Justin,<br><br><div class="gmail_quote">31 марта 2012 г. 18:18 пользователь Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> написал:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Start by inspecting the initial configuration in the vicinity of these atoms. Something is likely clashing here.</blockquote><div><br>Yes, I've checked both of the proteins and found that the problem atoms were situated exactly in the docked region of the both proteins. So It seems that there are some clashes between atoms in the docked site. By the way this site of the first protein ( Receptor) consist of 2 flexible loops and the rigid helix from the second protein. ( fragment of G-protein) Might the energy minimisation solve this problem generally ? ( e.g by means of CG minimisation to very low forces aplied on atoms). Is there any possible ways to change conformation of the flexible loops during minimisation\ equilibration phases without aplication of any external forces?<br>
<br>James<br></div></div><br>