From tennantm1%frgen.dnet@smithkline.com Mon Apr 1 22:39:02 1993 Date: Tue, 30 Mar 93 03:39:02 -0500 Message-Id: <9303300839.AA07850@smithkline.com> From: tennantm1%frgen.dnet@smithkline.com (Mike Tennant. Harlow x3328) To: "chemistry@ccl.net"%INET.dnet@smithkline.com Subject: PROFANAL Dear Netters, Does anybody know how I can get hold of the progs profmake and profanal (Gribskov, McLachlan and Eisenberg. PNAS. 84, 4355-4358, (1987). (preferably for an SG!, but I'm prepared for anything within reason!) Mike Tennant Email: tennantm1@smithkline.com | | Email: tennant%hau410.uk.smithkline.com@smithkline.com | | Email: smithkline.com!hau410.uk.smithkline.com!tennant | |*****************************************************************************| | "EXTERMINATE ALL RATIONAL THOUGHT" - William S. Burroughs, The Naked Lunch | ------------------------------------------------------------------------------- From bewilson@Kodak.COM Tue Apr 2 02:38:55 1993 Date: Tue, 30 Mar 93 07:38:55 -0500 Message-Id: <9303301238.AA23757@Kodak.COM> From: bewilson@Kodak.COM (Bruce E. Wilson, Eastman Chemical Company, (bewilson@kodak.com)) To: "chemistry@ccl.net"@Kodak.COM Subject: Molefiles and Smiles strings > In response to Henry Rzepa's query on molfile formats and Gopher attributes, > I would like to put in a plug for SMILES representation as well as MDL > molfiles. SMILES is becoming a standard and having a simple text string > for a structure (given that 2-D and 3-D structures can be rapidly generated > now using CONCORD and other programs) can be very usefulin many situations. I agree that SMILES are a very useful representation, and also a very compact one. The question I have is how are people dealing with the lack of configuration information in the SMILES string? While I hate to break up the simplicity of the SMILES string, adding information like Z/E and configuration about aliphitic rings could make a potentially large difference. I know that Weiningers developed some extensions to SMILES to handle some of these cases, I've worked on some ideas of my own, but I wonder how widespread this really is. Any comments are welcome. If there are a significant number of comments to me, I will summarize. Thanks. Bruce Wilson (bewilson@kodak.com) From msrag@csv.warwick.ac.uk Tue Apr 2 15:09:43 1993 Date: Tue, 30 Mar 1993 14:09:43 +0100 From: Dr D Buttar Message-Id: <14699.199303301309@violet.csv.warwick.ac.uk> To: chemistry@ccl.net Subject: Polyrate Query I have been trying to use the program polyrate(version 4.5.1) to determine rate constants from ab initio data. I have however not been able to set up an input file that reads in vibrational frequencies directly. I was wondering if anyone else has used this program and if they have used the option in the electronic structure input file that allows frequencies to be read in directly. An example input file of this type would be much appreciated. David Buttar. From c62@aixfile1.urz.uni-heidelberg.de Tue Apr 2 21:31:32 1993 Date: Tue, 30 Mar 1993 19:31:32 +0200 From: c62@aixfile1.urz.uni-heidelberg.de (Andreas Schulz) Message-Id: <9303301731.AA33104@ix.urz.uni-heidelberg.de> To: chemistry@ccl.net Subject: NBO analyses Dear All Does anybody have a description of the NBO analyses in MOPAC6. Thanks in advance A.Schulz Email: c62@ix.urz.uni-heidelberg.de Phys.Chem.Dept. University Heidelberg From PEARLMAN@VAX.PHR.UTEXAS.EDU Tue Apr 2 10:04:42 1993 Date: Tue, 30 Mar 1993 16:04:42 -0600 (CST) From: PEARLMAN@VAX.PHR.UTEXAS.EDU Message-Id: <930330160442.2a8@VAX.PHR.UTEXAS.EDU> Subject: Stereochemistry and SMILES To: chemistry@ccl.net I, too, wish to encourage the use of the SMILES chemical line notation! Bruce Wilson posted a recent message expressing concern about whether or not stereochemical information can be included within SMILES strings. The answer is YES! In fact there are two ways: 1. Daylight Chemical Information Systems distributes SMILES-based software and defines what I would call the "official SMILES syntax." That syntax did not, at first, support stereochemistry. However, about two years ago, Daylight (Dave Weininger) extended the syntax to allow specification of *local* stereochemistry (i.e., defined in terms of connection-table sequence rather than chemical conventions such as Cahn-Ingold-Prelog). This is precisely the type of stereo- chemical specification needed for substructural searching but may not be the most convenient for chemists who wish to describe a complete molecular structure using the familiar R/S, E/Z, cis/trans definitions. 2. About six years ago, I wanted to use SMILES as input to our CONCORD program (for 2D to 3D conversion) and defined an extension to the original (non-stereochemical) SMILES syntax. It supports the C-I-P stereochemical notation. To distinguish it from the official SMILES syntax, I refer to it as "conversational SMILES" (since it supports the terminology with which chemists converse about structures) but many other people refer to it as "CONCORD SMILES" (since it was first used within CONCORD). Please NOTE that CONCORD accepts BOTH the official Daylight stereochemical SMILES and the "conversational SMILES". I believe (but am not positive) that the SMILES interpretter available from Daylight also accepts both "dialects." SMILES is (are?) great! I encourage you to learn about how SMILES could possibly be of use to you. I'd be glad to answer questions but contacting Daylight would probably be best. --- Bob Pearlman P.S. CONCORD v 3.0.0 has recently been delivered to Tripos. By default, it automatically performs extremely efficient geometry optimizations to relieve close-contacts between non-bonded atoms. Many other significant improvements have been made but I dare not list them here! :-) From hotline@MSI.COM Tue Apr 2 12:00:48 1993 Message-Id: <9303302200.AA09262@support> From: Technical Support Hotline Date: Tue, 30 Mar 1993 17:00:48 -0500 Organization: Molecular Simulations Inc. To: chemistry@ccl.net Subject: Re: batching files in MOPAC > Date: 3/25/93 5:16 PM > From: Dr. Gene A. Nelson > Date: Thu, 25 Mar 93 10:18:48 -0500 > From: au195@cleveland.freenet.edu (Dr. Gene A. Nelson) > To: chemistry@ccl.net > Subject: Batching files in MOPAC > Reply-To: au195@cleveland.freenet.edu (Dr. Gene A. Nelson) > Sender: chemistry-request@ccl.net > Errors-To: owner-chemistry@ccl.net > Precedence: bulk > > Dear Netters, > > I am running MOPAC 5.0 in the Quanta3.3 software from MSI. I would like to run > > the files through automatically. Does anyone have a batch file t do this for > this system? > > Thanks > Mary Ellen > > -- > Gene Nelson, Ph.D., Biophysics Company (Pen Based Computing and > Science Advocacy), 7374 Brookside Parkway, Cleveland, Ohio, USA > 44130 - 5468 Phone [Voice/Data/FAX] (216) 891 - 8809 > Internet Address (same as above!): Reply-To: au195@po.CWRU.edu > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator > OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net > CHEMISTRY-SEARCH@ccl.net --- search the archives, read help.search file first > --- For the benefit of those other readers of the OSC chemistry mailing list who may also be doing something similar, here is a TCL record script that can be adapted. This will be a part of the upcoming Quanta update. Please note that I am >not< on this mailing list, and I was only made aware of this message from a friend who forwarded it to me. Questions about MSI products should be sent to hotline@msi.com. -------cut here------ * QUANTA script that automates the process of performing MOPAC * calculations on a number of molecules. It reads in all the MSF * files in the current directory and sends them to MOPAC. * This procedure illustrates the TCL commands foreach, glob, and proc. It * also shows how to obtain the root name of a file using the set and file * commands. * qm opens an MSF file and performs a MOPAC calculation on it !proc qm {molecule} { mole open $molecule.msf exec mopac > CALC > title "MOPAC calculation " > PM3 > zmatauto > dummy 0 > symmetry 0 > charge 0 > options 0 > ok > NONE > $molecule.ain > ok > WAIT > report 0 > conf 0 > coord 1 > charge 1 > csr 0 > dipole 0 > map 0 > clean 0 > ok > OVER > exit mole remove } * loop over all .msf files in the current directory !foreach file [!glob *.msf] { !set ext [!file rootname $file] !qm $ext } -------cut here------ -- ******************************************* * * * MOLECULAR SIMULATIONS HOTLINE SUPPORT * * 16 New England Executive Park * * Burlington, MA 01803-5297 * * Tel (617) 229-8879 / 1-800-756-4674 * * FAX (617) 229-9092 * * E-Mail hotline@msi.com * * * *******************************************