<div style="line-height:1.7;color:#000000;font-size:14px;font-family:arial"><br><br><div>--<br><span class="Apple-style-span" style="font-family: Arial,Helvetica; line-height: normal;"><div><span class="Apple-style-span" style="font-family: Arial,Helvetica; line-height: normal;">Xianqiang Sun</span></div><div><span class="Apple-style-span" style="font-family: Arial,Helvetica; line-height: normal;"><br></span></div><div>Email: xianqiang@theochem.kth.se</div>Division of Theoretical Chemistry and Biology <br>School of Biotechnology&nbsp;<br>Royal Institute of Technology<br>S-106 91 Stockholm, Sweden</span>
&nbsp;
</div><div id="divNeteaseMailCard"></div><br><pre><br>At&nbsp;2012-01-04&nbsp;04:04:46,"Justin&nbsp;A.&nbsp;Lemkul"&nbsp;&lt;jalemkul@vt.edu&gt;&nbsp;wrote:
&gt;
&gt;
&gt;xianqiang&nbsp;wrote:
&gt;&gt;&nbsp;You&nbsp;do&nbsp;not&nbsp;need&nbsp;to&nbsp;fix&nbsp;the&nbsp;copper&nbsp;in&nbsp;the&nbsp;calculation.&nbsp;There&nbsp;are&nbsp;must&nbsp;be&nbsp;
&gt;&gt;&nbsp;some&nbsp;negative&nbsp;charged&nbsp;residues&nbsp;around&nbsp;the&nbsp;copper.&nbsp;Therefore,&nbsp;the&nbsp;copper&nbsp;
&gt;&gt;&nbsp;will&nbsp;located&nbsp;at&nbsp;the&nbsp;place&nbsp;where&nbsp;it&nbsp;should&nbsp;be.
&gt;&gt;&nbsp;
&gt;
&gt;I&nbsp;agree&nbsp;that&nbsp;a&nbsp;position&nbsp;restraint&nbsp;on&nbsp;copper&nbsp;is&nbsp;not&nbsp;appropriate,&nbsp;but&nbsp;I&nbsp;strongly&nbsp;
&gt;disagree&nbsp;with&nbsp;the&nbsp;assumption&nbsp;that&nbsp;it&nbsp;will&nbsp;simply&nbsp;be&nbsp;held&nbsp;in&nbsp;place&nbsp;by&nbsp;virtue&nbsp;of&nbsp;
&gt;negative&nbsp;charges.&nbsp;&nbsp;I&nbsp;know&nbsp;of&nbsp;many&nbsp;cases&nbsp;where&nbsp;the&nbsp;MM&nbsp;approximations&nbsp;and&nbsp;
&gt;electrostatic&nbsp;interactions&nbsp;were&nbsp;insufficient&nbsp;to&nbsp;preserve&nbsp;active-site&nbsp;geometry.&nbsp;
&gt;There&nbsp;are&nbsp;a&nbsp;number&nbsp;of&nbsp;QM/MM&nbsp;studies&nbsp;that&nbsp;have&nbsp;concluded&nbsp;that&nbsp;fixed&nbsp;point&nbsp;charges&nbsp;
&gt;on&nbsp;such&nbsp;species&nbsp;suffer&nbsp;from&nbsp;many&nbsp;limitations,&nbsp;not&nbsp;the&nbsp;least&nbsp;of&nbsp;which&nbsp;are&nbsp;
&gt;inductive&nbsp;effects&nbsp;and&nbsp;the&nbsp;inability&nbsp;to&nbsp;account&nbsp;for&nbsp;orbital&nbsp;geometry.&nbsp;&nbsp;A&nbsp;series&nbsp;
&gt;of&nbsp;distance&nbsp;restraints&nbsp;between&nbsp;ligating&nbsp;residues&nbsp;and&nbsp;the&nbsp;copper&nbsp;ion&nbsp;itself&nbsp;may&nbsp;
&gt;be&nbsp;the&nbsp;best&nbsp;approach&nbsp;for&nbsp;"standard"&nbsp;MD&nbsp;simulations.
&gt;
&gt;-Justin
&gt;
&gt;--&nbsp;
&gt;========================================
&gt;
&gt;Justin&nbsp;A.&nbsp;Lemkul
&gt;Ph.D.&nbsp;Candidate
&gt;ICTAS&nbsp;Doctoral&nbsp;Scholar
&gt;MILES-IGERT&nbsp;Trainee
&gt;Department&nbsp;of&nbsp;Biochemistry
&gt;Virginia&nbsp;Tech
&gt;Blacksburg,&nbsp;VA
&gt;jalemkul[at]vt.edu&nbsp;|&nbsp;(540)&nbsp;231-9080
&gt;http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
&gt;</pre><pre><br></pre><pre>I agree your opinion on some degree. But I think he should do the simulation with the copper at reasonable place  without restraint at first. If it is not work, the electrostatic interaction may be not  strong enough for locating the copper. Then, he can redo the calculation with distance restraint between the  copper and residues nearby. So the choice should depend on the system he worked on.</pre><pre>regards</pre><pre> 
&gt;========================================
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