From chemistry-request@server.ccl.net Thu Sep 21 03:43:25 2000 Received: from lancelot.imb-jena.de (lancelot.imb-jena.de [192.124.248.76]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA02737 for ; Thu, 21 Sep 2000 03:43:24 -0400 Received: (from pineda@localhost) by lancelot.imb-jena.de (980427.SGI.8.8.8/8.8.8) id JAA29304; Thu, 21 Sep 2000 09:43:13 +0200 (CEST) From: "Felipe Pineda" Message-Id: <10009210943.ZM223296@lancelot.imb-jena.de> Date: Thu, 21 Sep 2000 09:43:13 +0000 In-Reply-To: Irena Bonin "CCL:solvation energies" (Sep 20, 6:14am) References: <20000920131447.2737.rocketmail@web220.mail.yahoo.com> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Irena Bonin , chemistry@ccl.net Subject: Re: CCL:solvation energies Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi Irena! Electrostatic (polar) solvation free energies -> look for UHBD (FDPB continuum solvent model) or the TINKER package (GB model) or AMBER 6 (GB too) For the non-polar (SA dependent) solvation free energies: TINKER too and many other packages implemmenting the Connolly algorithm. Best regards Felipe -- ********************************************************************** * Felipe Pineda,PhD * * Institut fuer Molekulare Biotechnologie * * AG Theoretische Biophysik * * Beutenbergstrasse 11, Jena Tel.: +49-3641-65-6491 * * Postfach 100 813, D-07708 Jena, Germany Fax: +49-3641-656495 * ********************************************************************** ********************************************************************** * DISCLAIMER: Unless indicated otherwise, everything in this note is * * my personal opinion, not an official statement of my employer * ********************************************************************** From chemistry-request@server.ccl.net Thu Sep 21 05:19:28 2000 Received: from Salicet.ucd.ie (mail.ucd.ie [137.43.1.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA03353 for ; Thu, 21 Sep 2000 05:19:27 -0400 X-Confirm-reading-to: Laurence.Cuffe@ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON by Salicet.ucd.ie (PMDF V5.2-32 #40440) id <0G1800F01CJXKA@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Thu, 21 Sep 2000 10:19:17 +0100 (BST) Received: from elvira ([137.43.24.26]) by Salicet.ucd.ie (PMDF V5.2-32 #40440) with SMTP id <0G1800EB7CJXZ6@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Thu, 21 Sep 2000 10:19:09 +0100 (BST) Date: Thu, 21 Sep 2000 10:19:08 +0100 From: Laurence Cuffe Subject: CCL:Babel g98 to g94 To: CHEMISTRY@ccl.net Message-id: <0G1800EB8CJXZ6@Salicet.ucd.ie> Organization: University College Dublin MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.01d) Content-type: text/plain; charset=US-ASCII Priority: normal On a unix system the command: sed 's/ 0 / /' myfile.log myfileg94.log will strip out the extra field in the standard orientation section of a g98 log file (myfile.log) and write the result into myfileg94.log This makes it readable to gausview version1 and presumably babel. In a windows system I think something similar should work i.e. edit the file and do a global search and replace for blankblankzeroblank blank and replace it by two blanks. Hope this crude fix helps Larry Cuffe From chemistry-request@server.ccl.net Thu Sep 21 03:45:16 2000 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA02761 for ; Thu, 21 Sep 2000 03:45:15 -0400 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id JAA01938 for ; Thu, 21 Sep 2000 09:45:04 +0200 (MET DST) Message-ID: <005701c0239e$e67c88e0$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: "CCL" Subject: A Babel of Babels Date: Thu, 21 Sep 2000 09:38:11 +0200 Organization: Ist. Chimica Farmaceutica 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear CCLers, In order to translate or manage chemical files you can check also our free software VEGA. See: http://users.unimi.it/~ddl/ Best regards Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-29502230 Fax +39-02-29514197 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Thu Sep 21 10:47:28 2000 Received: from bastille.cchem.berkeley.edu (bastille.cchem.berkeley.edu [128.32.198.211]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA06201 for ; Thu, 21 Sep 2000 10:47:28 -0400 Received: from localhost (rjd@localhost) by bastille.cchem.berkeley.edu (8.9.3/8.9.3) with SMTP id HAA25140; Thu, 21 Sep 2000 07:47:13 -0700 Date: Thu, 21 Sep 2000 07:47:12 -0700 (PDT) From: "Robert J. Doerksen" To: Laurence Cuffe cc: CHEMISTRY@ccl.net Subject: Re: CCL:Babel g98 to g94 In-Reply-To: <0G1800EB8CJXZ6@Salicet.ucd.ie> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Laurence and CCL, Re. sed and other such useful "unix-like" tools, do not forget that versions for ms-windows are available, for example at http://www.weihenstephan.de/~syring/win32/UnxUtils.html Sometimes the win32 versions have even more features than other unix-os versions! Cheers, Robert Dr. Robert J. Doerksen ************************************************* Head-Gordon Group work phone (510) 643-2935 Department of Chemistry or (510) 642-9304 University of California fax (510) 643-1255 Berkeley, CA, USA 94720 e-mail: rjd@bastille.cchem.berkeley.edu **** webpage: http://www.cchem.berkeley.edu/~mhggrp/doerksen/rjdhome.htm On Thu, 21 Sep 2000, Laurence Cuffe wrote: > Date: Thu, 21 Sep 2000 10:19:08 +0100 > From: Laurence Cuffe > To: CHEMISTRY@ccl.net > Subject: CCL:Babel g98 to g94 > > On a unix system the command: > sed 's/ 0 / /' myfile.log myfileg94.log > will strip out the extra field in the standard orientation section of a > g98 log file (myfile.log) and write the result into myfileg94.log > This makes it readable to gausview version1 and presumably babel. > In a windows system I think something similar should work i.e. edit > the file and do a global search and replace for blankblankzeroblank > blank and replace it by two blanks. > Hope this crude fix helps > Larry Cuffe > > -= 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 Thu Sep 21 16:24:30 2000 Received: from georgetown.edu (postoffice.georgetown.edu [141.161.1.110]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA07482 for ; Thu, 21 Sep 2000 16:24:29 -0400 Received: from mailhost.georgetown.edu (mailhost.georgetown.edu [141.161.1.103]) by georgetown.edu (8.10.0.Beta12/8.10.0.Beta12) with ESMTP id e8LKOSj29703; Thu, 21 Sep 2000 16:24:29 -0400 (EDT) Received: from giccs.georgetown.edu (giccs196.giccs.georgetown.edu [141.161.231.196]) by mailhost.georgetown.edu (8.10.0.Beta12/8.10.0.Beta12) with ESMTP id e8LKOS312504; Thu, 21 Sep 2000 16:24:28 -0400 (EDT) Message-ID: <39CA95C8.450D8835@giccs.georgetown.edu> Date: Thu, 21 Sep 2000 16:12:08 -0700 From: Shaomeng Wang X-Mailer: Mozilla 4.51 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, wangs Subject: How to produce a gif file from mol or mol2 for chemical structures Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, Does anyone know a program that can automatically produce a gif file >from a mol or mol2 file for a chemical structure? We have many chemical structures and would like to produce gif file for each of them automatically for display purpose. Thank you very much and I will summarize to CCL users. Shaomeng Wang Georgetown University From chemistry-request@server.ccl.net Thu Sep 21 12:36:12 2000 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA06654 for ; Thu, 21 Sep 2000 12:36:11 -0400 Received: (from jochen@localhost) by bacchus.pc1.uni-duesseldorf.de (8.9.3/8.8.7) id SAA04336; Thu, 21 Sep 2000 18:35:49 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14794.14564.468869.808931@bacchus.pc1.uni-duesseldorf.de> Date: Thu, 21 Sep 2000 18:35:48 +0200 (CEST) From: Jochen Kuepper To: "Robert J. Doerksen" Cc: CHEMISTRY@ccl.net Subject: CCL:Babel g98 to g94 In-Reply-To: References: <0G1800EB8CJXZ6@Salicet.ucd.ie> X-Mailer: VM 6.72 under 21.1 (patch 12) "Channel Islands" XEmacs Lucid X-Face: -%Z4EZ6iY'4m:wiK:!v Re. sed and other such useful "unix-like" tools, do not forget > that versions for ms-windows are available, for example at > > http://www.weihenstephan.de/~syring/win32/UnxUtils.html > > Sometimes the win32 versions have even more features than other > unix-os versions! Sure, because they are derived from the GNU-tools, widely used in Un*x-world;-)) Jochen -- Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43 Raum 02.29 40225 Düsseldorf, Germany phone ++49-211-8113681 http://www.Jochen-Kuepper.de fax ++49-211-8115195 From chemistry-request@server.ccl.net Thu Sep 21 22:54:55 2000 Received: from galileu.dqfex.ufpe.br (root@galileu.dqfex.ufpe.br [150.161.40.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA09754 for ; Thu, 21 Sep 2000 22:54:52 -0400 Received: from dqfex.ufpe.br (xaxado.dqf.ufpe.br [150.161.5.235]) by galileu.dqfex.ufpe.br (8.9.3/8.8.7) with ESMTP id XAA05284 for ; Thu, 21 Sep 2000 23:54:31 -0300 Message-ID: <39CAC9AD.9DB004@dqfex.ufpe.br> Date: Thu, 21 Sep 2000 23:53:33 -0300 From: Sidney Ramos X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en,en-US,pt-BR MIME-Version: 1.0 To: CCL List Subject: Error via Link L502!!! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Users, I have been trying to calculate the rotation barrier in a benzamidoxime by the method B3LYP/6-31G* using the keyword "Scan" in the Gaussian 98, however after the last step the program stop and write the messages bellow: > Requested convergence on MAX density matrix=1.00D-06. > Integral accuracy reduced to 1.0D-05 until final iterations. > Problem detected with inexpensive integrals. > Switching to full accuracy and repeating last cycle. > Warning! Spurious integrated density: > NE= 72 NElCor= 0 Integral= 0.00000 Tolerance=1.00D-03 > Consistency failure #2 in CalDSu. > Error termination via Lnk1e in /net/frevo/export/local/bin//g98/l502.exe. > Job cpu time: 0 days 7 hours 32 minutes 24.1 seconds. > File lengths (MBytes): RWF= 29 Int= 0 D2E= 0 Chk= 11 Scr= 1 How do I solve this problem? Thanks for any help! Sidney Ramos DQF - CCEN - UFPE