From owner-hyperchem@hyper.com Thu Jan 9 18:51:25 1997 From: "Forrest Stevens" To: hyperchem@hyper.com Subject: Two problems with hyperchem Our research group has been using Hyperchem (release 2) off and on, and we are now considering upgrading to the current version. However, there are two problems we have experienced, and we want to find out if we will also have these problems in the current release. 1) We are modeling molecules adsorbed on graphite, so need a graphite surface to place molecules on. We have tried to model graphite by building a sheet of aromatic carbon rings, but after sketching, "add H and model build" causes the sheet to curl and fold drastically. 2) We are trying to model a molecule which contains a Pt atom with four subtituents in a square planar geometry. Although release 2 does not have a "square planar" geometry option, we thought we could get it by choosing octahedral geometry and adding some constraints, but this has been ineffective. In addtion, we would welcome any comments on the usefulness of Hyperchem 5 for low-level modeling of interactions between molecules and surfaces. Forrest Stevens stevensf@heb.chem.utah.edu University of Utah ---------------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Jan 10 18:06:45 1997 Date: Fri, 10 Jan 1997 10:27:08 -0800 From: Laurence Lavelle Subject: Solution to problem with snapshot files. Hi Joel, Victoria and HC users, Joel and I had communicated about the snapshot file problem many times but came up with no explanation. Occasionally users had the following message: "Dynamics snapshot file x.snp incompatible with system" The x.hin file would open, but snapshots could not be played back. This error message was 'random' and could not be duplicated. It appears that this error message only occurs if one opens a molecular dynamics file when the current force field is different from that used during the molecular dynamics. For example, MD using MM+, close file, select different force field (e.g. ZINDO/1) reopen MD file and error message occurs and MD playback is not possible. Close MD file, change force field back to MM+, open MD file and everything is OK. I don't know if this 'bug' is the case for all the combinations of force fields, perhaps HyperChem support can test this out and provide a more detailed response. Laurence Lavelle """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Laboratory of Structural Biology & Molecular Medicine Molecular Biology Institute Los Angeles, CA90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone:(310)206-8270 Fax:(310)825-0982 http://www.mbi.ucla.edu/people/lavelle/lavelle.html """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" ---------------------------------------------------------------------- From owner-hyperchem@hyper.com Mon Jan 13 19:17:09 1997 Date: Mon, 13 Jan 1997 13:50:47 -0500 (EST) From: Mark Schwartz Subject: PBC screening Does anyone know how to screen electrostaic charges using periodic boundry conditions? ---------------------------------------------------------------------- From owner-hyperchem@hyper.com Thu Jan 16 11:57:32 1997 Date: Thu, 16 Jan 1997 11:23:29 -0100 From: Nico Scharnagl Subject: Copying ISIS-Sketch Hi hyperchemists, With the new version of HyperChem (5.0) I#m trying to copy the molecule = as an ISIS-sketch to the clipboard and aftwerwards to paste it into = ISIS. Only thing that happens is an unrecoverable application error. = Additional nothing is saved in the clipboard. Any idea? Additional another question. In "getting started" on page 169 it is = written that the Monte Carlo results can be copied to the clipboard for = use in other applications. But this doesn't work. I've not found any way = to copy the results. Many thanks for help from Germany Nico Scharnagl ****************************************************************** * Dr. Nico Scharnagl ! e-mail: Nico.Scharnagl@gkss.de * * GKSS-Forschungszentrum/CGE ! CompuServe: 100022.3444 * * P.O. Box 1160 ! phone : +49 4152 872422 (voice) * * D-21494 Geesthacht, Germany ! fax : +49 4152 872444 * ****************************************************************** ---------------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Jan 17 15:29:35 1997 Date: Fri, 17 Jan 97 10:52:30 -0500 From: barclay (Victoria Barclay) Subject: Re: Copy/Paste ISIS Hi Nico and newsgroup, > With the new version of HyperChem (5.0) I#m trying to copy the molecule = > as an ISIS-sketch to the clipboard and aftwerwards to paste it into = > ISIS. Only thing that happens is an unrecoverable application error. = > Additional nothing is saved in the clipboard. Any idea? You and a couple of others who have contacted our Support Desk directly will be happy to know that we have made available a patch for this particular problem. Please download the patch from our ftp site, ftp.hyper.com, in the support directory. The README file should be straightforward. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@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 Sun Jan 19 20:34:20 1997 Date: Sun, 19 Jan 97 17:15:52 -0500 From: barclay (Victoria Barclay) Subject: Re: Two problems with hyperchem > From: "Forrest Stevens" > Subject: Two problems with hyperchem > > Our research group has been using Hyperchem (release 2) off and on, > and we are now considering upgrading to the current version. > However, there are two problems we have experienced, and we want to > find out if we will also have these problems in the current release. > Hi Forrest and HyperChemists, Hypercube does not support HyperChem 2 (due to the terms negotiated under the separation from AutoDesk, which was the original distributor of HyperChem 2 and 3; see March 94 archives) so I can only comment on how later releases handle this problem. > 1) We are modeling molecules adsorbed on graphite, so need a graphite > surface to place molecules on. We have tried to model graphite > by building a sheet of aromatic carbon rings, but after > sketching, "add H and model build" causes the sheet to curl and fold > drastically. For HyperChem releases 4, 4.5, and 5, graphite is calculated without the "curl" you describe. Sometimes unexpected geometries arise at the next stage, when geometry optimization is selected. Especially with simpleer potentials such as MM+, this can result in an unexpected geometry. Although you may have imposed constraints in the model builder, these do not apply during geometry optimization. To improve the optimization, you may find it necessary to impose restraints--not just constraints. Just to emphasize the semantics: "constraints" -- affect the model builder "restraints" -- affect the geometry optimization. These settings are accessed in different ways; and the latter one means that certain atoms in the molecule must be "named selections" which are specified as Restraints under the Setup menu. Unfortunately, from what I can glean, HyperChem 2 does not have restraints--it only has constraints. > 2) We are trying to model a molecule which contains a Pt atom with > four subtituents in a square planar geometry. Although release 2 > does not have a "square planar" geometry option, we thought we could > get it by choosing octahedral geometry and adding some constraints, > but this has been ineffective. The "Constrain Geometry" dialog constrains the Model Build stage in release 4 to the follwoing geometries: linear, trigonal, tetrahedral, bipyramidal, and octahedral. In release 5, this is broadened to include square planar as well. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@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 Jan 20 20:58:53 1997 Date: Mon, 20 Jan 1997 15:27:52 -0600 (CST) From: "XIE, NING" Subject: result uncertainties Hi, Victoria & hyperchemists, I have a question about the result I got using hyperchem. I tried to calculate the HOMO and LUMO energies of some para substituted thioanisoles, such as p-CH3OPhSCH3, p-CH3PhSCH3, PhSCH3, p-FPhSCH3, P-ClPhSCH3 and p-NO2PhSCH3. I need the uncertainties of these orbital energies, but I couldn't find related information nowhere in the log file. Does anybody have a hint? Thank you for you help. NING ---------------------------------------------------------------------- From owner-hyperchem@hyper.com Tue Jan 21 16:49:53 1997 Date: Tue, 21 Jan 1997 10:05:08 -0400 From: facien03@abello.dic.uchile.cl (Juan S. Gomez-Jeria.) Subject: Display menu. Dear Sirs (of Hyperchem): It would be highly desirable if you may modify the following menu: DISPLAY-LABELS-ATOMS, by adding the option "Other" obviously to be able to label our atoms as we need (sometimes the other options already implemented do not give the answer!). Yours sincerely, Juan S. Gomez-Jeria Associate Professor Universidad de Chile Facultad de Ciencias Casilla 653 Santiago CHILE. e-mail: facien03@abello.dic.uchile.cl Phone: (562)-672-7261. Fax: (562)-271-3888 ---------------------------------------------------------------------- From owner-hyperchem@hyper.com Thu Jan 23 19:03:40 1997 Date: Thu, 23 Jan 97 13:30:55 -0500 From: barclay (Victoria Barclay) Subject: square planar Hi again Forrest and HyperChemists, > > 2) We are trying to model a molecule which contains a Pt atom with > > four subtituents in a square planar geometry. Although release 2 > > does not have a "square planar" geometry option, we thought we could > > get it by choosing octahedral geometry and adding some constraints, > > but this has been ineffective. > > The "Constrain Geometry" dialog constrains the Model Build stage > in release 4 to the follwoing geometries: > linear, trigonal, tetrahedral, bipyramidal, and octahedral. > In release 5, this is broadened to include square planar as well. My answer should be amended to read that releases 4, 4.5 and 5 *all* have linear, trigonal, tetrahedral, bipyramidal, square planar and octahedral. (The Reference Manual for release 4 does not list this as an option, but it *is* there in the software.) And although the square planar geometry is available, it only works for mono-dentate ligands--something I ought to have brought up at that juncture. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ---------------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Jan 24 13:20:13 1997 Date: Fri, 24 Jan 1997 13:02:36 +0100 From: Jerzy Malecki Subject: polarizabilities Hi hyperchemists, Does anyone know how get results on polarizabilities (first and second order) ? Jerzy Malecki Institute of Molecular Physics Polish Academy of Sciences Smoluchowskiego 17, 60179 PL Poznan, Poland Phone: (4861) 612360 Fax: (4861) 684524 ---------------------------------------------------------------------- From owner-hyperchem@hyper.com Sun Jan 26 22:43:54 1997 Date: Sun, 26 Jan 97 18:12:37 -0500 From: barclay (Victoria Barclay) Subject: polarizabilities >Date: Fri, 24 Jan 1997 13:02:36 +0100 >From: Jerzy Malecki >Does anyone know how get results on polarizabilities (first and second order)? Hi Jerzy and HyperChemists, Polarizabilities are not yet included as an option in our log file output. I have entered this item on our "wish list." No guarantees, but at least it is there. Similarly, I have made note of the request by Juan S. Gomez-Jeria regarding more flexibility in Display-Labels-Atoms. Thanks for the input! Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@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 Sun Jan 26 23:22:34 1997 Date: Sun, 26 Jan 97 18:17:31 -0500 From: barclay (Victoria Barclay) Subject: result uncertainties Hi Ning and HyperChemists, > From: "XIE, NING" > Subject: result uncertainties > > Hi, Victoria & hyperchemists, > > I have a question about the result I got using hyperchem. I tried to > calculate the HOMO and LUMO energies of some para substituted > thioanisoles, such as p-CH3OPhSCH3, p-CH3PhSCH3, PhSCH3, p-FPhSCH3, > P-ClPhSCH3 and p-NO2PhSCH3. I need the uncertainties of these orbital > energies, but I couldn't find related information nowhere in the log > file. Does anybody have a hint? There are no "uncertainties" as such reported for computed values because the values are calculated to the level of machine precision. What I think you are really driving at here--the accuracy of such calculations--depends on the method you use, the parameter set you have, and the system you are considering. This becomes a matter of looking at the scientific literature for related calculations, e.g., ZINDO calculations of sulfur-containing compounds (if ZINDO is the method you chose). You might also be able to run sample calculations for known or standard species, and thus obtain some idea of the level to which you can trust the type of numbers predicted. Sometimes the results must be interpreted in a qualitative fashion rather than expecting quantitative answers. Besides the usual library search for reports on related calculations, you might find the archives of the Computational Chemistry List (CCL) helpful; I have seen discussion of _ab initio_ methods as well as PM3 and AM1 methods and parameter sets. Their web site is http://ccl.osc.edu/chemistry.html Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@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 Jan 30 01:47:52 1997 Date: Wed, 29 Jan 1997 18:07:09 -0600 (CST) From: "XIE, NING" Subject: MnO4- LUMO Hi, there, I'm trying to calculate the LUMO evergy of MnO4- (permanganate). After 75 cycles It still doesn't arrive convergence and the structure is not tetrahedron. When I set constrain all the bond angle at tetrahedron angel, the bond angles are changed. Anybody has an idea ? Thank you for you time. ning ---------------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Jan 31 17:52:42 1997 Date: Fri, 31 Jan 97 10:02:45 -0500 From: barclay (Victoria Barclay) To: hyperchem@hyper.com Subject: permanganate Hi Ning and HyperChemists, > I'm trying to calculate the LUMO evergy of MnO4- (permanganate). After 75 cycles > It still doesn't arrive convergence and the structure is not tetrahedron. > When I set constrain all the bond angle at tetrahedron angel, the bond angles > are changed. Anybody has an idea ? Ah, good, a chance to practice restraint. Try the following: draw MnO_4 (with "allow ions" toggled on), select the Mn atom, and then do the following menu operations: Build/Constrain Geometry --> tetrahedral Build/Add H & Model Build then select and Edit/Cut the extra H's This will give you a good set of angles to begin the geometry optimization with... but before you begin, you will have to set up the restraints. To do this, select each one of the O--Mn--O angles and do a Select/Name Selection on it by specifying "other" and giving it a unique name. (You will be making 6 selections, since there are 6 unique angles.) Once you have chosen the method and specified charge and multiplicity, from the Setup/Restraints menu, add all 6 of the named selections. Then do Compute/Geometry Optimization. Regards, Victoria ------------ Victoria Barclay, Ph.D. Manager, Scientific Support Email to: barclay@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ---------------------------------------------------------------------- From owner-hyperchem@hyper.com Fri Jan 31 17:02:03 1997 Date: Fri, 31 Jan 1997 13:32:14 +0100 From: Dirk Dettmering Subject: Hyperchem 5.0 Dear Users of Hyperchem, I'm a PhD-candidate at the department of pharmacy at the Philipps-university of Marburg, Germany, and member of the research group of PD. Dr. Peter Imming. Our research group plans to investigate the interaction of newly synthezised drug compounds with the target enzyme. Therefore we are looking for a not to complex software package which can be run on Intel based= computers. I've heard about the new release of hyperchem 5.0 and it's new features. But on the web pages of Hypercube I couldn't get the information about the import and export filters supported by hyperchem 5.0 especially concerning the interchange of data with software packages like sybel running on SGI workstations. It could be also very helpful for our research group to learn from users about the kind of application they are using hyperchem for and how exact the results are. Thanks to all answering people in advance. Yours sincerly Dirk Dettmering **************************************************************************** *********** * Dirk Dettmering Email: Dettmer@pharmazie.uni-marburg.de * * Philipps-Universit=E4t Marburg - FB Pharmazie und Lebensmittelchemie = * * Philipps University Marburg - Department of Pharmacy - Germany = * **************************************************************************** ***********