From MROZEK@Trurl.ch.uj.edu.pl Mon Aug 1 15:31:30 1994 From: Organization: Faculty of Chemistry, UJ To: hyperchem@HYPER.COM Date: Mon, 1 Aug 1994 11:31:30 -0400 Subject: MEP units Dear netters, I went through all the manuals and did not find a single reference to the units in which the molecular electrostatic potential is computed in Hyperchem. I enetred the list quite recently so please accept my apologies if this problem was already discussed. TIA Janusz Mrozek ==================================================== Janusz Mrozek, Department of Theoretical Chemistry & Department of Computational Methods in Chemistry Faculty of Chemistry, Jagiellonian University 3 R. Ingardena St. 30-060 Cracow, Poland ==================================================== ________________________________________________________________________ From twwells!telesci!moscom!rit!cci632!sjfc!schwartz@rutgers.edu Tue Aug 2 13:54:21 1994 From: sjfc.edu!schwartz@hyper.hyper.com (Leslie Schwartz) Subject: UV spectra To: hyperchem@HYPER.COM Date: Tue, 2 Aug 1994 09:54:21 -0400 Dear Graham Hurst and HyperChem netters, I am still using release 2. I am trying to calculate the transition energy between the ground and first excited singlet states for a number of substituted inorganic complexes and organic molecules in order to relate their geometry and other features to their UV absorption spectra. My procedure is to : 1) do an AM1 calculation while optimizing the ground state geometry using the Polak-Ribiere method, 2) perform a single point calculation on the optimized ground state geometry using AM1 and CI to obtain the energy of the lowest energy state, 3) perform a single point calculation on the optimized ground state geometry using AM1 and CI to obtain the energy of the next lowest energy state, and 4) subtract the energies obtained from steps 2) and 3). I get less and less believable results from this method when I apply it to a series of molecules of ever increasing complexity. I believe that my problem may be that while HyperChem 2 allows me to optimize the geometry of the lowest energy state before using CI to calculate its energy, it does not allow me to optimize the geometry of the next lowest energy state. Do the higher versions of HyperChem allow for geometry optimization of excited states? Am I missing something that I should be doing? I would be very grateful for any help that you all might offer - I am learning as I go along, but am stuck at this point. Sincerely, Leslie Schwartz Chemistry Department St. John Fisher College Rochester, N.Y. 14618 e-mail: schwartz@sjfc.edu telephone: (716) 385-8237 ________________________________________________________________________ From J_RABER@ACAD.LVC.EDU Tue Aug 9 17:03:06 1994 Date: Tue, 9 Aug 1994 13:03:06 -0400 From: ACAD.LVC.EDU!J_RABER@hyper.hyper.com To: hyperchem@HYPER.COM Cc: J_RABER@ACAD.LVC.EDU Subject: File Saving errors Hello everyone. I am currently working with the RuBisCo enzyme. I retrieved ten different PDB files and that is what I am working with. I tranfered these files over to the .hin format so I can deal with them more easily. This way I can save all of the necesssary connectivity and bonding information that I want. I am also doing all of this under the amber force field. I am currently trying to insert different inhibitors into the active site. I am overlaying the new inhibitors with the ones currently there and then deleting the origonal inhibitor. I am runnning into the problem of my files not saving. I got about one third of the ones to work, but that isn't going to be enough. I keep getting the error "unable to write file....". This is really frustrating. Does anyone know what could be the problem, and how to fix it? If so I would appreciate a response. Thanks in advance for all of your help. ******************************************************************************* Jeffrey Raber Tel: (717)-274-9407 BioChemistry Major Fax: (717)-228-2453 ATTN: Jeff Raber Lebanon Valley College Annville, PA Mail: 24 Fox Chase Lane E-Mail: J_RABER@ACAD.LVC.EDU Lebanon, PA 17042 ________________________________________________________________________ From hurst@hyper.hyper.com Tue Aug 9 19:45:01 1994 Date: Tue, 9 Aug 1994 15:45:01 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: , hyperchem@HYPER.COM Subject: Re: MEP units > Dear netters, > I went through all the manuals and did not find a single > reference to the units in which the molecular electrostatic potential > is computed in Hyperchem. I enetred the list quite recently so please > accept my apologies if this problem was already discussed. > TIA > Janusz Mrozek The electrostatic potential is given in atomic units. 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 jmeehan@cc.utas.edu.au Tue Aug 9 22:57:03 1994 Date: Tue, 9 Aug 1994 18:57:03 -0400 From: John Meehan Subject: Size of spheres???? To: hyperchem@HYPER.COM G'day everyone, I was wondering if it is possible to easily change the size of the spheres. Am I right in assuming that these CPK models represent the VDW Radii of the atoms....and if so can they be altered in the respective parameter files? I want to be able to keep the ratios of size between the elements the same....but decrease their overall size a little. Somewhere between the spheres and disks format so that they are not overlapping. Is this an option in HC 4 (I cannot upgrade from 2 to 4 yet :-( ......soon :-) )? Cheers John ---------------------------------------------- John Meehan O CH2-COOH Department of Biochemistry " / University of Tasmania, HO-P-O-C-COOH Australia | \ HO CH2-COOH PHOSPHOCITRIC ACID ---- A powerful, natural inhibitor of Pathological Biomineralization ---------------------------------------------- ________________________________________________________________________ From hurst@hyper.hyper.com Wed Aug 10 17:21:28 1994 Date: Wed, 10 Aug 1994 13:21:28 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: J_RABER@ACAD.LVC.EDU Subject: Re: File Saving errors Cc: hyperchem@HYPER.COM Hi Jeffrey, You asked: > Date: Tue, 9 Aug 1994 13:03:06 -0400 > From: J_RABER@ACAD.LVC.EDU > To: hyperchem@hyper.com > Cc: J_RABER@ACAD.LVC.EDU > Subject: File Saving errors > > Hello everyone. > > I am currently working with the RuBisCo enzyme. I retrieved ten > different PDB files and that is what I am working with. I tranfered these > files over to the .hin format so I can deal with them more easily. This way I > can save all of the necesssary connectivity and bonding information that I > want. I am also doing all of this under the amber force field. I am > currently trying to insert different inhibitors into the active site. I am > overlaying the new inhibitors with the ones currently there and then deleting > the origonal inhibitor. I am runnning into the problem of my files not > saving. I got about one third of the ones to work, but that isn't going to be > enough. I keep getting the error "unable to write file....". This is really > frustrating. Does anyone know what could be the problem, and how to fix it? > If so I would appreciate a response. Thanks in advance for all of your help. > > ****************************************************************************** > Jeffrey Raber Tel: (717)-274-9407 > BioChemistry Major Fax: (717)-228-2453 ATTN: Jeff Raber > Lebanon Valley College > Annville, PA Mail: 24 Fox Chase Lane > E-Mail: J_RABER@ACAD.LVC.EDU Lebanon, PA 17042 Have you checked how much free space you have or if you are trying to write to a write-protected disk? I suspect that you have simply run out of disk space since you files are roughly a half MB each. If these are okay send the full text of the error message to support@hyper.com. Cheers, 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 hurst@hyper.hyper.com Thu Aug 11 14:36:55 1994 Date: Thu, 11 Aug 1994 10:36:55 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: John Meehan , hyperchem@HYPER.COM Subject: Re: Size of spheres???? John Meehan asks: > G'day everyone, > I was wondering if it is possible to easily change the size of the > spheres. Am I right in assuming that these CPK models represent the VDW > Radii of the atoms....and if so can they be altered in the respective > parameter files? Not easily - you would have to modify chem.exe! The radii are 0.75 * vdW where vdW were available, or we used the covalent radius if we couldn't find a vdW radius. The Molecule Presentations module of ChemPlus *does* have the radii in editable text files, and you can define three sets of radii to easily switch between them (the sets are Ball & Stick, CPK Spheres and Custom). You need to have HyperChem 3 or 4 to run ChemPlus though (send email to info@hyper.com for more information about ChemPlus). > I want to be able to keep the ratios of size between the elements > the same....but decrease their overall size a little. Somewhere between the > spheres and disks format so that they are not overlapping. Is this an option > in HC 4 (I cannot upgrade from 2 to 4 yet :-( ......soon :-) )? HyperChem uses the *same* radii for disks and spheres, it just doesn't calculate sphere intersections for disks (for speed). If you want to adjust radii for display you need ChemPlus. > Cheers > John 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 berger@wuchem.wustl.edu Mon Aug 15 20:04:29 1994 Date: Mon, 15 Aug 1994 16:04:29 -0400 From: wuchem.wustl.edu!berger@hyper.hyper.com To: "hyperchem@hyper.com"@WUGATE.wustl.edu Subject: Using vibrational analysis in a script My version 3 manual doesn't list a command for doing vibrational analysi in a script. Is there such a command? Thanks. Dan Berger Washington University St. Louis ________________________________________________________________________ From hurst@hyper.hyper.com Tue Aug 16 14:50:35 1994 Date: Tue, 16 Aug 1994 10:50:35 -0400 From: hurst@hyper.hyper.com (Graham Hurst) To: berger@wuchem.wustl.edu Subject: Re: Using vibrational analysis in a script Cc: hyperchem@HYPER.COM Dan Berger asks: > My version 3 manual doesn't list a command for doing vibrational analysi > in a script. Is there such a command? Since it was new in Release 3, it is documented in the New Features manual. (Autodesk elected to provide Release 2 documention with a New Features manual for Release 3 - Release 4 by Hypercube has unified, up-to-date documentation.) Some of the new commands related to vibrational analysis were do-vibrational-analysis, menu-compute-vibrations and menu-compute-vibrational-spectrum. Also look for ones starting with "ir-". I recall that the online help descriptions of scripts was newer than the New Features manual for R3 (the README mentions the differences). R4 added several more script commands from user requests. 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 DBellnie@hs1.buffalo.edu Tue Aug 16 19:59:00 1994 From: "Bellnier, David" To: hyperchem@HYPER.COM Date: Tue, 16 Aug 1994 15:59:00 -0400 I am relatively new to the field of analytical/physical chem. My question is this: is there a measure of the AMPHIPHILICITY (amphiphilic moment???) of a small (nonprotein) molecule. For instance, porphyrin molecules with carboxylic acid on one side of the molecule and a carbon chain of varying length on the opposite side. Can this be measured experimentally or calculated with Hyperchem? ________________________________________________________________________ From DBellnie@hs1.buffalo.edu Wed Aug 17 16:19:00 1994 From: "Bellnier, David" To: hyperchem@HYPER.COM Date: Wed, 17 Aug 1994 12:19:00 -0400 Is there a way to estimate amphiphilicity (amphiphilic moment?) of a molecule using Hyperchem/ChemPlus? ________________________________________________________________________ From michael.moller Mon Aug 29 20:07:33 1994 Date: Mon, 29 Aug 1994 16:07:33 -0400 From: BRI.NRC.CA!michael.moller@hyper.hyper.com (Michael Moller) To: hyperchem@hyper.HYPER.COM Subject: survey: new compute servers for HyperChem Dear HyperChemists: As you may already know, Hypercube is now offering a networked back-end option. With this option, you can off-load the molecular mechanics and quantum mechanics calculations to a remote (presumably faster) machine on your network, while seeing the results displayed just as if the calculations were being done on your PC. So far, Hypercube is offering back-ends for three machines: SGI, RS6000 and DEC Alpha. We would like to find out what other machines there are that users of HyperChem would like to have back-ends made available. If you have a particular machine that you would like to see supported, please send a message to: moller@hyper.hyper.com We will use your responses to help determine which, if any, other hardware combinations will be supported in the future. Please indicate whether or not you currently have or plan to have the machine(s) you mention, and whether or not you would be interested in making a purchase if such a back-end becomes available. Thank you in advance for your replies, Michael Moller Staff Scientist Hypercube, Inc.