From chemistry-request@ccl.net Thu Jun 12 15:19:47 2003 Received: from salmon.maths.tcd.ie (salmon.maths.tcd.ie [134.226.81.11]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h5CJJkkr030669 for ; Thu, 12 Jun 2003 15:19:47 -0400 Received: from boole.maths.tcd.ie by salmon.maths.tcd.ie with SMTP id ; 12 Jun 2003 20:19:46 +0100 (BST) Date: Thu, 12 Jun 2003 20:19:45 +0100 (BST) From: Gemma Kinsella To: chemistry/at/ccl.net Subject: Charmm solvent parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I am interested in using some different solvents with the charmm force field, such as CCL4,CHCL3. I was wondering if there were charmm parameters available for these and if so where could I obtain them?? Many thanks, Gemma Kinsella From chemistry-request@ccl.net Thu Jun 12 04:27:49 2003 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5C8Rmkr008586 for ; Thu, 12 Jun 2003 04:27:49 -0400 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Thu, 12 Jun 2003 09:27:46 +0100 Date: Thu, 12 Jun 2003 09:27:46 +0100 Message-ID: <3EA4FB980003BC9A/at/hawk.dcu.ie> In-Reply-To: <20030611140414.93845.qmail/at/web21108.mail.yahoo.com> From: noel.oboyle2/at/mail.dcu.ie Subject: RE: File format conversion To: "Gurpreet Singh" Cc: chemistry/at/ccl.net 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 h5C8Rnkr008587 Hello, You don't say exactly what format your x-ray data is in. Babel (available > from the web - get BabelWin also) can convert between many formats including Gaussian. If your x-ray data is in .cif format (e.g. as found in the Cambridge Crystallography Database) you will need to download Mercury from their website at http://www.ccdc.cam.ac.uk/prods/mercury/index.html. This will open .cif files and save them as .pdb (also known as .ent files), which may then be converted using Babel. Hope that helps, Noel O'Boyle Dublin City University > >Dear CCLers, > We are trying to do an optimization of the >x-ray >Hydrogen positions of alanine (for example) and >compare them to >Neutron Diffraction data using Gaussian98. However, >the output >(Input Orientation or Standard Orientation) is not in >the same >format (ie fractional or cartesian coordinates) as >that of the >x-ray/neutron diffraction data. > > > In the calculation, some of the larger >atoms (ie >Carbon and Nitrogen ) are frozen (ie not to be >optimized) and we >do not want those coordinates to change. They are >supposed to >remain invariant. > > Is there any way to get the Gaussian >output in >fractional/cartesian coordinates so as to compare with >the input >file? > >Thank YOu > >Gurpreet Singh >Project Assistant, >National Chemical Laboratory, >Pune, >India > > > > > >-= This is automatically added to each message by mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: >line >and send your message to: CHEMISTRY/at/ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net > >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl/at/ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Thu Jun 12 13:02:20 2003 Received: from frontend-1.cgpmail.ua.pt (mail.ua.pt [193.136.80.79]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5CH2Fkr025085 for ; Thu, 12 Jun 2003 13:02:20 -0400 X-UA: Message Inspected for Viruses by RAV Received: from [192.168.69.132] (HELO backend-2.cgpmail.ua.pt) by frontend-1.cgpmail.ua.pt (CommuniGate Pro SMTP 4.0.6) with ESMTP id 10174151 for chemistry^at^ccl.net; Thu, 12 Jun 2003 18:02:14 +0100 Received: from [193.136.83.38] (account ) by backend-2.cgpmail.ua.pt (CommuniGate Pro WebUser 4.0.6) with HTTP id 5495867 for ; Thu, 12 Jun 2003 18:00:03 +0100 From: "Nelson Fonseca" Subject: CCL: Mapping Intermolecular Interactions To: X-Mailer: CommuniGate Pro Web Mailer v.4.0.6 Date: Thu, 12 Jun 2003 18:00:03 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Content-Transfer-Encoding: 8bit Experience is what you get when you don't get what you want. -- Dan Stanford-- Dear cclers: Is there any free software than can calculate the best docking conformation between 2 molecules based on intermolecular interactions given by any Force Field? Thanks in advance --------------------- --------------------- Nelson Fonseca Dep. of Chemistry University of Aveiro Portugal ---------------------