From chemistry-request: at :ccl.net Wed May 11 19:09:22 2005 Received: from postoffice10.mail.cornell.edu (postoffice10.mail.cornell.edu [132.236.56.14]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BN9IUq032296 for ; Wed, 11 May 2005 19:09:18 -0400 Received: from [192.168.0.139] (ip.253.34.140-dhcp.chem.cornell.edu [128.253.34.140]) by postoffice10.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id j4BLxxqZ012086; Wed, 11 May 2005 18:00:04 -0400 (EDT) In-Reply-To: References: Mime-Version: 1.0 (Apple Message framework v728) Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: Cc: chemistry %a% ccl.net From: Geoff Hutchison Subject: Re: CCL:Tinker input file Date: Wed, 11 May 2005 17:59:57 -0400 To: lhhu %a% yangtze.hku.hk X-Mailer: Apple Mail (2.728) X-Spam-Status: No, score=0.5 required=5.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j4BN9MUq032300 On May 11, 2005, at 4:16 AM, lhhu %a% yangtze.hku.hk wrote: > I would like to use free TINKER to calculated molecular dynamics. > But the input file of tinker seems difficult to generate because > the int or xyz file need to be assigned force field atom type > first. Can anyone tell me about the most convenient way to generate > the input xyz or int file? Is there any free program I can use? Use Open Babel (or the original Babel): Open Babel: http://openbabel.sf.net/ Babel 1.6 (and older): http://www.ccl.net/cca/software/UNIX/babel/ Some atom types may or may not be assigned automatically depending on which force field you wish to use and what format you used originally. However, it's a great time-saver. Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruqa Group http://abruna.chem.cornell.edu/