From chemistry-request@server.ccl.net Fri Jan 12 13:44:51 2001 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0CIiop24775 for ; Fri, 12 Jan 2001 13:44:51 -0500 Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay2.scripps.edu (8.11.0/TSRI-4.0r) with ESMTP id f0CIgna17990; Fri, 12 Jan 2001 10:42:49 -0800 (PST) Received: (from case@localhost) by gamow.scripps.edu (8.9.1a/TSRI-2.8) id KAA157735; Fri, 12 Jan 2001 10:42:49 -0800 (PST) Date: Fri, 12 Jan 2001 10:42:49 -0800 From: David Case To: CHEMISTRY@ccl.net Cc: xxh0541@hotmail.com Subject: Re: CCL: united atom force fields in Amber Message-ID: <20010112104249.B157584@gamow.scripps.edu> References: <3A5CE2B9.B09726E1@mcmaster.ca> <3A5E9C27.368CEB0C@hotmail.com> <20010112090725.A156683@gamow.scripps.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <20010112090725.A156683@gamow.scripps.edu>; from case@scripps.edu on Fri, Jan 12, 2001 at 09:07:25AM -0800 On Fri, Jan 12, 2001, David Case wrote: > > > How to just add polar hydrogen (united atom) to residues, and how to > > assign the kollman united atom charges using AMBER6.0? > > Run xleap -s (to ignore the default startup file), then type > "source leaprc.ff91". This will load in the "parm91" (Weiner et al. united > atom force field). Because this force field is so old (developed in > 1983-84) it is not used much anymore; be sure this is what you really want > before spending a lot of time at it. Amber6 is really designed with more > recent force fields in mind. .ooops...this answer was incorrect. A more complex procedure is needed to really get the original 1984 polar-hydrogen-only force field. The procedure mentioned above actually gets the all-atom 1986 force field. (They are both called Weiner et al....) My apologies for any confusion this has caused. ...dac -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ==================================================================