From CUNDARIT@MSUVX1.MEMST.EDU Sun Aug 11 16:58:27 1993 Date: 11 Aug 1993 22:58:27 -0600 (CST) From: CUNDARIT@memstvx1.memst.edu Subject: aromatic amine To: chemistry@ccl.net Message-Id: <01H1MWRSDG8G9AO2SV@MSUVX1.MEMST.EDU> Sorry for the bandwidth guys, but I have to ask a repeat question. A while back, I asked about which of the MOPAC Hamiltonians was best for aromatic amines. As I recall, Doug Smith and co. had a paper in some journal, but I can't recall the ref. If any body has seen the paper, the ref would be most useful. Tom Cundari From szilagyi@miat0.vein.hu Thu Aug 12 12:27:18 1993 Date: Thu, 12 Aug 93 10:27:18 +0200 From: Szilagyi Robert Message-Id: <9308120827.AA15227@miat0.vein.hu> To: chemistry@ccl.net Subject: semi-empirical parameters Dear Netters, I'm interested in the bibliographic references of the parametrization of MNDO, AM1 semi-empirical methods on the first (or/and second) row transition metals, exspecially Cr and its neighbours. Has anyone a summary about this topic ? Thanks for every answer, Robert C. Szilagyi Dept. Chem. Univ. Veszprem Hungary szilagyi@iris.inc.bme.hu From schuetz@ips.id.ethz.ch Thu Aug 12 12:59:07 1993 From: Martin Schuetz Message-Id: <9308120900.AA25781@sitter> Subject: Re: nice? To: JKONG@ac.dal.ca Date: Thu, 12 Aug 1993 10:59:07 +0200 (MET DST) > > Dear netters, > > This query has been posted twice on newsgroup comp.unix.aix but > no response yet. > > The commands "nice" and "renice" seemingly do not work on our two > ibm risc/6000's(580 and 355). The commands we tried are > > renice 20 pid > /usr/bin/nice -n 15 job > nice +15 job (csh) > > The speed of the jobs simply were not affected in the existance of > other jobs. > > And also we don't know how to schdedule the queues. The queues we > use now are printer queues. We want a couple of queues with different > priorities to meet the demands of different types of jobs. > > We would very appreciate any suggestions. > I would recommend you to run your low priority jobs at FIXED low priority. Code to set a running job at (low) fixed priority is included in this mail. From iacrs2.unibe.ch, PD NQS source code for the RS6K is available which Hope this helps... ---cut here #include #include main(int argc, char *argv[]) { pid_t procid; int prio,oldprio; if (argc==3) { sscanf(argv[1],"%d",&procid); argc--; argv++; sscanf(argv[1],"%d",&prio); argc--; argv++; } else { printf("Enter PID: "); scanf("%d", &procid); printf("-> %d\n", procid); printf("Enter Priority: "); scanf("%d", &prio); }; if (prio<120) { printf("prio %d not fixed priority, not in range 120-127",prio); exit(1); } oldprio=setpri(procid,prio); if (oldprio>-1) printf("pid %d: %d -> %d\n", procid,oldprio,prio); else printf("error occured setting %d to %d\n",procid,prio); } -- Martin Schuetz Phone: +41 1 256 55 66 Interdisciplinary Project Center FAX: +41 1 261 04 68 for Supercomputing, ETH Zuerich Switzerland E-mail: schuetz@ips.id.ethz.ch or mgs@ips.id.ethz.ch From DSMITH@uoft02.utoledo.edu Thu Aug 12 04:18:01 1993 Date: Thu, 12 Aug 1993 09:18:01 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: aromatic amine To: CUNDARIT@memstvx1.memst.edu Message-Id: <01H1NIEZOAJ60005AM@UOFT02.UTOLEDO.EDU> The reference is: D. A. Smith, C. W. Ulmer, II, M. J. Gilbert, "Structural Studies of Aromatic Amines and the DNA Intercalating Compounds m-AMSA and o-AMSA: Comparison of MNDO, AM1, and PM3 to Experimental and Ab Initio Results," J. Comput. Chem. 1992, 13, 640-650. The simple answer to Tom's question is that AM1 reproduced geometries best. This paper has generated more interest than anything else we have published in the past two years. Reprints are available - email me your address. Doug Douglas A. Smith Assistant Professor of Chemistry and of Medicinal and Biological Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From rrk@iris3.chem.fsu.edu Thu Aug 12 06:07:58 1993 Date: Thu, 12 Aug 93 10:07:58 -0400 From: rrk@iris3.chem.fsu.edu (Randal R. Ketchem) Message-Id: <9308121407.AA07775@iris3.chem.fsu.edu> To: CHEMISTRY@ccl.net Subject: Re: NMR chemical shift refinement >I am actually writting up my PhD thesis on the determination of biomolecular >structures by NMR. I would like to include something about >structure refinement based on chemical shift information. >Does someone know some recent references on this subject? [stuff deleted] Ketchem, Hu and Cross have a paper accepted in Science which should be out in September. "High-Resolution Conformation of Gramicidin A in a Lipid Bilayer by Solid-State NMR". The structure was determined by using oriented chemical shift, chemical shift tensor magnitudes and orientations, N-H dipolar splittings and N-C dipolar splittings. The structure was refined to optimize the intramolecular hydrogen bonds while not deviating from the experimental data by a technique developed in this lab. The technique relies heavily on the chemical shift information. Send email to the address below for more information on the refinement technique. Randal R. Ketchem Institute of Molecular Biophysics 904.644.7798 (voice) Florida State University 904.644.8281 (FAX) Tallahassee, FL 32306-3015 rrk@sb.fsu.edu (email) From ramon@ce.ifisicam.unam.mx Thu Aug 12 04:55:41 1993 Message-Id: <199308121556.AA20418@oscsunb.ccl.net> From: Ramon Garduno Subject: Summary on Cremer-Pople inquiry To: chemistry@ccl.net (POST MSGS) Date: Thu, 12 Aug 93 9:55:41 CDT Hi netters: I am in debt with all of you that responded to my query about Cremer-Pople parameters and how to calculate them. In turn, I send to you this summary of responses. I have edited some of them in the sake of space. ---------------------------------------------------------------------------- The module CARNAL (Bill Ross, UCSF, ross@cgl.ucsf.edu), which is not yet a standard module of the AMBER package, can calculate the Cremer-Pople puckering. Cheers, Vidana C. Epa Biomolecular Research Institute, 343 Royal Parade, Parkville, Victoria 3052, Australia. e-mail: vepa@tigger.mel.dbe.csiro.au tel : (61) - 3 - 342 - 4300 fax : (61) - 3 - 342 - 4301 ---------------------------------------------------------------------------- I wrote a copy of the pucker program myself that you are welcome to. The only problem I have ever had was reproducing the phase values. They depend on the ORDERING of the coordinates in the file. That is, if you give the ring as C1-C2-C3-C4-C5-O5 you will get a different phase value than if you list it O5-C1-C2-C3-C4-C5 etc. All the amplitudes are correct. If you play with the input you will get the published values. I do not think this is an error in the program. It is just a feature of the math. Good luck Rob Woods Robert J. Woods, Ph.D. Glycobiology Institute Department of Biochemistry University of Oxford South Parks Road Oxford, OX1 3QU PROGRAM SOURCE DELETED SINCE I DO NOT KNOW Y ROB WANTS IT IN THE PUBLIC DOMAIN __________________________________________________________________________ There is a program with name "Ring" available via QCPE. The QCPE-Program No. is 110. It was developed by Dieter Cremer. It reads X-ray or cartesian coordinates in. You' ll get the puckering coordinates, dihdral angles, bondangles and a distance matrix. I am using this PC-program for several weeks succesfully. Ciao Antje Hoellwarth __________________________________________________________________________ I haven't used that method, but I have "programmed" the Altona/Sundaralingam method and the method in Saenger into my spreadsheet (WingZ, Mac II) without any problems. I didn't think that the Cremer-Pople version was that more difficult? Leonore Leonore A. Findsen |owned by: College of Pharmacy |Pico: DS B Y 11 L+ C+ T I+ F+ H A- S V University of Toledo |Smokey:DM Bd X 10 L+ C+ T I+ F+ H A- S V+++ INTERNET: LFindse@uoft02.utoledo.edu|Catcode by Eric Williams:wd6cmu@netcom.com VOICE: (419) 537-2729 | FAX: (419) 537-4940 |usual disclaimers apply __________________________________________________________________________ There is a code called mdXvu available from the quantum chemistry program exchange (QCPE) that calculates cremer pople parameters for 5 and 6 membered rings. The program accepts PDB files as input and is graphical and intercative. It should compile and run on any system supporting X11. Just load the molecule, display it, enter the command cpp6 for a 6 membered ring and pick the atoms O5,C1,C2,C3,C4,C5 to get the CP parameters. Please contact Richard counts at QCPE (countsr@ucs.indiana.edu) for full details. I wrote this code, but since I now work for a commercial modelling company I dont support it ! Bye for Now Mark J Forster __________________________________________________________________________ Song Liu's message was deleted because his program is not released yet! __________________________________________________________________________ -- ________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA, UNAM || bitnet: rgard@unamvm1 Lab. de Cuernavaca || email: ramon@ifisicam.unam.mx Apdo. Postal 139-B || 62191 Cuernavaca, Morelos || FAX: (73)173077 MEXICO || (73)111603 ______________________________ EOF _____________________________________ From ramon@ce.ifisicam.unam.mx Thu Aug 12 04:57:12 1993 Message-Id: <199308121558.AA20438@oscsunb.ccl.net> From: Ramon Garduno Subject: Summary on LogP inquiry To: chemistry@ccl.net (POST MSGS) Date: Thu, 12 Aug 93 9:57:12 CDT Hi netters: I thank all of you that responded to my inquiry about LogP calculations. In turn, I send to you this summary of responses. I have edited some of them in the sake of space. __________________________________________________________________________ It depends on what you want to do with the logP value. The CompuDrug and Daylight Chemical Information (MedChem) software vare both fairly expensive. A good inexpensive (US$200) option is the Hint! program of Abraham and Kellogg (Virginia Commonwealth University). Glen Kellogg can be reached by email (gkellogg@gems.vcu.edu). It can also plot lipophilicity contours around molecules and can create lipophilic fields for use in CoMFA. Cheers, Dave Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. __________________________________________________________________________ I have been interested in the log(P) calculators but also have had difficulty getting information. Also, I'm not sure how accurate they are. When I need to calculate a log(P), I usually do it "by hand" from the data provided by Rekker in his "Hydrophobic Fragmental Constant" work. I am well versed in the method and find it generally gives good answers. We have published a couple of papers with this approach. I'll give you the references in case they might be useful to you: "Development of Hydrophobicity Parameters to Analyze Proteins Which Bear Post- or Cotranslational Modifications", Black, S.D., and Mould, D.R. (1991) Anal. Biochem. 193, 72-82. "Development of Hydrophobicity Parameters for Prenylated Proteins", Black, S.D. (1992) Biochem. Biophys. Res. Commun. 186, 1437-1442. Cheers, =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= __________________________________________________________________________ One package for calculating LogP is Polaris from Molecular Simulations Inc. This program employs the protein dipole-Langevin dipole method of Arieh Warshel. This method has been successful in calculating free energies of solvation, free energies of binding, delta pKa, and LogP values. Nick Reynolds Molecular Simulations Inc. 16 New England Executive Park Burlington, MA 01803-5297 USA 1-617-229-9800 __________________________________________________________________________ You can reach compudrug sales person Harlod Borgsted at (716) 292-6830. I think that this is a New York number. By the way, we have the ProLogP software and would like to comment on a few items. First, It may be limited in that some compounds containing unique fragments will not compute with this software. The method is a fragment addition method where it splits your compound into parts that it has in it's datbase and then adds up the LogP values. Also, Charged compounds and some particular ringsystems cannot be used. And most importantly, isomers are given the same LogP values. Example- move a hudroxyl para, ortho or meta on an aromatic group. The log P will be the same! Or move a hydroxyl around a steroid ring, all will have the same LogP. We compaired to the Daylight Chemical LogP stuff (much more expensive) and found similar limitations. The values were not the same (even close to each other) between the packages). So. for use in QSAR, we do not use either of these. We have found a LogP method that works from the atom level rather than the fragment level and have used it to some extent. It handles all compounds but still has the isomer problem. Contact: Arup K. Ghose at Sterling Winthrop Research group, 81Columbia Turnpike, Rensselaer, NY, 12124 phone: (215) 983-5499 Ref is: J. Med. Chem. 1991, around Jan 17 or so. (sorry I don't have exactly) He developed the software and should give you a copy if you send a tape. Contact him first to set up arrangement. Good luck, Tom PS see the Hansch paper of a few months ago to review usefullness of logP. Debnath, A. K.; Hansch, C.; Kim, K. H.; Martin, Y. C. Mechanistic interpretation of the genotoxicity of nitrofurans (antibacterial agents) using quantitative structure-activity relationships and comparative molecular field analysis. Journal of Medicinal Chemistry. 1993 Apr 16; 36(8): 1007-1016. ################################################## Tom Wiese Department of Biochemistry Wayne State University School of Medicine 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-5605 FAX: (313) 577-2765 email: tom@sgih.roc.wayne.edu ################################################## -- ________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA, UNAM || bitnet: rgard@unamvm1 Lab. de Cuernavaca || email: ramon@ifisicam.unam.mx Apdo. Postal 139-B || 62191 Cuernavaca, Morelos || FAX: (73)173077 MEXICO || (73)111603 ______________________________ EOF _____________________________________ From muino@nitrogen.oscs.montana.edu Thu Aug 12 06:54:04 1993 Date: Thu, 12 Aug 1993 12:54:04 -0600 (MDT) From: Pedro Muino Subject: Conformers of tryptophan To: lista quimica Message-Id: Dear netters: I am trying to find a reference for any ab initio study of rotational conformers of tryptophan, but I had no luck so far. Can anybody provide some information?? Thanks, Pedro From jkl@ccl.net Thu Aug 12 10:29:03 1993 From: Jan Labanowski Date: Thu, 12 Aug 1993 14:29:03 -0400 Message-Id: <199308121829.AA07539@krakow.ccl.net> To: INFORMATION@ccl.net, ABOUT@ccl.net, COMPUTATIONAL@ccl.net, Subject: re re: comp chem newsletter INFORMATION ABOUT COMPUTATIONAL CHEMISTRY LIST. PLEASE... READ IT CAREFULLY. I. WHAT IS THE COMPUTATIONAL CHEMISTRY LIST? The COMPUTATIONAL CHEMISTRY LIST is an e-mail exploder which allows computational chemistry researchers to exchange information and experience. It was created to promote contact between researchers involved in chemistry-related computation. This list is not restricted to any particular chemistry software or methodology and anyone is welcome to subscribe. It works on the principle, "WHAT ANYBODY POSTS, EVERYBODY GETS." All posting to this list is archived and available for downloading as described below. The list of subscribers, however, will not be made available. Examples of topics for the list are: - reports on bugs in chemistry software and possible work- arounds - new chemistry software announcements - announcements of computational chemistry-related workshops and symposia - new methods and techniques in computational chemistry - questions and answers about solving computational chemistry problems - programs and utilities - information on the availability of particular software, data, etc. - hardware-related issues relevant to the computational chemistry community - opinions about services and products Examples of topics which SHOULD NOT appear on this list are: - personal attacks - topics unrelated to computational chemistry - announcements of "vaporware" - annoucements of job openings or CV's. These are handled off line (see point V for more information). - address inquiries (you can post address inquiry only when you exhausted all other ways (i.e., looking up ACS Directory of Chemistry Departments in your library, contacting list coordinator, contacting the Postmaster at the target machine) Rules for commercial software announcements are described later in this file. II. HOW TO SUBSCRIBE/UNSUBSCRIBE. To subscribe (or to unsubscribe) to the Computational Chemistry List, send a short e-mail message to CHEMISTRY-REQUEST@ccl.net or CHEMISTRY-REQUEST@oscsunb.ccl.net stating your name, affiliation and electronic mail address. You can also send these directly to jkl@ccl.net or JKL@OHSTPY.BITNET. Please, DO NOT SEND THESE MESSAGES TO EVERYBODY. III. HOW TO POST TO THE COMPUTATIONAL CHEMISTRY LIST. The list is uncensored, i.e. nobody screens the messages before they are posted. The machine delivers them automatically. Before you post to the list, be sure that your message is correct (use editor!) and adheres to the rules. Use lines shorter than 80 characters since many mailers truncate longer lines. Remember that what you post will be received by many people in many countries. However, do not feel overly paralyzed about this. Communication is a two-way street. Be concise though. Not everybody has superworkstations connected to a high-speed network. However, do not be overly concise. If you have a question to the list, describe your problem, and why you need it --- try to educate and be educated. Also, summarize to the list the responses you got. We want to know what you know. The most important part of your posting is the "Subject:" field. Your message will not be accepted by the list without it. If you do not know how to create a Subject: field in your message, ask your system administrator. If your computer system is unable to create it, contact the list coordinator (chemistry-request@ccl.net) and it will be posted for you. The Subject: should not be longer than 40 characters. People screen incoming e-mail by the "Subject:" line, so make it clear. If you are posting a long file (e.g. a program), please split it into chunks which are smaller than 50 kBytes. Always identify part number and total number of parts in the "Subject:" line (e.g. NiceDraw Part 2 of 5). To post an article to the the list just send your electronic mail to CHEMISTRY@ccl.net or CHEMISTRY@oscsunb.ccl.net the way you normally do. It will be automatically distributed to all subscribers. However, remember that you might not get a copy of your own post since many mailers suppress messages with the same From: and To: lines. To ensure getting your own post place your own e-mail address on the Cc: line or ask your system manager for help (depending on the system, some e-mail defaults needs be changed). If you are not sure that your post is successful, or if you have problems or suggestions, contact us first at: chemistry-request@ccl.net or jkl@ccl.net or JKL@OHSTPY.BITNET or chemistry-request@oscsunb.ccl.net. We are here to help you. IV. COMMERCIAL SOFTWARE ANNOUNCEMENTS. Commercial Software - software that was sold to anyone for more than the cost of handling and documentation (up to few hundreds dollars). Commercial Posting - commercial software advertisements posted by the people who develop or sell the software. Postings responding to user questions, as well as bug reports, requests for comments, and tips on efficient software use are not considered commercial postings and are highly encouraged. Commercial software reviews or evaluations conducted by people not associated with the software vendor/developer are also encouraged. Rules for Commercial Postings: Short (25 lines or less) commercial postings are allowed. They should include a straightforward "Subject:" line. Reposts are not allowed unless new features/releases become available. Please make them informative, since they are useless otherwise. Announcements of "vaporware" (software that is not yet working or available) are not allowed in any form. You can submit commercial postings of any length to list owners at chemistry-request@ccl.net or chemistry-request@oscsunb.ccl.net List owners will make these available for automatic download and will periodically post the index with such announcements. V. EMPLOYMENT (POSITIONS OFFERED AND WANTED) To limit traffic on the list to matters of general interest the announcements of positions wanted and positions offered will be handled off line. Simply, instead of sending them to CHEMISTRY@ccl.net you will send them to CHEMISTRY-REQUEST@ccl.net (or jkl@ccl.net or JKL@OHSTPY.BITNET). I will be collecting these announcements in files: positions.wanted and positions.offered which can be obtained from our archives (see Part VI. ARCHIVES). I will try to post a short summary of these files from time to time. Please include the description of position offered/wanted, degree needed/acquired, salary, contact address, etc. The announcements can be any length, but remember that people do not read lengthily essays. When the offer is no longer current, please send me a request to remove it from the archive (to chemistry-request@ccl.net or JKL@OHSTPY.BITNET). VI. ARCHIVES OF THE COMPUTATIONAL CHEMISTRY LIST. You can retrieve index, previous postings, free software, positions wanted and offered, and the help file through electronic mail by sending a simple message to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET. You can also ftp to the archives as described later. The body of your message should consist of one or more lines having the following format (only lowercase letters !!!): send from chemistry Substitute with one of the items given below: help - this text index - digest of "From:" and "Subject:" lines from postings for the current year (i.e., 1993), file names where you can find the original postings. directory - directory of all files in the archive with sizes index.91 - as index but for old posting for 1991. index.92 - as index but for old posting for 1992. software - index to free software in our archives index.software - similar to index above but for software announcements which did not appear in the general distribution ("commercial software announcements") positions.wanted - positions wanted (i.e., people looking for a job) positions.offered - positions offered (i.e., jobs available) yy/mm/dd - postings for a given day yy/mm/dd.software - longer (commercial) software announcements which were not generally distributed (see rules for commercial postings above) For example, to get this help file send a line: send help from chemistry The postings are organized in files named after the day of original contribution in the format yy/mm/dd For example, the first general posting to the list appeared on January 11, 1991, and so its code is: 91/01/11 To get it, you would simply send a line: send 91/01/11 from chemistry The software announcements are coded similarly, e.g.: send 91/02/06.software from chemistry Before you request individual postings, it is a good idea to get the index, for example: send index from chemistry - or - send software from chemistry The index and archives are updated almost daily. If you need something urgently, and it is not available yet, contact us directly at jkl@ccl.net or JKL@OHSTPY.BITNET or jkl@oscsunb.ccl.net Also, archive retrieval details will probably change in the future, depending on volume. If something does not work, download the help file first. It will always contain updated information. Also remember that you can send as many requests as you wish within a single e-mail message to oscpost@ccl.net or OSCPOST@OHSTPY.BITNET or oscpost@oscsunb.ccl.net A good place for starters is: send help from chemistry send index from chemistry send software from chemistry send directory from chemistry These files can also be obtained from anonymous ftp at www.ccl.net (or 128.146.36.48). Here is how you get them using ftp: ftp www.ccl.net (or ftp 128.146.36.48) login: anonymous password: your_e-mail_address (please !) ftp> cd pub/chemistry ftp> ls -l (to get the listing of all files which are there) ftp> get file_you_want (e.g. get index) ftp> quit Of course, you need to know ftp to use it efficiently. Here are some more popular commands: ascii - set text mode (for text files) binary - set binary mode (for binary files) - very important if you retrieve compressed (*.Z) or tar files. cd - change directory get - get a file from the remote machine to your current directory (no * allowed in the name) glob - toggle (glob/noglob) the use of wildcard character (*) in filenames help - list commands of ftp ls - list files in the current directory mget - get all files fitting the pattern (* allowed) prompt - toggle asking (yes/no) for each file in mget command pwd - tells in which diretory you are now quit, bye - end the ftp session For example, to get a file with messages posted between June 20 and 29 of 1992 you would do: ftp www.ccl.net (or ftp 128.146.36.48) login: anonymous password: your_e-mail_address (please !) ftp> cd pub/chemistry/92/06 (all files for June 92 reside there) ftp> ascii (messages are text files) ftp> glob (you do not want to be asked for each file) ftp> mget 2* (will get 20, 21, ... 29) ftp> quit (bye, bye... www.ccl.net) VII. SEARCHING THE FILES IN THE ARCHIVES BY KEYWORDS The archives can be search by keywords, regular expressions, etc. Since the syntax of the search queries is complex (though not difficult), the search procedures are described in a separate file: help.search To retrieve information of searching the archives of the list, send a one line message: send help.search from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET or retrieve file help.search from the anonymous ftp on www.ccl.net in directory /pub/chemistry. VIII.DISCLAIMERS. The list is organized as a service to computational chemistry researchers and is not aimed at monetary gains of lawyers. By posting to this list you agree that the content represents your personal opinion. In no event should Ohio Supercomputer Center (OSC) be liable for the opinions or materials posted. The OSC is not reviewing the materials submitted to this list and cannot stop their distribution. The software and messages distributed by the Computational Chemistry List come without any warranty. They may be perfect or totally wrong, and if you decide to use it, you do it on you own risk. List owners: David J. Heisterberg (djh@ccl.net, DJH@OHSTPY.BITNET, ph. 614-292-6036) Jan K. Labanowski (jkl@ccl.net, JKL@OHSTPY.BITNET, ph. 614-292-9279) Ohio Supercomputer Center 1224 Kinnear Rd Columbus, OH 43212-1163 FAX: 614-292-7168 From xlh@wag.caltech.edu Thu Aug 12 07:28:57 1993 Date: Thu, 12 Aug 93 14:28:57 -0700 From: Xinlei Hua Message-Id: <9308122128.AA15368@sgi1> To: chemistry@ccl.net Subject: sum up of chem eq. software Dear Netters, Thank you very much for the responses to my inquiry about the softwares that can write chemical equations. Below is a summary of the responses I got. Also I included e-mail address of those who responded in the bracket as sources and wish to express my thanks to them. REACCS (Molecular Design) (after: marc@david.saclay.cea.fr) CAMEO program from Bill Jorgensen's group for organic reactions. (after: jas@medinah.atc.ucarb.com (Jack Smith)) and (after: dave@terminus.chem.yale.edu) SECS system which was developed by Todd Wipke at UC Santa Cruz (wipke@secs.ucsc.edu) (after: dave@carbon.chem.csiro.au) A Hypercard stack called MacElements Utilities 1.01 and is on the sumex macintosh archive (ie only for Mac). (after: rzepa@ic.ac.uk) ************************************* Xinlei Hua 139-74 Beckman Institute Caltech Pasadana, CA 91125 (818)395-2723 ************************************* From stoutepf@lldmpc.dnet.dupont.com Thu Aug 12 13:57:10 1993 Date: Thu, 12 Aug 93 17:57:10 -0400 Message-Id: <9308122157.AA07816@esds01.es.dupont.com> From: stoutepf@lldmpc.dnet.dupont.com (Pieter Stouten, +1-302-695-3515) To: "chemistry@ccl.net"@esds01.dnet.dupont.com Subject: Conformations of phenyl sulphonyl amides I am interested in the different conformations that phenyl sulphonyl amides (C6H5-SO2-NH-R) can adopt. I would appreciate any references to this topic, e.g. ab initio, semi-emperical calculations, crystal structure analyses, etc. Thanks in advance, Pieter. Pieter Stouten Computer Aided Drug Design Group The Du Pont Merck Pharmaceutical Company Phone: +1 (302) 695 3515 ARA/Fax: +1 (302) 695 4324 E-mail: stoutepf@chemsci1.es.dupont.com E-mail: stoutepf@lldmpc.dnet.dupont.com From B_DUKE@DARWIN.NTU.EDU.AU Fri Aug 13 10:59:53 1993 Date: Fri, 13 Aug 1993 10:59:53 GMT From: B_DUKE@DARWIN.NTU.EDU.AU (Brian Duke) Message-Id: <930813105953.f53f@DARWIN.NTU.EDU.AU> Subject: G92 and NQS - problem solved. To: CHEMISTRY@ccl.net G'day, comp chem netters. The problem I had with NQS and Gaussian92 on a RS6K is solved. You need to go into the nqs utility qmgr and set data_limit = ( unlimited ) 'queue name' This is the per process maximum data segment size limit. Nobody seems to know why this happens, but it works. Anyone with any ideas? My thanks go to several people for their responses, but particularly to Kent Milfield from Texas and David Mosley from Namur, Belgium, both of whom solved the problem, and to Doug Fox from Gaussian who constantly kept pointing me in the right direction and has been most helpful in many areas. My final script to run g92 is:- #!/bin/csh # # Submit a Gaussian 92 job to an nqs batch queue. # # $1 -- name of input file. # # GAUSS_WORK should be set in your .login to your # working directory for G92 # cd $GAUSS_WORK # cat <$1.job cd $GAUSS_WORK g92 <$1.com >$1.log END # echo Now submit it. # qsub -q molecule -nr -eo -r $1 -x -o $1.batch-log $1.job # molecule is the only queue I want to use, but this could # be an argument rm $1.job One problem with the subg92 file from Gaussian is that it only works if the data *.com file is in your home directory. The variable GAUSS_WORK gets over this problem. It is setenv'ed in .login. The script (I call it sub_g92) can be put anywhere on your path. The use of extra arguments as in subg92 can easily be added to the script above. It is also a good idea to add ENVIRONMENT=NONBATCH in /etc/environment. This sets the variable before entering .cshrc and .login. You can then use if (ENVIRONMENT != "BATCH" ) then .. endif to set any commands that use the terminal or are otherwise not needed in the NQS call. NQS sets ENVIRONMENT to BATCH, but it is not set otherwise. Here in Darwin, Northern Territory, Australia, I am at least 2000 km from the nearest computational quantum chemist (except Mike McKee from Auburn who is currently visiting for a few days and has just gone out doing the tourist thing in Kakadu!). The Ohio list really helps to get over the "tyranny of distance". Thanks, folks! Regards, Brian Brian Salter-Duke (Brian Duke) School of Chemistry and Earth Sciences, Northern Territory University GPO Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 FAX 089-410460 E-mail B_DUKE@DARWIN.NTU.EDU.AU From ipcakc@vigyan.ernet.in Tue Aug 13 03:28:24 1993 To: CHEMISTRY@ccl.net Subject: hexatriene Date: 13 Aug 93 08:28:24 EST (Fri) From: ipcakc@vigyan.iisc.ernet.in Message-Id: <9308130828.AA20568@vigyan.iisc.ernet.in> Dear netters Can anyone out there will let me know the amoount of work that has been done on 1,3,5hexatriene and cyclohexadiene, specifically ab initio. I have finished a portion of the calculations namely rearrangement and in the stage of finishing the isomerisation. Please let me know about it . Sumathy department of inorganic and physical chemistry indian institute of science bangalore 560 012 india  Thanking you in advance.