From chemistry-request@server.ccl.net Mon Aug 26 04:13:40 2002 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7Q8Der13315 for ; Mon, 26 Aug 2002 04:13:40 -0400 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.1-1 #40925) id <0H1F00601YUQ0X@mailhost2.tudelft.nl> for chemistry@ccl.net; Mon, 26 Aug 2002 10:13:40 +0200 (MEST) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.1-1 #40925) with ESMTP id <0H1F002EBYUPDQ@mailhost2.tudelft.nl> for chemistry@ccl.net; Mon, 26 Aug 2002 10:13:37 +0200 (MEST) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.12.5/8.12.5) with ESMTP id g7Q8DRp2010711 for ; Mon, 26 Aug 2002 10:13:37 +0200 (MEST) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Mon, 26 Aug 2002 10:13:37 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Mon, 26 Aug 2002 10:13:25 +0000 (MET-1MEST) Date: Mon, 26 Aug 2002 10:13:21 +0200 From: Stefan Bromley Subject: 2 centre intermolecular hydrogen potential? To: chemistry@ccl.net Message-id: <3D69FF3E.26637.1334D941@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Dear CCL, does anyone know of a good atomic centred (2-centre) non-bonded intermolecular potential for hydrogen (H2) and, in particular, its performance in MC/MD simulations (e.g. adsorption, diffusion) compared to the often used centre-of-mass (one-centre) Lennard- Jones intermolecular potential which neglects the internal vibrational degrees of freedom of the H2 molecular. Best regards, Stefan ________________________________________________________ Dr Stefan T. Bromley Laboratory of Applied Organic Chemistry and Catalysis DelftChemTech, Delft University of Technology Julianalaan 136, 2628 BL Delft The Netherlands Phone : + 31 1527 89418 e-mail : S.T.Bromley@tnw.tudelft.nl ________________________________________________________ From chemistry-request@server.ccl.net Sun Aug 25 19:20:45 2002 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7PNKjr06509 for ; Sun, 25 Aug 2002 19:20:45 -0400 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KLQ57QWKGW00092S@trentu.ca> for chemistry@ccl.net; Sun, 25 Aug 2002 19:20:39 EDT Date: Sun, 25 Aug 2002 19:22:40 -0400 From: elewars Subject: Re: CCL:History question To: chemistry@ccl.net Message-id: <3D6966BF.D0E9D4C9@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: <38EED9506B1@virgil.ruc.dk> 2002 Aug 25 Hello, That is an interesting question, because the exact source of the assertion never seems to be given. I can only suggest you try to track it down using: T. S. Kuhn, "Black-Body Radiation and the Quantum Discontinuity 1894-1912", U. of Chicago Press, 1978. (Kuhn became controversial for his idea idea of paradigm (a trendy word he popularized) shifts, in his "The Structure of Scientific Revolutions") J. Mehra and H. Rechenberg, "The Historical development of Quantum Theory", Vols. 1 and 2. Springer- Verlag, New York, 1982. (Possibly the definitive work on the history of QM). E. Segre, "From X-Rays to Quarks" Freeman, New York, 1980. A history of modern physics by the 1959 physics Nobel cowinner. B. Bederson, "More Things in Heaven and Earth: a Celebration of Physics at the Millenium", Springer- Verlag, New York, 1999. Useful may be the extensive references in the remarkable novel "Night Thoughts of a Classical Physicist", by Russell McCormmach, Harvard U Press, 1982. As far as an actual quotation goes: "By the beginning of the twentieth century, most scientists felt satisfied that all their important problems were more or less solved. ... it seemed that all that was needed was to fill in a few details. How wrong they were." From "To light such a candle", Oxford U Press, 1998, p. 290; by the Canadian physical chemist and historian Keith Laidler. E. Lewars ======================= Jens Spanget-Larsen wrote: > Dear CCL, > > we are occasionally told that towards the end of the 19th century, > some scientists (physicists?) tended to believe that after Newton's > Mechanics and Maxwell's Equations all fundamental discoveries in > physics were made and that future work would only deal with details. > They even discouraged young people to enter the field! But then, of > course, came the turn of the century with, in 1895-1905, X-rays, > Zeeman effect, radioactivity, the electron, quantum theory, and > theory of relativity. > > I would be grateful for information on literature that documents this > story. Any quotations? > > Yours, Jens >--< > > NB! Please note new mail address: > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > JENS SPANGET-LARSEN Office: +45 4674 2710 > Department of Chemistry Fax: +45 4674 3011 > Roskilde University (RUC) Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget@ruc.dk > DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Mon Aug 26 05:35:45 2002 Received: from smtpscan-nl1.vscan.dsm-group.com ([163.175.162.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7Q9Zir16717 for ; Mon, 26 Aug 2002 05:35:44 -0400 Received: from nlgln20ntms920.GLN20.DSM-GROUP.COM (localhost [127.0.0.1]) by smtpscan-nl1.vscan.dsm-group.com (8.9.3/8.8.5-1.2.2m-19990317) with ESMTP id LAA11599 for ; Mon, 26 Aug 2002 11:35:43 +0200 (MET DST) Received: by nlgln20ntms920.gln20.dsm-group.com with Internet Mail Service (5.5.2653.19) id ; Mon, 26 Aug 2002 11:35:06 +0200 Message-ID: <6D47A7D05774D411959200508BDF739A024383E3@nlgln50ntms001.gln51.dsm-group.com> From: "Coussens, Betty" To: "'chemistry@ccl.net'" Subject: problem with TDDFT in Gaussian98 Date: Mon, 26 Aug 2002 11:35:05 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear all, I am performing TDDFT calculations using Gaussian98 Rev. A9 on a Windows NT IBM machine and I have problems using the keyword Add=N for computing additional states after succesful termination of a job wih Nstates=M. Instead of giving the additional states the Gaussian output appears to contain the excitation energies and oscillator strengths of the same first three states that were produced in the run before, i.e. using the keyword NStates=M. Any idea what's going on? Thanks in advance! Betty Disclaimer 1. This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. 2. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately. This e-mail is confidential and may be legally privileged. DSM does not guarantee that the information sent and/or received by or with this e-mail is correct and does not accept any liability for damages related thereto. From chemistry-request@server.ccl.net Mon Aug 26 08:33:50 2002 Received: from ws0e.pc.chemie.tu-darmstadt.de ([130.83.242.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7QCXnr23749 for ; Mon, 26 Aug 2002 08:33:49 -0400 Received: from localhost (hatice@localhost) by ws0e.pc.chemie.tu-darmstadt.de (SGI-8.9.3/8.9.3) with ESMTP id OAA11807 for ; Mon, 26 Aug 2002 14:33:48 +0200 (CDT) Date: Mon, 26 Aug 2002 14:33:48 +0200 From: "Dr. Hatice Can" To: chemistry@ccl.net Subject: CASSCF: StateAverage calculations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Members, I am doing CASSCF calculations on a cation. I am not clear about why state average calculations is done. What for is it? Is it really necessary? If you would sent any suggestions or literature name, I will be glad. Thank you in advnace, and the responses will be summarised. Regards, Hatice ***************************************************************************** Dr. Hatice Can Darmstadt University of Technology Chemistry Department Physical Chemistry I Petersenstrase 20 64287 Darmstadt Germany Phone: (+49) 6151 16 5397 Fax: (+49) 6151 16 4298 E-mail: hatice@pc.chemie.tu-darmstadt.de WWW: http://www.pc.chemie.tu-darmstadt.de/staff/hatice/ ***************************************************************************** From chemistry-request@server.ccl.net Mon Aug 26 13:25:46 2002 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7QHPjr04324 for ; Mon, 26 Aug 2002 13:25:45 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #12) id 17jNcS-0006kg-00 for chemistry@ccl.net; Mon, 26 Aug 2002 19:25:40 +0200 Message-ID: <3D6A6474.3000504@mpi-bpc.mpg.de> Date: Mon, 26 Aug 2002 19:25:08 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: CCL list Subject: adding protons Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCL-ers, This email would be better sent to AMBER list but it seems that the AMBER list is out of order these days. I have a pdb file with a piece of RNA. I will run dynamics with it. The problem is that the pdb does not have protons. I tried to use protonate for the purpose but it does not work at all for nucleic acids. On the other hand Leap is adding by default the protons. So, the question is: Is the default add by Leap reliable or should I use o more reliable way. If the latter can somebody suggest a freeware that can be used for this purpose? Maybe also a bit of discussion about the importance of initial positions of the protons for a MD run ....especially for Nucleic Acids. Thanks a lot in advance for any kind of Replies. Best regards, vlad -- Vlad Cojocaru Max Planck Institut for Biophysical Chemistry Deparment: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de From chemistry-request@server.ccl.net Mon Aug 26 09:48:37 2002 Received: from maties1.sun.ac.za ([146.232.128.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7QDmXr26810 for ; Mon, 26 Aug 2002 09:48:36 -0400 Received: from exchimc.sun.ac.za ([146.232.129.34]) by maties1.sun.ac.za with esmtp (Exim 4.05) id 17jKDk-0006cO-00; Mon, 26 Aug 2002 15:47:56 +0200 Received: by exchimc.sun.ac.za with Internet Mail Service (5.5.2656.59) id ; Mon, 26 Aug 2002 15:47:13 +0200 Message-ID: <2827D92BF3C4D311A3DA00805FB785230435AB7A@exchange01.sun.ac.za> From: Dillen J Prof To: "'Jens Spanget-Larsen'" Cc: "'chemistry@ccl.net'" Subject: RE: History question Date: Mon, 26 Aug 2002 15:44:02 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain; charset="iso-8859-1" X-Scanner: exiscan for exim4 (http://duncanthrax.net/exiscan/) *17jKDk-0006cO-00*7uoQ4G93HDo* Jens, There is a (very good) book by Barbara Lovett Cline: "The questioners: physicists and the quantum theory" (Thomas Crowell Co, New York, 1965) where it is said that a statement of this type was communicated by the "head of the physics department" to Max Planck when he wanted to enter the university. The book mentions that this happened in 1875. No name is given for this departmental head, but Planck started his studies at Munich, and moved on to Berlin at a later stage. Jan > -----Original Message----- > From: Jens Spanget-Larsen [mailto:spanget@virgil.ruc.dk] > Dear CCL, > > we are occasionally told that towards the end of the 19th century, > some scientists (physicists?) tended to believe that after Newton's > Mechanics and Maxwell's Equations all fundamental discoveries in > physics were made and that future work would only deal with details. > They even discouraged young people to enter the field! But then, of > course, came the turn of the century with, in 1895-1905, X-rays, > Zeeman effect, radioactivity, the electron, quantum theory, and > theory of relativity. > > From chemistry-request@server.ccl.net Mon Aug 26 11:04:21 2002 Received: from mail.ccmsi.us ([143.132.103.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7QF4Lr30088 for ; Mon, 26 Aug 2002 11:04:21 -0400 Received: from Falcon [10.30.6.25] by mail.ccmsi.us (SMTPD32-7.07) id A372640080; Mon, 26 Aug 2002 10:04:18 -0500 Message-ID: <000701c24d11$dadf5f50$19061e0a@ccmsi.us> From: "Yevgeniy Podolyan" To: Subject: 11th Conference on Current Trends in Computational Chemistry Date: Mon, 26 Aug 2002 10:04:20 -0500 Organization: Jackson State University 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 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear Colleagues! This is to remind you that the registration deadline for the 11th Conference on Current Trends in Computational Chemistry is approaching very fast. Please, visit our conference web site (http://ccmsi.us/cctcc) for details and registration. We hope to see you in November. Sincerely, 11th CCTCC Organizing Committee From chemistry-request@server.ccl.net Mon Aug 26 19:44:38 2002 Received: from mail.staff.site.ntu.edu.au ([138.80.69.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7QNiar25872 for ; Mon, 26 Aug 2002 19:44:37 -0400 Received: from mail.staff.site.ntu.edu.au ([138.80.49.23]) by mail.staff.site.ntu.edu.au with Microsoft SMTPSVC(5.0.2195.5329); Tue, 27 Aug 2002 09:14:34 +0930 Received: by mail.staff.site.ntu.edu.au (sSMTP sendmail emulation); Tue, 27 Aug 2002 09:14:02 +0930 Date: Tue, 27 Aug 2002 09:14:02 +0930 From: Brian Salter-Duke To: Comp Chem List Subject: WATOC02 Poster on B2H2 Message-ID: <20020826234402.GA1612@BSALTERDUKE1> Mail-Followup-To: Comp Chem List Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.99i X-OriginalArrivalTime: 26 Aug 2002 23:44:35.0578 (UTC) FILETIME=[88B565A0:01C24D5A] I seek help in tracking down the author of a poster that was presented at the recent WATOC02 meeting in Lugano. The poster was presented at the first poster session. I had my own poster at that session and did not have enough time to talk to the presenter of a poster on B2H2. Naturally I assumed that details were in the abstract book, but I later discovered that this poster was a late poster, details were not in the abstracts book and the WATOC organisers had not kept records of the late posters. The poster was in the small room upstairs and was nearest to the door in the row facing the right (looking from the door) wall. So, if the author of that poster is on this list, could they please contact me. If anyone at WATOC remembers this poster and the author, please contact me also. I really do need to know where this work is going to be published. Many thanks and best regards, Brian. -- Brian Salter-Duke (Brian Duke) b_duke@octa4.net.au Honorary Fellow in Chemistry, NT University, Darwin, NT 0909, Australia. Post: Box 1028, Humpty Doo, NT 0836, Australia. Phone 08-89881600. Fax 08-89881302. http://www.octa4.net.au/linden/brian/ From chemistry-request@server.ccl.net Mon Aug 26 15:54:01 2002 Received: from mole.chem.iupui.edu ([134.68.136.192]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7QJs0r11602 for ; Mon, 26 Aug 2002 15:54:00 -0400 Received: from mole.chem.iupui.edu (mole.chem.iupui.edu [134.68.136.192]) by mole.chem.iupui.edu (8.9.1/8.9.1) with ESMTP id OAA812161; Mon, 26 Aug 2002 14:53:45 -0500 (EST) Date: Mon, 26 Aug 2002 14:53:45 -0500 From: Daquan Gao To: Vlad Cojocaru cc: CCL list Subject: Re: CCL:adding protons In-Reply-To: <3D6A6474.3000504@mpi-bpc.mpg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In my opinion, the initial hydrogen positions are not very important, except that it might flip the chirality if the hydrogen is on a chiral center and the initial position is "too bad". I don't have any freeware for this, macromodel does a good job if the correct connectivity is given (meaning the bonds between the heavy atoms are correct), but not free. I think reinventing the wheel by writing a small script is not that hard. Basically you look for the plane of the three atoms if the hydrogen is connected to a carbon in between two other heavy atoms, and then form a perpendicular plane. Then put hydrogens in the plane. Checking number of hydrogens that are already there and connectivity is probably somewhat tedious. regards, daquan On Mon, 26 Aug 2002, Vlad Cojocaru wrote: > Dear CCL-ers, > This email would be better sent to AMBER list but it seems that the > AMBER list is out of order these days. > I have a pdb file with a piece of RNA. I will run dynamics with it. > The problem is that the pdb does not have protons. I tried to use > protonate for the purpose but it does not work at all for nucleic acids. > On the other hand Leap is adding by default the protons. So, the > question is: Is the default add by Leap reliable or should I use o more > reliable way. If the latter can somebody suggest a freeware that can be > used for this purpose? > Maybe also a bit of discussion about the importance of initial > positions of the protons for a MD run ....especially for Nucleic Acids. > Thanks a lot in advance for any kind of Replies. > Best regards, > vlad > > -- > Vlad Cojocaru > Max Planck Institut for Biophysical Chemistry > Deparment: 060 > Am Fassberg 11, 37077 Goettingen, Germany > tel: ++49-551-201.1389 > e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Mon Aug 26 15:51:01 2002 Received: from email03.aon.at ([195.3.96.93]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g7QJoTr11446 for ; Mon, 26 Aug 2002 15:51:01 -0400 Received: (qmail 27746 invoked from network); 26 Aug 2002 19:50:14 -0000 Received: from m885p003.adsl.highway.telekom.at ([62.47.142.131]) (envelope-sender ) by qmail3rs.highway.telekom.at (qmail-ldap-1.03) with SMTP for ; 26 Aug 2002 19:50:14 -0000 Subject: Workstation help From: "Mag.phar. Klaus Leisser" To: chemistry@ccl.net Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Evolution/1.0.2 Date: 26 Aug 2002 21:51:11 +0200 Message-Id: <1030391472.5636.11.camel@gandalf> Mime-Version: 1.0 Hello everybody, For a new small startup doing computational chemistry and biology (mostly alignment, number crunching) I am going to buy a new workstation. Could anyone help me in deciding which hardware to buy (is the intel xeon worth the high price compared to a pentium 4 ?) or does anybody know a source on the net where I could find help ? Thanks and best greetings from Vienna, Klaus Klaus Leisser leisser.klaus@aon.at From chemistry-request@server.ccl.net Mon Aug 26 21:20:53 2002 Received: from ptah.u.arizona.edu (IDENT:daemon@[128.196.133.224]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7R1Kqr03483 for ; Mon, 26 Aug 2002 21:20:53 -0400 Received: from localhost (okwon@localhost) by ptah.u.arizona.edu (8.11.6+Sun/8.10.2) with ESMTP id g7R1KlH01417 for ; Mon, 26 Aug 2002 18:20:50 -0700 (MST) X-Authentication-Warning: ptah.u.arizona.edu: okwon owned process doing -bs Date: Mon, 26 Aug 2002 18:20:47 -0700 (MST) From: Ohyun Kwon To: chemistry@ccl.net Subject: iop option in G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers; I would like to print out MO coefficients and eigenvalues in higher precision in G98. Does anybody know which IOP option I should use for this purpose? Thank you for your kind attention in advance. Best wishes, Ohyun Kwon, Ph.D University of Arizona Tucson, AZ