From dufner@ws01.pc.chemie.th-darmstadt.de Wed Jun 8 06:24:37 1994 Received: from rs2.hrz.th-darmstadt.de for dufner@ws01.pc.chemie.th-darmstadt.de by www.ccl.net (8.6.4/930601.1506) id GAA07288; Wed, 8 Jun 1994 06:04:40 -0400 Received: from ws01.pc.chemie.th-darmstadt.de by rs2.hrz.th-darmstadt.de with SMTP id AA41223 (5.65c/IDA-1.4.4 for <@rs2.hrz.th-darmstadt.de:chemistry@ccl.net>); Wed, 8 Jun 1994 12:04:18 +0200 Received: by ws01.pc.chemie.th-darmstadt.de (931110.SGI/930416.SGI.AUTO) for @rs2.hrz.th-darmstadt.de:chemistry@ccl.net id AA16392; Wed, 8 Jun 94 12:04:15 +0200 Date: Wed, 8 Jun 94 12:04:15 +0200 From: dufner@ws01.pc.chemie.th-darmstadt.de (Hagen Dufner) Message-Id: <9406081004.AA16392@ws01.pc.chemie.th-darmstadt.de> To: chemistry@ccl.net Subject: optimization with G92 Hi netters, I do geometry optimization with Gaussian92 and run almost after every optimization step in the following error: ERROR ON Z-MATRIX CARD NUMBER 7 ANGLE Alpha IS OUTSIDE THE VALID RANGE OF 0 TO 180. What should I do to get out of this dilemma. Should I 1) fix this angle until all other coordinates are optimized or 2) correct it in the following manner and start a new optimization: d / old angle(b-c-d) = oa b - c old torsion(a-b-c-d) = ot / a new angle = 360-oa = na new torsion = -ot In this way I have "mirrored" the regarded coordinate at the a,b,c-plane (not really because of different angle oa and na). Any help is appriciated. # #+----------------------------------------------+ #| Hagen Dufner | #| Technische Hochschule Darmstadt | #| Physikalische Chemie I | #| Petersenstr. 20 | #| 64287 Darmstadt, Germany | #| Phone: (+int) 6151 165397 | #| Fax: (+int) 6151 164298 | #| Network : | #+----------------------------------------------+ From GREULACH@pcmail.uni-trier.de Wed Jun 8 09:24:27 1994 Received: from apollo11.Uni-Trier.De for GREULACH@pcmail.uni-trier.de by www.ccl.net (8.6.4/930601.1506) id IAA09230; Wed, 8 Jun 1994 08:51:10 -0400 Received: from servrz02.uni-trier.de by apollo11.Uni-Trier.De (5.65/2.00) id AA01201; Wed, 8 Jun 94 14:50:52 +0200 Received: From NETWARESERVER/WORKQUEUE by servrz02.uni-trier.de via Charon-4.0-VROOM with IPX id 100.940608145040.352; 08 Jun 94 14:50:55 -200 Message-Id: To: chemistry@ccl.net From: "GREULACH UWE" Organization: University of Trier Date: 8 Jun 94 14:50:36 GMT+2 Subject: Amplifier and potentiostat for microelectrodes Priority: normal X-Mailer: Pegasus Mail v2.3 (R5). Hi netters, I'm still searching for an amplifier (pico- or femtoammeter) (and if it is possible) in conjunction with a potentiostat for voltammetry with a Pt- microdisk electrode. It should be possible to measure in the area of femtoamp currents and to registrate cyclic voltammograms by using high scan rates. The electrochemical experiments will be done with a three-electrode system from Metrohm. Does anybody know something about such instruments from EG&G, BAS, ERC, Radiometer or anything else??? Thank you very much for your answers and please send them to Greulach@pcmail.uni-tier.de Bye and all the best, Hansi Nirmaier From ghislain@jupiter.sun.csd.unb.ca Wed Jun 8 09:32:07 1994 Received: from unb.ca for ghislain@jupiter.sun.csd.unb.ca by www.ccl.net (8.6.4/930601.1506) id IAA09006; Wed, 8 Jun 1994 08:25:03 -0400 Received: from jupiter.sun.csd.unb.ca by unb.ca (4.1/SMI-4.1-940224-08:05) id AA15470; Wed, 8 Jun 94 09:25:01 ADT Received: from [131.202.47.1] by jupiter.sun.csd.unb.ca (4.1/SMI-4.1-940126-11:10) id AA18925; Wed, 8 Jun 94 09:24:59 ADT Date: Wed, 8 Jun 94 09:24:58 ADT Message-Id: <9406081224.AA18925@jupiter.sun.csd.unb.ca> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@ccl.net From: ghislain@jupiter.sun.csd.unb.ca (Ghislain Deslongchamps) Subject: Sun SCSI disk on Indigo = OK Dear Netters, Thank you for all the useful responses despite my ill-placed posting. I really appreciate your help. I was able to get the Sun SCSI disk to work fine on my SGI Indigo. It turned out to be simple once I entrenched myself in the man pages and followed your advice: I simply reformatted the disk (fx -x "dksc(0,5)" i.e. it's on SCSI controller 0, SCSI address 5), then I made a filesystem and mounted it (Add_disk 5). Et voila! The SGI disk (1Gb internal 3.5" fast SCSI) was $4400 canadian. The Sun disk (1.05Gb external SCSI) was $1320 !!! Gratefully Yours, Ghis :-) +++++++++++++++++++++++++++++++++++++++++++++++++++++ + Ghislain Deslongchamps, Assistant Professor + + Department of Chemistry + + University of New Brunswick + + Fredericton, N.B. CANADA E3B 5A3 + + e-mail: GHISLAIN@UNB.CA + + phone: 506-453-4795 (or 453-4792) + + FAX: 506-453-4599 + +++++++++++++++++++++++++++++++++++++++++++++++++++++ From xiang@auriga.rose.brandeis.edu Wed Jun 8 11:24:21 1994 Received: from auriga.rose.brandeis.edu for xiang@auriga.rose.brandeis.edu by www.ccl.net (8.6.4/930601.1506) id KAA11127; Wed, 8 Jun 1994 10:56:51 -0400 Received: by auriga.rose.brandeis.edu (5.57/Ultrix3.0-C) id AA00715; Wed, 8 Jun 94 10:59:01 -0400 Date: Wed, 8 Jun 94 10:59:01 -0400 From: xiang@auriga.rose.brandeis.edu (Xiaoou Xiang) Message-Id: <9406081459.AA00715@auriga.rose.brandeis.edu> To: chemistry@ccl.net Subject: Monte Carlo Dear Netters: Could any of you tell me where to obtain Monte Carlo simulation programs for molecular mechanics calculations? Phil Xiang Biophysics program Brandeis University From PA13808%UTKVM1.BITNET@phem3.acs.ohio-state.edu Wed Jun 8 11:29:08 1994 Received: from phem3 for PA13808%UTKVM1.BITNET@phem3.acs.ohio-state.edu by www.ccl.net (8.6.4/930601.1506) id LAA11245; Wed, 8 Jun 1994 11:03:16 -0400 From: Received: from UTKVM1.BITNET (MAILER@UTKVM1) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HDAPKW0AQO99PKKU@phem3.acs.ohio-state.edu>; Wed, 8 Jun 1994 11:02:58 EDT Received: from UTKVM1 (PA13808) by UTKVM1.BITNET (Mailer R2.10 ptf000) with BSMTP id 5737; Wed, 08 Jun 94 11:02:11 LCL Date: Wed, 08 Jun 94 10:40:27 LCL Subject: G92 LICENSING PROBLEM To: netters Message-id: <01HDAPKW0AQQ99PKKU@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT I am at a large state university(U of TENN). The admin has policy of support ing a central comp center rather helping faculty to purchase individual work stations. In order to satisfy the needs of a number of faculty who need ab initio calc as PART of their research prog I have been trying to replace G90 by G92 on an IBM 3090 at the central comp center. The UT lawyers and The Gaussian lawyers have not been able to come to an agreement concerning the licensing. The problem seems to concern any legal problem which might arise out of the use of G92 !!!! would under TENN law have to be fought according to the laws here whereas G. is incorporated i in Illinois. I have heard that other UNIV have had similar problems. I would like to here from anyone who has had this problem particularly if they have been able to solve it. Our position has become desperate because we need calc of geom and freq at at least the MP2 level and it is in these areas that G92 is much superior to G90. I would also like to here about other prog which are capable of doing MP2 or CCD geom opt and freq calc as efficiently or more so than G92 which are easily available for a SUN or IBM/6000 work stn The future of several grad students and at least one professor depends on getting this problem resolved speedily !!!! John E. Bloor(PA13808 at utkvm1.bitnet or utkvm1.utk.edu or phone 615-573-5176) From xiang@auriga.rose.brandeis.edu Wed Jun 8 14:24:39 1994 Received: from auriga.rose.brandeis.edu for xiang@auriga.rose.brandeis.edu by www.ccl.net (8.6.4/930601.1506) id OAA15871; Wed, 8 Jun 1994 14:11:17 -0400 Received: by auriga.rose.brandeis.edu (5.57/Ultrix3.0-C) id AA01487; Wed, 8 Jun 94 14:13:22 -0400 Date: Wed, 8 Jun 94 14:13:22 -0400 From: xiang@auriga.rose.brandeis.edu (Xiaoou Xiang) Message-Id: <9406081813.AA01487@auriga.rose.brandeis.edu> To: chemistry@ccl.net Subject: Monte Carlo,again... Dear Max and other Netters: I posted this question earlier: >>Could any of you tell me where to obtain Monte Carlo simulation programs for >>molecular mechanics calculations? Let me be more specific. I want to use Monte Carlo method to sample the conformational space of a small drug molecule to find the global and local minima. The molecular mechanics programs I have are AMBER and CHARMM, none of which came with Monte Carlo utility. Phil Xiang Biophysics program Brandeis University From shenkin@still3.chem.columbia.edu Wed Jun 8 15:24:39 1994 Received: from still3.chem.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.4/930601.1506) id OAA16704; Wed, 8 Jun 1994 14:52:30 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA05904; Wed, 8 Jun 94 14:52:18 -0400 From: "Peter Shenkin" Message-Id: <9406081452.ZM5902@still3.chem.columbia.edu> Date: Wed, 8 Jun 1994 14:52:07 -0400 In-Reply-To: xiang@auriga.rose.brandeis.edu (Xiaoou Xiang) "CCL:Monte Carlo,again..." (Jun 8, 2:13pm) References: <9406081813.AA01487@auriga.rose.brandeis.edu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: xiang@auriga.rose.brandeis.edu (Xiaoou Xiang), chemistry@ccl.net Subject: Re: CCL:Monte Carlo,again... Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Jun 8, 2:13pm, Xiaoou Xiang wrote: > Subject: CCL:Monte Carlo,again... > >>Could any of you tell me where to obtain Monte Carlo simulation programs > >> for > >>molecular mechanics calculations? > > Let me be more specific. I want to use Monte Carlo method to sample the > conformational space of a small drug molecule to find the global and local > minima. The molecular mechanics programs I have are AMBER and CHARMM, none > of > which came with Monte Carlo utility. Phil, BatchMin/MacroModel supports Monte Carlo conformational search, as well as MD and minimization, in the context of AMBER*, MM2*, MM3* or OPLSA* force-fields. It should be well suited to your application. The cost to academics is quite low. For more info: finger mmod@still3.chem.columbia.edu and send me email if you have questions. Caveat: I work on the program, so I'm prejudiced in its favor. -P. -- ********** After the revolution, everyone will have a home page... ********** Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ***** (... but the Internet will be too busy for anyone to access it.) ****** From CHAKRAVO@ucs.indiana.edu Wed Jun 8 20:24:31 1994 Received: from PO3.indiana.edu for CHAKRAVO@ucs.indiana.edu by www.ccl.net (8.6.4/930601.1506) id TAA19796; Wed, 8 Jun 1994 19:30:47 -0400 Message-Id: <199406082330.TAA19796@www.ccl.net> Received: from LOCAL:.prism.DECnet by PO3.Indiana.EDU; id AA13031 (5.65c+jsm/2.5.1jsm); Wed, 8 Jun 1994 18:24:31 -0500 Date: Wed, 8 Jun 94 18:30:47 EST From: Subhas Chakravorty X-To: PO%"chemistry@ccl.net" Subject: MOPAC To: chemistry@ccl.net Which is the mos recent version MOPAC93, MOPAC7 , MOPAC6 perhaps there is an ftp site where I can read about these versions. I intend to email the entire MOPAC to a friend in India. Please email me the info . I thank you in advance Subhas Chakravorty PS: ALL my gopher searches landed up with sites for MOPAC6. So I am wondering if thats the current one! which is free software but copyrighted. From SBOESCH@aardvark.ucs.uoknor.edu Wed Jun 8 21:24:27 1994 Received: from aardvark.ucs.uoknor.edu for SBOESCH@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.4/930601.1506) id VAA20325; Wed, 8 Jun 1994 21:21:15 -0400 From: Message-Id: <199406090121.VAA20325@www.ccl.net> Date: Wed, 8 Jun 94 20:21 CDT Subject: NQS problem To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear Netters, This message is directed to those who use NQS on an IBM RISC/6000. The other day we had an rather odd occurence. One of our users was running two different jobs in differenct queues ( one was an amber job, the other a gaussian job). At appoximately the same time both his jobs were ejected from the queue, but they continued to run. The *.batch-log files appeared in his directories, but they contained no information as to why the jobs were ejected from the queue. Although we have not been running NQS very long, the experience we do have suggests that a job will not be ejected from the queue unless the job either finished successfully or terminates abnormally. The first thought that comes to mind is that the jobs exceeded the time limit in their respective queues, however, that was not the case. The amber job had run approximately 4 hours and it was in a 24 hour queue and the gaussian job was being run in an unlimited time queue. If anyone has experienced this before or has any suggestions I would be most appreciative. Thanks very much. SBOESCH@aardvark.ucs.uoknor.edu S.E. Boesch Department of Chemistry & Biochemistry University of Oklahoma Norman, Oklahoma