From owner-chemistry(+ at +)ccl.net Mon Nov 6 20:46:46 1995 Received: from bedrock.ccl.net for owner-chemistry # - at - # ccl.net by www.ccl.net (8.6.10/950822.1) id UAA05496; Mon, 6 Nov 1995 20:35:33 -0500 Received: from cheetah.it.wsu.edu for brian ":at:" bert.chem.wsu.edu by bedrock.ccl.net (8.7.1/950822.1) id UAA18713; Mon, 6 Nov 1995 20:35:30 -0500 (EST) Received: from bert.chem.wsu.edu (bert.chem.wsu.edu [134.121.43.22]) by cheetah.it.wsu.edu (8.6.12/WSUit-1.1) with SMTP id RAA10418 for ; Mon, 6 Nov 1995 17:35:32 -0800 Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA19107; Mon, 6 Nov 1995 17:35:57 -0800 From: brian-: at :-bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9511070135.AA19107.,at,.bert.chem.wsu.edu> Subject: Re: CCL:G:Parametrization for Zinc / charges & vdW radius To: vis(+ at +)gensia.com (Viswanadhan) Date: Mon, 6 Nov 1995 15:57:04 -0800 (PST) In-Reply-To: from "Viswanadhan" at Nov 6, 95 04:49:15 am X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Sender: brian $#at#$ bert.chem.wsu.edu Viswanadhan wrote: : : : I would like to use CHELPG charges which necessitates the use of right : vdW radii. For neutral Zinc, the Bondi radius (J. Phys. Chem. 68. 441) : is 1.39 A, which is clearly not appropriate. Can any one point to recent : references or suggest a method? I will be happy to summarize the : responses (with regard to vdW radii & modeling the charge in the active : site of an enzyme for the Zinc ion). : : Vellarkad N. Viswanadhan : Yes, what does constitute "good" vdW radii. In our work on Fe-S centers in proteins we've noticed that the actual charges calculated by CHELPG vary significantly depending on whether you use Breneman&Wiberg radii or Gavizotti&Spackman radii. Generally, Breneman & Wiberg based charges seem "better behaved" in our systems. Also, we've noticed that many groups use radii designed for other purposes and "plug" these into the CHELPG algorithm. What are the rationals people use in choosing their radii? -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | ||--------------------| brian: at :bert.chem.wsu.edu | || \\ WSU || Biochem/Biophysics | brian_beck:~at~:wsu.edu | |\ - *|| WSU , 206 Fulmer | URL http://elmo.chem.wsu.edu/~brian | | | || Pullman, WA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | =============================================================================