From chemistry-request@server.ccl.net Thu Apr 11 06:18:16 2002 Received: from igor.urz.unibas.ch ([131.152.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3BAIFj11421 for ; Thu, 11 Apr 2002 06:18:15 -0400 Received: from proinformatix.com (yutang.pz.unibas.ch [131.152.84.72]) by igor.urz.unibas.ch (PMDF V6.1-1 #40761) with ESMTP id <0GUE008IQFA7U1@igor.urz.unibas.ch> for chemistry@ccl.net; Thu, 11 Apr 2002 12:18:07 +0200 (MET DST) Date: Thu, 11 Apr 2002 12:18:18 +0200 From: Sergio Manzetti Subject: ZN ions To: CCL Reply-to: sergio@proinformatix.com Message-id: <3CB562EA.6010703@proinformatix.com> MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en-us User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 Dear CCLrs I am trying to simulate a ZN peptidase. The problem is that the ZN ion, which is directed by an anterior sulphur atom to donate certain orbitals to one carboxylate oxygen and one carbonyl oxygen for polarization effect to carry out catalysis, is presented in the GROMOS96 force fields as a structural ion. Indeed, you could say that I am expecting an EVB/QM model of the ZN ion in a MD program, however I was thinking it could be possible to reduce the current hexacoordinated state to tetra coordinated state somehow. I have been advised to create a topology of the tetra coordinated state manually, but this is rather tedious because of the state of the protein-inhibitor complex. Are there options to modify the parameters in the GROMOS force field to your knowledge? Sergio