From chemistry-request@server.ccl.net Mon May 27 01:29:20 2002 Received: from biosino.org ([202.127.18.238]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4R5TJ122504 for ; Mon, 27 May 2002 01:29:20 -0400 Received: from mao [202.127.18.233] by biosino.org (SMTPD32-6.04) id A408E20268; Mon, 27 May 2002 13:28:40 +0800 Date: Mon, 27 May 2002 13:30:15 +0800 From: "xmao@biosino.org" To: "chemistry@ccl.net" Subject: problem about imaginary frequency X-mailer: FoxMail 3.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <200205271328411.SM00279@mao> chemistryDear Everyone: I met a problem when using partial optimization to search for the TS, and I got some intermediates that have a imaginary frequency value near -1200cm-1, but here is always a imaginary frequency value near -50~-70cm-1. The first imaginary frequency is related to the breakage of the chemical bond, while the second one is a distort frequency. I wonder if my intermediates are the TS. Thanks a lot. Best Regards, mao From chemistry-request@server.ccl.net Mon May 27 02:36:29 2002 Received: from century.fen.bilkent.edu.tr ([139.179.97.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4R6aR123401 for ; Mon, 27 May 2002 02:36:27 -0400 Received: from fen.bilkent.edu.tr (fenII-121.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id JAA04973 for ; Mon, 27 May 2002 09:32:41 +0300 (EET DST) Message-ID: <3CF1D469.6020203@fen.bilkent.edu.tr> Date: Mon, 27 May 2002 09:38:33 +0300 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: G98/StepSize Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Gaussian Users, I am trying to optimize a tricky system and would like to reduce the stepsize in the optimization. I thought, the input should read something like "fopt=(stepsize=3)" but I am getting a syntaz error. I also tried without "=" and without brackets but it does not work. Can somebody please advise me how to use this keyword? Thanks, Ulrike Salzner From chemistry-request@server.ccl.net Mon May 27 09:01:58 2002 Received: from century.fen.bilkent.edu.tr ([139.179.97.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4RD1v131828 for ; Mon, 27 May 2002 09:01:57 -0400 Received: from fen.bilkent.edu.tr (fenII-121.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id PAA14765 for ; Mon, 27 May 2002 15:58:15 +0300 (EET DST) Message-ID: <3CF22EC4.4010608@fen.bilkent.edu.tr> Date: Mon, 27 May 2002 16:04:04 +0300 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: g98/stepsize Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Thanks everybody, I got lots of replies explaining that the keyword is not implemented, although it is described in the manual. "IOP(1/8=x)" works fine. Regards, Ulrike Salzner From chemistry-request@server.ccl.net Mon May 27 09:55:32 2002 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4RDtV100545 for ; Mon, 27 May 2002 09:55:32 -0400 Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id PAA23766; Mon, 27 May 2002 15:52:55 +0200 (MEST) for chemistry@ccl.net Date: Mon, 27 May 2002 15:52:55 +0200 (MEST) Message-Id: <200205271352.PAA23766@resu1.ulb.ac.be> From: Pierre Mignon To: chemistry@ccl.net Subject: free energy ... X-Mailer: Webmail ULB v2.1 Hello all ! I am looking for good references dealing about the problem of free energy calculation in bio-molecules, I have already found some, but I would be interested in a review or a article about the general aspects of the avances in the last decade. Thank you in advance. Mignon Pierre PhD student Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 35 16 Fax + 32 2 629 33 17 e-mail pmignon@vub.ac.be From chemistry-request@server.ccl.net Mon May 27 07:22:24 2002 Received: from llar.net.uniovi.es ([156.35.11.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4RBMN130033 for ; Mon, 27 May 2002 07:22:23 -0400 Received: from CONVERSION-DAEMON.llar.net.uniovi.es by llar.net.uniovi.es (PMDF V6.1 #39514) id <01KI82HH5S4W00FQAT@llar.net.uniovi.es> for chemistry@ccl.net; Mon, 27 May 2002 13:22:09 +0200 (MET) Received: from correo.uniovi.es (sci.cpd.uniovi.es [156.35.10.6]) by llar.net.uniovi.es (PMDF V6.1 #39514) with ESMTP id <01KI82HFIHXY00GEBF@llar.net.uniovi.es> for chemistry@ccl.net; Mon, 27 May 2002 13:22:07 +0200 (MET) Received: from correo.uniovi.es (pcc134.quimica.uniovi.es [156.35.54.35]) by correo.uniovi.es (8.9.3/8.9.2) with ESMTP id NAA19135 for ; Mon, 27 May 2002 13:22:07 +0200 (MET DST) Date: Mon, 27 May 2002 13:27:21 +0200 From: =?iso-8859-1?Q?Hayd=E9e=20Vald=E9s=20Gonz=E1lez?= Subject: NBO+ECP with GAMESS To: chemistry@ccl.net Message-id: <3CF21818.8085FEDB@correo.uniovi.es> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (Win95; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en Dear users, I am trying to run some NBO calculations with GAMESS. When using all-electron-basis sets, things are ok but when using ECPs I got the following error message ENCODING THE EFFECTIVE CORE POTENTIAL FORMULAE BASIS FUNCTIONS ARE MAX TYPE D PROJECTION OPERATOR MAX TYPE S 1. BASIC ANGULAR INTS......... 0.00 SECONDS 2. LOCAL OPERATOR INTS........ 0.01 SECONDS 3. PROJECTION OPERATOR INTS... 0.00 SECONDS 4. SPECIAL ANGULAR INTS....... 0.00 SECONDS DAWRIT HAS REQUESTED A RECORD WITH LENGTH DIFFERENT THAN BEFORE - ABORT FORCED. DAF RECORD 92 NEW LENGTH = 0 OLD LENGTH = 434 EXECUTION OF GAMESS TERMINATED ABNORMALLY AT Fri May 24 04:24:28 2002 Has any of you ever had such a problem? Thanks in advance, H. Valdes hvg@correo.uniovi.es From chemistry-request@server.ccl.net Mon May 27 07:23:19 2002 Received: from mail.chemie.fu-berlin.de (root@[160.45.24.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4RBNI130061 for ; Mon, 27 May 2002 07:23:19 -0400 Received: from diels.chemie.fu-berlin.de ([160.45.24.148]) (1664 bytes) by mail.chemie.fu-berlin.de via sendmail with P:esmtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Mon, 27 May 2002 13:23:18 +0200 (CEST) (Smail-3.2.0.111) Date: Mon, 27 May 2002 13:23:14 +0200 From: Michael Patzschke To: chemistry@ccl.net Subject: SAPT In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g4RBNJ130062 Dear CCl'ers, I would like to perform some calculations using the SAPT code (http://www.physics.udel.edu/~mas/group.htm) by Krzysztof Szalewicz's and coworkers. The program is interfaced with many SCF-codes, I would prefer using GAMESS. Unfortunately the interface depends on a rather old version on GAMESS (which I don't have). Therefore my questions: Is someone of You aware of a newer version of SAPT running with a newer version of GAMESS ? Or does anybody know where to get older version of GAMESS. Obviously I tried the GAMESS home-page but the oldest version there is from 2000. I figure that what I need is a version from 1997. Best regards, Michael Patzschke ------------------------------------------------------------------------- Michael Patzschke | email: michaelp@chemie.fu-berlin.de Privat: | Freie Universität Berlin - Institut für Chemie Waghäuseler Str. 9/10 | Physikalische und Theoretische Chemie 10715 Berlin | Takustr. 3, 14195 Berlin, Germany ------------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon May 27 03:36:30 2002 Received: from igc.phys.chem.ethz.ch ([129.132.218.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4R7aT124756 for ; Mon, 27 May 2002 03:36:30 -0400 Received: from humagne.ethz.ch (humagne [129.132.218.162]) by igc.phys.chem.ethz.ch (8.11.4/8.11.4) with ESMTP id g4R7aSx25595 for ; Mon, 27 May 2002 09:36:28 +0200 (MEST) Received: (from portmann@localhost) by humagne.ethz.ch (8.11.4/8.11.4) id g4R7aS916848 for chemistry@ccl.net; Mon, 27 May 2002 09:36:28 +0200 (MEST) Date: Mon, 27 May 2002 09:36:28 +0200 (MEST) Message-Id: <200205270736.g4R7aS916848@humagne.ethz.ch> From: Stefan Portmann Reply-To: info@watoc02.ch Subject: WATOC'02: Last Call for Contributions! Content-Type: text Dear Madam or Sir 6th WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS (WATOC'02) August 4-9, 2002, Palazzo dei Congressi, Lugano, Switzerland More than 100 talks and over 400 poster presentations in Theory, Computation and Information Science in Chemistry, Biochemistry and Materials Science. Don't miss this great event! Last Call for Contributions: Please submit an abstract for your contribution until the end of May using the online form at http://www.watoc02.ch (Deadline: May 31, 2002). WATOC'02 special issue of THEOCHEM: We are pleased to announce that Elsevier will publish a WATOC'02 special issue of THEOCHEM to appear in Spring 2003. You are therefore invited to submit a full paper. Information and Registration: http://www.watoc02.ch. Registrations are accepted until June 14, 2002. We are looking forward to see you in Lugano. Hans Peter Luethi and Stefan Portmann ETH Zurich From chemistry-request@server.ccl.net Mon May 27 15:44:11 2002 Received: from ms1.uibk.ac.at ([138.232.1.201]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4RJiB107008 for ; Mon, 27 May 2002 15:44:11 -0400 Received: from localhost (web-mail2.uibk.ac.at [138.232.1.226] Hannes.Loeffler@uibk.ac.at) by ms1.uibk.ac.at (8.11.3/E2) with ESMTP id g4RJi7k44137199 for ; Mon, 27 May 2002 21:44:07 +0200 (CEST) Received: from 62.47.210.138 ( [62.47.210.138]) as user c72409@mail1.uibk.ac.at by web-mail2.uibk.ac.at with HTTP; Mon, 27 May 2002 21:44:07 +0200 Message-ID: <1022528647.3cf28c8732f9c@web-mail2.uibk.ac.at> Date: Mon, 27 May 2002 21:44:07 +0200 From: Hannes Loeffler To: chemistry@ccl.net Subject: mean residence times (again) MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 62.47.210.138 Hello all, I recently asked how to calculate mean residence times and got several useful pointers to the literature. Now I mostly understand how to implement the computations myself but still are unsure about some issues. Obviously, the mean residence time is computed from a correlation function. Thus the same assumption applies as for other time correlation functions (or the MSD as I recently learned from this list): it is independent(?) of the chosen time origin and to improve statistics one may average over several time origins (overlapping windows). I hope that's right. Impey et al. introduced a book-keeping value t^star to account for molecules leaving only temporarily from the region of interest. Other authors set this value to zero. Anyway, I'm still unsure what I should do if such a molecule leaves for a (much) longer time then t^star and returns after some time. Should the residence time correlation function increase again? Or should this water be considered as to have never been in the region of interest at the time origin (in this case the correlation function is strictly decreasing)? I hope somebody can enlighten me, Hannes. -- Hannes Loeffler | tel: +43-(0)512-507-5166 | fax: +43-(0)512-507-2714 http://www-c724.uibk.ac.at/staff/loeffler/ | mailto:Hannes.Loeffler@uibk.ac.at Institute for General, Inorganic and Theoretical Chemistry University of Innsbruck, Austria From chemistry-request@server.ccl.net Mon May 27 18:42:44 2002 Received: from meta4.mbasis.com ([216.98.157.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4RMgi110074 for ; Mon, 27 May 2002 18:42:44 -0400 Received: by meta4.mbasis.com with Internet Mail Service (5.5.2653.19) id ; Mon, 27 May 2002 15:38:15 -0700 Message-ID: From: Rami Reddy To: "'Pierre Mignon'" , chemistry@ccl.net Subject: RE: free energy ... Date: Mon, 27 May 2002 15:38:14 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain The following references will provide the information about free energy calculation in bio-molecules. 1) M. Rami Reddy, Mark Erion, and Atul Agarwal' Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities' Reviews in Computational Chemistry, Edited by Lipkowitz and Boyd, Volume 16, Pages 217-303. 2) Free Energy Calculations in Rational Drug Design (a total of 19 chapters in this text book and all are related to free energy calculations), edited by M. Rami Reddy and Mark Erion, Kluwer Academic/Plenum Publishers, New York, 2001. -----Original Message----- From: Pierre Mignon [mailto:pmignon@vub.ac.be] Sent: Monday, May 27, 2002 6:53 AM To: chemistry@ccl.net Subject: CCL:free energy ... Hello all ! I am looking for good references dealing about the problem of free energy calculation in bio-molecules, I have already found some, but I would be interested in a review or a article about the general aspects of the avances in the last decade. Thank you in advance. Mignon Pierre PhD student Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 35 16 Fax + 32 2 629 33 17 e-mail pmignon@vub.ac.be -= 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