From chemistry-request@server.ccl.net Sun Dec 2 06:44:42 2001 Received: from hotmail.com ([64.4.31.108]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB2Bigi13571 for ; Sun, 2 Dec 2001 06:44:42 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sun, 2 Dec 2001 03:44:29 -0800 Received: from 213.120.56.37 by pv1fd.pav1.hotmail.msn.com with HTTP; Sun, 02 Dec 2001 11:44:29 GMT X-Originating-IP: [213.120.56.37] From: "Glen Hoddle" To: chemistry@ccl.net Subject: Gaussian Solvation Models Date: Sun, 02 Dec 2001 11:44:29 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 02 Dec 2001 11:44:29.0735 (UTC) FILETIME=[B3B9B370:01C17B26] I have a problem with ALL the solvation models in Gaussian when I try to optimise anything with bromine that involves and alpha or beta lactones. I have fully characterised the gas phase calculations at HF, B3LYP and MP2 using various basis sets (big and small). However every time I try to optimise any structure using the solvation models in Gaussian, it either fails to converge or carbon dioxide is released. My question is: has anyone tried to vary the VDW radius instead of using the standard values. And does this work? Or is it a problem with my ‘ Odd’ alpha or beta lactones system. Thanbkyou for anyhelp I recive. Dr Glen Hoddle _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Sun Dec 2 16:26:35 2001 Received: from garaged.fis.unam.mx ([132.248.33.226]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB2LQYi18800 for ; Sun, 2 Dec 2001 16:26:34 -0500 Received: from yahoo.com (localhost [127.0.0.1]) by garaged.fis.unam.mx (8.11.6/8.11.6) with ESMTP id fB19R9p05063 for ; Sat, 1 Dec 2001 03:27:09 -0600 Sender: max@garaged.fis.unam.mx Message-ID: <3C08A26D.DC63379E@yahoo.com> Date: Sat, 01 Dec 2001 03:27:09 -0600 From: Max Valdez X-Mailer: Mozilla 4.78 [es] (X11; U; Linux 2.4.9-ac18 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: XYZ "movie" to any other movie format? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers Does anyone knows any program to transform XYZ movies to any other format read by CMD or any common visualization tool ?? I Can read up to 200 steps on Molden, but not a "big" 5,000 steps xyz dynamics, I guess it would be easy to recompile molden, but there must be a better way to do it, specially to make some analisys of the dynamics. Hope somebody can help me, I will summarize. Max From chemistry-request@server.ccl.net Sun Dec 2 17:36:08 2001 Received: from mail-02.med.umich.edu ([141.214.93.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB2Ma8i19829 for ; Sun, 2 Dec 2001 17:36:08 -0500 Received: from gwia-02-MTA by mail-02.med.umich.edu with Novell_GroupWise; Sun, 02 Dec 2001 17:35:59 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.1 Date: Sun, 02 Dec 2001 17:35:40 -0500 From: "Renxiao Wang" To: Subject: Summary: Available complex structure database Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fB2Ma8i19830 Dear CCLers, About a week ago, I posted this: -------------------------------------------- I am looking for on-line databases which maintain a collection of all the complex structures from PDB. Basically a complete list is desired. If all the entries are organized in a logic way, that will be a major plus. I have checked "PDBSum" at http://www.biochem.ucl.ac.uk/bsm/pdbsum/ and "Relibase" at http://relibase.ebi.ac.uk/. Both of them provide some forms of useful information. I will appreciate it very much if anyone has other clues. I will certainly put back the summary. -------------------------------------------- And here are the clues I have received: > From mao@ramana.chem.yale.edu: http://binddb.org/ http://www.bindingdb.org/bind/index.jsp > From mn1@helix.nih.gov: We are working on something like this. Please ask back in a couple of months or so. > From didier.rognan@aspirine.u-strasbg.fr: We have a list of about 2,000 non-redundant PDB entries retrieved from the PDB with the following keywords: 'COMPLEX', 'WITH', 'INHIBITOR'. If you are interested in either the list or a tar archive of all selected entries, just let me know. > From maria.brandl@pharma.novartis.com: the problem with compiling such a data-base is that most of brainpower put into their assembly is considered as private property. Really sorry for that. Thank everybody who has answered. Hope these help. Regards, Renxiao Wang, Ph.D. University of Michigan Medical School