From chemistry-request@server.ccl.net Tue Jun 22 14:53:23 1999 Received: from mailserv.mta.ca (root@mailserv.mta.ca [138.73.101.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA21289 for ; Tue, 22 Jun 1999 14:53:23 -0400 Received: from m0336.mta.ca (host-22-226.mta.ca [138.73.22.226]) by mailserv.mta.ca (8.9.3/8.9.3) with SMTP id PAA06781 for ; Tue, 22 Jun 1999 15:42:41 -0300 (ADT) Date: Tue, 22 Jun 1999 15:42:41 -0300 (ADT) Message-Id: <1.5.4.16.19990622154342.74b70018@mailserv.mta.ca> X-Sender: mculf@mailserv.mta.ca X-Mailer: Windows Eudora Light Version 1.5.4 (16) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: Miroslava Culf Subject: Deleting files Dear all, I need a program for Unix environment that would automatically delete all files in certain directories that are older then, i.e. last used longer then some time ago (for example 1 month). Does anybody have such a program available either as an UNIX shell program or in any other way. Thanks very much for your help, Mira ____________________________________________________________ Miroslava Cuperlovic-Culf, Ph.D. 65 York St. Computer Services Department/Chemistry Department Mount Allison University Sackville, NB E4L 1E4 Canada e-mail: mculf@mta.ca tel. 506-364-2411 ____________________________________________________________ From chemistry-request@server.ccl.net Wed Jun 23 20:12:56 1999 Received: from office.un.md (root@office.un.md [212.0.211.34]) by server.ccl.net (8.8.7/8.8.7) with SMTP id UAA17800 for ; Wed, 23 Jun 1999 20:12:55 -0400 Received: from un.md ([212.0.205.38]) by office.un.md (8.6.13/8.6.12xla) with SMTP id TAA04835 for ; Wed, 23 Jun 1999 19:04:27 +0300 Date: Wed, 23 Jun 1999 19:04:41 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.15) S/N B6042885 Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <10794.990623@mail.ru> To: CHEMISTRY@ccl.net Subject: Help need -- a copy of journal Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit +======================---------------- --- -- - - - - . | Hello Chemistry, : . Could anybody help me? I need two articles, but I couldn't find them in our library. Could anybody scan them and send to me? (Please, send big attaches, more than 200Kb to mmpsf@cni.md). If so, here are the references: * P.Pulay, G. Fogarosi, J.E.Boggs J.Am.Chem.Soc., 101, 2550-2560 (1979) * G. Fogarosi, X.Zhou, P.W.Taylor, P.Pulay J.Am.Chem.Soc., 114, 8191-8201 (1992) This two articles describes "natural internal coordinates" and their application for ring systems. If anybody could provide me link to the Internet resource, I will be thankful. Best regards, Mike mailto:MikePeleah@mail.ru ... Too many mind. Abort, Retry, Ignore? . : | . - - - - -- --- ----------------======================+ From chemistry-request@server.ccl.net Wed Jun 23 20:13:02 1999 Received: from anorg.chem.uva.nl (anorg.chem.uva.nl [145.18.129.200]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA17805 for ; Wed, 23 Jun 1999 20:13:01 -0400 Received: from hk-pc11 (hk-pc11.chem.uva.nl [145.18.129.149]) by anorg.chem.uva.nl (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id MAA24020 for ; Wed, 23 Jun 1999 12:58:43 GMT Message-Id: <3.0.6.32.19990623130053.007b4440@anorg.chem.uva.nl> X-Sender: sirik@anorg.chem.uva.nl X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 23 Jun 1999 13:00:53 +0200 To: chemistry@ccl.net From: sirik Deerenberg Subject: end of my contract Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCL, My contract has come to an end and for now I won't be working in the field of Molecular Modelling. Maybe in the future. I want to thank you for all the informative e-mails. So, please take me out of the CCL-list. Best regards, Sirik Deerenberg Sirik Deerenberg Institute for Molecular Chemistry, Department of Homogeneous Catalysis and Inorganic Chemistry, Nieuwe Achtergracht 166, 1018 WV, Amsterdam, The Netherlands. Tel. +31 20 5255005/6510 e-mail: sirik@anorg.chem.uva.nl From chemistry-request@server.ccl.net Wed Jun 23 20:16:30 1999 Received: from ex1.ncsa.uiuc.edu (ex1.ncsa.uiuc.edu [141.142.2.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA17983 for ; Wed, 23 Jun 1999 20:16:30 -0400 Received: from mx1.ncsa.uiuc.edu (mx1.ncsa.uiuc.edu [141.142.2.8]) by ex1.ncsa.uiuc.edu (8.9.3/8.9.3) with ESMTP id KAA09534 for ; Wed, 23 Jun 1999 10:51:29 -0500 (CDT) Received: from thymine.ncsa.uiuc.edu (thymine.ncsa.uiuc.edu [141.142.221.22]) by mx1.ncsa.uiuc.edu (8.9.3/8.9.3) with ESMTP id KAA19854 for ; Wed, 23 Jun 1999 10:51:29 -0500 (CDT) Received: (from dsteiger@localhost) by thymine.ncsa.uiuc.edu (980427.SGI.8.8.8/8.8.5) id KAA09889; Wed, 23 Jun 1999 10:51:28 -0500 (CDT) Date: Wed, 23 Jun 1999 10:51:28 -0500 (CDT) From: "D. Steiger" To: chemistry@server.ccl.net Subject: Charge density functions for large molecules? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-md5sum: 318840b8fbe9f8653acf4138329b0a92 X-md5sum-Origin: mx1.ncsa.uiuc.edu I would like to derive as accurately as possible the charge density function for a molecule with 3,500 atoms. Does anybody know of any references that discusses this problem. Don Steiger dsteiger@cysteine.ncsa.uiuc.edu From chemistry-request@server.ccl.net Wed Jun 23 20:16:31 1999 Received: from ex1.ncsa.uiuc.edu (ex1.ncsa.uiuc.edu [141.142.2.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA17985 for ; Wed, 23 Jun 1999 20:16:30 -0400 Received: from mx1.ncsa.uiuc.edu (mx1.ncsa.uiuc.edu [141.142.2.8]) by ex1.ncsa.uiuc.edu (8.9.3/8.9.3) with ESMTP id KAA09177 for ; Wed, 23 Jun 1999 10:44:07 -0500 (CDT) Received: from thymine.ncsa.uiuc.edu (thymine.ncsa.uiuc.edu [141.142.221.22]) by mx1.ncsa.uiuc.edu (8.9.3/8.9.3) with ESMTP id KAA18725 for ; Wed, 23 Jun 1999 10:44:06 -0500 (CDT) Received: (from dsteiger@localhost) by thymine.ncsa.uiuc.edu (980427.SGI.8.8.8/8.8.5) id KAA09874; Wed, 23 Jun 1999 10:44:06 -0500 (CDT) Date: Wed, 23 Jun 1999 10:43:58 -0500 (CDT) From: "D. Steiger" To: chemistry@server.ccl.net Subject: Continuous charge density function for large molecules. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-md5sum: 6df9012b2b7cb3c55963499a26309bba X-md5sum-Origin: mx1.ncsa.uiuc.edu I would like to obtain an accurate as possible charge density function for a molecule that contains 3,500 atoms. Can anyone point me to any references that discuss methods for solving this type of problem. Don Steiger dsteiger@cysteine.ncsa.uiuc.edu From chemistry-request@server.ccl.net Wed Jun 23 20:17:38 1999 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA18068 for ; Wed, 23 Jun 1999 20:17:37 -0400 Received: from red5 (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with SMTP id NAA02896; Wed, 23 Jun 1999 13:18:31 -0700 (PDT) Message-Id: <4.1.19990623131619.01e07310@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Wed, 23 Jun 1999 13:22:31 -0700 To: Bernd Engels , chemistry@server.ccl.net (Computational Chemistry List) From: Laurence Lavelle Subject: Re: CCL:summary_errors in comp chem. In-Reply-To: <199906110829.KAA17242@rs5.thch.uni-bonn.de> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 10:29 AM 6/11/99 +0200, Bernd Engels wrote: >Below please find a summary of the responses >I got to the following question: > >>I am looking for systems which are theoretically >>difficult. I am interested in all kind of systems, >>i.e. in systems which makes problems for DFT and/or >>Coupled Clusters and/or Moller-Plesset etc. >>there should be a lot of systems which are >>really problematic and (what a pity) where the >>problems where never published. > > >Thanks a lot to all who have answered. >It was really interesting. >Bernd Engels > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >Dear Prof. Engels, > > I have started to put together a web accessible database of molecules and >particular theoretical methods which produce poor results. It doesn't have >many species in it yet. I have it running on a small web server which is >currently at: > >http://h194161.nist.gov/sicklist/sicklist.html Any updates on this address. My access is blocked on asking for user ID & password. >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >Dear Bernd, > >At the last ACS meeting, Karl Irikura reported that his group at NIST is >developing several resources to be made readily available in support of QC >applications: > > http://www.nist.gov/compchem > >One of these developments is to collect examples of known failures of >specific methods into a "Quantum Chemistry Sicklist Database." This sounds >very much like what you are looking for: I did not find a link on this topic. Any suggestions. Thanks Laurence """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Department of Chemistry & Biochemistry and Molecular Biology Institute Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Office): (310) 825-2083 Room 3048A Young Hall Fax: (310) 206-4038 Phone (Lab): (310) 206-8270 Room 269B MBI http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" From chemistry-request@server.ccl.net Wed Jun 23 20:18:41 1999 Received: from darkwing.uoregon.edu (root@darkwing.uoregon.edu [128.223.142.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA18117 for ; Wed, 23 Jun 1999 20:18:40 -0400 Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id OAA26095 for ; Tue, 22 Jun 1999 14:53:05 -0700 (PDT) Date: Tue, 22 Jun 1999 14:53:04 -0700 (PDT) From: "Dale A. Braden" To: chemistry@ccl.net Subject: Re: CCL:Gaussian AIM Calculation Failure In-Reply-To: <80256794.005867D4.00@gbrhn001.ici-group.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Steve, I had this problem also, and there is no cure using G94 or G98. Jerzy Cioslowski was kind enough to look at one of my output files, and he told me that the topology of the electron density in the metal sandwich compounds I was modeling was beyond the current capability of the AIM code. The PROMEGA algorithm contained in the AIMPAC package distributed by Bader (http://www.chemistry.mcmaster.ca/aimpac/) worked in my cases, but it only treats one atom at a time, and is very slow. Best wishes, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From chemistry-request@server.ccl.net Wed Jun 23 20:24:33 1999 Received: from ce.fis.unam.mx (ce.fis.unam.mx [132.248.33.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA18296 for ; Wed, 23 Jun 1999 20:24:32 -0400 Received: from ce.fis.unam.mx ([132.248.33.121]) by ce.fis.unam.mx with ESMTP (8.7.1/8.7.1) id RAA27140; Tue, 22 Jun 1999 17:00:05 -0700 (PDT) Message-ID: <3770156C.8E0DBB38@ce.fis.unam.mx> Date: Tue, 22 Jun 1999 16:59:56 -0600 From: Max Valdez Organization: Centro de Ciencias Fisicas, UNAM X-Mailer: Mozilla 4.6 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: jmmckel@ibm.net, CHEMISTRY@ccl.net Subject: Re: CCL:G94W/G98W References: <376F97FC.2A13@ibm.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCL! About your question John: I have usead a 6311G** with 942 basis functions for a pentapentide. I would like to hear about some others. Best Regards Max Valdez > CCLers... > > Just a curiosity... > > What's the biggest basis set anyone has used with G94W or G98W ? > > Thanks! > > John McKelvey > > -= 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 From chemistry-request@server.ccl.net Wed Jun 23 20:29:44 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA18367 for ; Wed, 23 Jun 1999 20:29:43 -0400 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay1.scripps.edu (8.9.3/TSRI-3.0.2r) with ESMTP id RAA15142 for ; Wed, 23 Jun 1999 17:01:58 -0700 (PDT) Received: from scripps.edu (localhost [127.0.0.1]) by elvis.scripps.edu (8.9.2/TSRI-3.0) with ESMTP id RAA63081 for ; Wed, 23 Jun 1999 17:01:58 -0700 (PDT) Sender: yadavm@scripps.edu Message-ID: <37717576.4C77E789@scripps.edu> Date: Wed, 23 Jun 1999 17:01:58 -0700 From: Maneesh Yadav X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Dock woes Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have posted before but I don't know if my message got out (or if this was considered appropriate for the list) I am currently using UCSF Dock 4.0 and have been having a nunmber of problems lately... I am testing with an internal cavity in a protien, and seems to me that the scoring method that gives the best indication of ligand fit is the contact score. The chemical screening/matching stuff just doesn't seem to work...any comments on this? Another thing, when I leave dock to run overnight, I come back in the morning to see it running unusably slow on my octane because it's chattering way too much to virtual memory. Is it not freeing unused memory or something? Any tips for using it on a ~100k compund database? Many Thanks, Maneesh Yadav From chemistry-request@server.ccl.net Wed Jun 23 20:26:06 1999 Received: from smtp01.kent.edu (kent.edu [131.123.77.110]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA18333 for ; Wed, 23 Jun 1999 20:26:04 -0400 Received: from kent.edu ([131.123.16.53]) by smtp01.kent.edu (8.9.1/8.9.1) with SMTP id QAA10649 for ; Wed, 23 Jun 1999 16:29:04 -0400 Date: Wed, 23 Jun 1999 16:29:04 -0400 Message-Id: <199906232029.QAA10649@smtp01.kent.edu> X-Sender: scabanis@pop.kent.edu X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@server.ccl.net From: Steve Cabaniss Subject: ACS Symposium: COMP METHODS IN ENVIRONMENTAL CHEM COMPUTATIONAL METHODS IN ENVIRONMENTAL CHEMISTRY Division of Environmental Chemistry 219th American Chemical Society (ACS) National Meeting March 26-31, 2000 San Francisco, CA Rapidly evolving progress in computer hardware and software has promoted the application of sophisticated chemical models to complex environmental problems. This symposium will showcase the application of computational methods, including molecular modeling of pollutant properties and reactions, kinetic simulations of complex reactions, and aqueous equilibrium modeling. Oral presentations will emphasize A) novel algorithms and models which could be applied to environmental problems, B) models and algorithms first applied to environmental problems in the last five years and C) prospective environmental applications for which only preliminary results are available. Short abstracts (required by ACS) and extended abstracts no longer than 4 pages (required by the Division of Environmental Chemistry, see divisional web page http://gemini.tntech.edu/~mjw5030/acspage.html) must be submitted by November 3, 1999 to: Steve Cabaniss Department of Chemistry Kent State University Kent, OH 44242 (330)672-3731 FAX (330)672-3816 email: scabanis@kent.edu Steve Cabaniss Chemistry Dept. Kent State University Kent, OH 44242 (330) 672-3731 From chemistry-request@server.ccl.net Wed Jun 23 21:22:18 1999 Received: from out1.ibm.net (out1.ibm.net [165.87.194.252]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA19075 for ; Wed, 23 Jun 1999 21:22:17 -0400 From: jmmckel@ibm.net Received: from puccini (slip166-72-87-33.ny.us.ibm.net [166.72.87.33]) by out1.ibm.net (8.8.5/8.6.9) with SMTP id BAA167402 for ; Thu, 24 Jun 1999 01:18:45 GMT Message-ID: <37714184.27AB@ibm.net> Date: Wed, 23 Jun 1999 21:20:20 +0100 Reply-To: jmmckel@ibm.net X-Mailer: Mozilla 3.04 (WinNT; I) MIME-Version: 1.0 To: Chemistry@server.ccl.net Subject: MOPAC_2000 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit CCLers... This may not be news to many of you, but in regards to a recent posting about atomic charges for large systems... Mopac_2000 can now do a 1SCF on a 4150 atom system on a PII-400/NT machine in less than 1 hour... answer is the same as by MOPAC6, if it could be done. The 4150 atom can be done using MPI on a 16 processor SGI-O2K in 7(seven) minutes. A 7,000 atom and a 11,000 atom system is being used for debugging, with a 17,000 atom case standing by. John McKelvey From chemistry-request@server.ccl.net Wed Jun 23 23:29:02 1999 Received: from mserv1b.u-net.net (mserv1b.u-net.net [195.102.240.137]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA20013 for ; Wed, 23 Jun 1999 23:29:02 -0400 Received: from [195.102.83.47] (helo=Biofocusn) by mserv1b.u-net.net with smtp (Exim 2.10 #61) id 10wiYe-0000Cc-00 for CHEMISTRY@ccl.net; Wed, 23 Jun 1999 09:39:00 +0100 Message-ID: <000f01bebd53$dbef9780$2f5366c3@Biofocusn.u-net.com> Reply-To: "Dr Adrian Stevens" From: "Dr Adrian Stevens" To: Subject: MMFF94 validation in Sybyl and Cerius2 Date: Wed, 23 Jun 1999 09:39:06 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Dear All, Has anyone checked the implementation of the MMFF94 force field in both Sybyl and Cerius2? My concern follows some contrasting results observed when a client and myself both modelled the same compound in the cis and trans forms (about a butadiene moiety in the structure). The difference in conformational energies obtained from the two packages was staggering! Although both companies claim to have incorporated the force field into their MM engines, they do not produce comparable results; both in terms of energy differences and of the predicted lowest energy conformation. One test I ran on Sybyl came from the Gundertofte MM comparison paper (Gundertofte K, et al, J. Comp. Chem., vol.17, no.4, 429-449 (1996)) and looked at the cis and trans forms of butadiene. The energy difference between these two forms agreed with the literature result within 0.1 kcal. I'm awaiting the clients test on the same system. If anyone has **independently** examined the force field in these packages, I'd be very keen to hear if the results were comparable. Many thanks Adrian.