From chemistry-request@server.ccl.net Thu Sep 7 02:37:37 2000 Received: from songsim.cuk.ac.kr ([203.229.207.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA01499 for ; Thu, 7 Sep 2000 02:37:35 -0400 Received: from songsim.cuk.ac.kr ([210.179.239.118]) by songsim.cuk.ac.kr (8.9.3/8.9.3) with ESMTP id PAA21949 for ; Thu, 7 Sep 2000 15:32:02 +0900 (KST) Sender: young@songsim.cuk.ac.kr Message-ID: <37D59270.FC8E573D@songsim.cuk.ac.kr> Date: Tue, 07 Sep 1999 15:32:17 -0700 From: young Organization: The Catholic University of Korea X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: GORMACS compiling Content-Type: text/plain; charset=iso-2022-kr Content-Transfer-Encoding: 7bit Dear CCLers I have some problems to compile the GROMACS on unix. Some error messges were remained. make: file `Makefile' line 6: Must be a separator (: or ::) for rules (bu39) make: file `/usr3/MD/GROMACS/src/makef/Makefile.def' line 10: Must be a separator (: or ::) for rules (bu39) make: file `/usr3/MD/GROMACS/src/makef/Makefile.SGI' line 60: Must be a separator (: or ::) for rules (bu39) make: file `/usr3/MD/GROMACS/src/makef/Makefile.SGI' line 60: Syntax error I already installed GNU software My machine is SGI sorkstation, IRIX6.2 R5000 (INDY). Could you help me...? -- ================================= Jee-Young Lee The Catholic University of Korea Department of Chemistry Ph.D candidate TEL. +82-32-3403-674 ================================= From chemistry-request@server.ccl.net Thu Sep 7 08:59:57 2000 Received: from inf6serv.rug.ac.be (inf6serv.rug.ac.be [157.193.40.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA03895 for ; Thu, 7 Sep 2000 08:59:55 -0400 Received: from eduserv2.rug.ac.be (eduserv2.rug.ac.be [157.193.40.10]) by inf6serv.rug.ac.be (8.9.0/8.9.0) with ESMTP id OAA13565 for ; Thu, 7 Sep 2000 14:55:00 +0200 (MET DST) Received: from localhost (tkuppens@localhost) by eduserv2.rug.ac.be (8.9.3/8.9.3) with ESMTP id OAA16264 for ; Thu, 7 Sep 2000 14:54:59 +0200 (MET DST) Date: Thu, 7 Sep 2000 14:54:59 +0200 (MET DST) From: Tom Kuppens To: chemistry@ccl.net Subject: Summary: NMR Literature Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, a week or two ago I posted a question about NMR-literature. Here's the summary. Many thanks goes out to Donald B. Boyd, Sergio E. Galembeck, Dave Giesen, Ned C. Haubein, Thomas Heine, Kieran F. Lim, Trevor D. Power, Georg Schreckenbach, Leo Woodcock. The original message. >Hi all, > >I'm starting a project on NMR ab-initio calculations. >Does someone have an idea of a good starting point in the literature ? > >regards > >Tom Kuppens Summary - J. Comp. Chem. 1999 Vol. 20 / Nr.12 - T. Helgaker et al., Chem Rev 99 (1999),293-352 - ACS symp. series: vol. 732, 1999, 'Modelling NMR Chemical Shifts', edited by Facelli and de Dios - papers by Ned Martin : UNCWilmington as well as Paul Scheyler at UGA - The Encyclopdeia of Computational (i think, or Quantum) Chemistry - D. B. Chesnut, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1996, Vol. 8, pp. 245-297. The Ab Initio Computation of Nuclear Magnetic Resonance Chemical Shielding. - M. Pecul et al., J. Chem. Phys., 2000, 112(18) - K.B. Wiberg et al., J. org. chem, 1999, 64 6394-6400 - K.B. Wiberg et al., J. comp. Chem, 1999, 20(12) 1299-1303 - Kollwitz, M; Haser, M; Gauss, J., JOURNAL OF CHEMICAL PHYSICS, 1998 MAY 22, V108 N20:8295-8301. Greetings, Tom Kuppens tom@hartree4.rug.ac.be http://studwww.rug.ac.be/~tkuppens/chem.html ----------------------------------------------------------------------...- Windows NT has detected that the mouse has moved. Reboot the computer for these changes to take effect. -- George Dau From chemistry-request@server.ccl.net Thu Sep 7 11:22:12 2000 Received: from panic.csc.cuhk.edu.hk (root@panic.csc.cuhk.edu.hk [137.189.6.35]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA04543 for ; Thu, 7 Sep 2000 11:22:10 -0400 Received: from l (dialup3-043.csc.cuhk.edu.hk [137.189.210.43]) by panic.csc.cuhk.edu.hk (8.9.3/8.9.3) with SMTP id XAA15600 for ; Thu, 7 Sep 2000 23:17:10 +0800 (HKT) Message-ID: <007801c018de$c5495e20$2bd2bd89@l> Reply-To: "Kiniu WONG Kin-Yiu" From: "Kiniu WONG Kin-Yiu" To: Subject: can I know how Gaussian optimizes the wavefunction by STABE=Opt if there is internal stability? Date: Thu, 7 Sep 2000 23:17:35 +0800 Organization: Physics CUHK MIME-Version: 1.0 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear all, I have another question about "STABLE=OPT". Gaussian will optimise the wavefuntion until it's stable, and then from the output I can know the new lower energy. But, it seems that when there is internal instability, I can't know how it optimises the wavefunction such that it could obtain this new energy. So, my question is that can I know how Gaussian optimises the wavefunction by STABLE=Opt if there is internal stability? Thanks in advance! Best wishes, Kiniu WONG Kin-Yiu Undergraduate student Department of Physics The Chinese University of Hong Kong Email: kiniu@cuhk.edu.hk or kyiwong@phy.cuhk.edu.hk From chemistry-request@server.ccl.net Thu Sep 7 11:56:53 2000 Received: from myamlak.ch.uj.edu.pl (myamlak.ch.uj.edu.pl [149.156.71.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA04760 for ; Thu, 7 Sep 2000 11:56:52 -0400 Received: from localhost (borowski@localhost) by myamlak.ch.uj.edu.pl (8.9.3/8.9.3) with ESMTP id RAA23258 for ; Thu, 7 Sep 2000 17:53:15 +0200 (MET DST) Date: Thu, 7 Sep 2000 17:53:15 +0200 (MET DST) From: Tomasz Borowski X-Sender: borowski@myamlak.ch.uj.edu.pl To: chemistry@ccl.net Subject: EPR for TM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All! Does anyone know a good review paper (book, web site etc.) considering EPR phenomena for Transition Metal ions and their complexes? I'm mostly interested in the theory of it. kind regards, Tomek Borowski From chemistry-request@server.ccl.net Thu Sep 7 13:43:40 2000 Received: from panic.csc.cuhk.edu.hk (root@panic.csc.cuhk.edu.hk [137.189.6.35]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05287 for ; Thu, 7 Sep 2000 13:43:39 -0400 Received: from l (dialup4-020.csc.cuhk.edu.hk [137.189.211.20]) by panic.csc.cuhk.edu.hk (8.9.3/8.9.3) with SMTP id BAA04243 for ; Fri, 8 Sep 2000 01:38:39 +0800 (HKT) Message-ID: <001e01c018f2$89863480$14d3bd89@l> Reply-To: "Kiniu WONG Kin-Yiu" From: "Kiniu WONG Kin-Yiu" To: Subject: one more questions about an error in Gaussian Date: Fri, 8 Sep 2000 01:39:06 +0800 Organization: Physics CUHK MIME-Version: 1.0 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi, Sorry to bother again. There's one more questions about Gaussian. Recently, I've calculated the ground energy of a cation which contains about 50 atoms by CISD. However, there was an error termination at the end. The Route Section and the error output are attached at the end of email. I don't know the reason. Can anyone help me? Thanks a lot! # UCISD/6-31G(d) SCF=Tight Guess=Mix ------------------------------------------------------ ---- ---- ---- SCF Done: E(UHF) = -1662.87165162 A.U. after 39 cycles Convg = 0.8574D-08 -V/T = 2.0012 S**2 = 1.6627 Annihilation of the first spin contaminant: S**2 before annihilation 1.6627, after 1.8035 Range of M.O.s used for correlation: 39 550 NBasis= 550 NAE= 119 NBE= 118 NFC= 38 NFV= 0 NROrb= 512 NOA= 81 NOB= 80 NVA= 431 NVB= 432 Estimate disk for full transformation 76475988068 words. Semi-Direct transformation. ModeAB= 2 MOrb= 512 LenV= 45858810 LASXX= 9165849841 LTotXX= 9165849841 LenRXX= 9165849841 LTotAB= 17247043584 MaxLAS= 19899475200 LenRXY= 19899475200 NonZer= 18331699682 LenScr= 27543408333 LnRSAI= 0 LnScr1= 0 MaxDsk= -1 Total= 56608733374 SrtSym= F ITran= 5 JobTyp=1 Pass 1: I= 1 to 512. LAS= 19899475200 but cannot sort more than 2147483647 items. Error termination via Lnk1e in /usr/local/g98/l804.exe. Job cpu time: 0 days 8 hours 47 minutes 25.8 seconds. File lengths (MBytes): RWF=***** Int= 0 D2E= 0 Chk= 5 Scr=***** ---------------------------------------------------------------------- Regards, Kiniu WONG Kin-Yiu Undergraduate student Department of Physics The Chinese University of Hong Kong Email: kiniu@cuhk.edu.hk or kyiwong@phy.cuhk.edu.hk From chemistry-request@server.ccl.net Thu Sep 7 13:44:49 2000 Received: from helma.informatik.uni-freiburg.de (root@helma.informatik.uni-freiburg.de [132.230.167.155]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05299 for ; Thu, 7 Sep 2000 13:44:48 -0400 Received: (from ch@localhost) by helma.informatik.uni-freiburg.de (8.9.3/8.9.3) id TAA01960; Thu, 7 Sep 2000 19:39:49 +0200 Date: Thu, 7 Sep 2000 19:39:49 +0200 From: Christoph Helma To: comp-bio@net.bio.net, molmodel@net.bio.net, toxicol@net.bio.net, chemistry@ccl.net Subject: ANNOUNCEMENT: The Predictive Toxicology Challenge 2000-2001 Message-ID: <20000907193949.G23712@helma.informatik.uni-freiburg.de> Reply-To: helma@informatik.uni-freiburg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit User-Agent: Mutt/1.2i ***************************** ANNOUNCEMENT ****************************** * * * THE PREDICTIVE TOXICOLOGY CHALLENGE 2000-2001 * * * ************************************************************************* We initiated the Predictive Toxicology Challenge (PTC) to stimulate the development of advanced SAR techniques for predictive toxicology models with nocongeneric compounds. The goal of this competition is to predict the rodent carcinogenicity of new compounds based on the experimental results of the US National Toxicology Program (NTP). The PTC will last >from 2000 to 2001 and consist of four stages. In Phase I chemical structures and carcinogenicity evaluations from the NTP will be provided by the organizers. Participants can submit new chemical and structural descriptors for these molecules before March 01, 2001. These submissions will be used by the model-developers in Phase II. In Phase II predictive toxicology models based on descriptors from Phase I may be submitted until June 01, 2001. Each submission must include an estimation of the model accuracy according to the rules given on the website and a translation of the model, which is understandable by toxicologists. In Phase III the submitted models will be evaluated on quantitative (performance) and qualitative (toxicological relevance) scales. From all submissions we will select a subset of "optimal" models. From these we will (a) identify models that are particular relevant to toxicology and (b) descriptors that were particular useful for predicting carcinogenicity. Finally, the results of the Predictive Toxicology Challenge 2000-2001 will be presented at a workshop of the PKDD/ECML conferences in September 2001 in Freiburg. Detailed information about the Predictive Toxicology Challenge can be obtained from the website http://www.informatik.uni-freiburg.de/~ml/ptc/. PS: This message was crossposted to several newsgroups and mailinglists to reach a broad audience. Please accept my apologies if you receive multiple copies of this message. -- Christoph Helma Machine Learning Lab Institute for Computer Science Albert-Ludwigs-Universität Freiburg Am Flughafen 17 D-79110 Freiburg/Br. Germany T: +49-761-203-8013, F: +49-761-203-8007 helma@informatik.uni-freiburg.de http://helma.informatik.uni-freiburg.de/ From chemistry-request@server.ccl.net Thu Sep 7 15:52:53 2000 Received: from po.cwru.edu (po.CWRU.Edu [129.22.4.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA05860 for ; Thu, 7 Sep 2000 15:52:48 -0400 Received: from gavin (chem51286.CHEM.CWRU.Edu [129.22.200.86]) by po.cwru.edu with SMTP (8.8.8+cwru/CWRU-3.6) id PAA16285; Thu, 7 Sep 2000 15:52:46 -0400 (EDT) (from hxt10@po.cwru.edu for ) Message-ID: <002001c01905$829e09a0$56c81681@cwru.edu> From: "Hui-Hsu (Gavin) Tsai" To: Subject: torsion-torsion cross terms Date: Thu, 7 Sep 2000 15:55:01 -0400 HI, CCLers: Can anyone tell me the non-harmonic potential form for the torsion-torsion cross terms in the classical force field calculation? Thanks! Gavin From chemistry-request@server.ccl.net Thu Sep 7 18:05:23 2000 Received: from cougar.it.wsu.edu (root@cougar.it.wsu.edu [134.121.1.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA06381 for ; Thu, 7 Sep 2000 18:05:23 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id PAA09645; Thu, 7 Sep 2000 15:05:18 -0700 (PDT) Message-ID: <001b01c01917$b4d0f830$b4297986@chem.wsu.edu> From: "Phillip Matz" To: "Kiniu WONG Kin-Yiu" , References: <001e01c018f2$89863480$14d3bd89@l> Subject: Re: CCL:one more questions about an error in Gaussian Date: Thu, 7 Sep 2000 15:05:17 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi, What version of Gaussian are you using? If it is anything less than G98 (such as G94) and your system default route does not change the calculation method to "direct" then you are probably running out of disk space. I encountered similar problems with G94 and calculations on phenanthroline some time ago. Try running the same calculations with "SCF=(tight, direct)". Let me know if it works or if somebody else has an alternative suggestion. Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Kiniu WONG Kin-Yiu" To: Sent: Thursday, September 07, 2000 10:39 AM Subject: CCL:one more questions about an error in Gaussian > Hi, > > Sorry to bother again. There's one more questions about Gaussian. > Recently, I've calculated the ground energy of a cation which contains about > 50 atoms by CISD. However, there was an error termination at the end. The > Route Section and the error output are attached at the end of email. I > don't know the reason. Can anyone help me? Thanks a lot! > > > # UCISD/6-31G(d) SCF=Tight Guess=Mix > ------------------------------------------------------ > ---- > ---- > ---- > SCF Done: E(UHF) = -1662.87165162 A.U. after 39 cycles > Convg = 0.8574D-08 -V/T = 2.0012 > S**2 = 1.6627 > Annihilation of the first spin contaminant: > S**2 before annihilation 1.6627, after 1.8035 > Range of M.O.s used for correlation: 39 550 > NBasis= 550 NAE= 119 NBE= 118 NFC= 38 NFV= 0 > NROrb= 512 NOA= 81 NOB= 80 NVA= 431 NVB= 432 > Estimate disk for full transformation 76475988068 words. > Semi-Direct transformation. > ModeAB= 2 MOrb= 512 LenV= 45858810 > LASXX= 9165849841 LTotXX= 9165849841 LenRXX= 9165849841 > LTotAB= 17247043584 MaxLAS= 19899475200 LenRXY= 19899475200 > NonZer= 18331699682 LenScr= 27543408333 LnRSAI= 0 > LnScr1= 0 MaxDsk= -1 Total= 56608733374 > SrtSym= F ITran= 5 > JobTyp=1 Pass 1: I= 1 to 512. > LAS= 19899475200 but cannot sort more than 2147483647 items. > Error termination via Lnk1e in /usr/local/g98/l804.exe. > Job cpu time: 0 days 8 hours 47 minutes 25.8 seconds. > File lengths (MBytes): RWF=***** Int= 0 D2E= 0 Chk= 5 Scr=***** > ---------------------------------------------------------------------- > > Regards, > Kiniu WONG Kin-Yiu > Undergraduate student > Department of Physics > The Chinese University of Hong Kong > Email: kiniu@cuhk.edu.hk or kyiwong@phy.cuhk.edu.hk > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >