<div>Hi Vladimir ,</div>
<div> </div>
<div>The problem with docking inorganic molecules into protein structures is with at atom typing ie Charges to be placed on the atoms..fully charged, partial charges. Most forcefields are either biased to proteins or inorganic molecules and metals. There is no comprehensive forcefield that covers all. You will need to check the forcefield library for the atoms and molecules covered. In general people approximate the charges. Run the expts, see if the molecule is distorted. Rerun expts to overcome after charge modifications for adjusting the distortions. </div>
<div> </div>
<div>regards,</div>
<div> </div>
<div>Sunil.</div>
<div> <br><br> </div>
<div><span class="gmail_quote">On 31/05/2008, <b class="gmail_sendername"><a href="mailto:molmodel-request@oat.bio.indiana.edu">molmodel-request@oat.bio.indiana.edu</a></b> <<a href="mailto:molmodel-request@oat.bio.indiana.edu">molmodel-request@oat.bio.indiana.edu</a>> wrote:</span>
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<br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Fri, 30 May 2008 18:16:04 -0400<br>From: Vladimir Petrov <<a href="mailto:vpetrov@sco.com">vpetrov@sco.com</a>><br>
Subject: [Molecular-modelling] Re: inorganic mol. docking<br>To: <a href="mailto:molmodel@net.bio.net">molmodel@net.bio.net</a><br>Message-ID: <g1pub4$iql$<a href="mailto:1@aioe.org">1@aioe.org</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>X-no-archive: yes<br><a href="mailto:sudha.mrig@gmail.com">sudha.mrig@gmail.com</a> wrote:<br>> I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a<br>> protein molecule.<br><br>I guess, you'd have to familiarize yourself with basics of General<br>
Chemistry first, and then decide how to dock ZnSO4 "in organic molecule"<br>into the protein structure...<br><br><br>------------------------------<br><br>_______________________________________________<br>Molmodel mailing list<br>
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