From chemistry-request@server.ccl.net Fri Jan 12 12:09:26 2001 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0CH9Qp24600 for ; Fri, 12 Jan 2001 12:09:26 -0500 Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay1.scripps.edu (8.11.0/TSRI-4.0r) with ESMTP id f0CH7P425523; Fri, 12 Jan 2001 09:07:25 -0800 (PST) Received: (from case@localhost) by gamow.scripps.edu (8.9.1a/TSRI-2.8) id JAA157211; Fri, 12 Jan 2001 09:07:25 -0800 (PST) Date: Fri, 12 Jan 2001 09:07:25 -0800 From: David Case To: xin_hu Cc: CHEMISTRY@ccl.net Subject: Re: CCL:basis set optimiser in solid Message-ID: <20010112090725.A156683@gamow.scripps.edu> References: <3A5CE2B9.B09726E1@mcmaster.ca> <3A5E9C27.368CEB0C@hotmail.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <3A5E9C27.368CEB0C@hotmail.com>; from xxh0541@hotmail.com on Thu, Jan 11, 2001 at 11:54:48PM -0600 On Thu, Jan 11, 2001, xin_hu wrote: > Can I > load a pdb file of protein, assign the residues with charges, > and save the file as pdb or other type formate? if can, what's > kind of charge it is assigned? The standard libraries have alternate charge states (protonated and unprotonated) for his, glu and asp. You could make others and add to the library, or manually modify charges using a spread-sheet like interface. The file can be saved as PDB or Amber format. All of this is done in LEaP, which has an on-line manual, a printed Users' Guide and a tutorial section. > 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. ...good luck...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 ==================================================================