From chemistry-request@ccl.net Tue Apr 6 13:50:28 2004 Received: from mta3.appstate.edu (mailhub.appstate.edu [152.10.1.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i36IoOjR022392 for ; Tue, 6 Apr 2004 13:50:25 -0500 Received: from ws3.appstate.edu (ws3.appstate.edu [152.10.1.42]) by mta3.appstate.edu (8.12.8/8.12.8) with ESMTP id i36IoBdD018068 for ; Tue, 6 Apr 2004 14:50:13 -0400 Received: from kohn.appstate.edu (cohn.chem.appstate.edu [152.10.114.100]) by appstate.edu (PMDF V6.2-X26 #30685) with ESMTP id <01L8M3PGNFZEBHC0WG(at)appstate.edu> for CHEMISTRY(at)ccl.net; Tue, 06 Apr 2004 14:50:10 -0400 (EDT) Date: Tue, 06 Apr 2004 14:50:07 -0400 From: Steve Williams Subject: CCL: onoim in g03 X-Sender: willsd(at)imap.appstate.edu To: CHEMISTRY(at)ccl.net Message-id: <5.1.0.14.0.20040406143036.02c3a058(at)imap.appstate.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; format=flowed; charset=us-ascii X-MailScanner-Information: Please contact the Helpdesk @ 6266 for more information X-MailScanner-ASU-mta3: Found to be clean X-MailScanner-SpamCheck: X-MailScanner-From: willsd(at)appstate.edu X-Spam-Status: No, hits=0.0 required=5.0 tests=LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I am trying to learn to do onoim calculations in g03. My test molecule is a rather large Re(V) complex that is a +2 singlet cation. I am trying a two layer oniom with the Re and the 6 atoms it is bound to (1 N, 4 P, 1 Cl) as the high layer (b3lyp/lanl2dz) with the rest done at am1. I found that the default guess did not work (stopped with an error before guess computation began) so switched to guess=harris and got rid of that error. I now have persistent bad file IO crashes. These usually indicate lack of disk space, but I do not think that is the case on this machine as I have been able to run some rather large CAS calculations, and single layer calculations run fine (b3lyp/lanl2dz on whole complex is slow but does run; geometry optimizations eventually converge...); none of these large calculations required any fooling with maxdisk. I am running on a 64 bit Itanium cluster so splitting rwf file has not been needed with other jobs. The top of my input is below: %mem=120MW %nproc=4 # opt oniom=(rb3lyp/lanl2dz:ram1) geom=connectivity guess=harris first try at oniom calculation for one of grant's biggies 2 1 2 1 0 1 C 0 9.649231 -0.243106 -0.297205 L C 0 8.621088 -0.302810 -1.225543 L C 0 7.252282 -0.215031 -0.805502 L with lots more geometry below. G03 does seem to read this file as intended (it confirms which atoms are in the high and low layer, confirms that the whole molecule is a +2 singlet, that the high layer is a +2 singlet, and that the low layer is a neutral singlet. The last few lines before G03 crashes are : ONIOM: Cut between C /H 120 and P 26 factor= 0.773169 0.773169 ONIOM: saving gridpoint 17 ONIOM: generating point 3 -- low level on real system. Standard basis: VSTO-3G (5D, 7F) Atomic number 75 exceeds maximum of 54 in STO -- maximum used. There are 349 symmetry adapted basis functions of A symmetry. Integral buffers will be 131072 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned on. 349 basis functions, 1047 primitive gaussians, 349 cartesian basis functions 179 alpha electrons 179 beta electrons nuclear repulsion energy 5857.5087847753 Hartrees. NAtoms= 130 NActive= 130 NUniq= 130 SFac= 1.00D+00 NAtFMM= 60 Big=T FileIO operation on non-existent file. FileIO: IOper= 2 IFilNo(1)= -516 Len= 61075 IPos= 61075 Q=***************** dumping /fiocom/, unit = 1 NFiles = 51 SizExt = 524288 WInBlk = 2048 defal = T LstWrd = 4567040 FType=2 FMxFil=10000 Number 0 501 502 503 507 508 511 520 Base 4167680 432128 448512 600064 610304 3831808 1906688 3848192 Then there is good bit of related (diagnostic?) stuff. Can anyone help me debug this oniom job? I realize that this has almost certainly appeared on CCL in the not too distant past, but CCL searches are currently disabled so I have not been able to find those messages. Thanks in advance for any help... Steve Steve Williams A. R. Smith Department of Chemistry Appalachian State University Boone, NC 28608 USA 828-262-2965 From chemistry-request@ccl.net Wed Apr 7 07:21:53 2004 Received: from acomp.usf.edu (nova.acomp.usf.edu [131.247.100.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i37CLqjR001731 for ; Wed, 7 Apr 2004 07:21:53 -0500 Received: from [131.247.212.13] (HELO WillsToy) by acomp.usf.edu (CommuniGate Pro SMTP 4.1.5) with ESMTP id 19618524 for chemistry(at)ccl.net; Tue, 06 Apr 2004 15:50:35 -0400 From: "will" To: Subject: autodock 3.05 intallation... Please help Date: Tue, 6 Apr 2004 15:48:43 -0400 Message-ID: <003c01c41c10$46983090$0dd4f783@WillsToy> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_003D_01C41BEE.BF869090" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2616 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_003D_01C41BEE.BF869090 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I'm totally new to unix based systems, but my PI has put me in charge of getting autodock up and running in our lab. I am trying to install autodock on the latest version of cygwin on my Toshiba winxp laptop. Having very limited knowledge on unix, I've done the best I can to compile autodock and autogrid from the src directory. Unfortunately, I'm not sure what exactly to edit in the makefile. All of the websites referenced for compiling/installing autodock on a linux system no longer exist for some reason. I've gone into the makefile of autodock and done the best I can as far as changing what was apparent, but still get the following error: ./libad.a(rep.o)(.text$... :rep.cc: undefined reference to operator delete (void*) a lot of those undefined reference lines collect2: ld returned 1 exit status make: *** [autodock3] Error 1 any help or if someone could simply send me a copy of their makefile that would work for my architecture would be greatly appreciated. Will University of South Florida Ewlowe(at)helios.acomp.usf.edu ------=_NextPart_000_003D_01C41BEE.BF869090 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I’m totally new to unix based systems, but my PI has put me in = charge of getting autodock up and running in our lab. =  I am trying to install autodock on the latest version of cygwin on my Toshiba winxp laptop.  Having very limited knowledge = on unix, I’ve done = the best I can to compile autodock and autogrid > from the src directory.  Unfortunately, I’m not = sure what exactly to edit in the makefile.  All of the websites referenced = for compiling/installing autodock on a linux system no longer exist for some reason.  I’ve gone into the makefile of autodock = and done the best I can as far as changing what was apparent, but still get the = following error:

 

./libad.a(rep.o)(.text$...  = :rep.cc: undefined reference to operator delete = (void*)       &nbs= p;    a lot of those undefined reference = lines

 

collect2: ld returned 1 = exit status

make: *** [autodock3] Error 1

 

any help or if someone could simply send me a copy of their makefile that would work for my architecture would be greatly appreciated.  

 

Will

University of = South = Florida

Ewlowe(at)helios.acomp.usf.edu

------=_NextPart_000_003D_01C41BEE.BF869090-- From chemistry-request@ccl.net Wed Apr 7 02:24:39 2004 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i377OdjR019248 for ; Wed, 7 Apr 2004 02:24:39 -0500 Received: from gwdu70.gwdg.de ([134.76.8.20]) by mailer.gwdg.de with esmtp (TLSv1:DES-CBC3-SHA:168) (Exim 4.20) id 1BB7QR-00083D-4G for chemistry*at*ccl.net; Wed, 07 Apr 2004 09:24:43 +0200 Date: Wed, 7 Apr 2004 09:24:37 +0200 (MEST) From: Frauke Meyer To: chemistry*at*ccl.net Subject: EMBO-course "Protein simulations and drug design" Shanghai Sept 2004 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Level: / X-Spam-Report: Content analysis: 0.0 points, 6.0 required X-Virus-Scanned: (clean) by exiscan+sophie Hi all computational biologists/chemists, Apply Now: EMBO - Practical course on Methods for protein simulations and drug design in Shanghai at the Drug Discovery and Design Center from 13-24 Sept 2004 !!!! www.dddc.ac.cn/embo04 !!!! Topics: * Molecular Dynamics (protein dynamics, membrane proteins, implicit selvent etc) * Computer-aided drug design (free energy calculations, dockign and scoring etc) * Hybrid quantum/molecular mechanics Speakers: Jeremy Smith, Biocomputing, University of Heidelberg Wilfried van Gunsteren, IGC, ETH Zuerich Bert de Groot, MPI for Biophysical Chemistry, Goettingen Phil Biggin, Molecular Biophysics, University of Oxford Jianpeng Ma, Baylor College of Medicine, Houston Daan van Aalten, Drug Design, University of Dundee Johan Aqvist, Cell and Mol. Biology, University of Uppsala Jonathan Essex, University of Southampton Martin Stahl, Roche, Basel Gerhard Klebe, Drug Design, University of Marburg Ursula Roethlisberger, University of Lausanne Gerrit Groenhof, University of Groningen Qi Chen, Lilly Research Laboratories, Indianapolis and others Best wishes, Frauke --- Frauke Meyer Drug Discovery and Design Center Shanghai Institute of Materia Medica 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park Shanghai 201203 Tel: +86 21 50806600*1201, Fax: +86 21 50806600*1205 http://www.dddc.ac.cn, e-mail:frauke.meyer*at*mpi-bpc.mpg.de From chemistry-request@ccl.net Wed Apr 7 09:53:27 2004 Received: from mail1.hrz.uni-bielefeld.de (mail1.hrz.uni-bielefeld.de [129.70.4.88]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i37ErQjR011352 for ; Wed, 7 Apr 2004 09:53:27 -0500 Received: from conversion-daemon.mail1.hrz.uni-bielefeld.de by mail1.hrz.uni-bielefeld.de (iPlanet Messaging Server 5.2 HotFix 1.15 (built Apr 28 2003)) id <0HVT00L012LSPQ-.at.-mail1.hrz.uni-bielefeld.de> for chemistry-.at.-ccl.net; Wed, 07 Apr 2004 16:53:32 +0200 (MEST) Received: from uni-bielefeld.de (localhost [127.0.0.1]) by mail1.hrz.uni-bielefeld.de (iPlanet Messaging Server 5.2 HotFix 1.15 (built Apr 28 2003)) with ESMTP id <0HVT002J32P7KP-.at.-mail1.hrz.uni-bielefeld.de> for chemistry-.at.-ccl.net; Wed, 07 Apr 2004 16:53:31 +0200 (MEST) Received: from [129.187.181.37] by mail1.hrz.uni-bielefeld.de (mshttpd); Wed, 07 Apr 2004 16:53:31 +0200 Date: Wed, 07 Apr 2004 16:53:31 +0200 From: Andreas Serr Subject: gaussian 03 on macintosh To: chemistry-.at.-ccl.net Message-id: <3130b530f280.30f2803130b5-.at.-uni-bielefeld.de> MIME-version: 1.0 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.15 (built Apr 28 2003) Content-type: text/plain; charset=us-ascii Content-language: de Content-transfer-encoding: 7BIT Content-disposition: inline X-Accept-Language: de Priority: normal Dear all, we are considering using Gaussian 03 on a Mac OS X system. Has anybody experience in that field? In particular: - G03M is not optimised for Mac G5 architecture, so does it make sense to run it on G5 rather than on G4? - is GaussView M working fine with G5 computers? - does anyone have experience/benchmark tests for Gaussian running on Mac (G5/G4/...) in comparison with Gaussian on Intel Xeon-dual process. @ 2 GHz (Linux system) Regards, Andy andreas.serr-.at.-uni-bielefeld.de From chemistry-request@ccl.net Wed Apr 7 15:15:08 2004 Received: from marconi.rtp.epa.gov (marconi.rtp.epa.gov [134.67.208.99]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i37KF8jR025864 for ; Wed, 7 Apr 2004 15:15:08 -0500 Received: from epahub11.rtp.epa.gov (epahub11.rtp.epa.gov [134.67.213.52]) by epamail.epa.gov (PMDF V5.2-32 #42056) with ESMTP id <0HVT00O0SHBX8I!at!epamail.epa.gov> for CHEMISTRY!at!ccl.net; Wed, 7 Apr 2004 16:09:33 -0400 (EDT) Date: Wed, 07 Apr 2004 16:09:31 -0400 From: Fan.Huajun!at!epamail.epa.gov Subject: CCL: EPA DSSTox database available To: CHEMISTRY!at!ccl.net Message-id: MIME-version: 1.0 X-Mailer: Lotus Notes Release 5.0.12 February 13, 2003 Content-type: text/plain; charset=US-ASCII X-MIMETrack: Serialize by Router on EPAHUB11/USEPA/US(Release 6.0.2CF1|June 9, 2003) at 04/07/2004 04:09:33 PM Hi All, I am posting this for Dr Richard. If you need any further information, please feel free to contact her. ****************************************************************************** ACD Labs has recently posted links to our current DSSTox database offerings, as well as posted ACD ChemFolder files augmented with IUPAC names and ACD properties for open-access download at: http://www.acdlabs.com/download/db/weblibdb.html In addition, to introduce features of "Web Librarian", ACD's web-based chemical relational database product, to the larger user community (based on the ChemFolder application), they offer free, structure-searchable on-line access to all of our DSSTox DBs at the above website. We thank them for their valuable contribution to the DSSTox effort. If you visit and use the above site, please provide ACD Labs with feedback on this public service. Regards to all, Ann Richard ****************************************************************************** Ann M Richard Mail Drop B143-06 Environmental Carcinogenesis Division National Health and Environmental Effects Research Laboratory US Environmental Protection Agency Research Triangle Park, NC 27711 tel: 919-541-3934 fax: 919-685-3263 email: richard.ann!at!epa.gov ****************************************************************************** From chemistry-request@ccl.net Wed Apr 7 13:58:19 2004 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i37IwJjR023555 for ; Wed, 7 Apr 2004 13:58:19 -0500 Received: from [165.91.177.61] (HELO yubopclab) by mail.chem.tamu.edu (CommuniGate Pro SMTP 4.1.8) with SMTP id 1278743 for chemistry!at!ccl.net; Wed, 07 Apr 2004 13:58:25 -0500 Message-ID: <000c01c41cd2$4acbda00$3db15ba5@yubopclab> From: "Yubo Fan" To: Subject: Calculate N2 with different basis sets Date: Wed, 7 Apr 2004 13:58:19 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C41CA8.61C4FE00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C41CA8.61C4FE00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I tried to use different basis sets to calculate N2 molecule but failed. = How can I set the Gaussian 03 input file to run this type of homoatomic = molecules? Thanks. Sincerely, Yubo ------=_NextPart_000_0009_01C41CA8.61C4FE00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,
 
I tried to use different basis sets to = calculate N2=20 molecule but failed. How can I set the Gaussian 03 input file to run = this type=20 of homoatomic molecules? Thanks.
 
Sincerely,
 
Yubo
------=_NextPart_000_0009_01C41CA8.61C4FE00-- From chemistry-request@ccl.net Wed Apr 7 17:30:25 2004 Received: from web20909.mail.yahoo.com (web20909.mail.yahoo.com [216.136.226.231]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i37MUOjR000744 for ; Wed, 7 Apr 2004 17:30:24 -0500 Message-ID: <20040407223031.87190.qmail..at..web20909.mail.yahoo.com> Received: from [128.227.192.230] by web20909.mail.yahoo.com via HTTP; Wed, 07 Apr 2004 15:30:31 PDT Date: Wed, 7 Apr 2004 15:30:31 -0700 (PDT) From: Anatoli Korkin Subject: Comparison ab initio vs DFT and semi-empirical methods To: chemistry..at..ccl.net Cc: jlabanow..at..nd.edu MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Colleagues, I will appreciate if you send me refenece(s) of your, or someone else's paper or review, where computed properties (desirably many) calculated with different methods are tabulated for comparison of the performance of the higher level ab initio approaches (e.g. CC, MP4, and/or CI) vs DFT and/or semi-empirical methods. I will send a summary to the list, if there is interest. Thank you very much for your help and consideration. Best regards, Anatoli Korkin __________________________________ Do you Yahoo!? Yahoo! Small Business $15K Web Design Giveaway http://promotions.yahoo.com/design_giveaway/