From jlbchamp@cco.caltech.edu Thu Jan 5 20:04:57 1995 Date: Thu, 5 Jan 1995 16:50:45 -0800 To: hyperchem@hyper.com From: jlbchamp@cco.caltech.edu (J.L. Beauchamp) Subject: Hyperchem Menus Deletion We are running the current version of Hyperchem for Windows and are using a video card to copy molecular dynamics sequences to video tape for playback in classes and seminars. Does anyone know if the menus can be removed for the playback of a molecular dynamics sequence (full screen VGA)? J.L. Beauchamp California Institute of Technology 127-72 Pasadena, CA 91125 Phone: 818-395-6525 FAX: 818-568-8641 EMail: jlbchamp@cco.caltech.edu ________________________________________________________________________ From riusal@redvax1.dgsca.unam.mx Fri Jan 6 01:06:31 1995 Date: Thu, 5 Jan 1995 21:08:52 -0600 (CST) From: Rius Alonso Carlos-FQ To: "J.L. Beauchamp" Cc: hyperchem@hyper.com Subject: Re: Hyperchem Menus Deletion I have done some work with Hyperchem and video tape for classes , I have used two methods 1./ With a videocamera Hi8 and a slow shutter speed ( lower than 30) the images of the tape are of aceptable quality with the advantage that you can focus on the image and use the zoom to open or close the image, in this way you can tape exactly what you want. 2./ The second method is to use the video card I am using TVATOR pro and the quality is good it has a mode by software of overscan and most of the menu is out of the screen. The quality of the image is better than the first method but you have much less flexibility. Sincerely your Dr. Carlos Rius Faculty Of Chemistry UNAM Mexico On Thu, 5 Jan 1995, J.L. Beauchamp wrote: > We are running the current version of Hyperchem for Windows and are using a > video card to copy molecular dynamics sequences to video tape for playback > in classes and seminars. Does anyone know if the menus can be removed for > the playback of a molecular dynamics sequence (full screen VGA)? > J.L. Beauchamp > California Institute of Technology 127-72 > Pasadena, CA 91125 > Phone: 818-395-6525 > FAX: 818-568-8641 > EMail: jlbchamp@cco.caltech.edu > > ________________________________________________________________________ From llavelle@watson.Princeton.EDU Mon Jan 9 15:35:54 1995 Date: Mon, 09 Jan 1995 13:52:43 EST To: hyperchem@hyper.com Subject: Easy access to molecular structures. Greetings for 1995. Additions to the Wish List. (To improve what is already an excellent package!) Easy access to molecular structures by including structures from the Brookhaven Protein Data Bank. This feature is already available in other software packages, e.g., MacImdad. ________________________________________________________________________ From pstein@css1.css.edu Tue Jan 10 15:26:40 1995 From: "paul stein" Date: Tue, 10 Jan 95 13:45:04 CST To: hyperchem@hyper.com Subject: Re: Easy access to molecular structures. On Mon, 09 Jan 1995 13:52:43 EST, wrote: >Greetings for 1995. > >Additions to the Wish List. (To improve what is already an excellent >package!) > >Easy access to molecular structures by including structures from the >Brookhaven Protein Data Bank. This feature is already available in other >software packages, e.g., MacImdad. Protein structures can be downloaded directly from the Brookhaven Protein Data Bank, using the internet. Access to the pdb database is made easier using Molecules R Us which allows full text searches of the database. I wish I could give more detailed instructions on how to find this, but I use Mosaic and was given the program with Molecules R Us as one of the bookmarks already in place. Make sure to download the files as Text files. I have had no problems reading these in hyperchem. Paul Stein ________________________________________________________________________ From llavelle@watson.Princeton.EDU Thu Jan 12 12:48:34 1995 Date: Thu, 12 Jan 1995 11:34:53 EST To: hyperchem@hyper.com Subject: Response to various questions about, "Easy access to molecular structures". 1) MacImdad is a program (for mac and pc) developed by Dr. Michael Levitt and distributed by Molecular Applications Group. It includes the entire Brookhaven Protein Data Bank reduced to 8% of its normal size and is updated for additional fees. 2) It appears that SciProtein (for HyperChem) from SciVision will do the same thing. Thank you to Paul Stein for advice on downloading directly from the Brookhaven PDB. Laurence Lavelle Depts. of Chemistry and Molecular Biology Princeton University Princeton NJ 08540 Tel:(609)258-3935 Fax:(609)258-3980 ________________________________________________________________________ From MARTINN@UNCWIL.EDU Tue Jan 17 13:04:34 1995 Date: Tue, 17 Jan 1995 12:44:07 -0400 (EDT) Subject: Questions about Hyperchem and ChemPlus To: hyperchem@hyper.com Hi, Recently after performing AM1 minimizations, when we viewed the orbitals, a double set of similar (but slightly different) lines (orbitals) was displayed on the screen. I do not know what to make of the two sets of data. In an unrelated question, has anyone found a way to store the output from QSAR calculations (Log P, etc) in a spreadsheet such as Excel? That would make our work a lot easier. Thanks for your help. Ned H. Martin Department of Chemistry University of North Carolina at Wilmington ________________________________________________________________________ From jstucker@whale.st.usm.edu Wed Jan 18 14:30:50 1995 Date: Wed, 18 Jan 1995 12:45:26 -0600 (CST) From: Jerry Stacy Tucker Subject: PDB Files To: Hyperchem Discussion Hi, This is in response to a recent message about PDB files. I am attempting to locate a PDB file for cystatin to open in HyperChem. I have searched the gopher at BNL; I was only able to find journal references and a .gif file. I believe there is a PDB file for cystatin. If this file is available at the Brookhaven Database where else should I look. Thanks for any information. Stacy Tucker University of Southern Mississippi Department of Chemistry and Biochemistry ________________________________________________________________________ From 94970459@vax1.dcu.ie Thu Jan 19 01:07:46 1995 Date: Wed, 18 Jan 1995 22:19:04 +0000 (GMT) From: KANEPCHEM <94970459@vax1.dcu.ie> Subject: single point calculations To: hyperchem@hyper.com Hi, When I carry out a geometry optimisation on a class of macrocyclic compounds known as calixarenes I sometimes find that the optimisation does not converge after the maximum no. of cycles has taken place but if I restart the optimisation it converges immediately after one cycle i.e. the gradient decreases by a much greater difference than those decreases just before the optimisation reached its maximum no. of cycles. A related problem is that I often that when an optimisation does converge the values that I obtain for the energy and gradient values are than those obtain- ed when I carry out a single point calculation on the optimised structure. In this work I use: i) the MM+ force field ii) the following algorithms (in the order given): a) steepest descent b) Polak-Ribiere c) block diagonal Newton-Raphson Any help would be greatly appreciated. Paddy Kane Dublin City University Ireland ________________________________________________________________________ From jlbchamp@cco.caltech.edu Fri Jan 20 14:40:47 1995 Date: Fri, 20 Jan 1995 11:34:40 -0800 To: hyperchem@hyper.com From: jlbchamp@cco.caltech.edu (J.L. Beauchamp) Subject: Internal Energies We have been carrying out trajectory calculations of polyatomic molecules colliding with large biological ions and evaluating the conversion of relative translational energy into internal excitation. Does anyone have an easy approach for extracting the total internal excess energy of the two molecules (separately) after the collision from the calculated results? Thanks for your input. Jack Beauchamp J.L. Beauchamp California Institute of Technology 127-72 Pasadena, CA 91125 Phone: 818-395-6525 FAX: 818-568-8641 EMail: jlbchamp@cco.caltech.edu ________________________________________________________________________ From emcgoran@ewu.edu Thu Jan 26 07:06:28 1995 Date: Wed, 25 Jan 1995 18:00:43 -0800 From: emcgoran@ewu.edu (Ernie McGoran) Subject: hbond/nonbond energy output To: hyperchem Hello: hope you can help. I am not able to get a HyperChem script to return (on the status line) hbond-energy ornonbond-energy, script messages # 323 and 324 following a single-point calculation with MM+ parameters on a deca-peptide. Whether or not a log file is activated doesn't seem to matter. The VDW and the electrostatic contributions are output to a log file, but I see no listing for H-bond, which will be the largest contribution to the electrostatic portion of the energy, and I presume the latter could be used as a good approximation to the H-bond energy. Does the single-point calculation have to be done with a different parameter set, or I am I missing something else? Thanks in advance for any ideas. Ernie McGoran | Phone: (509) 359-7931 Dept. of Chem./Biochem.MS 74 | FAX: (509) 359-6937 Eastern Washington University | email: emcgoran@ewu.edu Cheney, WA 99004 ________________________________________________________________________ From JSL@mmf.ruc.dk Sat Jan 28 09:03:44 1995 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: hyperchem@hyper.com Date: Sat, 28 Jan 1995 14:18:36 +0100 Subject: Halogens in ZINDO/S Hello HyperChem-users! I am interested in information on ZINDO/S parameters for Chlorine. Also information on parameters for Bromine and Iodine would be most welcome! Yours sincerely, Jens >--< _________________________________ _________________________________ | | | | Jens Spanget-Larsen | Phone: +45 46757711 | | Associate Professor, dr.scient. | - direct: +45 46757781 * 2710 | | Department of Chemistry (17.2) | - private: +45 42840320 | | Roskilde University | Fax: +45 46757721 [Dept.] | | RUC, P.O. Box 260 | - +45 46757401 [RUC] | | DK-4000 Roskilde, Denmark | Internet: JSL@mmf.ruc.dk | |_________________________________|_________________________________|