From dsg@hartree.quantchem.kuleuven.ac.be Tue Dec 13 04:19:33 1994 Received: from hartree.quantchem.kuleuven.ac.b for dsg@hartree.quantchem.kuleuven.ac.be by www.ccl.net (8.6.9/930601.1506) id DAA22689; Tue, 13 Dec 1994 03:58:58 -0500 From: Received: by hartree.quantchem.kuleuven.ac.be id AA29451 (5.67a/IDA-1.5 for CHEMISTRY@ccl.net); Tue, 13 Dec 1994 09:53:47 +0100 Date: Tue, 13 Dec 1994 09:53:47 +0100 Message-Id: <199412130853.AA29451@hartree.quantchem.kuleuven.ac.be> To: CHEMISTRY@ccl.net Subject: L-J parameter of acetic acid Hi Netters, Can anbody give the reference for the L-J parameter of acetic acid? debasis dsg@hartree.quantchem.kuleuven.ac.be From pesquer@lpct.u-bordeaux.fr Tue Dec 13 08:19:36 1994 Received: from ausone.lpct.u-bordeaux.fr for pesquer@lpct.u-bordeaux.fr by www.ccl.net (8.6.9/930601.1506) id IAA24457; Tue, 13 Dec 1994 08:12:21 -0500 From: Message-Id: <199412131312.IAA24457@www.ccl.net> Received: from mac4.lpct.u-bordeaux.fr by ausone.lpct.u-bordeaux.fr with SMTP (1.38.193.4/16.2) id AA12390; Tue, 13 Dec 1994 14:12:37 +0100 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Mailer: Eudora F1.4.2 Date: Tue, 13 Dec 1994 14:18:48 +0000 To: chemistry@ccl.net Subject: nalyse of ARCHIVE file from GAUSSIAN92 > >Dear CCL, > >We created an archive file named ARCHIVE with rhe GAUSSIAN 92 program >(keyword FREQ). We try to analyse the results. What are the units(D A-1,the >axis orientation and the arrangement(order) in the file for the dipole >derivatives components? >We have not the Browse Quantum Chemistry Database System Users Guide. If >one can send this documentation(by EUDORA by exemple) we were very >grateful. > >Thank you Very much. >Yours. > >M.P. > > > >**************************************************** >* >* Michel PESQUER E-Mail: pesquer@lpct.u-bordeaux.fr >* >**************************************************** >* Labo: Physicochimie theorique. - U.B.I. - >33405 Talence Cedex >* >* Tel 56 84 63 12 Fax 56 84 66 45 >**************************************************** >* Delegation Regionale du CNRS. - B.P.105 - 33402 Talence Cedex >* >* Tel 56 37 80 80 Fax 57 96 10 56 >* >*************************************************** > > > > ----- End of the message ----- **************************************************** * * Michel PESQUER E-Mail: pesquer@lpct.u-bordeaux.fr * **************************************************** * Labo: Physicochimie theorique. - U.B.I. - 33405 Talence Cedex * * Tel 56 84 63 12 Fax 56 84 66 45 **************************************************** * Delegation Regionale du CNRS. - B.P.105 - 33402 Talence Cedex * * Tel 56 37 80 80 Fax 57 96 10 56 * *************************************************** From lin@gkcl.ists.ca Tue Dec 13 11:20:56 1994 Received: from gkcl.ists.ca for lin@gkcl.ists.ca by www.ccl.net (8.6.9/930601.1506) id KAA27123; Tue, 13 Dec 1994 10:40:30 -0500 Received: by gkcl.ists.ca (5.61/1.34) id AA11985; Tue, 13 Dec 94 10:39:45 -0500 From: lin@gkcl.ists.ca (Delin Shen) Message-Id: <9412131539.AA11985@gkcl.ists.ca> Subject: Summary: Computation Using PC To: chemistry@ccl.net Date: Tue, 13 Dec 94 10:39:44 ADT X-Mailer: ELM [version 2.2 PL0] Dear Netters, Several Days ago, I posted a question on computation using pc. From the suggestions I received, it seems to me MOPAC under LINUX is a good choice. Thank you very much for your help. >Dear Netters, > > Does anyone have experience doing comptation >(ab inition and semiempirical methods) using 486 PC >with UNIX operating system, which program is most >suitable for this purpose? Any help will be appreciated. > >Lin >Chemistry Department >York University >Toronto, Canada > I don't know of anything that runs under Unix on a PC but there's quite a bit in the way of semi-empirical programs that will run under Windows including Hyperchem which I use. There is always MOPAC which is available for free and is a DOS program so if your unix can run a DOS window you'ld be OK with it. The only ab initio package that I know of that will run on a PC is Gaussian 92, which runs under Windows. You'ld better have a very fast PC at least 66 MHz. They do sell a density functional package add-on for Gaussian 92 which might haelp the speed problem. It's not at all obvious that they have optimized Gaussian 92 for a PC. I suspect a brute force translation from a high speed workstation. If you hear of any other ab initio programs that will run on a PC of any sort please let me know Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario (613) 541-6000 X6175 Hello, In reply to your quey, I have used MOPAC 6 running on the Linux operating system (free unix), on a 486DX/2 @66MHz, 8 Mb of RAM, and 420 Mb disk. With MOPAC running there isn't enough memory to run X-Windows very quickly, but in text mode response is fine. I had an 80Mb install of Linux done from CD-ROM, but it can also be downloaded from the Network (FTP to tsx-11.mit.edu /pub/linux, to get more information, or Linux itself). The only problem I found was the MOPAC binary was compiled with a limit of 38 heavy atoms, 38 light atoms, 60 atoms total, 150 Molecular orbitals total. For the drug based work I was doing some structures were larger than this. MOPAC6 for Linux can (I think) be found on www.ccl.net and definately on solaris.ims.ac.jp by FTP. Good Luck, Regards, Martin. ---------------------------------------------------------------- | Martin Hargreaves, ch11mh@surrey.ac.uk| | Undergraduate Computational Chemist | | WWW Server Admin http://www.chem.surrey.ac.uk| ---------------------------------------------------------------- Delin Shen said: > From: lin@gkcl.ists.ca (Delin Shen) > Subject: [COMP-CHEM:7942] CCL:Computation Using PC > > Dear Netters, > > Does anyone have experience doing comptation > (ab inition and semiempirical methods) using 486 PC > with UNIX operating system, which program is most > suitable for this purpose? Any help will be appreciated. > > Lin > Chemistry Department > York University > Toronto, Canada > Hello We are using FreeBSD 1.1.5 and 2.0 with 486 machines (24 machines). We have ported mopac6, mopac7 and two gamess versions to this OS without problems. Semiempirical methods run fine on PC's, abinitio calculations suffer from the I/O limitations of the PC architeture but works. Other public applications like rasmol compile easily too. You can download FreeBSD from freebsd.cdrom.com for free, a good configuration for comp chem is a 486DX2 with 16M ram and the amount of disk you use for calculations. Pedro Very good question! I'll be rather interested to see the summary. Sincerely, Ayaz Bakasov. Hi Lin, We are routinely using PC-s (both 386 and 486) running Linux for computational chemistry calculations using mopac 6.0 and gamess-US. In case you need any further information don't hestitate to contact me. Regards, Peeter -- Peeter Burk, Ph.D. Jakobi 2, EE2400 Tartu, Estonia Institute of Chemical Physics Phone (372-7) 441-453 Tartu University Fax (372-7) 441-453 Estonia E-mail peeter@chem.ut.ee Gentleman, In regards to using a 486 with UNIX, there isn't much you can do. However, if you can open a Telnet connection over to a center that is running GAUSSIAN92 or GAMESS or another program, then that is what I would recommend. There hasn't been much released for the PC DOS, much less the PC UNIX, but I have heard that some software is supposed to be released in _late_ 1995. Hope this was at least informative. Charles B. Bettini NCSSM Dear Dr. Lin : We have a version UNIMOL that does ab initio calculations on PC 80486 at SCF and MP2 levels. Also under development is a DISTRIBUTED COMPUTING version on 2 or more 486's thru LAN. PLEASE REPLY TO : gadre@unipune.ernet.in or gadre@parcom.ernet.in FAX : 0091-212-337551 or 333899 if you are interested. Thanks..............................Shridhar Gadre 12.12.94 From mrigank@imtech.ernet.in Tue Dec 13 13:23:26 1994 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.9/930601.1506) id MAA29754; Tue, 13 Dec 1994 12:25:44 -0500 Received: (from root@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id WAA02100 for chemistry@ccl.net; Tue, 13 Dec 1994 22:55:14 +0500 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA20760; Tue, 13 Dec 94 22:45:12+050 Message-Id: <9412131745.AA20760@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Tue, 13 Dec 94 09:14:46 +0530 Date: Tue, 13 Dec 94 09:14:46 +0530 From: Mrigank To: chemistry@ccl.net Subject: Boc, OMe and chloroform parameters X-Vms-Mail-To: CHEM,WATOC,WSN Hi Does anyone has Boc OCH3 anc chloform parametres for AMBER ? I have a peptide where these are first and last groups respectively. Boc OCH3 H H H O \|/ | C H--C--H H \ | | H-->C--C--O-C==O H H / | C /|\ H H H I am also interested in parameters of chloroform as we want to see chloroform peptide interaction. Thanks Mrigank ---- /Mrigank \/ Phone +91 172 40957 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 40958, +91 172 28032 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From bru@ucsd.edu Tue Dec 13 14:19:42 1994 Received: from ucsd.edu for bru@ucsd.edu by www.ccl.net (8.6.9/930601.1506) id OAA01442; Tue, 13 Dec 1994 14:05:17 -0500 Received: from [137.110.103.89] by ucsd.edu; id LAA07598 sendmail 8.6.9/UCSD-2.2-sun via SMTP Tue, 13 Dec 1994 11:05:09 -0800 for Message-Id: <199412131905.LAA07598@ucsd.edu> X-Sender: ebruner@sdcc13.ucsd.edu (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 12 Dec 1994 12:02:30 -0800 To: chemistry@ccl.net From: bru@ucsd.edu (Eric Bruner) Subject: Unsubscribe Please unsubcribe Eric Bruner. Eric Bruner University of California 3912 Via Tranquilo San Diego CA, 92122-1742 at E-mail bru@ucsd.edu Phone 619-550-0652 San Diego or 619-558-0312 From jstewart@fujitsuI.fujitsu.com Tue Dec 13 16:20:03 1994 Received: from mail.barrnet.net for jstewart@fujitsuI.fujitsu.com by www.ccl.net (8.6.9/930601.1506) id PAA03087; Tue, 13 Dec 1994 15:26:46 -0500 Received: from fujitsu1.fujitsu.com by mail.barrnet.net (8.6.8/BARRNET-8.6.6) id MAA15907; Tue, 13 Dec 1994 12:26:44 -0800 Received: by fujitsu1.fujitsu.com (4.1/SMI-4.1) id AA19158; Tue, 13 Dec 94 12:27:03 PST Date: Tue, 13 Dec 94 12:27:03 PST From: jstewart@fujitsu.com (Dr. James Stewart) Message-Id: <9412132027.AA19158@fujitsu1.fujitsu.com> To: chemistry@ccl.net Subject: MOPAC, bug in POLAR BUG IN MOPAC 93 AND MOPAC 7 POLAR calculations involving electrooptic Pockels effect (EOPE) and optical rectification (OR) give incorrect beta values. Second harmonic generation (SHG) beta values are correct. The fault was due to a programming error caused by myself. The bug was found by Prof. Henry Kurtz, one of the authors of the POLAR routine. To correct the fault, modify subroutine BEOPOR to replace the line COMMON /COORD/ COORD(3,NUMATM) with COMMON /GEOM / GEO(3,NUMATM), COORD(3,NUMATM) This correction should be made to all copies of MOPAC 93 and MOPAC 7. The fault appeared when iterated beta calculations were done. The following data-sets can be used to verify (1) that the fault exists, and (2) that the bug-fix is done correctly. James J. P. Stewart. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Test data sets: POLAR(iwflb=0,beta=1) 1scf Formaldehyde (Second harmonic generation) O 0.00000000 0 0.0000000 0 0.0000000 0 0 0 0 -0.2902 C 1.21651960 0 0.0000000 0 0.0000000 0 1 0 0 0.2922 H 1.10612798 0 123.5116221 0 0.0000000 0 2 1 0 -0.0010 H 1.10612798 0 123.5116221 0 180.0000000 0 2 1 3 -0.0010 POLAR(iwflb=2,beta=1,gamma=0) 1scf Formaldehyde (Electrooptic Pockels Effect) O 0.00000000 0 0.0000000 0 0.0000000 0 0 0 0 -0.2902 C 1.21651960 0 0.0000000 0 0.0000000 0 1 0 0 0.2922 H 1.10612798 0 123.5116221 0 0.0000000 0 2 1 0 -0.0010 H 1.10612798 0 123.5116221 0 180.0000000 0 2 1 3 -0.0010 POLAR(iwflb=3,beta=1,gamma=0) 1scf Formaldehyde (Optical rectification) O 0.00000000 0 0.0000000 0 0.0000000 0 0 0 0 -0.2902 C 1.21651960 0 0.0000000 0 0.0000000 0 1 0 0 0.2922 H 1.10612798 0 123.5116221 0 0.0000000 0 2 1 0 -0.0010 H 1.10612798 0 123.5116221 0 180.0000000 0 2 1 3 -0.0010 Faulty results: (Second harmonic generation) AVERAGE BETA (SHG) VALUE AT 0.50000 EV = 50.39719 (Electrooptic Pockels Effect) AVERAGE BETA VALUE AT 0.50000 EV = 7.50247 (Optical rectification) AVERAGE BETA VALUE AT 0.50000 EV = 7.55551 Correct results: (Second harmonic generation) AVERAGE BETA (SHG) VALUE AT 0.50000 EV = 50.39719 (Electrooptic Pockels Effect) AVERAGE BETA VALUE AT 0.50000 EV = 49.84824 (Optical rectification) AVERAGE BETA VALUE AT 0.50000 EV = 49.85153 From jbrown@iris7.carb.nist.gov Tue Dec 13 17:30:04 1994 Received: from ENH.NIST.GOV for jbrown@iris7.carb.nist.gov by www.ccl.net (8.6.9/930601.1506) id QAA04912; Tue, 13 Dec 1994 16:37:41 -0500 Received: from iris7.carb.nist.gov by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01HKLNXQW128002JQF@ENH.NIST.GOV>; Tue, 13 Dec 1994 16:34:25 EDT Received: by iris7.carb.nist.gov (920330.SGI/920502.SGI) for @enh.nist.gov:chemistry@ccl.net id AA01808; Tue, 13 Dec 94 16:36:18 -0500 Date: Tue, 13 Dec 1994 16:34:13 -0500 (EST) From: "Dr. James Brown" Subject: LJ parameters for metals To: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT I am looking for Lennard-Jones parameters for Mn, Co, Cd, and Ni. Any ideas where I could find them? I'll post a summary. Thanks, James Brown Center for Advanced Research in Biotechnology Rockville, MD From jesus@canarylab.chem.nyu.edu Tue Dec 13 17:39:30 1994 Received: from axp1.acf.nyu.edu for jesus@canarylab.chem.nyu.edu by www.ccl.net (8.6.9/930601.1506) id RAA06055; Tue, 13 Dec 1994 17:15:19 -0500 Received: from canarylab.chem.nyu.edu ("port 1081"@CANARYLAB.CHEM.NYU.EDU) by ACFcluster.NYU.EDU (PMDF V4.3-13 #8043) id <01HKLP6QHLIOX6X94V@ACFcluster.NYU.EDU>; Tue, 13 Dec 1994 17:09:56 -0400 (EDT) Received: by canarylab.chem.nyu.edu (940406.SGI/931108.SGI.AUTO.ANONFTP) for @acfcluster.nyu.edu:CHEMISTRY@ccl.net id AA04994; Tue, 13 Dec 94 17:17:30 -0500 Date: Tue, 13 Dec 1994 17:17:30 -0500 From: jesus@canarylab.chem.nyu.edu (Jesus M. Castagnetto Mizuaray) Subject: Coalition to Ban Dihydrogen Monoxide Homepage (fwd) To: CHEMISTRY@ccl.net Message-id: <9412132217.AA04994@canarylab.chem.nyu.edu> Content-transfer-encoding: 7BIT Follows something (funny?) from http://samsara.circus.com/~no_dhmo/. Can't decide yet if it's a big joke or some example of misinformation and paranoia against chemicals. >>> INCLUDED MESSAGE Ban Dihydrogen Monoxide! The Invisible Killer Dihydrogen monoxide is colorless, odorless, tasteless, and kills uncounted thousands of people every year. Most of these deaths are caused by accidental inhalation of DHMO, but the dangers of dihydrogen monoxide do not end there. Prolonged exposure to its solid form causes severe tissue damage. Symptoms of DHMO ingestion can include excessive sweating and urination, and possibly a bloated feeling, nausea, vomiting and body electrolyte imbalance. For those who have become dependent, DHMO withdrawal means certain death. 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Even after washing, produce remains contaminated by this chemical. as an additive in certain "junk-foods" and other food products. Companies dump waste DHMO into rivers and the ocean, and nothing can be done to stop them because this practice is still legal. The impact on wildlife is extreme, and we cannot afford to ignore it any longer! The Horror Must Be Stopped! The American government has refused to ban the production, distribution, or use of this damaging chemical due to it's "importance to the economic health of this nation." In fact, the navy and other military organizations are conducting experiments with DHMO, and designing multi-billion dollar devices to control and utilize it during warfare situations. Hundreds of military research facilities receive tons of it through a highly sophisticated underground distribution network. Many store large quantities for later use. It's Not Too Late! Act NOW to prevent further contamination. Find out more about this dangerous chemical. What you don't know CAN hurt you and others throughout the world. Send email to no_dhmo@circus.com, or a SASE to: Coalition to Ban DHMO 211 Pearl St. Santa Cruz CA, 95060 Back to the Circus home page Ban Dihydrogen Monoxide! / The Coalition / no_dhmo@circus.com >>> END INCLUDED MESSAGE ----- Jesus M. Castagnetto Mizuaray | "Organic Chemistry: The practice Dep.of Chemistry - New York University | of transmuting vile substances 4 Washington Pl, Room 514. NY 10003 | into publications" (The Last Word- jesus@canarylab.chem.nyu.edu | The Ultimate Scientific Dictionary)