From harttigu@ava.bcc.orst.edu Sun Feb 1 22:09:14 1998 Received: from ava.bcc.orst.edu for harttigu@ava.bcc.orst.edu by www.ccl.net (8.8.3/950822.1) id VAA06966; Sun, 1 Feb 1998 21:46:19 -0500 (EST) Received: from bcc.orst.edu (slip77.UCS.ORST.EDU [128.193.5.77]) by ava.bcc.orst.edu (8.8.7/8.8.7) with ESMTP id SAA00059 for ; Sun, 1 Feb 1998 18:44:38 -0800 (PST) Message-ID: <34D5330F.490A5429@bcc.orst.edu> Date: Sun, 01 Feb 1998 18:44:31 -0800 From: Ulrich Harttig X-Mailer: Mozilla 4.03 [en] (WinNT; I) MIME-Version: 1.0 To: CCL Subject: AMBER94-FF comparisons Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I have adapted the AMBER94 (Cornell et al. J. Am. Chem. Soc. 117, 5179-5197) forcefield for Hyperchem 5.02 and would like to test the accuracy of this implementation. Unfortunately I have no access to other programs which use the AMBER94 forcefield. I hope someone here can help me by running some quick calculations on their favorite Amber program. I am thinking about single-point calulations of some smaller proteins without cofactors (1crn.pdb, 1ps2.pdb, 1ubq.pdb, I can provide the PDB files if necessary) and without water molecules. Pointers to references with similar calulations will also be appreciated. Thank you for your help. Ulrich Harttig, Ph.D. Marine/Freshwater Biomedical Sciences Center Oregon State University, 232 Wiegand Hall, Corvallis, OR, 97331 Phone: 541-737-6514 Fax: 541-737-1877 From jrh@qc.ag-berlin.mpg.de Sun Feb 1 19:01 EST 1998 Received: from bedrock.ccl.net for jrh@qc.ag-berlin.mpg.de by www.ccl.net (8.8.3/950822.1) id TAA06708; Sun, 1 Feb 1998 19:01:31 -0500 (EST) Received: from helios.qc.ag-berlin.mpg.de (helios.QC.AG-Berlin.MPG.DE [141.20.74.13]) by bedrock.ccl.net (8.8.6/8.8.6/OSC 1.0) with SMTP id TAA16112 for ; Sun, 1 Feb 1998 19:01:31 -0500 (EST) Received: by helios.qc.ag-berlin.mpg.de (AIX 3.2/UCB 5.64/4.03) id AA29432; Mon, 2 Feb 1998 01:01:31 +0100 Date: Mon, 2 Feb 1998 01:01:31 +0100 From: jrh@qc.ag-berlin.mpg.de (Joerg-Ruediger Hill) Message-Id: <9802020001.AA29432@helios.qc.ag-berlin.mpg.de> To: chemistry@www.ccl.net Subject: Viewmol 2.1 released Viewmol 2.1 has been released. What is Viewmol ? Viewmol is a graphical front end for some quantum chemical as well as for some molecular modelling programs. It is able to visualize results of such calcula- tions. The program is able to show the geometry of a molecule, to trace a geo- metry optimization or a MD trajectory, to animate normal vibrations of a mole- cule or to show them as arrows, to draw IR, Raman, and inelastic neutron scat- tering spectra of a molecule, an MO energy level or density of states diagram, basis functions, molecular orbitals, and electron densities of a molecule and to show forces acting on each atom in a certain configuration. All drawings generated by Viewmol can be saved as TIFF, HPGL, or PostScript files. Anima- tions of normal modes can be converted to a video (MPEG) or animated GIF file, e. g. for inclusion into World Wide Web documents (requires additional pro- grams available on the Internet). The program can also be used as an interface to the freeware ray tracing program Rayshade. A file containing a description of the scene for this program may be generated and the ray tracing program can be used from within Viewmol. At present Viewmol includes input filters for Discover, DMol/DSolid/DMol3, Gaussian 9x, Gulp, and Turbomole outputs as well as for PDB files. It is easy to write additional input filters for other output formats. What is new in version 2.1 ? - perspective drawing mode with shadows - ability to move view point - automatic determination of bond orders - output of resolution independent Postscript files even for drawings with shaded surfaces - ability to read observed spectra and overlay them over the calculated ones - ability to annotate the drawing in the main window - no hard wired limits on the number of bonds per atom anymore (metal organic complexes should now work) - speed up of drawing of isosurfaces - ability to save a number of configurational settings directly from the program without need to edit X resources - improved input filter for Gaussian 9x and Turbomole - introduction of output filters to write structures in different formats - Viewmol now runs more or less with Lesstif - a lot of bug fixes What operating systems does Viewmol run on ? Viewmol was developed using Linux, but it was also ported (or better recompiled) on a number of other operating systems. Currently, pre- compiled binaries are available for Linux (dynamically linked with Lesstif, statically linked with Motif), AIX, and IRIX. The program should also run on OSF1 and HP-UX, but due to a lack of direct access to such hardware I couldn't test it. Where do I get Viewmol ? Viewmol can be downloaded from the Computational Chemistry List archive (USA): - ftp://ftp.ccl.net/pub/chemistry/software/SOURCES/C/viewmol or from Akademische Software Kooperation Karlsruhe (Europe): - ftp://ftp.ask.uni-karlsruhe.de/pub/education/chemistry The source code and the precompiled binaries for Linux will also be available from Sunsite (USA) or your friendly neighbourhood mirror: - ftp://sunsite.unc.edu/pub/Linux/apps/graphics/visualization For the second site it may take a few days before the site administrators have moved the code to the given location. Joerg-Ruediger Hill (jrh@qc.ag-berlin.mpg.de)