From chemistry-request@ccl.net Thu Aug 13 00:10:35 1992 From: hyper!slee (Thomas Slee) Subject: HyperChem Users' E-Mail Group To: chemistry@ccl.net Date: Wed, 12 Aug 1992 17:21:55 -0400 Status: RO HyperChem users' e-mail group ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A HyperChem users' e-mail group has been put in place by Autodesk. The e-mail group is designed primarily for, but not limited to, HyperChem users. Any and all scientific and technical issues related to the use of HyperChem are appropriate for discussion on this group, and we hope that it will become a valuable resource for HyperChem users. News and developments concerning HyperChem will also be posted to this group. The group is unmoderated, so that any message sent to the group is sent automatically to all other members of the group. As usual, any information on this group is to be taken "as is" without representation or warranty of any kind, either express or implied. The entire risk as to the use of this information is assumed by the user. ADDRESSES TO USE ================ To be added to or removed from the group, please mail to hyperchem-request@autodesk.com To post a message to the group, please mail to hyperchem@autodesk.com. Karyn Kambur (Autodesk) and Tom Slee (Hypercube), Group administrators. --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Aug 13 05:47:42 1992 Date: Wed, 12 Aug 92 18:36:49-1795 From: Dr. James Stewart To: chemistry@ccl.net Subject: WARNING_message_in_MOPAC Status: R Recently, Rafael G. Ramirez inquired about the enigmatic message ` WARNING -- GEOMETRY IS NOT AT A STATIONARY POINT' which sometimes appears in the MOPAC output. This message is not explained in the MOPAC manual. Here is a brief explanation, taken >from the next MOPAC manual. Sometimes GNORM may be very small and at the same time the geometry might not be at a stationary point. This can easily happen when (a) less than (3N-6) coordinates are flagged for optimization, (b) SYMMETRY has been used incorrectly, or (c) (less common) only (3N-6) coordinates are flagged for optimization and dummy atoms are used. If any one of these three conditions, occurs, then the warning message, ` WARNING -- GEOMETRY IS NOT AT A STATIONARY POINT' will be printed. A less common, but not unknown, situation arises when internal coordinates are used. In this strange situation, the internal derivatives might all be zero, but the Cartesian derivatives are large. An example of such a system is given here: geo-ok GRADIENTS 1scf DEBUG DCART Formaldehyde, for Demonstration Purposes O 0.0000000 0 0.000000 0 0.000000 0 0 0 0 C 1.2075307 1 0.000000 0 0.000000 0 1 0 0 H 1.2109988 1 103.394948 1 0.000000 0 2 1 0 H 1.0903826 1 180.000000 1 -90.000000 1 2 1 3 In this strange system, the bond-angle of the second hydrogen is 180 degrees, and the dihedral is 0 degrees. Obviously, the derivative of the dihedral will be zero. The derivative of the angle is not so obvious. If the angle changes, then the fourth atom will move out of the plane of the other three atoms, therefore the energy will change in the same way regardless of whether the angle increases or decreases, therefore the derivative of the angle must be zero. Because of the unusual nature of this type of system, users may be unaware of the danger. If such a system is detected, a warning will be given and the job stopped. For all other cases, the ` WARNING -- GEOMETRY IS NOT AT A STATIONARY POINT' message will be printed on completion of the calculation. I hope this is of some help. Several MOPAC users have sent me reports of errors in the program; these will be corrected in MOPAC 7. However, in order to help maintain a useful program, if you know of bugs in MOPAC, please send them (the bugs that is) to me at "jstewart@fai.com". Bugs are welcome, bug fixes are welcome, and comments regarding the Manual (what is vague, inaccurate, or missing) are welcome James J. P. Stewart --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Aug 13 07:52:55 1992 Date: Thu, 13 Aug 92 10:18:33 CET From: To: Status: R Dear netters, I am just beginning my work on dynamik NMR. Are you know any computer programs on that topic ? I only know the programs DNMR3 and DNMR5 from QCPE. Perhaps you can tell me, where I can get other programs and what it costs. I am glad to hear from you soon. Thank you very much ! Rainer Fuhler. ******************************************************************************** Rainer Fuhler Heinrich-Heine-University Duesseldorf Institute for Inorganic Chemistry 1 Universitaetsstr. 1 W-4000 Duesseldorf Germany Internet : fuhlerr@ze8.rz.uni-duesseldorf.de ******************************************************************************** --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Aug 13 13:25:02 1992 Date: Thu, 13 Aug 92 08:32:00 CDT From: sam@ncsa.uiuc.edu (Sam Milosevich) To: chemistry@ccl.net, defrees@almaden.ibm.com Subject: lists of lists Status: R > Date: Wed, 12 Aug 92 09:00:16 PDT > From: "Doug DeFrees" > To: chemistry@ccl.net > > Is there anywhere a list of lists? ... If you know of a > public list or forum or newsgroup that directly addresses chemistry or > physics please send a note to the list. USEnet net-news groups directed to chemistry and physics include the following. sci.chem sci.physics sci.engr.chem sci.physics.fusion bionet.* sci.med.physics Also, see USEnet newsgroup "news.lists" for postings on Publicly Accessible Mailing Lists by spaf@cs.purdue.EDU (Gene Spafford) List of Periodic Informational Postings by jik@athena.mit.edu (Jonathan I. Kamens) You could also check the USEnet "news.announce.newusers" conference. ---Sam * Sam Milosevich, Research Scientist, Eli Lilly and Company * * Phone: +1-317-276-9118; FAX: +1-317-276-5431 (attn: Sam) * * E-mail: sam@ncsa.uiuc.edu (NCSA Partners), sam@lilly.com * * X.400: G=Samuel; S=Milosevich; P=Lilly; A=ATTmail; C=US; * --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Aug 13 15:17:49 1992 Date: Thu, 13 Aug 92 17:14:09 +0200 From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) To: chemistry@ccl.net Subject: Molecular Graphics and the Design of Bioactive Compounds Status: R Preliminary Announcement: /--\ ================================ \--/ || ... Molecular Graphics Society \ / \ : : \ / \. ... : 12th Annual Conference | . . : | . ...: ================================ / \ / : : / \ / :..: || Interlaken, June 8-11, 1993 /--\ SWITZERLAND \--/ Molecular Graphics and the Design of Bioactive Compounds The conference will focus on molecular graphics applied to the design of bioactive compounds. Methods, applications, and the most recent research in this exciting area of computational chemistry will be presented. The preliminary program will be distributed in the 1st Circular October '92. Interlaken is a beautiful place located in the swiss alps. Besides the scientific program, touristic facilities are provided. Contact: Dr. H.P.Weber Tel. +41 61 324 4343 Sandoz Pharma AG Fax. +41 61 324 2686 CH 4002 Basel SWITZERLAND electronic Mail mgs@comp.bioz.unibas.ch +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Aug 13 16:34:57 1992 Date: Thu, 13 Aug 92 09:52:09 PDT From: d3f012@gator.pnl.gov Subject: Argus bug report To: chemistry@ccl.net Status: R Argus users: Bug: Greg Schenter (Pacific Northwest Laboratory) reports that data files without the "savescf" used (in the $control block) will flag an error in the properties driver when the program is looking for a .scf file The error message looks like: ** FATAL ERROR ** SCFRead : reading rank returned stat 0 should be 4 errno = 0 Exiting Program The program's standard default had the savescf variable set to FALSE, when it should have been TRUE. The default behavior of Argus should be to save the SCF at least once, at the end of the SCF. Fix: simply include "savescf xxx" (where xxx is some number) in all your data files. Using xxx as a very large number will simply cause the program to save the SCF every xxx SCF cycles, or once at the end of the SCF, whichever comes first. ie: make sure all you data decks have something like the following: $control ... savescf 1000 ... $end Obviously, for larger more expensive calculations, you may always opt to save the SCF more frequently, like every 5 cycles. I'll be updating all executables and user documentation to reflect this soon. Since this bug can be circumvented by a simple data deck change, I'll wait until the next minor revision to include this fix in the code. Mark Thompson Pacific Northwest Laboratory internet: d3f012@pnlg.pnl.gov voice : 509-375-6734 FAX : 508-375-6631 --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Aug 13 16:43:26 1992 Date: Thu, 13 Aug 92 12:58:19 -0400 From: dchin%emperor@harvard.harvard.edu (Donovan Chin) To: chemistry@ccl.net Subject: CHARMM bulletin board Status: R Dear Netters; There is now a bulletin board service (bbs) for users of the CHARMM (Chemistry at HARvard Macromolecular Mechanics) modeling software. This bbs will be dedicated to the applications of charmm and the science behind it. --> This service will be available to anyone who uses charmm. <-- --> It is designed so that users can share charmm information, <-- --> or scripts, with others quickly and efficiently via e-mail. <-- ----- --> So far, several leading industrial charmm user groups have aggreed <-- --> to participate. These include; NIH, IBM, ELI-LILLY, Merck, Exxon,<-- --> Polygen/MSI etc. Several academic institutions as well. <-- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +The charmm bbs will be called: + + + + charmm-bbs@emperor.harvard.edu + + + +Any personal msgs and REQUESTS TO JOIN can be sent to: + + + + charmm-bbs-sysop@emperor.harvard.edu + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ----------------- Any charmm related questions/comments or scripts you would like to share, are simply posted to the bbs in the form of e-mail. All subscribers will recieve all e-mail that is sent to the bbs. For example: mail charmm-bbs@emperor.harvard.edu subject/ body of letter etc.. Stay tuned as a major release of CHARMm (CHARMm 22) from Polygen/MSI is eminant. Regards, Donovan Chin =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-= Donovan Chin Ph.d Phone: 617.496.6820 Fax: 617.495.9857 Harvard University e-mail dchin@emperor.harvard.edu Department of Chemistry 12 Oxford St. Cambridge, MA 02138, USA =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-= --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Aug 13 18:23:17 1992 Date: Thu, 13 Aug 92 10:06:27 PDT From: d3f012@gator.pnl.gov Subject: Argus: molecule size To: chemistry@ccl.net Status: R Argus users: The response to the availability of Argus has been overwhelming. Thanks for your support. I have had several inquiries regarding size limitations for molecules run with Argus. THERE ARE NO HARDWIRED ARRAYS IN ARGUS. THERE IS NO SIZE LIMITATION TO THE MOLECULES YOU CAN ATTEMPT TO RUN. I have frequently run ~500 atom systems on a Cray YMP with no difficulty. Caveats: You are limited by the memory of your system, cpu performance, intrinsic limitations of the algorithms and theories employed. (ie. you probably don't want to do a Hartree Fock calc on an entire protein. It would be ridiculously expensive and probably give meaningless results). If you use Argus on a system where cpu time costs real $$, like a Cray YMP, please test the code on small inexpensive systems (like the test data decks) before you tackle a huge expensive calculation. The ab initio integrals code is not blazingly fast. It was originally included in the code to test some new model Hamiltonians. Don't expect to run large abinitio calculations with the efficiency of codes like Gaussian, Disco, Gamess, etc. *************************************************************************** If you don't like to see the status reports appear on the screen during a run, simply include the "silent" option in the $print control block, run your job in the background, and Argus will run silently. ie. $print silent $end *************************************************************************** Mark Thompson Pacific Northwest Laboratory internet : d3f012@pnlg.pnl.gov voice : 509-375-6734 FAX : 509-375-6631 --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Aug 13 19:25:42 1992 Date: Thu, 13 Aug 92 14:59:59 EDT From: swl26@cas.org (Steve Layten x3451) Subject: Re: lists of lists To: chemistry@ccl.net Status: R The message from sam@ncsa.uiuc.edu (Sam Milosevich) with Subject "lists of lists" triggered a memory. There is a list of lists, which is: at site ftp.nisc.sri.com, in file: netinfo/interest-groups It looks like it was last updated 28 Jan 92, and contains several groups with the word "chemistry" in the description, including this one: o NFNET-L Biological Nitrogen Fixation MIRCEN o CHMINF-L on LISTSERV@IUBVM.BITNET Chemical Information Sources o Chemistry@ccl.net Computational Chemistry List o cryonics o dibug@avogadro.barnard.columbia.edu Biosym Technologies Software Users o FORENS-L@FAUVAX.BITNET o ORGCHE-L o TEXTILES@TREARN.BITNET See the file for information on what is "covered" in the list, and how to subscribe, etc. Steve Layten -- Steven W. Layten, Senior Engineer Chemical Abstracts Service, PO Box 3012, Columbus, OH 43210 +1 614 447 3600 INET: swl26@cas.org BITNET: swl26@cas UUCP: osu-cis!chemabs!swl26 # # # Speaking only for myself, and NOT for Chemical Abstracts Service! # # # --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Aug 13 20:32:12 1992 To: chemistry@ccl.net From: "Larry Wier" Organization: Saint Bonaventure University Date: 13 Aug 92 14:50:54 DST Subject: Re: Chemistry lists Status: R > Date: Wed, 12 Aug 92 09:00:16 PDT > From: "Doug DeFrees" > To: chemistry@ccl.net > Netters: > > I was prompted by the recent note about an organic chemistry list to > wonder what other lists or forums might exist on the internet which > directly address chemistry or physics. This list for computational > chemists is a good example as is the organic chemistry list (though > there seems to be some question about it) and the nascent macromodel > list that was mentioned here recently. > > Is there anywhere a list of lists? (I doubt it.) If you know of a > public list or forum or newsgroup that directly addresses chemistry or > physics please send a note to the list. > > > Doug DeFrees > IBM Almaden Research Center > > --- > Administrivia: This message is automatically appended by the mail exploder. > CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only > OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net > --- > Doug, An annotated list of lists was just discussed on the Chemical Info list. See below. Larry Wier =================================== Date: Tue, 4 Aug 1992 17:43:00 BST Reply-To: "CHEMICAL INFORMATION SOURCES DISCUSSION LIST" Sender: "CHEMICAL INFORMATION SOURCES DISCUSSION LIST" From: "Bernard J. Treves Brown" Subject: List of Chemistry Discussion Groups - A Correction To: Multiple recipients of list CHMINF-L Greeting! I sent a message to the list about Diane Kovacs' Directory of Academic Email Conferences last week; but, unfortunately, the information I had was out of date. A couple of people have written to me with problems, sincere apologies to them and any others who have had trouble. For ftp purposes: site: ksuvxa.kent.edu signon: anonymous password: your user i.d. CD LIBRARY GET ACADLIST.FILE6 (or .FILE5) EMAIL: send GET ACADLIST FILE6 to LISTSERV@KENTVM N.B. This is not a mistake - use stops with ftp, NOT with Email A description of the files available follows: Bernard Treves Brown DIAS, UMIST, Manchester, UK. ********************************************************** Academic Electronic Conferences ------------------------------------------------------------------ CONTENTS: (The entire directory is available in binhexed Macintosh Word 4.0 as ACADWHOL HQX ) Social Sciences and Humanities (entries 1-473) ACADLIST FILE1: Anthropology-Education ACADLIST FILE2: Futurology-Latin American Studies ACADLIST FILE3: Library and Information Science-Music ACADLIST FILE4: Political Science-Writing (All four files are available in binhexed Macintosh Word 4.0 as ACADSOCH HQX ) Biological Sciences (entries 1-127) ACADLIST FILE5 Physical Sciences (entries 1-94) ACADLIST FILE6 Business, Miscellaneous Academia, News and Weather (entries 1-64) ACADLIST.FILE7 There is also a description of how to subscribe to lists ACADLIST README and a list of changes and new lists in the compilation ACADLIST CHANGES =============================== I hope this helps. ============================== Dr Larry Wier Dept of Chemistry St Bonaventure University St Bonaventure, N.Y. 14778 (716)375-2116 INTERNET:lwier@sbu.edu ============================== --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Aug 13 22:25:39 1992 From: reg%sdchemw2.ucsd@chem.UCSD.EDU (Richard E. Gillilan) Subject: Re: lists of lists To: chemistry@ccl.net Date: Thu, 13 Aug 92 15:31:49 PDT Status: R > > > > Is there anywhere a list of lists? ... If you know of a > > public list or forum or newsgroup that directly addresses chemistry or > > physics please send a note to the list. Here are a few, I would also like to know about any others: ------------------------------------------- Computational chemistry related news groups ------------------------------------------- to subscribe, send mail to: comment ...................................................................... chemistry-request@ccl.net (you know) gromos-request@igc.ethz.ch (Gromos users) dibug-request@comp.bioz.unibas.ch (BIOSYM users) amber-request@cgl.ucsf.edu (Amber users) sybylreq@quant.chem.rpi.edu (Sybyl users) spasms-users-request@cgl.ucsf.edu (Spasms users) mmodinfo-request@uoft02.utoledo.edu (Macromodel) * ga-molecule-request@tammy.harvard.edu (Genetic algorithms) * send message SUBSCRIBE MMODINFO --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net ---