIESSEN" Subject: MM+ bug SGI To: hyperchem@www Organization: Department of Biology, RUGroningen Dear Joel Recently, I downloaded the MMplus update for SGI Hyperchem 4.5, decompressed and replaced the appropriate file in /usr/sbin for the new version. Hyperchem normally starts, but when I start a geometry optimisation with MM+, the system freezes. The problem does not occur when I replace the new version with the older one. The replacement protocol as indicated in the home-page MM+ bug is straightforward. Therefore, I wonder what is happening? sincerely yours Arnold Driessen Dr. A.J.M. Driessen, Department of Microbiology, University of Groningen, Kerklaan 30, 9751 NN HAREN, The Netherlands Tel. +31-50-3632164; Fax +31-50-3632154; E-mail A.J.M.DRIESSEN@BIOL.RUG.NL _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jun 13 14:56:49 1996 Date: Thu, 13 Jun 96 11:22:38 -0400 From: polowin (Joel Polowin) To: "A.J.M.DRIESSEN" Subject: MM+ bug SGI Cc: hyperchem@hyper.com > Date: Thu, 13 Jun 1996 14:15:16 MET+02 > From: "A.J.M.DRIESSEN" > > Recently, I downloaded the MMplus update for SGI Hyperchem 4.5, > decompressed and replaced the appropriate file in /usr/sbin for the > new version. Hyperchem normally starts, but when I start a geometry > optimisation with MM+, the system freezes. The problem does not occur > when I replace the new version with the older one. > > The replacement protocol as indicated in > the home-page MM+ bug is straightforward. Therefore, I wonder what is > happening? When the update file was placed on our server, the file permissions were accidentally set to exclude "execute" permission. (This has now been corrected.) To let the module that you downloaded work, you just have to add execute permission: chmod a+x hc45_mmplus Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jun 13 20:46:01 1996 Date: Thu, 13 Jun 1996 14:56:23 -0700 From: "Marco A. Lopez" Organization: CSULB To: hyperchem@www Subject: Nonaqueous solvent molecules in HYPERCHEM Hello. I am interested in using to run MD calculations in solvents other than water. How may I do such a calculation in HYPERCHEM? Is it possible? -- Marco A. Lopez, Ph.D. Office (310)985-4936 Department of Chemistry & Biochemistry Lab (310)985-1545 College of Natural Sciences & Mathematics Fax (310)985-8557 California State University, Long Beach e-mail lopezm@csulb.edu _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Jun 14 13:56:44 1996 Date: Fri, 14 Jun 1996 16:09:50 +0100 From: cos4@cfdvs3.univ-bpclermont.fr To: HYPERCHEM@hyper.com Subject: Message to the semi-empirical calculations users (AM1 or PM3). The Energy displayed by Hyperchem PM3 calculations is likely the Total energy of the molecule. Is it possible to get ,like in the Mopac version of PM3: 1- The final heat of formation in Kcal/mol. 2- The bond orders between the atoms. Thank you. _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Jun 14 14:36:27 1996 Date: Fri, 14 Jun 96 10:19:01 -0400 From: polowin (Joel Polowin) To: "Marco A. Lopez" , hyperchem@www Subject: Re: Nonaqueous solvent molecules in HYPERCHEM > Date: Thu, 13 Jun 1996 14:56:23 -0700 > From: "Marco A. Lopez" > > Hello. I am interested in using to run MD calculations in solvents other > than water. How may I do such a calculation in HYPERCHEM? Is it > possible? Pre-defined files for periodic boxes of solvents other than water are not distributed with HyperChem, but creating your own solvent boxes is relatively straightforward. To find the number of solvent molecules appropriate for your box, you will need the box volume (length x width x height) and the molecular weight and density of your solvent. Then: # molecules = (volume x density x Avogadro's constant) / molecular weight For example, for a periodic box 18.62 A in each dimension, filled with water at 25'C, the density is 1.00 g/cm3 and the molecular weight is 18.02 g/mol. Substituting into the above, and including the conversion from A to cm: # molecules = (18.62 A)^3 x (1 cm/10^8 A)^3 x 1.00 g/cm^3 x 6.023E23 / 18.02 g/mol = 215.8 which matches the 216 water molecules found in the standard periodic box. The solvent molecules should be oriented randomly in the box and the entire system equilibrated. You can do this by running Molecular Dynamics on the system. You can then add a solute molecule to the system; you will probably want to delete one or more solvent molecules to make space for it, as HyperChem does with its standard water boxes. An equilibrated box of solvent molecules can be saved as a file, and re-used as you wish. 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 Jun 17 13:35:03 1996 Date: Fri, 14 Jun 96 16:48:04 -0400 From: polowin (Joel Polowin) To: cos4@cfdvs3.univ-bpclermont.fr, HYPERCHEM@hyper.com Subject: Re: Message to the semi-empirical calculations users (AM1 or PM3). > From: cos4@cfdvs3.univ-bpclermont.fr > Date: Fri, 14 Jun 1996 16:09:50 +0100 > > The Energy displayed by Hyperchem PM3 calculations is likely the Total > energy of the molecule. Is it possible to get ,like in the Mopac version > of PM3: > 1- The final heat of formation in Kcal/mol. > 2- The bond orders between the atoms. The energy shown on the status line after a semi-empirical calculation is the binding energy, i.e., the total energy minus the isolated atomic energy. All of the separate energy factors, as well as the heat of formation, can be saved in a log file, or output using script commands; please see the _Reference Manual_. It is not possible to calculate bond orders automatically with HyperChem, but they can be calculated manually from the density matrices (also in the log file). The bond order between atoms A and B is the sum of the squares of the elements in the density matrix with rows for atom A's orbitals and columns for atom B's orbitals, or vice versa. If you are doing UHF calculations, you must add the elements of the alpha and beta matrices together before squaring. I tried this for C2H4 as model-built, with an AM1 single-point calculation, and got a calculated C--C bond order of 2.0004. 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 Jun 17 17:05:06 1996 From: Sabbir Ahmed Organization: Kingston University (Science) To: sybyl@extreme.chem.rpi.edu, orgchem@extreme.chem.rpi.edu, hyperchem@hyper.com, biosci@net.bio.net, bionet@net.bio.net Date: Mon, 17 Jun 1996 18:03:08 GMT0BST Subject: Re.: New electronic journal in med. chem. Apologies to people who have already recieved this message from other mailservers. Announcing the arrival of a new (peer reviewed) electronic journal in the general area of medicinal chemistry titled 'Electronic Medicinal Chemistry Journal' (EMCJ). This is also a call for papers allied to any field related to Medicinal Chemistry for possible inclusion into future editions of EMCJ. For further information regarding EMCJ, please refer to : http://www.electronicjournals.co.uk (UK and Europe) http://www.he.net/~proton Sabbir Ahmed Dr. Sabbir Ahmed School of Applied Chemistry Kingston University Penrhyn Road Kingston upon Thames Kingston Surrey, KT1 2EE United Kingdom Tele. : +44 (0)181 547 2000 ext. 2433 Fax. : +44 (0)181 547 7562 E-mail : CH_S534@KINGSTON.AC.UK _______________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jun 18 22:24:52 1996 From: tbender@ccs.carleton.ca (timothy bender) Subject: McAfee antivirus To: hyperchem@hyper.com Date: Tue, 18 Jun 96 19:30:37 EDT ---------------------------------------------------------------------- Tim Bender, B.Sc | To know chemistry, Student, Department of Chemistry | is to know a little Carleton University, Ottawa, Ont, Canada | piece of nature ... Email address: tbender@ccs.carleton.ca | ---------------------------------------------------------------------- My question, to anyone with an answer is, has anyone ever had a problem when running hyperchem on windows95 when the McAfee antivirus program is also installed? Tim :-) _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jun 19 14:51:03 1996 Date: Wed, 19 Jun 96 10:19:57 -0400 From: polowin (Joel Polowin) To: tbender@ccs.carleton.ca (timothy bender), hyperchem@hyper.com Subject: Re: McAfee antivirus > From: tbender@ccs.carleton.ca (timothy bender) > Date: Tue, 18 Jun 96 19:30:37 EDT > > My question, to anyone with an answer is, has anyone ever had a > problem when running hyperchem on windows95 when the McAfee antivirus > program is also installed? I have had no reports of trouble, but that doesn't mean that it could not happen... I have had one report that McAfee VSHIELD 2.1.3L made HyperChem crash under Windows 3.11, but I have not been able to find a copy of that version to check; I tried VSHIELD 2.1.3D and had no trouble. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jun 27 20:48:51 1996 Date: Thu, 27 Jun 1996 13:37:02 -0700 From: "Marco A. Lopez" Organization: CSULB To: hyperchem@www Subject: Semi-Empirical calculations Hello. I wish to reproduce the values calculated using AM1 for the series of molecules shown on Table 8.1, p 102-103 in th book "Computational Chemistry" that came with Hyperchem. When we ran the geometry optimization of benzoic acid, we did not get the -68.0 kcal/mol, we got -1690 kcal/mol; the value we got for norbornadiene was -1523 kcal/mol, not the +67.7 kcal/mol in that Table. What is it that we are not doing correctly? Perhaps there is some assumption being made, or there is something we are not setting correctly. We will appreciate any help you can offer. Thank You. Marco Lopez -- Marco A. Lopez, Ph.D. Office (310)985-4936 Department of Chemistry & Biochemistry Lab (310)985-1545 College of Natural Sciences & Mathematics Fax (310)985-8557 California State University, Long Beach e-mail lopezm@csulb.edu _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Jun 28 17:56:55 1996 Date: Fri, 28 Jun 96 13:48:16 -0400 From: polowin (Joel Polowin) To: "Marco A. Lopez" , hyperchem@www Subject: Re: Semi-Empirical calculations > Date: Thu, 27 Jun 1996 13:37:02 -0700 > From: "Marco A. Lopez" > > Hello. I wish to reproduce the values calculated using AM1 for the > series of molecules shown on Table 8.1, p 102-103 in th book > "Computational Chemistry" that came with Hyperchem. When we ran the > geometry optimization of benzoic acid, we did not get the -68.0 kcal/mol, > we got -1690 kcal/mol; the value we got for norbornadiene was -1523 > kcal/mol, not the +67.7 kcal/mol in that Table. What is it that we are > not doing correctly? Perhaps there is some assumption being made, or > there is something we are not setting correctly. We will appreciate any > help you can offer. Thank You. The values given in that table are heats of formation; the values reported on the status line, and which you appear to give above, are binding energies, equal to the difference between the total energy of the system minus the sum of the energies of the isolated atoms. All of these values are available from the log files or through script commands. The values that I get for total energies from these two structures are lower than the values that you report, even if I just run single-point AM1 calculations on the structures after model-building them and without optimising them. Please double-check that you are optimising your structures completely; the status line should say whether the optimisation was complete or not. 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.