From jtgolab@amoco.com Wed Mar 3 04:16:26 1993 Date: Wed, 3 Mar 1993 10:16:26 -0600 From: jtgolab@amoco.com Message-Id: <9303031616.AA15187@vacc47.nap.amoco.com> To: aec@howdy.wustl.edu Subject: Re: Molecular Visualization The best (IMHO) public domain software for visualizing molecules comes from Florida State University. With a little software cobbling, one can take XYZ coordinates and display a molecule. If one has Gaussian files it is even easier. Once the molecule is displayed, one can rotate it, display 3-D data (i.e. orbital densities), even make movies. The software is called "SciAn" and Eric Pepke is one of its creators. I enclose a short recent message from Eric announcing the lastest version of the SciAn complete with directions for downloading it. It takes no time at all (about 30 minutes) to install on UNIX machines - if you read the README file and know a (very) little about UNIX. Good Luck. :Joe jtgolab@nap.amoco.com -------- Eric Pepke's Message of 3/2/93 > From: PEPKE@scri.fsu.edu > To: scian@scri.fsu.edu > Subject: SciAn version 0.742 available for downloading > Status: RO > > SciAn version 0.742 is now available for downloading from ftp.scri.fsu.edu. > It's in the pub/SciAn/release directory. > > Following are the release notes for this version. > > Eric Pepke INTERNET: pepke@scri.fsu.edu > Supercomputer Computations Research Institute MFENET: pepke@fsu > Florida State University SPAN: scri::pepke > Tallahassee, FL 32306-4052 BITNET: pepke@fsu > > Disclaimer: My employers seldom even LISTEN to my opinions. > Meta-disclaimer: Any society that needs disclaimers has too many lawyers. > > -------------------- > > This is the release of version 0.74 of SciAn. > Please let us know if you have any problems. > > The following is a summary of the changes since release 0.73: > > Visualization Objects > Bugs in several visualization objects, including the point cloud, mesh, > and balls objects, have been fixed > > Visualize As... > The VisualizeAs... window has been changed to allow selection of > the visualization technique at the top. This simplifies the display > and allows all types of visualization techniques to be seen. > > Deformation > A bug in deformation has been fixed. > > The following is a summary of the changes since release 0.722: > > PDB reader > Some bugs have been fixed in the protein data bank reader > > PLOT-3D > The unformatted part of the PLOT-3D is working, but you need FORTRAN > to compile it. > > Vector Datasets > Some scalar visualization techniques, such as isosurfaces, work on > vector data without a modifier. They use the absolute value of the > dataset. It is also possible to color by the absolute value of the > field. More flexibility will be provided later through modifiers. > > Contours > Contours have been changed somewhat > > Point Cloud > A couple of features have been added to the point cloud > > The following is a summary of the changes since release 0.721: > > Installation > The installation process has been automated even more, and it should > never be neccessary to edit machine.h by hand unless there's something > really strange going on. > > Scripts > Several bugs involving scripts were fixed. > > Cursor > A bug which caused the cursor to remain hidden after a recording > block has been exited was fixed. > > Manual > We've gotten closer to releasing a manual. One more edit, and we > should have it. > > Things we Haven't Forgotten > Keyframe editing, saved palettes, saved visualization state, fully > debugged sockets, Gaussian 90 reader, individually movable and reflectable objects. We haven't forgotten any of this stuff. I wanted to have all of this done by this time, but things happened to get in the way, and they will be late. > > Eric Pepke > pepke@scri.fsu.edu > Report bugs to: scian-bugs@scri.fsu.edu, but first read README. ----- From abby@mercury.aichem.arizona.edu Wed Mar 3 06:42:18 1993 Date: Wed, 3 Mar 93 13:42:18 -0700 From: abby@mercury.aichem.arizona.edu (Abby Parrill) Message-Id: <9303032042.AA17107@mercury.aichem.arizona.edu> To: chemistry@ccl.net Subject: MM2 Parameters for cyclopropyl esters I am currently using MM2 (87) on a set of substituted molecules. One of the substituents giving me problems is cyclopropyl. MM2 has some parameters for atom type 22 (cyclopropane carbon) but not next to an ester. I attempted the reasoning by analogy approach to "quesstimate" some parameters and ended up with some unreasonable energies. Has anyone developed (or read about) reasonable parameters for this type of system? Many thanks. **************************************************************************** ****** ****** ****** University of Arizona ****** ****** Artificial Intelligence in Chemistry ****** ****** Abby Parrill(abby@mercury.aichem.arizona.edu) ****** ****** ****** **************************************************************************** From mlorenz@ecn.purdue.edu Wed Mar 3 17:25:28 1993 Date: Wed, 3 Mar 93 22:25:28 -0500 From: mlorenz@ecn.purdue.edu (Michael Lorenz) Message-Id: <9303040325.AA16448@cn.ecn.purdue.edu> To: CHEMISTRY@ccl.net Subject: MOPAC-Optimizing the Transition State I've been using MOPAC to do conformational analysis (i.e. barriers to rotation) on certain group of phenylene compounds. I've been using the SADDLE keyword to get the T.S. and then invoking the IRC command to determine the reaction path. Is this the best way? According to the manual, i need to transition state opt. so i can do a force calculation and then invoke the IRC. I can't find a stationary point at the T.S. When i tighten the convergence criteria on the SADDLE calculation i get an an error message telling me to consult a programmer. Does anyone have any suggestions? Thanks Mike Lorenz